Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003885.1 Hibiscus syriacus cultivar Beakdansim tig00008386_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: 757743
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 4
Found at i:168645 original size:23 final size:20
Alignment explanation
Indices: 168547--168686 Score: 69
Period size: 21 Copynumber: 6.9 Consensus size: 20
168537 TTTTTTATTA
168547 TTATTTTA--TTTATTTGT-T
1 TTATTTTATCTTTATTT-TCT
*
168565 TTATTTCTATATTT-TTTTC-
1 TTATTT-TATCTTTATTTTCT
*
168584 TTCTTTT-TC-TTATTTTTCT
1 TTATTTTATCTTTA-TTTTCT
*
168603 TTATTTTTTATATTTATTTTACT
1 TTA--TTTTATCTTTATTTT-CT
*
168626 TACTATTTTATCTTTGTTTTCT
1 T--TATTTTATCTTTATTTTCT
* **
168648 TTATCTTATCTTTTATTTAAT
1 TTATTTTATC-TTTATTTTCT
* *
168669 TTGTTTTCTCTTTATTTT
1 TTATTTTATCTTTATTTT
168687 AATTTAATTA
Statistics
Matches: 93, Mismatches: 14, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
16 2 0.02
17 1 0.01
18 12 0.13
19 10 0.11
20 18 0.19
21 21 0.23
22 8 0.09
23 19 0.20
25 2 0.02
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (20 bp):
TTATTTTATCTTTATTTTCT
Found at i:168728 original size:15 final size:15
Alignment explanation
Indices: 168710--168739 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
168700 AATTTATTTC
168710 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
168725 TTACCTTTTTATCTA
1 TTACCTTTTTATCTA
168740 ACATGGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (15 bp):
TTACCTTTTTATCTA
Found at i:170345 original size:36 final size:36
Alignment explanation
Indices: 170305--170375 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
170295 AAAATATCGA
170305 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
*
170341 CATTGGTGTAGTTAATTATTCTAGGTAAACTATAT
1 CATTGGTGTAGCTAATTATTCTAGGTAAACTATAT
170376 ATAATAATCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (36 bp):
CATTGGTGTAGCTAATTATTCTAGGTAAACTATATT
Found at i:176303 original size:170 final size:173
Alignment explanation
Indices: 175983--176304 Score: 481
Period size: 170 Copynumber: 1.9 Consensus size: 173
175973 TTAATGTGGT
* * * * *
175983 AATTAATAAAATTGATATAATTGCACGTTTGGCCACTCTTACTTATATATTTTATCAATTTGATC
1 AATTAATAAAATTGATATAATTACACATTCGACCAC-CTTACTTATATATTCTATCAATTTGATC
* * *
176048 CTAATTTTATTAAATTAAAATAAATTTAACCTTCTAATCGGATGATGTCATGTGTCATTACAAAA
65 CTAATTTTATTAAATTAAAATAAATTTAACCTTCTAATAGGATGATATCATATGTCATTACAAAA
176113 AAAATTAAGAGAACTTAAGAATTTGATAGAAGTGTTGATATGTC
130 AAAATTAAGAGAACTTAAGAATTTGATAGAAGTGTTGATATGTC
176157 AATTAATAAAATTGATATAATTACACATTCGACCA-C-T-CTTATATATTCTATCAATTTGATCC
1 AATTAATAAAATTGATATAATTACACATTCGACCACCTTACTTATATATTCTATCAATTTGATCC
* * **
176219 TAATTTTATTAAATTAAAATAAATTTAACCTTCTAATATGATGATATCATATGTCGTTACGCCAA
66 TAATTTTATTAAATTAAAATAAATTTAACCTTCTAATAGGATGATATCATATGTCATTAC-AAAA
*
176284 AAAATTAAG-GAAGTTAAGAAT
130 AAAATTAAGAGAACTTAAGAAT
176305 GAGGACCATG
Statistics
Matches: 134, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
170 90 0.67
171 12 0.09
172 1 0.01
174 31 0.23
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (173 bp):
AATTAATAAAATTGATATAATTACACATTCGACCACCTTACTTATATATTCTATCAATTTGATCC
TAATTTTATTAAATTAAAATAAATTTAACCTTCTAATAGGATGATATCATATGTCATTACAAAAA
AAATTAAGAGAACTTAAGAATTTGATAGAAGTGTTGATATGTC
Found at i:176628 original size:24 final size:25
Alignment explanation
Indices: 176582--176632 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
176572 TATTAAATTA
*
176582 AAATCAAAATAAAATATACATTTTT
1 AAATAAAAATAAAATATACATTTTT
*
176607 AAATAAAAATAAAA-ATATATTTTT
1 AAATAAAAATAAAATATACATTTTT
176631 AA
1 AA
176633 GTTAAGATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
AAATAAAAATAAAATATACATTTTT
Found at i:176672 original size:25 final size:27
Alignment explanation
Indices: 176634--176687 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 27
176624 TATTTTTAAG
* *
176634 TTAAGATAAGAATAA-AATATA-TATA
1 TTAAGATAAAAATAAGAATAAATTATA
*
176659 TTAAGTTAAAAATAAGAATAAATTATA
1 TTAAGATAAAAATAAGAATAAATTATA
176686 TT
1 TT
176688 TAATAATTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 13 0.54
26 5 0.21
27 6 0.25
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (27 bp):
TTAAGATAAAAATAAGAATAAATTATA
Found at i:176672 original size:61 final size:59
Alignment explanation
Indices: 176557--176865 Score: 217
Period size: 61 Copynumber: 5.3 Consensus size: 59
176547 AAATTAAGAT
* * * *
176557 AAAATATAATATATTTATTAAA-TTAAAATCAA-AATAAAATATA-CATT---TTTAAATA
1 AAAATAAAATATATTT-TTAAAGTTAAGAT-AAGAATAAAATATATTATTAAGTTAAAATA
176612 AAAATAAAAATATATTTTT-AAGTTAAGATAAGAATAAAATATATATATTAAGTTAAAAATA
1 AAAAT-AAAATATATTTTTAAAGTTAAGATAAGAATAAAATATAT-TATTAAGTT-AAAATA
* * * * ** * * ** *
176673 AGAATAAATTATA-TTTAATAATTTAATTTAAAAATATAATATATGTAACAAGTTAAGATA
1 AAAATAAAATATATTTTTA-AAGTTAAGATAAGAATAAAATATAT-TATTAAGTTAAAATA
* * * *
176733 AAAATAAAATA-ATTTTTTAAAAGTTAGGATAAGAATAAAATATATTTTTAAGTTAAGACA
1 AAAATAAAATATA-TTTTT-AAAGTTAAGATAAGAATAAAATATATTATTAAGTTAAAATA
* * * * * * * *
176793 ATAATAAAATATATTTTTAAACTTAATATAAGATTAAAAAATATT-TTTAGTTGAGATA
1 AAAATAAAATATATTTTTAAAGTTAAGATAAGAATAAAATATATTATTAAGTTAAAATA
176851 AAAATAAAATA-ATTT
1 AAAATAAAATATATTT
176866 AAATATTAAG
Statistics
Matches: 200, Mismatches: 39, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
54 4 0.02
55 24 0.12
56 10 0.05
57 7 0.04
58 20 0.10
59 26 0.13
60 49 0.25
61 59 0.29
62 1 0.00
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (59 bp):
AAAATAAAATATATTTTTAAAGTTAAGATAAGAATAAAATATATTATTAAGTTAAAATA
Found at i:176831 original size:30 final size:30
Alignment explanation
Indices: 176542--176865 Score: 162
Period size: 30 Copynumber: 11.1 Consensus size: 30
176532 TCTTATAATA
* *
176542 TTTTAAAATTAAGATAA-AATATAATATAT
1 TTTTAAACTTAAGATAAGAATAAAATATAT
*
176571 TTATTAAA-TTAAAATCAA-AATAAAATATACAT
1 TT-TTAAACTTAAGAT-AAGAATAAAATAT--AT
*
176603 TTTTAAA--TAA-A-AA-TA-AAAATATAT
1 TTTTAAACTTAAGATAAGAATAAAATATAT
*
176627 TTTT-AAGTTAAGATAAGAATAAAATATAT
1 TTTTAAACTTAAGATAAGAATAAAATATAT
* * * *
176656 ATATT-AAGTTAAAAATAAGAATAAATTATA-
1 -TTTTAAACTT-AAGATAAGAATAAAATATAT
* * ** * *
176686 TTTAATAATTTAATTTAAAAATATAATATA-
1 TTTTA-AACTTAAGATAAGAATAAAATATAT
* * * *
176716 TGTAACAAGTTAAGATAAAAATAAAATA-ATT
1 TTTTA-AACTTAAGATAAGAATAAAATATA-T
* *
176747 TTTTAAAAGTTAGGATAAGAATAAAATATAT
1 TTTT-AAACTTAAGATAAGAATAAAATATAT
* * *
176778 TTTT-AAGTTAAGACAATAATAAAATATAT
1 TTTTAAACTTAAGATAAGAATAAAATATAT
* * *
176807 TTTTAAACTTAATATAAGATTAAAAAATAT
1 TTTTAAACTTAAGATAAGAATAAAATATAT
* * *
176837 TTTT--AGTTGAGATAAAAATAAAATA-AT
1 TTTTAAACTTAAGATAAGAATAAAATATAT
176864 TT
1 TT
176866 AAATATTAAG
Statistics
Matches: 236, Mismatches: 40, Indels: 40
0.75 0.13 0.13
Matches are distributed among these distances:
23 2 0.01
24 6 0.03
25 3 0.01
26 8 0.03
27 9 0.04
28 16 0.07
29 47 0.20
30 86 0.36
31 53 0.22
32 6 0.03
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (30 bp):
TTTTAAACTTAAGATAAGAATAAAATATAT
Found at i:176902 original size:18 final size:18
Alignment explanation
Indices: 176871--176915 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
176861 AATTTAAATA
* * *
176871 TTAAGATGTGAATTTAAT
1 TTAAGATATTAATTTAAG
*
176889 TTAATATATTAATTTAAG
1 TTAAGATATTAATTTAAG
176907 TTAAGATAT
1 TTAAGATAT
176916 ATATAATATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TTAAGATATTAATTTAAG
Found at i:182878 original size:955 final size:952
Alignment explanation
Indices: 181312--183473 Score: 3612
Period size: 955 Copynumber: 2.3 Consensus size: 952
181302 TGCTTGGCTG
181312 TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGTTTTATTTGCAAATAAAATTTAGGGTAAATTA
1 TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGTTTTATTTGCAAATAAAATTTAGGGTAAATTA
* * *
181377 TCCCATGATCATTTAATTTTTTTTGAAGAAACTTTTATTAAAACAAACCTTAATTAAGAGTTTCG
66 CCCCACGATCATTTAA-TTTTTTTGAAGAAAATTTTATTAAAACAAACCTTAATTAAGAGTTTCG
* * *
181442 TTAAAAACTTTTCTAAACCAAAATATAGTCCACGAGATCAAACTCCTAACACAATACAAATTGTA
130 TTAAAAACTTTTCTAAACCAAAATATAGTCCACAAG-TCAAACCCCTAACACAATACAAACTGTA
* *
181507 CCCCAATGCTGTAAAACACAAGAGTAAGACTAGACGAA-CCCCATCTAAAAATCTACAATCACCA
194 CCCCAATGCTGTAAAACACAAGAGCAAGACTAGACGAACCCCCATCTAAAAATCTACAACCACCA
181571 CCATCAGGGGCTTAACGTACCCCTGCTGATAAGACACTAGGGGTGTTTGGATCAATGAATGTGTG
259 CCATCAGGGGCTTAACGTACCCCTGCTGATAAGACACTAGGGGTGTTTGGATCAATGAATGTGTG
* *
181636 ATTCCCATAGAAATGTAATCCACATTCCCAAGTTTGATTGGTCGGGAATCTCATTCCCGGTAATG
324 ATTCCCATAGAAATGGAATCCACATTCCCAAGTTTGATTGGCCGGGAATCTCATTCCCGGTAATG
* *
181701 TTTTATTACCAATAGTAGATTTTCTGGGATATATTACCAGGAATGCCATTAACTTCATTTTCTTA
389 TTTTATTACCAATAGTAAATTTTCTGGGATATATTACCAGGAATGCCATTAACTCCATTTTCTTA
* * * *
181766 GGTATTGTTGGATTACCGGCGTTTTGGACAAAAAATGCCCTTAATTTTTTTTTTCTAAAAAATAT
454 AGTATTATTGGATTACCGGCGTTTTGAACAAAAAATGCACTTAA-TTTTTTTTTCTAAAAAATAT
* * *
181831 CATTCTTCTGTCATTGAATAATAAAAATTCTATGAAAGTTAAATTATAAATTTATCCTTAAACTA
518 AATTCTTCTGTCATTGAATAATAAAAATTCTACGAAAGTTAAATTACAAATTTATCCTTAAACTA
181896 TTTTAGATTTACAAAAAAATCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAAATT
583 TTTTAGATTTACAAAAAAATCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAAATT
181961 TTCCCTTTCATTAAACCTTTTTATATTTTCAATTTTGT-AAAAACATATATATAAATGTTATGAA
648 TTCCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAACATATATATAAATGTTATGAA
182025 TTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAAACAAATATATAATA
713 TTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTT-AAAAAAACAAATATATAATA
*
182090 AGGTCAATTTGGTCAAATATACATTTCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTT
777 AGGACAATTTGGTCAAATATACATTTCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTT
* * * * *
182155 ACATTCCTGTTAAACCAACCAAACACAAAATACAATATTCTTAGTAATCTTTTTCTCTGGTAATC
842 ACATTCCTGTTAAACCAACCAAACACAAAATACAACATTCTCAGTAATCCTATTCTCTAGTAATC
* * *
182220 TTACATTCCCACTGGTAATTTTACATTTCGTGAACCAAACGCACCC
907 TTACATTCCCACTGATAATCTTACATTCCGTGAACCAAACGCACCC
*
182266 TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGATTTATTTGCAAATAAAATTTAGGGTAAATTA
1 TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGTTTTATTTGCAAATAAAATTTAGGGTAAATTA
* * *
182331 CCCCACAATAATTTAATTTTTTTGAAGAAAATTTTATTAAAATAAACCTTAATTAAGAGTTTCGT
66 CCCCACGATCATTTAATTTTTTTGAAGAAAATTTTATTAAAACAAACCTTAATTAAGAGTTTCGT
182396 TAAAAACTTTTCTAAACCAAAATATAGTCCACAAAGTCAAACCCCTAACACAATACAAACTGTAC
131 TAAAAACTTTTCTAAACCAAAATATAGTCCAC-AAGTCAAACCCCTAACACAATACAAACTGTAC
* *
182461 CCCAATACTGTAAAACACAAGAGCAAGACTAGACGAACCCCCATCTAAAAACCTACAACCACCAC
195 CCCAATGCTGTAAAACACAAGAGCAAGACTAGACGAACCCCCATCTAAAAATCTACAACCACCAC
*
182526 CATGAGGGGCTTAACGTACCCCTGCTGATAAGACACTAGGGGGTGTTTGGATCAATGAATGTGTG
260 CATCAGGGGCTTAACGTACCCCTGCTGATAAGACACTA-GGGGTGTTTGGATCAATGAATGTGTG
* * ** * *
182591 ATTCCCATAGGAATGGAATTCACATTCTTATGTTTGGTTGGCCGGGAATCTCATTCCCGGTAATG
324 ATTCCCATAGAAATGGAATCCACATTCCCAAGTTTGATTGGCCGGGAATCTCATTCCCGGTAATG
* * * * * * *
182656 TTTTATTATCAATAGTAAATTTTTTGGGGTATATTATCAGGAATGCCATTACCTCCCTTTTTTTT
389 TTTTATTACCAATAGTAAATTTTCTGGGATATATTACCAGGAATGCCATTAACT-CCATTTTCTT
182721 AAGTATTATTGGATTACCGGCGTTTTGAACAAAAAATGCACTTAA-TTTTTTTTCTAAAAAAATA
453 AAGTATTATTGGATTACCGGCGTTTTGAACAAAAAATGCACTTAATTTTTTTTTCT-AAAAAATA
*
182785 TAATTCTTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTACAAATTTATCCTTAAACT
517 TAATTCTTCTGTCATTGAATAATAAAAATTCTACGAAAGTTAAATTACAAATTTATCCTTAAACT
*
182850 ATTTTAGATTTACAAAAAAATTTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAAAT
582 ATTTTAGATTTACAAAAAAATCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAAAT
* *
182915 TTTCCCTTTCATTAAATCTTTTTATATTTTCAATTTTGTAAAAAATATATATATAAATGTTATGA
647 TTTCCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAACATATATATAAATGTTATGA
*
182980 ATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAATAAATATATAATA
712 ATTTAATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATATAATA
183045 AGGACAATTTGGTCAAATATACATTTCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTT
777 AGGACAATTTGGTCAAATATACATTTCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTT
*
183110 ACATTCCTGTTAAACTAACCAAACACAAAATACAACATTCTCAGTAATCCTATTCTCTAGTAATC
842 ACATTCCTGTTAAACCAACCAAACACAAAATACAACATTCTCAGTAATCCTATTCTCTAGTAATC
*
183175 TTACATTCCCACTGATAATCTTACATTCCGTGAACTAAACGCACCC
907 TTACATTCCCACTGATAATCTTACATTCCGTGAACCAAACGCACCC
183221 TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGTTTTATTTGCAAATAAAATTTAGGGTAAATTA
1 TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGTTTTATTTGCAAATAAAATTTAGGGTAAATTA
*** *
183286 CCCCACGATCATTTAATTTCTTTTGAA-ATTTTTTTTATTAAAACAAACCTTAATTAAGAATTTC
66 CCCCACGATCATTTAATTT-TTTTGAAGA-AAATTTTATTAAAACAAACCTTAATTAAGAGTTTC
* * *
183350 GTTAAAAACTTTTCTAAACCAAAATATAATCCACGAGGTCAAACCCCTAGCACAATACAAACTGT
129 GTTAAAAACTTTTCTAAACCAAAATATAGTCCAC-AAGTCAAACCCCTAACACAATACAAACTGT
** *
183415 AATCCAATGCTGTAAAACACAAGAGCAAGACTAGACGAACCCCCCTCTAAAAATCTACA
193 ACCCCAATGCTGTAAAACACAAGAGCAAGACTAGACGAACCCCCATCTAAAAATCTACA
183474 GTCATCACCC
Statistics
Matches: 1128, Mismatches: 72, Indels: 14
0.93 0.06 0.01
Matches are distributed among these distances:
953 141 0.12
954 150 0.13
955 568 0.50
956 269 0.24
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (952 bp):
TAAGTTTTATCGTGTTTCCTTGAAGTCTTTCTGTTTTATTTGCAAATAAAATTTAGGGTAAATTA
CCCCACGATCATTTAATTTTTTTGAAGAAAATTTTATTAAAACAAACCTTAATTAAGAGTTTCGT
TAAAAACTTTTCTAAACCAAAATATAGTCCACAAGTCAAACCCCTAACACAATACAAACTGTACC
CCAATGCTGTAAAACACAAGAGCAAGACTAGACGAACCCCCATCTAAAAATCTACAACCACCACC
ATCAGGGGCTTAACGTACCCCTGCTGATAAGACACTAGGGGTGTTTGGATCAATGAATGTGTGAT
TCCCATAGAAATGGAATCCACATTCCCAAGTTTGATTGGCCGGGAATCTCATTCCCGGTAATGTT
TTATTACCAATAGTAAATTTTCTGGGATATATTACCAGGAATGCCATTAACTCCATTTTCTTAAG
TATTATTGGATTACCGGCGTTTTGAACAAAAAATGCACTTAATTTTTTTTTCTAAAAAATATAAT
TCTTCTGTCATTGAATAATAAAAATTCTACGAAAGTTAAATTACAAATTTATCCTTAAACTATTT
TAGATTTACAAAAAAATCTATAATTAAAATTTTATATGAAGTTCAGGGGTTAAAATAAAATTTTC
CCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAAACATATATATAAATGTTATGAATTT
AATTTTTTTAAAGAAAATATATAAATATTTTCCAACTTGTTAAAAAAACAAATATATAATAAGGA
CAATTTGGTCAAATATACATTTCAATAATCTTTTATTCCTTTAACCAAACACGGTAATCTTACAT
TCCTGTTAAACCAACCAAACACAAAATACAACATTCTCAGTAATCCTATTCTCTAGTAATCTTAC
ATTCCCACTGATAATCTTACATTCCGTGAACCAAACGCACCC
Found at i:184886 original size:22 final size:23
Alignment explanation
Indices: 184853--184911 Score: 84
Period size: 22 Copynumber: 2.5 Consensus size: 23
184843 TTAAATAATT
*
184853 TTTATCTTTTTAAAATTTTATAGA
1 TTTA-CTTTTTAAAATTTTATAAA
184877 TTTA-TTTTTAAAATTTTATAAA
1 TTTACTTTTTAAAATTTTATAAA
184899 TTTACTTCTTTAA
1 TTTACTT-TTTAA
184912 TATAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
22 21 0.66
23 2 0.06
24 9 0.28
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (23 bp):
TTTACTTTTTAAAATTTTATAAA
Found at i:189939 original size:16 final size:16
Alignment explanation
Indices: 189918--189951 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
189908 TTACTATTCA
*
189918 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
189934 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
189950 CG
1 CG
189952 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:200289 original size:3 final size:3
Alignment explanation
Indices: 200281--200381 Score: 184
Period size: 3 Copynumber: 33.7 Consensus size: 3
200271 GTTTTACCCA
*
200281 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
200329 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
200377 TAT TA
1 TAT TA
200382 AATATATATT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 94 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:200907 original size:18 final size:18
Alignment explanation
Indices: 200884--200920 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
200874 ACAGAACCGA
200884 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
200902 AGAGAAAGAAAAAAAAAC
1 AGAGAAAGAAAAAAAAAC
200920 A
1 A
200921 ACAACAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.78, C:0.05, G:0.16, T:0.00
Consensus pattern (18 bp):
AGAGAAAGAAAAAAAAAC
Found at i:201861 original size:22 final size:21
Alignment explanation
Indices: 201822--201864 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
201812 AGAATTTTTC
**
201822 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
201843 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
201865 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:202553 original size:17 final size:17
Alignment explanation
Indices: 202531--202570 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
202521 CTTTTCAAAT
202531 TTTTTATATATTTATTA
1 TTTTTATATATTTATTA
* *
202548 TTTTTATATTTTTTTTA
1 TTTTTATATATTTATTA
202565 TATTTT
1 T-TTTT
202571 CTTATTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTTTATATATTTATTA
Found at i:209675 original size:18 final size:17
Alignment explanation
Indices: 209647--209687 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
209637 AGATGGCAAT
*
209647 CATTCTTTACATTTTATTA
1 CATT-TTTACATTTCA-TA
209666 CATTTTTACATTTCATA
1 CATTTTTACATTTCATA
209683 CATTT
1 CATTT
209688 ACTATATTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 10 0.48
19 4 0.19
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (17 bp):
CATTTTTACATTTCATA
Found at i:213234 original size:14 final size:13
Alignment explanation
Indices: 213217--213254 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
213207 AATATATAAT
213217 AAAAAAGAAAAGA
1 AAAAAAGAAAAGA
*
213230 AAAAAAAAGAAAGA
1 AAAAAAGA-AAAGA
213244 AAAAAAGAAAA
1 AAAAAAGAAAA
213255 AGGGGGTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAGA
Found at i:213242 original size:19 final size:18
Alignment explanation
Indices: 213220--213256 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
213210 ATATAATAAA
213220 AAAGAAAAGAAAAAAAAAG
1 AAAGAAAA-AAAAAAAAAG
*
213239 AAAGAAAAAAAGAAAAAG
1 AAAGAAAAAAAAAAAAAG
213257 GGGGTCAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAAAAAG
Found at i:214509 original size:83 final size:83
Alignment explanation
Indices: 214370--214887 Score: 858
Period size: 83 Copynumber: 6.4 Consensus size: 83
214360 GATATCTTAG
214370 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
214435 ATGATCTGGTTGGACAGA
66 CTGATCTGATTGGACAGA
214453 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
214518 CTGATCTGATTTGACAGA
66 CTGATCTGATTGGACAGA
* * *
214536 ACCCATCATCGAATTTGGAAGATGAATGTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
214601 CTGATCTGATTTGACAGA
66 CTGATCTGATTGGACAGA
*
214619 ACCCATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214684 CTGA--T--TT-GACAGA
66 CTGATCTGATTGGACAGA
*
214697 ACCCATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
214762 CTGA--T--TTGG-CAGA
66 CTGATCTGATTGGACAGA
* *
214775 AACAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAATTAT
1 ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
*
214840 CTGATCTGATTGGATAGA
66 CTGATCTGATTGGACAGA
214858 ACCAATCATTGAATTTGGAAGATGAATTTG
1 ACCAATCATTGAATTTGGAAGATGAATTTG
214888 CTCATAGTAG
Statistics
Matches: 416, Mismatches: 13, Indels: 12
0.94 0.03 0.03
Matches are distributed among these distances:
78 148 0.36
79 3 0.01
80 1 0.00
81 1 0.00
82 4 0.01
83 259 0.62
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.36
Consensus pattern (83 bp):
ACCAATCATTGAATTTGGAAGATGAATTTGTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTGGACAGA
Found at i:215915 original size:114 final size:114
Alignment explanation
Indices: 215607--216584 Score: 1498
Period size: 114 Copynumber: 8.6 Consensus size: 114
215597 AATCTATCAC
* *
215607 TTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
* * *
215672 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATCCATC-AT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
* * *
215720 TTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
* *
215785 AGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
*
215834 TTGATGGATTATCTTTTCCAGAGAAAGTTCAAAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
*
215899 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
* *
215948 TTGATGGATCATCTTTTCCAGAGAAAGTTCAAAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
*
216013 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
*
216062 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
*
216127 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
*
216176 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
*
216241 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTGAATTCATCAAA
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
* *
216290 TTGATGGATTATCTTTTCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1 TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
* * * * *
216355 AGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATC-AT
66 AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
* * * * *
216403 TTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAG
1 TTGATGGATTATCTTTTCCAGAG-AAAGTTCATAATGAGAAGAAC-C--CATCTGAAGAAGGAAG
* * * * *
216467 AAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATC-AT
62 AAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
* * ** * *
216519 TTGATGGATCATCATCCCCAGCAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AGAAG
1 TTGATGGATTATCTTTTCCAG-AGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAG
216583 AA
65 AA
216585 TTTATTCAAT
Statistics
Matches: 821, Mismatches: 37, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
112 1 0.00
113 150 0.18
114 563 0.69
116 86 0.10
117 20 0.02
118 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (114 bp):
TTGATGGATTATCTTTTCCAGAGAAAGTTCATAATGAGAAGAACCCATCTGAAGAAGGAAGAAGA
AGTTCATAATGAGAAGAATTTGTTCAACCTTTTTCCTGAATTCATCAAA
Found at i:216728 original size:3 final size:3
Alignment explanation
Indices: 216720--216802 Score: 148
Period size: 3 Copynumber: 27.7 Consensus size: 3
216710 TTTTTACCCA
*
216720 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
216768 TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
216803 AATATATATT
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:217326 original size:17 final size:17
Alignment explanation
Indices: 217304--217338 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
217294 ACAGAACCGA
217304 AGAGAAAGAAAAAAAAC
1 AGAGAAAGAAAAAAAAC
217321 AGAGAAAGAAAAAAAAC
1 AGAGAAAGAAAAAAAAC
217338 A
1 A
217339 ACAACAAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (17 bp):
AGAGAAAGAAAAAAAAC
Found at i:218275 original size:22 final size:21
Alignment explanation
Indices: 218236--218278 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
218226 AGAATTTTTC
**
218236 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
218257 TTTTATATATATTCATAAATAT
1 TTTTAT-TATATTCATAAATAT
218279 ATATAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:219527 original size:21 final size:19
Alignment explanation
Indices: 219503--219558 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
219493 TCATCAAAAT
219503 AATAATTATTAAAATATTTAA
1 AATAATTATT--AATATTTAA
*
219524 AATATATTTATTAATATTTAT
1 AATA-A-TTATTAATATTTAA
219545 AATAA-TA-TAATATT
1 AATAATTATTAATATT
219559 ATATTTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
17 7 0.22
18 2 0.06
20 1 0.03
21 16 0.50
22 1 0.03
23 5 0.16
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
AATAATTATTAATATTTAA
Found at i:219550 original size:12 final size:12
Alignment explanation
Indices: 219500--219552 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
219490 TTTTCATCAA
*
219500 AATAATAATTATT
1 AATAATATTTA-T
*
219513 AA-AATATTTAA
1 AATAATATTTAT
219524 AAT-ATATTTAT
1 AATAATATTTAT
219535 --TAATATTTAT
1 AATAATATTTAT
219545 AATAATAT
1 AATAATAT
219553 AATATTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
9 1 0.03
10 8 0.24
11 9 0.27
12 13 0.39
13 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
AATAATATTTAT
Found at i:219562 original size:22 final size:21
Alignment explanation
Indices: 219515--219568 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
219505 TAATTATTAA
* *
219515 AATATTTAAAATATATTTATT
1 AATATTTATAATATATATATT
219536 AATATTTATAATAATATAATATT
1 AATATTTATAAT-ATAT-ATATT
219559 -ATATTTATAA
1 AATATTTATAA
219569 AGGAAAATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 11 0.38
22 14 0.48
23 4 0.14
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATATTTATAATATATATATT
Found at i:233255 original size:18 final size:20
Alignment explanation
Indices: 233222--233260 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
233212 GACAATGGAT
233222 TATTTTATTGTAATATTAAA
1 TATTTTATTGTAATATTAAA
233242 TATTTTA-T-TAATATTAAA
1 TATTTTATTGTAATATTAAA
233260 T
1 T
233261 GTCACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TATTTTATTGTAATATTAAA
Found at i:233656 original size:20 final size:20
Alignment explanation
Indices: 233631--233679 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
233621 TTTTCCCAAT
*
233631 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
233651 TCGCAACGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
233671 TCGCAACGC
1 TCGCAACGC
233680 AAATTGGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:233715 original size:41 final size:41
Alignment explanation
Indices: 233670--233758 Score: 142
Period size: 41 Copynumber: 2.2 Consensus size: 41
233660 GAATAAGTAA
*
233670 ATCGCAACGCAAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACACAAATTGGGAAAATCGCAATGCGATACTGACT
* * *
233711 ATCGCAATACGAATTTGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACACAAATTGGGAAAATCGCAATGCGATACTGACT
233752 ATCGCAA
1 ATCGCAA
233759 TGCGATTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (41 bp):
ATCGCAACACAAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:233716 original size:20 final size:20
Alignment explanation
Indices: 233691--233764 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
233681 AATTGGGAAA
233691 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
* * **
233711 ATCGCAATACGA-ATTTGGAAA
1 ATCGCAATGCGATA-CT-GACT
233732 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
233752 ATCGCAATGCGAT
1 ATCGCAATGCGAT
233765 TTTCCTAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 1 0.02
20 27 0.63
21 14 0.33
22 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:233759 original size:41 final size:41
Alignment explanation
Indices: 233681--233759 Score: 149
Period size: 41 Copynumber: 1.9 Consensus size: 41
233671 TCGCAACGCA
233681 AATTGGGAAAATCGCAATGCGATACTGACTATCGCAATACG
1 AATTGGGAAAATCGCAATGCGATACTGACTATCGCAATACG
*
233722 AATTTGGAAAATCGCAATGCGATACTGACTATCGCAAT
1 AATTGGGAAAATCGCAATGCGATACTGACTATCGCAAT
233760 GCGATTTTCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (41 bp):
AATTGGGAAAATCGCAATGCGATACTGACTATCGCAATACG
Found at i:233778 original size:41 final size:41
Alignment explanation
Indices: 233692--233825 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
233682 ATTGGGAAAA
* ** *
233692 TCGCAATGCGATACTGACTATCGCAATACGAATTTGGA-AAA
1 TCGCAATGCGATACTGACTATCGCAATGCG-ATTTTCATAAT
*
233733 TCGCAATGCGATACTGACTATCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATACTGACTATCGCAATGCGATTTTCATAAT
* * **
233774 TCGCATTGCGAT--TTACGTATTCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATACTGAC-TA-TCGCAATGCGATTTTCATAAT
233815 TCGCAATGCGA
1 TCGCAATGCGA
233826 ATACGTAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
39 3 0.04
40 6 0.08
41 70 0.89
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (41 bp):
TCGCAATGCGATACTGACTATCGCAATGCGATTTTCATAAT
Found at i:233783 original size:21 final size:21
Alignment explanation
Indices: 233753--233825 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
233743 ATACTGACTA
*
233753 TCGCAATGCGATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
233774 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
233794 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
233815 TCGCAATGCGA
1 TCGCAATGCGA
233826 ATACGTAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:233840 original size:20 final size:20
Alignment explanation
Indices: 233815--233926 Score: 138
Period size: 20 Copynumber: 5.5 Consensus size: 20
233805 TTTTCATAAT
233815 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
233835 TCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAA-TACGTAAA
* *
233855 TCGCAATGCGAATTAAGAAAA
1 TCGCAATGCGAA-TACGTAAA
233876 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
233896 TCGCAATGCGAAT-CTTACCA
1 TCGCAATGCGAATACGTA-AA
233916 TCGCAATGCGA
1 TCGCAATGCGA
233927 TTTACATAGC
Statistics
Matches: 82, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.74
21 18 0.22
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:233865 original size:61 final size:61
Alignment explanation
Indices: 233616--233934 Score: 179
Period size: 61 Copynumber: 5.2 Consensus size: 61
233606 ACAGTGTCGT
** * * * *
233616 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAACGCGAATAAGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAATGCGAATTAGTAAATCGCAA
* * *** * * * *
233677 CGCAAATTGGGA-AAATCGCAATGCG-ATAC-TGACTATCGCAATACGAATTTGGAAAATCGCAA
1 TGC-GATTTTCATAAATCGCAATGCGAATACGT-A-AATCGCAATGCGAA-TTAGTAAATCGCAA
** * * * * * * * * **
233739 TGCGATACTGACT--ATCGCAATGCGATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGATTTTCA-TAAATCGCAATGCGA-ATACGTAAATCGCAATGCGAATTA-GTAAATCGCAA
* *
233800 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGAATTAGTAAATCGCAA
1 TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAATGCGAATTAGTAAATCGCAA
* * * *
233861 TGCGA-ATTAAGAAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCT--TACCATCGCAA
1 TGCGATTTTCA-TAAATCGCAATGCGAATACGTAAATCGCAATGCGAAT-TAGTA-AATCGCAA
*
233922 TGCGATTTACATA
1 TGCGATTTTCATA
233935 GCGCCATTCG
Statistics
Matches: 186, Mismatches: 55, Indels: 34
0.68 0.20 0.12
Matches are distributed among these distances:
59 1 0.01
60 12 0.06
61 129 0.69
62 40 0.22
63 3 0.02
64 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (61 bp):
TGCGATTTTCATAAATCGCAATGCGAATACGTAAATCGCAATGCGAATTAGTAAATCGCAA
Found at i:233887 original size:41 final size:41
Alignment explanation
Indices: 233815--233908 Score: 138
Period size: 41 Copynumber: 2.3 Consensus size: 41
233805 TTTTCATAAT
* *
233815 TCGCAATGCGAA-TACGTAAATCGCAACGCGAATTA-GTAAA
1 TCGCAATGCGAATTAAGAAAATCGCAACGCGAA-TACGTAAA
*
233855 TCGCAATGCGAATTAAGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTAAGAAAATCGCAACGCGAATACGTAAA
233896 TCGCAATGCGAAT
1 TCGCAATGCGAAT
233909 CTTACCATCG
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
40 14 0.29
41 35 0.71
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTAAGAAAATCGCAACGCGAATACGTAAA
Found at i:234600 original size:33 final size:34
Alignment explanation
Indices: 234558--234623 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
234548 TTTCATTTCG
234558 CGTTGCGATAGTCATTT-CGCGTTGCGATTCTCT
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
234591 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
234624 ATTATCTCGT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 17 0.53
34 15 0.47
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (34 bp):
CGTTGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:234625 original size:20 final size:19
Alignment explanation
Indices: 234522--234648 Score: 129
Period size: 19 Copynumber: 6.8 Consensus size: 19
234512 CAAAATCACA
234522 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
234541 TTGTGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
**
234560 TTGCGATAGTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
*
234579 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCGCG
**
234593 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCG
* *
234613 TTGCGATTCTCATTATCTCG
1 TTGCGATTTTCATT-TCGCG
234633 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
234649 AACCAAAAGA
Statistics
Matches: 89, Mismatches: 12, Indels: 14
0.77 0.10 0.12
Matches are distributed among these distances:
14 10 0.11
16 2 0.02
17 2 0.02
19 43 0.48
20 31 0.35
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:236815 original size:21 final size:21
Alignment explanation
Indices: 236791--236857 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
236781 TCATTCCTCG
236791 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
236812 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
236833 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
236854 AGAG
1 AGAG
236858 CCCGACTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:236815 original size:42 final size:42
Alignment explanation
Indices: 236764--236857 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
236754 CCACTCTTAT
* *
236764 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
236806 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
236848 CATTCAAGAG
1 CGTTCAAGAG
236858 CCCGACTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:238226 original size:14 final size:14
Alignment explanation
Indices: 238207--238242 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
238197 ATTGTTTAAT
238207 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
238221 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
238235 TGATTTGT
1 TGATTTGT
238243 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:238369 original size:19 final size:18
Alignment explanation
Indices: 238345--238403 Score: 63
Period size: 19 Copynumber: 3.4 Consensus size: 18
238335 AAAAAGTACT
238345 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
*
238363 GATCGCAA--CGAGA-G-A
1 -ATCGCAATGCGAAATGAA
238378 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
238397 ATCGCAA
1 ATCGCAA
238404 CGAGAGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 7 0.21
15 1 0.03
16 5 0.15
17 5 0.15
19 15 0.45
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:238382 original size:33 final size:33
Alignment explanation
Indices: 238345--238434 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
238335 AAAAAGTACT
*
238345 ATCGCAATGCGAAATGAAGATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
238378 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
238411 ATCGCAACGCGAAATTAAATTCGC
1 ATCGCAATGCGAAATGAAAATCGC
238435 GTTGCGATTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:238383 original size:14 final size:14
Alignment explanation
Indices: 238364--238419 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
238354 CGAAATGAAG
238364 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
238378 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
238397 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
238411 ATCGCAACG
1 ATCGCAACG
238420 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.21, G:0.25, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:238452 original size:19 final size:19
Alignment explanation
Indices: 238430--238518 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 19
238420 CGAAATTAAA
238430 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
238449 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
238464 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
238482 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
238496 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
238515 TTCG
1 TTCG
238519 TAATGCGATT
Statistics
Matches: 50, Mismatches: 10, Indels: 20
0.62 0.12 0.25
Matches are distributed among these distances:
14 20 0.40
16 3 0.06
17 3 0.06
19 24 0.48
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:238476 original size:33 final size:32
Alignment explanation
Indices: 238434--238541 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 32
238424 ATTAAATTCG
238434 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
238467 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
* *
238500 CGTTGCGATTTTCATTTCGTAATGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
238533 CGTTGCGAT
1 CGTTGCGAT
238542 AGTAATTTCC
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
31 3 0.04
33 61 0.91
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:238550 original size:66 final size:67
Alignment explanation
Indices: 238427--238560 Score: 198
Period size: 66 Copynumber: 2.0 Consensus size: 67
238417 ACGCGAAATT
* ** *
238427 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTT-CGCATTG
1 AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
238491 CG
66 CG
* * *
238493 AAATTCGCGTTGCGATTTTCATTTCGTAATGCGATTCTCTCGTTGCGATAGTAATTTCCGCGTTG
1 AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
238558 CG
66 CG
238560 A
1 A
238561 TAGACATTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
66 51 0.85
67 9 0.15
ACGTcount: A:0.17, C:0.22, G:0.21, T:0.40
Consensus pattern (67 bp):
AAATTCGCGTTGCGATTTTCATTTCGCAATGCGATTCCCTCGTTGCGATAGTAATTTCCGCATTG
CG
Found at i:240849 original size:12 final size:12
Alignment explanation
Indices: 240832--240856 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
240822 TCTTCGGGGA
240832 CTTTTTCTTCTT
1 CTTTTTCTTCTT
240844 CTTTTTCTTCTT
1 CTTTTTCTTCTT
240856 C
1 C
240857 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:241065 original size:24 final size:24
Alignment explanation
Indices: 241031--241084 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
241021 CTGAAACATC
*
241031 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
241055 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
241079 ATCAAA
1 ATCAAA
241085 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:241895 original size:20 final size:20
Alignment explanation
Indices: 241870--241940 Score: 88
Period size: 20 Copynumber: 3.5 Consensus size: 20
241860 TTTCCTAATT
*
241870 CGCAATGTGAATAAGTAAAA
1 CGCAATGCGAATAAGTAAAA
*
241890 CGCAATGCGAATAAGTAAAT
1 CGCAATGCGAATAAGTAAAA
** *
241910 CGCAATGCGAATTTGGAAAA
1 CGCAATGCGAATAAGTAAAA
241930 TCGCAATGCGA
1 -CGCAATGCGA
241941 TACTGACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
20 34 0.77
21 10 0.23
ACGTcount: A:0.42, C:0.15, G:0.23, T:0.20
Consensus pattern (20 bp):
CGCAATGCGAATAAGTAAAA
Found at i:242014 original size:20 final size:20
Alignment explanation
Indices: 241925--242016 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
241915 TGCGAATTTG
* *
241925 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
241945 GACTATCGCAACGAGATAAT
1 GAAAATCGCAACGAGATACT
* *
241965 ACAAAATCGCAACGAGATTCT
1 -GAAAATCGCAACGAGATACT
*** *
241986 GACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
242006 GAAAATCGCAA
1 GAAAATCGCAA
242017 TCATCTTCAA
Statistics
Matches: 54, Mismatches: 17, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.21
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:242296 original size:20 final size:20
Alignment explanation
Indices: 242230--242297 Score: 57
Period size: 20 Copynumber: 3.4 Consensus size: 20
242220 CAACGGGGAA
*
242230 ATCGCAACGCCAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
242250 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
*
242270 ATTGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
242290 ATCGCAAC
1 ATCGCAAC
242298 TAGAAAATCG
Statistics
Matches: 33, Mismatches: 13, Indels: 4
0.66 0.26 0.08
Matches are distributed among these distances:
19 5 0.15
20 23 0.70
21 5 0.15
ACGTcount: A:0.40, C:0.24, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:242495 original size:14 final size:14
Alignment explanation
Indices: 242476--242513 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
242466 CACCAATTAA
242476 ACAAATCAATATTT
1 ACAAATCAATATTT
* *
242490 ACAAATCATTTTTT
1 ACAAATCAATATTT
242504 ACAAATCAAT
1 ACAAATCAAT
242514 TAAACAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (14 bp):
ACAAATCAATATTT
Found at i:244464 original size:33 final size:32
Alignment explanation
Indices: 244422--244510 Score: 151
Period size: 33 Copynumber: 2.7 Consensus size: 32
244412 ATGGCTATCA
244422 CAATGTGAAATGCAAATCGCAACGACAAAATCG
1 CAATGTGAAATG-AAATCGCAACGACAAAATCG
244455 CAATGTGAAATGAAAATCGCAACGACAAAATCG
1 CAATGTGAAATG-AAATCGCAACGACAAAATCG
*
244488 CAATGCGAAATGAAATCGCAACG
1 CAATGTGAAATGAAATCGCAACG
244511 CGAAACACAA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
32 11 0.20
33 43 0.80
ACGTcount: A:0.46, C:0.20, G:0.19, T:0.15
Consensus pattern (32 bp):
CAATGTGAAATGAAATCGCAACGACAAAATCG
Found at i:244505 original size:18 final size:18
Alignment explanation
Indices: 244449--244515 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 18
244439 CGCAACGACA
*
244449 AAATCGCAATGTGAAATG
1 AAATCGCAATGCGAAATG
*
244467 AAAATCGCAA--CGACA--
1 -AAATCGCAATGCGAAATG
244482 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAATG
*
244500 AAATCGCAACGCGAAA
1 AAATCGCAATGCGAAA
244516 CACAAATCGC
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.22
16 4 0.10
17 3 0.08
18 15 0.38
19 9 0.22
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.13
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Found at i:244532 original size:19 final size:18
Alignment explanation
Indices: 244482--244532 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
244472 CGCAACGACA
**
244482 AAATCGCAATGCGAAATG
1 AAATCGCAATGCGAAAAC
*
244500 AAATCGCAACGCGAAACAC
1 AAATCGCAATGCGAAA-AC
*
244519 AAATCGCATTGCGA
1 AAATCGCAATGCGA
244533 TTTTCATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.43, C:0.24, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATCGCAATGCGAAAAC
Found at i:244544 original size:19 final size:19
Alignment explanation
Indices: 244522--244618 Score: 79
Period size: 19 Copynumber: 5.6 Consensus size: 19
244512 GAAACACAAA
244522 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
244541 TCGCGTTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
244557 TCG--TTGTGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
244574 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
244590 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
244607 TCGTATTGCGAT
1 TCGCATTGCGAT
244619 AGCCATTTCC
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 11 0.18
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 22 0.36
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:244568 original size:33 final size:33
Alignment explanation
Indices: 244527--244618 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
244517 ACAAATCGCA
*
244527 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
244560 TTGTGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
244593 TTGCGATTTTCATTTCGTATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
244619 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:244598 original size:14 final size:14
Alignment explanation
Indices: 244544--244602 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
244534 TTTCATTTCG
244544 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
244558 CGTTGTGATTTTCATTT
1 CGTTGCGA-TTT--TGT
244575 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
244591 CGTTGCGATTTT
1 CGTTGCGATTTT
244603 CATTTCGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 17 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 5 0.14
ACGTcount: A:0.10, C:0.15, G:0.24, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:244654 original size:20 final size:20
Alignment explanation
Indices: 244605--244654 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
244595 GCGATTTTCA
* *
244605 TTTCGTATTGCGATAGCCAT
1 TTTCGTGTTGAGATAGCCAT
* * *
244625 TTCCGCGTTGAGATAGTCAT
1 TTTCGTGTTGAGATAGCCAT
244645 TTTCGTGTTG
1 TTTCGTGTTG
244655 CGAAAGTAAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.42
Consensus pattern (20 bp):
TTTCGTGTTGAGATAGCCAT
Found at i:245165 original size:18 final size:18
Alignment explanation
Indices: 245139--245178 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
245129 GTCGATCAGA
* *
245139 TGATGGCTCTGGGTGAGG
1 TGATAGCTCTGGGCGAGG
245157 TGATAGCTCTGGGCGAGG
1 TGATAGCTCTGGGCGAGG
245175 TGAT
1 TGAT
245179 GGATCCCGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.12, G:0.45, T:0.28
Consensus pattern (18 bp):
TGATAGCTCTGGGCGAGG
Found at i:246529 original size:20 final size:20
Alignment explanation
Indices: 246481--246539 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
246471 AATAGTTTCT
** *
246481 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
246501 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
246521 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
246540 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:247082 original size:20 final size:20
Alignment explanation
Indices: 247031--247144 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
247021 GATTATGTAT
*
247031 TATCGCGTTGCAAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
247051 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
247071 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* * *
247092 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
247112 TATCGCATTGC-AATAGTCAG
1 TATCGCGTTGCGAA-AGTCAG
*
247132 TATCGCATTGCGA
1 TATCGCGTTGCGA
247145 TTTTCCCAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
19 4 0.05
20 57 0.75
21 13 0.17
22 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:247117 original size:61 final size:61
Alignment explanation
Indices: 247011--247148 Score: 170
Period size: 61 Copynumber: 2.3 Consensus size: 61
247001 CGCTTTGAAA
* * * * *
247011 ATCGTATTGCGATTATGTATTATCGCGTTGCAAAAGTCAGAATCGCGTTGCGAA-AGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGC-AATAGTCAGT
* * * * *
247072 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCAATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCAATAGTCAGT
247133 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
247149 CCCAATTCGC
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 2 0.03
61 62 0.97
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCAAAAGTAAGAATCGCATTGCAATAGTCAGT
Found at i:247568 original size:18 final size:20
Alignment explanation
Indices: 247535--247573 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
247525 GACAATGGAT
247535 TATTTTATTGTAATATTAAA
1 TATTTTATTGTAATATTAAA
247555 TATTTTA-T-TAATATTAAA
1 TATTTTATTGTAATATTAAA
247573 T
1 T
247574 GTCACATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 11 0.58
19 1 0.05
20 7 0.37
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TATTTTATTGTAATATTAAA
Found at i:248028 original size:32 final size:32
Alignment explanation
Indices: 247992--248066 Score: 150
Period size: 32 Copynumber: 2.3 Consensus size: 32
247982 TTATGGTGTA
247992 GAATAGTTTAAAGTTTATAGCTGGATGACATG
1 GAATAGTTTAAAGTTTATAGCTGGATGACATG
248024 GAATAGTTTAAAGTTTATAGCTGGATGACATG
1 GAATAGTTTAAAGTTTATAGCTGGATGACATG
248056 GAATAGTTTAA
1 GAATAGTTTAA
248067 TAATAAACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (32 bp):
GAATAGTTTAAAGTTTATAGCTGGATGACATG
Found at i:254427 original size:46 final size:46
Alignment explanation
Indices: 254374--254485 Score: 197
Period size: 46 Copynumber: 2.4 Consensus size: 46
254364 GGAATTTTCT
* *
254374 CAATTTAATGAAGTAGGTGGAGTAGGTGACAATAATGTATGACTAG
1 CAATTTAATGGAGTAGGTGGAGTAGGTGACAATAATATATGACTAG
*
254420 CAATTTAATGGAGTAGGTGGAGTAGGTGGCAATAATATATGACTAG
1 CAATTTAATGGAGTAGGTGGAGTAGGTGACAATAATATATGACTAG
254466 CAATTTAATGGAGTAGGTGG
1 CAATTTAATGGAGTAGGTGG
254486 TAATAATGTA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.35, C:0.06, G:0.30, T:0.29
Consensus pattern (46 bp):
CAATTTAATGGAGTAGGTGGAGTAGGTGACAATAATATATGACTAG
Found at i:256229 original size:23 final size:22
Alignment explanation
Indices: 256203--256266 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
256193 CAGCTCAAAT
256203 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
256226 AATTACACCGGAGTGCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
256249 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
256267 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:256407 original size:103 final size:103
Alignment explanation
Indices: 256282--256602 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
256272 TAATGTCCAT
*
256282 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
256347 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
256385 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAACGATAAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
256450 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
256488 AAGAACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
256553 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
256591 AAGGACCACATA
1 AAGGACCACATA
256603 GACCCTCTAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:257121 original size:18 final size:19
Alignment explanation
Indices: 257084--257120 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
257074 TTTTTTATTA
*
257084 TGGGGGAATCGGTTCCCCC
1 TGGGGGAATCGATTCCCCC
*
257103 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
257121 TCTAGCGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.11, C:0.30, G:0.35, T:0.24
Consensus pattern (19 bp):
TGGGGGAATCGATTCCCCC
Found at i:263269 original size:23 final size:23
Alignment explanation
Indices: 263243--263295 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
263233 ATTATACCTA
263243 AGTGCCACGTAGAATTGCACCGG
1 AGTGCCACGTAGAATTGCACCGG
*
263266 AGTGCCACGTAGAATTGCACCGT
1 AGTGCCACGTAGAATTGCACCGG
263289 AGTGCCA
1 AGTGCCA
263296 TATAATAATG
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:0.26, C:0.26, G:0.28, T:0.19
Consensus pattern (23 bp):
AGTGCCACGTAGAATTGCACCGG
Found at i:263434 original size:103 final size:103
Alignment explanation
Indices: 263311--263631 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
263301 TAATGTCCAT
*
263311 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
263376 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* * *
263414 AAAGACCACATATCATTCCTTAAGAATCATATACATATATCAACGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
263479 GACTTCACACATGTTCCAAAGAATACATATATGTCTCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
263517 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
263582 GACCTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
263620 AAGGACCACATA
1 AAGGACCACATA
263632 GACCCTCTAC
Statistics
Matches: 207, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 207 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:264150 original size:19 final size:20
Alignment explanation
Indices: 264113--264150 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
264103 TTTTTTATTA
*
264113 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGATTCCCCCC
*
264133 TGGGGGTATCGATTCCCC
1 TGGGGGAATCGATTCCCC
264151 TCTAGCGTTC
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:0.11, C:0.32, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGATTCCCCCC
Found at i:274374 original size:29 final size:29
Alignment explanation
Indices: 274294--274363 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
274284 AATTGAAATA
* *
274294 AAAATCAAA-GTTTAATGTTATAATTGAC
1 AAAATTAAAGGTTCAATGTTATAATTGAC
*
274322 AAAATTGAAGGTTCAATGTTATAATTGAC
1 AAAATTAAAGGTTCAATGTTATAATTGAC
274351 AAAATTAAAGGTT
1 AAAATTAAAGGTT
274364 GAATTGTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 7 0.19
29 30 0.81
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (29 bp):
AAAATTAAAGGTTCAATGTTATAATTGAC
Found at i:276363 original size:23 final size:21
Alignment explanation
Indices: 276326--276379 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
276316 CGGTTCAACC
*
276326 TAAATTTTTT-TTATTTTTTAT
1 TAAATTTTTTAGTA-TTTTTAT
276347 TAAATGTTTTTAGTATTTTTAT
1 TAAAT-TTTTTAGTATTTTTAT
*
276369 TTAATTTTTTA
1 TAAATTTTTTA
276380 AATAATTATG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.38
22 16 0.55
23 2 0.07
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
TAAATTTTTTAGTATTTTTAT
Found at i:281668 original size:11 final size:11
Alignment explanation
Indices: 281638--281668 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
281628 AAATTGATAG
*
281638 GTTGGCTTCAA
1 GTTGGCTTTAA
281649 GTTGGCTTTAA
1 GTTGGCTTTAA
281660 GTTGGCTTT
1 GTTGGCTTT
281669 CTTATTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.13, G:0.29, T:0.45
Consensus pattern (11 bp):
GTTGGCTTTAA
Found at i:282386 original size:45 final size:45
Alignment explanation
Indices: 282322--282414 Score: 186
Period size: 45 Copynumber: 2.1 Consensus size: 45
282312 TAAGTGTTGT
282322 TGAAATTCAGAAAATCTCATCCTTAGAGTTCAATTTCCAAGAAAC
1 TGAAATTCAGAAAATCTCATCCTTAGAGTTCAATTTCCAAGAAAC
282367 TGAAATTCAGAAAATCTCATCCTTAGAGTTCAATTTCCAAGAAAC
1 TGAAATTCAGAAAATCTCATCCTTAGAGTTCAATTTCCAAGAAAC
282412 TGA
1 TGA
282415 CCTAAACTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (45 bp):
TGAAATTCAGAAAATCTCATCCTTAGAGTTCAATTTCCAAGAAAC
Found at i:286820 original size:24 final size:24
Alignment explanation
Indices: 286793--286870 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
286783 AGGATACCCA
286793 ATAAAGTCTAAAAATTTAGAATAC
1 ATAAAGTCTAAAAATTTAGAATAC
** *
286817 ATAAAAG-C--AAAAGCTAGGATACCC
1 AT-AAAGTCTAAAAATTTAGAATA--C
286841 GATAAAGTCTAAAAATTTAGAATAC
1 -ATAAAGTCTAAAAATTTAGAATAC
286866 ATAAA
1 ATAAA
286871 AGCAAAAGCT
Statistics
Matches: 41, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 10 0.24
24 13 0.32
25 8 0.20
27 10 0.24
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (24 bp):
ATAAAGTCTAAAAATTTAGAATAC
Found at i:286838 original size:22 final size:22
Alignment explanation
Indices: 286809--286901 Score: 80
Period size: 22 Copynumber: 4.0 Consensus size: 22
286799 TCTAAAAATT
286809 TAGAATACATAAAAGCAAAAGC
1 TAGAATACATAAAAGCAAAAGC
* **
286831 TAGGATACCCGAT-AAAGTCTAAAAATT
1 TAGAATA--C-ATAAAAG-C--AAAAGC
286858 TAGAATACATAAAAGCAAAAGC
1 TAGAATACATAAAAGCAAAAGC
* *
286880 TAGAACACGTAAAAGCAAAAGC
1 TAGAATACATAAAAGCAAAAGC
286902 AAAAGCATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
22 30 0.54
24 8 0.14
25 8 0.14
27 10 0.18
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.16
Consensus pattern (22 bp):
TAGAATACATAAAAGCAAAAGC
Found at i:286838 original size:49 final size:49
Alignment explanation
Indices: 286782--286882 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
286772 GCATTAAACA
286782 TAGGATACCCAATAAAGTCTAAAAATTTAGAATACATAAAAGCAAAAGC
1 TAGGATACCCAATAAAGTCTAAAAATTTAGAATACATAAAAGCAAAAGC
*
286831 TAGGATACCCGATAAAGTCTAAAAATTTAGAATACATAAAAGCAAAAGC
1 TAGGATACCCAATAAAGTCTAAAAATTTAGAATACATAAAAGCAAAAGC
286880 TAG
1 TAG
286883 AACACGTAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.21
Consensus pattern (49 bp):
TAGGATACCCAATAAAGTCTAAAAATTTAGAATACATAAAAGCAAAAGC
Found at i:292870 original size:2 final size:2
Alignment explanation
Indices: 292863--292896 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
292853 ACTTGGAATT
*
292863 TG TG TG TG TG TG TG TG TG TG CG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
292897 AACTACAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:298640 original size:72 final size:72
Alignment explanation
Indices: 298526--298737 Score: 288
Period size: 72 Copynumber: 3.0 Consensus size: 72
298516 TTTGACTCCG
* * *
298526 ATGCCTTAGCCAACAGAG---CACCATCCACCACAGTAGTTTCTTGCAAAAGCGTCTCTTTATTT
1 ATGCCTTAGCCAACAGAGAATCACCATCCACCACAGTAGTTTCTTGCAAAAGCGCCTCTTCACTT
298588 TCAGAAA
66 TCAGAAA
*
298595 ATGCCTTAGTCAACAGAGAATCACCATCCACCACAGTAGTTTCTTGCAAAAGCGCCTCTTCACTT
1 ATGCCTTAGCCAACAGAGAATCACCATCCACCACAGTAGTTTCTTGCAAAAGCGCCTCTTCACTT
*
298660 TCAGAAG
66 TCAGAAA
* * * * * *
298667 ATGCCTTAGCCAACAAAGAATCACCGTTCACCACACTAGTTTCTTGCAAAAGCACTTC-TCTACT
1 ATGCCTTAGCCAACAGAGAATCACCATCCACCACAGTAGTTTCTTGCAAAAGCGCCTCTTC-ACT
298731 TTCAGAA
65 TTCAGAA
298738 GCATCATTCA
Statistics
Matches: 127, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
69 17 0.13
71 2 0.02
72 108 0.85
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.26
Consensus pattern (72 bp):
ATGCCTTAGCCAACAGAGAATCACCATCCACCACAGTAGTTTCTTGCAAAAGCGCCTCTTCACTT
TCAGAAA
Found at i:301507 original size:21 final size:20
Alignment explanation
Indices: 301472--301527 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 20
301462 AAACCGGTTT
* *
301472 TACCGGTTTTTAGCCCGTTC
1 TACCGATTTTCAGCCCGTTC
*
301492 -ACCCCGATTTTCAGCCGGTTC
1 TA--CCGATTTTCAGCCCGTTC
301513 TACCGATTTTCAGCC
1 TACCGATTTTCAGCC
301528 GATTCATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 1 0.03
20 13 0.43
21 15 0.50
22 1 0.03
ACGTcount: A:0.14, C:0.34, G:0.18, T:0.34
Consensus pattern (20 bp):
TACCGATTTTCAGCCCGTTC
Found at i:309872 original size:374 final size:372
Alignment explanation
Indices: 309185--309881 Score: 1020
Period size: 374 Copynumber: 1.9 Consensus size: 372
309175 AGACAAATCG
* * * *
309185 TGACTATAGAATAATGATTTATTAAGTCTTTCGACTATTAAAAGTTATAAAATAATTATTTAATT
1 TGACTATAGAATAATGATTTATTAAGTATTTCGACTATTAAAAGTTATAAAATAATCATATAACT
*
309250 ATAAGAAACTACTTTTTTAGTCCCTTAACTATTAAAAGTTACAAAATAGTCACCGACTATTCATT
66 ATAAGAAACTACTTTTTTAGTCCATTAACTATTAAAAGTTACAAAATAGTCACCGACTATTCATT
* * * * *
309315 ATGTTCTAAACTCCTCCTCTTTCGTTAAAAATTAATGTCAGTATGAGATGTACGTTTACTTGTTG
131 ATATTCCAAACTCCTCCTCTTTCGTTAAAAATTAACGTCAGTATGAGATGTACGTTAACTTATTG
* * * * * *
309380 ACTGAGATATGATAAAAAATGATATCATTATCTCAATCAACTATCATATCTCAATTAGCATGTTA
196 ACTGAGATATGATAAAAAATGATATCATAATCTCAAACAACTATCATATCGCAATAAACATGCTA
*
309445 ACGTCCAACTTAACTGGCCGTTAATTTTTTAACGAAAAATGATGAGTTTGGAACATAATGAATCT
261 ACGTCCAACTTAACTGACCGTTAATTTTTTAACGAAAAATGATGAGTTTGGAACATAATGAATCT
309510 TAGAGTGATCATTTTACGTTAATGGGTAAAGTACACAAATGGTCCTC
326 TAGAGTGATCATTTTACGTTAATGGGTAAAGTACACAAATGGTCCTC
* * * * *
309557 TGACTATAGGATAATGTTTTATTAAGTATTTTGACTATTAAAAGTTATAAAATAGTCATATGACT
1 TGACTATAGAATAATGATTTATTAAGTATTTCGACTATTAAAAGTTATAAAATAATCATATAACT
* ** * *
309622 ATAGGAAGTTACTTTTTTTAGTCCATTGACTATTAAAAGTTACAAAAT-GATCACTCGATTATTC
66 ATAAGAAACTAC-TTTTTTAGTCCATTAACTATTAAAAGTTACAAAATAG-TCAC-CGACTATTC
* * * *
309686 ATTATATTCCAAGA-TCCTTCTTTTTCGTTAAAAATTGACGTCGGTATGAGATGTACGTTAACTT
128 ATTATATTCCAA-ACTCCTCCTCTTTCGTTAAAAATTAACGTCAGTATGAGATGTACGTTAACTT
* * *
309750 ATTGACTGAGATATGATAAAATATGATATCATAATCTTAAACAACTATCATATCGCAGTAAACAT
192 ATTGACTGAGATATGATAAAAAATGATATCATAATCTCAAACAACTATCATATCGCAATAAACAT
* *
309815 GCTAACGTCTAACTTAACTGACCGTTAATTTTTTAACGAAAAATGATGATTTTGGAACATAATGA
257 GCTAACGTCCAACTTAACTGACCGTTAATTTTTTAACGAAAAATGATGAGTTTGGAACATAATGA
309880 AT
322 AT
309882 GGTAGGCTGT
Statistics
Matches: 285, Mismatches: 36, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
372 66 0.23
373 37 0.13
374 181 0.64
375 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (372 bp):
TGACTATAGAATAATGATTTATTAAGTATTTCGACTATTAAAAGTTATAAAATAATCATATAACT
ATAAGAAACTACTTTTTTAGTCCATTAACTATTAAAAGTTACAAAATAGTCACCGACTATTCATT
ATATTCCAAACTCCTCCTCTTTCGTTAAAAATTAACGTCAGTATGAGATGTACGTTAACTTATTG
ACTGAGATATGATAAAAAATGATATCATAATCTCAAACAACTATCATATCGCAATAAACATGCTA
ACGTCCAACTTAACTGACCGTTAATTTTTTAACGAAAAATGATGAGTTTGGAACATAATGAATCT
TAGAGTGATCATTTTACGTTAATGGGTAAAGTACACAAATGGTCCTC
Found at i:323055 original size:3 final size:3
Alignment explanation
Indices: 323044--323107 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
323034 TTTTTTTTCG
** *
323044 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
323089 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
323108 CAAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:323085 original size:32 final size:32
Alignment explanation
Indices: 323041--323105 Score: 105
Period size: 32 Copynumber: 2.0 Consensus size: 32
323031 GGTTTTTTTT
*
323041 TCGTTATTTTATTATTATTATTATTA-TTATTA
1 TCGTTATCTTATTATT-TTATTATTATTTATTA
323073 TCGTTATCTTATTATTTTATTATTATTTATTA
1 TCGTTATCTTATTATTTTATTATTATTTATTA
323105 T
1 T
323106 TACAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.29
32 22 0.71
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
TCGTTATCTTATTATTTTATTATTATTTATTA
Found at i:324288 original size:20 final size:23
Alignment explanation
Indices: 324241--324294 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
324231 TCAGTCATTA
*
324241 ATTTATATATTATGTTTGCTGAT
1 ATTTATATATTATGGTTGCTGAT
324264 A-TTATA-ATT-TGGTTG-TGAT
1 ATTTATATATTATGGTTGCTGAT
324283 ATTTATAT-TTAT
1 ATTTATATATTAT
324295 TTCGTTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 4 0.15
22 5 0.19
23 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (23 bp):
ATTTATATATTATGGTTGCTGAT
Found at i:325282 original size:22 final size:22
Alignment explanation
Indices: 325257--325300 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
325247 TCAAACGATG
*
325257 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
325279 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
325301 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:326844 original size:31 final size:32
Alignment explanation
Indices: 326808--326869 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
326798 ATTTTACATG
326808 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
326839 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
326870 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:328295 original size:26 final size:25
Alignment explanation
Indices: 328266--328343 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
328256 AAATTTTGAC
328266 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
328292 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
328312 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
328338 ATTCTT
1 ATTCTT
328344 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:328304 original size:20 final size:20
Alignment explanation
Indices: 328281--328355 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
328271 ATCTCTTTGA
328281 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
328301 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
328327 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
328346 CACCTTGAAA
1 GACCTTGAAA
328356 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:329844 original size:23 final size:24
Alignment explanation
Indices: 329818--329862 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
329808 TGAAAGGAGC
*
329818 AATA-TTTTCAAAACTTTTGATTA
1 AATATTTTTCAAAACTATTGATTA
329841 AATATTTTTCAAAACTATTGAT
1 AATATTTTTCAAAACTATTGAT
329863 ATTTTCAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (24 bp):
AATATTTTTCAAAACTATTGATTA
Found at i:330157 original size:4 final size:4
Alignment explanation
Indices: 330148--330197 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
330138 GATCGAGAAA
*
330148 ACAT ACAT ACAT ACAT ACAT ATAT AC-- ACAT ACAT ACAT ACAT A-AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
330193 ACAT A
1 ACAT A
330198 AAATTTGCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 36 0.88
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:330178 original size:22 final size:21
Alignment explanation
Indices: 330152--330195 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
330142 GAGAAAACAT
330152 ACATACATACATACATATATAC
1 ACATACATACATACATA-ATAC
330174 ACATACATACATACATAATAC
1 ACATACATACATACATAATAC
330195 A
1 A
330196 TAAAATTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.25
Consensus pattern (21 bp):
ACATACATACATACATAATAC
Found at i:330682 original size:105 final size:105
Alignment explanation
Indices: 330541--330730 Score: 283
Period size: 105 Copynumber: 1.8 Consensus size: 105
330531 TGAGAATTTT
* *
330541 AAAACAAATTGCGTCTCACTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTGCGTCTCACTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
330605 TTAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
66 TT-AAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
* * * * *
330646 AAAACAAATTTCGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGAATTTGTTTCACA
1 AAAACAAATTGCGTCTCACTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* *
330711 TTAAACAAAGTTGATCTCAC
66 TTAAACAAAATTAATCTCAC
330731 TTGAGATCGT
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
105 73 0.97
106 2 0.03
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (105 bp):
AAAACAAATTGCGTCTCACTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TTAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC
Found at i:330787 original size:36 final size:34
Alignment explanation
Indices: 330747--330844 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 34
330737 TCGTTTCCTC
*
330747 AAAAACAAACTTTGTCTCGCTTGAGACAATTTCTCT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCT-T
** *
330783 AAAAACAAATTTTGTCTCATTTGAGACTATATCTT
1 AAAAACAAA-TTTGTCTCGCTTGAGACAATATCTT
*
330818 -AAAGCAAATTTCGTCTCGCTTGAGACA
1 AAAAACAAATTT-GTCTCGCTTGAGACA
330845 TCATTTTCTC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 3 0.06
34 19 0.37
35 1 0.02
36 29 0.56
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (34 bp):
AAAAACAAATTTGTCTCGCTTGAGACAATATCTT
Found at i:331170 original size:56 final size:55
Alignment explanation
Indices: 331086--331217 Score: 187
Period size: 56 Copynumber: 2.4 Consensus size: 55
331076 AAGACAATTT
331086 CTTTTGAAAAAATCTTTGAGTTTGTTCCTCTTG-A-AAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAG-TTGTTC
* * *
331140 CTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAGTTGTTT
1 CTTTTG-A-AAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGTTC
*
331197 CGTTTGAAAAAATCTTTGAGT
1 CTTTTGAAAAAATCTTTGAGT
331218 CTATTTATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
54 6 0.09
55 14 0.20
56 25 0.36
57 11 0.16
58 13 0.19
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (55 bp):
CTTTTGAAAAAATCTTTGAGTTTGTTCCTCTTGAATAAAAATCTTTGAGTTGTTC
Found at i:331232 original size:27 final size:27
Alignment explanation
Indices: 331086--331217 Score: 185
Period size: 29 Copynumber: 4.8 Consensus size: 27
331076 AAGACAATTT
331086 CTTTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
*
331113 CTCTTGAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAATCTTTGAGTTTGTTC
*
331140 CTTTTGAATAAAAATCTTGGAGTTTGTTC
1 CTTTTG-A-AAAAATCTTTGAGTTTGTTC
*
331169 CTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTG-A-AAAAATCTTTGAGTTTGTTC
*
331197 CGTTTGAAAAAATCTTTGAGT
1 CTTTTGAAAAAATCTTTGAGT
331218 CTATTTATTT
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
26 13 0.14
27 32 0.33
28 11 0.11
29 40 0.42
ACGTcount: A:0.28, C:0.11, G:0.16, T:0.45
Consensus pattern (27 bp):
CTTTTGAAAAAATCTTTGAGTTTGTTC
Found at i:331251 original size:93 final size:92
Alignment explanation
Indices: 331173--331359 Score: 299
Period size: 93 Copynumber: 2.0 Consensus size: 92
331163 TTGTTCCTTT
331173 TGAATAAAAATCTTTGAG-TTGTTTCGTTTG-A-AAAAATCTTTGAGTCTATTTATTTTGAAACA
1 TGAA-AAAAATCTTTGAGATTGTTTCGTTTGAACAAAAATCTTTGAGTCTATTTATTTTGAAACA
331235 AAGTTTTGTCTCTCTTGAGACAATTTTG
65 AAGTTTTGTCTCTCTTGAGACAATTTTG
* *
331263 TGAAAAAAATCTTTGAGATTGTTTCTTTTGAAACAAAAATCTTTGAGTCTATTTCTTTTGAAACA
1 TGAAAAAAATCTTTGAGATTGTTTCGTTTG-AACAAAAATCTTTGAGTCTATTTATTTTGAAACA
* *
331328 AAGTTTTGTCTCTCTTAAGACAATTTCG
65 AAGTTTTGTCTCTCTTGAGACAATTTTG
331356 TGAA
1 TGAA
331360 GAATATTTGA
Statistics
Matches: 89, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
89 13 0.15
90 15 0.17
92 1 0.01
93 60 0.67
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (92 bp):
TGAAAAAAATCTTTGAGATTGTTTCGTTTGAACAAAAATCTTTGAGTCTATTTATTTTGAAACAA
AGTTTTGTCTCTCTTGAGACAATTTTG
Found at i:331301 original size:30 final size:30
Alignment explanation
Indices: 331267--331329 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
331257 ATTTTGTGAA
*
331267 AAAAATCTTTGAGAT-TGTTTCTTTTGAAAC
1 AAAAATCTTTGAG-TCTATTTCTTTTGAAAC
331297 AAAAATCTTTGAGTCTATTTCTTTTGAAAC
1 AAAAATCTTTGAGTCTATTTCTTTTGAAAC
331327 AAA
1 AAA
331330 GTTTTGTCTC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (30 bp):
AAAAATCTTTGAGTCTATTTCTTTTGAAAC
Found at i:331397 original size:145 final size:146
Alignment explanation
Indices: 331228--331494 Score: 482
Period size: 147 Copynumber: 1.8 Consensus size: 146
331218 CTATTTATTT
*
331228 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTG-AAAAAAATCTTTGAGATTGTTTCTTTT
1 TGAAACAAAGTTTTGTCTCCCTTGAGACAATTTTGTGAAAAAAAATCTTTGAGATTGTTTCTTTT
* *
331292 GAAACAAAAATCTTTGAGTCTATTTCTTTTGAAACAAAGTTTTGTCTCTCTTAAGACAATTTCGT
66 GAAACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTCGT
331357 GAAGAATATTTGAGTC
131 GAAGAATATTTGAGTC
331373 TGAAACAAAGTTTTGTCTCCCTTGAGACAATTTTGTGAAAAAAAAATCTTTGAGATTGTTTCTTT
1 TGAAACAAAGTTTTGTCTCCCTTGAGACAATTTTGTG-AAAAAAAATCTTTGAGATTGTTTCTTT
*
331438 TGAAACAAAAATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
65 TGAAACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
331495 TATTTTCTTT
Statistics
Matches: 116, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
145 36 0.31
147 80 0.69
ACGTcount: A:0.32, C:0.13, G:0.15, T:0.40
Consensus pattern (146 bp):
TGAAACAAAGTTTTGTCTCCCTTGAGACAATTTTGTGAAAAAAAATCTTTGAGATTGTTTCTTTT
GAAACAAAAATCTTTGAGTCTATTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGACAATTTCGT
GAAGAATATTTGAGTC
Found at i:331448 original size:30 final size:30
Alignment explanation
Indices: 331408--331477 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 30
331398 GACAATTTTG
*
331408 TGAAAAAAAAATCTTTGAGAT-TGTTTCTTT
1 TGAAACAAAAATCTTTGAG-TCTGTTTCTTT
331438 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
1 TGAAACAAAAATCTTTGAGTCTGTTTCTTT
*
331468 GGAAACAAAA
1 TGAAACAAAA
331478 TTTTGTCTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 36 0.97
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (30 bp):
TGAAACAAAAATCTTTGAGTCTGTTTCTTT
Found at i:331838 original size:66 final size:65
Alignment explanation
Indices: 331757--331880 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 65
331747 GATGTAATCC
* * *
331757 ATCTTTGAGTCTGTTTCTTTTGAAATGAAA-TTTTATCTCTTAATGACAATTTCTTTTGAGAAAA
1 ATCTTTGAGTCTGTTTCCTTTGAAA-CAAACTTTTATCTCTCAA-GACAATTTCTTTTGAGAAAA
331821 AA
64 AA
* * *
331823 ATCTTTGAGTTTGTTTCCTTTGAAACAAACTTTTGTCTCTCGAGACAATTTCTTTTGA
1 ATCTTTGAGTCTGTTTCCTTTGAAACAAACTTTTATCTCTCAAGACAATTTCTTTTGA
331881 AAATACACAC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
65 18 0.35
66 33 0.65
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.46
Consensus pattern (65 bp):
ATCTTTGAGTCTGTTTCCTTTGAAACAAACTTTTATCTCTCAAGACAATTTCTTTTGAGAAAAAA
Found at i:331905 original size:66 final size:64
Alignment explanation
Indices: 331801--331924 Score: 144
Period size: 65 Copynumber: 1.9 Consensus size: 64
331791 ATCTCTTAAT
* * * * *
331801 GACAATTTCTTTTGAGAAAAAAATCTTTGAGTTTGTTTCCT-TTGAAACAAACTTTTGTCTCTCG
1 GACAATTTCTTTTGAGAAAAAAACCTTCGAGATCGTTT-CTATTAAAACAAA-TTTTGTCTCTCG
331865 A
64 A
*
331866 GACAATTTCTTTTGA-AAATACACACCTTCGAGATCGTTTCTATTAAAACAAATTTTGTC
1 GACAATTTCTTTTGAGAAA-A-AAACCTTCGAGATCGTTTCTATTAAAACAAATTTTGTC
331925 CCCCTTTAGG
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
64 3 0.06
65 25 0.50
66 22 0.44
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (64 bp):
GACAATTTCTTTTGAGAAAAAAACCTTCGAGATCGTTTCTATTAAAACAAATTTTGTCTCTCGA
Found at i:332041 original size:15 final size:16
Alignment explanation
Indices: 332000--332047 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
331990 CTTTGAGTCG
332000 TTTCCCTTGAAACAAATT
1 TTTCCCTTGAAAC--ATT
332018 TTGTCCCTTGAAACA-T
1 TT-TCCCTTGAAACATT
*
332034 TTTCCCTTAAAACA
1 TTTCCCTTGAAACA
332048 AGAACATCTG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 11 0.39
16 3 0.11
17 1 0.04
18 2 0.07
19 11 0.39
ACGTcount: A:0.31, C:0.25, G:0.06, T:0.38
Consensus pattern (16 bp):
TTTCCCTTGAAACATT
Found at i:332478 original size:66 final size:65
Alignment explanation
Indices: 332357--332495 Score: 172
Period size: 66 Copynumber: 2.1 Consensus size: 65
332347 ACAAAACAAA
* * ** *
332357 CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACGC
1 CATCTTTGAGAACGTTTCCCTTAAAACAAATTTTGTCTCACTTGAGACAATTTCCCATGAAACGC
* * * *
332422 CGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCGCTTGAGACAA-TTCCCTTTAAAT
1 C-ATCTTTGAGAACGTTTCCCTT-AAAACAAATTTTGTCTCACTTGAGACAATTTCCCATGAAAC
332486 GC
64 GC
332488 CATCTTTG
1 CATCTTTG
332496 GGTTGTTTCC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
65 8 0.13
66 32 0.51
67 23 0.37
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (65 bp):
CATCTTTGAGAACGTTTCCCTTAAAACAAATTTTGTCTCACTTGAGACAATTTCCCATGAAACGC
Found at i:332704 original size:28 final size:28
Alignment explanation
Indices: 332654--332707 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
332644 TCAAAATCCA
* * *
332654 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTCTCCATTGAAACAC
*
332682 ATCTTTGAGTTGGTCTCCCTTGAAAC
1 ATCTTTGAGTTGGTCTCCATTGAAAC
332708 CATTATCCCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.17, T:0.43
Consensus pattern (28 bp):
ATCTTTGAGTTGGTCTCCATTGAAACAC
Found at i:332789 original size:46 final size:45
Alignment explanation
Indices: 332736--332929 Score: 165
Period size: 46 Copynumber: 4.4 Consensus size: 45
332726 CCAGCCGTCC
* * *
332736 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCATAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGGCCAGAACTCT
* * *
332782 TCATCACGTATGAGCCGTGTCATTC-CC--CGA---CCAGATCTCT
1 TCATCACGTATGAGCCGTGTTA-TCACCTTAGATGGCCAGAACTCT
* ** * *
332822 TCATCACGTATGAGCCGTG---TCACCCTAGATAACCAG-CCGTCC
1 TCATCACGTATGAGCCGTGTTATCACCTTAGATGGCCAGAAC-TCT
* *
332864 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTATGAGCCGTGTTATCACC-TTAGATGGCCAGAACTCT
332910 TCATCACGTATGAGCCGTGT
1 TCATCACGTATGAGCCGTGT
332930 CATTCCCGAC
Statistics
Matches: 117, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
36 2 0.02
37 2 0.02
39 2 0.02
40 27 0.23
41 1 0.01
42 23 0.20
43 2 0.02
45 5 0.04
46 50 0.43
47 3 0.03
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.27
Consensus pattern (45 bp):
TCATCACGTATGAGCCGTGTTATCACCTTAGATGGCCAGAACTCT
Found at i:332870 original size:42 final size:42
Alignment explanation
Indices: 332778--333054 Score: 216
Period size: 42 Copynumber: 6.6 Consensus size: 42
332768 ATGGCCATAA
* *
332778 CTCTTCATCACGTATGAGCCGTGTCATTCCC-CG---ACCAGAT
1 CTCTTCATCACGTATGAGCCGTGTCA--CCCTAGATAACCAGAC
332818 CTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAG-C
1 CTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAGAC
* * * * ** *
332859 CGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAA
1 C-TCTTCATCACGTATGAGCCGTG---TCACC-CTAGATAACCAGAC
*
332906 CTCTTCATCACGTATGAGCCGTGTCATTCCC--G---ACCAGAT
1 CTCTTCATCACGTATGAGCCGTGTCA--CCCTAGATAACCAGAC
**
332945 CTCTTCATCACGTATGAATCGTGTCACCCTAGATAACCAG-C
1 CTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAGAC
* * *
332986 CGTCCTCATCACGTAGGAGCCGTGTCACCCTTAGATGACCAGAC
1 C-TCTTCATCACGTATGAGCCGTGTCACCC-TAGATAACCAGAC
** *
333030 CTCTTCATTGCGTATGAGCAGTGTC
1 CTCTTCATCACGTATGAGCCGTGTC
333055 GTCCCCACCA
Statistics
Matches: 189, Mismatches: 28, Indels: 37
0.74 0.11 0.15
Matches are distributed among these distances:
37 3 0.02
38 3 0.02
39 31 0.16
40 26 0.14
41 2 0.01
42 54 0.29
43 32 0.17
44 2 0.01
45 7 0.04
46 28 0.15
47 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (42 bp):
CTCTTCATCACGTATGAGCCGTGTCACCCTAGATAACCAGAC
Found at i:333221 original size:3 final size:3
Alignment explanation
Indices: 333210--333272 Score: 78
Period size: 3 Copynumber: 22.0 Consensus size: 3
333200 TTTTTTTTCG
** *
333210 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
333256 TTA TT- TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
333273 CAAATTTTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
2 5 0.10
3 46 0.90
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:334454 original size:20 final size:23
Alignment explanation
Indices: 334407--334460 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
334397 TCAGTCATTA
*
334407 ATTTATATATTATGTTTGCTGAT
1 ATTTATATATTATGGTTGCTGAT
334430 A-TTATA-ATT-TGGTTG-TGAT
1 ATTTATATATTATGGTTGCTGAT
334449 ATTTATAT-TTAT
1 ATTTATATATTAT
334461 TTCGTTTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
19 5 0.19
20 12 0.44
21 4 0.15
22 5 0.19
23 1 0.04
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (23 bp):
ATTTATATATTATGGTTGCTGAT
Found at i:335444 original size:22 final size:22
Alignment explanation
Indices: 335419--335462 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
335409 TCAAACGATG
*
335419 CAATGTGTGTTATTTTAAGTGA
1 CAATGTATGTTATTTTAAGTGA
* * *
335441 CAATTTATTTTATTTTATGTGA
1 CAATGTATGTTATTTTAAGTGA
335463 ATGTAAATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.27, C:0.05, G:0.16, T:0.52
Consensus pattern (22 bp):
CAATGTATGTTATTTTAAGTGA
Found at i:337597 original size:24 final size:24
Alignment explanation
Indices: 337570--337702 Score: 94
Period size: 23 Copynumber: 5.7 Consensus size: 24
337560 CATTTAAATG
*
337570 ATAAACGAATACAAATAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
* * * **
337594 ATAAATGGACAGATGTAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
*
337618 ATAAACAAACAC-AATAAACGAA-
1 ATAAACGAACACAAATAAACGAAC
* * *
337640 AGTAAACAAACATAAATGAACG-AC
1 A-TAAACGAACACAAATAAACGAAC
* * *
337664 GTAAACGAAAAC-AATAAATGAAC
1 ATAAACGAACACAAATAAACGAAC
* *
337687 TTAAACGAACATAAAT
1 ATAAACGAACACAAAT
337703 GAAAATAGAT
Statistics
Matches: 81, Mismatches: 23, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
22 7 0.09
23 38 0.47
24 36 0.44
ACGTcount: A:0.59, C:0.15, G:0.11, T:0.14
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:340311 original size:2 final size:2
Alignment explanation
Indices: 340304--340333 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
340294 CTTAACGTAA
340304 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
340334 CACACATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:369964 original size:29 final size:29
Alignment explanation
Indices: 369927--370019 Score: 168
Period size: 29 Copynumber: 3.2 Consensus size: 29
369917 TAAAGAAGTA
*
369927 AATTTATAATTTATTAGAGAAGACGAATT
1 AATTAATAATTTATTAGAGAAGACGAATT
369956 AATTAATAATTTATTAGAGAAGACGAATT
1 AATTAATAATTTATTAGAGAAGACGAATT
*
369985 AATTAATAATTTATTAGAGAAGACAAATT
1 AATTAATAATTTATTAGAGAAGACGAATT
370014 AATTAA
1 AATTAA
370020 ATTTTATGGG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 62 1.00
ACGTcount: A:0.49, C:0.03, G:0.12, T:0.35
Consensus pattern (29 bp):
AATTAATAATTTATTAGAGAAGACGAATT
Found at i:371873 original size:21 final size:21
Alignment explanation
Indices: 371824--371877 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
371814 TATCGCAAAT
* *
371824 TCGCGTTACAATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
371845 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
371866 TCGCGTTGCGAT
1 TCGCGTTGCGAT
371878 TTTCCATTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:371919 original size:22 final size:22
Alignment explanation
Indices: 371889--371960 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
371879 TTCCATTTCG
371889 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * * **
371911 CGTTACGAT--TTTTCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
371930 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
371952 CGTTGCGAT
1 CGTTGCGAT
371961 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:371934 original size:41 final size:41
Alignment explanation
Indices: 371889--371978 Score: 162
Period size: 41 Copynumber: 2.2 Consensus size: 41
371879 TTCCATTTCG
*
371889 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTTCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
*
371930 CGTTGCGATAGTCTACAGTTGTCGTTGCGATTTTCCAAATT
1 CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
371971 CGTTGCGA
1 CGTTGCGA
371979 AAATCGCGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
CGTTGCGATAGTCTACAGTTGTCGTTACGATTTTCCAAATT
Found at i:371938 original size:19 final size:19
Alignment explanation
Indices: 371910--371978 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
371900 TCTACAGTTG
* *
371910 TCGTTACGATTTTTCAAAT
1 TCGTTGCGATTTTACAAAT
* **
371929 TCGTTGCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTACAAAT
*
371950 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTACAAAT
371970 TCGTTGCGA
1 TCGTTGCGA
371979 AAATCGCGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 18 0.47
20 5 0.13
21 5 0.13
22 10 0.26
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Done.