Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008480.1 Hibiscus syriacus cultivar Beakdansim tig00111311_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: 2515485
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:577610 original size:64 final size:65
Alignment explanation
Indices: 577536--577691 Score: 217
Period size: 65 Copynumber: 2.4 Consensus size: 65
577526 ACACCATAAT
*
577536 TCGAATGCATTTTGTGTACCGATGCACA-ACCATGCATCGATGCACTCCT-GATTTTATTGAAAC
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTT-TTGAAAC
577599 A
65 A
* * * *
577600 TCGAATGCATTTTATGTACTGATGCAAAGACCATGCATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
* * *
577665 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGCATTTTGTGTACCGATGCAC
577692 CCCAAGTGTA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 25 0.32
65 50 0.63
66 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (65 bp):
TCGAATGCATTTTGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGATCTTTTGAAACA
Found at i:580297 original size:24 final size:24
Alignment explanation
Indices: 580265--580315 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
580255 CTTTCGCTTT
580265 AATTGAGCTCAAATTTTAGGCATC
1 AATTGAGCTCAAATTTTAGGCATC
*
580289 AATTGAGCTCAAATTTTAGGCTTC
1 AATTGAGCTCAAATTTTAGGCATC
580313 AAT
1 AAT
580316 CGAACTTCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (24 bp):
AATTGAGCTCAAATTTTAGGCATC
Found at i:580549 original size:30 final size:30
Alignment explanation
Indices: 580524--580608 Score: 161
Period size: 30 Copynumber: 2.8 Consensus size: 30
580514 GGTTCAAACT
580524 GGTTTTGCCGGTTTTCAGCCGGTTCACCCC
1 GGTTTTGCCGGTTTTCAGCCGGTTCACCCC
580554 GGTTTTGCCGGTTTTCAGCCGGTTCACCCC
1 GGTTTTGCCGGTTTTCAGCCGGTTCACCCC
*
580584 GGTTTTCCCGGTTTTCAGCCGGTTC
1 GGTTTTGCCGGTTTTCAGCCGGTTC
580609 TTCCGGTTCT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.06, C:0.32, G:0.27, T:0.35
Consensus pattern (30 bp):
GGTTTTGCCGGTTTTCAGCCGGTTCACCCC
Found at i:589620 original size:42 final size:42
Alignment explanation
Indices: 589559--589723 Score: 217
Period size: 42 Copynumber: 4.0 Consensus size: 42
589549 AGCAAATCCG
*
589559 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTT-TGGTCCA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT-CA
*
589601 TCAGTAAGTCTTTCAAGCATGATGATGAAATCCTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
* *
589643 TCAGTAAGCCTTTCGAGCATGATGATTAAATCCTTCGGGTCA
1 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
** * * * *
589685 TTTGTGAGTCTCTCGAGCAAGATGAT-AAATCCTTTGGGT
1 TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGT
589724 TATCCATAAG
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
41 12 0.11
42 95 0.86
43 3 0.03
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (42 bp):
TCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGTCA
Found at i:590151 original size:53 final size:53
Alignment explanation
Indices: 590071--590323 Score: 321
Period size: 53 Copynumber: 4.8 Consensus size: 53
590061 ATCACACCAT
* *
590071 AAGATTGTTCGAGTTATACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGTAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
590124 AAGATTGTTCGAGTTTTACTCCCTGAAGTAATAGGGAGCGAACCCGTAGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* * *
590177 AAGATTGTTCGAGTTCTACTCCCTAAAGCAAGAGGGAGTGAACCCGTGGGCAG
1 AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
** ****
590230 AAGATTGTTCGAGTTCTAC-CCCTTGAAGCAAGAGGGAGCGAACCAATTTTTAG
1 AAGATTGTTCGAGTTCTACTCCC-TGAAGCAAGAGGGAGCGAACCCGTAGGCAG
* *
590283 AAGATTGTTCGAGTTCCTTAATCCCTTAA-CAAGAGGGAGCG
1 AAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCG
590324 GACCTGTCAT
Statistics
Matches: 176, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
52 3 0.02
53 152 0.86
54 13 0.07
55 5 0.03
56 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (53 bp):
AAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAG
Found at i:594474 original size:58 final size:59
Alignment explanation
Indices: 594374--594494 Score: 210
Period size: 58 Copynumber: 2.1 Consensus size: 59
594364 AAAACGTAAA
*
594374 TCAAATAAAAGAAATCATAGTTCAAATACTTAAACACTAATAGTGTAAACAACCATAGT
1 TCAAATAAAAGAAATCATAGTTCAAATACTAAAACACTAATAGTGTAAACAACCATAGT
594433 TCAAATAAAAGACAA-CATAGTT-AAATACTAAAACACTAATAGTGTAAACAACCATAGT
1 TCAAATAAAAGA-AATCATAGTTCAAATACTAAAACACTAATAGTGTAAACAACCATAGT
594491 TCAA
1 TCAA
594495 TATCATGACC
Statistics
Matches: 60, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
58 39 0.65
59 19 0.32
60 2 0.03
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (59 bp):
TCAAATAAAAGAAATCATAGTTCAAATACTAAAACACTAATAGTGTAAACAACCATAGT
Found at i:601319 original size:3 final size:3
Alignment explanation
Indices: 601311--601366 Score: 94
Period size: 3 Copynumber: 18.3 Consensus size: 3
601301 ATATATATAT
601311 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA GATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
*
601360 AAA ATA A
1 ATA ATA A
601367 AAACGAGATA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:601761 original size:90 final size:90
Alignment explanation
Indices: 601578--602414 Score: 1057
Period size: 90 Copynumber: 9.3 Consensus size: 90
601568 TTAGTTCTCC
* * * *
601578 TTTGAAAATATCCTGCACTGAAGGTCTTATGGATGACTCGAAGG-CTTTAACATCTTGCACTGAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
* * *
601642 GGTCTTACAGATGATCCAAAGGCTT
66 GGTCTTACAGATGACCCGAAGGATT
* *
601667 TTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGGA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
601732 GGTCTTACAGATGACCCGAAGGATT
66 GGTCTTACAGATGACCCGAAGGATT
* * * * * *
601757 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATTGCTCGAATGACTTTAACTTTTTGCACTAAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
601822 GGTCTTACAGATGACCCGAAGGACTT
66 GGTCTTACAGATGACCCGAAGGA-TT
* *
601848 TCTGAAAACATCCTGCATTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
*
601913 GGTCTTACAGATGACCCAAAGGATT
66 GGTCTTACAGATGACCCGAAGGATT
601938 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
* * *
602003 GGTCTTACATATGACCCAAAGGGACT
66 GGTCTTACAGATGACCCGAA-GGATT
602029 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
* * *
602094 AGTCTTACAAATGACCCGAAGGACT
66 GGTCTTACAGATGACCCGAAGGATT
** * *
602119 TTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGG-TTTTAACATCTTGCACTGAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
602183 GGTCTTACAGATGA-CCGAAGGATT
66 GGTCTTACAGATGACCCGAAGGATT
** **
602207 TTTGAAAACATCCTGCACTGTAGGTCTTACAGATGATCCGAAGG-CTTTGAAAACATCCTT-CAC
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTT---AACAT-CTTGCAC
* ** * *
602270 TGTAGGTCTTATGGATAACCCGAATG--T
62 TGAAGGTCTTACAGATGACCCGAAGGATT
* * * * * * *
602297 TTTGAAAACATCATGCACTGAAGGTCTTA-GAGATGACCCGATGG-TTTTGAAAAATCCTGCACT
1 TTTGAAAACATCCTGCACTGTAGGTCTTATG-GATGGCCCGAAGGACTTT--AACATCTTGCACT
* ** * *
602360 GTAGGTCTTATGGATGGCCTGAAGG--T
63 GAAGGTCTTACAGATGACCCGAAGGATT
* *
602386 TTTGAAAACATCATGCACTGAAGGTCTTA
1 TTTGAAAACATCCTGCACTGTAGGTCTTA
602415 CAGATGATCC
Statistics
Matches: 680, Mismatches: 58, Indels: 20
0.90 0.08 0.03
Matches are distributed among these distances:
88 57 0.08
89 132 0.19
90 293 0.43
91 189 0.28
92 9 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (90 bp):
TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
GGTCTTACAGATGACCCGAAGGATT
Found at i:601885 original size:181 final size:180
Alignment explanation
Indices: 601578--602337 Score: 1045
Period size: 181 Copynumber: 4.2 Consensus size: 180
601568 TTAGTTCTCC
* * * *
601578 TTTGAAAATATCCTGCACTGAAGGTCTTATGGATGACTCGAAGGCTTTAACATCTTGCACTGAAG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGACTTTAACATCTTGCACTGAAG
* *
601643 GTCTTACAGATGATCCAAAGG-CTTTTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCG
66 GTCTTACAGATGACCCAAAGGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCG
*
601707 AAGGACTTTAACATCTTGCACTGGAGGTCTTACAGATGACCCGAAGGATT
131 AAGGACTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATT
* * * *
601757 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATTG-CTCGAATGACTTTAACTTTTTGCACTAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGA-TGACCCGAA-GACTTTAACATCTTGCACTGA
* * *
601821 AGGTCTTACAGATGACCCGAAGGACTTTCTGAAAACATCCTGCATTGTAGGTCTTATGGATGGCC
64 AGGTCTTACAGATGACCCAAAGGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCC
*
601886 CGAAGGACTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCAAAGGATT
129 CGAAGGACTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATT
*
601938 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCGAAGGACTTTAACATCTTGCACTGAA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAA-GACTTTAACATCTTGCACTGAA
*
602003 GGTCTTACATATGACCCAAAGGGAC-TTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCC
65 GGTCTTACAGATGACCCAAA-GGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCC
* * *
602067 CGAAGGACTTTAACATCTTGCACTGAAAGTCTTACAAATGACCCGAAGGACT
129 CGAAGGACTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATT
** **
602119 TTTGAAAACATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTTTTAACATCTTGCACTGAAG
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGACTTTAACATCTTGCACTGAAG
* ** **
602184 GTCTTACAGATGA-CCGAAGGA-TTTTTGAAAACATCCTGCACTGTAGGTCTTACAGATGATCCG
66 GTCTTACAGATGACCCAAAGGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCG
* ** * *
602247 AAGG-CTTTGAAAACATCCTT-CACTGTAGGTCTTATGGATAACCCGAATG--T
131 AAGGACTTT---AACAT-CTTGCACTGAAGGTCTTACAGATGACCCGAAGGATT
* *
602297 TTTGAAAACATCATGCACTGAAGGTCTTA-GAGATGACCCGA
1 TTTGAAAACATCCTGCACTGTAGGTCTTATG-GATGACCCGA
602338 TGGTTTTGAA
Statistics
Matches: 523, Mismatches: 47, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
177 4 0.01
178 82 0.16
179 41 0.08
180 102 0.20
181 290 0.55
182 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.29
Consensus pattern (180 bp):
TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCGAAGACTTTAACATCTTGCACTGAAG
GTCTTACAGATGACCCAAAGGACTTTTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCG
AAGGACTTTAACATCTTGCACTGAAGGTCTTACAGATGACCCGAAGGATT
Found at i:603742 original size:54 final size:54
Alignment explanation
Indices: 603530--603739 Score: 294
Period size: 54 Copynumber: 3.9 Consensus size: 54
603520 ATAATCACTG
*
603530 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGTTTCTGCACAGAT
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
* * * * *
603584 GTTCGTAAAACGTTTGACAACATATTCATCATTTCTTGTGGTTTCTGCACAGAT
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
* * * *
603638 GTTCGTAAATCATTTGACAACACATTCATCATTTCTTGTGGCTTCTGCCCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
** * *
603692 GTTCATAAAGTATTTGACAACACATTCATCCTTTCCTATGGCTTCTGC
1 GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGC
603740 CCAAATTTCT
Statistics
Matches: 141, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 141 1.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.37
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCATTTCCTGTGGCTTCTGCACAGAT
Found at i:606378 original size:72 final size:71
Alignment explanation
Indices: 606261--606396 Score: 182
Period size: 72 Copynumber: 1.9 Consensus size: 71
606251 AGTATAATAG
* **
606261 GCTAGCTGAATATTATCCATAAAGCCAGGGCTATTAACCAATTGCTCTAGAGGGACAACTCAAGC
1 GCTAGCTGAATATTATCCATAAAGCCAGAGAGATTAACCAATTGCTCTAG-GGGACAACTCAAGC
606326 ATAACAT
65 ATAACAT
* ** * **
606333 GCTAGTTGAATATTATCCATAAAGTTAGAGAGATTAACCAATTGCTTTAGGGGGTAACTCAAGC
1 GCTAGCTGAATATTATCCATAAAGCCAGAGAGATTAACCAATTGCTCTAGGGGACAACTCAAGC
606397 TTTATTGTAT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
71 12 0.22
72 43 0.78
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.26
Consensus pattern (71 bp):
GCTAGCTGAATATTATCCATAAAGCCAGAGAGATTAACCAATTGCTCTAGGGGACAACTCAAGCA
TAACAT
Found at i:608486 original size:12 final size:12
Alignment explanation
Indices: 608462--608495 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
608452 GCAAAGATGC
608462 AAATATAAAATGA
1 AAATAT-AAATGA
*
608475 AAATGTAAATGA
1 AAATATAAATGA
608487 AAATATAAA
1 AAATATAAA
608496 AATACAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AAATATAAATGA
Found at i:608504 original size:20 final size:21
Alignment explanation
Indices: 608481--608550 Score: 65
Period size: 20 Copynumber: 3.4 Consensus size: 21
608471 ATGAAAATGT
608481 AAATG-AAA-ATATAAAAATAC
1 AAATGCAAACATA-AAAAATAC
*
608501 AAATGCAAACATAAAAAATGC
1 AAATGCAAACATAAAAAATAC
* **
608522 AAATGTAATGA-AAAAAATAC
1 AAATGCAAACATAAAAAATAC
*
608542 GAATGCAAA
1 AAATGCAAA
608551 TGCAACAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
20 19 0.47
21 18 0.45
22 3 0.08
ACGTcount: A:0.64, C:0.09, G:0.10, T:0.17
Consensus pattern (21 bp):
AAATGCAAACATAAAAAATAC
Found at i:617194 original size:30 final size:29
Alignment explanation
Indices: 617128--617196 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
617118 TTTTATTTCA
*
617128 TTTTAGTACCATGACGTTAAAAACTTAAC
1 TTTTAGTACCATGACATTAAAAACTTAAC
*
617157 TTTTAGTACCCTGACATTAAAAA-TTAAC
1 TTTTAGTACCATGACATTAAAAACTTAAC
617185 GTGTTTAGTACC
1 -T-TTTAGTACC
617197 TAAGCTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 5 0.14
29 22 0.61
30 9 0.25
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (29 bp):
TTTTAGTACCATGACATTAAAAACTTAAC
Found at i:617722 original size:21 final size:21
Alignment explanation
Indices: 617684--617733 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
617674 TTAATAGATT
617684 ATTTCATTTTAAAAAAATA-AA
1 ATTT-ATTTTAAAAAAATATAA
*
617705 ATTTATTTTAAACTAAATATAA
1 ATTTATTTTAAA-AAAATATAA
*
617727 AATTATT
1 ATTTATT
617734 CAAATATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 8 0.32
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTTATTTTAAAAAAATATAA
Found at i:617952 original size:28 final size:28
Alignment explanation
Indices: 617912--617979 Score: 92
Period size: 23 Copynumber: 2.6 Consensus size: 28
617902 ACATGTGTTT
617912 TCTAATTATCTTTTTGTTTTTTTATTAA
1 TCTAATTATCTTTTTGTTTTTTTATTAA
617940 TCTAATTATC----T-TTTTTTTATTAA
1 TCTAATTATCTTTTTGTTTTTTTATTAA
*
617963 TATAATTATCTTTTTGT
1 TCTAATTATCTTTTTGT
617980 AAGTATCAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
23 21 0.62
24 1 0.03
27 1 0.03
28 11 0.32
ACGTcount: A:0.24, C:0.07, G:0.03, T:0.66
Consensus pattern (28 bp):
TCTAATTATCTTTTTGTTTTTTTATTAA
Found at i:618084 original size:25 final size:25
Alignment explanation
Indices: 618056--618107 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
618046 AGTTAGTTTC
618056 GAATAATTCAAAATTTATAAGTCTT
1 GAATAATTCAAAATTTATAAGTCTT
* * * *
618081 GAATAATTTAAATTTTGTAAGTTTT
1 GAATAATTCAAAATTTATAAGTCTT
618106 GA
1 GA
618108 TTAACCCAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (25 bp):
GAATAATTCAAAATTTATAAGTCTT
Found at i:618317 original size:15 final size:15
Alignment explanation
Indices: 618289--618322 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
618279 TTAATATGTA
618289 TATTCAATTTATTTT
1 TATTCAATTTATTTT
618304 TATT-AATTTAATTTT
1 TATTCAATTT-ATTTT
618319 TATT
1 TATT
618323 TTTAGCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTCAATTTATTTT
Found at i:618752 original size:12 final size:12
Alignment explanation
Indices: 618735--618760 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
618725 TTGAGGGTTG
618735 TTCATCTTCTTC
1 TTCATCTTCTTC
618747 TTCATCTTCTTC
1 TTCATCTTCTTC
618759 TT
1 TT
618761 ATCCTTTTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCATCTTCTTC
Found at i:619856 original size:20 final size:20
Alignment explanation
Indices: 619833--619872 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
619823 ATTAGCTAGA
* *
619833 ATGGACTATCATGTTAGCAC
1 ATGGACCATCAAGTTAGCAC
*
619853 ATGGACCGTCAAGTTAGCAC
1 ATGGACCATCAAGTTAGCAC
619873 CGTAAACTAC
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:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
ATGGACCATCAAGTTAGCAC
Found at i:624583 original size:59 final size:60
Alignment explanation
Indices: 624500--624659 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 60
624490 GAAATGTCCA
* * *
624500 AAAAGTCTGAGGA-TCAATTTAGAATGA-AGGTCATAGTTTGGGGACGAAAATGAAATG-TT
1 AAAAGTTTGAGGACT-AATTTAGAATGATA-GTCATAGTTTAGAGACGAAAATGAAATGTTT
* *
624559 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGATGAAATTGAAATGTTT
1 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGACGAAAATGAAATGTTT
* * *
624619 AGAAGTTTTG-GGACTAATTTAAAATGAGTA-TCATAGATTAG
1 AAAAG-TTTGAGGACTAATTTAGAATGA-TAGTCATAGTTTAG
624660 GGACATATGA
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
59 48 0.55
60 34 0.39
61 6 0.07
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (60 bp):
AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGACGAAAATGAAATGTTT
Found at i:624740 original size:15 final size:17
Alignment explanation
Indices: 624717--624753 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
624707 TTAGAAAAGA
*
624717 ATTTATAAAAA-T-AAT
1 ATTTTTAAAAACTGAAT
624732 ATTTTTAAAAACTGAAT
1 ATTTTTAAAAACTGAAT
624749 ATTTT
1 ATTTT
624754 ATAATGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 1 0.05
17 8 0.42
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTTTAAAAACTGAAT
Found at i:624811 original size:15 final size:15
Alignment explanation
Indices: 624772--624811 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
624762 TGGATGGTTG
624772 TAAAATATTTCCTGT
1 TAAAATATTTCCTGT
*
624787 TAATAA-ATTTCCTTT
1 TAA-AATATTTCCTGT
624802 TAAAATATTT
1 TAAAATATTT
624812 TCAAAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAATATTTCCTGT
Found at i:626205 original size:15 final size:15
Alignment explanation
Indices: 626187--626222 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
626177 CCATACGATA
*
626187 AGGTGCCATAGAAAT
1 AGGTGACATAGAAAT
626202 AGGTGACATAGAAAT
1 AGGTGACATAGAAAT
626217 AGGTGA
1 AGGTGA
626223 AGATCCCGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.08, G:0.31, T:0.19
Consensus pattern (15 bp):
AGGTGACATAGAAAT
Found at i:630031 original size:29 final size:29
Alignment explanation
Indices: 629999--630078 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
629989 ACCCATTTTG
* *
629999 AATTAATTACTAGAATAGCACCAAAACCA
1 AATTATTTACCAGAATAGCACCAAAACCA
*
630028 AATTATTTACCAGAATAGCACCAAAACCG
1 AATTATTTACCAGAATAGCACCAAAACCA
630057 AATTATTTACCAGAATAGCACC
1 AATTATTTACCAGAATAGCACC
630079 GGTCAACGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.46, C:0.23, G:0.09, T:0.23
Consensus pattern (29 bp):
AATTATTTACCAGAATAGCACCAAAACCA
Found at i:630133 original size:18 final size:18
Alignment explanation
Indices: 630093--630134 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
630083 AACGGTCAAT
*
630093 GGGTCGGGTCAACGGGTT
1 GGGTCGGGTCAACGGGTC
*
630111 AGGTCGGGTCAACGGGTC
1 GGGTCGGGTCAACGGGTC
630129 GGGTCG
1 GGGTCG
630135 TGACCGGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.19, G:0.50, T:0.19
Consensus pattern (18 bp):
GGGTCGGGTCAACGGGTC
Found at i:631231 original size:59 final size:60
Alignment explanation
Indices: 631148--631307 Score: 168
Period size: 59 Copynumber: 2.7 Consensus size: 60
631138 GAAATGTCCA
* * *
631148 AAAAGTCTGAGGA-TCAATTTAGAATGA-AGGTCATAGTTTGGGGACGAAAATGAAATG-TT
1 AAAAGTTTGAGGACT-AATTTAGAATGATA-GTCATAGTTTAGAGACGAAAATGAAATGTTT
* * *
631207 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTATAGATGAAATTGAAATGTTT
1 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGACGAAAATGAAATGTTT
* * *
631267 AGAAGTTTTG-GGACTAATTTAAAATGAGTA-TCATAGATTAG
1 AAAAG-TTTGAGGACTAATTTAGAATGA-TAGTCATAGTTTAG
631308 GGACATATGA
Statistics
Matches: 86, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
59 47 0.55
60 33 0.38
61 6 0.07
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (60 bp):
AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGACGAAAATGAAATGTTT
Found at i:631388 original size:15 final size:17
Alignment explanation
Indices: 631365--631401 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
631355 TTAGAAAAGA
*
631365 ATTTATAAAAA-T-AAT
1 ATTTTTAAAAACTAAAT
631380 ATTTTTAAAAACTAAAT
1 ATTTTTAAAAACTAAAT
631397 ATTTT
1 ATTTT
631402 ATAATGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 1 0.05
17 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTTAAAAACTAAAT
Found at i:631459 original size:15 final size:15
Alignment explanation
Indices: 631420--631459 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
631410 TGGATGGTTG
631420 TAAAATATTTCCTGT
1 TAAAATATTTCCTGT
*
631435 TAATAA-ATTTCCTTT
1 TAA-AATATTTCCTGT
631450 TAAAATATTT
1 TAAAATATTT
631460 TCAAAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAATATTTCCTGT
Found at i:636619 original size:30 final size:29
Alignment explanation
Indices: 636585--636653 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
636575 CATTTTACAC
* *
636585 AAATAGTACCCTTTTTTAAAATAATTACCA
1 AAATAGTACCC-ATTTCAAAATAATTACCA
* * *
636615 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGTACCCATTTCAAAATAATTACCA
*
636644 GAATAGTACC
1 AAATAGTACC
636654 AAAACCGAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 22 0.69
30 10 0.31
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.30
Consensus pattern (29 bp):
AAATAGTACCCATTTCAAAATAATTACCA
Found at i:636693 original size:28 final size:28
Alignment explanation
Indices: 636630--636711 Score: 112
Period size: 28 Copynumber: 2.9 Consensus size: 28
636620 GCACCCATTT
*
636630 CGAATTAATTACCAGAATAGTACCAAAAC
1 CGAATTATTTACCAGAATAG-ACCAAAAC
636659 CGAATTATTTACCAGAATA-ACACAAAAC
1 CGAATTATTTACCAGAATAGAC-CAAAAC
*
636687 TGAATTATTTACCAGAATAGCACCA
1 CGAATTATTTACCAGAATAG-ACCA
636712 GTCAACGGTC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
27 2 0.04
28 24 0.50
29 20 0.42
30 2 0.04
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (28 bp):
CGAATTATTTACCAGAATAGACCAAAAC
Found at i:636753 original size:18 final size:18
Alignment explanation
Indices: 636730--636770 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
636720 TCAACGATCG
636730 GGTCGGGTCAACGGGTCA
1 GGTCGGGTCAACGGGTCA
*
636748 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCA
636766 GGTCG
1 GGTCG
636771 TGACCGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.12, C:0.22, G:0.49, T:0.17
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCA
Found at i:637906 original size:59 final size:60
Alignment explanation
Indices: 637823--637982 Score: 177
Period size: 59 Copynumber: 2.7 Consensus size: 60
637813 GAAATGTCCA
* * *
637823 AAAAGTCTGAGGA-TCAATTTAGAATGA-AGGTCATAGTTTGGGGACGAAAATGAAATG-TT
1 AAAAGTTTGAGGACT-AATTTAGAATGATA-GTCATAGTTTAGAGACGAAAATGAAATGTTT
* *
637882 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGATGAAATTGAAATGTTT
1 AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGACGAAAATGAAATGTTT
* * *
637942 AGAAGTTTTG-GGACTAATTTAAAATGAGTA-TCATAGATTAG
1 AAAAG-TTTGAGGACTAATTTAGAATGA-TAGTCATAGTTTAG
637983 GGACATATGA
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
59 48 0.55
60 34 0.39
61 6 0.07
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (60 bp):
AAAAGTTTGAGGACTAATTTAGAATGATAGTCATAGTTTAGAGACGAAAATGAAATGTTT
Found at i:638062 original size:15 final size:17
Alignment explanation
Indices: 638039--638075 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
638029 TTAGAAAAGA
*
638039 ATTTATAAAAA-T-AAT
1 ATTTTTAAAAACTGAAT
638054 ATTTTTAAAAACTGAAT
1 ATTTTTAAAAACTGAAT
638071 ATTTT
1 ATTTT
638076 ATAATGTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 10 0.53
16 1 0.05
17 8 0.42
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
ATTTTTAAAAACTGAAT
Found at i:638133 original size:15 final size:15
Alignment explanation
Indices: 638094--638133 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
638084 TGGATGGTTG
638094 TAAAATATTTCCTGT
1 TAAAATATTTCCTGT
*
638109 TAATAA-ATTTCCTTT
1 TAA-AATATTTCCTGT
638124 TAAAATATTT
1 TAAAATATTT
638134 TCAAAAGTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.50
Consensus pattern (15 bp):
TAAAATATTTCCTGT
Found at i:639470 original size:16 final size:16
Alignment explanation
Indices: 639451--639481 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
639441 TATAAATTAA
639451 ATTAATGGTGCTCATT
1 ATTAATGGTGCTCATT
*
639467 ATTAGTGGTGCTCAT
1 ATTAATGGTGCTCAT
639482 CGGTACTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (16 bp):
ATTAATGGTGCTCATT
Found at i:640387 original size:21 final size:20
Alignment explanation
Indices: 640350--640388 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
640340 TTTTCAATTA
* *
640350 TATCAATTTTTTGTTTTAGG
1 TATCAATATTTTCTTTTAGG
640370 TATCTAATATTTTCTTTTA
1 TATC-AATATTTTCTTTTA
640389 TTAAATTACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.23, C:0.08, G:0.08, T:0.62
Consensus pattern (20 bp):
TATCAATATTTTCTTTTAGG
Found at i:642770 original size:28 final size:28
Alignment explanation
Indices: 642730--642783 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
642720 TCTCTAACCG
*
642730 TGGACTCTATAGCAAGGTGAACAAATTT
1 TGGACTCCATAGCAAGGTGAACAAATTT
642758 TGGACTCCATAGCAAGGTGAACAAAT
1 TGGACTCCATAGCAAGGTGAACAAAT
642784 ATTTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (28 bp):
TGGACTCCATAGCAAGGTGAACAAATTT
Found at i:644027 original size:24 final size:24
Alignment explanation
Indices: 643955--644110 Score: 116
Period size: 24 Copynumber: 6.5 Consensus size: 24
643945 TATTGATCAA
* * *
643955 TCCTATATTAGTGCATTTATACAC
1 TCCTGTATTAGTGCATTTGTGCAC
* ** * *
643979 TCCTATATTAGTGTGTTTATACAC
1 TCCTGTATTAGTGCATTTGTGCAC
*
644003 TCCTGTATTAGTGCAATTGTGCAC
1 TCCTGTATTAGTGCATTTGTGCAC
* * *
644027 TCCCGTATTAGTATCA-ATGTGCAC
1 TCCTGTATTAGT-GCATTTGTGCAC
* *
644051 TCCTGAATCAGTGCATTTGTGCAC
1 TCCTGTATTAGTGCATTTGTGCAC
* * * *
644075 TCTTGAATCAGTACATTTGTGCAC
1 TCCTGTATTAGTGCATTTGTGCAC
* *
644099 TCATATATTAGT
1 TCCTGTATTAGT
644111 ACCATTACGT
Statistics
Matches: 108, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
23 2 0.02
24 104 0.96
25 2 0.02
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (24 bp):
TCCTGTATTAGTGCATTTGTGCAC
Found at i:644150 original size:25 final size:24
Alignment explanation
Indices: 644001--644152 Score: 78
Period size: 24 Copynumber: 6.3 Consensus size: 24
643991 GTGTTTATAC
* *
644001 ACTCCTGTATTAGTGCAATT-GTGC
1 ACTCCTGTATTAGTAC-ATTCGTGT
* * *
644025 ACTCCCGTATTAGTATCAAT-GTGC
1 ACTCCTGTATTAGTA-CATTCGTGT
* * * * *
644049 ACTCCTGAATCAGTGCATTTGTGC
1 ACTCCTGTATTAGTACATTCGTGT
* * * * *
644073 ACTCTTGAATCAGTACATTTGTGC
1 ACTCCTGTATTAGTACATTCGTGT
* *
644097 ACTCATATATTAGTACCATTACGT-T
1 ACTCCTGTATTAGTA-CATT-CGTGT
644122 -CTCCTGTATTTAGTACATTCGTGT
1 ACTCCTGTA-TTAGTACATTCGTGT
644146 ACTCCTG
1 ACTCCTG
644153 GCATAATTTG
Statistics
Matches: 103, Mismatches: 18, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
23 6 0.06
24 78 0.76
25 17 0.17
26 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (24 bp):
ACTCCTGTATTAGTACATTCGTGT
Found at i:647164 original size:18 final size:18
Alignment explanation
Indices: 647138--647184 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
647128 AGCTGCAATG
*
647138 GCTGTTTCTGAACCTGTT
1 GCTGCTTCTGAACCTGTT
*
647156 GCTGCTTCTGAATCTGTT
1 GCTGCTTCTGAACCTGTT
**
647174 ATTGCTTCTGA
1 GCTGCTTCTGA
647185 TCGATTGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.45
Consensus pattern (18 bp):
GCTGCTTCTGAACCTGTT
Found at i:651054 original size:2 final size:2
Alignment explanation
Indices: 651047--651082 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
651037 TGTTTTTGTA
651047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
651083 TATCATCAAT
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):
AT
Found at i:652782 original size:35 final size:34
Alignment explanation
Indices: 652741--652819 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 34
652731 CAACACAGTC
652741 TTCAATTTCATTTTAAACCCCAAATTCCAAAATAA
1 TTCAATTT-ATTTTAAACCCCAAATTCCAAAATAA
* *
652776 TTCAATTATATTTTAAACCCCAAATTCTAAAATAC
1 TTCAATT-TATTTTAAACCCCAAATTCCAAAATAA
*
652811 TTTAATTTA
1 TTCAATTTA
652820 GAGTTTAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
34 2 0.05
35 37 0.93
36 1 0.03
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.39
Consensus pattern (34 bp):
TTCAATTTATTTTAAACCCCAAATTCCAAAATAA
Found at i:666264 original size:16 final size:16
Alignment explanation
Indices: 666243--666286 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
666233 ATTAATTAAT
666243 AATATAAATTTACTCA
1 AATATAAATTTACTCA
666259 AATATAAATTTACTCA
1 AATATAAATTTACTCA
666275 AATATAAATTTA
1 AATATAAATTTA
666287 AGAAATTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (16 bp):
AATATAAATTTACTCA
Found at i:668919 original size:53 final size:54
Alignment explanation
Indices: 668850--668954 Score: 158
Period size: 53 Copynumber: 2.0 Consensus size: 54
668840 GAGTGCATTG
*
668850 ATGCATAAAATGCATTCGATGTTTT-AAAAAAGCCTGAGTGCATCCATGCATCA
1 ATGCATAAAATGCATTCGATGTTTTCAAAAAACCCTGAGTGCATCCATGCATCA
* * * *
668903 ATGCATTAAATTCATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCAT
1 ATGCATAAAATGCATTCGATGTTTTCAAAAAACCCTGAGTGCATCCATGCAT
668955 TGTATGTGCA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 23 0.50
54 23 0.50
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (54 bp):
ATGCATAAAATGCATTCGATGTTTTCAAAAAACCCTGAGTGCATCCATGCATCA
Found at i:669030 original size:20 final size:20
Alignment explanation
Indices: 669005--669057 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
668995 TTATTCAATG
*
669005 GTGCATCGATGCATGGATTA
1 GTGCATCGATACATGGATTA
*
669025 GTGCATCGATACATGGATTG
1 GTGCATCGATACATGGATTA
669045 GTGCATCGATACA
1 GTGCATCGATACA
669058 CTCTTTTGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
GTGCATCGATACATGGATTA
Found at i:672684 original size:11 final size:11
Alignment explanation
Indices: 672662--672696 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
672652 GTTTGATGCT
672662 TTCTCT-TTGA
1 TTCTCTATTGA
672672 TTCTCTATTGA
1 TTCTCTATTGA
672683 TTCT-TATTGA
1 TTCTCTATTGA
672693 TTCT
1 TTCT
672697 TGTTTATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.14, C:0.17, G:0.09, T:0.60
Consensus pattern (11 bp):
TTCTCTATTGA
Found at i:673002 original size:45 final size:46
Alignment explanation
Indices: 672926--673032 Score: 137
Period size: 45 Copynumber: 2.3 Consensus size: 46
672916 GGTTCACTAA
* *
672926 GAGTGCATCGATGCATAAAATGCATTCGATGTTTT-A-AAATAGCCT
1 GAGTGCATCGATGCATAAAATACATTCGATGTTTTCATAAA-ACCCT
* * * *
672971 GAGTGTATCCATGCATTAAATACATTTGATGTTTTCATAAAACCCT
1 GAGTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCCT
673017 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
673033 GGTATGTGTA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
45 30 0.58
46 19 0.37
47 3 0.06
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (46 bp):
GAGTGCATCGATGCATAAAATACATTCGATGTTTTCATAAAACCCT
Found at i:675695 original size:23 final size:23
Alignment explanation
Indices: 675667--675730 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
675657 AACTCGTATA
*
675667 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCAAGTAG
675690 AAATGCACCGAAGTGCCAAGTAG
1 AAATGCACCGAAGTGCCAAGTAG
**
675713 AAATATACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
675731 TATAAAATGT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.39, C:0.23, G:0.23, T:0.14
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCAAGTAG
Found at i:675770 original size:23 final size:23
Alignment explanation
Indices: 675728--675779 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
675718 TACCGAAGTG
* *
675728 CCATAT-AAAATGTCCATAAGGA
1 CCATATAAAAATCTCCATAAGAA
*
675750 CCATATAAAAATCTCCTTAAGAA
1 CCATATAAAAATCTCCATAAGAA
675773 CCATATA
1 CCATATA
675780 CATATTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (23 bp):
CCATATAAAAATCTCCATAAGAA
Found at i:675832 original size:21 final size:20
Alignment explanation
Indices: 675781--675832 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
675771 AACCATATAC
675781 ATAT-TCCAAATGACCAAAT
1 ATATGTCCAAATGACCAAAT
* **
675800 ATGTGTCTCAAATGACCGCAT
1 ATATGTC-CAAATGACCAAAT
675821 ATATGCTCCAAA
1 ATATG-TCCAAA
675833 AGATTACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 19 0.73
22 2 0.08
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (20 bp):
ATATGTCCAAATGACCAAAT
Found at i:684811 original size:4 final size:4
Alignment explanation
Indices: 684802--684838 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
684792 CATAAATGGT
684802 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
684839 CTAGCTTTGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:686826 original size:23 final size:23
Alignment explanation
Indices: 686796--686847 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
686786 TTAGGGCTGT
*
686796 AGGGCCTACCTGAGAATGATCTC
1 AGGGCCTACCCGAGAATGATCTC
686819 AGGGCCTACCCGAGAATGATCTC
1 AGGGCCTACCCGAGAATGATCTC
686842 AGGGCC
1 AGGGCC
686848 GCAGAGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.17
Consensus pattern (23 bp):
AGGGCCTACCCGAGAATGATCTC
Found at i:695190 original size:37 final size:37
Alignment explanation
Indices: 695137--695241 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
695127 CATTTTCGTC
695137 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
695174 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
695211 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
695242 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:695783 original size:21 final size:20
Alignment explanation
Indices: 695721--695791 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
695711 TCTTTTATTA
*
695721 TTAT-TATTTTACTTATATAT
1 TTATATATTTTAC-TATTTAT
* *
695741 ATATATGCTTTTACT-TTT-T
1 TTATAT-ATTTTACTATTTAT
695760 TTATATATTTTACTCATTTAT
1 TTATATATTTTACT-ATTTAT
*
695781 TTATCTATTTT
1 TTATATATTTT
695792 CTTTTTATCT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
18 7 0.17
19 6 0.15
20 8 0.20
21 13 0.32
22 6 0.15
ACGTcount: A:0.25, C:0.08, G:0.01, T:0.65
Consensus pattern (20 bp):
TTATATATTTTACTATTTAT
Found at i:697101 original size:19 final size:19
Alignment explanation
Indices: 697077--697113 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
697067 ACCTTACTAA
697077 CTCTTTTCATTTT-TTTCCT
1 CTCTTTT-ATTTTATTTCCT
697096 CTCTTTTATTTTATTTCC
1 CTCTTTTATTTTATTTCC
697114 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
CTCTTTTATTTTATTTCCT
Found at i:700913 original size:184 final size:184
Alignment explanation
Indices: 700576--701113 Score: 909
Period size: 184 Copynumber: 2.9 Consensus size: 184
700566 ATTAAATCCG
700576 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
700641 ATAGATTATG-TTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTTAAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
700705 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTTAGTGATTTATCCCTC
131 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
*
700759 TAAAGCTGAGCTATTCCACTAAGGTAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
700824 ATAGATTATGTTTAAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
66 ATAGATTATGTTTAAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* *
700889 TTTGTCAGGCCAAAGACTTTGTGATGAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
*
700943 TAAAGCTGAGCTATTTCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
* ** * * * *
701008 ATATATTACATTCAAATC-ATGACATTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTTCT
66 ATAGATTATGTTTAAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
* * * *
701072 TTTTTCAGGTCAAAGGCTTTGTGATGAGATGAGCCCTTCAGT
131 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
701114 TAAACCTGAT
Statistics
Matches: 335, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
183 155 0.46
184 180 0.54
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (184 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTTAAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTATCCCTC
Found at i:702346 original size:72 final size:76
Alignment explanation
Indices: 702254--702415 Score: 192
Period size: 72 Copynumber: 2.2 Consensus size: 76
702244 ATGCAGATGA
* * * *
702254 TTATCTCACTCAA-ATTTGTTTTTCTTAAAACATA-CTTTGTCTCACTTGAGACTATTTT-TCTC
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACA-AGATTTGTCTCACTTGAGACCATTTTCACTC
702316 GAAA-AAAG-AT
65 GAAAGAAAGCAT
** *
702326 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACAAGATTTGTCTCGTTTGAGACCGTTTTCACTCG
1 TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCATTTTCACTCG
*
702390 AAAGAAGGCAT
66 AAAGAAAGCAT
702401 TTCATTTCACTCAAG
1 TT-ATTTCACTCAAG
702416 GCTTTTTTGT
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
71 1 0.01
72 48 0.63
73 8 0.11
74 3 0.04
75 4 0.05
76 12 0.16
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (76 bp):
TTATTTCACTCAAGATTTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACCATTTTCACTCG
AAAGAAAGCAT
Found at i:702490 original size:39 final size:39
Alignment explanation
Indices: 702447--702599 Score: 119
Period size: 39 Copynumber: 3.6 Consensus size: 39
702437 TTTTATCTTG
*
702447 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
702486 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
*
702538 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* *
702576 CTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
702600 TAAACATTGA
Statistics
Matches: 89, Mismatches: 11, Indels: 28
0.70 0.09 0.22
Matches are distributed among these distances:
38 2 0.02
39 45 0.51
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 24 0.27
52 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:702668 original size:105 final size:104
Alignment explanation
Indices: 702502--702820 Score: 518
Period size: 105 Copynumber: 3.1 Consensus size: 104
702492 ACAGTTTCTC
* *
702502 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
702567 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
702606 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
702671 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * * *
702711 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTACCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
702773 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
702812 TTGAAAACA
1 TTGAAAACA
702821 ATTTAACGAA
Statistics
Matches: 203, Mismatches: 11, Indels: 5
0.93 0.05 0.02
Matches are distributed among these distances:
101 48 0.24
103 1 0.00
104 52 0.26
105 102 0.50
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:702773 original size:36 final size:36
Alignment explanation
Indices: 702724--702794 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 36
702714 AAAACATTTC
* * *
702724 CCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTA
1 CCTTGAAACGAATTTTATCTCCCTTGAGACAGTTTA
*
702760 CCTTGAAACGAATTTTGTCTCCCTTGAGACAGTTT
1 CCTTGAAACGAATTTTATCTCCCTTGAGACAGTTT
702795 CTCTCCAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.39
Consensus pattern (36 bp):
CCTTGAAACGAATTTTATCTCCCTTGAGACAGTTTA
Found at i:703196 original size:105 final size:105
Alignment explanation
Indices: 702995--703439 Score: 695
Period size: 105 Copynumber: 4.3 Consensus size: 105
702985 ATATCGTGAC
* * * * *
702995 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
* *
703060 AATTTCAGAGCCAATTTCAACTTTACAACGAAGGATATTGG
65 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
703101 ACTTCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCACTGCTTGTCAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
703166 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
703206 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTC-CT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTC-
703270 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
703311 ACTCCAGACAACGCAAGTTCAACTCCACGATGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
703372 AT-TCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
703411 ACTCGAGACAACACAAGTTCAACTTCACG
1 ACTCCAGACAACGCAAGTTCAACTTCACG
703440 GCCAATTTCA
Statistics
Matches: 318, Mismatches: 19, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
100 62 0.19
101 2 0.01
103 3 0.01
104 3 0.01
105 203 0.64
106 45 0.14
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:704034 original size:20 final size:20
Alignment explanation
Indices: 704009--704046 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
703999 TCAACACACA
704009 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
704029 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
704047 TTTACTCATT
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:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:721313 original size:23 final size:23
Alignment explanation
Indices: 721287--721343 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
721277 GTTTAAGGCC
* *
721287 TTATTTAATTTTTAAA-ATAAAAA
1 TTATTTAAATTATAAATAT-AAAA
721310 TTATTTTAAATTATAAATATAAAA
1 TTA-TTTAAATTATAAATATAAAA
*
721334 TTATTCAAAT
1 TTATTTAAAT
721344 ATTCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 9 0.31
24 18 0.62
25 2 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TTATTTAAATTATAAATATAAAA
Found at i:721374 original size:21 final size:21
Alignment explanation
Indices: 721350--721403 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
721340 AAATATTCAA
*
721350 AAAAATTAATATAAAAATAAT
1 AAAAATGAATATAAAAATAAT
* * * *
721371 AAAAATGAAAATTAAATTACT
1 AAAAATGAATATAAAAATAAT
721392 AAAAATGAATAT
1 AAAAATGAATAT
721404 GCATTTAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAATGAATATAAAAATAAT
Found at i:722478 original size:21 final size:22
Alignment explanation
Indices: 722433--722480 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
722423 AAATATTTAA
*
722433 AAAAATAAAAATAAAAACTATT
1 AAAAATAAAAATAAAAACTACT
* *
722455 AAAAATAAAAAT-TAAATTACT
1 AAAAATAAAAATAAAAACTACT
722476 AAAAA
1 AAAAA
722481 ATTAAACATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACTACT
Found at i:722644 original size:14 final size:14
Alignment explanation
Indices: 722625--722676 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
722615 TATTAAAAAA
722625 TAAAAATATATTTT
1 TAAAAATATATTTT
* *
722639 TAAAAAGATA-TAT
1 TAAAAATATATTTT
*
722652 TATCAAA-ATATTTT
1 TA-AAAATATATTTT
722666 TAAAAATATAT
1 TAAAAATATAT
722677 ACATGTAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 10 0.33
14 20 0.67
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (14 bp):
TAAAAATATATTTT
Found at i:722689 original size:27 final size:27
Alignment explanation
Indices: 722629--722690 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
722619 AAAAAATAAA
*
722629 AATATATTTTTAAAAAGATATATTATC
1 AATATATTTTTAAAAAGATATATCATC
* * *
722656 AAAATATTTTTAAAAATATATA-CATGT
1 AATATATTTTTAAAAAGATATATCAT-C
722683 AATATATT
1 AATATATT
722691 GATATATTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (27 bp):
AATATATTTTTAAAAAGATATATCATC
Found at i:732811 original size:19 final size:21
Alignment explanation
Indices: 732766--732823 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
732756 ACCCCCATGA
732766 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TT-AAG
732789 GGGAACCGATTCCCCC-T-AG
1 GGGAACCGATTCCCCCTTAAG
* *
732808 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
732824 CGAGGTTCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.48
21 1 0.03
23 16 0.48
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTTAAG
Found at i:736779 original size:90 final size:90
Alignment explanation
Indices: 736626--736803 Score: 295
Period size: 90 Copynumber: 2.0 Consensus size: 90
736616 CCTAACACAC
*
736626 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTCTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTCTATTATTTCAAATTAATTAAATCTAT
* *
736691 ATTTAATTAATTGGAATTTAATAAT
66 ATTTAATTAATTGAAATTAAATAAT
* *
736716 CCTTTTATATCCAAGTTACCCTAATTATATTAGGGATTT-TATTATTTCAAATTAATTAAATCTA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTCTATTATTTCAAATTAATTAAATCTA
736780 TATTTAATTAATTGAAATTAAATA
65 TATTTAATTAATTGAAATTAAATA
736804 TTCGGGATTA
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 79 0.96
91 3 0.04
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.46
Consensus pattern (90 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTCTATTATTTCAAATTAATTAAATCTAT
ATTTAATTAATTGAAATTAAATAAT
Found at i:741421 original size:30 final size:30
Alignment explanation
Indices: 741387--741445 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
741377 TCTGACCCGT
741387 TGACC-TTAACTCGAACTGTTGACTTTGACA
1 TGACCGTTAAC-CGAACTGTTGACTTTGACA
* * *
741417 TGACCGTTGACCTACCTGTTGACTTTGAC
1 TGACCGTTAACCGAACTGTTGACTTTGAC
741446 CCAAAAAGTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.34
Consensus pattern (30 bp):
TGACCGTTAACCGAACTGTTGACTTTGACA
Found at i:743715 original size:42 final size:42
Alignment explanation
Indices: 743650--743757 Score: 171
Period size: 42 Copynumber: 2.6 Consensus size: 42
743640 TTTCCTTGAA
* *
743650 TTCCCGTATTTGTTTCACGTAATTCGTTTTCCGGAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATT
* * *
743692 TTTCCGTGTTTGTTTTACGTAATTTGTTTTCCGAAAAATATT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATT
743734 TTCCCGTGTTTGTTTCACGTAATT
1 TTCCCGTGTTTGTTTCACGTAATT
743758 AATTTTCCAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.19, C:0.17, G:0.15, T:0.49
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATATT
Found at i:744080 original size:52 final size:52
Alignment explanation
Indices: 743975--744148 Score: 124
Period size: 54 Copynumber: 3.2 Consensus size: 52
743965 ATATTTATAA
* **
743975 TAATAATAT-A-ATATTATATTTTTAATATTATATAA-A-ATAATCAATTATAATT
1 TAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAAT-AAAAAT-ATT
744027 TAATAATATAAGATATTATATTTTTATTTTAATAATATATAATAAAAATATT
1 TAATAATATAAGATATTATATTTTTATTTTAATAATATATAATAAAAATATT
* * * * *
744079 TATATATTTAATAATGAATAATATTATTTATATATTTAAATAATATTTTAATAAAGATATT
1 TA-ATA-AT-ATAA-G-ATATTA-TATTT-T-TATTTTAATAATA-TATAATAAAAATATT
744140 TAA-AATATA
1 TAATAATATA
744149 CTAATTAATA
Statistics
Matches: 100, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
52 18 0.18
53 14 0.14
54 19 0.19
55 4 0.04
56 1 0.01
57 8 0.08
58 6 0.06
59 2 0.02
60 13 0.13
61 15 0.15
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.48
Consensus pattern (52 bp):
TAATAATATAAGATATTATATTTTTATTTTAATAATATATAATAAAAATATT
Found at i:744090 original size:28 final size:28
Alignment explanation
Indices: 743956--744117 Score: 84
Period size: 28 Copynumber: 5.5 Consensus size: 28
743946 ATTATTTATT
743956 TATTTATTAATATTT-ATA-ATAATAATATAA
1 TATTTA-T-ATATTTAATATATAATAA-A-AA
*
743986 TA-TTATATTTTTAATAT-TATATAAAATAA
1 TATTTATATATTTAATATATA-AT-AAA-AA
* * **
744015 TCAATTATA-ATTTAATAATATAAGATATTA
1 T-ATTTATATATTTAAT-ATATAATA-AAAA
* *
744045 TATTTTTATTTTAATAATATATAATAAAAA
1 TATTTATATATT--TAATATATAATAAAAA
* *
744075 TATTTATATATTTAATA-ATGAATAATAT
1 TATTTATATATTTAATATAT-AATAAAAA
744103 TATTTATATATTTAA
1 TATTTATATATTTAA
744118 ATAATATTTT
Statistics
Matches: 104, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
27 7 0.07
28 32 0.31
29 15 0.14
30 28 0.27
31 16 0.15
32 6 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (28 bp):
TATTTATATATTTAATATATAATAAAAA
Found at i:744102 original size:19 final size:19
Alignment explanation
Indices: 744080--744132 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
744070 AAAAATATTT
*
744080 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
744099 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
744121 ATAT-TTTAATAA
1 ATATATTTAATAA
744133 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:744103 original size:60 final size:59
Alignment explanation
Indices: 743956--744141 Score: 177
Period size: 60 Copynumber: 3.1 Consensus size: 59
743946 ATTATTTATT
* * *
743956 TATTTATTAATATTT-ATAATAATAATATAATA-TTATATTTTTAATATTATATAA-AATAA
1 TATTTA-T-ATATTTAATAATAATAATATTATATTTATA-TTTTAATAATATATAATAAAAA
* *
744015 TCAATTATA-ATTTAATAAT-ATAAGATATTATATTTTTATTTTAATAATATATAATAAAAA
1 T-ATTTATATATTTAATAATAAT-A-ATATTATATTTATATTTTAATAATATATAATAAAAA
* * *
744075 TATTTATATATTTAATAATGAATAATATTAT-TTATATATTTAAATAATATTTTAATAAAGA
1 TATTTATATATTTAATAAT-AATAATATTATATT-TATATTTTAATAATA-TATAATAAAAA
744136 TATTTA
1 TATTTA
744142 AAATATACTA
Statistics
Matches: 106, Mismatches: 10, Indels: 20
0.78 0.07 0.15
Matches are distributed among these distances:
57 6 0.06
58 7 0.07
59 32 0.30
60 43 0.41
61 16 0.15
62 2 0.02
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (59 bp):
TATTTATATATTTAATAATAATAATATTATATTTATATTTTAATAATATATAATAAAAA
Found at i:744153 original size:23 final size:23
Alignment explanation
Indices: 744127--744171 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
744117 AATAATATTT
744127 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
744150 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
744172 ATATAACACT
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:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:744494 original size:15 final size:14
Alignment explanation
Indices: 744474--744507 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
744464 AAATGTAATT
*
744474 CATTTTACGGAAAA
1 CATTTTTCGGAAAA
744488 CATTTTTCGGAAAA
1 CATTTTTCGGAAAA
*
744502 CGTTTT
1 CATTTT
744508 CCAGAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (14 bp):
CATTTTTCGGAAAA
Found at i:744541 original size:20 final size:20
Alignment explanation
Indices: 744504--744542 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
744494 TCGGAAAACG
**
744504 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
744524 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
744543 CAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:744558 original size:15 final size:15
Alignment explanation
Indices: 744516--744561 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
744506 TTCCAGAAAT
744516 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
744531 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
744545 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
744560 GT
1 GT
744562 TCCAGTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:744723 original size:18 final size:20
Alignment explanation
Indices: 744692--744729 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
744682 AATTTATAAA
*
744692 TTATAATTATATAA-AATGT
1 TTATAATTAAATAATAATGT
744711 TTAT-ATTAAATAATAATGT
1 TTATAATTAAATAATAATGT
744730 ATAATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
TTATAATTAAATAATAATGT
Found at i:746352 original size:30 final size:27
Alignment explanation
Indices: 746290--746361 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
746280 ATTCAAATTT
* *
746290 TCGAACTAATTCGGTTAATCGATCGAA
1 TCGAATTAGTTCGGTTAATCGATCGAA
*
746317 TCGAATTAGTTCGGTTAATTCGATCGGTCA
1 TCGAATTAGTTCGGTTAA-TCGATC-G-AA
746347 TCGAATTAGTTCGGT
1 TCGAATTAGTTCGGT
746362 CGATTAACGG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 16 0.41
28 6 0.15
29 1 0.03
30 16 0.41
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (27 bp):
TCGAATTAGTTCGGTTAATCGATCGAA
Found at i:746694 original size:187 final size:187
Alignment explanation
Indices: 746455--746828 Score: 574
Period size: 187 Copynumber: 2.0 Consensus size: 187
746445 TTAAATTTTT
* * * * *
746455 AATATTAAATATATAATATATAACATATGTGTTTAGCCCAAATAATTTAAAACTCAATTAATAAT
1 AATATTAAATATATAATATATAACATATGGGCTAAGCCAAAATAATTTAAAACCCAATTAATAAT
*
746520 TTAAGATTCAATAACTTTTA-AACCTAAATCAATATTAATTAATTAAAAAAATTAAAT-AAATTG
66 TTAAGATCCAATAACTTTTACAA-CTAAATCAATATTAATTAATT-AAAAAATTAAATAAAATTG
*
746583 TTATTTTATAATTATATATTATTTAAATTAATTATAAAATGTTTTTTTGAATTAAAAAA
129 TTATTTTATAATTATATATTATTTAAATTAATTATAAAATATTTTTTTGAATTAAAAAA
* *
746642 AATATTATATATATTATATATAACATATGGGCTAAGCCAAAACT-ATTTAAAACCCAATTAATAA
1 AATATTAAATATATAATATATAACATATGGGCTAAGCCAAAA-TAATTTAAAACCCAATTAATAA
* ** * *
746706 TTTAAGATCCAATAACTTTTACAATTAAATCAATATTAATTAATTAAAATTTTATATAAAATTTT
65 TTTAAGATCCAATAACTTTTACAACTAAATCAATATTAATTAATTAAAAAATTAAATAAAATTGT
746771 TATTTTATAATTATATATTATTTAAATTAATTATAAAATATTTTTTTGAATTAAAAAA
130 TATTTTATAATTATATATTATTTAAATTAATTATAAAATATTTTTTTGAATTAAAAAA
746829 TATTTAATTT
Statistics
Matches: 170, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
186 9 0.05
187 158 0.93
188 3 0.02
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (187 bp):
AATATTAAATATATAATATATAACATATGGGCTAAGCCAAAATAATTTAAAACCCAATTAATAAT
TTAAGATCCAATAACTTTTACAACTAAATCAATATTAATTAATTAAAAAATTAAATAAAATTGTT
ATTTTATAATTATATATTATTTAAATTAATTATAAAATATTTTTTTGAATTAAAAAA
Found at i:746812 original size:20 final size:20
Alignment explanation
Indices: 746778--746835 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
746768 TTTTATTTTA
* *
746778 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
**
746798 TAATTATAAAATATTT-TTT
1 TAATTATAAAATATTTAAAT
*
746817 TGAATTAAAAAATATTTAA
1 T-AATTATAAAATATTTAA
746836 TTTTTATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 2 0.07
20 28 0.93
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Found at i:749899 original size:3 final size:3
Alignment explanation
Indices: 749891--749969 Score: 106
Period size: 3 Copynumber: 26.0 Consensus size: 3
749881 AATTTTAATC
* *
749891 TTA TTA TTA TTA TTA TTA TTA TTA ATG TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
749938 TTGT TTA TTAA TTA TTA TTA TTA TTA TTA TTA
1 TT-A TTA TT-A TTA TTA TTA TTA TTA TTA TTA
749970 ATTACATATT
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
2 2 0.03
3 61 0.90
4 5 0.07
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:755335 original size:4 final size:4
Alignment explanation
Indices: 755328--755364 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
755318 ACATCAACAT
755328 ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
755365 TATATGATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
4 29 0.94
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:755335 original size:16 final size:17
Alignment explanation
Indices: 755314--755366 Score: 65
Period size: 16 Copynumber: 3.1 Consensus size: 17
755304 ATTGAGAAAA
755314 ACATACATCA-ACATAT
1 ACATACATCATACATAT
755330 ACATACATACATACATACAT
1 ACATACAT-CATACAT--AT
755350 ACATACA-CATACATAT
1 ACATACATCATACATAT
755366 A
1 A
755367 TATGATACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.33
17 2 0.06
18 11 0.33
20 9 0.27
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (17 bp):
ACATACATCATACATAT
Found at i:755779 original size:36 final size:35
Alignment explanation
Indices: 755723--755863 Score: 149
Period size: 36 Copynumber: 3.9 Consensus size: 35
755713 TGAGAATTTT
755723 AAAACAAATTTTTGTCTCGCTTGAGATAATTTTTCTC
1 AAAACAAA-TTTTGTCTCGCTTGAGA-AATTTTTCTC
* * * *
755760 AAAACAAATTTTGACTCGCTTGAGACAGTTTTCTA
1 AAAACAAATTTTGTCTCGCTTGAGAAATTTTTCTC
* *
755795 AAAATAAATTTTGTTTCGCTTGAGACAATTTCTT-TC
1 AAAACAAATTTTGTCTCGCTTGAGA-AATTT-TTCTC
* * * *
755831 GAAACAAATTTCGTCTCACTTGAGACATTTTTC
1 AAAACAAATTTTGTCTCGCTTGAGAAATTTTTC
755864 CTTTGAGATA
Statistics
Matches: 85, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
34 2 0.02
35 33 0.39
36 40 0.47
37 10 0.12
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (35 bp):
AAAACAAATTTTGTCTCGCTTGAGAAATTTTTCTC
Found at i:755807 original size:71 final size:72
Alignment explanation
Indices: 755723--755863 Score: 187
Period size: 71 Copynumber: 2.0 Consensus size: 72
755713 TGAGAATTTT
* * *
755723 AAAACAAATTTTTGTCTCGCTTGAGATAATTT-TTCTCAAAACAAATTTTGACTCGCTTGAGACA
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTT-TCAAAACAAATTTCGACTCACTTGAGACA
755787 GTTTTCTA
65 GTTTTCTA
* * * * *
755795 AAAATAAA-TTTTGTTTCGCTTGAGACAATTTCTTTCGAAACAAATTTCGTCTCACTTGAGACAT
1 AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAACAAATTTCGACTCACTTGAGACAG
755859 TTTTC
66 TTTTC
755864 CTTTGAGATA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
71 51 0.85
72 9 0.15
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (72 bp):
AAAACAAATTTTTGTCTCGCTTGAGACAATTTCTTTCAAAACAAATTTCGACTCACTTGAGACAG
TTTTCTA
Found at i:755941 original size:103 final size:102
Alignment explanation
Indices: 755832--756167 Score: 385
Period size: 104 Copynumber: 3.2 Consensus size: 102
755822 ATTTCTTTCG
*
755832 AAACAAATTTCGTCTCACTTGAGACATTTTTCCTTTGAGATACAAAATTTGAATTTGTTTCACAT
1 AAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAAATTTGAATTTGTTTCACAT
*
755897 TAAACAAAGTTGATCTCATTTGAGATCGCTTTCTCTTA
66 TAAACAAAGTTGATCTCACTTGAGATCG-TTTCTCTTA
* * * * *
755935 AAACAAACTTCGTCTTGCTTGAGACATTTTTTCCTTTGATATA-AAATTTTGAATTTGATTCAC-
1 AAACAAATTTCGTCTCGCTTGAGACA-TTTTTCCTTTGAGATACAAAATTTGAATTTGTTTCACA
* * * * *
755998 TTGAAACAAAAATTAATCTCACTTGAGATTGTTATTTTTTCA
65 TT-AAAC-AAAGTTGATCTCACTTGAGATCGTT-TCTCTT-A
* *
756040 AAACAATTTTCGTCTCGTTTGAGACATTTTTCCTTTGAGAATAC-AAATTTCGAATTTGATTTCA
1 AAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAG-ATACAAAATTT-GAATTTG-TTTCA
* *
756104 AATTAAACAAAGTTGATCTCACTTGAGATCGTTT-TCTCAA
63 CATTAAACAAAGTTGATCTCACTTGAGATCGTTTCTCT-TA
*
756144 AAACAAACGTT-GTCTCGCTTGAGA
1 AAACAAA-TTTCGTCTCGCTTGAGA
756168 TAATTTCTCT
Statistics
Matches: 193, Mismatches: 28, Indels: 23
0.79 0.11 0.09
Matches are distributed among these distances:
102 2 0.01
103 47 0.24
104 71 0.37
105 34 0.18
106 29 0.15
107 8 0.04
108 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (102 bp):
AAACAAATTTCGTCTCGCTTGAGACATTTTTCCTTTGAGATACAAAATTTGAATTTGTTTCACAT
TAAACAAAGTTGATCTCACTTGAGATCGTTTCTCTTA
Found at i:756238 original size:36 final size:36
Alignment explanation
Indices: 756120--756245 Score: 121
Period size: 36 Copynumber: 3.5 Consensus size: 36
756110 ACAAAGTTGA
** * *
756120 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACGTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAATGTTT
* * ** *
756156 TCTCGCTTGAGATAATTTCTCT-AAAAGTAATTTTT
1 TCTCACTTGAGACAATTTCTCTAAAAACAAATGTTT
**
756191 GTCTCGTTTGAGACAATTTCTCTAAAAACAAATGTTT
1 -TCTCACTTGAGACAATTTCTCTAAAAACAAATGTTT
756228 TCTCACTTGAGACAATTT
1 TCTCACTTGAGACAATTT
756246 TTCAAATTAT
Statistics
Matches: 71, Mismatches: 16, Indels: 6
0.76 0.17 0.06
Matches are distributed among these distances:
35 14 0.20
36 47 0.66
37 10 0.14
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAATGTTT
Found at i:756249 original size:210 final size:204
Alignment explanation
Indices: 755734--756251 Score: 480
Period size: 210 Copynumber: 2.5 Consensus size: 204
755724 AAACAAATTT
* * * *
755734 TTGTCTCGCTTGAGATAATTTTTCTCAAAACAAATTTTGACTCGCTTGAGACAGTTT-TCTAAAA
1 TTGTCTCGCTTGAGATAATTTCTCT-AAAATAAATTTTG-CTCGTTTGAGACAATTTCTCTAAAA
* * *
755798 ATAAATTTTGTTTCGCTTGAGACAATTTCTTTCGAAACAAATTTCGTCTCACTTGAGACATTTTT
64 A-AAATTTT-TCTCACTTGAGACAA-TT-TTTCAAAACAAATTTCGTCTCACTTGAGACATTTTT
* *
755863 CCTTTGAGATACAAAATTTGAATTTGTTTCACATTAAACAAAGTTGATCTCATTTGAGATCGCTT
125 CCTTTGAGATACAAAATTTGAATTTGTTTCAAATTAAACAAAGTTGATCTCACTTGAGATCGCTT
*
755928 TCTCTTAAAACAAAC
190 TCTCTAAAAACAAAC
* ** * * * ** **
755943 TTCGTCTTGCTTGAGACATTTTTTCCTTTGATATAAAATTTTG--AATTTGATTC-A---CT-TG
1 TT-GTCTCGCTTGAG--ATAATTT-CTCTAAAAT-AAATTTTGCTCGTTTGAGACAATTTCTCT-
** * * * **
756001 AAACAAAAATTAATCTCACTTGAGATTGTTATTTTTTCAAAACAATTTTCGTCTCGTTTGAGACA
60 AAA-AAAAATTTTTCTCACTTGAGA----CAATTTTTCAAAACAAATTTCGTCTCACTTGAGACA
756066 TTTTTCCTTTGAGAATAC-AAATTTCGAATTTGATTTCAAATTAAACAAAGTTGATCTCACTTGA
120 TTTTTCCTTTGAG-ATACAAAATTT-GAATTTG-TTTCAAATTAAACAAAGTTGATCTCACTTGA
*
756130 GATCGTTTTCTC-AAAAACAAAC
182 GATCGCTTTCTCTAAAAACAAAC
*
756152 GTTGTCTCGCTTGAGATAATTTCTCTAAAAGTAATTTTTGTCTCGTTTGAGACAATTTCTCTAAA
1 -TTGTCTCGCTTGAGATAATTTCTCTAAAA-TAAATTTTG-CTCGTTTGAGACAATTTCTCTAAA
756217 AACAAATGTTTTCTCACTTGAGACAATTTTTCAAA
63 AA-AAAT-TTTTCTCACTTGAGACAATTTTTCAAA
756252 TTATGAATTT
Statistics
Matches: 239, Mismatches: 43, Indels: 53
0.71 0.13 0.16
Matches are distributed among these distances:
206 23 0.10
207 15 0.06
208 48 0.20
209 41 0.17
210 70 0.29
212 9 0.04
213 19 0.08
214 14 0.06
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (204 bp):
TTGTCTCGCTTGAGATAATTTCTCTAAAATAAATTTTGCTCGTTTGAGACAATTTCTCTAAAAAA
AATTTTTCTCACTTGAGACAATTTTTCAAAACAAATTTCGTCTCACTTGAGACATTTTTCCTTTG
AGATACAAAATTTGAATTTGTTTCAAATTAAACAAAGTTGATCTCACTTGAGATCGCTTTCTCTA
AAAACAAAC
Found at i:756298 original size:32 final size:30
Alignment explanation
Indices: 756262--756323 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
756252 TTATGAATTT
756262 GTTTCACTGGAAACAAACATCATCTTTGAGTC
1 GTTTCACTGGAAAC-AA-ATCATCTTTGAGTC
** * *
756294 GTTTCTTTTGAAACAAATGATCTTTGAGTC
1 GTTTCACTGGAAACAAATCATCTTTGAGTC
756324 TATTTCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 13 0.50
31 2 0.08
32 11 0.42
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (30 bp):
GTTTCACTGGAAACAAATCATCTTTGAGTC
Found at i:756319 original size:30 final size:31
Alignment explanation
Indices: 756283--756341 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
756273 AACAAACATC
*
756283 ATCTTTGAGTC-GTTTCTTTTGAAACAAATG
1 ATCTTTGAGTCTATTTCTTTTGAAACAAATG
756313 ATCTTTGAGTCTATTTCTTTTGAAACAAA
1 ATCTTTGAGTCTATTTCTTTTGAAACAAA
756342 ACTTTGTCTC
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (31 bp):
ATCTTTGAGTCTATTTCTTTTGAAACAAATG
Found at i:756449 original size:100 final size:101
Alignment explanation
Indices: 756313--756493 Score: 260
Period size: 100 Copynumber: 1.8 Consensus size: 101
756303 GAAACAAATG
* *
756313 ATCTTTGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGACAGATTT-TATTGAAA-A
1 ATCTTTGAGTATATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGAAAG-TTTCTATTGAAAGA
*
756376 ATCTTTGAGTGTGTTTCACCTAAAACAAAAAGAAAAA
65 ATCTTTGAGTATGTTTCACCTAAAACAAAAAGAAAAA
* * * *
756413 ATCTTTGAGTATGTTTC-TTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTCTTTTGAAAGA
1 ATCTTTGAGTATATTTCTTTTGA-AACAAAACTTTGTCTCTCTTGAGAAAGTTTCTATTGAAAGA
756477 ATCTTTGAGTATGTTTC
65 ATCTTTGAGTATGTTTC
756494 TTTGGAAACA
Statistics
Matches: 71, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
99 8 0.11
100 46 0.65
101 17 0.24
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (101 bp):
ATCTTTGAGTATATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGAAAGTTTCTATTGAAAGAA
TCTTTGAGTATGTTTCACCTAAAACAAAAAGAAAAA
Found at i:756582 original size:66 final size:64
Alignment explanation
Indices: 756407--756585 Score: 234
Period size: 64 Copynumber: 2.8 Consensus size: 64
756397 AAAACAAAAA
* *
756407 GAAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTCTTTT
1 GAAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGAAAGTTCCTTTT
* * *
756471 GAAAGAATCTTTGAGTATGTTTCTTTGGAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTTT
1 GAAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGAAAGTTCCTTTT
* * ***
756535 GAAGAAAAATCTTTAAGTCTGTTT-TTATGAAAACAAAGGCTTGTCTCTTTT
1 G-A-AAAAATCTTTGAGTATGTTTCTT-TGAAAACAAAATTTTGTCTCTTTT
756586 AAAAATATTT
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
64 60 0.60
65 3 0.03
66 37 0.37
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.44
Consensus pattern (64 bp):
GAAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGAAAGTTCCTTTT
Found at i:756607 original size:24 final size:26
Alignment explanation
Indices: 756575--756637 Score: 76
Period size: 24 Copynumber: 2.4 Consensus size: 26
756565 AAACAAAGGC
*
756575 TTGTCTCTTTT-AAAAA-TATTTGAG
1 TTGTTTCTTTTAAAAAATTATTTGAG
*
756599 TTGTTTCTTTTGAAAAAATTCTTTGAG
1 TTGTTTCTTTT-AAAAAATTATTTGAG
756626 TCTGTTTCTTTT
1 T-TGTTTCTTTT
756638 GAACCAAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 10 0.30
26 5 0.15
27 8 0.24
28 10 0.30
ACGTcount: A:0.22, C:0.10, G:0.13, T:0.56
Consensus pattern (26 bp):
TTGTTTCTTTTAAAAAATTATTTGAG
Found at i:756728 original size:91 final size:91
Alignment explanation
Indices: 756602--756807 Score: 260
Period size: 91 Copynumber: 2.3 Consensus size: 91
756592 ATTTGAGTTG
* * *
756602 TTTCTTTTGAAAAAATTCTTTGAGTCTGTTTCTTTTGAACCAAAGTTTTGTTTCTCTTAAGACA-
1 TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGTCTCTCTTAAGACAG
756666 ATTTCGTGA-AAAAATCTTTGAGACA
66 ATTTCGTGAGAAAAATCTTTGAGACA
* *
756691 TTTCTTTTGAAACCAAAATCTTTGAGTTTGTTTCTTTTGAAACAAAGTTTTGTCTCTCTTGAGAC
1 TTTCTTTTGAAA--AAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGTCTCTCTTAAGAC
* * *
756756 AGTTTTTCTTGAGAAAAATCTTTGAGTC-
64 AG-ATTTCGTGAGAAAAATCTTTGAGACA
756784 TGTTCATTTTG--AAAAATCTTTGAG
1 T-TTC-TTTTGAAAAAAATCTTTGAG
756808 ATTGTGTATC
Statistics
Matches: 102, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
89 12 0.12
91 59 0.58
93 9 0.09
94 17 0.17
95 5 0.05
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.45
Consensus pattern (91 bp):
TTTCTTTTGAAAAAAATCTTTGAGTCTGTTTCTTTTGAAACAAAGTTTTGTCTCTCTTAAGACAG
ATTTCGTGAGAAAAATCTTTGAGACA
Found at i:757262 original size:134 final size:134
Alignment explanation
Indices: 757020--757267 Score: 329
Period size: 134 Copynumber: 1.9 Consensus size: 134
757010 AATCATTATC
* *
757020 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCTCCCGACCAGATCTCCTCAT
1 CCTAAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCTCCCGACCAGATCTCCTCAT
* * * **
757085 CGCATAGGAGCCATGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCAC
66 CACATAGGAACCATGTCACCCCTAGACAACCAAACGTCCTCATCGCGTAGGAACCGAGTTATCAC
757150 CCTT
131 CCTT
* * * *
757154 CCTAAAGATGACCAGAACTCTTCATCACATATGAGTCGTGTCAT-TCCCCGACCATATTTTCTCA
1 CCTAAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCT-CCCGACCAGATCTCCTCA
* * * *
757218 TCACATAGGAACCGTGTCACCCTTAGACGACCATAAC-TCTTCATCGCGTA
65 TCACATAGGAACCATGTCACCCCTAGACAACCA-AACGTCCTCATCGCGTA
757268 TGAGCCGTGT
Statistics
Matches: 97, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
133 1 0.01
134 95 0.98
135 1 0.01
ACGTcount: A:0.26, C:0.33, G:0.17, T:0.25
Consensus pattern (134 bp):
CCTAAAGATGACCAGAACTCTTCATCACATATGAGCCGTGTCATCTCCCGACCAGATCTCCTCAT
CACATAGGAACCATGTCACCCCTAGACAACCAAACGTCCTCATCGCGTAGGAACCGAGTTATCAC
CCTT
Found at i:757388 original size:3 final size:3
Alignment explanation
Indices: 757380--757443 Score: 76
Period size: 3 Copynumber: 21.0 Consensus size: 3
757370 AATTTTAATC
* * *
757380 TTA TTA TTA TTA TTA TTA ATG TTA TTA TTA TTA TTA TT- TTGT TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
757425 TTAA TTA TTA TTA TTA TTA
1 TT-A TTA TTA TTA TTA TTA
757444 CTAATTACAT
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
2 2 0.04
3 46 0.87
4 5 0.09
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:757425 original size:18 final size:21
Alignment explanation
Indices: 757374--757440 Score: 91
Period size: 21 Copynumber: 3.1 Consensus size: 21
757364 CTATTTAATT
*
757374 TTAATCTTATTATTATTATTA
1 TTAATGTTATTATTATTATTA
757395 TTAATGTTATTATTATTATTA
1 TTAATGTTATTATTATTATTA
*
757416 TT-TTGTTTATTAATTATTATTA
1 TTAATG-TTATT-ATTATTATTA
757438 TTA
1 TTA
757441 TTACTAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
20 2 0.05
21 27 0.66
22 12 0.29
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (21 bp):
TTAATGTTATTATTATTATTA
Found at i:769584 original size:14 final size:14
Alignment explanation
Indices: 769565--769592 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
769555 ATTATTTGCC
769565 ACGACATTGTCGTT
1 ACGACATTGTCGTT
769579 ACGACATTGTCGTT
1 ACGACATTGTCGTT
769593 GTACGTCGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
ACGACATTGTCGTT
Found at i:773362 original size:20 final size:20
Alignment explanation
Indices: 773337--773379 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
773327 TCTAAAAGCC
*
773337 CATTTAGGATCATATAGATG
1 CATTTAGGAGCATATAGATG
*
773357 CATTTAGGAGCATATAGTTG
1 CATTTAGGAGCATATAGATG
773377 CAT
1 CAT
773380 GTGGTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGAGCATATAGATG
Found at i:797639 original size:26 final size:25
Alignment explanation
Indices: 797602--797659 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
797592 TCAAATAAAG
* * *
797602 TTTTT-TTTAATATTAGTTTGATTAA
1 TTTTTATTAAATATTAG-TTAATGAA
797627 TTTTTATTAAATATTAGTTAATGAA
1 TTTTTATTAAATATTAGTTAATGAA
797652 TTTTTATT
1 TTTTTATT
797660 CCCAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 19 0.66
26 10 0.34
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (25 bp):
TTTTTATTAAATATTAGTTAATGAA
Found at i:799965 original size:20 final size:20
Alignment explanation
Indices: 799940--799991 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
799930 TAGTGTTAAG
799940 GTATCGATACCCAAAGGTGA
1 GTATCGATACCCAAAGGTGA
*
799960 GTATCGATACCCAAATGTGA
1 GTATCGATACCCAAAGGTGA
799980 GTATCGATACCC
1 GTATCGATACCC
799992 TCGTTCAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
GTATCGATACCCAAAGGTGA
Found at i:813887 original size:3 final size:3
Alignment explanation
Indices: 813879--813911 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
813869 TAGTATTACC
*
813879 TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
813912 AAATGTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:822569 original size:21 final size:22
Alignment explanation
Indices: 822530--822576 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
822520 TCTTGTTTTC
*
822530 TTTCTTTTATAAAGTTTTTACT
1 TTTCTTTTATAAAGCTTTTACT
*
822552 TTTCTTTT-TCAAGCTTTTACT
1 TTTCTTTTATAAAGCTTTTACT
822573 TTTC
1 TTTC
822577 AAGTTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.64
Consensus pattern (22 bp):
TTTCTTTTATAAAGCTTTTACT
Found at i:830118 original size:6 final size:6
Alignment explanation
Indices: 830109--830139 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
830099 CGAAAAACAG
830109 TATTGC TATTGC TATTGC TATTGC TA-TGC TA
1 TATTGC TATTGC TATTGC TATTGC TATTGC TA
830140 ATGATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.48
Consensus pattern (6 bp):
TATTGC
Found at i:831730 original size:20 final size:20
Alignment explanation
Indices: 831705--831752 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
831695 AGAACAAGTG
*
831705 TCGATATTATCCCAATAGTA
1 TCGATACTATCCCAATAGTA
831725 TCGATACTATCCCAATAGTA
1 TCGATACTATCCCAATAGTA
831745 TCGATACT
1 TCGATACT
831753 CTACCTGCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
TCGATACTATCCCAATAGTA
Found at i:832980 original size:14 final size:14
Alignment explanation
Indices: 832961--832998 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
832951 ATTAATTATG
832961 ATTATAGTTATACA
1 ATTATAGTTATACA
832975 ATTATAGTTATACA
1 ATTATAGTTATACA
*
832989 AGTATA-TTAT
1 ATTATAGTTAT
832999 TCGATTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (14 bp):
ATTATAGTTATACA
Found at i:838562 original size:15 final size:15
Alignment explanation
Indices: 838538--838579 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
838528 CCCTATTTTG
838538 TAAATAAAAA-TAAA
1 TAAATAAAAATTAAA
838552 TAAAGTAAAAATTAAA
1 TAAA-TAAAAATTAAA
* *
838568 AAAATTAAAATT
1 TAAATAAAAATT
838580 TATTAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 4 0.17
15 13 0.54
16 7 0.29
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (15 bp):
TAAATAAAAATTAAA
Found at i:839396 original size:20 final size:20
Alignment explanation
Indices: 839371--839413 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
839361 GAACATCCTA
*
839371 GAATCGATTCGAGTCAACTC
1 GAATCGATTCGAGCCAACTC
*
839391 GAATCGATTTGAGCCAACTC
1 GAATCGATTCGAGCCAACTC
839411 GAA
1 GAA
839414 CCGAACTGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (20 bp):
GAATCGATTCGAGCCAACTC
Found at i:839423 original size:20 final size:20
Alignment explanation
Indices: 839385--839423 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
839375 CGATTCGAGT
* **
839385 CAACTCGAATCGATTTGAGC
1 CAACTCGAACCGAACTGAGC
839405 CAACTCGAACCGAACTGAG
1 CAACTCGAACCGAACTGAG
839424 TCAAACTAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.28, G:0.21, T:0.18
Consensus pattern (20 bp):
CAACTCGAACCGAACTGAGC
Found at i:840372 original size:36 final size:36
Alignment explanation
Indices: 840331--840400 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
840321 AAGTCTCTAC
**
840331 AGGTTCAGCTTCGATCAAGCTGGTAATTCCTTATAT
1 AGGTTCAGCACCGATCAAGCTGGTAATTCCTTATAT
*
840367 AGGTTCAGCACCGATCAAGTTGGTAATTCCTTAT
1 AGGTTCAGCACCGATCAAGCTGGTAATTCCTTAT
840401 GGACCTAAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (36 bp):
AGGTTCAGCACCGATCAAGCTGGTAATTCCTTATAT
Found at i:843279 original size:15 final size:15
Alignment explanation
Indices: 843259--843294 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
843249 CACGAGTCCA
843259 GATCGGCTTACTCTG
1 GATCGGCTTACTCTG
843274 GATCGGCTTACTCTG
1 GATCGGCTTACTCTG
843289 GATCGG
1 GATCGG
843295 ATCTATTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.14, C:0.25, G:0.31, T:0.31
Consensus pattern (15 bp):
GATCGGCTTACTCTG
Found at i:849041 original size:19 final size:19
Alignment explanation
Indices: 849014--849218 Score: 392
Period size: 19 Copynumber: 10.8 Consensus size: 19
849004 GGTACAAACA
*
849014 TACTATAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849033 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
*
849052 TATTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849071 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849090 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849109 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849128 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849147 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849166 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849185 TACTGTAAGGAAGTTAACG
1 TACTGTAAGGAAGTTAACG
849204 TACTGTAAGGAAGTT
1 TACTGTAAGGAAGTT
849219 GCTAGTCTGT
Statistics
Matches: 183, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 183 1.00
ACGTcount: A:0.37, C:0.10, G:0.26, T:0.27
Consensus pattern (19 bp):
TACTGTAAGGAAGTTAACG
Found at i:856403 original size:5 final size:5
Alignment explanation
Indices: 856395--856443 Score: 82
Period size: 5 Copynumber: 10.0 Consensus size: 5
856385 ATTTCTTTTC
*
856395 TATCA TATCA TATCA TATCA -CTCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
856444 CTCATATCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
4 3 0.07
5 38 0.93
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (5 bp):
TATCA
Found at i:856430 original size:29 final size:29
Alignment explanation
Indices: 856395--856451 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
856385 ATTTCTTTTC
856395 TATCATATCATATCATATCACTCATATCA
1 TATCATATCATATCATATCACTCATATCA
856424 TATCATATCATATCATATCACTCATATC
1 TATCATATCATATCATATCACTCATATC
856452 CTTATTCATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.37, C:0.25, G:0.00, T:0.39
Consensus pattern (29 bp):
TATCATATCATATCATATCACTCATATCA
Found at i:856854 original size:23 final size:23
Alignment explanation
Indices: 856817--856880 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
856807 CAGCTCGTCT
856817 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACGTAG
* * *
856840 AATTGCACCGTAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACGTAG
*
856863 AAATGCACCAAAGTGCCA
1 AAATGCACCGAAGTGCCA
856881 TATAAGGTTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACGTAG
Found at i:864333 original size:22 final size:22
Alignment explanation
Indices: 864305--864384 Score: 98
Period size: 22 Copynumber: 3.7 Consensus size: 22
864295 TGCACTGTAT
864305 GGTGCATCG-ATGCACTAGTGCA
1 GGTGCAT-GAATGCACTAGTGCA
864327 GGTGCATGAATGCAC---TGCA
1 GGTGCATGAATGCACTAGTGCA
864346 TGGTGCATCG-ATGCACTAGTGCA
1 -GGTGCAT-GAATGCACTAGTGCA
864369 GGTGCATGAATGCACT
1 GGTGCATGAATGCACT
864385 GCAGGGATGC
Statistics
Matches: 51, Mismatches: 0, Indels: 14
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.08
20 13 0.25
21 3 0.06
22 27 0.53
23 4 0.08
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (22 bp):
GGTGCATGAATGCACTAGTGCA
Done.