Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 106 of 129
Found at i:19107130 original size:26 final size:26
Alignment explanation
Indices: 19107094--19107144 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
19107084 TTTATTTTGA
* **
19107094 AAATTTAAAATAAAAGGACTTAAATT
1 AAATATAAAATAAAACCACTTAAATT
19107120 AAATATAAAATAAAACCACTTAAAT
1 AAATATAAAATAAAACCACTTAAAT
19107145 CCAAAATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.27
Consensus pattern (26 bp):
AAATATAAAATAAAACCACTTAAATT
Found at i:19110364 original size:25 final size:26
Alignment explanation
Indices: 19110303--19110398 Score: 87
Period size: 25 Copynumber: 3.9 Consensus size: 26
19110293 GAGCTTTTAT
* *
19110303 TTTATTATATATATA-TATATATATA
1 TTTATTATATATATATTTTTTATATA
** *
19110328 TAAAATA-ATATATATTTTTTATATTA
1 TTTATTATATATATATTTTTTATA-TA
19110354 TTT-TTAT-TATATA-TTTTTA-ATA
1 TTTATTATATATATATTTTTTATATA
*
19110376 TTTATTATATACATATTTTTTAT
1 TTTATTATATATATATTTTTTAT
19110399 TTTTTATATT
Statistics
Matches: 55, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
22 5 0.09
23 5 0.09
24 18 0.33
25 24 0.44
26 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTATTATATATATATTTTTTATATA
Found at i:19110381 original size:13 final size:13
Alignment explanation
Indices: 19110333--19110381 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
19110323 ATATATAAAA
19110333 TAATATATATTTT
1 TAATATATATTTT
*
19110346 TTATAT-TATTTT
1 TAATATATATTTT
*
19110358 TATTATATATTTT
1 TAATATATATTTT
*
19110371 TAATATTTATT
1 TAATATATATT
19110382 ATATACATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
12 10 0.33
13 20 0.67
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TAATATATATTTT
Found at i:19110404 original size:25 final size:24
Alignment explanation
Indices: 19110339--19110405 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
19110329 AAAATAATAT
*
19110339 ATATTTTTTATATTATTT-TTATTAT
1 ATATTTTTTAT-TT-TTTATTATTAC
* *
19110364 ATA-TTTTTAATATTTATTATATAC
1 ATATTTTTTATTTTTTATTAT-TAC
19110388 ATATTTTTTATTTTTTAT
1 ATATTTTTTATTTTTTAT
19110406 ATTTTTCACT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 3 0.09
23 5 0.15
24 11 0.32
25 15 0.44
ACGTcount: A:0.30, C:0.01, G:0.00, T:0.69
Consensus pattern (24 bp):
ATATTTTTTATTTTTTATTATTAC
Found at i:19113530 original size:19 final size:18
Alignment explanation
Indices: 19113501--19113537 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
19113491 TTATCTATAA
19113501 TAATTATTATAATGTAAT
1 TAATTATTATAATGTAAT
*
19113519 TAATTAATTATAATTTAAT
1 TAATT-ATTATAATGTAAT
19113538 ATTGTATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TAATTATTATAATGTAAT
Found at i:19113919 original size:14 final size:13
Alignment explanation
Indices: 19113894--19113938 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
19113884 GATCTACACA
19113894 ATATTAAATTAATT
1 ATATT-AATTAATT
19113908 ATGATTAATTAATT
1 AT-ATTAATTAATT
*
19113922 ATATTATAATAATT
1 ATATTA-ATTAATT
19113936 ATA
1 ATA
19113939 AATGATACGC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 21 0.75
15 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
ATATTAATTAATT
Found at i:19114206 original size:15 final size:16
Alignment explanation
Indices: 19114170--19114207 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
19114160 TGTTAGAGTC
*
19114170 TATGATAGTTTATAAA
1 TATGATAATTTATAAA
*
19114186 TTTGATAATTT-TAAA
1 TATGATAATTTATAAA
19114201 TATGATA
1 TATGATA
19114208 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (16 bp):
TATGATAATTTATAAA
Found at i:19115715 original size:26 final size:25
Alignment explanation
Indices: 19115657--19115704 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
19115647 TTTATTTTTT
19115657 AATAA-AAAATAAAAATACAAAATA
1 AATAACAAAATAAAAATACAAAATA
*
19115681 AATAACAAAATATAAAATATAAAA
1 AATAACAAAATA-AAAATACAAAA
19115705 AACTAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.24
25 6 0.29
26 10 0.48
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (25 bp):
AATAACAAAATAAAAATACAAAATA
Found at i:19116137 original size:3 final size:3
Alignment explanation
Indices: 19116131--19116168 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
19116121 TTTTTTCCTT
* *
19116131 TTA TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA GTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19116169 TCTTTTCAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:19116584 original size:2 final size:2
Alignment explanation
Indices: 19116525--19116571 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
19116515 AACAAATCTA
*
19116525 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19116567 -T AT AT
1 AT AT AT
19116572 TACAACATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:19117547 original size:2 final size:2
Alignment explanation
Indices: 19117540--19117567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19117530 TACCTTTGAC
19117540 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
19117568 TACAAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19118156 original size:16 final size:16
Alignment explanation
Indices: 19118135--19118168 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
19118125 ATATTTTCTT
19118135 AAATAT-AATTTTAAAA
1 AAATATGAA-TTTAAAA
19118151 AAATATGAATTTAAAA
1 AAATATGAATTTAAAA
19118167 AA
1 AA
19118169 TTAAGAAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATATGAATTTAAAA
Found at i:19118167 original size:17 final size:16
Alignment explanation
Indices: 19118135--19118168 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
19118125 ATATTTTCTT
*
19118135 AAATATAATTTTAAAA
1 AAATATAATTTAAAAA
19118151 AAATATGAATTTAAAAA
1 AAATAT-AATTTAAAAA
19118168 A
1 A
19118169 TTAAGAAGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
AAATATAATTTAAAAA
Found at i:19119239 original size:28 final size:28
Alignment explanation
Indices: 19119151--19119235 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 28
19119141 AACTAATTAT
* *
19119151 TTAATATAATATCTAAATTTAAAAATTTT
1 TTAATATAATATATAAA-TTAAAAATTTA
19119180 TTAATATAATATATAAATTATAAAATTTA
1 TTAATATAATATATAAATTA-AAAATTTA
19119209 TTAATA-AATATA-ATAATTAAAAATTTA
1 TTAATATAATATATA-AATTAAAAATTTA
19119236 ATTATCTATT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
27 9 0.17
28 14 0.27
29 29 0.56
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAATATAATATATAAATTAAAAATTTA
Found at i:19119337 original size:30 final size:28
Alignment explanation
Indices: 19119267--19119342 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 28
19119257 TTTAAAATTA
*
19119267 ATCAAATTAAAAATTTTAAAATTTAAAT
1 ATCATATTAAAAATTTTAAAATTTAAAT
19119295 ATCATATTAAAAATATTTAAAATTTAAAT
1 ATCATATTAAAAAT-TTTAAAATTTAAAT
*
19119324 ATCGTATTTAAAAATTTTA
1 ATCATA-TTAAAAATTTTA
19119343 CTATAATTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
28 13 0.30
29 23 0.52
30 8 0.18
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (28 bp):
ATCATATTAAAAATTTTAAAATTTAAAT
Found at i:19122668 original size:3 final size:3
Alignment explanation
Indices: 19122660--19122685 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19122650 TAAACTCTTT
19122660 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
19122686 TCAAAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19134517 original size:16 final size:16
Alignment explanation
Indices: 19134496--19134527 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
19134486 TCATATTTTT
19134496 TAGGTAGCATGCACAA
1 TAGGTAGCATGCACAA
19134512 TAGGTAGCATGCACAA
1 TAGGTAGCATGCACAA
19134528 GAAGCATCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.19
Consensus pattern (16 bp):
TAGGTAGCATGCACAA
Found at i:19136885 original size:16 final size:18
Alignment explanation
Indices: 19136842--19136885 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
19136832 TTTTTTTATT
*
19136842 TTATATTTAT-AAATGTA
1 TTATATTAATAAAATGTA
19136859 TTATATTAATAAAAT-TA
1 TTATATTAATAAAATGTA
19136876 TTAT-TTAATA
1 TTATATTAATA
19136886 CTTTAATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 6 0.24
17 15 0.60
18 4 0.16
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATATTAATAAAATGTA
Found at i:19137354 original size:13 final size:14
Alignment explanation
Indices: 19137338--19137379 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
19137328 ATTTTTATAT
19137338 ATTATA-TTAATAA
1 ATTATATTTAATAA
*
19137351 ATTATTATTTAATAC
1 ATTA-TATTTAATAA
19137366 ATTA-ATTTAATAA
1 ATTATATTTAATAA
19137379 A
1 A
19137380 ATATTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 13 0.52
14 2 0.08
15 10 0.40
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTATATTTAATAA
Found at i:19137358 original size:16 final size:15
Alignment explanation
Indices: 19137337--19137386 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
19137327 TATTTTTATA
19137337 TATTATATTAATAAAT
1 TATTAT-TTAATAAAT
*
19137353 TATTATTTAATACAT
1 TATTATTTAATAAAT
*
19137368 TA--ATTTAATAAAA
1 TATTATTTAATAAAT
19137381 TATTAT
1 TATTAT
19137387 ATTGATATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 11 0.38
15 12 0.41
16 6 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTATTTAATAAAT
Found at i:19138020 original size:80 final size:81
Alignment explanation
Indices: 19137905--19138062 Score: 205
Period size: 80 Copynumber: 2.0 Consensus size: 81
19137895 GTATTTAGGG
* *
19137905 CAATCAATTCAGAAAAGTGCAATCAATTAAGGGTTTTATATTTAAGGA-AATCGATTGGTCTTTG
1 CAATCAATTCAGAAAAGTGCAATCAATTAAGGGTTTTATATTT-AGGACAATCAATGGGTCTTTG
*
19137969 ATATTAGAGGTTTATGA
65 AAATTAGAGGTTTATGA
* * * *
19137986 CAATCAATTCA-AAAAGTGCAGTCGATTGAA-GGTTTTATGTTTAGGACAATTAATGGGTCTTTG
1 CAATCAATTCAGAAAAGTGCAATCAATT-AAGGGTTTTATATTTAGGACAATCAATGGGTCTTTG
*
19138049 AAATTAGGGGTTTA
65 AAATTAGAGGTTTA
19138063 GATTAGTGAA
Statistics
Matches: 67, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
79 4 0.06
80 50 0.75
81 13 0.19
ACGTcount: A:0.34, C:0.09, G:0.22, T:0.35
Consensus pattern (81 bp):
CAATCAATTCAGAAAAGTGCAATCAATTAAGGGTTTTATATTTAGGACAATCAATGGGTCTTTGA
AATTAGAGGTTTATGA
Found at i:19139082 original size:31 final size:31
Alignment explanation
Indices: 19139047--19139128 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
19139037 CTGTGCTAAT
*
19139047 ACAAAATTTGAAATTTAGTCCCTATACTTGC
1 ACAAAATTTGAAATTTAGTCCATATACTTGC
* *
19139078 ACAAAATTTAAAATTTAGTCCATGTACTTGC
1 ACAAAATTTGAAATTTAGTCCATATACTTGC
*
19139109 ACGAAATTTGAAATTTAGTC
1 ACAAAATTTGAAATTTAGTC
19139129 TCTCTAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (31 bp):
ACAAAATTTGAAATTTAGTCCATATACTTGC
Found at i:19145560 original size:12 final size:10
Alignment explanation
Indices: 19145515--19145554 Score: 55
Period size: 9 Copynumber: 3.9 Consensus size: 10
19145505 GATGTTAATG
19145515 TTTTTCTTTT
1 TTTTTCTTTT
19145525 TTTTT-TTTT
1 TTTTTCTTTT
19145534 TTTTTCCTTTGT
1 TTTTT-CTTT-T
19145546 TTTTTCTTT
1 TTTTTCTTT
19145555 AGTTTTCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.88
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:19147679 original size:14 final size:14
Alignment explanation
Indices: 19147660--19147686 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19147650 ATAAGTTAGC
19147660 AAAAAAATAAAAAT
1 AAAAAAATAAAAAT
19147674 AAAAAAATAAAAA
1 AAAAAAATAAAAA
19147687 AAGATTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:19149548 original size:28 final size:30
Alignment explanation
Indices: 19149516--19149571 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
19149506 GTGTTTACGT
* *
19149516 ATTTAAAAA-GAA-ATTTTTTTATAAATTA
1 ATTTAAAAATGAATAATTTTTTAAAAATTA
19149544 ATTTAAAAATGAATAATTTTTTAAAAAT
1 ATTTAAAAATGAATAATTTTTTAAAAAT
19149572 ATTAATGCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 3 0.12
30 12 0.50
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (30 bp):
ATTTAAAAATGAATAATTTTTTAAAAATTA
Found at i:19150027 original size:16 final size:16
Alignment explanation
Indices: 19150006--19150036 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19149996 TATTATACAT
19150006 TAATTTATATATTATA
1 TAATTTATATATTATA
*
19150022 TAATTTATATTTTAT
1 TAATTTATATATTAT
19150037 GAAAAAAAAA
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TAATTTATATATTATA
Found at i:19152701 original size:153 final size:153
Alignment explanation
Indices: 19152415--19152701 Score: 416
Period size: 153 Copynumber: 1.9 Consensus size: 153
19152405 ATCTAATATA
*
19152415 TTGGTATTTCAATACAAAATTAAATAATTTATATTAATTTACAGACATATGATCATAAATATAAG
1 TTGGTATTTCAATACAAAATTAAATAATTTATATTAATTTACAGACATATAATCATAAATATAAG
* * * ** * *
19152480 AAAATTATCTTAAAACTTAGTTTTAAGGGTTTATAAAAGCTCTTATTTGTAATAGTGTAAATATA
66 AAAATTACCTTAAAACATAGTTTTAAGGGTTTATAAAAGCTCTTATTTGTAAAAGTACAAACACA
19152545 TATAAGGTAAGTCAATAATTTTT
131 TATAAGGTAAGTCAATAATTTTT
* * * *
19152568 TTGGTCTTTTAATACGAAATTAAATAATTTATATTAATTTACGGACATATAATCATAAATATAAG
1 TTGGTATTTCAATACAAAATTAAATAATTTATATTAATTTACAGACATATAATCATAAATATAAG
* *
19152633 AAAATTACCTTGAAACATAGTTTTTAGGGTTTATGAAAA-CTCTTA-TTGTAAAAGTACAACACA
66 AAAATTACCTTAAAACATAGTTTTAAGGGTTTAT-AAAAGCTCTTATTTGTAAAAGTACAA-ACA
19152696 CATATA
129 CATATA
19152702 TATATATATT
Statistics
Matches: 118, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
152 11 0.09
153 103 0.87
154 4 0.03
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (153 bp):
TTGGTATTTCAATACAAAATTAAATAATTTATATTAATTTACAGACATATAATCATAAATATAAG
AAAATTACCTTAAAACATAGTTTTAAGGGTTTATAAAAGCTCTTATTTGTAAAAGTACAAACACA
TATAAGGTAAGTCAATAATTTTT
Found at i:19155188 original size:29 final size:29
Alignment explanation
Indices: 19155144--19155202 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
19155134 GTCTTCTCTC
* *
19155144 TATTAGTGTCCTTGCCTCTAATGCAGGCT
1 TATTAGTGTCCATGCCTCTAATGCAAGCT
19155173 TATTAGTGTCCATGCCTCTAATGCAAGCT
1 TATTAGTGTCCATGCCTCTAATGCAAGCT
19155202 T
1 T
19155203 CCTTGTGGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.19, T:0.37
Consensus pattern (29 bp):
TATTAGTGTCCATGCCTCTAATGCAAGCT
Found at i:19157369 original size:30 final size:33
Alignment explanation
Indices: 19157301--19157369 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 33
19157291 TATTAATAAT
19157301 AAAAAA-AAAATAAATAAAGTTTTTTAAAGGAA
1 AAAAAAGAAAATAAATAAAGTTTTTTAAAGGAA
19157333 AAAAAAGAAAA-AAA-AAA-TTTTTTAAA-GAA
1 AAAAAAGAAAATAAATAAAGTTTTTTAAAGGAA
19157362 AAGAAAAG
1 AA-AAAAG
19157370 GATATATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 5 0.14
30 14 0.40
31 3 0.09
32 9 0.26
33 4 0.11
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (33 bp):
AAAAAAGAAAATAAATAAAGTTTTTTAAAGGAA
Found at i:19160947 original size:60 final size:62
Alignment explanation
Indices: 19160863--19161091 Score: 211
Period size: 66 Copynumber: 3.7 Consensus size: 62
19160853 GTTTTTTATG
* * * *
19160863 TTAAAAAAAATTAATACTTTCAACTTTTCCTTAAAAATATTTTTTCTT-T-AAATTTTATTT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTCTTCTGAAATTTTAATT
* * * *
19160923 TTAAGAAAAATTGGTACTTCCAACTTTTCCTCAAAAATGCTTTTTTTTTTTTCTGAAATTTTAAT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA----TATTTTTTCTTCTGAAATTTTAAT
19160988 T
62 T
* * * * *
19160989 TCAAGAAAAATTGATACTTTCGACTTTTTCTCAAAAATA--TTTT-TT-AGAAATTTTTATCT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTCTTCTGAAATTTTAAT-T
* * * *
19161048 TCAAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATACTTTTT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
19161092 GAAAATTTTT
Statistics
Matches: 142, Mismatches: 18, Indels: 18
0.80 0.10 0.10
Matches are distributed among these distances:
58 16 0.11
59 33 0.23
60 40 0.28
62 1 0.01
64 9 0.06
65 1 0.01
66 42 0.30
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.48
Consensus pattern (62 bp):
TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTCTTCTGAAATTTTAATT
Found at i:19160975 original size:67 final size:66
Alignment explanation
Indices: 19160902--19161157 Score: 197
Period size: 66 Copynumber: 3.9 Consensus size: 66
19160892 CTTAAAAATA
* * * *
19160902 TTTTTTCTTTAAATTTTATTTTTAAGAAAAATTGGTACTTCCAACTTTTCCTCAAAAATGCTTTT
1 TTTTTTC-TGAAATTTTAATTTCAAGAAAAATTGATACTTCCAACTTTTCCTCAAAAATGCTTTT
19160967 TT
65 TT
* * *
19160969 TTTTTTCTGAAATTTTAATTTCAAGAAAAATTGATACTTTCGACTTTTTCTCAAAAA-------T
1 TTTTTTCTGAAATTTTAATTTCAAGAAAAATTGATACTTCCAACTTTTCCTCAAAAATGCTTTTT
*
19161027 A
66 T
* * ** * *
19161028 TTTTTT-AGAAATTTTTATCTTCAAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATACTTTT
1 TTTTTTCTGAAATTTTAAT-TTCAAGAAAAATTGATACTTCCAACTTTTCCTCAAAAATGCTTTT
19161091 TGAAAAT
65 T-----T
* * * * *
19161098 TTTTATTTTAGAAATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAAT
1 TTTT-TTCT-GAAATTTTAATTTCAAGAAAAATTGATACTTCCAACTTTTCCTCAAAAAT
19161158 ATTTTTTAAA
Statistics
Matches: 152, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
58 14 0.09
59 38 0.25
65 1 0.01
66 43 0.28
67 7 0.05
70 4 0.03
71 2 0.01
72 29 0.19
73 14 0.09
ACGTcount: A:0.34, C:0.11, G:0.06, T:0.48
Consensus pattern (66 bp):
TTTTTTCTGAAATTTTAATTTCAAGAAAAATTGATACTTCCAACTTTTCCTCAAAAATGCTTTTT
T
Found at i:19161032 original size:59 final size:58
Alignment explanation
Indices: 19160977--19161100 Score: 180
Period size: 59 Copynumber: 2.1 Consensus size: 58
19160967 TTTTTTTTCT
*
19160977 GAAATTTTAAT-TTCAAGAAAAATTGATACTTTCGACTTTTTCTCAAAAATATTTTTTA
1 GAAATTTTAATCTTCAAGAAAAATTGATACTTTCAACTTTTTCTC-AAAATATTTTTTA
* * *
19161035 GAAATTTTTATCTTCAAGAAAAATTGATACTTTTAACTTTTTCTCAAAATACTTTTT-
1 GAAATTTTAATCTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTA
19161092 GAAAATTTT
1 G-AAATTTT
19161101 TATTTTAGAA
Statistics
Matches: 60, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
57 1 0.02
58 28 0.47
59 31 0.52
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.46
Consensus pattern (58 bp):
GAAATTTTAATCTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATATTTTTTA
Found at i:19161041 original size:58 final size:56
Alignment explanation
Indices: 19160971--19161105 Score: 189
Period size: 58 Copynumber: 2.3 Consensus size: 56
19160961 GCTTTTTTTT
* * *
19160971 TTTTCTGAAATTTTAATTTCAAGAAAAATTGATACTTTCGACTTTTTCTCAAAAATAT
1 TTTT-TGAAATTTTTATTTCAAGAAAAATTGATACTTTCAACTTTTTCTC-AAAATAC
*
19161029 TTTTTAGAAATTTTTATCTTCAAGAAAAATTGATACTTTTAACTTTTTCTCAAAATAC
1 TTTTT-GAAATTTTTAT-TTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATAC
19161087 TTTTTGAAAATTTTTATTT
1 TTTTTG-AAATTTTTATTT
19161106 TAGAAATTTT
Statistics
Matches: 70, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
57 4 0.06
58 35 0.50
59 31 0.44
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.49
Consensus pattern (56 bp):
TTTTTGAAATTTTTATTTCAAGAAAAATTGATACTTTCAACTTTTTCTCAAAATAC
Found at i:19161131 original size:72 final size:73
Alignment explanation
Indices: 19161022--19161178 Score: 214
Period size: 72 Copynumber: 2.2 Consensus size: 73
19161012 CTTTTTCTCA
* * *
19161022 AAAATA-TT-TTTTAGAAATTTTTATCTTCAAGAAAAATTGATACTTTTAACTTTTTCT-CAAAA
1 AAAATATTTATTTTAGAAATTTTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAA
19161084 TACTTTTTG
66 TA-TTTTTG
* * *
19161093 AAAATTTTTATTTTAGAAA-TTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTAAAAAA
1 AAAATATTTATTTTAGAAATTTTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAA
*
19161157 TATTTTTT
66 TATTTTTG
19161165 AAAATATTTATTTT
1 AAAATATTTATTTT
19161179 TAAGAAAAAT
Statistics
Matches: 75, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
71 5 0.07
72 55 0.73
73 15 0.20
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (73 bp):
AAAATATTTATTTTAGAAATTTTTATCTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAA
TATTTTTG
Found at i:19161164 original size:63 final size:60
Alignment explanation
Indices: 19161141--19161373 Score: 179
Period size: 63 Copynumber: 3.7 Consensus size: 60
19161131 TGATACTTTC
* *
19161141 AACTTTTCCTAAAAAATA---TTTTTTAAAATATTTATTTTTAAGAAAAATT-AGTACTTCC
1 AACTTTTCCTAAAAAATATTTTTTTTTAAAAT-TTTATTTTCAAGAAAAATTGA-TACTTTC
* * *
19161199 AACTTTTTCTCAAAAATATATATAAATATATATTTTTAAACTTTTATTTTCAAAAAAAATTGATA
1 AAC-TTTTC-CTAAAA-A-ATAT---T-T-T-TTTTTAAAATTTTATTTTCAAGAAAAATTGATA
19161264 CTTTC
56 CTTTC
* * * * *
19161269 AACTTTTTCTCAAAAATACTTTTTTTCTGAAAAATTTTATTTTTAAGAAAAATTGATACTTTT
1 AACTTTTCCTAAAAAATA-TTTTTTT-T-TAAAATTTTATTTTCAAGAAAAATTGATACTTTC
19161332 AACTTTTTCAC-AAAAAATATTTTTTTTTAGAAATTTTATTTT
1 AAC-TTTTC-CTAAAAAATATTTTTTTTTA-AAATTTTATTTT
19161374 AGGAAAAGCA
Statistics
Matches: 139, Mismatches: 16, Indels: 36
0.73 0.08 0.19
Matches are distributed among these distances:
58 3 0.02
59 5 0.04
60 5 0.04
61 5 0.04
62 18 0.13
63 40 0.29
64 12 0.09
65 1 0.01
66 3 0.02
67 2 0.01
68 4 0.03
69 4 0.03
70 27 0.19
71 10 0.07
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (60 bp):
AACTTTTCCTAAAAAATATTTTTTTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTC
Found at i:19161175 original size:58 final size:58
Alignment explanation
Indices: 19161103--19161217 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
19161093 AAAATTTTTA
* *
19161103 TTTTAGAAATTTTATTTTCAAGGAAAATT-GATACTTTCAACTTTTCCTAAAAAATATT
1 TTTTAGAAATTTTATTTTCAAGAAAAATTAG-TACTTCCAACTTTTCCTAAAAAATATT
* * *
19161161 TTTTA-AAATATTTATTTTTAAGAAAAATTAGTACTTCCAACTTTTTCTCAAAAATAT
1 TTTTAGAAAT-TTTATTTTCAAGAAAAATTAGTACTTCCAACTTTTCCTAAAAAATAT
19161218 ATATAAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.08
58 45 0.90
59 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.45
Consensus pattern (58 bp):
TTTTAGAAATTTTATTTTCAAGAAAAATTAGTACTTCCAACTTTTCCTAAAAAATATT
Found at i:19161257 original size:70 final size:70
Alignment explanation
Indices: 19161156--19161286 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 70
19161146 TTCCTAAAAA
* *
19161156 ATATTTTTTAAAATATTTATTTTTAAGAAAAATT-AGTACTTCCAACTTTTTCTCAAAAATATAT
1 ATATTTTTTAAAATATTTATTTTCAAAAAAAATTGA-TACTTCCAACTTTTTCTCAAAAATATAT
19161220 ATAAAT
65 ATAAAT
* *
19161226 ATATATTTTTAAACT-TTTATTTTCAAAAAAAATTGATACTTTCAACTTTTTCTCAAAAATA
1 ATAT-TTTTTAAAATATTTATTTTCAAAAAAAATTGATACTTCCAACTTTTTCTCAAAAATA
19161287 CTTTTTTTCT
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
70 45 0.82
71 10 0.18
ACGTcount: A:0.42, C:0.10, G:0.02, T:0.46
Consensus pattern (70 bp):
ATATTTTTTAAAATATTTATTTTCAAAAAAAATTGATACTTCCAACTTTTTCTCAAAAATATATA
TAAAT
Found at i:19161387 original size:63 final size:63
Alignment explanation
Indices: 19161240--19161373 Score: 191
Period size: 63 Copynumber: 2.1 Consensus size: 63
19161230 ATTTTTAAAC
* * *
19161240 TTTTATTTTCAAAAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTTTTTTTCTGAAAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCACAAAAATACTTTTTTTCTGAAAAA
* * *
19161303 TTTTATTTTTAAGAAAAATTGATACTTTTAACTTTTTCACAAAAAATA-TTTTTTT-TTAGAAA
1 TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCAC-AAAAATACTTTTTTTCTGAAAAA
19161365 TTTTATTTT
1 TTTTATTTT
19161374 AGGAAAAGCA
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
62 14 0.22
63 43 0.67
64 7 0.11
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.51
Consensus pattern (63 bp):
TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCACAAAAATACTTTTTTTCTGAAAAA
Found at i:19161455 original size:3 final size:3
Alignment explanation
Indices: 19161447--19161490 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
19161437 ATCAATAAGC
19161447 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19161491 CAAATAAATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:19161876 original size:11 final size:11
Alignment explanation
Indices: 19161860--19161923 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
19161850 GTCAGAATCT
*
19161860 AAAAATTTTCC
1 AAAAAATTTCC
19161871 -AAAAATTTCC
1 AAAAAATTTCC
* *
19161881 TAGAAAAAATACC
1 -A-AAAAATTTCC
*
19161894 AAAAAATTTCA
1 AAAAAATTTCC
19161905 AAAAAATTTCC
1 AAAAAATTTCC
*
19161916 TAAAAATT
1 AAAAAATT
19161924 CTAGAACTAC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
10 9 0.21
11 24 0.57
12 1 0.02
13 8 0.19
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.28
Consensus pattern (11 bp):
AAAAAATTTCC
Found at i:19162628 original size:44 final size:44
Alignment explanation
Indices: 19162561--19163057 Score: 541
Period size: 44 Copynumber: 11.3 Consensus size: 44
19162551 AACAGCTTCG
* **
19162561 AAAAAATAAACAAGGCTCCTCTAATCAGAGGCTCAATGACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * *
19162605 AAAAAATAAACAACGTTCTTCTAAACAGAGGCTCAACAACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * **
19162649 AAAAAATAAACAAAGCTCCTATAATCAGAGGCTTAACAACTTCGA
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTT-TT
* * * **
19162694 AAAAAATAAACAAAGCTCCTCTAATTAAAGGTTCAATGACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * **
19162738 AAAAAATAAACAAAGCTCCTATAAACAGAGGCTCAATGACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * ** **
19162782 AAAAAATAAACAAAGCTCCTTTAATCAAAGGCTTTACAACTTCA
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * *
19162826 AAAAAATAAACAAAGCTTCTCTAATCAAAGGCTTAACAACTTTG
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * *
19162870 AAAAAATAAATAAAGCTCCTCTAATAAGAGGCTTAACAACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * * * *
19162914 GAAAAATAAACAAGGCTTCTCTAAACAAAGGCTCAATAA-TTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * *
19162957 GAAAAATAAACAAAGCTCCTCTAAACAGAAGCTCAACAAC-TTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * *
19163000 GAAAAATAAATAAAGCTCATTTAATCAGAGGCTCAACAACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
*
19163044 GAAAAATAAA-AAAG
1 AAAAAATAAACAAAG
19163058 GTTCCATGAC
Statistics
Matches: 384, Mismatches: 66, Indels: 7
0.84 0.14 0.02
Matches are distributed among these distances:
43 80 0.21
44 269 0.70
45 35 0.09
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.24
Consensus pattern (44 bp):
AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
Found at i:19162712 original size:133 final size:132
Alignment explanation
Indices: 19162548--19163057 Score: 598
Period size: 132 Copynumber: 3.9 Consensus size: 132
19162538 CAAAACTCAT
* * * **
19162548 CTTAACAGCTTCGAAAAAATAAACAAGGCTCCTCTAATCAGAGGCTCAATGACTTTTAAAAAATA
1 CTTAACAACTTCGAAAAAATAAACAAAGCTCCTCTAATCAAAGGCTCAACAACTTTTAAAAAATA
* * * *
19162613 AACAACGTTCTTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTATAATCAGA
66 AACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTATAATCAAA
19162678 GG
131 GG
* * **
19162680 CTTAACAACTTCGAAAAAAATAAACAAAGCTCCTCTAATTAAAGGTTCAATGACTTTTAAAAAAT
1 CTTAACAACTTCG-AAAAAATAAACAAAGCTCCTCTAATCAAAGGCTCAACAACTTTTAAAAAAT
* ** *
19162745 AAACAAAGCTCCTATAAACAGAGGCTCAATGACTTTTAAAAAATAAACAAAGCTCCTTTAATCAA
65 AAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTATAATCAA
19162810 AGG
130 AGG
* * * * *
19162813 CTTTACAACTTCAAAAAAATAAACAAAGCTTCTCTAATCAAAGGCTTAACAACTTTGAAAAAATA
1 CTTAACAACTTCGAAAAAATAAACAAAGCTCCTCTAATCAAAGGCTCAACAACTTTTAAAAAATA
* * * * * * *
19162878 AATAAAGCTCCTCTAATA-AGAGGCTTAACAACTTTTGAAAAATAAACAAGGCTTCTCTAAACAA
66 AACAAAGCTCCTCTAA-ACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTATAATCAA
19162942 AGG
130 AGG
* * * * * *
19162945 CTCAATAATTTTG-AAAAATAAACAAAGCTCCTCTAAACAGAA-GCTCAACAAC-TTTGAAAAAT
1 CTTAACAACTTCGAAAAAATAAACAAAGCTCCTCTAATCA-AAGGCTCAACAACTTTTAAAAAAT
* * * * *
19163007 AAATAAAGCTCATTTAATCAGAGGCTCAACAACTTTTGAAAAATAAA-AAAG
65 AAACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAG
19163058 GTTCCATGAC
Statistics
Matches: 326, Mismatches: 48, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
129 3 0.01
130 50 0.15
131 33 0.10
132 121 0.37
133 119 0.37
ACGTcount: A:0.47, C:0.18, G:0.10, T:0.24
Consensus pattern (132 bp):
CTTAACAACTTCGAAAAAATAAACAAAGCTCCTCTAATCAAAGGCTCAACAACTTTTAAAAAATA
AACAAAGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAAAATAAACAAAGCTCCTATAATCAAA
GG
Found at i:19164061 original size:20 final size:21
Alignment explanation
Indices: 19164017--19164063 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
19164007 TGAGTCTTCT
*
19164017 TTTTTTTATTTTTTCTTCTCA
1 TTTTTTTATTTTTTATTCTCA
*
19164038 -TTTTTTATTTTTTATT-TTA
1 TTTTTTTATTTTTTATTCTCA
19164057 TTTTTTT
1 TTTTTTT
19164064 TTCAAGCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.11, C:0.06, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTATTTTTTATTCTCA
Found at i:19171317 original size:15 final size:15
Alignment explanation
Indices: 19171294--19171323 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19171284 TATCTTATTG
*
19171294 AATGTAATGAATGAA
1 AATGCAATGAATGAA
19171309 AATGCAATGAATGAA
1 AATGCAATGAATGAA
19171324 GGTACATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.23
Consensus pattern (15 bp):
AATGCAATGAATGAA
Found at i:19173635 original size:58 final size:58
Alignment explanation
Indices: 19173571--19173994 Score: 500
Period size: 59 Copynumber: 7.2 Consensus size: 58
19173561 TCTTGTGTAG
*
19173571 GGAAAATTGATACTTTCAACTATTCCCCAAAAATCATTTTTTTGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTGAAATTTATTTTTAA
* * * **
19173629 GGAAAATTGATACTTACAACTTTTTCCTAAAAATCCCTTTTTTGAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTG-AAATTTATTTTTAA
* * *
19173688 GGAAAATTGATACTTTTAACTTTTCCCTAAAAAT-A-TTTTTTGAAAATTTCGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTG-AAATTT--ATTTTTAA
* * * *
19173747 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATCTTTTTTTTGAAAATTTACTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTG-AAATTTATTTTTAA
* * *
19173806 GAAAAATTGATACTTTCAACTTTTCTCCAAAAAT-ATTTTTTGGAAATTTATTTTTCTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTGAAATTTA----T-TTTTAA
* *
19173868 GGAAAATTGATACTTTCAACTTTTCCCTAAAAAT-ATTTTTTGGAAATTTTGATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTGAAA-TTT-ATTTTTAA
* * **
19173927 GGGAAATTGATACTTTCAACTTTTCCTCAAAAA-C-CCTTTTTGAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTGAAATTTATTTTTAA
19173983 GGAAAATTGATA
1 GGAAAATTGATA
19173995 AATAAAAATA
Statistics
Matches: 318, Mismatches: 35, Indels: 28
0.83 0.09 0.07
Matches are distributed among these distances:
56 19 0.06
57 24 0.08
58 53 0.17
59 154 0.48
60 1 0.00
61 14 0.04
62 49 0.15
63 3 0.01
64 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATCATTTTTTTGAAATTTATTTTTAA
Found at i:19174010 original size:11 final size:11
Alignment explanation
Indices: 19173994--19174055 Score: 54
Period size: 12 Copynumber: 5.3 Consensus size: 11
19173984 GAAAATTGAT
19173994 AAATAAAAATA
1 AAATAAAAATA
19174005 AAATAAAAAATA
1 AAAT-AAAAATA
*
19174017 AAGA-AAAGTAAAA
1 AA-ATAAA--AATA
19174030 AAATAAAAAATA
1 AAAT-AAAAATA
*
19174042 AAATAAAGATA
1 AAATAAAAATA
19174053 AAA
1 AAA
19174056 GGAATATTAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 16 0.38
12 17 0.40
13 6 0.14
14 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.15
Consensus pattern (11 bp):
AAATAAAAATA
Found at i:19174049 original size:25 final size:26
Alignment explanation
Indices: 19174004--19174055 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 26
19173994 AAATAAAAAT
19174004 AAAATAAAAAATAAAGAAAAG-TAAA
1 AAAATAAAAAATAAAGAAAAGATAAA
19174029 AAAATAAAAAATAAA-ATAAAGATAAA
1 AAAATAAAAAATAAAGA-AAAGATAAA
19174055 A
1 A
19174056 GGAATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 1 0.04
25 19 0.76
26 5 0.20
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.13
Consensus pattern (26 bp):
AAAATAAAAAATAAAGAAAAGATAAA
Found at i:19174102 original size:16 final size:16
Alignment explanation
Indices: 19174078--19174112 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
19174068 AAACCTAATC
19174078 TAATAAATAAATAAAT
1 TAATAAATAAATAAAT
*
19174094 TAATTAATAAATAAAT
1 TAATAAATAAATAAAT
19174110 TAA
1 TAA
19174113 AAAAAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATAAATAAATAAAT
Found at i:19174104 original size:12 final size:12
Alignment explanation
Indices: 19174079--19174112 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
19174069 AACCTAATCT
*
19174079 AATAAATAAATA
1 AATAAATTAATA
*
19174091 AATTAATTAATA
1 AATAAATTAATA
19174103 AATAAATTAA
1 AATAAATTAA
19174113 AAAAAAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAAATTAATA
Found at i:19175247 original size:20 final size:21
Alignment explanation
Indices: 19175222--19175262 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
19175212 CCTTTACCCA
19175222 ATTTGGGCCAAG-CCCAATTG
1 ATTTGGGCCAAGACCCAATTG
*
19175242 ATTTGGGCCAGGACCCAATTG
1 ATTTGGGCCAAGACCCAATTG
19175263 GGGTGTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.24
Consensus pattern (21 bp):
ATTTGGGCCAAGACCCAATTG
Found at i:19175380 original size:8 final size:8
Alignment explanation
Indices: 19175369--19175399 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
19175359 TTTTGTGTTT
*
19175369 TTTTTTTA
1 TTTTTTTG
19175377 TTTTTTTG
1 TTTTTTTG
19175385 TTTTTTTG
1 TTTTTTTG
19175393 TTTTTTT
1 TTTTTTT
19175400 TTTACCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.90
Consensus pattern (8 bp):
TTTTTTTG
Found at i:19175381 original size:21 final size:20
Alignment explanation
Indices: 19175355--19175402 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
19175345 CAACATTGTC
*
19175355 ATTTTTTTGTGTTTTTTTTTT
1 ATTTTTTTGT-TTTTTTGTTT
19175376 ATTTTTTTGTTTTTTTGTTT
1 ATTTTTTTGTTTTTTTGTTT
19175396 -TTTTTTT
1 ATTTTTTT
19175403 ACCAAAACTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 7 0.27
20 9 0.35
21 10 0.38
ACGTcount: A:0.04, C:0.00, G:0.08, T:0.88
Consensus pattern (20 bp):
ATTTTTTTGTTTTTTTGTTT
Found at i:19175467 original size:41 final size:41
Alignment explanation
Indices: 19175410--19175622 Score: 309
Period size: 41 Copynumber: 5.1 Consensus size: 41
19175400 TTTACCAAAA
* * * * *
19175410 CTCCTCTAAACGGAGGCTCAATGACTTTGAAAAGTAAATTA
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
* *
19175451 CTCCTCTAAACAGAGGCACCACGACTTTAAAAAATAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
*
19175492 CTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATTG
*
19175534 CTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
*
19175575 CTCCTCTAAACAGAGGCACCGCGACTTTGGAAAGAGTAAATTG
1 CTCCTCTAAACAGAGGCACCACGACTTT-GAAA-AGTAAATTG
19175618 CTCCT
1 CTCCT
19175623 TGACAATCAT
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
41 99 0.64
42 42 0.27
43 14 0.09
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
CTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTG
Found at i:19175551 original size:83 final size:83
Alignment explanation
Indices: 19175410--19175622 Score: 320
Period size: 83 Copynumber: 2.6 Consensus size: 83
19175400 TTTACCAAAA
* * * *
19175410 CTCCTCTAAACGGAGGCTCAATGACTTTG-AAAAGTAAATTACTCCTCTAAACAGAGGCACCACG
1 CTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
19175474 ACTTTAAAAAATAAATTG
66 ACTTTAAAAAATAAATTG
19175492 CTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 CTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
** *
19175557 ACTTTGGAAAGTAAATTG
66 ACTTTAAAAAATAAATTG
** *
19175575 CTCCTCTAAACAGAGGCACCGCGACTTTGGAAAGAGTAAATTGCTCCT
1 CTCCTCTAAACAGAGGCACCATGACTTT-GAAAAAGTAAATTGCTCCT
19175623 TGACAATCAT
Statistics
Matches: 119, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
82 26 0.22
83 75 0.63
84 18 0.15
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.23
Consensus pattern (83 bp):
CTCCTCTAAACAGAGGCACCATGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTAAAAAATAAATTG
Found at i:19180810 original size:22 final size:21
Alignment explanation
Indices: 19180798--19180840 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
19180788 ATAAATAAAT
19180798 AAAATTTTTTAAAAGAAAAAA
1 AAAATTTTTTAAAAGAAAAAA
*
19180819 AAAA-TTTTT-AAAGAAAAGA
1 AAAATTTTTTAAAAGAAAAAA
19180838 AAA
1 AAA
19180841 GGATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 5 0.24
21 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (21 bp):
AAAATTTTTTAAAAGAAAAAA
Found at i:19180826 original size:20 final size:20
Alignment explanation
Indices: 19180798--19180840 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
19180788 ATAAATAAAT
*
19180798 AAAATTTTTTAAAAGAAAA-A
1 AAAAATTTTT-AAAGAAAAGA
19180818 AAAAATTTTTAAAGAAAAGA
1 AAAAATTTTTAAAGAAAAGA
19180838 AAA
1 AAA
19180841 GGATATATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
AAAAATTTTTAAAGAAAAGA
Found at i:19183706 original size:3 final size:3
Alignment explanation
Indices: 19183661--19183693 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
19183651 AAAAGAGAGA
19183661 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
19183694 GTTGATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:19184422 original size:60 final size:59
Alignment explanation
Indices: 19184345--19184570 Score: 251
Period size: 60 Copynumber: 3.8 Consensus size: 59
19184335 GTTTTTTATG
* *
19184345 TTAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTCTTTAAATTTTATTT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT-TTTAAATTTTATTT
* *
19184405 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTCTTTTTTTTGGAAATTTTAATT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAT-AT-TTTTTTTT--AAATTTTATTT
* * * ** *
19184468 TCAAGGAAAATTGATACTTT-AGACTTTTTCTCAAAAATA-TTTTTTAGAAATTTTTATCT
1 TTAAGAAAAATTGATACTTTCA-ACTTTTCCTCAAAAATATTTTTTTTTAAA-TTTTATTT
* * *
19184527 TTAAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATACTTTTT
1 TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
19184571 GAAAATTTTT
Statistics
Matches: 144, Mismatches: 14, Indels: 17
0.82 0.08 0.10
Matches are distributed among these distances:
58 9 0.06
59 39 0.27
60 43 0.30
61 4 0.03
62 6 0.04
63 43 0.30
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (59 bp):
TTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTTTAAATTTTATTT
Found at i:19184540 original size:59 final size:57
Alignment explanation
Indices: 19184337--19184590 Score: 246
Period size: 63 Copynumber: 4.3 Consensus size: 57
19184327 ATTTGGAGGT
* * * *
19184337 TTTTTATGTTAAAAAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTCTTTAAA
1 TTTTTATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTT-TTGAAA
*
19184397 -TTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATGCTCTTTTTTTTGGAAA
1 TTTTTA-TTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAA-----TATTTTTT-GAAA
* * * *
19184460 TTTTAATTTCAAGGAAAATTGATACTTT-AGACTTTTTCTCAAAAATATTTTTTAGAAA
1 TTTTTATTTTAAGAAAAATTGATACTTTCA-ACTTTTCCTCAAAAATATTTTTT-GAAA
* * *
19184518 TTTTTATCTTTAAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATACTTTTTGAAAA
1 TTTTTAT-TTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTG-AAA
19184576 TTTTTATTTT-AGAAA
1 TTTTTATTTTAAGAAA
19184591 TTTTATTTTC
Statistics
Matches: 167, Mismatches: 15, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
56 5 0.03
57 4 0.02
58 38 0.23
59 34 0.20
60 37 0.22
62 3 0.02
63 41 0.25
64 4 0.02
65 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (57 bp):
TTTTTATTTTAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTGAAA
Found at i:19184798 original size:63 final size:59
Alignment explanation
Indices: 19184572--19184846 Score: 249
Period size: 60 Copynumber: 4.5 Consensus size: 59
19184562 ATACTTTTTG
* *
19184572 AAAAT-TTTTATTTTAGAA-ATTTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCTTAAA
1 AAAATATTTT-TTTTA-AATATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTT-TT-CA
* * * * *
19184633 AAAATATATTTTTTAAAT-CTTTATTTTTAAGAAAAATT-AGTACTTCCAACTTTTTCTAAA
1 AAAATATTTTTTTTAAATATTTTATTTTCAAGAAAAATTGA-TACTTTCAACTTTTT-T-CA
* *
19184693 AAGTATATATATTTTTTTAAA-CTTTTGTTTTCAAGAAAAATTGATACTTTCAACTTTTCTTCA
1 AA--A-ATAT-TTTTTTTAAATATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTT-TTCA
*
19184756 AAAATACTTTTTTTCTAAAATATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCA
1 AAAATA-TTTTTTT-T-AAATATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTT-TCA
19184819 AAAATATATCTTTTTT-AA-ATTTTATTTT
1 AAAATAT-T-TTTTTTAAATATTTTATTTT
19184847 AGGAAAATCA
Statistics
Matches: 182, Mismatches: 14, Indels: 37
0.78 0.06 0.16
Matches are distributed among these distances:
59 2 0.01
60 57 0.31
61 15 0.08
62 9 0.05
63 52 0.29
64 45 0.25
65 2 0.01
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (59 bp):
AAAATATTTTTTTTAAATATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTCA
Found at i:19184921 original size:3 final size:3
Alignment explanation
Indices: 19184913--19184938 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
19184903 ATCAATAAGC
19184913 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
19184939 CAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:19186082 original size:44 final size:44
Alignment explanation
Indices: 19186015--19186505 Score: 513
Period size: 44 Copynumber: 11.2 Consensus size: 44
19186005 AACAGCTTCG
* * **
19186015 AAAAAATAAACAAGGCTCCTCTAATTAGAGGCTCAATGACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * *
19186059 AAAAAATAAACAATGCTCTTCTAAACAGAGGCTCAACAACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * **
19186103 GAAAAATAAACAAAGCTCCTATAATCAGAGGCTTAACAACTTCG
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * **
19186147 AAAAAATAAACAAAGCT-CTCTAATTAAAGGTTCAATGACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * *
19186190 AAAAAATAAACAAAGCTCCTATAAACAGAGGCTCTACGACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * * * *
19186234 AAAATATAAATAAAGTTTCTCTAATCAGAGGCTCAATAAC-TTC
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * *
19186277 AGAAAAATAAACAAAGCTTCTCTAATCAGAGGCTCAACAACTGTG
1 A-AAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* *
19186322 AAAAAATAAACAAAGCTCCTCTAATAAGAGGCTTAACAACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * * * *
19186366 GAAAAATAAATAAGGCTTCTCTAAACAAAGGCTCAACAA-TTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
* * * *
19186409 GAAAAATAAATAAAGCTCCTCTAAACAGAAGCTCAACAAC-TTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
** * * *
19186452 GGAAAATAAATAAAGCTCATCTAATCAGAGACTCAACAACTTTT
1 AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
*
19186496 GAAAAATAAA
1 AAAAAATAAA
19186506 TAAGGTTTCA
Statistics
Matches: 372, Mismatches: 70, Indels: 10
0.82 0.15 0.02
Matches are distributed among these distances:
43 114 0.31
44 256 0.69
45 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.24
Consensus pattern (44 bp):
AAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACAACTTTT
Found at i:19186501 original size:175 final size:171
Alignment explanation
Indices: 19186015--19186505 Score: 574
Period size: 175 Copynumber: 2.8 Consensus size: 171
19186005 AACAGCTTCG
** * * * *
19186015 AAAAAATAAACAAGGCTCCTCTAATTAGAGGCTCAATGACTTTTAAAAAATAAACAATGCTCTTC
1 AAAAAATAAACAAGGCTCCTCTAAACAGAGGCTCAA-CACTTTT-AAAAATAAATAAAGCTCCTC
* *
19186080 TAAACAGAGGCTCAACAACTTTTGAAAAATAAACAAAGCTCCTATAATCAGAGGCTTAACAACTT
64 TAAACAGAGGCTCAACAAC-TTTGAAAAATAAACAAAGCT-CTCTAATCAGAGGCTCAACAACTT
* **
19186145 CGAAAAAATAAACAAAGCTCTCTAATTAAAGGTTCAATGACTTTT
127 TGAAAAAATAAACAAAGCTCTCTAATTAAAGGTTCAACAACTTTT
* * * * *
19186190 AAAAAATAAACAAAGCTCCTATAAACAGAGGCTCTACGACTTTTAAAATATAAATAAAGTTTCTC
1 AAAAAATAAACAAGGCTCCTCTAAACAGAGGCTCAAC-ACTTTTAAAA-ATAAATAAAGCTCCTC
* * * *
19186255 TAATCAGAGGCTCAATAACTTCAGAAAAATAAACAAAGCTTCTCTAATCAGAGGCTCAACAACTG
64 TAAACAGAGGCTCAACAACTT-TGAAAAATAAACAAAGC-TCTCTAATCAGAGGCTCAACAACTT
19186320 TGAAAAAATAAACAAAGCTCCTCTAA-TAAGAGGCTT-AACAACTTTT
127 TGAAAAAATAAACAAAGCT-CTCTAATTAA-AGG-TTCAACAACTTTT
* * * * *
19186366 GAAAAATAAATAAGGCTTCTCTAAACAAAGGCTCAACAATTTTGAAAAATAAATAAAGCTCCTCT
1 AAAAAATAAACAAGGCTCCTCTAAACAGAGGCTCAACACTTTT-AAAAATAAATAAAGCTCCTCT
* * * *
19186431 AAACAGAAGCTCAACAACTTTGGAAAATAAATAAAGCTCATCTAATCAGAGACTCAACAACTTTT
65 AAACAGAGGCTCAACAACTTTGAAAAATAAACAAAGCTC-TCTAATCAGAGGCTCAACAAC-TTT
19186496 G-AAAAATAAA
128 GAAAAAATAAA
19186506 TAAGGTTTCA
Statistics
Matches: 268, Mismatches: 38, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
173 2 0.01
174 49 0.18
175 163 0.61
176 52 0.19
177 2 0.01
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.24
Consensus pattern (171 bp):
AAAAAATAAACAAGGCTCCTCTAAACAGAGGCTCAACACTTTTAAAAATAAATAAAGCTCCTCTA
AACAGAGGCTCAACAACTTTGAAAAATAAACAAAGCTCTCTAATCAGAGGCTCAACAACTTTGAA
AAAATAAACAAAGCTCTCTAATTAAAGGTTCAACAACTTTT
Found at i:19187512 original size:19 final size:19
Alignment explanation
Indices: 19187465--19187521 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
19187455 TCACTTTGAG
19187465 TCTT-TTTTTTT-ATTTTT
1 TCTTCTTTTTTTCATTTTT
*
19187482 TCTTCTCATTTTTCATTTTT
1 TCTTCT-TTTTTTCATTTTT
19187502 TC-TCATTTTTTTCATTTTT
1 TCTTC-TTTTTTTCATTTTT
19187521 T
1 T
19187522 TCTTTTTCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.12
18 1 0.03
19 20 0.59
20 9 0.26
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (19 bp):
TCTTCTTTTTTTCATTTTT
Found at i:19187522 original size:20 final size:20
Alignment explanation
Indices: 19187468--19187524 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 20
19187458 CTTTGAGTCT
*
19187468 TTTTTTTTATTTTTTCTTCTCA
1 TTTTTTTCA-TTTTT-TTCTCA
19187490 --TTTTTCA-TTTTTTCTCA
1 TTTTTTTCATTTTTTTCTCA
19187507 TTTTTTTCATTTTTTTCT
1 TTTTTTTCATTTTTTTCT
19187525 TTTTCAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 6 0.19
18 4 0.13
19 7 0.23
20 14 0.45
ACGTcount: A:0.09, C:0.14, G:0.00, T:0.77
Consensus pattern (20 bp):
TTTTTTTCATTTTTTTCTCA
Found at i:19194797 original size:15 final size:15
Alignment explanation
Indices: 19194774--19194803 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
19194764 TATCTTATCG
*
19194774 AATGTAATGAATGAA
1 AATGCAATGAATGAA
19194789 AATGCAATGAATGAA
1 AATGCAATGAATGAA
19194804 GTTATATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.20, T:0.23
Consensus pattern (15 bp):
AATGCAATGAATGAA
Found at i:19198206 original size:59 final size:59
Alignment explanation
Indices: 19198011--19198247 Score: 248
Period size: 60 Copynumber: 4.0 Consensus size: 59
19198001 TGCTTTTATA
* * *
19198011 CAAGAAAAATTAATACTTTCAACTTTTTCTTAAAAATATATTTTTTTCAAA-TTTTATTTT
1 CAAGAAAAATTAATACTTTCAAC-TTTTCCTCAAAA-ATATTTTTTTAAAATTTTTATTTT
* ** * *
19198071 TAAGAAAAATTGGTACTTTCAACTTTAT-CTCAAAAATATTTTTTTCTGAAATTTTAATTTT
1 CAAGAAAAATTAATACTTTCAACTTT-TCCTCAAAAATA-TTTTTT-TAAAATTTTTATTTT
* * * *
19198132 TAA-AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAAAAATTTTTATCTT
1 CAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTTTTATTTT
* * * * *
19198190 CAAGGAAAATTAATACTTTTAACTTGTCCTC-AAACTATTTTTTGAAAATTTTTATTTT
1 CAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTTTTATTTT
19198248 AGAAATTTTA
Statistics
Matches: 151, Mismatches: 20, Indels: 14
0.82 0.11 0.08
Matches are distributed among these distances:
58 40 0.26
59 44 0.29
60 56 0.37
61 11 0.07
ACGTcount: A:0.37, C:0.11, G:0.04, T:0.48
Consensus pattern (59 bp):
CAAGAAAAATTAATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAAATTTTTATTTT
Found at i:19198246 original size:135 final size:135
Alignment explanation
Indices: 19198118--19198422 Score: 343
Period size: 135 Copynumber: 2.4 Consensus size: 135
19198108 ATTTTTTTCT
* *
19198118 GAAATTTTAATTTTTAA-AAAAATTGATACTTTCAACTTTTCCT-CAAA-A-ATAT-TTTTTAAA
1 GAAATTTT-ATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAGATATATATTTTTAAA
* *
19198178 AATTTTTATCTTCAAGGAAAATTAATACTTTTAACTTGTCCTCAAACTATTTTTTGAAAATTTTT
65 AATTTTTATCTTCAAGAAAAATTAATACTTCTAACTTGTCCTCAAACTATTTTTTGAAAATTTTT
19198243 ATTTTA
130 ATTTTA
*
19198249 GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAGATATATATTTTTAAAA
1 GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAGATATATATTTTTAAAA
* * ** * * * * * *
19198314 ATTTTTATTTTTAAGAAAAATTGGTACTTCTAACTTTTTCTCAAA--A----AT--ATATATAT-
66 ATTTTTATCTTCAAGAAAAATTAATACTTCTAACTTGTCCTCAAACTATTTTTTGAAAATTTTTA
19198370 TTTTA
131 TTTTA
*
19198375 -AACTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAA
1 GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCC-TAAAAA
19198423 TACTTTTTTT
Statistics
Matches: 151, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
125 39 0.26
126 11 0.07
127 5 0.03
129 1 0.01
130 7 0.05
131 33 0.22
132 3 0.02
133 2 0.01
134 4 0.03
135 46 0.30
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (135 bp):
GAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAGATATATATTTTTAAAA
ATTTTTATCTTCAAGAAAAATTAATACTTCTAACTTGTCCTCAAACTATTTTTTGAAAATTTTTA
TTTTA
Found at i:19198367 original size:62 final size:62
Alignment explanation
Indices: 19198244--19198519 Score: 287
Period size: 63 Copynumber: 4.5 Consensus size: 62
19198234 AAAATTTTTA
* * *
19198244 TTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAGATA-TATAT
1 TTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAA-ATACTATAT
*
19198306 TTTTAAAAATTTTTATTTTTAAGAAAAATTGGTAC-TTCTAACTTTTTCTCAAAAATA-TATAT
1 TTTTAAAAA-TTTTATTTTTAAGAAAAATTGATACTTTC-AACTTTTTCTCAAAAATACTATAT
* * * * * *
19198368 ATTTTTAAACTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATACT-TTT
1 -TTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTATAT
* * * * * *
19198430 TTTCTAAAAAATTTTATTTTTAA-AGAAAAGTGATACTTTTAACTTTTTCCCAAAAATATTTTTT
1 TTT-T-AAAAATTTTATTTTTAAGA-AAAATTGATACTTTCAACTTTTTCTCAAAAATACTATAT
*
19198494 TTTTGAAAATTTTA-TTTT-AGAAAAAT
1 TTTTAAAAATTTTATTTTTAAGAAAAAT
19198520 CATTGACAAA
Statistics
Matches: 182, Mismatches: 22, Indels: 22
0.81 0.10 0.10
Matches are distributed among these distances:
60 5 0.03
61 8 0.04
62 71 0.39
63 92 0.51
64 6 0.03
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (62 bp):
TTTTAAAAATTTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATACTATAT
Found at i:19198394 original size:125 final size:124
Alignment explanation
Indices: 19198244--19198519 Score: 364
Period size: 125 Copynumber: 2.2 Consensus size: 124
19198234 AAAATTTTTA
*
19198244 TTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAGATA-TATATTT
1 TTTTA-AAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAA-ATACT-TATTT
* * * *
19198308 T-TAAAAATTTTTATTTTT-AAGAAAAATTGGTACTTCTAACTTTTTCTCAAAAATATATATAT
63 TCTAAAAAATTTTATTTTTAAAG-AAAAGTGATACTTCTAACTTTTTCCCAAAAATAT-TATAT
* * *
19198370 TTTTAAACTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATACTTTTTTTCT
1 TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATACTTATTTTCT
* * *
19198435 AAAAAATTTTATTTTTAAAGAAAAGTGATACTTTTAACTTTTTCCCAAAAATATTTTTT
66 AAAAAATTTTATTTTTAAAGAAAAGTGATACTTCTAACTTTTTCCCAAAAATATTATAT
19198494 TTTTGAAAATTTTATTTT--AGAAAAAT
1 TTTT-AAAATTTTATTTTCAAGAAAAAT
19198520 CATTGACAAA
Statistics
Matches: 134, Mismatches: 12, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
123 8 0.06
124 15 0.11
125 103 0.77
126 8 0.06
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (124 bp):
TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAATACTTATTTTCT
AAAAAATTTTATTTTTAAAGAAAAGTGATACTTCTAACTTTTTCCCAAAAATATTATAT
Found at i:19198621 original size:4 final size:4
Alignment explanation
Indices: 19198612--19198649 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
19198602 TAATAATAAT
19198612 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
19198650 AACCCTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:19199167 original size:11 final size:11
Alignment explanation
Indices: 19199151--19199176 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19199141 TCGAAATATG
19199151 AAAATTTCCCA
1 AAAATTTCCCA
19199162 AAAATTTCCCA
1 AAAATTTCCCA
19199173 AAAA
1 AAAA
19199177 AAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTTCCCA
Found at i:19199265 original size:11 final size:11
Alignment explanation
Indices: 19199246--19199279 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19199236 TAAAAACTAT
*
19199246 TTTTGCTTCTA
1 TTTTCCTTCTA
19199257 TTTTCCTTCTA
1 TTTTCCTTCTA
*
19199268 TTTTCTTTCTA
1 TTTTCCTTCTA
19199279 T
1 T
19199280 GTGTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTTCCTTCTA
Found at i:19200470 original size:16 final size:17
Alignment explanation
Indices: 19200449--19200480 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19200439 CGAGTAGCAA
19200449 TTCTCTGAAAT-TTTAT
1 TTCTCTGAAATCTTTAT
19200465 TTCTCTGAAATCTTTA
1 TTCTCTGAAATCTTTA
19200481 AGTAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCTCTGAAATCTTTAT
Found at i:19202711 original size:21 final size:22
Alignment explanation
Indices: 19202685--19202726 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
19202675 CCCTCTTTTT
19202685 CATTATTT-TCGTT-CAAACTTA
1 CATTATTTCT-GTTGCAAACTTA
19202706 CATTATTTCTGTTGCAAACTT
1 CATTATTTCTGTTGCAAACTT
19202727 TGTGCATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (22 bp):
CATTATTTCTGTTGCAAACTTA
Found at i:19203590 original size:22 final size:24
Alignment explanation
Indices: 19203543--19203599 Score: 82
Period size: 22 Copynumber: 2.4 Consensus size: 24
19203533 TTTTATTTTT
19203543 ATATATTTATATTTATATTAAAAATA
1 ATAT-TTTATATTTATA-TAAAAATA
19203569 ATATTTTATATTTA-A-AAAAATA
1 ATATTTTATATTTATATAAAAATA
19203591 ATATTTTAT
1 ATATTTTAT
19203600 TAATTTCGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 16 0.52
24 1 0.03
25 10 0.32
26 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATTTTATATTTATATAAAAATA
Found at i:19210619 original size:3 final size:3
Alignment explanation
Indices: 19210613--19210643 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
19210603 AATAATAGTA
19210613 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
19210644 GGAAGGATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:19211397 original size:27 final size:27
Alignment explanation
Indices: 19211342--19211397 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
19211332 TGAATTGTAA
* * *
19211342 TAAAAATTATTATTAAATTTATTAGAT
1 TAAAAATTATTAATAAAATTATTAAAT
19211369 TAAAAATTATATAATAAAATT-TTAAAT
1 TAAAAATTAT-TAATAAAATTATTAAAT
19211396 TA
1 TA
19211398 TTTAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 17 0.68
28 8 0.32
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
TAAAAATTATTAATAAAATTATTAAAT
Found at i:19211423 original size:19 final size:19
Alignment explanation
Indices: 19211380--19211442 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 19
19211370 AAAAATTATA
19211380 TAATAAA-ATTT-T-AAAT
1 TAATAAATATTTATAAAAT
* *
19211396 TATTTAATATTTATAAAAT
1 TAATAAATATTTATAAAAT
* *
19211415 TAATAAATAATTA-AAAAC
1 TAATAAATATTTATAAAAT
19211433 TAATTAAATA
1 TAA-TAAATA
19211443 ATTTTTAAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 8 0.22
19 20 0.54
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATAAATATTTATAAAAT
Found at i:19211770 original size:2 final size:2
Alignment explanation
Indices: 19211763--19211802 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
19211753 AAATGAAATG
19211763 TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19211803 TAAAATTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19211788 original size:17 final size:17
Alignment explanation
Indices: 19211766--19211799 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
19211756 TGAAATGTAT
19211766 ATATATATATATATATA
1 ATATATATATATATATA
19211783 ATATATATATATATATA
1 ATATATATATATATATA
19211800 TATTAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:19212503 original size:20 final size:19
Alignment explanation
Indices: 19212472--19212555 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 19
19212462 TAATGTTAAA
*
19212472 AAAATTATAAAAATAATTTT
1 AAAA-TATAAAAAAAATTTT
19212492 AAAATATAAAAAAAGAGTTTT
1 AAAATATAAAAAAA-A-TTTT
*
19212513 -CAATATTAAAAAATAATTTT
1 AAAATA-TAAAAAA-AATTTT
* **
19212533 GAAATATCTAAAAAATTTT
1 AAAATATAAAAAAAATTTT
19212552 AAAA
1 AAAA
19212556 AATTGACAAG
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
19 18 0.34
20 18 0.34
21 16 0.30
22 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAAATATAAAAAAAATTTT
Found at i:19212504 original size:21 final size:21
Alignment explanation
Indices: 19212472--19212555 Score: 68
Period size: 20 Copynumber: 4.2 Consensus size: 21
19212462 TAATGTTAAA
*
19212472 AAAAT-TATAAAAATAATTTT
1 AAAATATAAAAAAATAATTTT
* *
19212492 AAAATATAAAAAAAGAGTTTT
1 AAAATATAAAAAAATAATTTT
* *
19212513 -CAATATTAAAAAATAATTTT
1 AAAATATAAAAAAATAATTTT
* **
19212533 GAAATAT-CTAAAA-AATTTT
1 AAAATATAAAAAAATAATTTT
19212552 AAAA
1 AAAA
19212556 AATTGACAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
19 9 0.18
20 25 0.49
21 17 0.33
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (21 bp):
AAAATATAAAAAAATAATTTT
Found at i:19212941 original size:26 final size:25
Alignment explanation
Indices: 19212887--19212953 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 25
19212877 ACAGAAAAAT
19212887 AATATAATATTTTTAA-A-TTTTATA
1 AATATAATA-TTTTAATATTTTTATA
19212911 AATATTTAATATTTTAATATTTTTAT-
1 AATA--TAATATTTTAATATTTTTATA
*
19212937 TATATAA-ATTTTAATAT
1 AATATAATATTTTAATAT
19212954 AATATTTTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
23 10 0.26
24 7 0.18
25 6 0.16
26 9 0.24
27 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
AATATAATATTTTAATATTTTTATA
Found at i:19212960 original size:28 final size:29
Alignment explanation
Indices: 19212886--19212963 Score: 95
Period size: 31 Copynumber: 2.6 Consensus size: 29
19212876 AACAGAAAAA
*
19212886 TAATATAATATTTTTAAATTTTATAAATATT
1 TAATATAATATTTTT--ATTATATAAATATT
19212917 TAATATTTTAATATTTTTATTATATAAAT-TT
1 TAATA---TAATATTTTTATTATATAAATATT
19212948 TAATATAATATTTTTA
1 TAATATAATATTTTTA
19212964 ATGATCATTT
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
28 11 0.26
31 12 0.28
32 10 0.23
34 10 0.23
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (29 bp):
TAATATAATATTTTTATTATATAAATATT
Found at i:19212978 original size:15 final size:14
Alignment explanation
Indices: 19212925--19212985 Score: 54
Period size: 14 Copynumber: 4.3 Consensus size: 14
19212915 TTTAATATTT
19212925 TAATATTTTTATTATA
1 TAATATTTTTA--ATA
19212941 TAA-A-TTTTAATA
1 TAATATTTTTAATA
19212953 TAATATTTTTAATGA
1 TAATATTTTTAAT-A
* * *
19212968 TCATTTTTTTATTA
1 TAATATTTTTAATA
19212982 TAAT
1 TAAT
19212986 TCATTTTACT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 6 0.16
13 1 0.03
14 16 0.42
15 12 0.32
16 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
TAATATTTTTAATA
Found at i:19213684 original size:15 final size:14
Alignment explanation
Indices: 19213665--19213701 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
19213655 GTGTATTTTG
19213665 TTTTTTAATTTAAT
1 TTTTTTAATTTAAT
*
19213679 TATTTTTAATTTCAT
1 T-TTTTTAATTTAAT
19213694 TTTTTTAA
1 TTTTTTAA
19213702 CAAAAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTTTAATTTAAT
Found at i:19215676 original size:24 final size:26
Alignment explanation
Indices: 19215629--19215707 Score: 71
Period size: 25 Copynumber: 3.3 Consensus size: 26
19215619 ATAGATTAAA
19215629 AAATTTTGTTATATAAATTAAATATG
1 AAATTTTGTTATATAAATTAAATATG
*
19215655 AAATTTT-TTA-A-AAATTTAA-AT-
1 AAATTTTGTTATATAAATTAAATATG
* **
19215676 AAATTTTGATATATATTTTAAATA-G
1 AAATTTTGTTATATAAATTAAATATG
*
19215701 ATATTTT
1 AAATTTT
19215708 TAATAAAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 7 0.17
22 4 0.10
23 8 0.19
24 6 0.14
25 10 0.24
26 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (26 bp):
AAATTTTGTTATATAAATTAAATATG
Found at i:19215679 original size:21 final size:24
Alignment explanation
Indices: 19215624--19215699 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
19215614 AATTGATAGA
19215624 TTAAA-AAATTTTGTTATATAAAT
1 TTAAATAAATTTTGTTATATAAAT
*
19215647 TAAATATGAAATTTT-TTA-A-AAAT
1 TTAA-AT-AAATTTTGTTATATAAAT
* *
19215670 TTAAATAAATTTTGATATAT-ATT
1 TTAAATAAATTTTGTTATATAAAT
19215693 TTAAATA
1 TTAAATA
19215700 GATATTTTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
21 7 0.16
22 4 0.09
23 20 0.47
24 2 0.05
25 3 0.07
26 7 0.16
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
TTAAATAAATTTTGTTATATAAAT
Found at i:19215710 original size:45 final size:46
Alignment explanation
Indices: 19215624--19215731 Score: 119
Period size: 47 Copynumber: 2.3 Consensus size: 46
19215614 AATTGATAGA
*
19215624 TTAAAAAATTTTGTTATATAAATTAAATATGAAATTTTTTAAAAAT
1 TTAAAAAATTTTGATATATAAATTAAATATGAAATTTTTTAAAAAT
** *
19215670 TTAAATAAATTTTGATATATATTTTAAATA-GATATTTTTAATAAAAAT
1 TTAAA-AAATTTTGATATATAAATTAAATATGAAATTTTT--TAAAAAT
*
19215718 ATTGATAAAATTTT
1 -TT-AAAAAATTTT
19215732 ATTATTAAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
46 13 0.25
47 21 0.40
48 7 0.13
49 9 0.17
50 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (46 bp):
TTAAAAAATTTTGATATATAAATTAAATATGAAATTTTTTAAAAAT
Found at i:19215880 original size:23 final size:21
Alignment explanation
Indices: 19215827--19215882 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 21
19215817 TTATCAATTT
19215827 AATTTTATT-AAAAATTTTAA
1 AATTTTATTAAAAAATTTTAA
19215847 AATTATT-TTAAAAAATTTTATA
1 AATT-TTATTAAAAAATTTTA-A
19215869 AATTTTACTTAAAA
1 AATTTTA-TTAAAA
19215883 GAAATTCATG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
20 6 0.19
21 14 0.45
22 5 0.16
23 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AATTTTATTAAAAAATTTTAA
Found at i:19219354 original size:23 final size:22
Alignment explanation
Indices: 19219321--19219371 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
19219311 TTCTTTAAGT
* *
19219321 AAAATTTATAAATTTTTTTAAA
1 AAAATTTATAAAATTTTTAAAA
*
19219343 ATAATTTAATAAAATTTTTAAAA
1 AAAATTT-ATAAAATTTTTAAAA
19219366 AAAATT
1 AAAATT
19219372 AAATCGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAATTTATAAAATTTTTAAAA
Found at i:19219373 original size:22 final size:23
Alignment explanation
Indices: 19219321--19219373 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
19219311 TTCTTTAAGT
* *
19219321 AAAATTTATAAATTTTTTTAAAA
1 AAAATTAATAAATATTTTTAAAA
* *
19219344 TAATTTAATAAA-ATTTTTAAAA
1 AAAATTAATAAATATTTTTAAAA
19219366 AAAATTAA
1 AAAATTAA
19219374 ATCGATAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAATTAATAAATATTTTTAAAA
Found at i:19222262 original size:14 final size:14
Alignment explanation
Indices: 19222245--19222285 Score: 50
Period size: 12 Copynumber: 2.9 Consensus size: 14
19222235 AAAAGTGATC
19222245 ATTAAAAATATTAT
1 ATTAAAAATATTAT
19222259 ATT-AAAAT-TTAT
1 ATTAAAAATATTAT
19222271 ATAATAAAAATATTA
1 AT--TAAAAATATTA
19222286 AATATTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.26
13 5 0.22
14 4 0.17
15 5 0.22
16 3 0.13
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTAAAAATATTAT
Found at i:19222692 original size:20 final size:21
Alignment explanation
Indices: 19222654--19222721 Score: 75
Period size: 20 Copynumber: 3.2 Consensus size: 21
19222644 TTTTTAAAAT
19222654 TTTTTTAGATATTTCAAAATTA
1 TTTTTTA-ATATTTCAAAATTA
* * *
19222676 TTTTTTAATA-TTGAAAACTC
1 TTTTTTAATATTTCAAAATTA
* *
19222696 TTTTTTTATATTTTAAAATTA
1 TTTTTTAATATTTCAAAATTA
19222717 TTTTT
1 TTTTT
19222722 AAAATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 16 0.42
21 15 0.39
22 7 0.18
ACGTcount: A:0.32, C:0.04, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTTTTAATATTTCAAAATTA
Found at i:19222723 original size:12 final size:12
Alignment explanation
Indices: 19222701--19222739 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
19222691 AACTCTTTTT
19222701 TTATATTTTAAAA
1 TTAT-TTTTAAAA
19222714 TTATTTTTAAAA
1 TTATTTTTAAAA
*
19222726 TT-TTTTTAACA
1 TTATTTTTAAAA
19222737 TTA
1 TTA
19222740 AAAATGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 10 0.42
12 10 0.42
13 4 0.17
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:19222728 original size:20 final size:19
Alignment explanation
Indices: 19222645--19222729 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 19
19222635 CTTAGTCAAT
*
19222645 TTTTAAAATTTTTTTAGATA
1 TTTTAAAATTTTTTTA-AAA
* *
19222665 TTTCAAAATTATTTTT-TAA
1 TTTTAAAATT-TTTTTAAAA
* * *
19222684 TATTGAAAACTCTTTTTTTATA
1 T-TTTAAAA-T-TTTTTTAAAA
19222706 TTTTAAAATTATTTTTAAAA
1 TTTTAAAATT-TTTTTAAAA
19222726 TTTT
1 TTTT
19222730 TTTAACATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
19 3 0.06
20 27 0.54
21 17 0.34
22 3 0.06
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (19 bp):
TTTTAAAATTTTTTTAAAA
Found at i:19223348 original size:17 final size:17
Alignment explanation
Indices: 19223322--19223358 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
19223312 TCATACTAAT
19223322 TATATATATATATATTA
1 TATATATATATATATTA
* *
19223339 TATATTTATATTTATTA
1 TATATATATATATATTA
19223356 TAT
1 TAT
19223359 TCATCAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATATATATATATATTA
Found at i:19223359 original size:9 final size:9
Alignment explanation
Indices: 19223322--19223358 Score: 51
Period size: 8 Copynumber: 4.3 Consensus size: 9
19223312 TCATACTAAT
19223322 TATATA-TA
1 TATATATTA
19223330 TATATATTA
1 TATATATTA
19223339 TATAT-TTA
1 TATATATTA
*
19223347 TATTTATTA
1 TATATATTA
19223356 TAT
1 TAT
19223359 TCATCAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
8 13 0.50
9 13 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TATATATTA
Found at i:19223359 original size:15 final size:15
Alignment explanation
Indices: 19223320--19223359 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
19223310 AATCATACTA
*
19223320 ATTATATATATATAT
1 ATTATATATTTATAT
19223335 ATTATATATTTATAT
1 ATTATATATTTATAT
19223350 -TTATTATATT
1 ATTA-TATATT
19223360 CATCAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTATATATTTATAT
Found at i:19223412 original size:2 final size:2
Alignment explanation
Indices: 19223405--19223430 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
19223395 AAATTTTAAT
19223405 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
19223431 CATTTCATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:19223772 original size:19 final size:19
Alignment explanation
Indices: 19223750--19223802 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
19223740 TTAACTTAAA
19223750 AATTATTTAATAAGTTTT-T
1 AATTATTTAATAA-TTTTAT
*
19223769 AATTATTTATTAATTTTAT
1 AATTATTTAATAATTTTAT
* *
19223788 AAATATTAAATAATT
1 AATTATTTAATAATT
19223803 AAAAATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 4 0.14
19 25 0.86
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
AATTATTTAATAATTTTAT
Found at i:19231614 original size:19 final size:20
Alignment explanation
Indices: 19231582--19231633 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
19231572 ATTCGAAATT
*
19231582 AATA-AAATATTATTTTTTTA
1 AATATAAATA-TATTATTTTA
19231602 AATATAAA-ATATTATTTTA
1 AATATAAATATATTATTTTA
19231621 AATATAAATATAT
1 AATATAAATATAT
19231634 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 17 0.59
20 9 0.31
21 3 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATATAAATATATTATTTTA
Found at i:19232492 original size:21 final size:22
Alignment explanation
Indices: 19232453--19232493 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
19232443 AACATGCACA
19232453 AAGTTTGCAACAGAAATAATTT
1 AAGTTTGCAACAGAAATAATTT
19232475 AAGTTTG-AAC-GAAAATAAT
1 AAGTTTGCAACAG-AAATAAT
19232494 GAAAAAGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 1 0.06
21 10 0.56
22 7 0.39
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (22 bp):
AAGTTTGCAACAGAAATAATTT
Found at i:19235646 original size:16 final size:17
Alignment explanation
Indices: 19235625--19235657 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19235615 TTTAGGCTTA
*
19235625 ATTATTT-TTTATTTAT
1 ATTATTTATTGATTTAT
19235641 ATTATTTATTGATTTAT
1 ATTATTTATTGATTTAT
19235658 TGATTTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTATTTATTGATTTAT
Found at i:19236043 original size:11 final size:11
Alignment explanation
Indices: 19236029--19236054 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19236019 TTGGTTTTTT
19236029 TTTTTGGGAAA
1 TTTTTGGGAAA
19236040 TTTTTGGGAAA
1 TTTTTGGGAAA
19236051 TTTT
1 TTTT
19236055 CAGATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (11 bp):
TTTTTGGGAAA
Found at i:19236129 original size:19 final size:20
Alignment explanation
Indices: 19236100--19236142 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
19236090 TTTCGGTGAC
19236100 TTTCTGGTGAA-ATTCAAAGT
1 TTTCTGGTGAAGATTC-AAGT
*
19236120 TTTC-GGTGAAGCTTCAAGT
1 TTTCTGGTGAAGATTCAAGT
19236139 TTTC
1 TTTC
19236143 AGCAACCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (20 bp):
TTTCTGGTGAAGATTCAAGT
Found at i:19236294 original size:15 final size:17
Alignment explanation
Indices: 19236257--19236298 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 17
19236247 CTTAAATCCT
19236257 AGAAAGAGGAAGAGATGAA
1 AGAAAG-GGAAGAGATG-A
19236276 AGAAAGGGAAGAGA-G-
1 AGAAAGGGAAGAGATGA
19236291 AGAAAGGG
1 AGAAAGGG
19236299 GAGGAGCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 8 0.35
17 1 0.04
18 8 0.35
19 6 0.26
ACGTcount: A:0.55, C:0.00, G:0.43, T:0.02
Consensus pattern (17 bp):
AGAAAGGGAAGAGATGA
Found at i:19236295 original size:19 final size:19
Alignment explanation
Indices: 19236257--19236296 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
19236247 CTTAAATCCT
*
19236257 AGAAAGAGGAAGAGATGAA
1 AGAAAGAGGAAGAGAAGAA
19236276 AGAAAG-GGAAGAGAGAGAA
1 AGAAAGAGGAAGAGA-AGAA
19236295 AG
1 AG
19236297 GGGAGGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (19 bp):
AGAAAGAGGAAGAGAAGAA
Found at i:19236776 original size:63 final size:60
Alignment explanation
Indices: 19236667--19237175 Score: 465
Period size: 63 Copynumber: 8.2 Consensus size: 60
19236657 TTTGTCAATG
* *
19236667 ATTTTTC-T-AAAATAAAATTTTCAAAAAAAAATATTTTT-GGAAAAAAGTTAAAAGTATC-
1 ATTTTTCTTAAAAATAAAATTTT-AAAAAAAAATATTTTTAAG-AAAAAGTTGAAAGTATCA
* * *
19236725 ACTTTTCTTTAAAAATAAAATTTTTTAGAAAAAAAGTATTTTTAAGGAAAAGTTGAAAGTATCA
1 ATTTTTC-TTAAAAATAAAA--TTTTA-AAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCA
* * * *
19236789 ATTTTTCTTGAAAATAAAAGTTTAAAAAATATATATATTTTTGAGAAAAAGTT-AGAAGTACCA
1 ATTTTTCTTAAAAATAAAATTTTAAAAAA-A-A-ATATTTTTAAGAAAAAGTTGA-AAGTATCA
* *
19236852 ATTTTTCTTAAAAATAAAAATTTTAAAAAATATATATTTTTTTAGAAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAAT-AAAATTTTAAAAAA-AAATA-TTTTTAAGAAAAAGTTGAAAGTATCA
* *
19236915 ATTTTTCTTAAAAATAAAATTTCTAAAATAAAAATTTTCAAAAAGTATTTTGAAG-AGAAGTTAA
1 ATTTTTCTTAAAAATAAAATTT-TAAAA-AAAAA---T-----A-T-TTTT-AAGAAAAAGTTGA
*
19236979 AAGTATTA
53 AAGTATCA
* * ** ** * *
19236987 ATTTTTCTTGAAGATAAAAAATT-CTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCA
1 ATTTTTCTTAAAAATAAAATTTTAAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCA
* * * * *
19237046 ATTTTCCTTAAAATTAAAATTTCAAAAAAAAATATTTTTGAGAAAAAGTTGAAAGTATTA
1 ATTTTTCTTAAAAATAAAATTTTAAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCA
* * *
19237106 ATTTTTCTTAAAAATAAAATTTGAAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCA
1 ATTTTTCTTAAAAATAAAATTTTAAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCA
19237166 ATTTTTCTTA
1 ATTTTTCTTA
19237176 TATAAAAGCA
Statistics
Matches: 371, Mismatches: 51, Indels: 56
0.78 0.11 0.12
Matches are distributed among these distances:
58 8 0.02
59 34 0.09
60 102 0.27
61 15 0.04
62 13 0.04
63 125 0.34
64 25 0.07
66 2 0.01
69 5 0.01
70 1 0.00
71 3 0.01
72 36 0.10
73 2 0.01
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.38
Consensus pattern (60 bp):
ATTTTTCTTAAAAATAAAATTTTAAAAAAAAATATTTTTAAGAAAAAGTTGAAAGTATCA
Found at i:19237017 original size:59 final size:58
Alignment explanation
Indices: 19236934--19237175 Score: 226
Period size: 60 Copynumber: 4.1 Consensus size: 58
19236924 AAAAATAAAA
* * * *
19236934 TTTC-TAAAAT-AAAAATTTTCAAAAAGTA-TTTTGAAGAGAAGTTAAAAGTATTAATT
1 TTTCTTAAAATAAAAAATTCT-AAAAAATATTTTTGAAGAAAAGTTGAAAGTATTAATT
* * *
19236990 TTTCTTGAAGATAAAAAATTCTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATT
1 TTTCTT-AAAATAAAAAATTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATTAATT
* * * *
19237049 TTCCTTAAAATTAAAATTTCAAAAAAAAATATTTTTG-AGAAAAAGTTGAAAGTATTAATT
1 TTTCTTAAAATAAAAAATTC--TAAAAAATATTTTTGAAG-AAAAGTTGAAAGTATTAATT
* * * *
19237109 TTTCTTAAAA-ATAAAATT-TGAAAAAAATATATTTTTAAGAAAAAATTGAAAGTATCAATT
1 TTTCTTAAAATAAAAAATTCT--AAAAAATAT-TTTTGAAG-AAAAGTTGAAAGTATTAATT
19237169 TTTCTTA
1 TTTCTTA
19237176 TATAAAAGCA
Statistics
Matches: 153, Mismatches: 22, Indels: 18
0.79 0.11 0.09
Matches are distributed among these distances:
56 4 0.03
57 1 0.01
58 31 0.20
59 47 0.31
60 70 0.46
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (58 bp):
TTTCTTAAAATAAAAAATTCTAAAAAATATTTTTGAAGAAAAGTTGAAAGTATTAATT
Found at i:19237101 original size:60 final size:60
Alignment explanation
Indices: 19236972--19237175 Score: 259
Period size: 60 Copynumber: 3.4 Consensus size: 60
19236962 TTTTGAAGAG
* * * * * * *
19236972 AAGTTAAAAGTATTAATTTTTCTTGAAGATAAAAAATTC--TAAAAAATATTTTTGAGGAA
1 AAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAATTTCAAAAAAAAATATTTTTGAGAAA
* *
19237031 AAGTTGAAAGTATCAATTTTCCTTAAAATTAAAATTTCAAAAAAAAATATTTTTGAGAAA
1 AAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAATATTTTTGAGAAA
* * * *
19237091 AAGTTGAAAGTATTAATTTTTCTTAAAAATAAAATTTGAAAAAAATATATTTTTAAGAAA
1 AAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAATATTTTTGAGAAA
*
19237151 AAATTGAAAGTATCAATTTTTCTTA
1 AAGTTGAAAGTATCAATTTTTCTTA
19237176 TATAAAAGCA
Statistics
Matches: 126, Mismatches: 17, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
58 7 0.06
59 24 0.19
60 95 0.75
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (60 bp):
AAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAAAATATTTTTGAGAAA
Found at i:19243378 original size:60 final size:60
Alignment explanation
Indices: 19243302--19243518 Score: 234
Period size: 58 Copynumber: 3.7 Consensus size: 60
19243292 CTTTTATATA
* * *
19243302 AAGAAAAATTAATACTTTCAACTTTTTCTTAAAAATATATTTTTT-TCAAATTTTATTTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTTCTCAAATTTTAATTTT
* * *
19243362 AAGAAAAATTGGTACTTTCAACTTTATCTCAAAAATATTTTTTTCTGAAATTTTAATTTT
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTCTCAAATTTTAATTTT
* * *
19243422 -A-AAAAATTGATACTTTCAACTTTTCCTCAAAAATA--TTTTT-T-AAATTTTTATCTTC
1 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTCTCAAATTTTAAT-TTT
* * * *
19243477 AAGGAAAAATTAATACTTTTAACTTGTCCTC-AAAATATTTTT
1 AA-GAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT
19243519 GAAAATTTTT
Statistics
Matches: 136, Mismatches: 14, Indels: 15
0.82 0.08 0.09
Matches are distributed among these distances:
54 9 0.07
55 3 0.02
56 6 0.04
57 6 0.04
58 55 0.40
59 10 0.07
60 47 0.35
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (60 bp):
AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTCTCAAATTTTAATTTT
Found at i:19243608 original size:62 final size:60
Alignment explanation
Indices: 19243530--19243803 Score: 288
Period size: 62 Copynumber: 4.5 Consensus size: 60
19243520 AAAATTTTTA
19243530 TTTTAGAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAGATATATAT
1 TTTTA-AAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAA-ATATATAT
* *
19243592 TTTTAAAATTTTTATTTTTAAGAAAAATTGGTAC-TTCTAACTTTTTCTCAAAAATATATATAT
1 TTTTAAAA-TTTTATTTTCAAGAAAAATTGATACTTTC-AACTTTTTCT-AAAAA-ATATATAT
* * * *
19243655 TTTTAAACTTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATACT-TTT
1 TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAATA-TATAT
* * * ** * *
19243715 TTTCTAAAAAATTTTATTTTTAA-AGAAAAGTGATACTTTTAACTTTTTCCCAAAAATATTTTT
1 TTT-T--AAAATTTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTTCTAAAAAATATATAT
19243778 TTTTGAAAATTTTATTTT--AGAAAAAT
1 TTTT-AAAATTTTATTTTCAAGAAAAAT
19243804 CATTGACAAA
Statistics
Matches: 183, Mismatches: 18, Indels: 25
0.81 0.08 0.11
Matches are distributed among these distances:
59 5 0.03
60 9 0.05
61 25 0.14
62 73 0.40
63 71 0.39
ACGTcount: A:0.38, C:0.09, G:0.05, T:0.48
Consensus pattern (60 bp):
TTTTAAAATTTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTCTAAAAAATATATAT
Found at i:19243886 original size:3 final size:3
Alignment explanation
Indices: 19243878--19243911 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
19243868 AATAAGTAGA
19243878 AAT AAT AAT AAT AAT AAT AAT AAAT AAAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AA
19243912 ATAAATAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 23 0.77
4 7 0.23
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:19243905 original size:4 final size:4
Alignment explanation
Indices: 19243896--19243932 Score: 67
Period size: 4 Copynumber: 9.5 Consensus size: 4
19243886 TAATAATAAT
19243896 AATA AATA AAT- AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AA
19243933 AACCCTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:19244450 original size:11 final size:11
Alignment explanation
Indices: 19244434--19244459 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19244424 TCGAAATATG
19244434 AAAATTTCCCA
1 AAAATTTCCCA
19244445 AAAATTTCCCA
1 AAAATTTCCCA
19244456 AAAA
1 AAAA
19244460 AAAATATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATTTCCCA
Found at i:19244548 original size:11 final size:11
Alignment explanation
Indices: 19244529--19244562 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
19244519 TAAAAACTAT
*
19244529 TTTTGCTTCTA
1 TTTTCCTTCTA
19244540 TTTTCCTTCTA
1 TTTTCCTTCTA
*
19244551 TTTTCTTTCTA
1 TTTTCCTTCTA
19244562 T
1 T
19244563 GTGTTTTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.09, C:0.21, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTTCCTTCTA
Found at i:19245752 original size:16 final size:17
Alignment explanation
Indices: 19245731--19245762 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19245721 CGAGTAGCAA
19245731 TTCTCTGAAAT-TTTAT
1 TTCTCTGAAATCTTTAT
19245747 TTCTCTGAAATCTTTA
1 TTCTCTGAAATCTTTA
19245763 AGTAAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (17 bp):
TTCTCTGAAATCTTTAT
Found at i:19247984 original size:21 final size:22
Alignment explanation
Indices: 19247958--19247999 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
19247948 CCCTCTTTTT
19247958 CATTATTT-TCGTT-CAAACTTA
1 CATTATTTCT-GTTGCAAACTTA
19247979 CATTATTTCTGTTGCAAACTT
1 CATTATTTCTGTTGCAAACTT
19248000 TGTGCATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (22 bp):
CATTATTTCTGTTGCAAACTTA
Done.