Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167937.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_2, 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: 35885061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 165000 characters in sequence are not A, C, G, or T
File 175 of 195
Found at i:29396899 original size:2 final size:2
Alignment explanation
Indices: 29396894--29396919 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29396884 TTTTTTTTTT
29396894 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
29396920 AGAGAGAGAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29396924 original size:2 final size:2
Alignment explanation
Indices: 29396919--29396947 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29396909 GTGTGTGTGT
29396919 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
29396948 CACAAAAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:29397289 original size:43 final size:43
Alignment explanation
Indices: 29397236--29397323 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
29397226 CATATTTACA
* *
29397236 TTCTACTAACCTAATAGATCTTGAATACGAATGCTTTTTATAC
1 TTCTACTAACCTAATAGATATTGAATACAAATGCTTTTTATAC
* * *
29397279 TTCTAGTAACCTAATGGATATTTAATACAAATGCTTTTTATAC
1 TTCTACTAACCTAATAGATATTGAATACAAATGCTTTTTATAC
29397322 TT
1 TT
29397324 AGCTTTATCT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.16, G:0.09, T:0.42
Consensus pattern (43 bp):
TTCTACTAACCTAATAGATATTGAATACAAATGCTTTTTATAC
Found at i:29403030 original size:11 final size:11
Alignment explanation
Indices: 29403014--29403038 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
29403004 TAGAAATAAG
29403014 TTTTTAAATTA
1 TTTTTAAATTA
29403025 TTTTTAAATTA
1 TTTTTAAATTA
29403036 TTT
1 TTT
29403039 ACTTTAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTAAATTA
Found at i:29403868 original size:22 final size:23
Alignment explanation
Indices: 29403832--29403880 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
29403822 ATTTAAATAG
*
29403832 AATTTTTTAAATAAAAATTATGA
1 AATTTTTTAAATAAAAATAATGA
* *
29403855 AATTTTTT-ATTAAAAATAATTA
1 AATTTTTTAAATAAAAATAATGA
29403877 AATT
1 AATT
29403881 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AATTTTTTAAATAAAAATAATGA
Found at i:29403913 original size:23 final size:20
Alignment explanation
Indices: 29403875--29403915 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
29403865 TAAAAATAAT
29403875 TAAATTAAAATTAAAATTGA
1 TAAATTAAAATTAAAATTGA
29403895 TAAATTGATAAATTGAAAATT
1 TAAATT-A-AAATT-AAAATT
29403916 TTTGTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 5 0.28
23 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
TAAATTAAAATTAAAATTGA
Found at i:29408255 original size:20 final size:20
Alignment explanation
Indices: 29408230--29408267 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29408220 ATATCTACAT
*
29408230 CACTATCGGCCTGCCTTGAC
1 CACTATCAGCCTGCCTTGAC
*
29408250 CACTATCAGCCTGTCTTG
1 CACTATCAGCCTGCCTTG
29408268 CTCATAAAAT
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:0.16, C:0.37, G:0.18, T:0.29
Consensus pattern (20 bp):
CACTATCAGCCTGCCTTGAC
Found at i:29411765 original size:5 final size:6
Alignment explanation
Indices: 29411751--29411783 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29411741 AAAACTCGAC
*
29411751 AAAATA AAAATA AAAATA AAAACA AAAA-A AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
29411784 GAGCATCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.09
Consensus pattern (6 bp):
AAAATA
Found at i:29415520 original size:20 final size:22
Alignment explanation
Indices: 29415490--29415532 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
29415480 ACCCCCTTTT
*
29415490 TTTTGTTATTTATA-TTTTTCA
1 TTTTGTTATTTAAAGTTTTTCA
29415511 TTTT-TTATTTAAAGTTTTTCA
1 TTTTGTTATTTAAAGTTTTTCA
29415532 T
1 T
29415533 ATTACGTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.70
Consensus pattern (22 bp):
TTTTGTTATTTAAAGTTTTTCA
Found at i:29415755 original size:15 final size:16
Alignment explanation
Indices: 29415735--29415798 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 16
29415725 ATATATTTTA
29415735 TTATTAATTTTA-ATC
1 TTATTAATTTTACATC
29415750 TTATT-A--TTACAT-
1 TTATTAATTTTACATC
*
29415762 TAATTAATTTTACATCC
1 TTATTAATTTTACAT-C
*
29415779 ATTATTATTTTTA-ATC
1 -TTATTAATTTTACATC
29415795 TTAT
1 TTAT
29415799 CACTCGTCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
12 7 0.18
13 3 0.08
14 1 0.03
15 15 0.38
16 1 0.03
17 2 0.05
18 10 0.26
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATTAATTTTACATC
Found at i:29421831 original size:24 final size:25
Alignment explanation
Indices: 29421795--29421864 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 25
29421785 CTGATAAAAA
**
29421795 TAAAATTGGATATAATAATGA-G-AT
1 TAAAATTAAATATAATAAT-ATGTAT
* *
29421819 TAAAATTAAATATAAAAATATGTTT
1 TAAAATTAAATATAATAATATGTAT
29421844 TAAAATGTAAATATAATAATA
1 TAAAAT-TAAATATAATAATA
29421865 GTGATGAGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 1 0.03
24 17 0.45
25 7 0.18
26 13 0.34
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
TAAAATTAAATATAATAATATGTAT
Found at i:29422324 original size:21 final size:21
Alignment explanation
Indices: 29422277--29422329 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
29422267 GTGATGGATT
* * *
29422277 ATTACATAATTTTTAATTGTA
1 ATTAAATAATTTTAAATTATA
29422298 ATTAAATAATTTTCAAATTATA
1 ATTAAATAATTTT-AAATTATA
*
29422320 A-TAAAAAATT
1 ATTAAATAATT
29422330 ACAGATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTAAATAATTTTAAATTATA
Found at i:29431728 original size:36 final size:36
Alignment explanation
Indices: 29431688--29431766 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 36
29431678 AATAAAAAAA
* * *
29431688 ATTTAAGCACTATGTTTTACATATCAGAAATGGAGT
1 ATTTAAGCACTATATTTTACATATCAGAAACGGACT
* * *
29431724 ATTTAAGCACTGTATTTTTCATATTAGAAACGGACT
1 ATTTAAGCACTATATTTTACATATCAGAAACGGACT
29431760 ATTTAAG
1 ATTTAAG
29431767 TGATATTTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (36 bp):
ATTTAAGCACTATATTTTACATATCAGAAACGGACT
Found at i:29434753 original size:20 final size:20
Alignment explanation
Indices: 29434713--29434754 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
29434703 AATGTAAATG
**
29434713 ATGTTAATATGCATTCGAGA
1 ATGTTAATATGCATAAGAGA
*
29434733 ATGTTAATATGCATAATAGA
1 ATGTTAATATGCATAAGAGA
29434753 AT
1 AT
29434755 TCCAAATGCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (20 bp):
ATGTTAATATGCATAAGAGA
Found at i:29435504 original size:322 final size:328
Alignment explanation
Indices: 29434772--29435504 Score: 801
Period size: 322 Copynumber: 2.2 Consensus size: 328
29434762 GCAGAAATAG
* * * *
29434772 AGTGTGAAAAGATTAAGAATAAAAATGCATTCTCTCAAAATGATGAA-GTACCTGAAATCATCAG
1 AGTGTGAAAAGATCAAGAATAAAAATGCATTCTCTCAAAATGATGAACATA-CAGAAATCATAAG
* * *
29434836 ATCTTGTGAATTATAGATCTTAAACCTTGCTTCTTTATCATCTTTAAGGGTATTACAACATATTA
65 ATCTTATGAATTATAGATCTTAAACCATGCTTCTTTATCATCTTTAAAGGTATTACAACATATTA
* * *
29434901 AACATTAGATATCATTAGTTTCAATTTAGAATTCTAGATTATTTTTTAATTAATATTTATATTTG
130 AAAATTAGATATCATTAGTTTCAATTTAGAATTCTAAATTATTTTTGAATTAATATTTATATTTG
* ** ** * ** * *
29434966 ATATTTAATTTTGGGAATGAATTTTTCACAAGTTCTACTAAGTGATGTAAAAGATGTATTAGTTG
195 ATATTTAATTTTGGAAACAAAAATTTCACAAGTGCTACTAAGTGACCTAAAAGATGTATAAGTTC
* *
29435031 AATATGCATTCGAGAATGTTAATGAAACTTTTAAAGTGTATCTTATGCTTCATAAAATTCTAAAC
260 AATATGCATTC---AATG-TAA-GAAAC-TTTAAAGTATATCTTATGCTTCATAAAACTCTAAAC
*
29435096 GCAAAAACAG
319 GCAAAAACAA
* * *
29435106 AGTGTGAAAAGATCAAGAATAAAGATGCATTTTCTTAAAATGATGAAGCAT-CAGAAATCATAAG
1 AGTGTGAAAAGATCAAGAATAAAAATGCATTCTCTCAAAATGATGAA-CATACAGAAATCATAAG
*
29435170 ATCTTATGAATTATAGATCTTAAA-CATGCTTCTTTATCAT-TTCTAAAGGTATTACAGCATATT
65 ATCTTATGAATTATAGATCTTAAACCATGCTTCTTTATCATCTT-TAAAGGTATTACAACATATT
* * ** *
29435233 AAAAATTGGATATCATTAGTTTCAA-TTCGTAATTCTAAATT-TTTTTGGTTTAATATTTATGTT
129 AAAAATTAGATATCATTAGTTTCAATTTAG-AATTCTAAATTATTTTTGAATTAATATTTATATT
* * * *
29435296 TGATATTTAATTTTTGAAACAAAAATTTCACAGGTGCTACTGAA-TGACCTAGATGATAGTATAA
193 TGATATTTAATTTTGGAAACAAAAATTTCACAAGTGCTACT-AAGTGACCTAAAAGAT-GTATAA
* * * * * * *
29435360 G-TCAATATGTATTC-ATG-AA-AAGC-TTAATGTATATTTTATGCTTGATGAAACTCTAAATGC
256 GTTCAATATGCATTCAATGTAAGAAACTTTAAAGTATATCTTATGCTTCATAAAACTCTAAACGC
*
29435420 AAAAGCAA
321 AAAAACAA
* * *
29435428 A-TGGTGAAAAGATGAAGAATAAAAATGCATTCTATCAAAATGAT-AACATAACAGAAGTCATAA
1 AGT-GTGAAAAGATCAAGAATAAAAATGCATTCTCTCAAAATGATGAACAT-ACAGAAATCATAA
* *
29435491 GATGTTTTGAATTA
64 GATCTTATGAATTA
29435505 AATATATGTT
Statistics
Matches: 338, Mismatches: 52, Indels: 30
0.80 0.12 0.07
Matches are distributed among these distances:
320 3 0.01
321 3 0.01
322 96 0.28
324 3 0.01
326 2 0.01
328 3 0.01
332 76 0.22
333 74 0.22
334 77 0.23
336 1 0.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (328 bp):
AGTGTGAAAAGATCAAGAATAAAAATGCATTCTCTCAAAATGATGAACATACAGAAATCATAAGA
TCTTATGAATTATAGATCTTAAACCATGCTTCTTTATCATCTTTAAAGGTATTACAACATATTAA
AAATTAGATATCATTAGTTTCAATTTAGAATTCTAAATTATTTTTGAATTAATATTTATATTTGA
TATTTAATTTTGGAAACAAAAATTTCACAAGTGCTACTAAGTGACCTAAAAGATGTATAAGTTCA
ATATGCATTCAATGTAAGAAACTTTAAAGTATATCTTATGCTTCATAAAACTCTAAACGCAAAAA
CAA
Found at i:29439747 original size:18 final size:18
Alignment explanation
Indices: 29439723--29439761 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
29439713 GTAAAAAATA
29439723 ATATATATAACTATAAATTT
1 ATATATAT-A-TATAAATTT
29439743 ATATATATATATAAATTT
1 ATATATATATATAAATTT
29439761 A
1 A
29439762 ATAATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
ATATATATATATAAATTT
Found at i:29456089 original size:3 final size:3
Alignment explanation
Indices: 29456083--29456108 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
29456073 AAAGAAAAAA
29456083 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
29456109 ATTATACGTA
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:29456294 original size:24 final size:25
Alignment explanation
Indices: 29456264--29456310 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
29456254 AATATTATTA
*
29456264 CATTTAAAAAAT-TGATTAAAAATG
1 CATTTAAAAAATACGATTAAAAATG
*
29456288 CATTTAAAATATACGATTAAAAA
1 CATTTAAAAAATACGATTAAAAA
29456311 CTTTAAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.32
Consensus pattern (25 bp):
CATTTAAAAAATACGATTAAAAATG
Found at i:29466363 original size:6 final size:6
Alignment explanation
Indices: 29466349--29466383 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
29466339 TCTTTCATCG
* *
29466349 AGGACT AGGAAT AGGACT AGGACC AGGACT AGGAC
1 AGGACT AGGACT AGGACT AGGACT AGGACT AGGAC
29466384 CACACCCTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.37, C:0.17, G:0.34, T:0.11
Consensus pattern (6 bp):
AGGACT
Found at i:29469753 original size:8 final size:8
Alignment explanation
Indices: 29469722--29469772 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
29469712 TAAAAGTTTT
29469722 ATTAAAAA
1 ATTAAAAA
* *
29469730 ATTAATAT
1 ATTAAAAA
* *
29469738 TTTGAAAA
1 ATTAAAAA
29469746 ATTAAAAAA
1 ATT-AAAAA
29469755 ATT-AAAA
1 ATTAAAAA
29469762 ATTAAAAA
1 ATTAAAAA
29469770 ATT
1 ATT
29469773 CATATTAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
7 7 0.21
8 19 0.58
9 7 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
ATTAAAAA
Found at i:29481407 original size:22 final size:22
Alignment explanation
Indices: 29481382--29481423 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29481372 TATAAAATAA
29481382 CATTTA-AAATTTCGACAAAACC
1 CATTTATAAATTT-GACAAAACC
*
29481404 CATTTATGAATTTGACAAAA
1 CATTTATAAATTTGACAAAA
29481424 AAAAAGTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.45, C:0.17, G:0.07, T:0.31
Consensus pattern (22 bp):
CATTTATAAATTTGACAAAACC
Found at i:29493350 original size:15 final size:15
Alignment explanation
Indices: 29493330--29493362 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
29493320 GCATCTTAAA
29493330 ATTAT-AATTATTTAT
1 ATTATAAATT-TTTAT
29493345 ATTATAAATTTTTAT
1 ATTATAAATTTTTAT
29493360 ATT
1 ATT
29493363 TTCAAACTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
ATTATAAATTTTTAT
Found at i:29497315 original size:4 final size:4
Alignment explanation
Indices: 29497301--29497433 Score: 65
Period size: 4 Copynumber: 33.2 Consensus size: 4
29497291 TTCTTGGTGT
* * * *
29497301 TTTA TTTTA TTTA TTTA TTTA TGTA TTT- TATT- TTTG TTTG GTTA TTTA
1 TTTA -TTTA TTTA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA TTTA TTTA
* ** *** * * *
29497349 TTTA TTTG TTTA TTTA TTT- CCTA TTTA TGCG TTCA TTTG TTTG TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* * * *
29497396 GTTA TTTA TTTGA TTGA TTGA TTGA TTTA TTTA TTTA T
1 TTTA TTTA TTT-A TTTA TTTA TTTA TTTA TTTA TTTA T
29497434 AAATATTTTT
Statistics
Matches: 101, Mismatches: 23, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
3 4 0.04
4 90 0.89
5 7 0.07
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.68
Consensus pattern (4 bp):
TTTA
Found at i:29499444 original size:10 final size:9
Alignment explanation
Indices: 29499406--29499476 Score: 53
Period size: 9 Copynumber: 8.2 Consensus size: 9
29499396 CTAATATAAC
29499406 TATTAAAA-
1 TATTAAAAT
29499414 TATTAAAAAT
1 TATT-AAAAT
*
29499424 TATT--TAT
1 TATTAAAAT
29499431 TATTAAAAT
1 TATTAAAAT
29499440 ATATTAAAAT
1 -TATTAAAAT
*
29499450 TATT--TAT
1 TATTAAAAT
*
29499457 TATTAAAAC
1 TATTAAAAT
*
29499466 TATTAATAT
1 TATTAAAAT
29499475 TA
1 TA
29499477 AAAAATAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
7 12 0.24
8 4 0.08
9 20 0.41
10 13 0.27
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (9 bp):
TATTAAAAT
Found at i:29499455 original size:26 final size:25
Alignment explanation
Indices: 29499406--29499471 Score: 105
Period size: 26 Copynumber: 2.6 Consensus size: 25
29499396 CTAATATAAC
29499406 TATTAAAATATTAAAAATTATTTAT
1 TATTAAAATATTAAAAATTATTTAT
*
29499431 TATTAAAATATATTAAAATTATTTAT
1 TATTAAAATAT-TAAAAATTATTTAT
29499457 TATTAAAACTATTAA
1 TATTAAAA-TATTAA
29499472 TATTAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 11 0.30
26 23 0.62
27 3 0.08
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTAAAATATTAAAAATTATTTAT
Found at i:29499460 original size:16 final size:15
Alignment explanation
Indices: 29499414--29499479 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
29499404 ACTATTAAAA
29499414 TATTAAAAATTATTTAT
1 TATT-AAAATTA-TTAT
29499431 TATT-AAA--A-TA-
1 TATTAAAATTATTAT
29499441 TATTAAAATTATTTAT
1 TATTAAAATTA-TTAT
* *
29499457 TATTAAAACTATTAA
1 TATTAAAATTATTAT
29499472 TATTAAAA
1 TATTAAAA
29499480 AATAATTATA
Statistics
Matches: 41, Mismatches: 2, Indels: 14
0.72 0.04 0.25
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
13 2 0.05
15 16 0.39
16 10 0.24
17 4 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAAATTATTAT
Found at i:29499477 original size:15 final size:16
Alignment explanation
Indices: 29499440--29499479 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
29499430 TTATTAAAAT
*
29499440 ATATTAAAATTATTTA
1 ATATTAAAACTATTTA
*
29499456 TTATTAAAACTA-TTA
1 ATATTAAAACTATTTA
29499471 ATATTAAAA
1 ATATTAAAA
29499480 AATAATTATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
ATATTAAAACTATTTA
Found at i:29499524 original size:19 final size:19
Alignment explanation
Indices: 29499497--29499536 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
29499487 ATATTTTAAT
29499497 AATAATATGAAAATATAAA
1 AATAATATGAAAATATAAA
* **
29499516 AATATTATGTTAATATAAA
1 AATAATATGAAAATATAAA
29499535 AA
1 AA
29499537 ATACTTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
AATAATATGAAAATATAAA
Found at i:29499575 original size:3 final size:3
Alignment explanation
Indices: 29499556--29499785 Score: 53
Period size: 3 Copynumber: 78.7 Consensus size: 3
29499546 ACAAAACTAT
* * *
29499556 TTA TTA TTC TT- TATA TTA TTTA TTA ATA -TA TTA ATA -TA TTA TTTA
1 TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * * *
29499601 TTA ATA ATA TTTA TTA TTA -TA ATA TT- TAA TTA -TA ATA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * *
29499644 TTTA TTA ATA -TA ATG TTA TTTA TTA ATA -TA TTA -TA TTA TTA TTTC
1 -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * * *
29499689 TTA ATA TTA TTTA TTA ATA -TA TTA -TA TTA ATA GTA -TA TTA TTTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* * *
29499733 TTA TTA ATA -TA TTA TT- TATA TT- TTA -TA ATA TTA TTTA TTA ATA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA -TTA TTA TTA
*
29499776 -TA ATA TTA TT
1 TTA TTA TTA TT
29499786 TATAAATAAA
Statistics
Matches: 174, Mismatches: 25, Indels: 56
0.68 0.10 0.22
Matches are distributed among these distances:
2 31 0.18
3 116 0.67
4 27 0.16
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:29499610 original size:18 final size:18
Alignment explanation
Indices: 29499587--29499794 Score: 153
Period size: 18 Copynumber: 12.2 Consensus size: 18
29499577 ATTAATATAT
29499587 TAATATATTATTTATTAA
1 TAATATATTATTTATTAA
29499605 TAATAT-TTA-TTATT-A
1 TAATATATTATTTATTAA
*
29499620 TAATAT-TTAATTA-TAA
1 TAATATATTATTTATTAA
29499636 T-AT-TATTATTTATTAA
1 TAATATATTATTTATTAA
*
29499652 T-ATAATGTTATTTATTAA
1 TAAT-ATATTATTTATTAA
**
29499670 TATATTATATTA-TTATTTC
1 TA-A-TATATTATTTATTAA
*
29499689 TTA-ATATTATTTA-T--
1 TAATATATTATTTATTAA
29499703 TAATATATTA--TATTAA
1 TAATATATTATTTATTAA
* *
29499719 TAGTATATTATTTATTAT
1 TAATATATTATTTATTAA
*
29499737 TAATATATTATTTA-TATT
1 TAATATATTATTTATTA-A
*
29499755 TTATAATATTATTTATTAA
1 TAAT-ATATTATTTATTAA
*
29499774 T-ATAATATTATTTATAAA
1 TAAT-ATATTATTTATTAA
29499792 TAA
1 TAA
29499795 AATTATGTTT
Statistics
Matches: 157, Mismatches: 13, Indels: 39
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.01
14 4 0.03
15 25 0.16
16 32 0.20
17 8 0.05
18 59 0.38
19 18 0.11
20 8 0.05
21 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (18 bp):
TAATATATTATTTATTAA
Found at i:29499656 original size:34 final size:33
Alignment explanation
Indices: 29499567--29499782 Score: 206
Period size: 34 Copynumber: 6.3 Consensus size: 33
29499557 TATTATTCTT
29499567 TATATTATTTATTAATATATTAATATATTATTTATTAA
1 TATATTATTTATT-AT-TA-T-A-ATATTATTTATTAA
*
29499605 TA-A-TATTTATTATTATAATATTTAATTA-TAA
1 TATATTATTTATTATTATAATA-TTATTTATTAA
* *
29499636 TATTATTATTTATTAATATAATGTTATTTATTAA
1 TA-TATTATTTATTATTATAATATTATTTATTAA
*
29499670 TATATTATATTATTATTTCTTAATATTATTTATTAA
1 TATATTAT-TTATTA-TT-ATAATATTATTTATTAA
* * *
29499706 TATATTATATTAATAGTATATTATT-TATTATTAA
1 TATATTAT-TTATTATTATAATATTAT-TTATTAA
*
29499740 TATATTATTTATATTTTATAATATTATTTATTAA
1 TATATTATTTAT-TATTATAATATTATTTATTAA
*
29499774 TATAATATT
1 TATATTATT
29499783 ATTTATAAAT
Statistics
Matches: 151, Mismatches: 16, Indels: 26
0.78 0.08 0.13
Matches are distributed among these distances:
31 8 0.05
32 7 0.05
33 18 0.12
34 73 0.48
35 5 0.03
36 37 0.25
37 1 0.01
38 2 0.01
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (33 bp):
TATATTATTTATTATTATAATATTATTTATTAA
Found at i:29499670 original size:88 final size:88
Alignment explanation
Indices: 29499571--29499775 Score: 252
Period size: 88 Copynumber: 2.4 Consensus size: 88
29499561 ATTCTTTATA
*
29499571 TTATTTATTAATATATTA-ATATATTATTTATTAATAATATTTATTATTATAATAT-TTAATTA-
1 TTATTTATTAATATATTATAT-TATTATTTATTAATAATATTTATTAATATAATATATTAA-TAG
29499633 TAATATTA-TTATTTATTAATATAATG
64 T-ATATTATTTA-TTATTAATATAATG
* * *
29499659 TTATTTATTAATATATTATATTATTATTTCTTAATATTATTTATTAATATATTATATTAATAGTA
1 TTATTTATTAATATATTATATTATTATTTATTAATAATATTTATTAATATAATATATTAATAGTA
29499724 TATTATTTATTATTAATAT-A--
66 TATTATTTATTATTAATATAATG
*
29499744 TTATTTA-T-AT-T-TTATAATATTATTTATTAATA
1 TTATTTATTAATATATTATATTATTATTTATTAATA
29499776 TAATATTATT
Statistics
Matches: 107, Mismatches: 6, Indels: 15
0.84 0.05 0.12
Matches are distributed among these distances:
81 19 0.18
82 1 0.01
83 2 0.02
84 1 0.01
85 7 0.07
87 1 0.01
88 66 0.62
89 10 0.09
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (88 bp):
TTATTTATTAATATATTATATTATTATTTATTAATAATATTTATTAATATAATATATTAATAGTA
TATTATTTATTATTAATATAATG
Found at i:29499776 original size:13 final size:13
Alignment explanation
Indices: 29499568--29499776 Score: 136
Period size: 13 Copynumber: 17.3 Consensus size: 13
29499558 ATTATTCTTT
29499568 ATATTATTTATTA
1 ATATTATTTATTA
*
29499581 ATA-TA-TTAAT-
1 ATATTATTTATTA
29499591 ATATTATTTATTA
1 ATATTATTTATTA
*
29499604 ATAATATTTATTA
1 ATATTATTTATTA
*
29499617 TTATAATATTTAATT-
1 --ATATTATTT-ATTA
*
29499632 ATAATA-TTATT-
1 ATATTATTTATTA
*
29499643 AT-TTATTAATATA
1 ATATTATTTAT-TA
*
29499656 ATGTTATTTATTA
1 ATATTATTTATTA
29499669 ATA-TA-TTA-TA
1 ATATTATTTATTA
* *
29499679 TTATTATTTCTTA
1 ATATTATTTATTA
29499692 ATATTATTTATTA
1 ATATTATTTATTA
29499705 ATA-TATTATATTA
1 ATATTATT-TATTA
*
29499718 ATAGTA--TATT-
1 ATATTATTTATTA
29499728 AT-TTA-TTATTA
1 ATATTATTTATTA
*
29499739 ATA-TA-TTATTT
1 ATATTATTTATTA
29499750 ATA-T-TTTA-TA
1 ATATTATTTATTA
29499760 ATATTATTTATTA
1 ATATTATTTATTA
29499773 ATAT
1 ATAT
29499777 AATATTATTT
Statistics
Matches: 160, Mismatches: 14, Indels: 44
0.73 0.06 0.20
Matches are distributed among these distances:
9 2 0.01
10 19 0.12
11 40 0.25
12 21 0.13
13 57 0.36
14 9 0.06
15 9 0.06
16 3 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (13 bp):
ATATTATTTATTA
Found at i:29499929 original size:19 final size:19
Alignment explanation
Indices: 29499905--29499965 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
29499895 TAATTTCATT
*
29499905 TTTATTAATCAATAAATTA
1 TTTATTTATCAATAAATTA
* *
29499924 TTTATTTATTAATCAATTAA
1 TTTATTTATCAATAAATT-A
29499944 TTT-TTTATCAAATAAA-TA
1 TTTATTTATC-AATAAATTA
29499962 TTTA
1 TTTA
29499966 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.12
19 21 0.62
20 9 0.26
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTATTTATCAATAAATTA
Found at i:29499931 original size:23 final size:23
Alignment explanation
Indices: 29499905--29499951 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
29499895 TAATTTCATT
29499905 TTTATTAATCAATAAATTATTTA
1 TTTATTAATCAATAAATTATTTA
* *
29499928 TTTATTAATCAATTAATTTTTTA
1 TTTATTAATCAATAAATTATTTA
29499951 T
1 T
29499952 CAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTATTAATCAATAAATTATTTA
Found at i:29515359 original size:13 final size:14
Alignment explanation
Indices: 29515326--29515365 Score: 55
Period size: 13 Copynumber: 2.8 Consensus size: 14
29515316 TTAAAGAAAT
29515326 AATATTAAACATATGA
1 AATA-TAAA-ATATGA
29515342 AATATAAAATAT-A
1 AATATAAAATATGA
29515355 AATATAAAATA
1 AATATAAAATA
29515366 AAAACTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
13 12 0.50
14 4 0.17
15 4 0.17
16 4 0.17
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (14 bp):
AATATAAAATATGA
Found at i:29526423 original size:11 final size:11
Alignment explanation
Indices: 29526407--29526452 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
29526397 TTAATCATTT
29526407 ATATATTTAAA
1 ATATATTTAAA
*
29526418 ATATATGTAAA
1 ATATATTTAAA
*
29526429 ATATA--TATA
1 ATATATTTAAA
*
29526438 ATATAATTAAA
1 ATATATTTAAA
29526449 ATAT
1 ATAT
29526453 TAAATAATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
9 8 0.27
11 22 0.73
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (11 bp):
ATATATTTAAA
Found at i:29526432 original size:20 final size:20
Alignment explanation
Indices: 29526409--29526453 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
29526399 AATCATTTAT
29526409 ATATTTAAAATAT-ATGTAAA
1 ATATTTAAAATATAAT-TAAA
* *
29526429 ATATATATAATATAATTAAA
1 ATATTTAAAATATAATTAAA
29526449 ATATT
1 ATATT
29526454 AAATAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
ATATTTAAAATATAATTAAA
Found at i:29526466 original size:18 final size:20
Alignment explanation
Indices: 29526425--29526468 Score: 58
Period size: 18 Copynumber: 2.3 Consensus size: 20
29526415 AAAATATATG
29526425 TAAAATATATATAATATAAT
1 TAAAATATATATAATATAAT
29526445 TAAAATAT-TA-AATAATAA-
1 TAAAATATATATAAT-ATAAT
29526463 TAAAAT
1 TAAAAT
29526469 TAATCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 9 0.39
19 6 0.26
20 8 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAATATATATAATATAAT
Found at i:29526929 original size:24 final size:24
Alignment explanation
Indices: 29526895--29526940 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
29526885 TAAAAGCTGA
* *
29526895 AATAGTTTTAAATTTTGAATAAGT
1 AATAGTATTAAATTTTAAATAAGT
29526919 AATAGTATTAAATTTTAAATAA
1 AATAGTATTAAATTTTAAATAA
29526941 TTATTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (24 bp):
AATAGTATTAAATTTTAAATAAGT
Found at i:29527413 original size:2 final size:2
Alignment explanation
Indices: 29527402--29527448 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
29527392 ACTCACACTT
*
29527402 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29527443 TA TA TA
1 TA TA TA
29527449 AAGAGGTGCA
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:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29527705 original size:37 final size:37
Alignment explanation
Indices: 29527664--29527777 Score: 92
Period size: 37 Copynumber: 3.1 Consensus size: 37
29527654 AAGATAAACT
29527664 ATATATTTAAATTATTATAAAAATTCATTTAAAAATA
1 ATATATTTAAATTATTATAAAAATTCATTTAAAAATA
* * ** * *
29527701 ATATATCTCTACATT-TGA-AAATTTTAATTTTAAAATA
1 ATATAT-T-TAAATTATTATAAAAATTCATTTAAAAATA
** *
29527738 TATATAACTAAATTATTAT-GAAATTCATTTAAAAA-A
1 -ATATATTTAAATTATTATAAAAATTCATTTAAAAATA
29527774 ATAT
1 ATAT
29527778 TTGTATAATT
Statistics
Matches: 57, Mismatches: 15, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
35 4 0.07
36 6 0.11
37 34 0.60
38 8 0.14
39 5 0.09
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (37 bp):
ATATATTTAAATTATTATAAAAATTCATTTAAAAATA
Found at i:29528388 original size:106 final size:106
Alignment explanation
Indices: 29528268--29528463 Score: 259
Period size: 107 Copynumber: 1.8 Consensus size: 106
29528258 CAAAATTTTC
* * * * *
29528268 TTATGAGTCAAATAGGAAGATAATCCACCTAGTATAT-GCATAAATAATTTTTATTATTTAAGCA
1 TTATGAGTCAAATAGGAAGATAATCCACCTA-AATATCACATAAATAAATTTTATCATGTAAGCA
* *
29528332 TGCATTATGTAATATAATATATATAAGTTTTTTAAAAAAATT
65 TGCATTATCTAATACAATATATATAAGTTTTTTAAAAAAATT
* * * *
29528374 TTATGTGTCAAATAGGAAGTTCATCCACCTAAATGTCCACATAAATAAATTTTATCATGTAAGCA
1 TTATGAGTCAAATAGGAAGATAATCCACCTAAATAT-CACATAAATAAATTTTATCATGTAAGCA
*
29528439 TGCATTCTCTAATACAATATATATA
65 TGCATTATCTAATACAATATATATA
29528464 TATATATATA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
105 3 0.04
106 28 0.37
107 45 0.59
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (106 bp):
TTATGAGTCAAATAGGAAGATAATCCACCTAAATATCACATAAATAAATTTTATCATGTAAGCAT
GCATTATCTAATACAATATATATAAGTTTTTTAAAAAAATT
Found at i:29528462 original size:2 final size:2
Alignment explanation
Indices: 29528455--29528481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29528445 CTCTAATACA
29528455 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29528482 CTACATTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29529271 original size:29 final size:29
Alignment explanation
Indices: 29529229--29529285 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
29529219 TAAAAAAAAG
*
29529229 AAACTTGTGAGATCTTGTCAATCTTTCAT
1 AAACTTGTGAGATCCTGTCAATCTTTCAT
* *
29529258 AAACTTGTGAGATCCTGTCCATGTTTCA
1 AAACTTGTGAGATCCTGTCAATCTTTCA
29529286 AGTGTTGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (29 bp):
AAACTTGTGAGATCCTGTCAATCTTTCAT
Found at i:29531744 original size:71 final size:71
Alignment explanation
Indices: 29531600--29531737 Score: 215
Period size: 71 Copynumber: 1.9 Consensus size: 71
29531590 ATTATTTAAT
* *
29531600 TTAATCATATTCATAATATCATCTTATCTTATCATTTCATAATCTTATGTACCAAACATATCTTA
1 TTAATCATATTCATAATATCATCTTATCTTATCATATCATAATCTTATGTACCAAACACATCTTA
29531665 ATGATA
66 ATGATA
* * *
29531671 TTAATCATATTCATAATATTATCTTATCTTATTC-TATCATAATTTTGTGTACCAAACACATCTT
1 TTAATCATATTCATAATATCATCTTATCTTA-TCATATCATAATCTTATGTACCAAACACATCTT
29531735 AAT
65 AAT
29531738 AGTATTATAT
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
71 59 0.97
72 2 0.03
ACGTcount: A:0.36, C:0.17, G:0.03, T:0.45
Consensus pattern (71 bp):
TTAATCATATTCATAATATCATCTTATCTTATCATATCATAATCTTATGTACCAAACACATCTTA
ATGATA
Found at i:29532939 original size:6 final size:6
Alignment explanation
Indices: 29532924--29532989 Score: 57
Period size: 6 Copynumber: 11.3 Consensus size: 6
29532914 CAATATAATC
* * *
29532924 AATA-A AATATA AATATA AATACA AATACA AATAT- AATATA TATATAA
1 AATATA AATATA AATATA AATATA AATATA AATATA AATATA AATAT-A
* *
29532971 AAAATA AA-ATA AAAATA AA
1 AATATA AATATA AATATA AA
29532990 CAAAAAAGGA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
5 14 0.27
6 34 0.65
7 4 0.08
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (6 bp):
AATATA
Found at i:29532956 original size:29 final size:25
Alignment explanation
Indices: 29532924--29532989 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 25
29532914 CAATATAATC
29532924 AATAAAATATAAATATAAATACAAATACA
1 AATAAAATATAAATAT-AA-A-AAATA-A
* *
29532953 AATATAATATATATATAAAAAATAA
1 AATAAAATATAAATATAAAAAATAA
29532978 AATAAAA-ATAAA
1 AATAAAATATAAA
29532990 CAAAAAAGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 4 0.12
25 7 0.21
26 5 0.15
27 1 0.03
28 2 0.06
29 14 0.42
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (25 bp):
AATAAAATATAAATATAAAAAATAA
Found at i:29532982 original size:23 final size:24
Alignment explanation
Indices: 29532924--29532989 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 24
29532914 CAATATAATC
29532924 AATAAAATATAAATATAAATACAAA
1 AATAAAATA-AAATATAAATACAAA
* * * *
29532949 TACAAATATAATATATATATA-AAA
1 AATAAA-ATAAAATATAAATACAAA
29532973 AATAAAATAAAA-ATAAA
1 AATAAAATAAAATATAAA
29532990 CAAAAAAGGA
Statistics
Matches: 32, Mismatches: 8, Indels: 5
0.71 0.18 0.11
Matches are distributed among these distances:
22 4 0.12
23 5 0.16
24 7 0.22
25 13 0.41
26 3 0.09
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (24 bp):
AATAAAATAAAATATAAATACAAA
Found at i:29533950 original size:3 final size:3
Alignment explanation
Indices: 29533944--29533979 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
29533934 TTATTAACAA
29533944 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29533980 GAAAGAAGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29534176 original size:115 final size:115
Alignment explanation
Indices: 29533974--29534182 Score: 366
Period size: 115 Copynumber: 1.8 Consensus size: 115
29533964 TAATAATAAT
* * *
29533974 AATAATGAAAGAAGGTTGGGCTTGAAATCTACATCCAATTAACAGTTGTTGGGCCTATAACCCAA
1 AATAATAAAAGAAGGTTGGGCCTGAAATCTACATCCAATTAACAGTTATTGGGCCTATAACCCAA
29534039 ACAACATAAATAAAATTGTAAAAAGCCCCAACATACATGCCTCCAAGGCC
66 ACAACATAAATAAAATTGTAAAAAGCCCCAACATACATGCCTCCAAGGCC
*
29534089 AATAATAAAATAAGGTTGGGCCT-AAAGTCTACATCCAATTAACAGTTATTGGGCCTATAACCCA
1 AATAATAAAAGAAGGTTGGGCCTGAAA-TCTACATCCAATTAACAGTTATTGGGCCTATAACCCA
29534153 AACAACATAAATAAAATTGTAAAAAGCCCC
65 AACAACATAAATAAAATTGTAAAAAGCCCC
29534183 GAACGCCTTC
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 3 0.03
115 86 0.97
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (115 bp):
AATAATAAAAGAAGGTTGGGCCTGAAATCTACATCCAATTAACAGTTATTGGGCCTATAACCCAA
ACAACATAAATAAAATTGTAAAAAGCCCCAACATACATGCCTCCAAGGCC
Found at i:29534576 original size:18 final size:18
Alignment explanation
Indices: 29534480--29534582 Score: 56
Period size: 18 Copynumber: 5.7 Consensus size: 18
29534470 AATTTATAAT
29534480 GATTTCAAAATT-TGCAAA
1 GATTTCAAAATTCT-CAAA
*
29534498 GATTT-AATATTCGT-AAA
1 GATTTCAAAATTC-TCAAA
* * *
29534515 GGTTTCTAAATT-TGCAGA
1 GATTTCAAAATTCT-CAAA
*
29534533 GATTCTC-AAATTCATAAAA
1 GATT-TCAAAATTC-TCAAA
*
29534552 GA-CTCAAAATTCTCAAA
1 GATTTCAAAATTCTCAAA
29534569 GATTTCAAAGATTC
1 GATTTCAAA-ATTC
29534583 AAGATTCGTA
Statistics
Matches: 63, Mismatches: 11, Indels: 21
0.66 0.12 0.22
Matches are distributed among these distances:
16 1 0.02
17 20 0.32
18 30 0.48
19 11 0.17
20 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.34
Consensus pattern (18 bp):
GATTTCAAAATTCTCAAA
Found at i:29534612 original size:34 final size:32
Alignment explanation
Indices: 29534574--29534648 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 32
29534564 TCAAAGATTT
* * *
29534574 CAAAGATTCAAGATTCGTAAGATTTTAAGTTTTA
1 CAAAGATTC-AGATTCATAAGATTTCAAG-TTCA
*
29534608 CAAAGATTTCAGATTTATAAGATTTCAAGTTCA
1 CAAAGA-TTCAGATTCATAAGATTTCAAGTTCA
29534641 CAAAGATT
1 CAAAGATT
29534649 TTAGATTTCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
32 2 0.06
33 9 0.25
34 22 0.61
35 3 0.08
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (32 bp):
CAAAGATTCAGATTCATAAGATTTCAAGTTCA
Found at i:29539091 original size:18 final size:18
Alignment explanation
Indices: 29539063--29539098 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
29539053 TTAATTACTC
29539063 TTTTCATAATTTTTTAAAA
1 TTTTCATAA-TTTTTAAAA
29539082 TTTT-ATAATTTTTAAAA
1 TTTTCATAATTTTTAAAA
29539099 AATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTCATAATTTTTAAAA
Found at i:29539099 original size:18 final size:19
Alignment explanation
Indices: 29539063--29539099 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29539053 TTAATTACTC
*
29539063 TTTTCATAATTTTTTAAAA
1 TTTTCATAATTTTTAAAAA
29539082 TTTT-ATAATTTTTAAAAA
1 TTTTCATAATTTTTAAAAA
29539100 ATAAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTCATAATTTTTAAAAA
Found at i:29539837 original size:34 final size:34
Alignment explanation
Indices: 29539757--29539837 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 34
29539747 CTTACCTTCC
** * *
29539757 ATAAATTCATTTTTTGAAAATTTTATGATTTTTT
1 ATAAATTCATTTTAAGAAAAGTTTACGATTTTTT
*
29539791 AAAAAATT-ATTTTAAGAAAAGTTTACGATTATTTT
1 -ATAAATTCATTTTAAGAAAAGTTTACGATT-TTTT
29539826 -TAAATTCATTTT
1 ATAAATTCATTTT
29539838 TAAAAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
33 5 0.13
34 23 0.61
35 10 0.26
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (34 bp):
ATAAATTCATTTTAAGAAAAGTTTACGATTTTTT
Found at i:29542936 original size:22 final size:22
Alignment explanation
Indices: 29542901--29542942 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29542891 GTGTGGTATC
*
29542901 TAAATTTTAAAAATTTTTAATA
1 TAAATTTTAAAAATTATTAATA
29542923 TAAA-TTTATAAAATTATTAA
1 TAAATTTTA-AAAATTATTAA
29542943 CTAATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATTTTAAAAATTATTAATA
Found at i:29543455 original size:27 final size:26
Alignment explanation
Indices: 29543391--29543458 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
29543381 GTTTATTTGA
*
29543391 ATAAAAATTAAAACATAAAAATGTTT
1 ATAAAAAATAAAACATAAAAATGTTT
29543417 ATAAATATAATAAAA-ATATAAAAT-TTT
1 ATAAA-A-AATAAAACATA-AAAATGTTT
29543444 ATTTAAAAAATAAAA
1 A--TAAAAAATAAAA
29543459 TAGTTTTAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
26 5 0.14
27 15 0.42
28 12 0.33
29 4 0.11
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.32
Consensus pattern (26 bp):
ATAAAAAATAAAACATAAAAATGTTT
Found at i:29544563 original size:18 final size:18
Alignment explanation
Indices: 29544540--29544578 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
29544530 AAAATTATTT
*
29544540 TTTAAAAAATTTATATAA
1 TTTAAAAAATTGATATAA
**
29544558 TTTAAATTATTGATATAA
1 TTTAAAAAATTGATATAA
29544576 TTT
1 TTT
29544579 TTAAGATATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
TTTAAAAAATTGATATAA
Found at i:29546767 original size:25 final size:24
Alignment explanation
Indices: 29546740--29546786 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
29546730 TACATTCACT
29546740 TTTTA-CTCTTAGTTTTTTACACAG
1 TTTTATCTCTTAGTTTTTT-CACAG
*
29546764 TTTTATTTCTTAGTTTTTTCACA
1 TTTTATCTCTTAGTTTTTTCACA
29546787 TGGTATCAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.60
Consensus pattern (24 bp):
TTTTATCTCTTAGTTTTTTCACAG
Found at i:29551292 original size:23 final size:23
Alignment explanation
Indices: 29551266--29551310 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
29551256 GCAGGGAGAA
29551266 AATATCATTGAAGATTCACTTAG
1 AATATCATTGAAGATTCACTTAG
29551289 AATATCATTGAAGATTCACTTA
1 AATATCATTGAAGATTCACTTA
29551311 TACCTATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.36
Consensus pattern (23 bp):
AATATCATTGAAGATTCACTTAG
Found at i:29557017 original size:9 final size:9
Alignment explanation
Indices: 29557003--29557038 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
29556993 TGAAAATAGG
29557003 AATAGCGGC
1 AATAGCGGC
*
29557012 AATAGCGGT
1 AATAGCGGC
29557021 AATAGCGGGC
1 AATAGC-GGC
29557031 AATAGCGG
1 AATAGCGG
29557039 ACCGTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.33, C:0.17, G:0.36, T:0.14
Consensus pattern (9 bp):
AATAGCGGC
Found at i:29557033 original size:19 final size:18
Alignment explanation
Indices: 29557003--29557038 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
29556993 TGAAAATAGG
29557003 AATAGCGGCAATAGCGGT
1 AATAGCGGCAATAGCGGT
29557021 AATAGCGGGCAATAGCGG
1 AATAGC-GGCAATAGCGG
29557039 ACCGTTATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.33, C:0.17, G:0.36, T:0.14
Consensus pattern (18 bp):
AATAGCGGCAATAGCGGT
Found at i:29557280 original size:19 final size:17
Alignment explanation
Indices: 29557256--29557300 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
29557246 AATTAATGAA
*
29557256 TAAAATTTTAATTAATTT
1 TAAAATTTTAAATAA-TT
*
29557274 TATAAATGTTAAATAATT
1 TA-AAATTTTAAATAATT
29557292 TAAAATTTT
1 TAAAATTTT
29557301 TGGTAATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.26
18 6 0.26
19 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
TAAAATTTTAAATAATT
Found at i:29557420 original size:21 final size:21
Alignment explanation
Indices: 29557391--29557437 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
29557381 TCAAATATAT
*
29557391 ATTTTATTA-T-TAAT-TTTA
1 ATTTTATTATTATAATAATTA
29557409 ATTTTATTATTATAATAATTA
1 ATTTTATTATTATAATAATTA
29557430 ATTTTATT
1 ATTTTATT
29557438 TTTACTGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 9 0.36
19 1 0.04
20 4 0.16
21 11 0.44
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
ATTTTATTATTATAATAATTA
Found at i:29557858 original size:21 final size:20
Alignment explanation
Indices: 29557820--29557859 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
29557810 AGATTATTTA
*
29557820 TTAAAAAAAAAATTTTTATT
1 TTAAAAAAAAAATATTTATT
*
29557840 TTAAAAAATAATATATTTAT
1 TTAAAAAA-AAAATATTTAT
29557860 AACTTTGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAAAAAAAATATTTATT
Found at i:29557943 original size:2 final size:2
Alignment explanation
Indices: 29557930--29557967 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
29557920 ATAAGAGTTG
* *
29557930 TA TA TG TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29557968 AAAGATAGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:29561232 original size:58 final size:61
Alignment explanation
Indices: 29561163--29561445 Score: 244
Period size: 58 Copynumber: 4.5 Consensus size: 61
29561153 TTTTTTAATG
*
29561163 ATTTTTC-T-AAAATAAAATTTCT-CAAAAAAT-TATTTTTGAGAAAAAATTGAAAGTATCA
1 ATTTTTCTTGAAAATAAAATTTCTAAAAAAAATATATTTTT-AGAAAAAATTGAAAGTATCA
** *
29561221 ATTTTT-TT-AAAATAAAAAAGT-T--AAAAAATATATTTTTAGGAAAAAATTGAAAGTATTA
1 ATTTTTCTTGAAAAT-AAAATTTCTAAAAAAAATATATTTTTA-GAAAAAATTGAAAGTATCA
* * * ** *
29561279 ATTTTTCTTAAAAATAAAATTTCTAAAATAAAAATTTCTAAAAGCATTTTGAGGGAAAGTTGAAA
1 ATTTTTCTTGAAAATAAAATTTCT-AAA-AAAAA----T---A-TATTTTTAGAAAAAATTGAAA
29561344 GTATCA
56 GTATCA
29561350 ATTTTTCTTGAAAATAAAAGTTTCTAAAAATAAA-ATATTTTTAGAAAAAAGTTGAAAGTATCA
1 ATTTTTCTTGAAAATAAAA-TTTCTAAAAA-AAATATATTTTTAGAAAAAA-TTGAAAGTATCA
*
29561413 ATTTTTCTTGAAAATAAAATTTTTAAAATAAAA
1 ATTTTTCTTGAAAATAAAATTTCTAAAA-AAAA
29561446 GTTATTAAGA
Statistics
Matches: 184, Mismatches: 18, Indels: 42
0.75 0.07 0.17
Matches are distributed among these distances:
57 8 0.04
58 44 0.24
59 12 0.07
60 6 0.03
62 21 0.11
63 34 0.18
64 5 0.03
68 1 0.01
70 2 0.01
71 40 0.22
72 11 0.06
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.37
Consensus pattern (61 bp):
ATTTTTCTTGAAAATAAAATTTCTAAAAAAAATATATTTTTAGAAAAAATTGAAAGTATCA
Found at i:29561308 original size:14 final size:15
Alignment explanation
Indices: 29561289--29561321 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
29561279 ATTTTTCTTA
29561289 AAAAT-AAAATTTCT
1 AAAATAAAAATTTCT
29561303 AAAATAAAAATTTCT
1 AAAATAAAAATTTCT
29561318 AAAA
1 AAAA
29561322 GCATTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAAAAATTTCT
Found at i:29567103 original size:56 final size:56
Alignment explanation
Indices: 29567044--29567282 Score: 250
Period size: 56 Copynumber: 4.2 Consensus size: 56
29567034 AGGTTAAATT
* * * *
29567044 TTTTCCTAAAT-AAAAATAATTTTTAAAATTTTTTGAGAAAAAATTGAATTATCAAT
1 TTTTCTTAAATAAAAAAT-ATTTTAAAAATTTTTTGAGAAAAAATTGAAATATCAAA
* * * * **
29567100 TTTTCTTAAATAAAAAAATATTTCAAAAAATGTTTGAGGAAAGGTTGAAATATC-AA
1 TTTTCTTAAAT-AAAAAATATTTTAAAAATTTTTTGAGAAAAAATTGAAATATCAAA
* * * *
29567156 TTTTCCTTAAATAAAAAATATTTCAAAAACTATTTGAGGAAAAATTGAAATATCAAA
1 TTTT-CTTAAATAAAAAATATTTTAAAAATTTTTTGAGAAAAAATTGAAATATCAAA
* * *
29567213 TTTTCTTAAATAAAAAATATTTCAAAAAATATTTTGAGAAAAAGTT-AAAGTATCAAAA
1 TTTTCTTAAATAAAAAATATTT-TAAAAATTTTTTGAGAAAAAATTGAAA-TATC-AAA
29567271 TTTTCTTAAATA
1 TTTTCTTAAATA
29567283 TAGCATCAAT
Statistics
Matches: 156, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
56 74 0.47
57 61 0.39
58 21 0.13
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (56 bp):
TTTTCTTAAATAAAAAATATTTTAAAAATTTTTTGAGAAAAAATTGAAATATCAAA
Found at i:29567192 original size:113 final size:115
Alignment explanation
Indices: 29567044--29567282 Score: 312
Period size: 113 Copynumber: 2.1 Consensus size: 115
29567034 AGGTTAAATT
** * * * *
29567044 TTTTCC-TAAAT-AAAAATAATTTTTAAAATTTTTTGAGAAAAAATTGAATTATCAATTTTTCTT
1 TTTTCCTTAAATAAAAAATAATTTCAAAAACTATTTGAGAAAAAATTGAAATATCAAATTTTCTT
* *
29567107 AAATAAAAAAATATTTCAAAAAAT-GTTTGAGGAAAGGTTGAAA-TATC-AA
66 AAAT-AAAAAATATTTCAAAAAATAGTTTGAGAAAAAGTT-AAAGTATCAAA
*
29567156 TTTTCCTTAAATAAAAAAT-ATTTCAAAAACTATTTGAGGAAAAATTGAAATATCAAATTTTCTT
1 TTTTCCTTAAATAAAAAATAATTTCAAAAACTATTTGAGAAAAAATTGAAATATCAAATTTTCTT
*
29567220 AAATAAAAAATATTTCAAAAAATATTTTGAGAAAAAGTTAAAGTATCAAAA
66 AAATAAAAAATATTTCAAAAAATAGTTTGAGAAAAAGTTAAAGTATC-AAA
29567271 TTTT-CTTAAATA
1 TTTTCCTTAAATA
29567283 TAGCATCAAT
Statistics
Matches: 111, Mismatches: 10, Indels: 10
0.85 0.08 0.08
Matches are distributed among these distances:
112 28 0.25
113 63 0.57
114 14 0.13
115 6 0.05
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (115 bp):
TTTTCCTTAAATAAAAAATAATTTCAAAAACTATTTGAGAAAAAATTGAAATATCAAATTTTCTT
AAATAAAAAATATTTCAAAAAATAGTTTGAGAAAAAGTTAAAGTATCAAA
Found at i:29569371 original size:27 final size:27
Alignment explanation
Indices: 29569340--29569393 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
29569330 CCATATAACC
29569340 ACTTATATCTAACATCACTTTAATAGT
1 ACTTATATCTAACATCACTTTAATAGT
*
29569367 ACTTATATCTAACATCATTTTAATAGT
1 ACTTATATCTAACATCACTTTAATAGT
29569394 TGATGATGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.17, G:0.04, T:0.43
Consensus pattern (27 bp):
ACTTATATCTAACATCACTTTAATAGT
Found at i:29608517 original size:28 final size:27
Alignment explanation
Indices: 29608450--29608523 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 27
29608440 TGAAAAAATT
* *
29608450 ACTAAAATTTTTTAAAAATTATGAAAAC
1 ACTAAAA-ATTTTAAAAATTATAAAAAC
*
29608478 ATTCAAAAATTTTAAAAATTA-AAAAAC
1 ACT-AAAAATTTTAAAAATTATAAAAAC
29608505 AACTAAAACATTTTAAAAA
1 -ACTAAAA-ATTTTAAAAA
29608524 AAAATCCAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 9 0.23
28 26 0.67
29 4 0.10
ACGTcount: A:0.59, C:0.08, G:0.01, T:0.31
Consensus pattern (27 bp):
ACTAAAAATTTTAAAAATTATAAAAAC
Found at i:29608568 original size:18 final size:20
Alignment explanation
Indices: 29608545--29608589 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
29608535 ATTCTATAAA
29608545 ATTAAAAAAAT-AAA-AATT
1 ATTAAAAAAATCAAACAATT
*
29608563 ATTAAAAAATTCAAACAATT
1 ATTAAAAAAATCAAACAATT
29608583 -TTAAAAA
1 ATTAAAAA
29608590 TTAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
19 10 0.42
20 4 0.17
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
ATTAAAAAAATCAAACAATT
Found at i:29608570 original size:10 final size:10
Alignment explanation
Indices: 29608555--29608665 Score: 51
Period size: 10 Copynumber: 11.5 Consensus size: 10
29608545 ATTAAAAAAA
29608555 TAAAAATTAT
1 TAAAAATTAT
29608565 TAAAAA--AT
1 TAAAAATTAT
29608573 TCAAACAATT-T
1 T-AAA-AATTAT
29608584 TAAAAATTA-
1 TAAAAATTAT
* * *
29608593 AAAAAAATCT
1 TAAAAATTAT
29608603 TAAGAAATTA-
1 TAA-AAATTAT
*
29608613 TAAAAACTT-C
1 TAAAAA-TTAT
*
29608623 TAAAAATTTT
1 TAAAAATTAT
29608633 TAAAAAATT-T
1 T-AAAAATTAT
*
29608643 CAAAAATTA-
1 TAAAAATTAT
*
29608652 T-AAAATAAT
1 TAAAAATTAT
29608661 TAAAA
1 TAAAA
29608666 TTTTTTTTAT
Statistics
Matches: 77, Mismatches: 10, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
8 9 0.12
9 26 0.34
10 29 0.38
11 13 0.17
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.32
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:29608661 original size:20 final size:19
Alignment explanation
Indices: 29608579--29608661 Score: 71
Period size: 20 Copynumber: 4.2 Consensus size: 19
29608569 AAATTCAAAC
* *
29608579 AATTTTAAAAATTAAAAAA
1 AATTTCAAAAATTATAAAA
29608598 AATCTT-AAGAAATTAT-AAA
1 AAT-TTCAA-AAATTATAAAA
* *
29608617 AACTTCTAAAAATTTTTAAAA
1 AATTTC-AAAAA-TTATAAAA
29608638 AATTTCAAAAATTATAAAA
1 AATTTCAAAAATTATAAAA
29608657 TAATT
1 -AATT
29608662 AAAATTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
18 2 0.04
19 20 0.38
20 22 0.42
21 8 0.15
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (19 bp):
AATTTCAAAAATTATAAAA
Found at i:29608762 original size:11 final size:10
Alignment explanation
Indices: 29608734--29608903 Score: 108
Period size: 9 Copynumber: 17.3 Consensus size: 10
29608724 TAAAATTAAG
29608734 AAAAATTC-A
1 AAAAATTCTA
29608743 AAAAA-TCTA
1 AAAAATTCTA
29608752 AAAAACTTCTA
1 AAAAA-TTCTA
* *
29608763 AAAACCTT-TT
1 AAAA-ATTCTA
29608773 AAAAATTCTA
1 AAAAATTCTA
* * *
29608783 ACAAATTTTC
1 AAAAATTCTA
29608793 AAAAATTCT-
1 AAAAATTCTA
*
29608802 AAAAATTCAA
1 AAAAATTCTA
29608812 AAATAATTACTA
1 AAA-AATT-CTA
*
29608824 AAAACTT-TGA
1 AAAAATTCT-A
*
29608834 GAAAATTC-A
1 AAAAATTCTA
29608843 AAAAA-T-TA
1 AAAAATTCTA
29608851 AAAAATTCTGA
1 AAAAATTCT-A
29608862 AAAAATT-TA
1 AAAAATTCTA
*
29608871 AAAAATTCCA
1 AAAAATTCTA
* *
29608881 AAAACTTTCAA
1 AAAA-ATTCTA
29608892 AAAAATT-TA
1 AAAAATTCTA
29608901 AAA
1 AAA
29608904 GTTTAAAATT
Statistics
Matches: 125, Mismatches: 20, Indels: 32
0.71 0.11 0.18
Matches are distributed among these distances:
8 9 0.07
9 40 0.32
10 38 0.30
11 33 0.26
12 5 0.04
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.28
Consensus pattern (10 bp):
AAAAATTCTA
Found at i:29608776 original size:20 final size:19
Alignment explanation
Indices: 29608734--29608894 Score: 96
Period size: 19 Copynumber: 8.3 Consensus size: 19
29608724 TAAAATTAAG
* * *
29608734 AAAAATTC-AAAAAATCTA
1 AAAAATTCTAAAAATTTTC
29608752 AAAAACTTCTAAAAACCTTTT-
1 AAAAA-TTCTAAAAA--TTTTC
29608773 AAAAATTCTAACAAATTTTC
1 AAAAATTCTAA-AAATTTTC
***
29608793 AAAAATTCTAAAAATTCAA
1 AAAAATTCTAAAAATTTTC
* *
29608812 AAATAATTACTAAAAACTTTG
1 AAA-AATT-CTAAAAATTTTC
* *
29608833 AGAAAATTC-AAAAA-ATTA
1 A-AAAATTCTAAAAATTTTC
* *
29608851 AAAAATTCTGAAAAAATTTA
1 AAAAATTCT-AAAAATTTTC
* *
29608871 AAAAATTCCAAAAACTTTC
1 AAAAATTCTAAAAATTTTC
29608890 AAAAA
1 AAAAA
29608895 AATTTAAAAG
Statistics
Matches: 116, Mismatches: 15, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
17 7 0.06
18 8 0.07
19 38 0.33
20 38 0.33
21 21 0.18
22 4 0.03
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATTCTAAAAATTTTC
Found at i:29608895 original size:20 final size:19
Alignment explanation
Indices: 29608734--29608895 Score: 125
Period size: 20 Copynumber: 8.3 Consensus size: 19
29608724 TAAAATTAAG
* *
29608734 AAAAATTC-AAAAAATCTA
1 AAAAATTCTAAAAACTTTA
*
29608752 AAAAACTTCTAAAAACCTTTT
1 AAAAA-TTCTAAAAA-CTTTA
* *
29608773 AAAAATTCTAACAAATTTTC
1 AAAAATTCTAA-AAACTTTA
*
29608793 AAAAATTCTAAAAA-TTCAA
1 AAAAATTCTAAAAACTT-TA
29608812 AAATAATTACTAAAAACTTTGA
1 AAA-AATT-CTAAAAACTTT-A
* *
29608834 GAAAATTC-AAAAA-ATTA
1 AAAAATTCTAAAAACTTTA
*
29608851 AAAAATTCTGAAAAAATTTA
1 AAAAATTCT-AAAAACTTTA
*
29608871 AAAAATTCCAAAAACTTTCA
1 AAAAATTCTAAAAACTTT-A
29608891 AAAAA
1 AAAAA
29608896 ATTTAAAAGT
Statistics
Matches: 117, Mismatches: 14, Indels: 24
0.75 0.09 0.15
Matches are distributed among these distances:
17 8 0.07
18 9 0.08
19 27 0.23
20 47 0.40
21 21 0.18
22 5 0.04
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAATTCTAAAAACTTTA
Found at i:29608903 original size:9 final size:9
Alignment explanation
Indices: 29608734--29608924 Score: 84
Period size: 9 Copynumber: 19.9 Consensus size: 9
29608724 TAAAATTAAG
*
29608734 AAAAATTCA
1 AAAAATTTA
*
29608743 AAAAATCTA
1 AAAAATTTA
29608752 AAAAACTTCTA
1 AAAAA-TT-TA
* *
29608763 AAAACCTTTT
1 AAAA-ATTTA
29608773 AAAAATTCTA
1 AAAAATT-TA
* *
29608783 ACAAATTTTC
1 A-AAAATTTA
29608793 AAAAATTCT-
1 AAAAATT-TA
*
29608802 AAAAATTCAA
1 AAAAATT-TA
29608812 AAATAATTACTA
1 AAA-AATT--TA
*
29608824 AAAACTTTGA
1 AAAAATTT-A
* *
29608834 GAAAATTCA
1 AAAAATTTA
29608843 AAAAA-TTA
1 AAAAATTTA
29608851 AAAAATTCTGA
1 AAAAATT-T-A
29608862 AAAAATTTA
1 AAAAATTTA
*
29608871 AAAAATTCCA
1 AAAAATT-TA
*
29608881 AAAACTTTCAA
1 AAAAATTT--A
29608892 AAAAATTT-
1 AAAAATTTA
*
29608900 AAAAGTTT-
1 AAAAATTTA
*
29608908 AAAATTTTA
1 AAAAATTTA
29608917 AAAAATTT
1 AAAAATTT
29608925 TAAATTTTTT
Statistics
Matches: 140, Mismatches: 25, Indels: 34
0.70 0.13 0.17
Matches are distributed among these distances:
8 21 0.15
9 49 0.35
10 29 0.21
11 36 0.26
12 5 0.04
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAAATTTA
Found at i:29608971 original size:19 final size:19
Alignment explanation
Indices: 29608734--29608983 Score: 76
Period size: 19 Copynumber: 12.9 Consensus size: 19
29608724 TAAAATTAAG
*
29608734 AAAAATTC--AAAAAATCTA
1 AAAAATTCTAAAAAAAT-TT
**
29608752 AAAAACTTCTAAAAACCTTTT
1 AAAAA-TTCTAAAAA-AATTT
* *
29608773 AAAAATTCTAACAAATTTT
1 AAAAATTCTAAAAAAATTT
*
29608792 CAAAAATTCT--AAAAATTC
1 -AAAAATTCTAAAAAAATTT
*
29608810 AAAAATAAT-TACTAAAAACTTT
1 AAAAAT--TCTA--AAAAAATTT
*
29608832 GAGAAAATTC--AAAAAATTA
1 -A-AAAATTCTAAAAAAATTT
*
29608851 AAAAATTCTGAAAAAATTT
1 AAAAATTCTAAAAAAATTT
* *
29608870 AAAAAATTC-CAAAAACTTT
1 -AAAAATTCTAAAAAAATTT
*
29608889 CAAAAAAATT-T--AAAAGTTT
1 ---AAAAATTCTAAAAAAATTT
* *
29608908 -AAAATTTTAAAAAATTTT
1 AAAAATTCTAAAAAAATTT
** * * *
29608926 AAATTTTTTTTAAAAACTTGT
1 AAA-AATTCTAAAAAAATT-T
*
29608947 AGAAATTCTAAAAAAATTT
1 AAAAATTCTAAAAAAATTT
29608966 AAAAATTC-AAAAATAATT
1 AAAAATTCTAAAAA-AATT
29608984 AAAGAAACTT
Statistics
Matches: 177, Mismatches: 28, Indels: 53
0.69 0.11 0.21
Matches are distributed among these distances:
15 6 0.03
16 1 0.01
17 13 0.07
18 24 0.14
19 52 0.29
20 46 0.26
21 21 0.12
22 8 0.05
23 1 0.01
24 5 0.03
ACGTcount: A:0.56, C:0.09, G:0.02, T:0.32
Consensus pattern (19 bp):
AAAAATTCTAAAAAAATTT
Found at i:29609027 original size:13 final size:13
Alignment explanation
Indices: 29609009--29609034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29608999 TTTTCAAAAA
29609009 TTTTTATAAATTT
1 TTTTTATAAATTT
29609022 TTTTTATAAATTT
1 TTTTTATAAATTT
29609035 GTAGAATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTTATAAATTT
Found at i:29609328 original size:19 final size:20
Alignment explanation
Indices: 29609297--29609357 Score: 88
Period size: 20 Copynumber: 3.1 Consensus size: 20
29609287 GTTTTGAATA
29609297 TTTTGAAGTTTTTAAAATTT
1 TTTTGAAGTTTTTAAAATTT
29609317 TTTTGAAGTTTTTAAAA-TT
1 TTTTGAAGTTTTTAAAATTT
* **
29609336 TTTAGAAAATTTTAAAATTT
1 TTTTGAAGTTTTTAAAATTT
29609356 TT
1 TT
29609358 AGAATTAAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 16 0.43
20 21 0.57
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.57
Consensus pattern (20 bp):
TTTTGAAGTTTTTAAAATTT
Found at i:29609329 original size:29 final size:29
Alignment explanation
Indices: 29609253--29609348 Score: 81
Period size: 29 Copynumber: 3.2 Consensus size: 29
29609243 TTTTGAAACT
*
29609253 AATTTTTTAT-AA-ATTTAAAAATTTTTTAAA
1 AATTTTTT-TGAATATTTTAAAA-TTTTT-AA
* * *
29609283 AATTGTTTTGAATATTTTGAAGTTTTTAA
1 AATTTTTTTGAATATTTTAAAATTTTTAA
29609312 AATTTTTTTGAAGT-TTTTAAAATTTTTAGA
1 AATTTTTTTGAA-TATTTTAAAATTTTTA-A
*
29609342 AAATTTT
1 AATTTTT
29609349 AAAATTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
29 26 0.48
30 22 0.41
31 6 0.11
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (29 bp):
AATTTTTTTGAATATTTTAAAATTTTTAA
Found at i:29609358 original size:19 final size:19
Alignment explanation
Indices: 29609306--29609361 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
29609296 ATTTTGAAGT
* **
29609306 TTTTAAAATTTTTTTGAAGT
1 TTTTAAAA-TTTTTAGAAAA
29609326 TTTTAAAATTTTTAGAAAA
1 TTTTAAAATTTTTAGAAAA
29609345 TTTTAAAATTTTTAGAA
1 TTTTAAAATTTTTAGAA
29609362 TTAAAGAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 25 0.76
20 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (19 bp):
TTTTAAAATTTTTAGAAAA
Found at i:29609410 original size:19 final size:20
Alignment explanation
Indices: 29609365--29609415 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
29609355 TTTAGAATTA
*
29609365 AAGAAAATTTAGA-ATTTTTT
1 AAGAAATTTTA-ATATTTTTT
29609385 AAGAAATTTTAATATTTTTT
1 AAGAAATTTTAATATTTTTT
*
29609405 GA-AAATTTTAA
1 AAGAAATTTTAA
29609416 AAAGTTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (20 bp):
AAGAAATTTTAATATTTTTT
Found at i:29609507 original size:20 final size:19
Alignment explanation
Indices: 29609484--29609615 Score: 65
Period size: 20 Copynumber: 6.8 Consensus size: 19
29609474 ATTTAAAAAA
* *
29609484 AATTTTAGAATTTTTTTGAG
1 AATTTTAAAAATTTTTT-AG
29609504 AATTTTTAAAAATTTTTTAG
1 AA-TTTTAAAAATTTTTTAG
* * *
29609524 AATTGCTTCATAGTTTTTTA-
1 AATT--TTAAAAATTTTTTAG
* ** *
29609544 AGTTTTAAATTTTTTTTTG
1 AATTTTAAAAATTTTTTAG
* *
29609563 AAGTTTTTAAAATTTTAT-G
1 AA-TTTTAAAAATTTTTTAG
*
29609582 AAATTTT-AAAA-TTTTTAT
1 -AATTTTAAAAATTTTTTAG
29609600 AATTTTAAAAAATTTT
1 AATTTT-AAAAATTTT
29609616 AATAATTTTT
Statistics
Matches: 84, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
17 10 0.12
18 13 0.15
19 12 0.14
20 25 0.30
21 24 0.29
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (19 bp):
AATTTTAAAAATTTTTTAG
Found at i:29609561 original size:21 final size:21
Alignment explanation
Indices: 29609537--29609578 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
29609527 TGCTTCATAG
29609537 TTTTTT-AAG-TTTTAAATTT
1 TTTTTTGAAGTTTTTAAATTT
*
29609556 TTTTTTGAAGTTTTTAAAATT
1 TTTTTTGAAGTTTTTAAATTT
29609577 TT
1 TT
29609579 ATGAAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 3 0.15
21 11 0.55
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTTTGAAGTTTTTAAATTT
Found at i:29609578 original size:19 final size:18
Alignment explanation
Indices: 29609556--29609609 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 18
29609546 TTTTAAATTT
*
29609556 TTTTTTGAAGTTTTTAAAA
1 TTTTTTGAA-ATTTTAAAA
*
29609575 TTTTATGAAATTTTAAAA
1 TTTTTTGAAATTTTAAAA
29609593 -TTTTT-ATAATTTTAAAA
1 TTTTTTGA-AATTTTAAAA
29609610 AATTTTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 1 0.03
17 14 0.45
18 8 0.26
19 8 0.26
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTTTGAAATTTTAAAA
Found at i:29609588 original size:27 final size:27
Alignment explanation
Indices: 29609566--29609625 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
29609556 TTTTTTGAAG
**
29609566 TTTTTAAAATTTTATGAAATTTTAAAA
1 TTTTTAAAATTTTAAAAAATTTTAAAA
*
29609593 TTTTTATAATTTTAAAAAATTTTAATAA
1 TTTTTAAAATTTTAAAAAATTTTAA-AA
29609621 TTTTT
1 TTTTT
29609626 GAGAAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 22 0.76
28 7 0.24
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (27 bp):
TTTTTAAAATTTTAAAAAATTTTAAAA
Found at i:29609606 original size:8 final size:8
Alignment explanation
Indices: 29609567--29609624 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 8
29609557 TTTTTGAAGT
29609567 TTTTAAAA
1 TTTTAAAA
29609575 TTTTATGAAA
1 TTTTA--AAA
29609585 TTTTAAAA
1 TTTTAAAA
*
29609593 TTTTTATAA
1 -TTTTAAAA
29609602 TTTTAAAAAA
1 TTTT--AAAA
29609612 TTTTAATAA
1 TTTTAA-AA
29609621 TTTT
1 TTTT
29609625 TGAGAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
8 14 0.33
9 13 0.31
10 15 0.36
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (8 bp):
TTTTAAAA
Found at i:29611940 original size:18 final size:18
Alignment explanation
Indices: 29611919--29611953 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29611909 TTAACTTAAC
*
29611919 TTTTTTATTATTAGACTG
1 TTTTTTATAATTAGACTG
29611937 TTTTTTATAATTAGACT
1 TTTTTTATAATTAGACT
29611954 AAATATGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (18 bp):
TTTTTTATAATTAGACTG
Found at i:29616410 original size:16 final size:15
Alignment explanation
Indices: 29616375--29616416 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
29616365 ATATAATTTG
29616375 ATAAATTATT-T-AT
1 ATAAATTATTATAAT
*
29616388 ATTAATTATTATAAT
1 ATAAATTATTATAAT
29616403 AATAAATTATTATA
1 -ATAAATTATTATA
29616417 GTTTATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 1 0.04
15 2 0.08
16 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAATTATTATAAT
Found at i:29617203 original size:22 final size:22
Alignment explanation
Indices: 29617087--29617224 Score: 77
Period size: 22 Copynumber: 6.2 Consensus size: 22
29617077 AATTTAGTAA
*
29617087 TAAATCATAAATAACTTAATA-
1 TAAATCATTAATAACTTAATAG
* * * * *
29617108 CAAATCAATGATAATTTAATAA
1 TAAATCATTAATAACTTAATAG
* * *
29617130 TTAATTATTGAA-AACTTAAAAG
1 TAAATCATT-AATAACTTAATAG
*
29617152 TAAA--ATAATATAACTTAGTAGTAG
1 TAAATCATTA-ATAACTTA--A-TAG
*
29617176 TTAATCATTAATAACTTAATAG
1 TAAATCATTAATAACTTAATAG
* * *
29617198 TAAATCAATGATAATTTAATAG
1 TAAATCATTAATAACTTAATAG
29617220 TAAAT
1 TAAAT
29617225 TGTGGATAAT
Statistics
Matches: 86, Mismatches: 22, Indels: 17
0.69 0.18 0.14
Matches are distributed among these distances:
19 1 0.01
20 3 0.03
21 22 0.26
22 41 0.48
23 3 0.03
24 5 0.06
25 8 0.09
26 3 0.03
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.36
Consensus pattern (22 bp):
TAAATCATTAATAACTTAATAG
Found at i:29617245 original size:89 final size:87
Alignment explanation
Indices: 29616976--29617257 Score: 257
Period size: 89 Copynumber: 3.2 Consensus size: 87
29616966 AGATCAATAA
* * ** *
29616976 AAAATAAGTGATAA-TTTAGTAGTTAATAATTGATAACTTAATAATAAATCAATGGCAACTTAAT
1 AAAATAA-TGATAACTTTAGTAGTTAATCATTAATAACTTAAT-ATAAATCAATGATAATTTAAT
* **
29617040 AGTAATTTAGTTTTAATTTAATAGT
64 AGTAAATT-GTGATAATTTAATAGT
* * * * * * *
29617065 -AATTACTTGATAAATTTAGTAATAAATCATAAATAACTTAATACAAATCAATGATAATTTAATA
1 AAAATA-ATGATAACTTTAGTAGTTAATCATTAATAACTTAATATAAATCAATGATAATTTAATA
* * * * * *
29617129 ATTAATTATTGAAAACTTAAAAGT
65 GTAAATT-GTGATAATTTAATAGT
29617153 AAAATAAT-ATAACTTAGTAGTAGTTAATCATTAATAACTTAATAGTAAATCAATGATAATTTAA
1 AAAATAATGATAACTT--TAGTAGTTAATCATTAATAACTTAATA-TAAATCAATGATAATTTAA
29617217 TAGTAAATTGTGGATAATTTAATA-T
63 TAGTAAATTGT-GATAATTTAATAGT
*
29617242 AAAACAATGATAACTT
1 AAAATAATGATAACTT
29617258 GATAATAAAT
Statistics
Matches: 151, Mismatches: 34, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
87 6 0.04
88 44 0.29
89 60 0.40
90 41 0.27
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (87 bp):
AAAATAATGATAACTTTAGTAGTTAATCATTAATAACTTAATATAAATCAATGATAATTTAATAG
TAAATTGTGATAATTTAATAGT
Found at i:29617351 original size:22 final size:22
Alignment explanation
Indices: 29617326--29617386 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
29617316 AAAAACTAAG
29617326 TAGTAAATCAATGATAACATAA
1 TAGTAAATCAATGATAACATAA
* *
29617348 TAGTAAATGC-ATAATAACATGA
1 TAGTAAAT-CAATGATAACATAA
* *
29617370 TAATAAATCATTGATAA
1 TAGTAAATCAATGATAA
29617387 TTTAGATGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.52, C:0.08, G:0.10, T:0.30
Consensus pattern (22 bp):
TAGTAAATCAATGATAACATAA
Found at i:29617527 original size:22 final size:22
Alignment explanation
Indices: 29617466--29617631 Score: 127
Period size: 22 Copynumber: 7.5 Consensus size: 22
29617456 AGTAACAAAT
* * **
29617466 TAGTTAATTATTAATAACTTTG
1 TAGTAAATCATTAATAACTTAA
* * *
29617488 TAATAAAATCATCAATAAATTAA
1 TAGT-AAATCATTAATAACTTAA
* *
29617511 TAGTAAATCA-GATATAACTTTA
1 TAGTAAATCATTA-ATAACTTAA
* *
29617533 TAATAAATCATTAATAACTTAG
1 TAGTAAATCATTAATAACTTAA
* *
29617555 CAGTAAATCATTAATAATTTAA
1 TAGTAAATCATTAATAACTTAA
* * * *
29617577 TAGTGACTCAGTCATAACTTAA
1 TAGTAAATCATTAATAACTTAA
* *
29617599 TAGTAAATTCATTCATAAATTAA
1 TAGTAAA-TCATTAATAACTTAA
29617622 TAGTAAATCA
1 TAGTAAATCA
29617632 ATGCTAATTT
Statistics
Matches: 111, Mismatches: 29, Indels: 8
0.75 0.20 0.05
Matches are distributed among these distances:
21 1 0.01
22 74 0.67
23 36 0.32
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.37
Consensus pattern (22 bp):
TAGTAAATCATTAATAACTTAA
Found at i:29617641 original size:67 final size:66
Alignment explanation
Indices: 29617493--29617651 Score: 160
Period size: 66 Copynumber: 2.4 Consensus size: 66
29617483 CTTTGTAATA
* * * *
29617493 AAATC-ATCAATAAATTAATAGTAAATCAGATATAACTTTATAATAAATCATTAATAACTTAGCA
1 AAATCAAT-AATAATTTAATAGTAAATCAGATATAACTTAATAATAAATCATTAATAAATTAACA
29617557 GT
65 GT
* * * * * *
29617559 AAATCATTAATAATTTAATAGTGACTCAG-TCATAACTTAATAGTAAATTCATTCATAAATTAAT
1 AAATCAATAATAATTTAATAGTAAATCAGAT-ATAACTTAATAATAAA-TCATTAATAAATTAAC
29617623 AGT
64 AGT
** *
29617626 AAATCAATGCTAATTTAGTAGTAAAT
1 AAATCAATAATAATTTAATAGTAAAT
29617652 TATTGATAAT
Statistics
Matches: 74, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
65 1 0.01
66 37 0.50
67 36 0.49
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (66 bp):
AAATCAATAATAATTTAATAGTAAATCAGATATAACTTAATAATAAATCATTAATAAATTAACAG
T
Found at i:29617648 original size:45 final size:45
Alignment explanation
Indices: 29617536--29617660 Score: 121
Period size: 45 Copynumber: 2.8 Consensus size: 45
29617526 AACTTTATAA
* * * *
29617536 TAAATCATTAATAACTTAGCAGTAAA-TCATTAATAATTTAATAG
1 TAAATCAATCATAACTTAGTAGTAAATTCATTAATAAATTAATAG
* * * * *
29617580 TGACTCAGTCATAACTTAATAGTAAATTCATTCATAAATTAATAG
1 TAAATCAATCATAACTTAGTAGTAAATTCATTAATAAATTAATAG
* *
29617625 TAAATCAATGC-TAATTTAGTAGTAAATT-ATTGATAA
1 TAAATCAAT-CATAACTTAGTAGTAAATTCATTAATAA
29617661 TTTAGCAATA
Statistics
Matches: 65, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
44 27 0.42
45 37 0.57
46 1 0.02
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.37
Consensus pattern (45 bp):
TAAATCAATCATAACTTAGTAGTAAATTCATTAATAAATTAATAG
Found at i:29617650 original size:22 final size:22
Alignment explanation
Indices: 29617502--29617696 Score: 88
Period size: 22 Copynumber: 8.8 Consensus size: 22
29617492 AAAATCATCA
* *
29617502 ATAAATTAATAGTAAATCAGAT-
1 ATAATTTAGTAGTAAATCA-ATG
* * *
29617524 ATAACTTTA-TAATAAATCATTA
1 ATAA-TTTAGTAGTAAATCAATG
* * * *
29617546 ATAACTTAGCAGTAAATCATTA
1 ATAATTTAGTAGTAAATCAATG
* * * * *
29617568 ATAATTTAATAGTGACTCAGTC
1 ATAATTTAGTAGTAAATCAATG
* * * *
29617590 ATAACTTAATAGTAAATTCATTC
1 ATAATTTAGTAGTAAA-TCAATG
* *
29617613 ATAAATTAATAGTAAATCAATG
1 ATAATTTAGTAGTAAATCAATG
* * *
29617635 CTAATTTAGTAGTAAATTATTG
1 ATAATTTAGTAGTAAATCAATG
* * * * *
29617657 ATAATTTAGCAATATATTATTG
1 ATAATTTAGTAGTAAATCAATG
*
29617679 ATAGTTTAGTAGTAAATC
1 ATAATTTAGTAGTAAATC
29617697 GCTGATAACA
Statistics
Matches: 135, Mismatches: 34, Indels: 8
0.76 0.19 0.05
Matches are distributed among these distances:
21 4 0.03
22 108 0.80
23 23 0.17
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.38
Consensus pattern (22 bp):
ATAATTTAGTAGTAAATCAATG
Found at i:29617705 original size:111 final size:111
Alignment explanation
Indices: 29617502--29617711 Score: 237
Period size: 111 Copynumber: 1.9 Consensus size: 111
29617492 AAAATCATCA
*
29617502 ATAAATTAATAGTAAATCAGATATAACTTTATAATAAATCATTAATAACTTAGCAGTAAATCATT
1 ATAAATTAATAGTAAATCAGATATAACTTTATAATAAATCATTAATAACTTAGCAATAAATCATT
* * *
29617567 AATAATTTAATAGTGACTCAGTCATAACTTAATAGTAAATTCATTC
66 AATAATTTAATAGTAAATCAGTCATAACATAATAGTAAATTCATTC
* * * * * * *
29617613 ATAAATTAATAGTAAATCA-ATGCTAA-TTTAGTAGTAAATTATTGATAATTTAGCAATATATTA
1 ATAAATTAATAGTAAATCAGAT-ATAACTTTA-TAATAAATCATTAATAACTTAGCAATAAATCA
* * * *
29617676 TTGATAGTTTAGTAGTAAATC-GCTGATAACATAATA
64 TTAATAATTTAATAGTAAATCAG-TCATAACATAATA
29617712 ATGAATCAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
110 7 0.09
111 74 0.91
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.37
Consensus pattern (111 bp):
ATAAATTAATAGTAAATCAGATATAACTTTATAATAAATCATTAATAACTTAGCAATAAATCATT
AATAATTTAATAGTAAATCAGTCATAACATAATAGTAAATTCATTC
Found at i:29617740 original size:22 final size:22
Alignment explanation
Indices: 29617699--29617741 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29617689 AGTAAATCGC
29617699 TGATAACATAATAATGAATCAA
1 TGATAACATAATAATGAATCAA
* * *
29617721 TGATAACTTAATTATTAATCA
1 TGATAACATAATAATGAATCA
29617742 TTTATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (22 bp):
TGATAACATAATAATGAATCAA
Found at i:29618074 original size:39 final size:39
Alignment explanation
Indices: 29617999--29618074 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 39
29617989 TTTTATCAAT
*
29617999 AATTACTAAAAGTATATCATAAGTTATCAAATTTATAAA
1 AATTACTAAAAGTATATCATAAGTTATCAAAATTATAAA
*
29618038 AATTACTAAAATTATAT-A-AATGGTTATCAAAATTATA
1 AATTACTAAAAGTATATCATAA--GTTATCAAAATTATA
29618075 TTATAAGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 2 0.06
38 1 0.03
39 30 0.91
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (39 bp):
AATTACTAAAAGTATATCATAAGTTATCAAAATTATAAA
Found at i:29618084 original size:21 final size:20
Alignment explanation
Indices: 29618019--29618112 Score: 61
Period size: 21 Copynumber: 4.7 Consensus size: 20
29618009 AGTATATCAT
*
29618019 AAGTTATC-AAATT-TATAA
1 AAGTTATCAAAATTATATTA
*
29618037 AAATTA-CTAAAATTATA-TA
1 AAGTTATC-AAAATTATATTA
29618056 AATGGTTATCAAAATTATATTA
1 AA--GTTATCAAAATTATATTA
* * * *
29618078 TAAGTTACCAAGATTTTATCA
1 -AAGTTATCAAAATTATATTA
29618099 AAGGTTATCAAAAT
1 AA-GTTATCAAAAT
29618113 CAAAATTATA
Statistics
Matches: 58, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
17 1 0.02
18 5 0.09
19 8 0.14
20 4 0.07
21 35 0.60
22 3 0.05
23 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.37
Consensus pattern (20 bp):
AAGTTATCAAAATTATATTA
Found at i:29618629 original size:17 final size:17
Alignment explanation
Indices: 29618590--29618622 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29618580 TAAAACACAT
29618590 GTTTAATAATAAAAAAA
1 GTTTAATAATAAAAAAA
*
29618607 GATTAATAATAAAAAA
1 GTTTAATAATAAAAAA
29618623 TATTTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
GTTTAATAATAAAAAAA
Found at i:29618645 original size:26 final size:25
Alignment explanation
Indices: 29618618--29618705 Score: 72
Period size: 25 Copynumber: 3.4 Consensus size: 25
29618608 ATTAATAATA
*
29618618 AAAAATATTTAAACTAAAATTTATT
1 AAAAATATTTAAAATAAAATTTATT
* *
29618643 -AAAAT-TTTAATAAATGAGAATTTAATAA
1 AAAAATATTT-A-AAAT-AAAATTT-AT-T
* *
29618671 AAAAATATTTAAATTAAATTTTATT
1 AAAAATATTTAAAATAAAATTTATT
29618696 AAAAATATTT
1 AAAAATATTT
29618706 TATTAAAAGT
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
23 3 0.06
24 6 0.12
25 13 0.27
26 8 0.16
27 7 0.14
28 3 0.06
29 6 0.12
30 3 0.06
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (25 bp):
AAAAATATTTAAAATAAAATTTATT
Found at i:29618683 original size:27 final size:25
Alignment explanation
Indices: 29618613--29618705 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
29618603 AAAAGATTAA
*
29618613 TAATAAAAAATATTTAAACTAAAATT
1 TAATAAAAAATATTTAAA-TGAAATT
* *
29618639 T-AT-TAAAATTTTAATAAATGAGAATT
1 TAATAAAAAATATT--TAAATGA-AATT
*
29618665 TAATAAAAAAATATTTAAATTAAATT
1 TAAT-AAAAAATATTTAAATGAAATT
* *
29618691 TTATTAAAAATATTT
1 TAATAAAAAATATTT
29618706 TATTAAAAGT
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
24 7 0.13
25 14 0.26
26 17 0.32
27 8 0.15
29 7 0.13
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (25 bp):
TAATAAAAAATATTTAAATGAAATT
Found at i:29618707 original size:14 final size:14
Alignment explanation
Indices: 29618688--29618721 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
29618678 TTTAAATTAA
29618688 ATTTTATTAAAAAT
1 ATTTTATTAAAAAT
*
29618702 ATTTTATTAAAAGT
1 ATTTTATTAAAAAT
29618716 ATTTTA
1 ATTTTA
29618722 GTCACTCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (14 bp):
ATTTTATTAAAAAT
Found at i:29618707 original size:26 final size:25
Alignment explanation
Indices: 29618618--29618707 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 25
29618608 ATTAATAATA
*
29618618 AAAAATA-TTTAAACTAAAATTTATT
1 AAAAATATTTTAAA-TTAAATTTATT
* *
29618643 -AAAAT-TTTAATAAATGAGAATTTAAT
1 AAAAATATTT--TAAATTA-AATTTATT
*
29618669 AAAAAAATATTTAAATTAAATTTTATT
1 AAAAATAT-TTTAAATTAAA-TTTATT
29618696 AAAAATATTTTA
1 AAAAATATTTTA
29618708 TTAAAAGTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
24 7 0.14
25 2 0.04
26 17 0.33
27 22 0.43
28 1 0.02
29 2 0.04
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (25 bp):
AAAAATATTTTAAATTAAATTTATT
Found at i:29619110 original size:41 final size:41
Alignment explanation
Indices: 29619053--29619137 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
29619043 ATTTACCATC
*
29619053 AAATATGCAGCAGAAAGAACACCCCGAATCTGATTCTGTAT
1 AAATATGCAGCAGAAAGAACACCCCAAATCTGATTCTGTAT
29619094 AAATATGCAGCAGAAAGAACACCCCAAATCTGATTCTGTAT
1 AAATATGCAGCAGAAAGAACACCCCAAATCTGATTCTGTAT
29619135 AAA
1 AAA
29619138 CGGGTAATAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.21
Consensus pattern (41 bp):
AAATATGCAGCAGAAAGAACACCCCAAATCTGATTCTGTAT
Found at i:29620021 original size:2 final size:2
Alignment explanation
Indices: 29620014--29620043 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29620004 CGTTGTCCCA
29620014 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
29620044 CTTGAAGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29629394 original size:10 final size:10
Alignment explanation
Indices: 29629371--29629420 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
29629361 TGAACCGGAT
*
29629371 AAGAAAGAAG
1 AAGAAAGAAA
*
29629381 AAGAAGGAAA
1 AAGAAAGAAA
29629391 AAGAAAG--A
1 AAGAAAGAAA
29629399 AAGAAAGAAA
1 AAGAAAGAAA
*
29629409 AAAAAAGAAA
1 AAGAAAGAAA
29629419 AA
1 AA
29629421 AAAATAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 8 0.24
10 26 0.76
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:29629421 original size:10 final size:10
Alignment explanation
Indices: 29629388--29629424 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
29629378 AAGAAGAAGG
29629388 AAAAAGAAAGA
1 AAAAAGAAA-A
29629399 AAGAAAGAAAA
1 AA-AAAGAAAA
29629410 AAAAAGAAAA
1 AAAAAGAAAA
29629420 AAAAA
1 AAAAA
29629425 TAATAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 13 0.52
11 5 0.20
12 7 0.28
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:29629767 original size:50 final size:48
Alignment explanation
Indices: 29629600--29629782 Score: 226
Period size: 49 Copynumber: 3.8 Consensus size: 48
29629590 TTGAAAATTT
* * * *
29629600 AAAAGGCTCATCTGAGCAGAGGCTCAACAATTTTAAAAT-TC-TCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
* * * *
29629646 AAAAAGCTCCTCTCAGCAAAGGCTTAACAACTTTATGAATCTTATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTA-AAATCTCATCTTG
*
29629695 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTCTCATCTTGG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TCTCATCTT-G
* *
29629745 AAAAGGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA
29629783 ATTTCATATC
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
46 29 0.25
47 3 0.03
48 3 0.03
49 45 0.39
50 36 0.31
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (48 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTCATCTTG
Found at i:29629804 original size:50 final size:49
Alignment explanation
Indices: 29629600--29629805 Score: 217
Period size: 49 Copynumber: 4.2 Consensus size: 49
29629590 TTGAAAATTT
* * * *
29629600 AAAAGGCTCATCTGAGCAGAGGCTCAACAA-TTTTAAAATTC--TCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTG
* * **
29629646 AAAAAGCTCCTCTCAGCAAAGGCTTAACAACTTTATGAA-TCTTATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTC-TATCTTG
*
29629695 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAATTCTCATCTTGG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCT-ATCTT-G
* *
29629745 AAAAGGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAAATTTCATATCTT-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAA-TTC-TATCTTG
*
29629795 TAAAAGCTCCT
1 AAAAAGCTCCT
29629806 TTAAAAAAAA
Statistics
Matches: 132, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
46 27 0.20
47 5 0.04
48 3 0.02
49 43 0.33
50 41 0.31
51 4 0.03
52 8 0.06
53 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (49 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATTCTATCTTG
Found at i:29641366 original size:10 final size:10
Alignment explanation
Indices: 29641351--29641376 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
29641341 TAATGAAATC
29641351 TTAAAATTTA
1 TTAAAATTTA
29641361 TTAAAATTTA
1 TTAAAATTTA
29641371 TTAAAA
1 TTAAAA
29641377 GGATAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:29642056 original size:201 final size:200
Alignment explanation
Indices: 29641819--29642326 Score: 672
Period size: 200 Copynumber: 2.5 Consensus size: 200
29641809 AATTTTGAAA
* * * * * *
29641819 AAAAAAAATTTTATTGTATTG-AAGTTTTTCTATAAATTTTCCAATACGTTAGTAATATTTTAAA
1 AAAAAAATTTTTATTCTATTGAAAATTTTT-TATAAATATT-CAATACATTGGTAATATTTTAAA
*
29641883 AAAAAATCTTCTCACCTAAGGATTTCGTAAAGCATCACTACTCGGAATACTTTTAGAATCCCATC
64 AAAAAATATTCTCACCTAAGGATTTCGTAAAGCATCACTACTCGGAATACTTTTAGAATCCCATC
*
29641948 ATTGGATAAAATTTCTTTTTTCCTTATTTATACTATTTTTAATAAATTAATTAATTTTTATTTAT
129 ATTAGATAAAATTTCTTTTTTCCTTATTTATACTATTTTTAATAAATTAATTAA-TTTTATTTAT
29642013 TATTCTAT
193 TATTCTAT
*** * * *
29642021 -AAATTTTTTTTATTCTATTGAAAACTTTTTATAAATATTACAATACACTGGTAATA-TTAAAAA
1 AAAAAAATTTTTATTCTATTGAAAATTTTTTATAAATATT-CAATACATTGGTAATATTTTAAAA
* * * * *
29642084 AAAAATATTCTCACATAGGGATTTCGTAAAGCATCACTACTCAGAATACTTTTAGAATCTCATTA
65 AAAAATATTCTCACCTAAGGATTTCGTAAAGCATCACTACTCGGAATACTTTTAGAATCCCATCA
29642149 TTAGATAAAATTTCTTTTTTCCTTATTTATACTATTTTTAATAAATTAATTAATTTTATTTATTA
130 TTAGATAAAATTTCTTTTTTCCTTATTTATACTATTTTTAATAAATTAATTAATTTTATTTATTA
29642214 TTCTAT
195 TTCTAT
*
29642220 AAAAAAAAAATTTTTATTCTATTGAAAATTTTTTATAAATACTTCAATACATTGGT-A-GTTTT-
1 ---AAAAAAATTTTTATTCTATTGAAAATTTTTTATAAATA-TTCAATACATTGGTAATATTTTA
* * *
29642282 AAAAAAAATATTCTCACCT-AGAGATTTCAT-AGGTATCACTACTCG
62 AAAAAAAATATTCTCACCTAAG-GATTTCGTAAAGCATCACTACTCG
29642327 AGTACCTTCG
Statistics
Matches: 265, Mismatches: 33, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
199 18 0.07
200 130 0.49
201 62 0.23
202 9 0.03
203 44 0.17
204 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.44
Consensus pattern (200 bp):
AAAAAAATTTTTATTCTATTGAAAATTTTTTATAAATATTCAATACATTGGTAATATTTTAAAAA
AAAATATTCTCACCTAAGGATTTCGTAAAGCATCACTACTCGGAATACTTTTAGAATCCCATCAT
TAGATAAAATTTCTTTTTTCCTTATTTATACTATTTTTAATAAATTAATTAATTTTATTTATTAT
TCTAT
Found at i:29643409 original size:12 final size:12
Alignment explanation
Indices: 29643388--29643428 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
29643378 CCGAATAAGG
*
29643388 AAAAAGAAAGAA
1 AAAAAAAAAGAA
29643400 AAAAAAAAAGAA
1 AAAAAAAAAGAA
* *
29643412 AAAAGAAAGGAA
1 AAAAAAAAAGAA
29643424 AAAAA
1 AAAAA
29643429 TAATAATAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:29650884 original size:34 final size:34
Alignment explanation
Indices: 29650841--29650911 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
29650831 CATGTCAAAG
* *
29650841 ATACAAATGTTGCTAATATAGCAACATTTTTCAT
1 ATACAAATGTCGCTAATATAACAACATTTTTCAT
* **
29650875 ATACAAATGTCGTTAATATAACGGCATTTTTCAT
1 ATACAAATGTCGCTAATATAACAACATTTTTCAT
29650909 ATA
1 ATA
29650912 TTAGTAGCTT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (34 bp):
ATACAAATGTCGCTAATATAACAACATTTTTCAT
Found at i:29652953 original size:26 final size:26
Alignment explanation
Indices: 29652918--29652968 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
29652908 CTTTAATAAT
* * *
29652918 AAAATTATCTCGATAATTGTATTAAC
1 AAAATCATCTCGAAAATTATATTAAC
*
29652944 AAAATCATCTTGAAAATTATATTAA
1 AAAATCATCTCGAAAATTATATTAA
29652969 ATACTGCCTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (26 bp):
AAAATCATCTCGAAAATTATATTAAC
Done.