Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 33
Found at i:3852527 original size:3 final size:3
Alignment explanation
Indices: 3852519--3852550 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
3852509 GATCCAGTTT
3852519 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
3852551 TTCACAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:3854037 original size:26 final size:26
Alignment explanation
Indices: 3853985--3854033 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
3853975 ATATAAACAA
*
3853985 TTATATTGAGTAATATTTTTAGAATG
1 TTATATTGAGTAATATTTTTAAAATG
3854011 TTATATT-A-TAATATTTTTTAAAA
1 TTATATTGAGTAATA-TTTTTAAAA
3854034 ATGTGTGCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 9 0.43
26 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (26 bp):
TTATATTGAGTAATATTTTTAAAATG
Found at i:3854312 original size:11 final size:11
Alignment explanation
Indices: 3854277--3854329 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
3854267 CTCTCAAACG
*
3854277 ATTA-TAAAAT
1 ATTATTAAATT
*
3854287 ATTTTTAAATT
1 ATTATTAAATT
3854298 -TTATTAAATT
1 ATTATTAAATT
* *
3854308 ATTATAAAATA
1 ATTATTAAATT
3854319 ATTATTAAATT
1 ATTATTAAATT
3854330 TATCAAACTT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 12 0.35
11 22 0.65
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:3854332 original size:31 final size:32
Alignment explanation
Indices: 3854206--3854338 Score: 100
Period size: 31 Copynumber: 4.3 Consensus size: 32
3854196 ATATATCTAA
* * *
3854206 TTATTAAATTATAATAAAAAAATTCATTAAAACT
1 TTATTAAACTATTATAAAATAATT-ATT-AAACT
3854240 TTA--AAACT-TT-TAAAATAATTATTAAAC-
1 TTATTAAACTATTATAAAATAATTATTAAACT
* * * * * *
3854267 CTCTCAAACGATTATAAAAT-ATTTTTAAATT
1 TTATTAAACTATTATAAAATAATTATTAAACT
*
3854298 TTATTAAATTATTATAAAATAATTATTAAA-T
1 TTATTAAACTATTATAAAATAATTATTAAACT
*
3854329 TTATCAAACT
1 TTATTAAACT
3854339 TTGTACAATG
Statistics
Matches: 77, Mismatches: 16, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.01
28 4 0.05
29 7 0.09
30 19 0.25
31 31 0.40
32 12 0.16
34 3 0.04
ACGTcount: A:0.50, C:0.08, G:0.01, T:0.42
Consensus pattern (32 bp):
TTATTAAACTATTATAAAATAATTATTAAACT
Found at i:3878925 original size:29 final size:28
Alignment explanation
Indices: 3878893--3878948 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
3878883 TAATTTACTA
3878893 TTGGACAGTTGCTGTTTTTCCTTCTTTTT
1 TTGGACAGTTGCTGTTTTTCCTT-TTTTT
*
3878922 TTGGACAGTTGTTGTTTTTCCTTTTTT
1 TTGGACAGTTGCTGTTTTTCCTTTTTT
3878949 ATTATGGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 4 0.15
29 22 0.85
ACGTcount: A:0.07, C:0.14, G:0.18, T:0.61
Consensus pattern (28 bp):
TTGGACAGTTGCTGTTTTTCCTTTTTTT
Found at i:3879168 original size:18 final size:17
Alignment explanation
Indices: 3879143--3879200 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
3879133 TTACAAATTA
3879143 TAATTATAATTTTTATT
1 TAATTATAATTTTTATT
*
3879160 TAGATTATAAACTTTTGATT
1 TA-ATTAT-AA-TTTTTATT
3879180 TAATTA-AATTATATTATT
1 TAATTATAATT-T-TTATT
3879198 TAA
1 TAA
3879201 CTTTTATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 2 0.06
17 5 0.15
18 12 0.35
19 6 0.18
20 9 0.26
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (17 bp):
TAATTATAATTTTTATT
Found at i:3879185 original size:19 final size:17
Alignment explanation
Indices: 3879143--3879189 Score: 51
Period size: 20 Copynumber: 2.6 Consensus size: 17
3879133 TTACAAATTA
*
3879143 TAATTATAATTTTTATT
1 TAATTATAATTTTGATT
3879160 TAGATTATAAACTTTTGATT
1 TA-ATTAT-AA-TTTTGATT
3879180 TAATTA-AATT
1 TAATTATAATT
3879190 ATATTATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 2 0.08
17 4 0.15
18 5 0.19
19 6 0.23
20 9 0.35
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (17 bp):
TAATTATAATTTTGATT
Found at i:3879841 original size:50 final size:50
Alignment explanation
Indices: 3879781--3879897 Score: 180
Period size: 50 Copynumber: 2.3 Consensus size: 50
3879771 AAGAGAGCAG
* *
3879781 CAAAGCTGCTACAAAACACCATCAATAGCAAACAACAAACCACCAATCAA
1 CAAAGTTGCTACAAAACACCATCAACAGCAAACAACAAACCACCAATCAA
* * * *
3879831 CAAAGTTGCTACAAAATACCCTCAACATCAAACATCAAACCACCAATCAA
1 CAAAGTTGCTACAAAACACCATCAACAGCAAACAACAAACCACCAATCAA
3879881 CAAAGTTGCTACAAAAC
1 CAAAGTTGCTACAAAAC
3879898 CACTCCAACC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 60 1.00
ACGTcount: A:0.50, C:0.31, G:0.06, T:0.14
Consensus pattern (50 bp):
CAAAGTTGCTACAAAACACCATCAACAGCAAACAACAAACCACCAATCAA
Found at i:3884633 original size:23 final size:23
Alignment explanation
Indices: 3884598--3884647 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
3884588 AAAGACAGAA
*
3884598 AAACGTGTCACAAAGGCAGAGAT
1 AAACGTGTCACAAAGGCAAAGAT
3884621 AAACGTG-CTACAAAGGCAAAGAT
1 AAACGTGTC-ACAAAGGCAAAGAT
3884644 AAAC
1 AAAC
3884648 ATATCATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (23 bp):
AAACGTGTCACAAAGGCAAAGAT
Found at i:3888349 original size:6 final size:6
Alignment explanation
Indices: 3888331--3888384 Score: 63
Period size: 6 Copynumber: 8.5 Consensus size: 6
3888321 TTGATTGCGA
* *
3888331 AAATTT GAAATTT AAATTT AAATTT AAAATTT AAAATTA AAATTA AAATTT
1 AAATTT -AAATTT AAATTT AAATTT -AAATTT -AAATTT AAATTT AAATTT
3888382 AAA
1 AAA
3888385 ATTCCGATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
6 26 0.59
7 18 0.41
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (6 bp):
AAATTT
Found at i:3888355 original size:19 final size:19
Alignment explanation
Indices: 3888331--3888387 Score: 87
Period size: 19 Copynumber: 3.0 Consensus size: 19
3888321 TTGATTGCGA
* *
3888331 AAATTTGAAATTTAAATTT
1 AAATTTAAAATTTAAAATT
3888350 AAATTTAAAATTTAAAATT
1 AAATTTAAAATTTAAAATT
*
3888369 AAAATTAAAATTTAAAATT
1 AAATTTAAAATTTAAAATT
3888388 CCGATTTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTTAAAATTTAAAATT
Found at i:3888385 original size:13 final size:13
Alignment explanation
Indices: 3888330--3888387 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
3888320 CTTGATTGCG
*
3888330 AAAATTTGAAATT
1 AAAATTTAAAATT
* *
3888343 TAAATTTAAATTT
1 AAAATTTAAAATT
3888356 AAAATTTAAAATT
1 AAAATTTAAAATT
3888369 AAAA-TTAAAATTT
1 AAAATTTAAAA-TT
3888382 AAAATT
1 AAAATT
3888388 CCGATTTGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
12 6 0.16
13 31 0.82
14 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
AAAATTTAAAATT
Found at i:3888651 original size:21 final size:18
Alignment explanation
Indices: 3888625--3888670 Score: 56
Period size: 21 Copynumber: 2.4 Consensus size: 18
3888615 TAAAAATAGT
3888625 AAAATAATGAGAAATAAAATA
1 AAAATAATGA-AAA-AAAA-A
*
3888646 AAAATAATGAAAAACAAA
1 AAAATAATGAAAAAAAAA
3888664 AAAATAA
1 AAAATAA
3888671 AAAAAGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 8 0.33
19 3 0.12
20 3 0.12
21 10 0.42
ACGTcount: A:0.76, C:0.02, G:0.07, T:0.15
Consensus pattern (18 bp):
AAAATAATGAAAAAAAAA
Found at i:3890505 original size:36 final size:35
Alignment explanation
Indices: 3890364--3890627 Score: 217
Period size: 34 Copynumber: 7.5 Consensus size: 35
3890354 AAAATGAAAA
*
3890364 TAAATACTATATAATATATATTTT-AGAAAAATGTTT
1 TAAA-ACTATATATTATATATTTTCA-AAAAATGTTT
*
3890400 TAAAACTATATATAATATA-TTTCAAAAATAT-TTT
1 TAAAACTATATATTATATATTTTCAAAAA-ATGTTT
* **
3890434 CAAAACCGTATATTATATAATTTT--AAAAATGTTT
1 TAAAACTATATATTATAT-ATTTTCAAAAAATGTTT
*
3890468 TAAAACTATATGTTATATAGTTTTCAAAAAATGTTT
1 TAAAACTATATATTATATA-TTTTCAAAAAATGTTT
*
3890504 TAAAA-T-TATATTATATGTTTTC-AAAAATGTTTTT
1 TAAAACTATATATTATATATTTTCAAAAAATG--TTT
* * * *
3890538 TTAAACTATTTATTATATATATTTTCCAAATAT-TTT
1 TAAAACTATATA-T-TATATATTTTCAAAAAATGTTT
* * *
3890574 AAAAACTATATAATATATATTTTCAAAATAT-TTT
1 TAAAACTATATATTATATATTTTCAAAAAATGTTT
*
3890608 AAAAAAAC-ATATATTATATA
1 --TAAAACTATATATTATATA
3890628 CATATTTTTC
Statistics
Matches: 189, Mismatches: 22, Indels: 35
0.77 0.09 0.14
Matches are distributed among these distances:
32 7 0.04
33 8 0.04
34 85 0.45
35 30 0.16
36 43 0.23
37 1 0.01
38 10 0.05
39 5 0.03
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (35 bp):
TAAAACTATATATTATATATTTTCAAAAAATGTTT
Found at i:3890620 original size:35 final size:34
Alignment explanation
Indices: 3890364--3890706 Score: 189
Period size: 34 Copynumber: 9.6 Consensus size: 34
3890354 AAAATGAAAA
* *
3890364 TAAATACTATATAATATATATTTT-AGAAAAATGTT
1 TAAAAACTATATAATATATATTTTCA-AAATAT-TT
*
3890399 TTAAAACTATAT-ATA-ATATATTTCAAAAATATTT
1 TAAAAACTATATAATATATAT-TTTC-AAAATATTT
* * * *
3890433 TCAAAACCGTATATTATATA-ATTTTAAAAATGTTT
1 T-AAAAAC-TATATAATATATATTTTCAAAATATTT
** *
3890468 T-AAAACTATATGTTATATAGTTTTCAAAAAATGTT
1 TAAAAACTATATAATATATA-TTTTCAAAATAT-TT
* * * *
3890503 TTAAAA-T-TATATTATATGTTTTCAAAAATGTTTT
1 TAAAAACTATATAATATATATTTTC-AAAAT-ATTT
** * *
3890537 TTTAAACTATTTATTATATATATTTTCCAAATATTT
1 TAAAAACTA--TATAATATATATTTTCAAAATATTT
3890573 TAAAAACTATATAATATATATTTTCAAAATATTT
1 TAAAAACTATATAATATATATTTTCAAAATATTT
* ***
3890607 TAAAAAAACATATATTATATACATATTTTTCAAAACGCTT
1 T--AAAAAC-TATA-TA-ATATATA-TTTTCAAAATATTT
* * *
3890647 AAAAAACTATATATTATATAAGTTTTCAAAAT-TAAT
1 TAAAAACTATATAATATAT-A-TTTTCAAAATAT-TT
3890683 TAGAAAACTAATATATATATATAT
1 TA-AAAACT-ATATA-ATATATAT
3890707 ATATATATAT
Statistics
Matches: 240, Mismatches: 40, Indels: 54
0.72 0.12 0.16
Matches are distributed among these distances:
32 9 0.04
33 14 0.06
34 62 0.26
35 38 0.16
36 43 0.18
37 24 0.10
38 28 0.12
39 11 0.05
40 11 0.05
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAAAACTATATAATATATATTTTCAAAATATTT
Found at i:3890690 original size:37 final size:35
Alignment explanation
Indices: 3890540--3890708 Score: 139
Period size: 36 Copynumber: 4.6 Consensus size: 35
3890530 ATGTTTTTTT
* * *
3890540 AAACTATTTATTATATATATTTTCCAAATATTTTAA
1 AAACTATATATTATATATATTTTCAAAATA-TTAAA
3890576 AAACTATATA--ATATATATTTTCAAAATATTTTAAAA
1 AAACTATATATTATATATATTTTCAAAATA--TT-AAA
**
3890612 AAAC-ATATATTATATACATATTTTTCAAAACGCTTAAA
1 AAACTATATATTATAT--ATA-TTTTCAAAA-TATTAAA
*
3890650 AAACTATATATTATATA-AGTTTTCAAAATTAATTAGA
1 AAACTATATATTATATATA-TTTTCAAAA-T-ATTAAA
3890687 AAACTAATATATATATATATAT
1 AAACT-ATATAT-TATATATAT
3890709 ATATATATAT
Statistics
Matches: 110, Mismatches: 10, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
34 17 0.15
35 8 0.07
36 25 0.23
37 14 0.13
38 13 0.12
39 23 0.21
40 10 0.09
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (35 bp):
AAACTATATATTATATATATTTTCAAAATATTAAA
Found at i:3890700 original size:2 final size:2
Alignment explanation
Indices: 3890693--3890721 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3890683 TAGAAAACTA
3890693 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3890722 CGTATATTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3892017 original size:249 final size:248
Alignment explanation
Indices: 3891262--3892021 Score: 901
Period size: 249 Copynumber: 3.1 Consensus size: 248
3891252 ATTTTATTGA
* ** * **
3891262 CAGATAGCCCTTCTTGCCTTGGGCTATGCTGTAAATGATGTGCCCAAGAGCTAAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTAAGCGTAGTCGAA
* * *
3891327 CCCAAAGGTCTTTGTTGG-CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTT
66 CTCAAAGGTCTTT-TGGGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT
*
3891391 AGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAAATAACCCTTCTAGCCTTGAGTTAT
130 AGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAGATAACCCTTCTAGCCTTGAGTTAT
*
3891456 GTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TTTGG
195 GCTGTAAATGATGT-CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGG
* * * * * *
3891510 CAGCTAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTAAGCGTAGTCGAA
* * * *
3891575 CTCAAAGGTCTTTGGTTGGA-AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT
66 CTCAAAGGTCTTT--TGGGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCT
* *
3891639 TAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGAGACAGATAACCCTTCTAGCCTTGAGTTA
129 TAGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAGATAACCCTTCTAGCCTTGAGTTA
* *
3891704 TGCTGTAAATGGTATG-CCCTCGAAGCTGAGTGTAATCGAACTTGGGGGTCTTTT-G
194 TGCTGTAAAT-G-ATGTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGG
* * * *
3891759 CAGATAGCCCTTCTAGCCTTAAGCTATGCTACAAATGATATGCCTTAGAGCTAAGTGTAGTCAAA
1 CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTAAGCGTAGTCGAA
* * * *
3891824 CTCGAAGGTCTTTTGGAGACAGATAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCT
66 CTCAAAGGTCTTTTGG-GACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTT
* * ** * * * *
3891889 CGAAGCTGAGTGTAATCGAACTCGGGGGTC-TTT-G-G-CAGATAGCCCTTCT-CCACTTAAGAT
130 AG-AGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAGATAACCCTTCTAGC-CTTGAGTT
* * * * * * *
3891949 ATGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGG
193 ATGCTGTAAATGATGTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC-TT--TTGG
*
3892008 CAAATAGCCCTTCT
1 CAGATAGCCCTTCT
3892022 TGTCTTGAGC
Statistics
Matches: 438, Mismatches: 60, Indels: 27
0.83 0.11 0.05
Matches are distributed among these distances:
244 3 0.01
245 28 0.06
246 31 0.07
247 3 0.01
248 71 0.16
249 273 0.62
250 26 0.06
251 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.29
Consensus pattern (248 bp):
CAGATAGCCCTTCTAGCCTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTAAGCGTAGTCGAA
CTCAAAGGTCTTTTGGGACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCTTA
GAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGGAGACAGATAACCCTTCTAGCCTTGAGTTATG
CTGTAAATGATGTCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTTGG
Found at i:3892021 original size:165 final size:166
Alignment explanation
Indices: 3891286--3892042 Score: 712
Period size: 165 Copynumber: 4.6 Consensus size: 166
3891276 TGCCTTGGGC
* ** * * *
3891286 TATGCTGTAAATGATGTGCCCAAGAGCTAAGCGTAGTCGAACCCAAAGGTCTTT-GTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* * * * *
3891350 AACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTAG-AGCTGAGTGTAGTCGAACTCG
66 AACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
* * *
3891414 AAGGTCTTTTGGAGACAAATAACCCTTCTAGCCTTGAGT
131 AAGGTCTTTT-G-G-CAGATAACCCTTCTACCCTTAAGT
* * * * * * * *
3891453 TATGTTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGC
1 TATGCTGCAAATGATGTGCCTTAG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGA
* * * * * * * * * *
3891514 TAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTC
65 TAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
* * *
3891578 AAAGGTCTTTGGTTGGAAGATAACCCTTCT-CGACTTAAGT
130 GAAGGTC-TT--TTGGCAGATAACCCTTCTAC-CCTTAAGT
* * * *
3891618 TATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG-AGACAGA
1 TATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGA
* * * *
3891682 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGGTATGCCCTCGAAGCTGAGTGTAATCGAACTT
65 TAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
** * * *
3891747 GGGGGTCTTTT-GCAGATAGCCCTTCTAGCCTTAAGC
130 GAAGGTCTTTTGGCAGATAACCCTTCTACCCTTAAGT
* * * * * * *
3891783 TATGCTACAAATGATATGCCTTAGAGCTAAGTGTAGTCAAACTCGAAGGTCTTTTGG-AGACAGA
1 TATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGA
*
3891847 TAACCCTTCTAGCCTTGAGTTATACTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
65 TAACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
** * *
3891912 GGGGGTC-TTTGGCAGATAGCCCTTCT-CCACTTAAGA
130 GAAGGTCTTTTGGCAGATAACCCTTCTACC-CTTAAGT
* * *
3891948 TATGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAAAT
1 TATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
* * * * *
3892013 AGCCCTTCTTGTCTTGAGCTATATTGCAAA
66 AACCCTTCTAGCCTTGAGTTATACTGCAAA
3892043 AAAAATGGCT
Statistics
Matches: 491, Mismatches: 83, Indels: 34
0.81 0.14 0.06
Matches are distributed among these distances:
164 35 0.07
165 344 0.70
166 6 0.01
167 23 0.05
168 58 0.12
169 25 0.05
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (166 bp):
TATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
AACCCTTCTAGCCTTGAGTTATACTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCG
AAGGTCTTTTGGCAGATAACCCTTCTACCCTTAAGT
Found at i:3898396 original size:49 final size:49
Alignment explanation
Indices: 3898324--3898422 Score: 182
Period size: 49 Copynumber: 2.0 Consensus size: 49
3898314 TGATCTCTGT
3898324 ATGATTCCCTCCCCCTTGTTCGATCTGGGGTGAGTTATTTACTACC-ACC
1 ATGATTCCCTCCCCCTTGTTCGATCTGGGGTGAGTTATTTA-TACCTACC
3898373 ATGATTCCCTCCCCCTTGTTCGATCTGGGGTGAGTTATTTATACCTACC
1 ATGATTCCCTCCCCCTTGTTCGATCTGGGGTGAGTTATTTATACCTACC
3898422 A
1 A
3898423 CCGACGTTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 4 0.08
49 45 0.92
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (49 bp):
ATGATTCCCTCCCCCTTGTTCGATCTGGGGTGAGTTATTTATACCTACC
Found at i:3898847 original size:11 final size:11
Alignment explanation
Indices: 3898840--3898864 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3898830 AACAAAAAAT
3898840 AATGAAAATAA
1 AATGAAAATAA
3898851 AATGAAAATAA
1 AATGAAAATAA
3898862 AAT
1 AAT
3898865 ACTATATAAT
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (11 bp):
AATGAAAATAA
Found at i:3899097 original size:11 final size:11
Alignment explanation
Indices: 3899039--3899097 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
3899029 TTAAAAATAT
*
3899039 AAATATTTTCA
1 AAATATTTTAA
3899050 AAATATTTTAA
1 AAATATTTTAA
*
3899061 AAAT-TATATAA
1 AAATAT-TTTAA
* *
3899072 TATATATTTTCA
1 -AAATATTTTAA
3899084 AAATATTTTAA
1 AAATATTTTAA
3899095 AAA
1 AAA
3899098 ACCATATATT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
10 1 0.03
11 30 0.79
12 6 0.16
13 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:3899097 original size:34 final size:31
Alignment explanation
Indices: 3898867--3899096 Score: 166
Period size: 33 Copynumber: 7.0 Consensus size: 31
3898857 AATAAAATAC
*
3898867 TATATAATATATATTTTAGAAAAATATTTTAAAA
1 TATAT-ATATATATTTT--CAAAATATTTTAAAA
3898901 CTATATATA-ATATATTTCAAAAATATTTTCAAAA
1 -TATATATATATAT-TTTC-AAAATATTTT-AAAA
* * * *
3898935 TCGTATATTATATAATTTTAAAAATGTTTTAAAC
1 T-ATATA-TATAT-ATTTTCAAAATATTTTAAAA
* *
3898969 TATATTTATATAGTTTTCAAAAATGTTTTAAAA
1 TATATATATATA-TTTTC-AAAATATTTTAAAA
* *
3899002 T-TATAT-TATGTTTTCAAAAATGTTTTTTTAAAA
1 TATATATATATATTTTC-AAAA---TATTTTAAAA
3899035 -ATATA-A-ATATTTTCAAAATATTTTAAAAA
1 TATATATATATATTTTCAAAATATTTT-AAAA
3899064 TTATATAATATATATTTTCAAAATATTTTAAAA
1 -TATAT-ATATATATTTTCAAAATATTTTAAAA
3899097 AACCATATAT
Statistics
Matches: 161, Mismatches: 14, Indels: 42
0.74 0.06 0.19
Matches are distributed among these distances:
28 5 0.03
29 4 0.02
30 10 0.06
31 12 0.07
32 21 0.13
33 50 0.31
34 36 0.22
35 16 0.10
36 5 0.03
37 2 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (31 bp):
TATATATATATATTTTCAAAATATTTTAAAA
Found at i:3899105 original size:35 final size:34
Alignment explanation
Indices: 3898859--3899112 Score: 117
Period size: 34 Copynumber: 7.6 Consensus size: 34
3898849 AAAATGAAAA
* *
3898859 TAAAATACTATATAATATATATTTTAGAAAAATATTT
1 TAAAA-ACCATATAATATATATTTT--CAAAATATTT
*
3898896 T-AAAACTATAT-ATA-ATATATTTCAAAAATATTT
1 TAAAAACCATATAATATATAT-TTTC-AAAATATTT
* * * * * *
3898929 TCAAAATCGTATATTATATAATTTTAAAAATGTTT
1 TAAAAACCATATAATATAT-ATTTTCAAAATATTT
* *
3898964 T--AAACTATAT-TTATATAGTTTTCAAAA-ATGTT
1 TAAAAACCATATAATATATA-TTTTCAAAATAT-TT
* * * *
3898996 TTAAAA--TTAT-AT-TATGTTTTCAAAAATGTTTTT
1 TAAAAACCATATAATATATATTTTC-AAAA--TATTT
*
3899029 TTAAAA--ATAT-A-A-ATATTTTCAAAATATTT
1 TAAAAACCATATAATATATATTTTCAAAATATTT
**
3899058 TAAAAATTATATAATATATATTTTCAAAATATTT
1 TAAAAACCATATAATATATATTTTCAAAATATTT
*
3899092 TAAAAAACCATATATTATATA
1 T-AAAAACCATATAATATATA
3899113 CATTTTTTCA
Statistics
Matches: 173, Mismatches: 23, Indels: 44
0.72 0.10 0.18
Matches are distributed among these distances:
29 9 0.05
30 5 0.03
31 17 0.10
32 29 0.17
33 33 0.19
34 35 0.20
35 34 0.20
36 8 0.05
37 3 0.02
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (34 bp):
TAAAAACCATATAATATATATTTTCAAAATATTT
Found at i:3899157 original size:36 final size:38
Alignment explanation
Indices: 3899091--3899161 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
3899081 TCAAAATATT
*
3899091 TTAAAAAACCATATATTATATACATTTTTTCAAAACGC
1 TTAAAAAACCATATATTATATACATGTTTTCAAAACGC
*
3899129 TTAAAAAACTATATATTATATA-A-GTTTTCAAAA
1 TTAAAAAACCATATATTATATACATGTTTTCAAAA
3899162 TTAATTAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 9 0.29
37 1 0.03
38 21 0.68
ACGTcount: A:0.48, C:0.11, G:0.03, T:0.38
Consensus pattern (38 bp):
TTAAAAAACCATATATTATATACATGTTTTCAAAACGC
Found at i:3900259 original size:170 final size:170
Alignment explanation
Indices: 3899977--3900315 Score: 678
Period size: 170 Copynumber: 2.0 Consensus size: 170
3899967 TTGAAGTTTG
3899977 GAACAATTATTGGGGTATATATATACACGGAATCTTATTCTTTTTCACCCATCGAACCTTTTTTT
1 GAACAATTATTGGGGTATATATATACACGGAATCTTATTCTTTTTCACCCATCGAACCTTTTTTT
3900042 GTTCTTCATGACACTTCCATTCTCTCTTCTTTTGACCACATTCCATTGCCTTCTATCATCCTCCT
66 GTTCTTCATGACACTTCCATTCTCTCTTCTTTTGACCACATTCCATTGCCTTCTATCATCCTCCT
3900107 TGTTAAACCAATCAAACCAAGCACATGGAAATGTAGACAT
131 TGTTAAACCAATCAAACCAAGCACATGGAAATGTAGACAT
3900147 GAACAATTATTGGGGTATATATATACACGGAATCTTATTCTTTTTCACCCATCGAACCTTTTTTT
1 GAACAATTATTGGGGTATATATATACACGGAATCTTATTCTTTTTCACCCATCGAACCTTTTTTT
3900212 GTTCTTCATGACACTTCCATTCTCTCTTCTTTTGACCACATTCCATTGCCTTCTATCATCCTCCT
66 GTTCTTCATGACACTTCCATTCTCTCTTCTTTTGACCACATTCCATTGCCTTCTATCATCCTCCT
3900277 TGTTAAACCAATCAAACCAAGCACATGGAAATGTAGACA
131 TGTTAAACCAATCAAACCAAGCACATGGAAATGTAGACA
3900316 AAGTATCATT
Statistics
Matches: 169, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
170 169 1.00
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (170 bp):
GAACAATTATTGGGGTATATATATACACGGAATCTTATTCTTTTTCACCCATCGAACCTTTTTTT
GTTCTTCATGACACTTCCATTCTCTCTTCTTTTGACCACATTCCATTGCCTTCTATCATCCTCCT
TGTTAAACCAATCAAACCAAGCACATGGAAATGTAGACAT
Found at i:3901584 original size:20 final size:20
Alignment explanation
Indices: 3901561--3901608 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3901551 ACAAAACTGA
* *
3901561 TAGTTTATACACTAAACACG
1 TAGTTTACACAATAAACACG
*
3901581 TAGTTTACCCAATAAACACG
1 TAGTTTACACAATAAACACG
3901601 TAGTTTAC
1 TAGTTTAC
3901609 CCAAATAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (20 bp):
TAGTTTACACAATAAACACG
Found at i:3901609 original size:20 final size:20
Alignment explanation
Indices: 3901573--3901612 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3901563 GTTTATACAC
3901573 TAAACACGTAGTTTACCCAA
1 TAAACACGTAGTTTACCCAA
3901593 TAAACACGTAGTTTACCCAA
1 TAAACACGTAGTTTACCCAA
3901613 ATAACTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (20 bp):
TAAACACGTAGTTTACCCAA
Found at i:3903087 original size:2 final size:2
Alignment explanation
Indices: 3903080--3903106 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3903070 GAAAGTTGAA
3903080 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
3903107 ATTCCATCGA
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:3906834 original size:12 final size:12
Alignment explanation
Indices: 3906817--3906847 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
3906807 GGTTTTCACA
3906817 AAAGAATTACTT
1 AAAGAATTACTT
3906829 AAAGAATTACTT
1 AAAGAATTACTT
3906841 AAAGAAT
1 AAAGAAT
3906848 ATCTTGTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.06, G:0.10, T:0.29
Consensus pattern (12 bp):
AAAGAATTACTT
Found at i:3908018 original size:34 final size:34
Alignment explanation
Indices: 3907979--3908059 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
3907969 TTCTTGAGAG
3907979 TTGTTTTCTCCTTTTTATCAAGAGAGAATTGTCA
1 TTGTTTTCTCCTTTTTATCAAGAGAGAATTGTCA
3908013 TTGTTTTCTCCTTTTTATCAAGAGAGAATTGTCA
1 TTGTTTTCTCCTTTTTATCAAGAGAGAATTGTCA
3908047 TTGTTTTCTCCTT
1 TTGTTTTCTCCTT
3908060 GTTAGACTGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.51
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTTATCAAGAGAGAATTGTCA
Found at i:3909754 original size:2 final size:2
Alignment explanation
Indices: 3909747--3909790 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3909737 TTGATTGATG
3909747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3909789 TA
1 TA
3909791 ATTAAGATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3909900 original size:2 final size:2
Alignment explanation
Indices: 3909893--3909923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3909883 TGATTGGTGG
3909893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3909924 ATTAAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3915009 original size:31 final size:32
Alignment explanation
Indices: 3914956--3915030 Score: 107
Period size: 31 Copynumber: 2.3 Consensus size: 32
3914946 GTCCAAGTAT
**
3914956 CCAAAACTTAATAAAAAAACGATAATGTAAGTGA
1 CCAAAACTTAAT--AAAAACGATAACATAAGTGA
3914990 CCAAAACTTAAT-AAAACGATAACATAAGTGA
1 CCAAAACTTAATAAAAACGATAACATAAGTGA
3915021 CCAAAACTTA
1 CCAAAACTTA
3915031 TGTTTCTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
31 27 0.69
34 12 0.31
ACGTcount: A:0.55, C:0.16, G:0.09, T:0.20
Consensus pattern (32 bp):
CCAAAACTTAATAAAAACGATAACATAAGTGA
Found at i:3916767 original size:25 final size:25
Alignment explanation
Indices: 3916739--3916789 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
3916729 AATTCGGTGA
3916739 CCGACCGAATTAATCAAACTAATTC
1 CCGACCGAATTAATCAAACTAATTC
3916764 CCGACCGAATTAATCAAACTAATTC
1 CCGACCGAATTAATCAAACTAATTC
3916789 C
1 C
3916790 GTTCGATCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.39, C:0.29, G:0.08, T:0.24
Consensus pattern (25 bp):
CCGACCGAATTAATCAAACTAATTC
Found at i:3917823 original size:4 final size:4
Alignment explanation
Indices: 3917816--3917844 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
3917806 ACGCACGCAC
3917816 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
3917845 TTAATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:3919834 original size:133 final size:132
Alignment explanation
Indices: 3919568--3919811 Score: 307
Period size: 133 Copynumber: 1.9 Consensus size: 132
3919558 TATCATGAAC
* * *
3919568 AATT-TTGATTCACTTCGCTGCTCTTCAGGGAAAGTTGAATCGAAGTTGATTTGCTTCACTGCTC
1 AATTATTGATTCACCTCACTGCTCTTCAGGGAAAGTTGAATCGAACTTGATTTGCTTCACTGCTC
* ** * * *
3919632 TTCAGGAAGACCAAATTTGAAAGAAGACGAGTCTGTTCCACTACTTTTTAGGGGAGATCACACTT
66 TTCAGGAAGACCAAATCTGAAAGAAGAAAACTCTGTTCCACTA-TTTTTAGAGGAGACCACACTT
3919697 AAA
130 AAA
* * * *
3919700 AATTATTGATTCACCTCACTGCTTTTTAGGG-AAGATTGAATCGAACTTGATTTTCTTCGCTGCT
1 AATTATTGATTCACCTCACTGCTCTTCAGGGAAAG-TTGAATCGAACTTGATTTGCTTCACTGCT
*
3919764 TTTCAGGAAGACCAAATCTGAAA-AAGGAAAACTCTGTTCCACT-TTTTT
65 CTTCAGGAAGACCAAATCTGAAAGAA-GAAAACTCTGTTCCACTATTTTT
3919812 GAGTAACCAG
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
131 5 0.05
132 9 0.09
133 83 0.86
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (132 bp):
AATTATTGATTCACCTCACTGCTCTTCAGGGAAAGTTGAATCGAACTTGATTTGCTTCACTGCTC
TTCAGGAAGACCAAATCTGAAAGAAGAAAACTCTGTTCCACTATTTTTAGAGGAGACCACACTTA
AA
Found at i:3921242 original size:9 final size:8
Alignment explanation
Indices: 3921214--3921276 Score: 51
Period size: 8 Copynumber: 8.0 Consensus size: 8
3921204 TTTCTTATTC
*
3921214 TTTTCATT
1 TTTTCTTT
3921222 TTTTC--T
1 TTTTCTTT
3921228 TTTTCTTT
1 TTTTCTTT
3921236 ATTTTC-TT
1 -TTTTCTTT
*
3921244 CTTTCTTT
1 TTTTCTTT
*
3921252 TTTTATTT
1 TTTTCTTT
*
3921260 TTTACTTTT
1 TTTTC-TTT
3921269 TTTTCTTT
1 TTTTCTTT
3921277 ATTCATTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
6 6 0.14
7 4 0.09
8 22 0.50
9 12 0.27
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTCTTT
Found at i:3921248 original size:16 final size:14
Alignment explanation
Indices: 3921214--3921276 Score: 63
Period size: 15 Copynumber: 4.1 Consensus size: 14
3921204 TTTCTTATTC
*
3921214 TTTTCATTTTTTCT
1 TTTTCTTTTTTTCT
3921228 TTTTCTTTATTTTCT
1 TTTTCTTT-TTTTCT
*
3921243 TCTTTCTTTTTTTATT
1 T-TTTCTTTTTTT-CT
3921259 TTTTACTTTTTTTTCT
1 TTTT-C-TTTTTTTCT
3921275 TT
1 TT
3921277 ATTCATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.17
15 14 0.34
16 13 0.32
17 7 0.17
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTCTTTTTTTCT
Found at i:3923936 original size:246 final size:248
Alignment explanation
Indices: 3923502--3923996 Score: 976
Period size: 246 Copynumber: 2.0 Consensus size: 248
3923492 ATGAGTATAT
3923502 GGGATATTGGATGTTAAGATGAGTTAAAATGGTATAAGTTGATTTGGATAAGTGTAGTTGAGTTT
1 GGGATATTGGATGTTAAGATGAGTTAAAATGGTATAAGTTGATTTGGATAAGTGTAGTTGAGTTT
3923567 AAAGGCTTTAAAGAATAGTAAAGTGAGGAAGTTGGCAAAGTTTTGGAAAATTTTTAGGTTAGATG
66 AAAGGCTTTAAAGAATAGTAAAGTGAGGAAGTTGGCAAAGTTTTGGAAAATTTTTAGGTTAGATG
3923632 AATAAGTTCTGGGCAAGGGGTATCGGTATTGGATGAACAGTGCTGATACTCCAAAGTAAATATAG
131 AATAAGTTCTGGGCAAGGGGTATCGGTATTGGATGAACAGTGCTGATACTCCAAAGTAAATATAG
3923697 ATGATAATTGGGTCTGGGTATCGATACTAGATGAAC-ATA-TGATACCATAAG
196 ATGATAATTGGGTCTGGGTATCGATACTAGATGAACAATATTGATACCATAAG
3923748 GGGATATTGGATGTTAAGATGAGTTAAAATGGTATAAGTTGATTTGGATAAGTGTAGTTGAGTTT
1 GGGATATTGGATGTTAAGATGAGTTAAAATGGTATAAGTTGATTTGGATAAGTGTAGTTGAGTTT
3923813 AAAGGCTTTAAAGAATAGTAAAGTGAGGAAGTTGGCAAAGTTTTGGAAAATTTTTAGGTTAGATG
66 AAAGGCTTTAAAGAATAGTAAAGTGAGGAAGTTGGCAAAGTTTTGGAAAATTTTTAGGTTAGATG
3923878 AATAAGTTCTGGGCAAGGGGTATCGGTATTGGATGAACAGTGCTGATACTCCAAAGTAAATATAG
131 AATAAGTTCTGGGCAAGGGGTATCGGTATTGGATGAACAGTGCTGATACTCCAAAGTAAATATAG
3923943 ATGATAATTGGGTCTGGGTATCGATACTAGATGAACAATATTGATACCATAAG
196 ATGATAATTGGGTCTGGGTATCGATACTAGATGAACAATATTGATACCATAAG
3923996 G
1 G
3923997 TAAAAGTGAA
Statistics
Matches: 247, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
246 231 0.94
247 3 0.01
248 13 0.05
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.31
Consensus pattern (248 bp):
GGGATATTGGATGTTAAGATGAGTTAAAATGGTATAAGTTGATTTGGATAAGTGTAGTTGAGTTT
AAAGGCTTTAAAGAATAGTAAAGTGAGGAAGTTGGCAAAGTTTTGGAAAATTTTTAGGTTAGATG
AATAAGTTCTGGGCAAGGGGTATCGGTATTGGATGAACAGTGCTGATACTCCAAAGTAAATATAG
ATGATAATTGGGTCTGGGTATCGATACTAGATGAACAATATTGATACCATAAG
Found at i:3924584 original size:14 final size:15
Alignment explanation
Indices: 3924559--3924588 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
3924549 CATTGCGGTA
3924559 TGATATTGATCTATG
1 TGATATTGATCTATG
3924574 TGATA-TGATCTATG
1 TGATATTGATCTATG
3924588 T
1 T
3924589 AAGTATGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
TGATATTGATCTATG
Found at i:3924998 original size:15 final size:15
Alignment explanation
Indices: 3924973--3925023 Score: 77
Period size: 15 Copynumber: 3.5 Consensus size: 15
3924963 CCATATAAGA
3924973 ATGTG-TCATGAGCT
1 ATGTGATCATGAGCT
3924987 ATGTGATCATGAGCT
1 ATGTGATCATGAGCT
* *
3925002 ATGTGATAATAAGCT
1 ATGTGATCATGAGCT
3925017 ATGTGAT
1 ATGTGAT
3925024 TTCATGCCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
14 5 0.15
15 29 0.85
ACGTcount: A:0.29, C:0.10, G:0.25, T:0.35
Consensus pattern (15 bp):
ATGTGATCATGAGCT
Found at i:3925017 original size:30 final size:28
Alignment explanation
Indices: 3924983--3925057 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 28
3924973 ATGTGTCATG
*
3924983 AGCTATGTGATCATGAGCTATGTGATAATA
1 AGCTATGTGATCATG-CCTATGTGAT-ATA
3925013 AGCTATGTGATTTCATGCCTATGTGATATA
1 AGCTATGTGA--TCATGCCTATGTGATATA
*
3925043 AG-TCATGTGAACATG
1 AGCT-ATGTGATCATG
3925058 TGAAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
28 4 0.10
29 1 0.03
30 21 0.52
31 9 0.22
32 5 0.12
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (28 bp):
AGCTATGTGATCATGCCTATGTGATATA
Found at i:3925161 original size:23 final size:23
Alignment explanation
Indices: 3925135--3925230 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
3925125 AAGTCGAGGG
*
3925135 TTCTATGCGGTCCTTCAGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
* * *
3925158 TTCTACGTGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCGGGACAA
* *
3925181 TTCTACGCGGTCCTTCGGGA-TA
1 TTCTATGCGGTCCTTCGGGACAA
* *
3925203 -TCTATGTGGTCATTCGGGAC-A
1 TTCTATGCGGTCCTTCGGGACAA
3925224 TTCTATG
1 TTCTATG
3925231 TGGTATTTCG
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
21 17 0.28
22 6 0.10
23 38 0.62
ACGTcount: A:0.17, C:0.24, G:0.25, T:0.34
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGACAA
Found at i:3925223 original size:44 final size:46
Alignment explanation
Indices: 3925135--3925225 Score: 123
Period size: 44 Copynumber: 2.0 Consensus size: 46
3925125 AAGTCGAGGG
* *
3925135 TTCTATGCGGTCCTTCAGGACAATTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCAGGACAATTCTACGTGGTCATTCGGGACAT
* * *
3925181 TTCTACGCGGTCCTTCGGGA-TA-TCTATGTGGTCATTCGGGACAT
1 TTCTACGCGGTCCTTCAGGACAATTCTACGTGGTCATTCGGGACAT
3925225 T
1 T
3925226 CTATGTGGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 21 0.52
45 1 0.03
46 18 0.45
ACGTcount: A:0.16, C:0.24, G:0.25, T:0.34
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCAGGACAATTCTACGTGGTCATTCGGGACAT
Found at i:3925240 original size:22 final size:22
Alignment explanation
Indices: 3925147--3925241 Score: 77
Period size: 23 Copynumber: 4.3 Consensus size: 22
3925137 CTATGCGGTC
* *
3925147 CTTCAGGACAATTCTACGTGGTC
1 CTTCGGGAC-ATTCTACGTGGTA
* *
3925170 CTTCGGGACATTTCTACGCGGTC
1 CTTCGGGACA-TTCTACGTGGTA
* *
3925193 CTTCGGGATA-TCTATGTGGT-
1 CTTCGGGACATTCTACGTGGTA
*
3925213 CATTCGGGACATTCTATGTGGTA
1 C-TTCGGGACATTCTACGTGGTA
*
3925236 TTTCGG
1 CTTCGG
3925242 TGTAATTTCT
Statistics
Matches: 61, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 16 0.26
22 16 0.26
23 28 0.46
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (22 bp):
CTTCGGGACATTCTACGTGGTA
Found at i:3925264 original size:67 final size:67
Alignment explanation
Indices: 3925136--3925265 Score: 147
Period size: 67 Copynumber: 1.9 Consensus size: 67
3925126 AGTCGAGGGT
* * * *
3925136 TCTATGCGGTCCTTCAGGACAATTCTACGTGGTCCTTCGGGACATTTCTACGCGGTCCTTCGGGA
1 TCTATGCGGTCATTCAGGACAATTCTACGTGGTACTTCGGGACATTTCTACGCGATACTTCGGGA
3925201 TA
66 TA
* * * * *
3925203 TCTATGTGGTCATTCGGGAC-ATTCTATGTGGTATTTCGGTGTA-ATTTCTATGCGATACTTCGG
1 TCTATGCGGTCATTCAGGACAATTCTACGTGGTACTTCGG-G-ACATTTCTACGCGATACTTCGG
3925266 TGCATTTTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
66 16 0.31
67 35 0.67
68 1 0.02
ACGTcount: A:0.17, C:0.22, G:0.25, T:0.36
Consensus pattern (67 bp):
TCTATGCGGTCATTCAGGACAATTCTACGTGGTACTTCGGGACATTTCTACGCGATACTTCGGGA
TA
Found at i:3935790 original size:18 final size:18
Alignment explanation
Indices: 3935767--3935812 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
3935757 ATAAAAGTAC
3935767 AAATAAAATGTAGAAA-GT
1 AAATAAAATGT-GAAATGT
3935785 AAATAAAACT-TGAAATGT
1 AAATAAAA-TGTGAAATGT
3935803 AAATAAAATG
1 AAATAAAATG
3935813 CAAATGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.20
18 19 0.76
19 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (18 bp):
AAATAAAATGTGAAATGT
Found at i:3935817 original size:17 final size:16
Alignment explanation
Indices: 3935767--3935818 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 16
3935757 ATAAAAGTAC
*
3935767 AAATAAAATGTAGAAAGT
1 AAATAAAATG-A-AATGT
3935785 AAATAAAACTTGAAATGT
1 AAATAAAA--TGAAATGT
3935803 AAATAAAATGCAAATG
1 AAATAAAATG-AAATG
3935819 CATGTCGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
16 2 0.07
17 5 0.17
18 20 0.67
19 1 0.03
20 2 0.07
ACGTcount: A:0.60, C:0.04, G:0.13, T:0.23
Consensus pattern (16 bp):
AAATAAAATGAAATGT
Found at i:3939985 original size:26 final size:26
Alignment explanation
Indices: 3939956--3940010 Score: 94
Period size: 26 Copynumber: 2.1 Consensus size: 26
3939946 ATACCCTAAT
3939956 TCATT-TAGCTTCAAAATCATCCCAAA
1 TCATTCTA-CTTCAAAATCATCCCAAA
3939982 TCATTCTACTTCAAAATCATCCCAAA
1 TCATTCTACTTCAAAATCATCCCAAA
3940008 TCA
1 TCA
3940011 AATCTTAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (26 bp):
TCATTCTACTTCAAAATCATCCCAAA
Found at i:3941498 original size:30 final size:31
Alignment explanation
Indices: 3941438--3941500 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 31
3941428 TCCACCTAAA
3941438 TACATCATTGATGCATGGCTGTGCGTAATTGT
1 TACATCATTGATGCATGGCTGT-CGTAATTGT
3941470 TACATCATTGATGCATGGCTGT-GTAATTGT
1 TACATCATTGATGCATGGCTGTCGTAATTGT
3941500 T
1 T
3941501 TATTATCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 9 0.29
32 22 0.71
ACGTcount: A:0.22, C:0.14, G:0.24, T:0.40
Consensus pattern (31 bp):
TACATCATTGATGCATGGCTGTCGTAATTGT
Found at i:3948874 original size:3 final size:3
Alignment explanation
Indices: 3948866--3948903 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3948856 AACTTTGAAC
3948866 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3948904 CCTTTATCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:3949066 original size:15 final size:15
Alignment explanation
Indices: 3949026--3949066 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
3949016 GTGAGTGATC
3949026 AAAATATTTTATATAA
1 AAAATATTTTA-ATAA
3949042 AAAATA--TTAATAA
1 AAAATATTTTAATAA
3949055 AAAATATTTTAA
1 AAAATATTTTAA
3949067 AAATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 4 0.17
16 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATTTTAATAA
Found at i:3949079 original size:13 final size:13
Alignment explanation
Indices: 3949034--3949079 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
3949024 TCAAAATATT
3949034 TTATATAAAAAATA
1 TTAT-TAAAAAATA
*
3949048 TTAATAAAAAATA
1 TTATTAAAAAATA
*
3949061 TT-TTAAAAATTA
1 TTATTAAAAAATA
3949073 TTATTAA
1 TTATTAA
3949080 TGAAGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 10 0.36
13 15 0.54
14 3 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTATTAAAAAATA
Found at i:3951702 original size:24 final size:23
Alignment explanation
Indices: 3951672--3951734 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
3951662 TGTTCGATAA
3951672 TATGTTCGTTAATGTTCATTCATT
1 TATGTTCGTTAAT-TTCATTCATT
* *
3951696 TATGTTCGTTTACTTTCATTCGTT
1 TATGTTCG-TTAATTTCATTCATT
*
3951720 TATGTTCGTTCATTT
1 TATGTTCGTTAATTT
3951735 ATGTTTAGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.15
24 25 0.74
25 4 0.12
ACGTcount: A:0.16, C:0.14, G:0.13, T:0.57
Consensus pattern (23 bp):
TATGTTCGTTAATTTCATTCATT
Found at i:3952086 original size:23 final size:20
Alignment explanation
Indices: 3952060--3952107 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 20
3952050 AATAAATTCT
*
3952060 TTTATGTTCGTTTGATTTGTTCA
1 TTTATGTTAGTTT-A-TT-TTCA
*
3952083 TTTACGTTAGTTTATTTTCA
1 TTTATGTTAGTTTATTTTCA
3952103 TTTAT
1 TTTAT
3952108 TGTGCTCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.36
21 2 0.09
22 1 0.05
23 11 0.50
ACGTcount: A:0.17, C:0.08, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTATGTTAGTTTATTTTCA
Found at i:3952149 original size:24 final size:25
Alignment explanation
Indices: 3952121--3952168 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3952111 GCTCTTTTGT
3952121 GTTCGTTTATGTTCATTTA-CATTC
1 GTTCGTTTATGTTCATTTATCATTC
* *
3952145 GTTCGTTTGTGTTCGTTTATCATT
1 GTTCGTTTATGTTCATTTATCATT
3952169 TAAATAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.56
Consensus pattern (25 bp):
GTTCGTTTATGTTCATTTATCATTC
Found at i:3953470 original size:57 final size:57
Alignment explanation
Indices: 3953406--3953520 Score: 203
Period size: 57 Copynumber: 2.0 Consensus size: 57
3953396 CATATTTGTG
* *
3953406 AGTAAATTGAAATATATCCTTTTTGCATATCTCAGATTGCGACCTCCTTCATAAACA
1 AGTAAATTGAAATATATCATTTATGCATATCTCAGATTGCGACCTCCTTCATAAACA
*
3953463 AGTAAATTGAAATATATCATTTATGCATATCTCAGATTGCGACCTCCTTTATAAACA
1 AGTAAATTGAAATATATCATTTATGCATATCTCAGATTGCGACCTCCTTCATAAACA
3953520 A
1 A
3953521 AAACCACTGG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 55 1.00
ACGTcount: A:0.36, C:0.19, G:0.10, T:0.35
Consensus pattern (57 bp):
AGTAAATTGAAATATATCATTTATGCATATCTCAGATTGCGACCTCCTTCATAAACA
Found at i:3956416 original size:21 final size:21
Alignment explanation
Indices: 3956385--3956562 Score: 193
Period size: 21 Copynumber: 8.5 Consensus size: 21
3956375 GTTTCCAGAT
* *
3956385 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
3956406 TCGCATTGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
3956427 TCGCAATGCAAACTTAGACTA
1 TCGCAATGCGAACTTGGACTA
*
3956448 TCGCAATGCAAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* * * *
3956469 TCGCAATGTG-AGTATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
3956489 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
3956510 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
3956531 TCGCAATGCGAA-TCTGGACTA
1 TCGCAATGCGAACT-TGGACTA
3956552 TCGCAATGCGA
1 TCGCAATGCGA
3956563 TAGTCGACTA
Statistics
Matches: 132, Mismatches: 19, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
20 16 0.12
21 115 0.87
22 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:3956441 original size:42 final size:41
Alignment explanation
Indices: 3956385--3956583 Score: 163
Period size: 42 Copynumber: 4.8 Consensus size: 41
3956375 GTTTCCAGAT
* * *
3956385 TCGCAACGCGAACTTCGACTATCGCATTGCGAACTTGGACTA
1 TCGCAATGCAAACTTCGACTATCGCAATGCGAA-TTGGACTA
* *
3956427 TCGCAATGCAAACTTAGACTATCGCAATGCAAACTTGGACTA
1 TCGCAATGCAAACTTCGACTATCGCAATGCGAA-TTGGACTA
** * * * *
3956469 TCGCAATG-TGAGTAT-GTA-AATCGCAATGCGATAGTCGACTA
1 TCGCAATGCAAACT-TCG-ACTATCGCAATGCGA-ATTGGACTA
* *
3956510 TCGCAATGCGAACTTGGACTATCGCAATGCGAATCTGGACTA
1 TCGCAATGCAAACTTCGACTATCGCAATGCGAAT-TGGACTA
* * *
3956552 TCGCAATGCGATA-GTCGACTATCGCATTGCGA
1 TCGCAATGC-AAACTTCGACTATCGCAATGCGA
3956584 TTTACATATT
Statistics
Matches: 126, Mismatches: 23, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
41 31 0.25
42 94 0.75
43 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.25
Consensus pattern (41 bp):
TCGCAATGCAAACTTCGACTATCGCAATGCGAATTGGACTA
Found at i:3956515 original size:62 final size:63
Alignment explanation
Indices: 3956385--3956577 Score: 221
Period size: 63 Copynumber: 3.1 Consensus size: 63
3956375 GTTTCCAGAT
* * * * * * * *
3956385 TCGCAACGCGAACTTCGACTATCGCATTGCGAACT-TGGACTATCGCAATGC-AAACTTAGACTA
1 TCGCAATGCAAACTTGGACTATCGCAATGCGAA-TATGGACAATCGCAATGCGATA-GTCGACTA
* * *
3956448 TCGCAATGCAAACTTGGACTATCGCAATGTGAGTATGTA-AATCGCAATGCGATAGTCGACTA
1 TCGCAATGCAAACTTGGACTATCGCAATGCGAATATGGACAATCGCAATGCGATAGTCGACTA
* * *
3956510 TCGCAATGCGAACTTGGACTATCGCAATGCGAATCTGGACTATCGCAATGCGATAGTCGACTA
1 TCGCAATGCAAACTTGGACTATCGCAATGCGAATATGGACAATCGCAATGCGATAGTCGACTA
3956573 TCGCA
1 TCGCA
3956578 TTGCGATTTA
Statistics
Matches: 110, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
62 51 0.46
63 59 0.54
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (63 bp):
TCGCAATGCAAACTTGGACTATCGCAATGCGAATATGGACAATCGCAATGCGATAGTCGACTA
Found at i:3956571 original size:21 final size:21
Alignment explanation
Indices: 3956488--3956818 Score: 158
Period size: 21 Copynumber: 15.9 Consensus size: 21
3956478 GAGTATGTAA
*
3956488 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* * *
3956509 ATCGCAATGCGA-ACTTGGACT
1 ATCGCATTGCGATA-GTCGACT
*
3956530 ATCGCAATGCGA-A-TCTGGACT
1 ATCGCATTGCGATAGTC--GACT
*
3956551 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
*
3956572 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
3956591 ATTCGCATTGCGATAGTCCAGGT
1 A-TCGCATTGCGATAGTCGA-CT
* * *
3956614 -TCGTATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGT-CGACT
*
3956635 -TCGCATTGCGATAGTAGACT
1 ATCGCATTGCGATAGTCGACT
*
3956655 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
3956674 ATTCGCATTGCGATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
*
3956697 -TCGCATTGTGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
*
3956717 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
3956736 ATTCGCATTGCGATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
* * *
3956759 -TTGCATTGCGATAGTCTAAGT
1 ATCGCATTGCGATAGTC-GACT
* * *
3956780 -TTGCATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGT-CGACT
*
3956801 -TCGCAATGCGATAGTCGA
1 ATCGCATTGCGATAGTCGA
3956819 AGTTCGCGTT
Statistics
Matches: 255, Mismatches: 27, Indels: 57
0.75 0.08 0.17
Matches are distributed among these distances:
18 6 0.02
19 10 0.04
20 45 0.18
21 179 0.70
22 7 0.03
23 6 0.02
24 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:3956774 original size:62 final size:62
Alignment explanation
Indices: 3956613--3956832 Score: 291
Period size: 62 Copynumber: 3.5 Consensus size: 62
3956603 ATAGTCCAGG
* *
3956613 TTCGTATTGCGATAGTCCAAGTTCGCATTGCGATAGTAGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
*
3956675 TTCGCATTGCGATAGTCCAAGTTCGCATTGTGATAGTCGACTATCGCATTGCGATTTACATA
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
* * * * * *
3956737 TTCGCATTGCGATAGTCCAAGTTTGCATTGCGATAGTCTAAGT-TTGCATTGCGATAGTCCA-A
1 TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTC-GACTATCGCATTGCGAT-TTACATA
* * *
3956799 GTTCGCAATGCGATAGTCGAAGTTCGCGTTGCGA
1 -TTCGCATTGCGATAGTCCAAGTTCGCATTGCGA
3956833 ATCTAGAAAC
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
62 107 0.76
63 34 0.24
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (62 bp):
TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATA
Found at i:3956805 original size:83 final size:83
Alignment explanation
Indices: 3956552--3956815 Score: 313
Period size: 83 Copynumber: 3.2 Consensus size: 83
3956542 ATCTGGACTA
* * *
3956552 TCGCAATGCGATAGT-CGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAGGTTC
1 TCGCATTGCGATAGTAC-ACTATCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTC
*
3956616 GTATTGCGATAGTCCAAGT
65 GCATTGCGATAGTCCAAGT
* *
3956635 TCGCATTGCGATAGTAGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCG
1 TCGCATTGCGATAGTACACTATCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTCG
* * *
3956700 CATTGTGATAGT-CGACT
66 CATTGCGATAGTCCAAGT
* * * *
3956717 ATCGCATTGCGAT-TTACA-TATTCGCATTGCGATAGTCCA-AGTTTGCATTGCGATAGTCTAAG
1 -TCGCATTGCGATAGTACACTA-TCGCATTGCGAT-GTACATA-TTCGCATTGCGATAGTCCAAG
*
3956779 TTTGCATTGCGATAGTCCAAGT
62 TTCGCATTGCGATAGTCCAAGT
*
3956801 TCGCAATGCGATAGT
1 TCGCATTGCGATAGT
3956816 CGAAGTTCGC
Statistics
Matches: 155, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
81 2 0.01
82 19 0.12
83 130 0.84
84 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (83 bp):
TCGCATTGCGATAGTACACTATCGCATTGCGATGTACATATTCGCATTGCGATAGTCCAAGTTCG
CATTGCGATAGTCCAAGT
Found at i:3956821 original size:21 final size:21
Alignment explanation
Indices: 3956592--3956832 Score: 244
Period size: 21 Copynumber: 11.6 Consensus size: 21
3956582 GATTTACATA
*
3956592 TTCGCATTGCGATAGTCCAGG
1 TTCGCATTGCGATAGTCCAAG
*
3956613 TTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
3956634 TTCGCATTGCGATAGT--AGAC
1 TTCGCATTGCGATAGTCCA-AG
* *
3956654 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
3956675 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
3956696 TTCGCATTGTGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
3956716 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
3956737 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
3956758 TTTGCATTGCGATAGTCTAAG
1 TTCGCATTGCGATAGTCCAAG
*
3956779 TTTGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
3956800 TTCGCAATGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
3956821 TTCGCGTTGCGA
1 TTCGCATTGCGA
3956833 ATCTAGAAAC
Statistics
Matches: 185, Mismatches: 24, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.01
20 33 0.18
21 148 0.80
22 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:3958444 original size:2 final size:2
Alignment explanation
Indices: 3958437--3958466 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3958427 AATATGCTTC
3958437 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
3958467 CAAAGTGATT
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:3966580 original size:5 final size:5
Alignment explanation
Indices: 3966570--3966595 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3966560 ATTCATATAT
3966570 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
3966596 GAAACTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:3967470 original size:17 final size:18
Alignment explanation
Indices: 3967444--3967490 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3967434 TATGGAATTG
* *
3967444 GATTTCAATTCC-TGACA
1 GATTCCAATTCCTTCACA
*
3967461 GATTCTAATTCCTTCACA
1 GATTCCAATTCCTTCACA
3967479 GATTCCAATTCC
1 GATTCCAATTCC
3967491 CTCAGAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:3968084 original size:16 final size:16
Alignment explanation
Indices: 3968063--3968099 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3968053 AGTGAGGCAT
* *
3968063 ACTTAACTATAAGCAA
1 ACTTAACCATAAACAA
3968079 ACTTAACCATAAACAA
1 ACTTAACCATAAACAA
3968095 ACTTA
1 ACTTA
3968100 TAAACATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (16 bp):
ACTTAACCATAAACAA
Found at i:3968324 original size:55 final size:55
Alignment explanation
Indices: 3968235--3968690 Score: 559
Period size: 55 Copynumber: 8.3 Consensus size: 55
3968225 ATTAAGATGC
* *
3968235 ACACGTAGTGCCTGTACGG-TAGTTCATCATCTCATGATGAATTCTGTGGTTTTGA
1 ACACTTAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCTGTGGTTTTGA
* * ***
3968290 ACATTTAGTGCCTGTACGGTTATTCATCAACTCATCATGAATTCCACGGTTTT-A
1 ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGA
* ** *
3968344 CACACTTAATGTATGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGTTTTGC
1 -ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGTTTTGA
* *
3968400 ACACTTAGTGCCTGTACGGTAATTCATCAACTCATGATGAATT-TCGTGGTTTTGC
1 ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGTTTTGA
* **
3968455 ACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTT-A
1 ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGA
*
3968509 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTAC-GTGGTTTT-A
1 -ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-CTGTGGTTTTGA
* * *
3968564 CACACTTAGTGCCTATACAGTTATTCATCAACTCATGATGAATT-TCGTGGTTTTGC
1 -ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGTTTTGA
* * * * *
3968620 AGACTTAGTGTCTGTACGGTCATTCATCAACTCATGATGAATTCCGTGGTTTTGC
1 ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGA
3968675 ACACTTAGTGCCTGTA
1 ACACTTAGTGCCTGTA
3968691 GTACACATAG
Statistics
Matches: 352, Mismatches: 38, Indels: 22
0.85 0.09 0.05
Matches are distributed among these distances:
54 1 0.00
55 348 0.99
56 3 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (55 bp):
ACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGTTTTGA
Found at i:3968427 original size:110 final size:110
Alignment explanation
Indices: 3968234--3968690 Score: 648
Period size: 110 Copynumber: 4.2 Consensus size: 110
3968224 TATTAAGATG
* * * * *
3968234 CACACGTAGTGCCTGTACGG-TAGTTCATCATCTCATGATGAA-TTCTGTGGTTTTGAACATTTA
1 CACACTTAGTGCATGTACGGTTA-TTCATCAACTCATGATGAATTTC-GTGGTTTTGCACACTTA
* **
3968297 GTGCCTGTACGGTTATTCATCAACTCATCATGAATTCCACGGTTTTA
64 GTGCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTA
* *
3968344 CACACTTAATGTATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTAGT
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTAGT
* * *
3968409 GCCTGTACGGTAATTCATCAACTCATGATGAATTTCGTGGTTTTG
66 GCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTA
* * *
3968454 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTTACACACTTAGT
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTAGT
* *
3968519 GCATGTACGGTTATTCATCAACTCATGATGAATTACGTGGTTTTA
66 GCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTA
* * * *
3968564 CACACTTAGTGCCTATACAGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCAGACTTAGT
1 CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTAGT
* * *
3968629 GTCTGTACGGTCATTCATCAACTCATGATGAATTCCGTGGTTTTG
66 GCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTA
*
3968674 CACACTTAGTGCCTGTA
1 CACACTTAGTGCATGTA
3968691 GTACACATAG
Statistics
Matches: 310, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
110 305 0.98
111 5 0.02
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (110 bp):
CACACTTAGTGCATGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTAGT
GCCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGGTTTTA
Found at i:3968508 original size:165 final size:164
Alignment explanation
Indices: 3968232--3968690 Score: 695
Period size: 165 Copynumber: 2.8 Consensus size: 164
3968222 TTTATTAAGA
* * * * *
3968232 TGCACACGTAGTGCCTGTACGGTAGTTCATCATCTCATGATGAA-TTCTGTGGTTTTGAACATTT
1 TGCACACTTAGTGCCTGTACGGTAATTCATCAACTCATGATGAATTTC-GTGGTTTTGCACACTT
* * *
3968296 AGTGCCTGTACGGTTATTCATCAACTCATCATGAATTCCACGGTTTTACACACTTAATGTATGTA
65 AGTG-CTGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTTACACACTTAATGCATGTA
*
3968361 CGGTTATTCATCAACTCATGATGAATTTCGTGGTTT
129 CGGTTATTCATCAACTCATGATGAATTACGTGGTTT
3968397 TGCACACTTAGTGCCTGTACGGTAATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTA
1 TGCACACTTAGTGCCTGTACGGTAATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTA
*
3968462 GTGCATGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTTACACACTTAGTGCATGTAC
66 GTGC-TGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTTACACACTTAATGCATGTAC
3968527 GGTTATTCATCAACTCATGATGAATTACGTGGTTT
130 GGTTATTCATCAACTCATGATGAATTACGTGGTTT
* * * * *
3968562 TACACACTTAGTGCCTATACAGTTATTCATCAACTCATGATGAATTTCGTGGTTTTGCAGACTTA
1 TGCACACTTAGTGCCTGTACGGTAATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTA
* * * * *
3968627 GTGTCTGTACGGTCATTCATCAACTCATGATGAATTCCGTGGTTTTGCACACTTAGTGCCTGTA
66 GTG-CTGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTTACACACTTAATGCATGTA
3968691 GTACACATAG
Statistics
Matches: 272, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
164 1 0.00
165 267 0.98
166 4 0.01
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.37
Consensus pattern (164 bp):
TGCACACTTAGTGCCTGTACGGTAATTCATCAACTCATGATGAATTTCGTGGTTTTGCACACTTA
GTGCTGTACGGTTATTCATCAACTCATGATGAATTCCATGGTTTTACACACTTAATGCATGTACG
GTTATTCATCAACTCATGATGAATTACGTGGTTT
Found at i:3974292 original size:13 final size:13
Alignment explanation
Indices: 3974274--3974299 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3974264 CTCCTAAGCT
3974274 TGATTGGAAATTA
1 TGATTGGAAATTA
3974287 TGATTGGAAATTA
1 TGATTGGAAATTA
3974300 CACCAACTTG
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:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (13 bp):
TGATTGGAAATTA
Found at i:3978740 original size:55 final size:55
Alignment explanation
Indices: 3978656--3979060 Score: 584
Period size: 55 Copynumber: 7.3 Consensus size: 55
3978646 TTTATTAAGA
* *
3978656 TGCACACGTAGTGCCTGTATGG-TAGTTCATCAACTCATGATGAATTTCGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTTCGTGGTTT
3978711 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGG-TTT
*
3978767 TGCACACTTAGTGCCTGTACGGTTATTCATCAAGTCATGATGAATTAT-GTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGTTT
* * *
3978822 TGCACACTTAGTGCATGTATGGTTATTCATCAACTCATGATGAATTACGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTT
* * * * *
3978877 TGCATACTTAGTACATGTACGGTTATTCATCAACTCATTATAAATTAT-GTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGTTT
3978932 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTAT-GTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATT-TCGTGGTTT
* * * * *
3978987 TGTACACTTAGTGTCTATACGATTATTCATCAACTCATGATGAATTCCGTGGTTT
1 TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTT
*
3979042 TGCACACTTAGTGCATGTA
1 TGCACACTTAGTGCCTGTA
3979061 GTACACGTAG
Statistics
Matches: 317, Mismatches: 27, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
55 262 0.83
56 54 0.17
57 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.20, T:0.39
Consensus pattern (55 bp):
TGCACACTTAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTTCGTGGTTT
Found at i:3982159 original size:13 final size:13
Alignment explanation
Indices: 3982141--3982170 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3982131 TTTTTCACTT
*
3982141 GGTTTTGAATTAG
1 GGTTTTGAATTAA
3982154 GGTTTTGAATTAA
1 GGTTTTGAATTAA
3982167 GGTT
1 GGTT
3982171 AAAGGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.23, C:0.00, G:0.30, T:0.47
Consensus pattern (13 bp):
GGTTTTGAATTAA
Found at i:3982379 original size:52 final size:52
Alignment explanation
Indices: 3982298--3982420 Score: 158
Period size: 52 Copynumber: 2.4 Consensus size: 52
3982288 AAAGTGATTT
* * * * *
3982298 TAGGTTAAAGTGGTATA-TGGTTTGTTAAGGTGAAAGTGGTGAAGGATTTTG
1 TAGGTTAAAGTGGTTTAGGGGTTTGTTAAGGTGAAAGTGATCAAGGATTGTG
* * * *
3982349 TATGTTAAAGTGGTTTAGGGGTTTTTTAAGGTGAGAGTGATCAAGGGTTGTG
1 TAGGTTAAAGTGGTTTAGGGGTTTGTTAAGGTGAAAGTGATCAAGGATTGTG
3982401 TAGGTTAAAGTGGTTTAGGG
1 TAGGTTAAAGTGGTTTAGGG
3982421 TAAGGTTCGA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 15 0.25
52 46 0.75
ACGTcount: A:0.25, C:0.01, G:0.37, T:0.37
Consensus pattern (52 bp):
TAGGTTAAAGTGGTTTAGGGGTTTGTTAAGGTGAAAGTGATCAAGGATTGTG
Found at i:3982420 original size:25 final size:25
Alignment explanation
Indices: 3982298--3982421 Score: 79
Period size: 26 Copynumber: 4.8 Consensus size: 25
3982288 AAAGTGATTT
* *
3982298 TAGGTTAAAGTGGTATATGG-TTTG
1 TAGGTTAAAGTGGTTTAGGGTTTTG
* ** *
3982322 TTAAGGTGAAAGTGGTGAAGGATTTTG
1 -T-AGGTTAAAGTGGTTTAGGGTTTTG
* *
3982349 TATGTTAAAGTGGTTTAGGGGTTTTT
1 TAGGTTAAAGTGGTTTA-GGGTTTTG
* * * ** *
3982375 TAAGGTGAGAGTGATCAAGGGTTGTG
1 T-AGGTTAAAGTGGTTTAGGGTTTTG
3982401 TAGGTTAAAGTGGTTTAGGGT
1 TAGGTTAAAGTGGTTTAGGGT
3982422 AAGGTTCGAT
Statistics
Matches: 71, Mismatches: 24, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
25 28 0.39
26 29 0.41
27 14 0.20
ACGTcount: A:0.25, C:0.01, G:0.36, T:0.38
Consensus pattern (25 bp):
TAGGTTAAAGTGGTTTAGGGTTTTG
Found at i:3983128 original size:24 final size:24
Alignment explanation
Indices: 3983050--3983134 Score: 66
Period size: 24 Copynumber: 3.5 Consensus size: 24
3983040 ACTTTCATTG
* *
3983050 TGAACTTT-AATTGGAATATGAAGT
1 TGAA-TTTGAATTAGAATATTAAGT
* * *
3983074 TGACTTTGAATTTCGAATA-TAATTT
1 TGAATTTGAA-TTAGAATATTAA-GT
* *
3983099 TAAATTTTAATTAGAATATTAAGT
1 TGAATTTGAATTAGAATATTAAGT
3983123 TGAATTTGAATT
1 TGAATTTGAATT
3983135 TGCATTTTAA
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 3 0.07
24 25 0.54
25 18 0.39
ACGTcount: A:0.38, C:0.04, G:0.14, T:0.45
Consensus pattern (24 bp):
TGAATTTGAATTAGAATATTAAGT
Found at i:3983168 original size:18 final size:18
Alignment explanation
Indices: 3983145--3983181 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3983135 TGCATTTTAA
*
3983145 AAACATTTAACAAACATT
1 AAACATTTAAAAAACATT
3983163 AAACATTTAAAAAACATT
1 AAACATTTAAAAAACATT
3983181 A
1 A
3983182 CATAATCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.27
Consensus pattern (18 bp):
AAACATTTAAAAAACATT
Found at i:3983850 original size:12 final size:12
Alignment explanation
Indices: 3983833--3983865 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
3983823 TGTGACGGTG
3983833 GACGTCTATCTT
1 GACGTCTATCTT
3983845 GACGTCTATCTT
1 GACGTCTATCTT
*
3983857 GACGCCTAT
1 GACGTCTAT
3983866 GAATTCTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (12 bp):
GACGTCTATCTT
Found at i:3985527 original size:35 final size:36
Alignment explanation
Indices: 3985453--3985523 Score: 103
Period size: 35 Copynumber: 2.0 Consensus size: 36
3985443 AATAATTATA
*
3985453 TAAATATTATTTTAATAAAAAATATAACATTATTTT
1 TAAATATTATTTTAATAAAAAATATAACAATATTTT
3985489 TAAATAATTA-TTT-ATAAAAAATATAACAA-ATTTT
1 TAAAT-ATTATTTTAATAAAAAATATAACAATATTTT
3985523 T
1 T
3985524 TAAAGAAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
34 6 0.18
35 15 0.45
36 8 0.24
37 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (36 bp):
TAAATATTATTTTAATAAAAAATATAACAATATTTT
Found at i:3985554 original size:22 final size:23
Alignment explanation
Indices: 3985493--3985555 Score: 83
Period size: 22 Copynumber: 2.8 Consensus size: 23
3985483 TATTTTTAAA
* *
3985493 TAATTATTTATAAAAAATATAAC
1 TAATTTTTTAAAAAAAATATAAC
* *
3985516 AAATTTTTTAAAGAAAATAT-AC
1 TAATTTTTTAAAAAAAATATAAC
3985538 TAATTTTTTAAAAAAAAT
1 TAATTTTTTAAAAAAAAT
3985556 TCTTACCAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 18 0.53
23 16 0.47
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (23 bp):
TAATTTTTTAAAAAAAATATAAC
Found at i:3987275 original size:42 final size:42
Alignment explanation
Indices: 3987229--3987334 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
3987219 TCAGTCAACT
*
3987229 TATCAACCAAAAACCAAACCAAACTTATCAAATCATCGAATA
1 TATCAACCAAAAACCAAACCAAACTCATCAAATCATCGAATA
* * * *
3987271 TATCAACCAAAACCCAAACCAAACTCGTGAAATCATCGAATT
1 TATCAACCAAAAACCAAACCAAACTCATCAAATCATCGAATA
* * * *
3987313 TGTCCACTAAGAACCAAACCAA
1 TATCAACCAAAAACCAAACCAA
3987335 GCTTTCGAAA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.48, C:0.28, G:0.06, T:0.18
Consensus pattern (42 bp):
TATCAACCAAAAACCAAACCAAACTCATCAAATCATCGAATA
Found at i:3990474 original size:22 final size:23
Alignment explanation
Indices: 3990449--3990497 Score: 82
Period size: 22 Copynumber: 2.2 Consensus size: 23
3990439 CGAACGGATG
3990449 TAAACGAACACAATAAACAAAC-
1 TAAACGAACACAATAAACAAACA
*
3990471 TAAACGAACACAATAAACGAACA
1 TAAACGAACACAATAAACAAACA
3990494 TAAA
1 TAAA
3990498 ACACAACACC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.63, C:0.20, G:0.06, T:0.10
Consensus pattern (23 bp):
TAAACGAACACAATAAACAAACA
Found at i:3990480 original size:13 final size:13
Alignment explanation
Indices: 3990449--3990493 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
3990439 CGAACGGATG
3990449 TAAACGAACACAA
1 TAAACGAACACAA
3990462 TAAAC-AA-AC--
1 TAAACGAACACAA
3990471 TAAACGAACACAA
1 TAAACGAACACAA
3990484 TAAACGAACA
1 TAAACGAACA
3990494 TAAAACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
9 5 0.18
10 2 0.07
11 4 0.14
12 2 0.07
13 15 0.54
ACGTcount: A:0.62, C:0.22, G:0.07, T:0.09
Consensus pattern (13 bp):
TAAACGAACACAA
Found at i:3990932 original size:15 final size:15
Alignment explanation
Indices: 3990912--3990944 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3990902 TGCTGATAGG
3990912 ATACCAGAATACAAA
1 ATACCAGAATACAAA
3990927 ATACCAGAATACAAA
1 ATACCAGAATACAAA
3990942 ATA
1 ATA
3990945 GTCTAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.18, G:0.06, T:0.15
Consensus pattern (15 bp):
ATACCAGAATACAAA
Found at i:3995418 original size:15 final size:15
Alignment explanation
Indices: 3995378--3995410 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3995368 GCTGAATAGG
*
3995378 ATACTAGAATACAAA
1 ATACCAGAATACAAA
3995393 ATACCAGAATACAAA
1 ATACCAGAATACAAA
3995408 ATA
1 ATA
3995411 GTATAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.18
Consensus pattern (15 bp):
ATACCAGAATACAAA
Found at i:3995567 original size:14 final size:14
Alignment explanation
Indices: 3995548--3995620 Score: 75
Period size: 14 Copynumber: 5.5 Consensus size: 14
3995538 CGATCGACCT
*
3995548 AAACATAAATGAAC
1 AAACATAAACGAAC
3995562 AAACATAAACGAAC
1 AAACATAAACGAAC
3995576 AAA-AGTAAACG---
1 AAACA-TAAACGAAC
3995587 -AACATAAACGAAC
1 AAACATAAACGAAC
**
3995600 AAACATAATTGAAC
1 AAACATAAACGAAC
3995614 AAACATA
1 AAACATA
3995621 TTACTGAACG
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
10 8 0.16
11 1 0.02
13 1 0.02
14 40 0.80
ACGTcount: A:0.63, C:0.16, G:0.08, T:0.12
Consensus pattern (14 bp):
AAACATAAACGAAC
Found at i:3998150 original size:45 final size:45
Alignment explanation
Indices: 3998100--3998243 Score: 209
Period size: 45 Copynumber: 3.2 Consensus size: 45
3998090 AATTTCTTAT
* *
3998100 CAATATACTTACCATTTATCCCATAAGCTCATAAGCTTAATTTTT
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAATTTTC
* *
3998145 CAATATACTTACCATTTATCCCATAAGCTCGTAAGATTAATTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAATTTTC
** *
3998190 CAATATACTTACCATTTATCATATAATCTCGTAAGCTT-ATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAATTTT-C
3998235 CAATATACT
1 CAATATACT
3998244 ATAAACCATA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
44 4 0.04
45 85 0.96
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGCTTAATTTTC
Found at i:3998624 original size:58 final size:57
Alignment explanation
Indices: 3998534--3998651 Score: 200
Period size: 58 Copynumber: 2.1 Consensus size: 57
3998524 CTATTTCATT
3998534 CATCCATGGTATCATATAACCATATATTTAACATTAGGGCAATTCATACCCAAAATAA
1 CATCCATGGTATCATATAACCATATATTTAACATTA-GGCAATTCATACCCAAAATAA
* * *
3998592 CATCCATGGTATCATATAACCATTTATTTAACATTAGGCAGTTCATACCCGAAATAA
1 CATCCATGGTATCATATAACCATATATTTAACATTAGGCAATTCATACCCAAAATAA
3998649 CAT
1 CAT
3998652 TAATGGTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
57 22 0.39
58 35 0.61
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (57 bp):
CATCCATGGTATCATATAACCATATATTTAACATTAGGCAATTCATACCCAAAATAA
Found at i:3998821 original size:24 final size:24
Alignment explanation
Indices: 3998789--3998837 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3998779 AGTCTTCCTG
3998789 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
*
3998813 ATGATGTATAAAATATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
3998837 A
1 A
3998838 ATGTCATGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Found at i:4002973 original size:29 final size:30
Alignment explanation
Indices: 4002919--4002977 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
4002909 CATTTCCCAT
* * *
4002919 CTTAACTTTTCAAAGTTTATACTTTGGTCA
1 CTTAACTTTTAAAAATTTATAATTTGGTCA
4002949 CTTAAC-TTTAAAAATTTATAATTTGGTCA
1 CTTAACTTTTAAAAATTTATAATTTGGTCA
4002978 TTCACAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (30 bp):
CTTAACTTTTAAAAATTTATAATTTGGTCA
Found at i:4004932 original size:23 final size:23
Alignment explanation
Indices: 4004905--4004950 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
4004895 TTTCTCATCT
4004905 TTTTTTCATTCTT-TTCTTTTTCTG
1 TTTTTTC-TTCTTCTT-TTTTTCTG
4004929 TTTTTTCTTCTTCTTTTTTTCT
1 TTTTTTCTTCTTCTTTTTTTCT
4004951 TCTTCTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.78
Consensus pattern (23 bp):
TTTTTTCTTCTTCTTTTTTTCTG
Found at i:4004933 original size:14 final size:13
Alignment explanation
Indices: 4004906--4005019 Score: 67
Period size: 14 Copynumber: 8.4 Consensus size: 13
4004896 TTCTCATCTT
4004906 TTTTTCATTCTTTTC
1 TTTTTC-TT-TTTTC
4004921 TTTTTCTGTTTTTTC
1 TTTTTC--TTTTTTC
*
4004936 TTCTTCTTTTTTTC
1 TTTTTC-TTTTTTC
*
4004950 TTCTTC-TTTTT-
1 TTTTTCTTTTTTC
*
4004961 GTTTTCTTATTTTC
1 TTTTTCTT-TTTTC
4004975 TTTTTCTATTTTT-
1 TTTTTCT-TTTTTC
4004988 TTCTTGT-TTTATTTC
1 TT-TT-TCTTT-TTTC
*
4005003 TTTTT-TTTTATC
1 TTTTTCTTTTTTC
4005015 TTTTT
1 TTTTT
4005020 AATATTATTT
Statistics
Matches: 83, Mismatches: 7, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
11 4 0.05
12 14 0.17
13 12 0.14
14 31 0.37
15 20 0.24
16 2 0.02
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTCTTTTTTC
Found at i:4004947 original size:28 final size:26
Alignment explanation
Indices: 4004916--4005011 Score: 81
Period size: 28 Copynumber: 3.6 Consensus size: 26
4004906 TTTTTCATTC
4004916 TTTTCTTTTTCTGTTTTTTCTTCTTCTTT
1 TTTTCTTTTTCT-TTTTTTCTTC-T-TTT
* *
4004945 TTTTCTTCTTCTTTTTGTT-TTC-TTA
1 TTTTCTTTTTCTTTTT-TTCTTCTTTT
*
4004970 TTTTCTTTTTCTATTTTTTTCTTGTTTT
1 TTTTCTTTTTC--TTTTTTTCTTCTTTT
*
4004998 ATTTCTTTTT-TTTT
1 TTTTCTTTTTCTTTT
4005012 ATCTTTTTAA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
25 16 0.29
26 2 0.04
27 7 0.12
28 18 0.32
29 13 0.23
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (26 bp):
TTTTCTTTTTCTTTTTTTCTTCTTTT
Found at i:4004973 original size:25 final size:24
Alignment explanation
Indices: 4004930--4005011 Score: 78
Period size: 25 Copynumber: 3.4 Consensus size: 24
4004920 CTTTTTCTGT
*
4004930 TTTTTCTTCTTCTTTTTTTCTTCTTC
1 TTTTT-TT-TTCTTATTTTCTTCTTC
*
4004956 TTTTTGTTTTCTTATTTTCTTTTTC
1 TTTTT-TTTTCTTATTTTCTTCTTC
* * *
4004981 TATTTTTTTCTTGTTTT-AT-TTC
1 TTTTTTTTTCTTATTTTCTTCTTC
4005003 TTTTTTTTT
1 TTTTTTTTT
4005012 ATCTTTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
22 11 0.22
23 1 0.02
24 11 0.22
25 19 0.39
26 7 0.14
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.80
Consensus pattern (24 bp):
TTTTTTTTTCTTATTTTCTTCTTC
Found at i:4004987 original size:54 final size:52
Alignment explanation
Indices: 4004907--4005011 Score: 133
Period size: 54 Copynumber: 2.0 Consensus size: 52
4004897 TCTCATCTTT
* *
4004907 TTTTCATTCTTTTCTTTTTCTGTTTTTTCTTCTTCTTTT-TTTCTTCTTCTTTTTG
1 TTTTCATTATTTTCTTTTTCT-ATTTTT-TTCTTCTTTTATTTCTT-TT-TTTTTG
*
4004962 TTTTC-TTATTTTCTTTTTCTATTTTTTTCTTGTTTTATTTCTTTTTTTTT
1 TTTTCATTATTTTCTTTTTCTATTTTTTTCTTCTTTTATTTCTTTTTTTTT
4005012 ATCTTTTTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
51 5 0.11
52 11 0.24
53 11 0.24
54 14 0.30
55 5 0.11
ACGTcount: A:0.04, C:0.14, G:0.03, T:0.79
Consensus pattern (52 bp):
TTTTCATTATTTTCTTTTTCTATTTTTTTCTTCTTTTATTTCTTTTTTTTTG
Found at i:4004991 original size:16 final size:16
Alignment explanation
Indices: 4004913--4005011 Score: 62
Period size: 17 Copynumber: 5.8 Consensus size: 16
4004903 CTTTTTTTCA
*
4004913 TTCTTTTCTTTTTCTGT
1 TTCTTTTCTTTTT-TAT
*
4004930 TTTTTCTTCTTCTTTT-T
1 TTCTT-TTCTT-TTTTAT
4004947 TTCTTCTTCTTTTTGT-T
1 TTCTT-TTCTTTTT-TAT
4004964 TTCTTATTTTCTTTTTCTAT
1 TTC---TTTTCTTTTT-TAT
4004984 TT-TTTTCTTGTTTTAT
1 TTCTTTTCTT-TTTTAT
4005000 TTCTTTT-TTTTT
1 TTCTTTTCTTTTT
4005012 ATCTTTTTAA
Statistics
Matches: 70, Mismatches: 3, Indels: 20
0.75 0.03 0.22
Matches are distributed among these distances:
15 3 0.04
16 17 0.24
17 27 0.39
18 6 0.09
19 12 0.17
20 5 0.07
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (16 bp):
TTCTTTTCTTTTTTAT
Found at i:4005019 original size:11 final size:10
Alignment explanation
Indices: 4004902--4005011 Score: 78
Period size: 12 Copynumber: 10.1 Consensus size: 10
4004892 TCATTTCTCA
4004902 TCTTTTTTTCAT
1 TCTTTTTTT--T
4004914 TCTTTTCTTTT
1 TCTTTT-TTTT
4004925 TCTGTTTTTTCT
1 TCT-TTTTTT-T
4004937 TCTTCTTTTTT
1 TCTT-TTTTTT
4004948 TCTTCTTCTTTT
1 TCTT-TT-TTTT
* * *
4004960 TGTTTTCTTA
1 TCTTTTTTTT
*
4004970 T-TTTCTTTT
1 TCTTTTTTTT
*
4004979 TCTATTTTTT
1 TCTTTTTTTT
4004989 TCTTGTTTTATT
1 TCTT-TTTT-TT
4005001 TCTTTTTTTT
1 TCTTTTTTTT
4005011 T
1 T
4005012 ATCTTTTTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
9 6 0.07
10 15 0.19
11 26 0.32
12 31 0.38
13 3 0.04
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.79
Consensus pattern (10 bp):
TCTTTTTTTT
Found at i:4007774 original size:45 final size:45
Alignment explanation
Indices: 4007717--4007815 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
4007707 AATTTCTTAT
*
4007717 CAATATATTTACCATTTATCCCATAAGCTCGTAAGATTAATTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGATTAATTTAC
* ** *
4007762 CAATATACTTACCATTTATCCCATAAGCTTGTAATCTTATTTTAC
1 CAATATACTTACCATTTATCCCATAAGCTCGTAAGATTAATTTAC
4007807 CAATATACT
1 CAATATACT
4007816 ATAAACCATA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (45 bp):
CAATATACTTACCATTTATCCCATAAGCTCGTAAGATTAATTTAC
Found at i:4008230 original size:57 final size:58
Alignment explanation
Indices: 4008106--4008231 Score: 182
Period size: 58 Copynumber: 2.2 Consensus size: 58
4008096 CTATTTCATT
*
4008106 CATCCATGGTATCATATAACCATATATTTAACATTAGGGCAATTCATACCCAAAATAA
1 CATCCATGGTATCATATAACCATATATTTAACATTAGGGCAATTCATACACAAAATAA
* * ** *
4008164 CATCCATGGTATCATATAACCATTTATTTAACATT-GGGCAGTTCATACATGAAATTA
1 CATCCATGGTATCATATAACCATATATTTAACATTAGGGCAATTCATACACAAAATAA
*
4008221 CATTCATGGTA
1 CATCCATGGTA
4008232 AAATATCACA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
57 27 0.44
58 34 0.56
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (58 bp):
CATCCATGGTATCATATAACCATATATTTAACATTAGGGCAATTCATACACAAAATAA
Found at i:4010471 original size:21 final size:20
Alignment explanation
Indices: 4010420--4010471 Score: 79
Period size: 19 Copynumber: 2.5 Consensus size: 20
4010410 TTAAATTCAC
4010420 ATTTTAACTTTAAAAATATAT
1 ATTTTAAC-TTAAAAATATAT
4010441 A-TTTAACTTAAAAATATAT
1 ATTTTAACTTAAAAATATAT
4010460 ATTTTAATCTTA
1 ATTTTAA-CTTA
4010472 TCTTAATTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.45
20 11 0.38
21 5 0.17
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTAACTTAAAAATATAT
Found at i:4012844 original size:7 final size:7
Alignment explanation
Indices: 4012832--4012875 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
4012822 TGTGTTTCTC
4012832 GTGATAT
1 GTGATAT
4012839 GTGATAT
1 GTGATAT
4012846 GTGATAT
1 GTGATAT
4012853 GTGATAT
1 GTGATAT
4012860 GTGATAT
1 GTGATAT
4012867 GTGATAT
1 GTGATAT
4012874 GT
1 GT
4012876 ATAAGTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.27, C:0.00, G:0.30, T:0.43
Consensus pattern (7 bp):
GTGATAT
Found at i:4014200 original size:32 final size:31
Alignment explanation
Indices: 4014164--4014239 Score: 98
Period size: 32 Copynumber: 2.4 Consensus size: 31
4014154 CAATATTAAT
* *
4014164 AATAATACTGATATTAGTATCGATACTACAA
1 AATAATACTGATACTAATATCGATACTACAA
* *
4014195 GAATAATATTGATACTAATATCGATACTATAA
1 -AATAATACTGATACTAATATCGATACTACAA
*
4014227 AACAATACTGATA
1 AATAATACTGATA
4014240 AACATAAATG
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 11 0.29
32 27 0.71
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AATAATACTGATACTAATATCGATACTACAA
Found at i:4021353 original size:28 final size:28
Alignment explanation
Indices: 4021321--4021398 Score: 138
Period size: 28 Copynumber: 2.8 Consensus size: 28
4021311 TCAGTTATCA
4021321 GTATTGATAGTGCTAAAGTAGTTTAACT
1 GTATTGATAGTGCTAAAGTAGTTTAACT
* *
4021349 GTATTGATAGTGTTGAAGTAGTTTAACT
1 GTATTGATAGTGCTAAAGTAGTTTAACT
4021377 GTATTGATAGTGCTAAAGTAGT
1 GTATTGATAGTGCTAAAGTAGT
4021399 ATTTGATACT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (28 bp):
GTATTGATAGTGCTAAAGTAGTTTAACT
Found at i:4032819 original size:16 final size:16
Alignment explanation
Indices: 4032798--4032869 Score: 81
Period size: 16 Copynumber: 4.4 Consensus size: 16
4032788 GGTATTACTC
*
4032798 GACCTGTTTTCAACCT
1 GACCTGTTTTTAACCT
* * *
4032814 GACCTGTTATGAACTT
1 GACCTGTTTTTAACCT
* *
4032830 GACATGTTTTTAACAT
1 GACCTGTTTTTAACCT
4032846 GACCTGTTTTTTAACCT
1 GACCTG-TTTTTAACCT
4032863 GACCTGT
1 GACCTGT
4032870 AAATGATCCG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
16 31 0.67
17 15 0.33
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.40
Consensus pattern (16 bp):
GACCTGTTTTTAACCT
Found at i:4036394 original size:120 final size:120
Alignment explanation
Indices: 4036176--4036446 Score: 420
Period size: 120 Copynumber: 2.3 Consensus size: 120
4036166 GTAAAAATTA
* * *
4036176 AACAATAGCTAAAAATTAAA-AAGTTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTCATAC
1 AACAGTAGCTACAAATTAAACAA-TTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTCATAA
4036240 AAGCAATCCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATC
65 AAGCAATCCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATC
* * *
4036296 AATAGTAGCTACAAATTAAACAATTTATTTAAA-CTGTAAATAAAGGCAGCTAACAACCTTATAA
1 AACAGTAGCTACAAATTAAACAATTTATTTAAATC-CTAAATAAAGGCAGCTAACAACCTCATAA
* * *
4036360 AAGTAATCTGAATGAACAACCAACAACACAAACAAGGACTATAGAGGAAACAAATC
65 AAGCAATCCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATC
*
4036416 AACAGTAGCTACAAATTAAACAGTTTATTTA
1 AACAGTAGCTACAAATTAAACAATTTATTTA
4036447 CCTCTTTTAG
Statistics
Matches: 138, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
119 1 0.01
120 135 0.98
121 2 0.01
ACGTcount: A:0.51, C:0.18, G:0.11, T:0.20
Consensus pattern (120 bp):
AACAGTAGCTACAAATTAAACAATTTATTTAAATCCTAAATAAAGGCAGCTAACAACCTCATAAA
AGCAATCCGAATGAACAACCAACAACACAAACAAGGACTACAGAGGAAACAAATC
Found at i:4036714 original size:25 final size:23
Alignment explanation
Indices: 4036665--4036714 Score: 55
Period size: 24 Copynumber: 2.1 Consensus size: 23
4036655 TTAGGGTTTT
*
4036665 TTAGGTTCGGGTTTGAATTCGGG
1 TTAGGTTCGGGTTTGAATTCAGG
* *
4036688 TTAGTGTTTGGGTTTTAGATTCAGG
1 TTAG-GTTCGGGTTTGA-ATTCAGG
4036713 TT
1 TT
4036715 TGGGTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 10 0.45
25 8 0.36
ACGTcount: A:0.14, C:0.06, G:0.34, T:0.46
Consensus pattern (23 bp):
TTAGGTTCGGGTTTGAATTCAGG
Found at i:4036717 original size:19 final size:19
Alignment explanation
Indices: 4036693--4036738 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
4036683 TCGGGTTAGT
4036693 GTTTGGGTTTTAGATTCAG
1 GTTTGGGTTTTAGATTCAG
* *
4036712 GTTTGGGTTTTAGATTTAT
1 GTTTGGGTTTTAGATTCAG
4036731 GTTTGGGT
1 GTTTGGGT
4036739 CCAGGTTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.13, C:0.02, G:0.33, T:0.52
Consensus pattern (19 bp):
GTTTGGGTTTTAGATTCAG
Found at i:4036756 original size:12 final size:12
Alignment explanation
Indices: 4036726--4036888 Score: 84
Period size: 12 Copynumber: 13.7 Consensus size: 12
4036716 GGGTTTTAGA
*
4036726 TTTATGTTTGGG
1 TTTAGGTTTGGG
**
4036738 TCCAGGTTTGGG
1 TTTAGGTTTGGG
*
4036750 TTTAGGTTCGGG
1 TTTAGGTTTGGG
** **
4036762 TTCGGGTTAAGG
1 TTTAGGTTTGGG
4036774 TTTAGGTTT-GG
1 TTTAGGTTTGGG
*
4036785 TTTAGGTTAGGG
1 TTTAGGTTTGGG
*
4036797 -TTAGGGTTAGGG
1 TTTA-GGTTTGGG
*
4036809 -TTAGGGTTAGGG
1 TTTA-GGTTTGGG
* *
4036821 TTTATGTTTAGG
1 TTTAGGTTTGGG
* *
4036833 TTTGGGTTT-AG
1 TTTAGGTTTGGG
* *
4036844 TTAAGGTTTAGG
1 TTTAGGTTTGGG
* *
4036856 TTTAGGTTCGGTT
1 TTTAGGTTTGG-G
4036869 TTTA-GTTTAGGG
1 TTTAGGTTT-GGG
4036881 TTTAGGTT
1 TTTAGGTT
4036889 CAAGTTAAGG
Statistics
Matches: 115, Mismatches: 29, Indels: 13
0.73 0.18 0.08
Matches are distributed among these distances:
11 21 0.18
12 82 0.71
13 12 0.10
ACGTcount: A:0.13, C:0.03, G:0.37, T:0.46
Consensus pattern (12 bp):
TTTAGGTTTGGG
Found at i:4036757 original size:6 final size:6
Alignment explanation
Indices: 4036741--4036863 Score: 99
Period size: 6 Copynumber: 20.8 Consensus size: 6
4036731 GTTTGGGTCC
* * * * * *
4036741 AGGTTT GGGTTT AGGTTC GGGTTC GGGTTA AGGTTT AGGTTT -GGTTT
1 AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT
* * * * *
4036788 AGG-TT AGGGTT AGGGTT AGGGTT AGGGTT AGGGTTT ATGTTT AGGTTT
1 AGGTTT AGGTTT AGGTTT AGGTTT AGGTTT A-GGTTT AGGTTT AGGTTT
* *
4036836 GGGTTT A-GTTA AGGTTT AGGTTT AGGTT
1 AGGTTT AGGTTT AGGTTT AGGTTT AGGTT
4036864 CGGTTTTTAG
Statistics
Matches: 99, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
5 14 0.14
6 80 0.81
7 5 0.05
ACGTcount: A:0.15, C:0.02, G:0.40, T:0.44
Consensus pattern (6 bp):
AGGTTT
Found at i:4036763 original size:18 final size:18
Alignment explanation
Indices: 4036742--4036863 Score: 110
Period size: 18 Copynumber: 6.9 Consensus size: 18
4036732 TTTGGGTCCA
*
4036742 GGTTTGGGTTTAGGTTCG
1 GGTTTGGGTTTAGGTTAG
* *
4036760 GGTTCGGGTTAAGGTTTA-
1 GGTTTGGGTTTAGG-TTAG
4036778 GGTTT-GGTTTAGGTTAG
1 GGTTTGGGTTTAGGTTAG
*
4036795 GGTTAGGG-TTAGGGTTAG
1 GGTTTGGGTTTA-GGTTAG
* *
4036813 GGTTAGGGTTTATGTTTA-
1 GGTTTGGGTTTA-GGTTAG
*
4036831 GGTTTGGGTTTA-GTTAA
1 GGTTTGGGTTTAGGTTAG
*
4036848 GGTTTAGGTTTAGGTT
1 GGTTTGGGTTTAGGTT
4036864 CGGTTTTTAG
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.07
17 25 0.29
18 46 0.53
19 9 0.10
ACGTcount: A:0.14, C:0.02, G:0.40, T:0.44
Consensus pattern (18 bp):
GGTTTGGGTTTAGGTTAG
Found at i:4037598 original size:14 final size:13
Alignment explanation
Indices: 4037569--4037631 Score: 65
Period size: 14 Copynumber: 4.5 Consensus size: 13
4037559 CATCCCTATA
*
4037569 TAATTTTTATTAAT
1 TAATATTTA-TAAT
4037583 TAACTATTTATAAT
1 TAA-TATTTATAAT
4037597 TAATATTATAATAAT
1 TAATATT-T-ATAAT
4037612 T-ATATATTATAAT
1 TAATAT-TTATAAT
4037625 TAATATT
1 TAATATT
4037632 AATATAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
13 11 0.26
14 20 0.47
15 12 0.28
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (13 bp):
TAATATTTATAAT
Found at i:4037658 original size:31 final size:30
Alignment explanation
Indices: 4037590--4037734 Score: 113
Period size: 31 Copynumber: 4.7 Consensus size: 30
4037580 AATTAACTAT
* *
4037590 TTAT-AATTAATATT-ATA-ATAATTATATA
1 TTATAAATTAATATTAATATA-AAATATATG
4037618 TTAT-AATTAATATTAATATAAAATATA-G
1 TTATAAATTAATATTAATATAAAATATATG
*
4037646 TCTATAACATTAATATTAATATAAACTATATG
1 T-TATAA-ATTAATATTAATATAAAATATATG
* *
4037678 TTATAAATTATATAGTATAGTTTATAAACTATA-G
1 TTATAAATTA-ATA-T-TA--ATATAAAATATATG
4037712 TTAATATAATTAATATTAATATA
1 TT-ATA-AATTAATATTAATATA
4037735 GTATAGTTTA
Statistics
Matches: 99, Mismatches: 5, Indels: 23
0.78 0.04 0.18
Matches are distributed among these distances:
28 15 0.15
29 12 0.12
30 6 0.06
31 33 0.33
32 3 0.03
33 4 0.04
34 4 0.04
35 17 0.17
36 5 0.05
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
TTATAAATTAATATTAATATAAAATATATG
Found at i:4037674 original size:24 final size:25
Alignment explanation
Indices: 4037629--4037675 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
4037619 TATAATTAAT
**
4037629 ATTAATATAAAATATAGTCTATAAC
1 ATTAATATAAAATATAAACTATAAC
*
4037654 ATTAATAT-TAATATAAACTATA
1 ATTAATATAAAATATAAACTATA
4037676 TGTTATAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
ATTAATATAAAATATAAACTATAAC
Found at i:4037702 original size:14 final size:14
Alignment explanation
Indices: 4037685--4037746 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
4037675 ATGTTATAAA
4037685 TTATATAGTATAGT
1 TTATATAGTATAGT
* *
4037699 TTATAAACTATAGT
1 TTATATAGTATAGT
* *
4037713 TAATATAATTAATA-T
1 TTATAT-AGT-ATAGT
*
4037728 TAATATAGTATAGT
1 TTATATAGTATAGT
4037742 TTATA
1 TTATA
4037747 AACTATATAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 3 0.08
14 23 0.61
15 9 0.24
16 3 0.08
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.47
Consensus pattern (14 bp):
TTATATAGTATAGT
Found at i:4037736 original size:43 final size:40
Alignment explanation
Indices: 4037687--4037777 Score: 128
Period size: 43 Copynumber: 2.2 Consensus size: 40
4037677 GTTATAAATT
*
4037687 ATATAGTATAGTTTATAAACTATAGTTAATATAATTAATATTA
1 ATATAGTATAGTTTATAAACTATA--TAATAT-ATTAATATAA
*
4037730 ATATAGTATAGTTTATAAACTATATACTATATTAATATAA
1 ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
4037770 ATTATAGT
1 A-TATAGT
4037778 TAAGATAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 10 0.22
41 11 0.24
43 24 0.53
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (40 bp):
ATATAGTATAGTTTATAAACTATATAATATATTAATATAA
Found at i:4037740 original size:29 final size:29
Alignment explanation
Indices: 4037707--4037799 Score: 78
Period size: 29 Copynumber: 3.0 Consensus size: 29
4037697 GTTTATAAAC
4037707 TATAGTTAATATAATTAATATTAATATAG
1 TATAGTTAATATAATTAATATTAATATAG
* * *
4037736 TATAGTTTATAAACTATATACTATATTAATATAAAT
1 TATAGTTAATATA--AT-TA--ATATTAATAT--AG
* *
4037772 TATAGTTAAGATAATTAACATTAATATA
1 TATAGTTAATATAATTAATATTAATATA
4037800 AACAATAGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
29 12 0.24
31 11 0.22
32 2 0.04
33 2 0.04
34 12 0.24
36 11 0.22
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAGTTAATATAATTAATATTAATATAG
Found at i:4037814 original size:20 final size:20
Alignment explanation
Indices: 4037789--4037828 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4037779 AAGATAATTA
4037789 ACATTAATATAAACAATAGT
1 ACATTAATATAAACAATAGT
*
4037809 ACATTAATATAAACTATAGT
1 ACATTAATATAAACAATAGT
4037829 TTGTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
ACATTAATATAAACAATAGT
Found at i:4037836 original size:65 final size:64
Alignment explanation
Indices: 4037693--4037840 Score: 156
Period size: 65 Copynumber: 2.3 Consensus size: 64
4037683 AATTATATAG
* * * ** ** *
4037693 TATAGTTTATAAACTATAGTTAATATAATTAATATTAATATAGTATAGTTTATAAACTATATAC
1 TATAGTTTATAAATTATAGTTAAGATAATTAACATTAATATACAATAGTACATAAACTATAAAC
*
4037757 TATA-TTAATATAAATTATAGTTAAGATAATTAACATTAATATAAACAATAGTACATTAA-TATA
1 TATAGTT--TATAAATTATAGTTAAGATAATTAACATTAATAT--ACAATAGTACATAAACTATA
4037820 AAC
62 AAC
*
4037823 TATAGTTTGTAAATTATA
1 TATAGTTTATAAATTATA
4037841 TACTATAGGT
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
63 2 0.03
64 4 0.06
65 41 0.59
66 10 0.14
67 12 0.17
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (64 bp):
TATAGTTTATAAATTATAGTTAAGATAATTAACATTAATATACAATAGTACATAAACTATAAAC
Done.