Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397269.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_12.1, 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: 5666189
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 144833 characters in sequence are not A, C, G, or T
File 13 of 14
Found at i:4934950 original size:61 final size:62
Alignment explanation
Indices: 4934871--4935027 Score: 174
Period size: 61 Copynumber: 2.6 Consensus size: 62
4934861 CCTCCACTGC
* * * ** * *
4934871 AAAAGGTAGACAATGGTTATACCTCTTTTGTAACCAGTAATGTAAGGTTATACCTTCA-TAA
1 AAAAGGTAGAGAAAGGTTATACCTCTTTTGCAAAAAATAATGTAAGGTTATACCTCCATTAA
* * *
4934932 AAAAGGTAGAGAAAGGTTATACCTCCTTTGCAAAAAATAGTGTAAGGTTATACCTCCATTAT
1 AAAAGGTAGAGAAAGGTTATACCTCTTTTGCAAAAAATAATGTAAGGTTATACCTCCATTAA
* * * *
4934994 AAAAGGTAGTGTAAGATTATACCTCTATTG-AAAA
1 AAAAGGTAGAGAAAGGTTATACCTCTTTTGCAAAA
4935028 GGCAAAGAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
61 53 0.66
62 27 0.34
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (62 bp):
AAAAGGTAGAGAAAGGTTATACCTCTTTTGCAAAAAATAATGTAAGGTTATACCTCCATTAA
Found at i:4934982 original size:31 final size:31
Alignment explanation
Indices: 4934911--4935018 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
4934901 TAACCAGTAA
* *
4934911 TGTAAGGTTATACCTTCA-TA-AAAAAGGTAG
1 TGTAAGGTTATACCTCCATTACAAAAA-ATAG
* * * *
4934941 AGAAAGGTTATACCTCCTTTGCAAAAAATAG
1 TGTAAGGTTATACCTCCATTACAAAAAATAG
* **
4934972 TGTAAGGTTATACCTCCATTATAAAAGGTAG
1 TGTAAGGTTATACCTCCATTACAAAAAATAG
*
4935003 TGTAAGATTATACCTC
1 TGTAAGGTTATACCTC
4935019 TATTGAAAAG
Statistics
Matches: 62, Mismatches: 14, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
30 14 0.23
31 43 0.69
32 5 0.08
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (31 bp):
TGTAAGGTTATACCTCCATTACAAAAAATAG
Found at i:4935114 original size:52 final size:52
Alignment explanation
Indices: 4935036--4935139 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 52
4935026 AAGGCAAAGA
*
4935036 AAGATTATACCTCCTAAAGAAAAGGTAGTGTGTTAAAGGTTGTGCTTAAACC
1 AAGATTATACCTCCTAAAGAAAAGGTAGTCTGTTAAAGGTTGTGCTTAAACC
* *
4935088 AAGATTATACCTCCTCAAGAAAAGGTAGTCTGTTAAAGGTTGTGTTTAAACC
1 AAGATTATACCTCCTAAAGAAAAGGTAGTCTGTTAAAGGTTGTGCTTAAACC
4935140 TGGTTAAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 49 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (52 bp):
AAGATTATACCTCCTAAAGAAAAGGTAGTCTGTTAAAGGTTGTGCTTAAACC
Found at i:4938802 original size:2 final size:2
Alignment explanation
Indices: 4938786--4938834 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
4938776 ATCAAACTAC
* *
4938786 TA TA TA CA TA CA 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
4938828 TA TA TA T
1 TA TA TA T
4938835 TACCACCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4945625 original size:15 final size:15
Alignment explanation
Indices: 4945605--4945634 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4945595 AACACTCATT
4945605 GCACAAATTTCACTG
1 GCACAAATTTCACTG
4945620 GCACAAATTTCACTG
1 GCACAAATTTCACTG
4945635 TTGACATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (15 bp):
GCACAAATTTCACTG
Found at i:4964507 original size:16 final size:17
Alignment explanation
Indices: 4964471--4964508 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
4964461 TAAACTTTTG
**
4964471 TTATTTTGGATTGGCTT
1 TTATTTTGGATTGGCAC
4964488 TTATTTTGG-TTGGCAC
1 TTATTTTGGATTGGCAC
4964504 TTATT
1 TTATT
4964509 GAATCTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.13, C:0.08, G:0.21, T:0.58
Consensus pattern (17 bp):
TTATTTTGGATTGGCAC
Found at i:4967452 original size:18 final size:19
Alignment explanation
Indices: 4967426--4967468 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
4967416 ATGATAAGTA
*
4967426 AAAAGAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
4967444 AAAATAATATTTTATGAAT
1 AAAATAATATTTTATAAAT
4967463 AAAATA
1 AAAATA
4967469 TNNNNNNNNN
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:4977192 original size:29 final size:29
Alignment explanation
Indices: 4977086--4977277 Score: 200
Period size: 28 Copynumber: 6.7 Consensus size: 29
4977076 TTAAGACAAC
* * * **
4977086 TCTTGTCTTTAATTGAGACAAAACATGTCA
1 TCTTGTC-TAAATTAAGACAAAACATATTT
*
4977116 TCTTGTCTAAATT--GA-ACAA-ATATGTT
1 TCTTGTCTAAATTAAGACAAAACATAT-TT
* *
4977142 TCTTGTCTAGATTAAGAC-AAACATATGT
1 TCTTGTCTAAATTAAGACAAAACATATTT
4977170 TCTTGTCTAAATTAAGACAAAACATATTTT
1 TCTTGTCTAAATTAAGACAAAACATA-TTT
*
4977200 TCTTGTCTAAATTAAGAC--AACATGTTTT
1 TCTTGTCTAAATTAAGACAAAACAT-ATTT
* *
4977228 TCTTTTCTAAATTAAGACAAAACATGTTT
1 TCTTGTCTAAATTAAGACAAAACATATTT
4977257 TCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAA
4977278 TATGCAAAAG
Statistics
Matches: 138, Mismatches: 14, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
25 3 0.02
26 15 0.11
27 2 0.01
28 47 0.34
29 39 0.28
30 32 0.23
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (29 bp):
TCTTGTCTAAATTAAGACAAAACATATTT
Found at i:4977217 original size:58 final size:59
Alignment explanation
Indices: 4977116--4977277 Score: 212
Period size: 58 Copynumber: 2.9 Consensus size: 59
4977106 AAACATGTCA
* * *
4977116 TCTTGTCTAAATT--GA-ACAA-ATATGTTTCTTGTCTAGATTAAGACAAACAT-ATGT
1 TCTTGTCTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGACAAACATGATGT
* *
4977170 TCTTGTCTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGAC-AACATGTTTT
1 TCTTGTCTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGACAAACATGATGT
* *
4977228 TCTTTTCTAAATTAAGACAAAACAT-GTTTTCTTGTCTAAATTAAGACAAA
1 TCTTGTCTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGACAAA
4977278 TATGCAAAAG
Statistics
Matches: 95, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
54 13 0.14
56 2 0.02
57 29 0.31
58 51 0.54
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (59 bp):
TCTTGTCTAAATTAAGACAAAACATATTTTTCTTGTCTAAATTAAGACAAACATGATGT
Found at i:4979672 original size:73 final size:73
Alignment explanation
Indices: 4979580--4979719 Score: 199
Period size: 73 Copynumber: 1.9 Consensus size: 73
4979570 CAAGAGATAG
* ** * * * *
4979580 TGTTAGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTGAGAGATAGAAATGACTTAATCGACTA
1 TGTTAGTCGACTAACAGCTTACTACCAAAAACTAGGTTCAGAGATAGAAACGACTTAATAGACTA
4979645 AGAAGTTT
66 AGAAGTTT
* *
4979653 TGTTAGTCGACTAACAGCTTACTACCAGAAACTAGGTTCAGAGATAGAGACGACTTAATAGACTA
1 TGTTAGTCGACTAACAGCTTACTACCAAAAACTAGGTTCAGAGATAGAAACGACTTAATAGACTA
4979718 AG
66 AG
4979720 TGGCAATGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 58 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.26
Consensus pattern (73 bp):
TGTTAGTCGACTAACAGCTTACTACCAAAAACTAGGTTCAGAGATAGAAACGACTTAATAGACTA
AGAAGTTT
Found at i:4979730 original size:73 final size:73
Alignment explanation
Indices: 4979580--4979739 Score: 194
Period size: 73 Copynumber: 2.2 Consensus size: 73
4979570 CAAGAGATAG
* ** * * * *
4979580 TGTTAGTCGACTAAGAGCTTACTGTCAAAAACTGGGTTGAGAGATAGAAATGACTTAATCGACTA
1 TGTTAGTCGACTAACAGCTTACTACCAAAAACTAGGTTCAGAGATAGAAACGACTTAATAGACTA
***
4979645 AGAAGTTT
66 AGAAGCAA
* *
4979653 TGTTAGTCGACTAACAGCTTACTACCAGAAACTAGGTTCAGAGATAGAGACGACTTAATAGACTA
1 TGTTAGTCGACTAACAGCTTACTACCAAAAACTAGGTTCAGAGATAGAAACGACTTAATAGACTA
**
4979718 AGTGGCAA
66 AGAAGCAA
4979726 TGTTAGTCGACTAA
1 TGTTAGTCGACTAA
4979740 AAGCATTCTG
Statistics
Matches: 73, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (73 bp):
TGTTAGTCGACTAACAGCTTACTACCAAAAACTAGGTTCAGAGATAGAAACGACTTAATAGACTA
AGAAGCAA
Found at i:4987466 original size:72 final size:72
Alignment explanation
Indices: 4987337--4987474 Score: 179
Period size: 73 Copynumber: 1.9 Consensus size: 72
4987327 AACATTGCCA
* * * * ** *
4987337 CTTAGTCTATTAGTCGTCTCTATCTCTGAACCTAGTTTCTGGTAGTAAGCTGTTAGTCGACTAAC
1 CTTAGTCGATTAGTCATCTCTATCTCTCAACCCAGTTTCTGACAGTAAGCTGCTAGTCGACTAAC
4987402 AAAACTT
66 AAAACTT
* *
4987409 CTTAGTCGATTAAGTCATTTCTATCTCTCAACCCAGTTTTTGACAGTAAGCT-CTAGTCGACTAA
1 CTTAGTCGATT-AGTCATCTCTATCTCTCAACCCAGTTTCTGACAGTAAGCTGCTAGTCGACTAA
4987473 CA
65 CA
4987475 CTATCTCTTG
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
72 23 0.41
73 33 0.59
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (72 bp):
CTTAGTCGATTAGTCATCTCTATCTCTCAACCCAGTTTCTGACAGTAAGCTGCTAGTCGACTAAC
AAAACTT
Found at i:5004479 original size:116 final size:117
Alignment explanation
Indices: 5004358--5004605 Score: 340
Period size: 116 Copynumber: 2.1 Consensus size: 117
5004348 TAATGATTAG
* * ** * * *
5004358 ATTATAAATAAAGTTTTAATA-TGCAAATTATTAATTATTAATATTTTAAGTAAATTATAAGTTA
1 ATTATAAATAAAATATTAATACT-CAAAAAATCAATTATTAATATTTTAA-AAAATTATAAATTA
5004422 TTAATA-TTTAAAAATA-AAATAAATAAAAACAAATAATCACAATAACATTTAA
64 TTAATATTTTAAAAATATAAATAAATAAAAACAAATAATCACAATAACATTTAA
* *
5004474 ATTATAAATAAAATATTCATACTTAAAAAATCAATTATTAATATTTTAAAAAATTATAAATTATT
1 ATTATAAATAAAATATTAATACTCAAAAAATCAATTATTAATATTTTAAAAAATTATAAATTATT
* * **
5004539 AATATTTTAAAAATATAAATAAATAAAAATAAATATTCTTAATAACATTTAA
66 AATATTTTAAAAATATAAATAAATAAAAACAAATAATCACAATAACATTTAA
5004591 ATTATAAATAAAATA
1 ATTATAAATAAAATA
5004606 ATGATATTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
115 18 0.16
116 50 0.43
117 48 0.41
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (117 bp):
ATTATAAATAAAATATTAATACTCAAAAAATCAATTATTAATATTTTAAAAAATTATAAATTATT
AATATTTTAAAAATATAAATAAATAAAAACAAATAATCACAATAACATTTAA
Found at i:5004504 original size:22 final size:23
Alignment explanation
Indices: 5004479--5004559 Score: 76
Period size: 22 Copynumber: 3.5 Consensus size: 23
5004469 TTTAAATTAT
* *
5004479 AAATA-AAATATTCATACTTAAA
1 AAATATAAATATTAATATTTAAA
* *
5004501 AAAT-CAATTATTAATATTTTAAA
1 AAATATAAATATTAATA-TTTAAA
*
5004524 AAATTATAAATTATTAATATTTTAA
1 AAA-TATAAA-TATTAATATTTAAA
5004549 AAATATAAATA
1 AAATATAAATA
5004560 AATAAAAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
22 13 0.27
23 10 0.21
24 7 0.15
25 10 0.21
26 8 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATAAATATTAATATTTAAA
Found at i:5004555 original size:24 final size:24
Alignment explanation
Indices: 5004496--5004558 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 24
5004486 ATATTCATAC
*
5004496 TTAAAAA-ATCAATTATTAATATT
1 TTAAAAATATAAATTATTAATATT
5004519 TTAAAAAATTATAAATTATTAATATT
1 TT-AAAAA-TATAAATTATTAATATT
5004545 TTAAAAATATAAAT
1 TTAAAAATATAAAT
5004559 AAATAAAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
23 2 0.06
24 12 0.33
25 5 0.14
26 17 0.47
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTAAAAATATAAATTATTAATATT
Found at i:5004599 original size:117 final size:116
Alignment explanation
Indices: 5004390--5004605 Score: 353
Period size: 117 Copynumber: 1.9 Consensus size: 116
5004380 GCAAATTATT
* *
5004390 AATTATTAATATTTTAAGTAAATTATAAGTTATTAATATTTAAAAATAAAATAAATAAAAACAAA
1 AATTATTAATATTTTAAGAAAATTATAAATTATTAATATTTAAAAATAAAATAAATAAAAACAAA
5004455 TAATCACAATAACATTTAAATTATAAATAAAATATTCATACTTAAAAAATC
66 TAATCACAATAACATTTAAATTATAAATAAAATATTCATACTTAAAAAATC
*
5004506 AATTATTAATATTTTAA-AAAATTATAAATTATTAATATTTTAAAAATATAAATAAATAAAAATA
1 AATTATTAATATTTTAAGAAAATTATAAATTATTAATA-TTTAAAAATA-AAATAAATAAAAACA
* **
5004570 AATATTCTTAATAACATTTAAATTATAAATAAAATA
64 AATAATCACAATAACATTTAAATTATAAATAAAATA
5004606 ATGATATTTT
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
115 18 0.20
116 27 0.29
117 47 0.51
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (116 bp):
AATTATTAATATTTTAAGAAAATTATAAATTATTAATATTTAAAAATAAAATAAATAAAAACAAA
TAATCACAATAACATTTAAATTATAAATAAAATATTCATACTTAAAAAATC
Found at i:5004657 original size:117 final size:115
Alignment explanation
Indices: 5004394--5004657 Score: 309
Period size: 117 Copynumber: 2.3 Consensus size: 115
5004384 ATTATTAATT
** * *
5004394 ATTAATATTTTAAGTAAATTATAAGTTATTAATATTTAAAAATAAAATAAATAAAAACAAATAAT
1 ATTAATA-TTTAAAAAAATTATAAATAATTAATATTTAAAAATAAAATAAATAAAAACAAATAAT
* *
5004459 CACAATAACATTTAAATTATAAATAAAATATTCATACTTAAAAAATCAATT
65 CACAATAACATTTAAATTATAAATAAAATAATCATACTTAAAAAATCAATG
* * * *
5004510 ATTAATATTTTAAAAAATTATAAATTATTAATATTTTAAAAATATAAATAAATAAAAATAAATAT
1 ATTAATATTTAAAAAAATTATAAATAATTAATA-TTTAAAAATA-AAATAAATAAAAACAAATAA
** * * **
5004575 TCTTAATAACATTTAAATTATAAATAAAATAATGATATTTTAAAATGTCAATG
64 TCACAATAACATTTAAATTATAAATAAAATAATCATA-CTTAAAAAATCAATG
5004628 ATTAA-ATTATAAATAAAATT-T-AATAATTAA
1 ATTAATATT-TAAA-AAAATTATAAATAATTAA
5004658 ATTATCAAAT
Statistics
Matches: 127, Mismatches: 16, Indels: 9
0.84 0.11 0.06
Matches are distributed among these distances:
115 22 0.17
116 17 0.13
117 62 0.49
118 20 0.16
119 6 0.05
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (115 bp):
ATTAATATTTAAAAAAATTATAAATAATTAATATTTAAAAATAAAATAAATAAAAACAAATAATC
ACAATAACATTTAAATTATAAATAAAATAATCATACTTAAAAAATCAATG
Found at i:5008205 original size:47 final size:47
Alignment explanation
Indices: 5008134--5009028 Score: 916
Period size: 47 Copynumber: 19.3 Consensus size: 47
5008124 ACATGGCAGG
* * * *
5008134 GTTCAAAGTTTGTGACACGTCATGGAGGGAATCTGTAACACTCCAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* *
5008181 GTTCAGAGTTTGTGACACACCATGGAGGGAATCTGTGACACGCTAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * *
5008228 GTTCAGAG-TT-TGATACGACATGGAGGGAATCTGTGACACGCTAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * *
5008273 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACACTCTAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * ** * *
5008320 GTTCAGAGTTTGTGACATGCCATGGAGGGAATTTGCCATACACCAGA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * *
5008367 GTTCAGAG-TT-TGACACGGCATGGAGGGAATCTGTGACACTCTAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* *
5008412 GTTCA-AGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGG
1 GTTCAGA-GTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * *
5008459 GTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGACAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * *
5008506 GTTCAGGGTTTGTGACACTCCATGGAGGGAATCTGTGACACGGCAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * *
5008553 GTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGAGATGCCA-A
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * ** *
5008599 GGTTCATAGTTTGCGATACGCCATGGAGGGAATCTAAGACACTCCAGA
1 -GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * *
5008647 GTTTAGAGTTTGTGACACGCCATGGAGGGAATCTATGACACACCAAA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * * *
5008694 ATTTAGAG-TT-TGACACGGCATGGAGGGAATTTGTGACACGCCAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
** * * * * *
5008739 GTTTTGTGTTTGTGACAAGCCATGGAGGGAATCCGTGACACGGCAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * * * *
5008786 GTTCAGGGTTTATGACACGCCATGGATGGAATTTGTGAGACGCCAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * *
5008833 GTTCAGAGTTTATGACACGCCATTGAGGGAATCTGTGACAC-CCTAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCC-AGA
* * * * * *
5008880 GTTTAGAG-TT-TGACACGCCATAGAGGAAATTTGTGACACGCTAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * ** *
5008925 GTTCAGAGTTTGTGACACGCCACGGAGGGAATTTGTGACACATCAGT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
* * * * * *
5008972 GTTCAGAG-TT-TGACATGCCATGGAGGAAATCTATGACATGCTAGG
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
*
5009017 GTTCAAAGTTTG
1 GTTCAGAGTTTG
5009029 ACACGTCAAC
Statistics
Matches: 714, Mismatches: 118, Indels: 32
0.83 0.14 0.04
Matches are distributed among these distances:
44 1 0.00
45 172 0.24
46 23 0.03
47 517 0.72
48 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (47 bp):
GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACGCCAGA
Found at i:5008371 original size:139 final size:141
Alignment explanation
Indices: 5008134--5009009 Score: 886
Period size: 139 Copynumber: 6.3 Consensus size: 141
5008124 ACATGGCAGG
* * *
5008134 GTTCAAAGTTTGTGACACGTCATGGAGGGAATCTGTAACACTCCAGAGTTCAGAGTTTGTGACAC
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCCAGAGTTCAGAGTTTGTGACAC
* * * * *
5008199 ACCATGGAGGGAATCTGTGACACGCTAGAGTTCAGAG-TT-TGATACGACATGGAGGGAATCTGT
66 GCCATGGAGGGAATCTGTGACACACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGT
5008262 GACACGCTAGT
131 GACACGCTAGT
* * *
5008273 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACACTCTAGAGTTCAGAGTTTGTGACAT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCCAGAGTTCAGAGTTTGTGACAC
* ** * *
5008338 GCCATGGAGGGAATTTGCCATACACCAGAGTTCAGAG-TT-TGACACGGCATGGAGGGAATCTGT
66 GCCATGGAGGGAATCTGTGACACACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGT
*
5008401 GACACTCTAGT
131 GACACGCTAGT
** * *
5008412 GTTCA-AGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGGCAGGGTTCAGGGTTTGTGACA
1 GTTCAGA-GTTTGTGACACGCCATGGAGGGAATCTGTGACACTCCAGAGTTCAGAGTTTGTGACA
* * *
5008476 CGCCATGGAGGGAATCTGTGACACGA-CAGGGTTCAGGGTTTGTGACACTCCATGGAGGGAATCT
65 CGCCATGGAGGGAATCTGTGACAC-ACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCT
*
5008540 GTGACACGGC-AGG
129 GTGACAC-GCTAGT
* * * * *
5008553 GTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGAGA-TGCCA-AGGTTCATAGTTTGCGAT
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACT-CCAGA-GTTCAGAGTTTGTGAC
** * *
5008616 ACGCCATGGAGGGAATCTAAGACACTCCAGAGTTTAGAGTTTGTGACACGCCATGGAGGGAATCT
64 ACGCCATGGAGGGAATCTGTGACACACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCT
* * * **
5008681 ATGACACACCAAA
129 GTGACACGCTAGT
* * * * * * ** * *
5008694 ATTTAGAG-TT-TGACACGGCATGGAGGGAATTTGTGACACGCCAGTGTTTTGTGTTTGTGACAA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCCAGAGTTCAGAGTTTGTGACAC
* ** * * * * *
5008757 GCCATGGAGGGAATCCGTGACACGGCAGGGTTCAGGGTTTATGACACGCCATGGATGGAATTTGT
66 GCCATGGAGGGAATCTGTGACACACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGT
* * *
5008822 GAGACGCCAGG
131 GACACGCTAGT
* * * *
5008833 GTTCAGAGTTTATGACACGCCATTGAGGGAATCTGTGACAC-CCTAGTGTTTAGAG-TT-TGACA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCC-AGAGTTCAGAGTTTGTGACA
* * * * * * * *
5008895 CGCCATAGAGGAAATTTGTGACACGCTAGGGTTCAGAGTTTGTGACACGCCACGGAGGGAATTTG
65 CGCCATGGAGGGAATCTGTGACACACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTG
*
5008960 TGACAC-ATCAGT
130 TGACACGCT-AGT
* * *
5008972 GTTCAGAG-TT-TGACATGCCATGGAGGAAATCTATGACA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACA
5009010 TGCTAGGGTT
Statistics
Matches: 611, Mismatches: 110, Indels: 34
0.81 0.15 0.05
Matches are distributed among these distances:
137 24 0.04
138 3 0.00
139 387 0.63
140 12 0.02
141 184 0.30
142 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (141 bp):
GTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACACTCCAGAGTTCAGAGTTTGTGACAC
GCCATGGAGGGAATCTGTGACACACCAGAGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGT
GACACGCTAGT
Found at i:5008472 original size:186 final size:186
Alignment explanation
Indices: 5008134--5009028 Score: 902
Period size: 186 Copynumber: 4.8 Consensus size: 186
5008124 ACATGGCAGG
* * * * *
5008134 GTTCAAAGTTTGTGACACGTCATGGAGGGAATCTGTAACACTCCAGAGTTCAGAGTTTGTGACAC
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
* * * * *
5008199 ACCATGGAGGGAATCTGTGACACGCTAGAGTTC-AGAG-TTTGATACGACATGGAGGGAATCTGT
66 GCCATGGAGGGAATCTGTGACACTC-AGTGTTCAAG-GTTTTGACACGCCATGGAGGGAATCTGT
* * *
5008262 GACACGCTAGTGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACACTCTAGA
129 GACACGCCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACACACTAGA
* ** * *
5008320 GTTCAGAGTTTGTGACATGCCATGGAGGGAATTTGCCATACACCAGAGTTCAGAG-TT-TGACAC
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
*
5008383 GGCATGGAGGGAATCTGTGACACTCTAGTGTTCAAGGTTTGTGACACGCCATGGAGGGAATCTGT
66 GCCATGGAGGGAATCTGTGACACTC-AGTGTTCAAGGTTT-TGACACGCCATGGAGGGAATCTGT
* * * *
5008448 GACACGGCAGGGTTCAGGGTTTGTGACACGCCATGGAGGGAATCTGTGACACGAC-AGG
129 GACACGCCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACAC-ACTAGA
* * * * * *
5008506 GTTCAGGGTTTGTGACACTCCATGGAGGGAATCTGTGACACGGCAGGGTTCAGGGTTTGTGACAC
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
* * *
5008571 GCCATGGAGGGAATCTGTGAGA-TGCCAAG-GTTCATA-GTTTGCGATACGCCATGGAGGGAATC
66 GCCATGGAGGGAATCTGTGACACT--C-AGTGTTCA-AGGTTT-TGACACGCCATGGAGGGAATC
** * * * * *
5008633 TAAGACACTCCAGAGTTTAGAGTTTGTGACACGCCATGGAGGGAATCT-ATGACACACCAAA
126 TGTGACACGCCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGA-GACACACTAGA
* * * * ** * *
5008694 ATTTAGAG-TT-TGACACGGCATGGAGGGAATTTGTGACACGCCAGTGTTTTGTGTTTGTGACAA
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
* * * * * *
5008757 GCCATGGAGGGAATCCGTGACACGGCAGGGTTCAGGGTTTATGACACGCCATGGATGGAATTTGT
66 GCCATGGAGGGAATCTGTGACAC-TCAGTGTTCAAGGTTT-TGACACGCCATGGAGGGAATCTGT
* * * * * *
5008822 GAGACGCCAGGGTTCAGAGTTTATGACACGCCATTGAGGGAATCTGTGACACCCTAGT
129 GACACGCCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACACACTAGA
* * * * *
5008880 GTTTAGAG-TT-TGACACGCCATAGAGGAAATTTGTGACACGCTAGGGTTCAGAGTTTGTGACAC
1 GTTCAGAGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
* * * * *
5008943 GCCACGGAGGGAATTTGTGACACATCAGTGTTC-AGAG-TTTGACATGCCATGGAGGAAATCTAT
66 GCCATGGAGGGAATCTGTGACAC-TCAGTGTTCAAG-GTTTTGACACGCCATGGAGGGAATCTGT
* * *
5009006 GACATGCTAGGGTTCAAAGTTTG
129 GACACGCCAGGGTTCAGAGTTTG
5009029 ACACGTCAAC
Statistics
Matches: 584, Mismatches: 108, Indels: 36
0.80 0.15 0.05
Matches are distributed among these distances:
184 73 0.12
185 11 0.02
186 381 0.65
187 8 0.01
188 107 0.18
189 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (186 bp):
GTTCAGAGTTTGTGACACGCCATGGAGGGAATTTGTGACACGCCAGAGTTCAGAGTTTGTGACAC
GCCATGGAGGGAATCTGTGACACTCAGTGTTCAAGGTTTTGACACGCCATGGAGGGAATCTGTGA
CACGCCAGGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTGAGACACACTAGA
Found at i:5008476 original size:24 final size:24
Alignment explanation
Indices: 5008398--5008574 Score: 111
Period size: 24 Copynumber: 7.5 Consensus size: 24
5008388 GGAGGGAATC
* * * *
5008398 TGTGACACTCTAGTGTTCAAGGTT
1 TGTGACACGCCAGGGTTCAGGGTT
* *
5008422 TGTGACACGCCATGG---AGGGAATC
1 TGTGACACGCCAGGGTTCAGGG--TT
*
5008445 TGTGACACGGCAGGGTTCAGGGTT
1 TGTGACACGCCAGGGTTCAGGGTT
* *
5008469 TGTGACACGCCATGG---AGGGAATC
1 TGTGACACGCCAGGGTTCAGGG--TT
*
5008492 TGTGACACGACAGGGTTCAGGGTT
1 TGTGACACGCCAGGGTTCAGGGTT
* * *
5008516 TGTGACACTCCATGG---AGGGAATC
1 TGTGACACGCCAGGGTTCAGGG--TT
*
5008539 TGTGACACGGCAGGGTTCAGGGTT
1 TGTGACACGCCAGGGTTCAGGGTT
5008563 TGTGACACGCCA
1 TGTGACACGCCA
5008575 TGGAGGGAAT
Statistics
Matches: 114, Mismatches: 24, Indels: 30
0.68 0.14 0.18
Matches are distributed among these distances:
21 11 0.10
23 41 0.36
24 50 0.44
26 12 0.11
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (24 bp):
TGTGACACGCCAGGGTTCAGGGTT
Found at i:5009880 original size:31 final size:31
Alignment explanation
Indices: 5009771--5009975 Score: 162
Period size: 31 Copynumber: 6.6 Consensus size: 31
5009761 ACCCCATGGT
* * *
5009771 TGGCGCGTTACAAGATTTGACTTGTTATGCA
1 TGGCGTGTAACAACATTTGACTTGTTATGCA
** *** *
5009802 TGGTATGTAATGGCATTTGACTT-TCTATAG-T
1 TGGCGTGTAACAACATTTGACTTGT-TAT-GCA
* * * *
5009833 TGGTGTGTCACCACATTTGACTTCTTATGCA
1 TGGCGTGTAACAACATTTGACTTGTTATGCA
* * *
5009864 TGGCGTGTAACAACATTTGACTTGATATTCC
1 TGGCGTGTAACAACATTTGACTTGTTATGCA
* * * *
5009895 TAGCGTGTAACAATATTTTACTTGTTATGTA
1 TGGCGTGTAACAACATTTGACTTGTTATGCA
* * *
5009926 GGGCGTGTAACCACATTTTACTTGTTATGCA
1 TGGCGTGTAACAACATTTGACTTGTTATGCA
*
5009957 TGGCGTGTAACCACATTTG
1 TGGCGTGTAACAACATTTG
5009976 TGCCGTGTTT
Statistics
Matches: 134, Mismatches: 36, Indels: 8
0.75 0.20 0.04
Matches are distributed among these distances:
30 2 0.01
31 130 0.97
32 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTGACTTGTTATGCA
Found at i:5015475 original size:63 final size:63
Alignment explanation
Indices: 5015401--5015520 Score: 159
Period size: 63 Copynumber: 1.9 Consensus size: 63
5015391 ACCACAACAC
* * * * *
5015401 GATGACGATGGTGCTCAATAGAGAGTTGACAAAGCTCATACAGTTTAGAGAGTTGAGTGACTT
1 GATGACAATGGTGCTCAACAGAGAGTTAACAAAGCTCATACAGTTCAGAGAGCTGAGTGACTT
* * * *
5015464 GATGACAATGGTGCTTAACAGAGAGTTAACAGAGTTGATACAGTTCAGAGAGCTGAG
1 GATGACAATGGTGCTCAACAGAGAGTTAACAAAGCTCATACAGTTCAGAGAGCTGAG
5015521 AGAGAAAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.25
Consensus pattern (63 bp):
GATGACAATGGTGCTCAACAGAGAGTTAACAAAGCTCATACAGTTCAGAGAGCTGAGTGACTT
Found at i:5024343 original size:18 final size:18
Alignment explanation
Indices: 5024320--5024355 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5024310 GATATGCTCT
5024320 TGACTTGGTCTTAACTGA
1 TGACTTGGTCTTAACTGA
5024338 TGACTTGGTCTTAACTGA
1 TGACTTGGTCTTAACTGA
5024356 GTAGAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (18 bp):
TGACTTGGTCTTAACTGA
Found at i:5031555 original size:10 final size:10
Alignment explanation
Indices: 5031540--5031575 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
5031530 AATAAACTTT
5031540 TATATGTATA
1 TATATGTATA
5031550 TATATGTATA
1 TATATGTATA
5031560 TATAT-TCATA
1 TATATGT-ATA
5031570 TATATG
1 TATATG
5031576 GTTGCCTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 1 0.04
10 23 0.96
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (10 bp):
TATATGTATA
Found at i:5034942 original size:16 final size:16
Alignment explanation
Indices: 5034921--5034951 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5034911 AAAATTTAAA
5034921 TTTTGATTCTTTTGAG
1 TTTTGATTCTTTTGAG
*
5034937 TTTTGATTGTTTTGA
1 TTTTGATTCTTTTGA
5034952 TATTTTTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.19, T:0.65
Consensus pattern (16 bp):
TTTTGATTCTTTTGAG
Found at i:5036429 original size:80 final size:81
Alignment explanation
Indices: 5036306--5036538 Score: 271
Period size: 80 Copynumber: 2.9 Consensus size: 81
5036296 CATAAGTTCC
* * ** *
5036306 ATTTATGAG-TTGT-AACATGT-ATGCCATAAGATATATGCATTGAGATAGTCATATACGCTATA
1 ATTTATGAGATTATGAA-ATGTCATGCCATAAGATGTATGTGTTGAGATAGTCATATACACTATA
* * **
5036368 GGCGAAGTGTGTAAGTG
65 GGCTAAGTATGTAAACG
* *
5036385 ATTTATGAGATTATGAAATG-CATGCCATGAGATGTATGTGTTGAGATAGTCATATACACTACCA
1 ATTTATGAGATTATGAAATGTCATGCCATAAGATGTATGTGTTGAGATAGTCATATACACTA-TA
*
5036449 -GCTAAGCATGTAAACG
65 GGCTAAGTATGTAAACG
* * *
5036465 ATTTATGAGATTATGAAATGTC-TACCATAAGATGTATGTGTTAAGATAGTCATATACACTATGG
1 ATTTATGAGATTATGAAATGTCATGCCATAAGATGTATGTGTTGAGATAGTCATATACACTATAG
5036529 GCTAAGTATG
66 GCTAAGTATG
5036539 ATGATGATTT
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
79 9 0.07
80 117 0.90
81 4 0.03
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (81 bp):
ATTTATGAGATTATGAAATGTCATGCCATAAGATGTATGTGTTGAGATAGTCATATACACTATAG
GCTAAGTATGTAAACG
Found at i:5040041 original size:16 final size:16
Alignment explanation
Indices: 5040020--5040058 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
5040010 CCCGGCCCCC
5040020 TTTTTTG-TACTTTTTA
1 TTTTTTGCTA-TTTTTA
5040036 TTTTTTGCTTATTTTTA
1 TTTTTTGC-TATTTTTA
5040053 TTTTTT
1 TTTTTT
5040059 AAAGTTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 12 0.57
18 2 0.10
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTTTGCTATTTTTA
Found at i:5040083 original size:17 final size:18
Alignment explanation
Indices: 5040030--5040104 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 18
5040020 TTTTTTGTAC
5040030 TTTTTAT-TTTTTGCTT-A
1 TTTTTATATTTTT-CTTAA
*
5040047 -TTTT-TATTTTT-TAAA
1 TTTTTATATTTTTCTTAA
*
5040062 GTTTTATATTTTTCTTAA
1 TTTTTATATTTTTCTTAA
*
5040080 TTTTTTGTATTTTCTCTTATA
1 -TTTTTATATTTT-TCTTA-A
5040101 TTTT
1 TTTT
5040105 GTATTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
14 1 0.02
15 2 0.04
16 13 0.28
17 7 0.15
18 3 0.07
19 10 0.22
20 9 0.20
21 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTTTATATTTTTCTTAA
Found at i:5040105 original size:19 final size:19
Alignment explanation
Indices: 5040063--5040111 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
5040053 TTTTTTAAAG
* *
5040063 TTTTATATTTTTCTTAATT
1 TTTTGTATTTTTCTTAATA
5040082 TTTTGTATTTTCTCTT-ATA
1 TTTTGTATTTT-TCTTAATA
5040101 TTTTGTATTTT
1 TTTTGTATTTT
5040112 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (19 bp):
TTTTGTATTTTTCTTAATA
Found at i:5040111 original size:26 final size:26
Alignment explanation
Indices: 5040088--5040138 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5040078 AATTTTTTGT
5040088 ATTTTCTCT-TATATTTTGTATTTTAA
1 ATTTT-TCTGTATATTTTGTATTTTAA
* *
5040114 ATTTTTTTGTATATTTTGTGTTTTA
1 ATTTTTCTGTATATTTTGTATTTTA
5040139 TTTTTGGCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 2 0.09
26 20 0.91
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.69
Consensus pattern (26 bp):
ATTTTTCTGTATATTTTGTATTTTAA
Found at i:5040513 original size:41 final size:41
Alignment explanation
Indices: 5040452--5040531 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
5040442 AATCTTTATT
*
5040452 TTTGGAAAATACTACACTTATAAAACTCCACAACTTTAAAA
1 TTTGAAAAATACTACACTTATAAAACTCCACAACTTTAAAA
* * * * *
5040493 TTTGAAAAATACTCCTCTTATGAGAGTCCACAACTTTAA
1 TTTGAAAAATACTACACTTATAAAACTCCACAACTTTAA
5040532 GAGAACTTTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (41 bp):
TTTGAAAAATACTACACTTATAAAACTCCACAACTTTAAAA
Found at i:5040644 original size:107 final size:106
Alignment explanation
Indices: 5040467--5040665 Score: 281
Period size: 107 Copynumber: 1.9 Consensus size: 106
5040457 AAAATACTAC
* * * * *
5040467 ACTTATAAAACTCCACAACTTTAAAATTTGAAAAATACTCCTCTTATGAGAGTCCACAACTTTAA
1 ACTTACAAAACTCCACAACTTTAAAATTTGAAAAATACTCATCCTACGAGAATCCACAACTTTAA
* *
5040532 GAGAACTTTGTAATTGTTTTTTTTTTTTTGAAAAGCACTCT
66 AAGAACTTTGAAATTGTTTTTTTTTTTTTGAAAAGCACTCT
* * * * *
5040573 ACTTACAAAACTCGACGATTTTAAAATTTTGAACAATACTCATCCTACGAGAATCTACAACTTTA
1 ACTTACAAAACTCCACAACTTTAAAA-TTTGAAAAATACTCATCCTACGAGAATCCACAACTTTA
5040638 AAAGAACTTTGAAATTGTTTTTTTTTTT
65 AAAGAACTTTGAAATTGTTTTTTTTTTT
5040666 AAATAACTCC
Statistics
Matches: 80, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
106 22 0.28
107 58 0.73
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.39
Consensus pattern (106 bp):
ACTTACAAAACTCCACAACTTTAAAATTTGAAAAATACTCATCCTACGAGAATCCACAACTTTAA
AAGAACTTTGAAATTGTTTTTTTTTTTTTGAAAAGCACTCT
Found at i:5040741 original size:103 final size:103
Alignment explanation
Indices: 5040370--5040743 Score: 274
Period size: 107 Copynumber: 3.5 Consensus size: 103
5040360 TTTAATGAGG
* ** * * * * *
5040370 CTCCACAAGTTTAAAAGAGTTGAAAAACACTCCTCATAAGAAGCTCCATAGCTTTAAAAGAATTT
1 CTCCACAACTTTAAAA-TTTTGAAAAATACTCCTCAT-ACAAG-TCCACAACTTTAAAAGAA-CT
** * * * * *
5040435 TTGAAATAATCTTTATTTTTGGAAAATACTAC-ACTTATAAAA
62 TTGAAATTGTTTTTTTTTTTTGAAAACACT-CTACTTACAAAA
* * *
5040477 CTCCACAACTTTAAAA-TTTGAAAAATACTCCTCTTATGAGAGTCCACAACTTTAAGAGAACTTT
1 CTCCACAACTTTAAAATTTTGAAAAATACTCCTCATA-CA-AGTCCACAACTTTAAAAGAACTTT
*
5040541 GTAATTGTTTTTTTTTTTTTGAAAAGCACTCTACTTACAAAA
64 GAAATTG-TTTTTTTTTTTTGAAAA-CACTCTACTTACAAAA
* * * * * * * *
5040583 CTCGACGATTTTAAAATTTTGAACAATACTCATCCTACGAGAATCTACAACTTTAAAAGAACTTT
1 CTCCACAACTTTAAAATTTTGAAAAATACTCCTCATAC-A-AGTCCACAACTTTAAAAGAACTTT
* ** *
5040648 GAAATTG-TTTTTTTTTTT-AAATA-ACTCCTTC-TATTAAG
64 GAAATTGTTTTTTTTTTTTGAAA-ACACT-CTACTTACAAAA
* *
5040686 CTCCACAACTTTAAAATTTTGAAAAATACTCCTCATACCAAGCTCCATAATTTTAAAA
1 CTCCACAACTTTAAAATTTTGAAAAATACTCCTCATA-CAAG-TCCACAACTTTAAAA
5040744 TAATTGAAAA
Statistics
Matches: 215, Mismatches: 41, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
102 1 0.00
103 51 0.24
104 15 0.07
105 60 0.28
106 27 0.13
107 61 0.28
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (103 bp):
CTCCACAACTTTAAAATTTTGAAAAATACTCCTCATACAAGTCCACAACTTTAAAAGAACTTTGA
AATTGTTTTTTTTTTTTGAAAACACTCTACTTACAAAA
Found at i:5040775 original size:43 final size:42
Alignment explanation
Indices: 5040683--5040782 Score: 121
Period size: 43 Copynumber: 2.4 Consensus size: 42
5040673 TCCTTCTATT
*
5040683 AAGCTCCACAACTTTAAAATTTTGAAAAATACTCCTCATACC
1 AAGCTCCACAACTTTAAAATATTGAAAAATACTCCTCATACC
* * * **
5040725 AAGCTCCATAATTTTAAAATAATTGAAAAATACTTCTTGTA-C
1 AAGCTCCACAACTTTAAAAT-ATTGAAAAATACTCCTCATACC
5040767 AAGTCTCCACAACTTT
1 AAG-CTCCACAACTTT
5040783 GAAAGAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
42 22 0.46
43 26 0.54
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.32
Consensus pattern (42 bp):
AAGCTCCACAACTTTAAAATATTGAAAAATACTCCTCATACC
Found at i:5044693 original size:31 final size:29
Alignment explanation
Indices: 5044615--5044671 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
5044605 ACTGTTTGTG
*
5044615 CGAGATTATAGTAAATGGGTATTTCCTAC
1 CGAGATTATGGTAAATGGGTATTTCCTAC
5044644 CGAGATTATGGTAAATGGGTATTTCCTA
1 CGAGATTATGGTAAATGGGTATTTCCTA
5044672 TCGTGAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.12, G:0.23, T:0.35
Consensus pattern (29 bp):
CGAGATTATGGTAAATGGGTATTTCCTAC
Found at i:5072787 original size:22 final size:19
Alignment explanation
Indices: 5072758--5072805 Score: 60
Period size: 22 Copynumber: 2.4 Consensus size: 19
5072748 ATGAGGAATG
5072758 AAAAAAGAAAAGTAAAGAGAA
1 AAAAAAGAAAA-T-AAGAGAA
*
5072779 AAGAAAAGAAAATAATAGAA
1 AA-AAAAGAAAATAAGAGAA
5072799 AAAAAAG
1 AAAAAAG
5072806 GTAACCTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 8 0.32
21 3 0.12
22 9 0.36
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.06
Consensus pattern (19 bp):
AAAAAAGAAAATAAGAGAA
Found at i:5079294 original size:16 final size:16
Alignment explanation
Indices: 5079273--5079306 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5079263 AATAGGAGAA
5079273 GAAATCATATGTCCTT
1 GAAATCATATGTCCTT
5079289 GAAATCATATGTCCTT
1 GAAATCATATGTCCTT
5079305 GA
1 GA
5079307 TACTCCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (16 bp):
GAAATCATATGTCCTT
Found at i:5083705 original size:27 final size:25
Alignment explanation
Indices: 5083673--5083729 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
5083663 ACATGGCTGG
5083673 GGCCATGGTCTATGATATACGTGGCAA
1 GGCCATGG-CT-TGATATACGTGGCAA
* * *
5083700 GGCCATGGGTTGATATATGTGGCTA
1 GGCCATGGCTTGATATACGTGGCAA
5083725 GGCCA
1 GGCCA
5083730 CAAGTGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 18 0.67
26 1 0.04
27 8 0.30
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (25 bp):
GGCCATGGCTTGATATACGTGGCAA
Found at i:5083745 original size:24 final size:25
Alignment explanation
Indices: 5083685--5083745 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
5083675 CCATGGTCTA
***
5083685 TGATATACGTGGCAAGGCCATGGGT
1 TGATATACGTGGCAAGGCCACAAGT
* *
5083710 TGATATATGTGGCTAGGCCACAAG-
1 TGATATACGTGGCAAGGCCACAAGT
5083734 TGATATACGTGG
1 TGATATACGTGG
5083746 TTGTGACCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 11 0.37
25 19 0.63
ACGTcount: A:0.26, C:0.15, G:0.33, T:0.26
Consensus pattern (25 bp):
TGATATACGTGGCAAGGCCACAAGT
Found at i:5089942 original size:40 final size:40
Alignment explanation
Indices: 5089898--5090010 Score: 131
Period size: 40 Copynumber: 2.8 Consensus size: 40
5089888 CAACCACAAC
**
5089898 TTCACAACATCACTGTCTTTTCAAGGTTAAAGCACAAACT
1 TTCACAACATCACTACCTTTTCAAGGTTAAAGCACAAACT
* * *
5089938 TTCACAA-AGTCTCTACCTTTTTAAGGTTAAAGCACAACCT
1 TTCACAACA-TCACTACCTTTTCAAGGTTAAAGCACAAACT
* *
5089978 TTCACAACATCTCTACC-TTTCTAAGGTCAAAGC
1 TTCACAACATCACTACCTTTTC-AAGGTTAAAGC
5090011 GTAATCCCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
39 4 0.06
40 58 0.92
41 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.31
Consensus pattern (40 bp):
TTCACAACATCACTACCTTTTCAAGGTTAAAGCACAAACT
Found at i:5090784 original size:17 final size:17
Alignment explanation
Indices: 5090758--5090793 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5090748 ATATAGATGA
* *
5090758 TCAAAGAAAGTTTAAGC
1 TCAAAAAAAGTTGAAGC
5090775 TCAAAAAAAGTTGAAGC
1 TCAAAAAAAGTTGAAGC
5090792 TC
1 TC
5090794 TAGAAGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.14, G:0.17, T:0.22
Consensus pattern (17 bp):
TCAAAAAAAGTTGAAGC
Found at i:5097019 original size:26 final size:24
Alignment explanation
Indices: 5096990--5097039 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
5096980 CAAACATCCA
5096990 CAAGGTCATACATTGACCGTTCAAGG
1 CAAGGTCATAC--TGACCGTTCAAGG
*
5097016 CAAGTTCATACTGACCGTTCAAGG
1 CAAGGTCATACTGACCGTTCAAGG
5097040 TAGGTTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 13 0.57
26 10 0.43
ACGTcount: A:0.30, C:0.24, G:0.22, T:0.24
Consensus pattern (24 bp):
CAAGGTCATACTGACCGTTCAAGG
Found at i:5099087 original size:67 final size:65
Alignment explanation
Indices: 5099026--5099155 Score: 163
Period size: 65 Copynumber: 2.0 Consensus size: 65
5099016 ATATTCTGTG
* * *
5099026 TACTACATGAGATGATTAAGTATGTAG-ATTAATGCCATAAGAATATATATGTGATGTATATTCC
1 TACTACATGAGATGATTAAGTA---AGCATAAATGCCATAAGAATACATATATGATGTATATTCC
5099090 ATA
63 ATA
* * * *
5099093 TACTATATGAGATGATTGAGTAAGCATAAATGCCATGAGAATACATATATGATGTAAATTCCA
1 TACTACATGAGATGATTAAGTAAGCATAAATGCCATAAGAATACATATATGATGTATATTCCA
5099156 CATATCTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
64 2 0.04
65 33 0.60
67 20 0.36
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (65 bp):
TACTACATGAGATGATTAAGTAAGCATAAATGCCATAAGAATACATATATGATGTATATTCCATA
Found at i:5102848 original size:70 final size:71
Alignment explanation
Indices: 5102709--5102904 Score: 188
Period size: 71 Copynumber: 2.8 Consensus size: 71
5102699 ACCTTTTTCC
* * ** * *
5102709 CCTTCATAGGATCGACTATAGTTGGTCTATAGTCGAT-TCTAGACTAGAATG-TTAGATTTTATT
1 CCTTCCTAAGATCGACTATAGAGGGTCAATAGTCGATCT-TGGACTAGAATGCTT-GATTTTATT
**
5102772 TGA-TTTT
64 CCATTTTT
* *
5102779 GCTTCAC-AAGATCGACTATAGAGGGTCAATAGTCGATCTTGGACTAGAATGCTTGCA-TTTCTT
1 CCTTC-CTAAGATCGACTATAGAGGGTCAATAGTCGATCTTGGACTAGAATGCTTG-ATTTTATT
5102842 CCATTTTT
64 CCATTTTT
* * *
5102850 CCTTCCTAAGATTGACTATAGAGGG-CACATAGTCGATCTTGGACCAAAATGCTTG
1 CCTTCCTAAGATCGACTATAGAGGGTCA-ATAGTCGATCTTGGACTAGAATGCTTG
5102905 GCTTTCCTTA
Statistics
Matches: 105, Mismatches: 14, Indels: 13
0.80 0.11 0.10
Matches are distributed among these distances:
70 51 0.49
71 54 0.51
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (71 bp):
CCTTCCTAAGATCGACTATAGAGGGTCAATAGTCGATCTTGGACTAGAATGCTTGATTTTATTCC
ATTTTT
Found at i:5102932 original size:71 final size:71
Alignment explanation
Indices: 5102780--5102936 Score: 187
Period size: 71 Copynumber: 2.2 Consensus size: 71
5102770 TTTGATTTTG
* * *
5102780 CTTCACAAGATCGACTATAGAGGGTCAATAGTCGATCTTGGACTAGAATGCTTGCATTTCTTCCA
1 CTTCACAAGATCGACTATAGAGGGTCAATAGTCGATCTTGGACCAAAATGCTTGCATTTCTTACA
* *
5102845 TTTTTC
66 TTTCTA
*
5102851 CTTC-CTAAGATTGACTATAGAGGG-CACATAGTCGATCTTGGACCAAAATGCTTGGC-TTTCCT
1 CTTCAC-AAGATCGACTATAGAGGGTCA-ATAGTCGATCTTGGACCAAAATGCTT-GCATTT-CT
5102913 TAC-TTTCTA
62 TACATTTCTA
*
5102922 TTTCACAAGATCGAC
1 CTTCACAAGATCGAC
5102937 CCTTTATGTG
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
70 3 0.04
71 63 0.86
72 7 0.10
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (71 bp):
CTTCACAAGATCGACTATAGAGGGTCAATAGTCGATCTTGGACCAAAATGCTTGCATTTCTTACA
TTTCTA
Found at i:5105345 original size:15 final size:15
Alignment explanation
Indices: 5105325--5105357 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
5105315 AGAGAGTAAG
5105325 TTGACTGAGTATTAC
1 TTGACTGAGTATTAC
5105340 TTGACTGAGTATTAC
1 TTGACTGAGTATTAC
5105355 TTG
1 TTG
5105358 GTATCTCACT
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:0.24, C:0.12, G:0.21, T:0.42
Consensus pattern (15 bp):
TTGACTGAGTATTAC
Found at i:5106387 original size:22 final size:22
Alignment explanation
Indices: 5106359--5106403 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5106349 AAATTTTGAA
5106359 CTTTGAATATGTCCAAAAGATG
1 CTTTGAATATGTCCAAAAGATG
5106381 CTTTGAATATGTCCAAAAGATG
1 CTTTGAATATGTCCAAAAGATG
5106403 C
1 C
5106404 CTGGAAAGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.31
Consensus pattern (22 bp):
CTTTGAATATGTCCAAAAGATG
Found at i:5113117 original size:21 final size:19
Alignment explanation
Indices: 5113091--5113131 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
5113081 AATTTAAAAC
5113091 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
5113112 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
5113131 A
1 A
5113132 CTTGACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:5118913 original size:35 final size:35
Alignment explanation
Indices: 5118854--5118970 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
5118844 ACAAGGTTAG
5118854 GCATAACCTTTACAACATGCCTTTTGCAAGATCAA
1 GCATAACCTTTACAACATGCCTTTTGCAAGATCAA
** * * * * * *
5118889 GTGTAACTTTTACAGCATGTCTTTTACAAGGTTAA
1 GCATAACCTTTACAACATGCCTTTTGCAAGATCAA
* *
5118924 GCATAACCTTTACAACATGCCTCTTGCAAGATTAA
1 GCATAACCTTTACAACATGCCTTTTGCAAGATCAA
5118959 GCATAACCTTTA
1 GCATAACCTTTA
5118971 TTAAGACATT
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 66 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.32
Consensus pattern (35 bp):
GCATAACCTTTACAACATGCCTTTTGCAAGATCAA
Found at i:5123019 original size:70 final size:70
Alignment explanation
Indices: 5122942--5123072 Score: 178
Period size: 70 Copynumber: 1.9 Consensus size: 70
5122932 TAGGGTATTT
*
5122942 ATCATGCATACTTAATCA-CTTCAAATA-G-TATATGAAATTTACATCACATATACAATCTTATA
1 ATCATGCATACTTAATCATC-TC--ATACGATATATGAAATTTACATCACATACACAATCTTATA
5123004 GTATATAC
63 GTATATAC
* * *
5123012 ATCATGCATACTTAATCATCTCATACGATATATGTAATTTACATCATATACATAATCTTAT
1 ATCATGCATACTTAATCATCTCATACGATATATGAAATTTACATCACATACACAATCTTAT
5123073 GGCATCCACC
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
68 3 0.06
69 1 0.02
70 49 0.91
71 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (70 bp):
ATCATGCATACTTAATCATCTCATACGATATATGAAATTTACATCACATACACAATCTTATAGTA
TATAC
Found at i:5137396 original size:18 final size:19
Alignment explanation
Indices: 5137373--5137415 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
5137363 AGACAAGTGA
5137373 AATATTTT-TAAATAAAAT
1 AATATTTTATAAATAAAAT
*
5137391 AATATTTTATTAATAAAAT
1 AATATTTTATAAATAAAAT
5137410 AATATT
1 AATATT
5137416 AAAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATATTTTATAAATAAAAT
Found at i:5137426 original size:19 final size:19
Alignment explanation
Indices: 5137383--5137428 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5137373 AATATTTTTA
** *
5137383 AATAAAATAATATTTTATT
1 AATAAAATAATATTAAAAT
5137402 AATAAAATAATATTAAAAT
1 AATAAAATAATATTAAAAT
*
5137421 ATTAAAAT
1 AATAAAAT
5137429 TTTATTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATAAAATAATATTAAAAT
Found at i:5141963 original size:19 final size:19
Alignment explanation
Indices: 5141922--5141961 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
5141912 TAATTAGATG
5141922 AAATTTGAGACTAAAGGAT
1 AAATTTGAGACTAAAGGAT
* *
5141941 AAATTTGATA-TAAAGGGT
1 AAATTTGAGACTAAAGGAT
5141959 AAA
1 AAA
5141962 ATGGTAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.03, G:0.20, T:0.28
Consensus pattern (19 bp):
AAATTTGAGACTAAAGGAT
Found at i:5142329 original size:29 final size:29
Alignment explanation
Indices: 5142294--5142638 Score: 299
Period size: 29 Copynumber: 11.9 Consensus size: 29
5142284 GGCAACTTTT
* *
5142294 ACATGTTTTGTCTTAATGTAGATAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * * *
5142323 ATATG-TTAGTCTTAATTTAAATAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5142351 GCATG-TTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5142379 ACATGTTTTGTCTTAATTTGGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * * * *
5142408 AAAAGTTTTGTTTTAATTTGGACAATAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* *
5142437 ACATATTTTCTCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* *
5142466 ACATG-TTTCTCTTAATTTGGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
** * *
5142494 ATGTGTTTTTTCTTAATTTCA-ACAAAAAAA
1 ACATGTTTTGTCTTAATTT-AGAC-AAGAAA
* * * *
5142524 AGCATG-ATCGTTTTAATTTAGACAAAAAA
1 A-CATGTTTTGTCTTAATTTAGACAAGAAA
* * * *
5142553 AAATGTTTTGTCTTCATCTAGAGAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5142582 ACATGTTTGTGTC--AATATTAGACAAGATA
1 ACATGTTT-TGTCTTAAT-TTAGACAAGAAA
* *
5142611 ACAAGTTTTGTCTTAATTAAGGACAAGA
1 ACATGTTTTGTCTTAATTTA-GACAAGA
5142639 GTTGTCTTAA
Statistics
Matches: 254, Mismatches: 50, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
28 81 0.32
29 140 0.55
30 31 0.12
31 2 0.01
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (29 bp):
ACATGTTTTGTCTTAATTTAGACAAGAAA
Found at i:5142524 original size:115 final size:116
Alignment explanation
Indices: 5142332--5142628 Score: 319
Period size: 115 Copynumber: 2.6 Consensus size: 116
5142322 AATATGTTAG
* * * *
5142332 TCTTAATTTAAATAAGAAAGCATGTTTGTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATT
1 TCTTAATTTAGACAAGAAAACATGTTTCTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATT
** * * * * * *
5142397 TGGACAAGAAAAA-AA-GTTTTGTTTTAATTTGGACAATAAAACATATTTTC
66 TCAACAAAAAAAAGAATG-ATCGTTTTAATTTAGACAAAAAAAAATATTTTC
* ** *
5142447 TCTTAATTTAGACAAGAAAACATGTTTCTCTTAATTTGGACAAGAAAATGTGTTTTTTCTTAATT
1 TCTTAATTTAGACAAGAAAACATGTTTCTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATT
* * *
5142512 TCAACAAAAAAAAGCATGATCGTTTTAATTTAGACAAAAAAAAATGTTTTG
66 TCAACAAAAAAAAGAATGATCGTTTTAATTTAGACAAAAAAAAATATTTTC
* * * * * * * *
5142563 TCTTCATCTAGAGAAGAAAACATGTTTGTGTCAATATTAGACAAGATAACAAGTTTTGTCTTAAT
1 TCTTAATTTAGACAAGAAAACATGTTTCTCTTAAT-TTAGACAAGAAAACATGTTTTGTCTTAAT
5142628 T
65 T
5142629 AAGGACAAGA
Statistics
Matches: 148, Mismatches: 31, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
115 67 0.45
116 56 0.38
117 25 0.17
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (116 bp):
TCTTAATTTAGACAAGAAAACATGTTTCTCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATT
TCAACAAAAAAAAGAATGATCGTTTTAATTTAGACAAAAAAAAATATTTTC
Found at i:5148947 original size:37 final size:37
Alignment explanation
Indices: 5148866--5148949 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 37
5148856 TTTTATGACT
* **
5148866 ATTAATATTTTTTTTAAGAAAAAGGAGTTTTTCTTGT
1 ATTAAAATTTTTTTTAAGAAAAAGGAGTTTTTCTTAC
*
5148903 A-TCAAATTTTTTTTGAA-AGAAAA-GAGTTTTTCTTAC
1 ATTAAAATTTTTTTT-AAGA-AAAAGGAGTTTTTCTTAC
5148939 ATTAAAATTTT
1 ATTAAAATTTT
5148950 GGTTTTATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 24 0.62
37 15 0.38
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.49
Consensus pattern (37 bp):
ATTAAAATTTTTTTTAAGAAAAAGGAGTTTTTCTTAC
Found at i:5153373 original size:22 final size:21
Alignment explanation
Indices: 5153318--5153379 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
5153308 CATTGTAGCA
*
5153318 AGATCCATTTTGGCTATAGTG
1 AGATCCATTTTGGCTACAGTG
* *
5153339 AGATCTATTTTGGCTGCAGTG
1 AGATCCATTTTGGCTACAGTG
*
5153360 AGAATCCATTTTGGCGACAG
1 AG-ATCCATTTTGGCTACAG
5153380 CTAAAACACG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 20 0.59
22 14 0.41
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (21 bp):
AGATCCATTTTGGCTACAGTG
Found at i:5157058 original size:29 final size:29
Alignment explanation
Indices: 5157016--5157296 Score: 289
Period size: 29 Copynumber: 9.6 Consensus size: 29
5157006 GGCAACTTTT
* *
5157016 ACATATTTTATCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5157045 ACATGTTTTGTCTTAATTTAGATAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * * *
5157074 ATAGGTTTTGTCTTAACTTAGACAAGAAG
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* *
5157103 ACATGTTTTGTCTTAATTTAGACTAGCAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5157132 ACATG-TTTGTCTTAATTTAGACAAAAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5157160 ACATGTGTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* *
5157189 ACATG-TTTGTTTTAATCTAGACAAGAAA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
* * * * **
5157217 ATATGGTTTGTTTTGTCCTAATCTAGAGAAGACC
1 ACA-----TGTTTTGTCTTAATTTAGACAAGAAA
* * *
5157251 ACATG-TTTGTCTCAAATTAGACAAGATA
1 ACATGTTTTGTCTTAATTTAGACAAGAAA
*
5157279 ACATGCTTTGTCTTAATT
1 ACATGTTTTGTCTTAATT
5157297 AAAGATAAAA
Statistics
Matches: 206, Mismatches: 38, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
28 68 0.33
29 116 0.56
33 2 0.01
34 20 0.10
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.38
Consensus pattern (29 bp):
ACATGTTTTGTCTTAATTTAGACAAGAAA
Found at i:5157164 original size:57 final size:57
Alignment explanation
Indices: 5157026--5157296 Score: 283
Period size: 57 Copynumber: 4.6 Consensus size: 57
5157016 ACATATTTTA
* *
5157026 TCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGA-TAAGAAAATAGGTTTTG
1 TCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACT-AGAAAACATG-TTTG
* * *
5157084 TCTTAACTTAGACAAGAAGACATGTTTTGTCTTAATTTAGACTAGCAAACATGTTTG
1 TCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACTAGAAAACATGTTTG
* * *
5157141 TCTTAATTTAGACAAAAAAACATGTGTTGTCTTAATTTAGACAAGAAAACATGTTTG
1 TCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACTAGAAAACATGTTTG
* * * * * ** **
5157198 TTTTAATCTAGACAAGAAAATATGGTTTGTTTTGTCCTAATCTAGAGAAGACCACATGTTTG
1 TCTTAATTTAGACAAGAAAACA-----TGTTTTGTCTTAATTTAGACTAGAAAACATGTTTG
* * * *
5157260 TCTCAAATTAGACAAGATAACATGCTTTGTCTTAATT
1 TCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATT
5157297 AAAGATAAAA
Statistics
Matches: 177, Mismatches: 30, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
57 85 0.48
58 46 0.26
59 1 0.01
62 45 0.25
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (57 bp):
TCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGACTAGAAAACATGTTTG
Found at i:5157226 original size:86 final size:87
Alignment explanation
Indices: 5157016--5157227 Score: 275
Period size: 86 Copynumber: 2.5 Consensus size: 87
5157006 GGCAACTTTT
* * * * * * *
5157016 ACATATTTTATCTTAATTTAGACAAGAAAACATGTTTTGTCTTAATTTAGATAAGAAAATAGGTT
1 ACATGTTTTGTCTTAATTTAGACAAGAAAACATGGTTTGTCTTAATTTAGACAAAAAAACAGGTG
*
5157081 TTGTCTTAACTTAGACAAGAAG
66 TTGTCTTAACTTAGACAAGAAA
* * *
5157103 ACATGTTTTGTCTTAATTTAGACTAGCAAACAT-GTTTGTCTTAATTTAGACAAAAAAACATGTG
1 ACATGTTTTGTCTTAATTTAGACAAGAAAACATGGTTTGTCTTAATTTAGACAAAAAAACAGGTG
*
5157167 TTGTCTTAATTTAGACAAGAAA
66 TTGTCTTAACTTAGACAAGAAA
* * *
5157189 ACATG-TTTGTTTTAATCTAGACAAGAAAATATGGTTTGT
1 ACATGTTTTGTCTTAATTTAGACAAGAAAACATGGTTTGT
5157228 TTTGTCCTAA
Statistics
Matches: 107, Mismatches: 17, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
85 22 0.21
86 56 0.52
87 29 0.27
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (87 bp):
ACATGTTTTGTCTTAATTTAGACAAGAAAACATGGTTTGTCTTAATTTAGACAAAAAAACAGGTG
TTGTCTTAACTTAGACAAGAAA
Found at i:5159797 original size:36 final size:36
Alignment explanation
Indices: 5159723--5159822 Score: 112
Period size: 36 Copynumber: 2.8 Consensus size: 36
5159713 GTCGTGATAG
* * * * *
5159723 AGGTTACATCTAATCCTA-CAAAACGCATGTTGTGA
1 AGGTTACACCTGATCCTATTAAAAGGCATGTTGTAA
*
5159758 AGGTTACACCTGATCCTATTAAAAGGCATGTTTTAA
1 AGGTTACACCTGATCCTATTAAAAGGCATGTTGTAA
* *
5159794 AGGTTACGCCTGATCCTCTTGAAAAGGCA
1 AGGTTACACCTGATCCTATT-AAAAGGCA
5159823 AGATGATAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
35 16 0.29
36 31 0.56
37 8 0.15
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (36 bp):
AGGTTACACCTGATCCTATTAAAAGGCATGTTGTAA
Found at i:5166096 original size:21 final size:22
Alignment explanation
Indices: 5166067--5166110 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5166057 AAGTGATTAA
5166067 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
5166088 TTTAGGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
5166110 T
1 T
5166111 ACTTTAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:5169028 original size:4 final size:4
Alignment explanation
Indices: 5168985--5169012 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
5168975 TCAGTAATAA
5168985 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
5169013 TTAAAAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:5181670 original size:10 final size:10
Alignment explanation
Indices: 5181651--5181690 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
5181641 AATACTTAAC
*
5181651 AGAATGAGAG
1 AGAAAGAGAG
*
5181661 AGAAAAAGAG
1 AGAAAGAGAG
*
5181671 AGAGAGAGAG
1 AGAAAGAGAG
5181681 AGAAAGAGAG
1 AGAAAGAGAG
5181691 TCAAAATGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.03
Consensus pattern (10 bp):
AGAAAGAGAG
Found at i:5182671 original size:33 final size:31
Alignment explanation
Indices: 5182627--5182689 Score: 81
Period size: 33 Copynumber: 2.0 Consensus size: 31
5182617 ATATAATATG
* *
5182627 GTCATATCATTATGCCACATCAGTATATCAT
1 GTCATATCATTATGACACATCAGCATATCAT
*
5182658 GTCATTATCCATTATGACATATCAGCATATCA
1 GTCA-TAT-CATTATGACACATCAGCATATCA
5182690 CGTTAACATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 4 0.15
32 3 0.11
33 20 0.74
ACGTcount: A:0.33, C:0.22, G:0.10, T:0.35
Consensus pattern (31 bp):
GTCATATCATTATGACACATCAGCATATCAT
Found at i:5183778 original size:2 final size:2
Alignment explanation
Indices: 5183771--5183807 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5183761 TAGGGCTTCC
*
5183771 TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5183808 CCATGTCCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5192955 original size:19 final size:19
Alignment explanation
Indices: 5192910--5192947 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5192900 ATGAACGAGA
5192910 AAAGAAAGAAAGGAGGAAG
1 AAAGAAAGAAAGGAGGAAG
*
5192929 AAAGAAAGAACGGAGGAAG
1 AAAGAAAGAAAGGAGGAAG
5192948 GGAGAAAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.61, C:0.03, G:0.37, T:0.00
Consensus pattern (19 bp):
AAAGAAAGAAAGGAGGAAG
Found at i:5198115 original size:28 final size:28
Alignment explanation
Indices: 5198078--5198355 Score: 335
Period size: 28 Copynumber: 9.8 Consensus size: 28
5198068 TTTCAAATGT
5198078 TTTGTCTTAATTTAGACAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATG
5198106 TTTGTCTTAATTTAGACAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATG
*
5198134 TTTGTCTTAATTTAGATAAGAAAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATG
*
5198162 TTTTGT-TTATTTTAGACAAGAAAACATG
1 -TTTGTCTTAATTTAGACAAGAAAACATG
* * *
5198190 CTTGTCTTAATGTAGACAAGATAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATG
* *
5198218 TTTGTCTTAATTTGGACAAGAAAATC-TA
1 TTTGTCTTAATTTAGACAAGAAAA-CATG
*
5198246 TTTGTCTTAATTTAAGACAAGAAAAATATG
1 TTTGTCTTAATTT-AGACAAG-AAAACATG
** * *
5198276 TTTTGTCTTAACCTAGACAAAAAAACATA
1 -TTTGTCTTAATTTAGACAAGAAAACATG
** *
5198305 TTTGTCTCCATTTAGACAAGATAACATG
1 TTTGTCTTAATTTAGACAAGAAAACATG
*
5198333 TTTTGTCTTAATTAAAGACAAGA
1 -TTTGTCTTAATT-TAGACAAGA
5198356 GTTATCTTAA
Statistics
Matches: 211, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
27 4 0.02
28 149 0.71
29 28 0.13
30 19 0.09
31 11 0.05
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (28 bp):
TTTGTCTTAATTTAGACAAGAAAACATG
Found at i:5213461 original size:8 final size:8
Alignment explanation
Indices: 5213422--5213487 Score: 61
Period size: 7 Copynumber: 8.9 Consensus size: 8
5213412 AAAACTGAAC
5213422 CTTCCTTT
1 CTTCCTTT
*
5213430 C-TCTTTT
1 CTTCCTTT
*
5213437 CTT-CTCT
1 CTTCCTTT
*
5213444 C-TCTTTT
1 CTTCCTTT
5213451 CTTCCTTT
1 CTTCCTTT
5213459 CTT-CTTT
1 CTTCCTTT
*
5213466 CCTCCTTT
1 CTTCCTTT
5213474 CTTCCTTT
1 CTTCCTTT
5213482 C-TCCTT
1 CTTCCTT
5213488 CCCTTCCTCT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
6 1 0.02
7 23 0.50
8 22 0.48
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (8 bp):
CTTCCTTT
Found at i:5213471 original size:15 final size:16
Alignment explanation
Indices: 5213448--5213487 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5213438 TTCTCTCTCT
*
5213448 TTTCTTCCTTTCTT-C
1 TTTCCTCCTTTCTTCC
5213463 TTTCCTCCTTTCTTCC
1 TTTCCTCCTTTCTTCC
5213479 TTT-CTCCTT
1 TTTCCTCCTT
5213488 CCCTTCCTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTCCTCCTTTCTTCC
Found at i:5213474 original size:23 final size:22
Alignment explanation
Indices: 5213424--5213483 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
5213414 AACTGAACCT
*
5213424 TCCTTTC-TCTTTTCTTCTCTC
1 TCCTTTCTTCCTTTCTTCTCTC
* *
5213445 TCTTTTCTTCCTTTCTTCTTTCC
1 TCCTTTCTTCCTTTCTTCTCT-C
5213468 TCCTTTCTTCCTTTCT
1 TCCTTTCTTCCTTTCT
5213484 CCTTCCCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.18
22 11 0.33
23 16 0.48
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (22 bp):
TCCTTTCTTCCTTTCTTCTCTC
Found at i:5234203 original size:25 final size:25
Alignment explanation
Indices: 5234169--5234224 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
5234159 GGTCTGTAAT
* *
5234169 ATATACGTGGCAAGGCCACGGGTTG
1 ATATATGTGGCAAGGCCACGAGTTG
* *
5234194 ATATATGTGGCTAGGCCATGAGTTG
1 ATATATGTGGCAAGGCCACGAGTTG
5234219 ATATAT
1 ATATAT
5234225 ATGGTTACAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (25 bp):
ATATATGTGGCAAGGCCACGAGTTG
Found at i:5238701 original size:20 final size:21
Alignment explanation
Indices: 5238659--5238704 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
5238649 ATCTGCCCAT
5238659 GAAAGAAAAGTAAAGAGAAAA
1 GAAAGAAAAGTAAAGAGAAAA
5238680 GAAAGAAAA-TAATAGA-AAAA
1 GAAAGAAAAGTAA-AGAGAAAA
5238700 GAAAG
1 GAAAG
5238705 TAACCTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.07
Consensus pattern (21 bp):
GAAAGAAAAGTAAAGAGAAAA
Found at i:5238829 original size:14 final size:13
Alignment explanation
Indices: 5238810--5238842 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5238800 GAAGAGAAAG
5238810 GAAGAAATGAGGAA
1 GAAGAAAT-AGGAA
5238824 GAAGAAATAGGAA
1 GAAGAAATAGGAA
5238837 -AAGAAA
1 GAAGAAA
5238843 GTTCAGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 5 0.26
14 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.30, T:0.06
Consensus pattern (13 bp):
GAAGAAATAGGAA
Found at i:5246344 original size:29 final size:29
Alignment explanation
Indices: 5246311--5246487 Score: 155
Period size: 29 Copynumber: 6.2 Consensus size: 29
5246301 GCAACTTTAG
*
5246311 CATGTTTTGTCTTAATTTGGACAAGAAAA
1 CATGTTTTGTCTTAATTTAGACAAGAAAA
* * ** *
5246340 CATGTTTTATTTTGCTTTACACAAGAAAA
1 CATGTTTTGTCTTAATTTAGACAAGAAAA
* * * * *
5246369 TATGTATTGTTTTAATTTAGAAAAAAAAA
1 CATGTTTTGTCTTAATTTAGACAAGAAAA
* * *
5246398 CATGTTTTCTCATAATTTAGACAAGACAA
1 CATGTTTTGTCTTAATTTAGACAAGAAAA
5246427 CATG---TGTCTTAATTTAGACAAGAAAA
1 CATGTTTTGTCTTAATTTAGACAAGAAAA
* ** *
5246453 GTATGTTTAATCTTAATCTAGAC-AGAAAA
1 -CATGTTTTGTCTTAATTTAGACAAGAAAA
5246482 CATGTT
1 CATGTT
5246488 AGACTCTCAA
Statistics
Matches: 114, Mismatches: 30, Indels: 9
0.75 0.20 0.06
Matches are distributed among these distances:
26 19 0.17
27 3 0.03
28 5 0.04
29 75 0.66
30 12 0.11
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (29 bp):
CATGTTTTGTCTTAATTTAGACAAGAAAA
Found at i:5247219 original size:29 final size:29
Alignment explanation
Indices: 5247165--5247344 Score: 186
Period size: 29 Copynumber: 6.3 Consensus size: 29
5247155 TGGCAACTTT
* *
5247165 AACATGTTTTGTCTTAATTTGGACAAGAA
1 AACATGTTTTCTCTTAATTTAGACAAGAA
* * *
5247194 AACATGTTTTCTTTTACTTTACACAAGAA
1 AACATGTTTTCTCTTAATTTAGACAAGAA
* * *
5247223 AATATGTTTTGTCTTAATTTAGACAAAAA
1 AACATGTTTTCTCTTAATTTAGACAAGAA
* *
5247252 AACATGTTTTCTCATAATTTAGACAAGAT
1 AACATGTTTTCTCTTAATTTAGACAAGAA
*
5247281 AACATG---TGTCTTAATTTAGACAAGAA
1 AACATGTTTTCTCTTAATTTAGACAAGAA
* ** * *
5247307 AAGTATGTTTAGTCTTAATCTAGATAAGAA
1 AA-CATGTTTTCTCTTAATTTAGACAAGAA
5247337 AACATGTT
1 AACATGTT
5247345 AGACNNNNNN
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
26 19 0.15
27 3 0.02
29 82 0.67
30 19 0.15
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (29 bp):
AACATGTTTTCTCTTAATTTAGACAAGAA
Found at i:5262071 original size:92 final size:92
Alignment explanation
Indices: 5261909--5262091 Score: 294
Period size: 92 Copynumber: 2.0 Consensus size: 92
5261899 TCTGCCTTAT
** *
5261909 CAAAACCCTAACTGCAAAATGGAATTTGAAGCTAGTTTGGAGTAGATCTGAGCTTAGATAACCAT
1 CAAAACCCTAACCCCAAAATGGAATTTAAAGCTAGTTTGGAGTAGATCTGAGCTTAGATAACCAT
* *
5261974 TATTAAGGTAAGATTACATCTTTTTAC
66 TATTAAGGTAAAAATACATCTTTTTAC
* * *
5262001 CAAAGCCCTAACCCCAAAATGGAATTTAAAGCTAGTTTGGAGTATATCTGAGCTTGGATAACCAT
1 CAAAACCCTAACCCCAAAATGGAATTTAAAGCTAGTTTGGAGTAGATCTGAGCTTAGATAACCAT
5262066 TATTAAGGTAAAAATACATCTTTTTA
66 TATTAAGGTAAAAATACATCTTTTTA
5262092 ACAATTTATT
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
92 83 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (92 bp):
CAAAACCCTAACCCCAAAATGGAATTTAAAGCTAGTTTGGAGTAGATCTGAGCTTAGATAACCAT
TATTAAGGTAAAAATACATCTTTTTAC
Found at i:5263082 original size:37 final size:37
Alignment explanation
Indices: 5263041--5263143 Score: 107
Period size: 37 Copynumber: 2.8 Consensus size: 37
5263031 TTGGTGTTGT
* *
5263041 GCATGATTTGAACATCTACCAATAACTTTGACTCAGA
1 GCATGATTTGAACATCCACCAATAACTTTCACTCAGA
* ** *
5263078 GCATGATTTGGACATCCGTCAATAACTTTCACTCATA
1 GCATGATTTGAACATCCACCAATAACTTTCACTCAGA
** * *
5263115 GTGTGATTTGAACCCTCCACCAATCACTT
1 GCATGATTTGAA-CATCCACCAATAACTT
5263144 CAATGTGTGC
Statistics
Matches: 52, Mismatches: 13, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
37 40 0.77
38 12 0.23
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (37 bp):
GCATGATTTGAACATCCACCAATAACTTTCACTCAGA
Found at i:5263193 original size:35 final size:37
Alignment explanation
Indices: 5263146--5263235 Score: 105
Period size: 35 Copynumber: 2.5 Consensus size: 37
5263136 AATCACTTCA
* * *
5263146 ATGTGTGCGATTTGACT-TTTCGTCAGTGGCTTAAGC-
1 ATGTGTGTGATTTGACTCTTT-GCCAATGGCTTAAGCT
*
5263182 AT-TGTGTGATTTGACTCTTTGCCAATGGCTTCAGCT
1 ATGTGTGTGATTTGACTCTTTGCCAATGGCTTAAGCT
*
5263218 TTGTGTGTGATTTGACTC
1 ATGTGTGTGATTTGACTC
5263236 CGTCGATTGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
35 25 0.54
36 6 0.13
37 15 0.33
ACGTcount: A:0.16, C:0.17, G:0.26, T:0.42
Consensus pattern (37 bp):
ATGTGTGTGATTTGACTCTTTGCCAATGGCTTAAGCT
Found at i:5270321 original size:15 final size:17
Alignment explanation
Indices: 5270298--5270339 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
5270288 GAAACCAAAA
*
5270298 TTTAGATTTTGA-TT-T
1 TTTATATTTTGATTTCT
5270313 TTTATATTTTGATTTCT
1 TTTATATTTTGATTTCT
5270330 TTTATATTTT
1 TTTATATTTT
5270340 TATTGAATCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 11 0.46
16 2 0.08
17 11 0.46
ACGTcount: A:0.19, C:0.02, G:0.07, T:0.71
Consensus pattern (17 bp):
TTTATATTTTGATTTCT
Found at i:5270787 original size:19 final size:19
Alignment explanation
Indices: 5270761--5270807 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
5270751 CTCTTCCAAC
5270761 TCATTTTTAACCAAAAAAT
1 TCATTTTTAACCAAAAAAT
* * *
5270780 TTATTTTTTACCAAAAACT
1 TCATTTTTAACCAAAAAAT
5270799 TCATTTTTA
1 TCATTTTTA
5270808 TGATTCTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.47
Consensus pattern (19 bp):
TCATTTTTAACCAAAAAAT
Found at i:5271728 original size:68 final size:68
Alignment explanation
Indices: 5271566--5271828 Score: 199
Period size: 68 Copynumber: 3.9 Consensus size: 68
5271556 TATGGTTGGT
* * * * * * *
5271566 ATGATGAATGCCATAAGATTTAAGTATATGAAGTAAATTCCATATACCATATGAGATGCTTAACT
1 ATGATAAATGCCATAAGA-TTATGTATATGATGTAAATTCTATATACCATATGAGATGATGAAGT
*
5271631 ATGC
65 ATAC
** *** * * * *
5271635 ATGATGTATATTATAAGACTGTGTATATGATGTAAACTCTATATACCATATGAGGTGATGAAGTA
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCTATATACCATATGAGATGATGAAGTA
5271700 TAC
66 TAC
* * * * * * *
5271703 ATGATAAATGCCATGAGATTATGTATGTGATGTATATTCTATATACAACATGAAATAATTG-AG-
1 ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCTATATACCATATGAGATGA-TGAAGT
*
5271766 AAAGC
65 ATA-C
* ** * *
5271771 ATGA-AGAATGCCATGAGATTATGTATATGATGTATTTTCCATATACCTTATGAGATGA
1 ATGATA-AATGCCATAAGATTATGTATATGATGTAAATTCTATATACCATATGAGATGA
5271829 GTAAGCTTGT
Statistics
Matches: 151, Mismatches: 40, Indels: 7
0.76 0.20 0.04
Matches are distributed among these distances:
67 3 0.02
68 132 0.87
69 16 0.11
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (68 bp):
ATGATAAATGCCATAAGATTATGTATATGATGTAAATTCTATATACCATATGAGATGATGAAGTA
TAC
Found at i:5299267 original size:23 final size:22
Alignment explanation
Indices: 5299241--5299295 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
5299231 ATCCTTGAGG
5299241 ATTTTCTTCATATT-CAGAAACAT
1 ATTTTCTTCAT-TTGCA-AAACAT
**
5299264 ATTTTAATCATTTGCAAAACAT
1 ATTTTCTTCATTTGCAAAACAT
*
5299286 ATTTACTTCA
1 ATTTTCTTCA
5299296 ATCAGTTTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (22 bp):
ATTTTCTTCATTTGCAAAACAT
Found at i:5299614 original size:34 final size:34
Alignment explanation
Indices: 5299517--5299619 Score: 118
Period size: 34 Copynumber: 3.0 Consensus size: 34
5299507 CAAGCAAACA
* * *
5299517 CTCACAATGGCTTTTTCCAAGCTCAACTATAACC
1 CTCACAATGGCTTTTTCTAAGCTCAACCACAACC
* **
5299551 CTTACAATGGC-TTTTCATAAGAGCAACCACAACC
1 CTCACAATGGCTTTTTC-TAAGCTCAACCACAACC
* *
5299585 CTCACAATAGCTTTTTCTAAGCTCTACCACAACC
1 CTCACAATGGCTTTTTCTAAGCTCAACCACAACC
5299619 C
1 C
5299620 ACATTAACTT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
33 5 0.09
34 46 0.82
35 5 0.09
ACGTcount: A:0.31, C:0.33, G:0.09, T:0.27
Consensus pattern (34 bp):
CTCACAATGGCTTTTTCTAAGCTCAACCACAACC
Found at i:5302848 original size:7 final size:7
Alignment explanation
Indices: 5302836--5302864 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5302826 TCTTAAAAAA
5302836 GGTGGCT
1 GGTGGCT
5302843 GGTGGCT
1 GGTGGCT
5302850 GGTGGCT
1 GGTGGCT
5302857 GGTGGCT
1 GGTGGCT
5302864 G
1 G
5302865 AGTAAATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.59, T:0.28
Consensus pattern (7 bp):
GGTGGCT
Found at i:5317021 original size:41 final size:41
Alignment explanation
Indices: 5316884--5317026 Score: 160
Period size: 41 Copynumber: 3.5 Consensus size: 41
5316874 TTGTAAACGT
* * * *
5316884 AACATCCTAGGGGCATGTAATCCATATCGATAGTAATATAG
1 AACATGCTAAGGGCATGTAACCCATATCGATAATAATATAG
* * * * *
5316925 AACATGCAAAGGGCATGTACCCCACATGGATAATATTATAG
1 AACATGCTAAGGGCATGTAACCCATATCGATAATAATATAG
* *
5316966 AACATGCTAAGGGCATGTAACCCATATCGATAATAGTACAG
1 AACATGCTAAGGGCATGTAACCCATATCGATAATAATATAG
* * *
5317007 AATATACTAGGGGCATGTAA
1 AACATGCTAAGGGCATGTAA
5317027 TTCATACAAA
Statistics
Matches: 84, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.24
Consensus pattern (41 bp):
AACATGCTAAGGGCATGTAACCCATATCGATAATAATATAG
Found at i:5318861 original size:22 final size:21
Alignment explanation
Indices: 5318746--5318921 Score: 68
Period size: 23 Copynumber: 7.9 Consensus size: 21
5318736 TAGCACAGGG
* **
5318746 CGTGTAACATGTTGTGAACATGG
1 CGTGTAACAT-TTTTGAA-ATAA
* **
5318769 CGTGTAACAAATTTTTGAACTTG
1 CGTGTAAC--ATTTTTGAAATAA
5318792 CGTGTAACATTTTT-AAATAA
1 CGTGTAACATTTTTGAAATAA
* * **
5318812 GGCATGTCACACTTTTTGAAATTG
1 --CGTGTAACA-TTTTTGAAATAA
5318836 CGTGTAACATTTTTGAATATAA
1 CGTGTAACATTTTTGAA-ATAA
* *
5318858 CGTGTATCATATTTT-AAACACGA
1 CGTGTAACAT-TTTTGAAATA--A
* * * *
5318881 AGTGTAATATTTTTTAAAAATGA
1 CGTGTAACA-TTTTT-GAAATAA
*
5318904 CGTGTAACATATTTGAAA
1 CGTGTAACATTTTTGAAA
5318922 AATGGCATGT
Statistics
Matches: 115, Mismatches: 25, Indels: 28
0.68 0.15 0.17
Matches are distributed among these distances:
20 3 0.03
21 19 0.17
22 31 0.27
23 46 0.40
24 11 0.10
25 5 0.04
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (21 bp):
CGTGTAACATTTTTGAAATAA
Found at i:5318924 original size:23 final size:23
Alignment explanation
Indices: 5318836--5318925 Score: 74
Period size: 23 Copynumber: 4.0 Consensus size: 23
5318826 TTTGAAATTG
* * *
5318836 CGTGTAACATTTTTG-AATATAA
1 CGTGTAACATATTTGAAAAATGA
* * * *
5318858 CGTGTATCATATTTTAAACACGA
1 CGTGTAACATATTTGAAAAATGA
* * * *
5318881 AGTGTAATATTTTTTAAAAATGA
1 CGTGTAACATATTTGAAAAATGA
5318904 CGTGTAACATATTTGAAAAATG
1 CGTGTAACATATTTGAAAAATG
5318926 GCATGTAATA
Statistics
Matches: 51, Mismatches: 16, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
22 12 0.24
23 39 0.76
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (23 bp):
CGTGTAACATATTTGAAAAATGA
Found at i:5319645 original size:21 final size:21
Alignment explanation
Indices: 5319621--5319661 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5319611 AGGATGATAC
5319621 TGTGACATTAGAGGGTGACAT
1 TGTGACATTAGAGGGTGACAT
** *
5319642 TGTGATGTTGGAGGGTGACA
1 TGTGACATTAGAGGGTGACA
5319662 CTATGATGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.07, G:0.39, T:0.29
Consensus pattern (21 bp):
TGTGACATTAGAGGGTGACAT
Found at i:5322823 original size:31 final size:31
Alignment explanation
Indices: 5322759--5323142 Score: 263
Period size: 31 Copynumber: 12.4 Consensus size: 31
5322749 TTATAAGGTC
* * * * * *
5322759 ACACGCTGAGTGGTGGTAGATTTGTGCCATG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * *
5322790 ACATGATGAGTGCTAGCAGATATATGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
*
5322821 ACACGCTGAGTGCTA-CTAGATTTAGGGCGTG
1 ACACGCTGAGTGCTAGC-AGATTTATGGCGTG
* ** * *
5322852 ACACGCTGACTGAAAGCAGATTTATGGGGTC
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * *
5322883 ACACGCTAAGTGCTAGCAAATATATGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* *
5322914 ACACGCTGAGTGCTACCAGATTTAAGGCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * ** * *
5322945 ACACACTGACTGAAAGCATATTTATAGG-GTC
1 ACACGCTGAGTGCTAGCAGATTTAT-GGCGTG
* * * *
5322976 ACACGCTGAGTGGTGGCAGATTTGTGCCGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * * *
5323007 ACACGCTAAGTGCTAGCACATATATGGTGTG
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * *
5323038 ACACACTGAGTGCTA-CTAGATTTAGGGTGTG
1 ACACGCTGAGTGCTAGC-AGATTTATGGCGTG
* ** * * *
5323069 ACACGCTGACTGAAAGCATATTTATGGGGTC
1 ACACGCTGAGTGCTAGCAGATTTATGGCGTG
* * * * *
5323100 ACATGCTAAGTTG-TGGTAGATTTATGCCGTG
1 ACACGCTGAG-TGCTAGCAGATTTATGGCGTG
*
5323131 ACATGCTGAGTG
1 ACACGCTGAGTG
5323143 TTGCCAGATT
Statistics
Matches: 265, Mismatches: 81, Indels: 15
0.73 0.22 0.04
Matches are distributed among these distances:
30 5 0.02
31 254 0.96
32 6 0.02
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.26
Consensus pattern (31 bp):
ACACGCTGAGTGCTAGCAGATTTATGGCGTG
Found at i:5322870 original size:62 final size:61
Alignment explanation
Indices: 5322716--5322922 Score: 175
Period size: 62 Copynumber: 3.3 Consensus size: 61
5322706 ATACTATCAT
* * * * * **
5322716 ATTTAGGGTGTGACACGCTGACTGAAAGTATATTTATAAGGTCACACGCTGAGTGGTGGTAG
1 ATTTAGGGCGTGACACGCTGACTGAAAGCAGATTTAT-GGGTCACACGCTGAGTGCTACTAG
* * * * * ** * *
5322778 ATTT-GTGCCATGACATGATGAGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTACTAG
1 ATTTAG-GGCGTGACACGCTGACTGAAAGCAGATTTATGG-GTCACACGCTGAGTGCTACTAG
* *
5322840 ATTTAGGGCGTGACACGCTGACTGAAAGCAGATTTATGGGGTCACACGCTAAGTGCTAGC-AA
1 ATTTAGGGCGTGACACGCTGACTGAAAGCAGATTTAT-GGGTCACACGCTGAGTGCTA-CTAG
* *
5322902 ATATATGGCGTGACACGCTGA
1 ATTTAGGGCGTGACACGCTGA
5322923 GTGCTACCAG
Statistics
Matches: 111, Mismatches: 29, Indels: 10
0.74 0.19 0.07
Matches are distributed among these distances:
61 2 0.02
62 105 0.95
63 4 0.04
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (61 bp):
ATTTAGGGCGTGACACGCTGACTGAAAGCAGATTTATGGGTCACACGCTGAGTGCTACTAG
Found at i:5322895 original size:93 final size:93
Alignment explanation
Indices: 5322798--5323046 Score: 336
Period size: 93 Copynumber: 2.7 Consensus size: 93
5322788 TGACATGATG
* * *
5322798 AGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTACTAGATTTAGGGCGTGACACGCTGACT
1 AGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACACTGACT
*
5322863 GAAAGCAGATTTATGGGGTCACACGCTA
66 GAAAGCAGATTTATAGGGTCACACGCTA
*
5322891 AGTGCTAGCAAATATATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACACTGACT
1 AGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACACTGACT
* *
5322956 GAAAGCATATTTATAGGGTCACACGCTG
66 GAAAGCAGATTTATAGGGTCACACGCTA
* * * * * * * * * * *
5322984 AGTGGTGGCAGATTTGTGCCGTGACACGCTAAGTGCTAGCACATATATGGTGTGACACACTGA
1 AGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACACTGA
5323047 GTGCTACTAG
Statistics
Matches: 137, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 137 1.00
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.24
Consensus pattern (93 bp):
AGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACACTGACT
GAAAGCAGATTTATAGGGTCACACGCTA
Found at i:5322943 original size:124 final size:123
Alignment explanation
Indices: 5322716--5323098 Score: 354
Period size: 124 Copynumber: 3.1 Consensus size: 123
5322706 ATACTATCAT
* * * * * * * * *
5322716 ATTTAGGGTGTGACACGCTGACTGAAAGTATATTTATAAGGTCACACGCTGAGTGGTGGTAGATT
1 ATTTAGGG-GTGACACGCTGACTGAAAGCAGATTTATGAGGTCACACGCTAAGTGCTAGCAAATA
* * * * * * * * * **
5322781 TGTGCCATGACATGATGAGTGCTAGCAGATATATGGCGTGACACGCTGAGTGCTA-CTAG
65 TATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACGCTGACTGAAAGC-AG
*
5322840 ATTTAGGGCGTGACACGCTGACTGAAAGCAGATTTATGGGGTCACACGCTAAGTGCTAGCAAATA
1 ATTTAGGG-GTGACACGCTGACTGAAAGCAGATTTATGAGGTCACACGCTAAGTGCTAGCAAATA
* *
5322905 TATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACACTGACTGAAAGCAT
65 TATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACGCTGACTGAAAGCAG
* * * *** * ** * *
5322964 ATTTATAGGGTCACACGCTGAGTGGTGGCAGATTTGTGCCGTGACACGCTAAGTGCTAGCACATA
1 ATTTA-GGGGTGACACGCTGACTGAAAGCAGATTTATGAGGTCACACGCTAAGTGCTAGCAAATA
* * * * * *
5323029 TATGGTGTGACACACTGAGTGCTACTAGATTTAGGGTGTGACACGCTGACTGAAAGCAT
65 TATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACGCTGACTGAAAGCAG
5323088 ATTTATGGGGT
1 ATTTA-GGGGT
5323099 CACATGCTAA
Statistics
Matches: 215, Mismatches: 42, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
124 212 0.99
125 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (123 bp):
ATTTAGGGGTGACACGCTGACTGAAAGCAGATTTATGAGGTCACACGCTAAGTGCTAGCAAATAT
ATGGCGTGACACGCTGAGTGCTACCAGATTTAAGGCGTGACACGCTGACTGAAAGCAG
Found at i:5323099 original size:124 final size:124
Alignment explanation
Indices: 5322867--5323142 Score: 390
Period size: 124 Copynumber: 2.2 Consensus size: 124
5322857 CTGACTGAAA
** * *
5322867 GCAGATTTATGGGGTCACACGCTAAGTGCTAGCAAATATATGGCGTGACACGCTGAGTGCTACCA
1 GCAGATTTATGCCGTGACACGCTAAGTGCTAGCAAATATATGGCGTGACACACTGAGTGCTACCA
*
5322932 GATTTAAGGCGTGACACACTGACTGAAAGCATATTTATAGGGTCACACGCTGAGTGGTG
66 GATTTAAGGCGTGACACACTGACTGAAAGCATATTTATAGGGTCACACGCTAAGTGGTG
* * * *
5322991 GCAGATTTGTGCCGTGACACGCTAAGTGCTAGCACATATATGGTGTGACACACTGAGTGCTACTA
1 GCAGATTTATGCCGTGACACGCTAAGTGCTAGCAAATATATGGCGTGACACACTGAGTGCTACCA
* * * * * *
5323056 GATTTAGGGTGTGACACGCTGACTGAAAGCATATTTATGGGGTCACATGCTAAGTTGTG
66 GATTTAAGGCGTGACACACTGACTGAAAGCATATTTATAGGGTCACACGCTAAGTGGTG
* * *
5323115 GTAGATTTATGCCGTGACATGCTGAGTG
1 GCAGATTTATGCCGTGACACGCTAAGTG
5323143 TTGCCAGATT
Statistics
Matches: 133, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 133 1.00
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (124 bp):
GCAGATTTATGCCGTGACACGCTAAGTGCTAGCAAATATATGGCGTGACACACTGAGTGCTACCA
GATTTAAGGCGTGACACACTGACTGAAAGCATATTTATAGGGTCACACGCTAAGTGGTG
Found at i:5323108 original size:93 final size:92
Alignment explanation
Indices: 5323011--5323204 Score: 199
Period size: 93 Copynumber: 2.1 Consensus size: 92
5323001 GCCGTGACAC
** * ** *
5323011 GCTAAGTGCTAGCACATATATGGTGTGACACACTGAGTGCTACTAGATTTAGGGTGTGACACGCT
1 GCTAAGTG-TAGCACATATATGCCGTGACACACTGAGTGCTACCAGATTTAGGACGTGACACACT
* *
5323076 GACTGAAAGCATATTTATGGGGTCACAT
65 GACTAAAAGCAGATTTATGGGGTCACAT
* * * * ** * * *
5323104 GCTAAGTTGTGGTAGATTTATGCCGTGACATGCTGAGTGTTGCCAGATTTAGTACGTGACACACT
1 GCTAAG-TGTAGCACATATATGCCGTGACACACTGAGTGCTACCAGATTTAGGACGTGACACACT
*
5323169 GACTAAAAGTAGATTTATGGGGTCACAT
65 GACTAAAAGCAGATTTATGGGGTCACAT
*
5323197 GCTGAGTG
1 GCTAAGTG
5323205 AAAGGAAAGT
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
92 2 0.02
93 77 0.95
94 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (92 bp):
GCTAAGTGTAGCACATATATGCCGTGACACACTGAGTGCTACCAGATTTAGGACGTGACACACTG
ACTAAAAGCAGATTTATGGGGTCACAT
Found at i:5323182 original size:124 final size:123
Alignment explanation
Indices: 5322867--5323208 Score: 310
Period size: 124 Copynumber: 2.8 Consensus size: 123
5322857 CTGACTGAAA
** * * * * * * * *** *
5322867 GCAGATTTATGGGGTCACACGCTAAGTGCTAGCAAATATATGGCGTGACACGCTGAGTGCTACCA
1 GCAGATTTATGCCGTGACACGCTAAGTGCTAGCACAGATATAGTGTGACACACTGACTAAAACTA
* * *
5322932 GATTTAAGGCGTGACACACTGACTGAAAGCATATTTATAGGGTCACACGCTGAGTGGTG
66 GATTT-AGGGGTGACACGCTGACTGAAAGCATATTTATAGGGTCACACGCTAAGTGGTG
* * * * ***
5322991 GCAGATTTGTGCCGTGACACGCTAAGTGCTAGCACATATATGGTGTGACACACTGAGTGCTACTA
1 GCAGATTTATGCCGTGACACGCTAAGTGCTAGCACAGATATAGTGTGACACACTGACTAAAACTA
* * *
5323056 GATTTAGGGTGTGACACGCTGACTGAAAGCATATTTATGGGGTCACATGCTAAGTTGTG
66 GATTTAGGG-GTGACACGCTGACTGAAAGCATATTTATAGGGTCACACGCTAAGTGGTG
* * * * * *
5323115 GTAGATTTATGCCGTGACATGCTGAGTG-TTGC-CAGATTTAGTACGTGACACACTGACTAAAAG
1 GCAGATTTATGCCGTGACACGCTAAGTGCTAGCACAGATATAGT--GTGACACACTGACTAAAAC
* * *
5323178 TAGATTTATGGGGTCACATGCTGAGTGAAAG
64 TAGATTTA-GGGGTGACACGCTGACTGAAAG
5323209 GAAAGTTATC
Statistics
Matches: 184, Mismatches: 30, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
122 7 0.04
123 6 0.03
124 168 0.91
125 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.28, T:0.27
Consensus pattern (123 bp):
GCAGATTTATGCCGTGACACGCTAAGTGCTAGCACAGATATAGTGTGACACACTGACTAAAACTA
GATTTAGGGGTGACACGCTGACTGAAAGCATATTTATAGGGTCACACGCTAAGTGGTG
Found at i:5323301 original size:23 final size:23
Alignment explanation
Indices: 5323249--5323308 Score: 77
Period size: 23 Copynumber: 2.6 Consensus size: 23
5323239 AGGTTATTCA
*
5323249 AGGGTGACATGCCATGCCCCAAT
1 AGGGTGACACGCCATGCCCCAAT
* *
5323272 AGGGTGACACGCCATGCGCTAAT
1 AGGGTGACACGCCATGCCCCAAT
5323295 -GGAGTGACACGCCA
1 AGG-GTGACACGCCA
5323309 CATGGTTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
22 2 0.06
23 31 0.94
ACGTcount: A:0.27, C:0.28, G:0.30, T:0.15
Consensus pattern (23 bp):
AGGGTGACACGCCATGCCCCAAT
Found at i:5327072 original size:31 final size:31
Alignment explanation
Indices: 5327037--5327302 Score: 352
Period size: 31 Copynumber: 8.6 Consensus size: 31
5327027 AGAAAGAAAT
5327037 AAATGTTGTTACACGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
*
5327068 AAATGTTGTTACATGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
*
5327099 AAATATTGTTACACGCCATGCATATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* * * * *
5327130 AAATGTTGTTACATGCAATGCCTAACAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* *
5327161 AAATGTTGTTACACGCCTTGCATATCAAGAA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* * * * *
5327192 AAATATTGTTACACGCAATGCATAACATGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* * * *
5327223 AAATATTGTTACATGCCATGCATAACAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* *
5327254 AAATGTTGTTACACGCCATGCACATCAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
5327285 AAATGTTGTTACACGCCA
1 AAATGTTGTTACACGCCA
5327303 ACGCTGACAC
Statistics
Matches: 205, Mismatches: 30, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 205 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATATCAAGTA
Found at i:5327196 original size:93 final size:93
Alignment explanation
Indices: 5327037--5327302 Score: 388
Period size: 93 Copynumber: 2.9 Consensus size: 93
5327027 AGAAAGAAAT
* * * *
5327037 AAATGTTGTTACACGCCATGCATATCAAGTAAAATGTTGTTACATGCCATGCATATCAAGTAAAA
1 AAATGTTGTTACATGCCATGCATAACAAGTCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
*
5327102 TATTGTTACACGCCATGCATATCAAGTA
66 TATTGTTACACGCCATGCATAACAAGTA
* * * *
5327130 AAATGTTGTTACATGCAATGCCTAACAAGTCAAATGTTGTTACACGCCTTGCATATCAAGAAAAA
1 AAATGTTGTTACATGCCATGCATAACAAGTCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
* * *
5327195 TATTGTTACACGCAATGCATAACATGTC
66 TATTGTTACACGCCATGCATAACAAGTA
* * *
5327223 AAATATTGTTACATGCCATGCATAACAAGTCAAATGTTGTTACACGCCATGCACATCAAGTCAAA
1 AAATGTTGTTACATGCCATGCATAACAAGTCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
*
5327288 TGTTGTTACACGCCA
66 TATTGTTACACGCCA
5327303 ACGCTGACAC
Statistics
Matches: 152, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
93 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (93 bp):
AAATGTTGTTACATGCCATGCATAACAAGTCAAATGTTGTTACACGCCATGCATATCAAGTAAAA
TATTGTTACACGCCATGCATAACAAGTA
Found at i:5328033 original size:47 final size:47
Alignment explanation
Indices: 5327959--5328276 Score: 291
Period size: 47 Copynumber: 6.8 Consensus size: 47
5327949 ACACTCTCTA
*
5327959 AACCCTGGCGTGTCACAGATTCCCTCCATGGCGTGTCACAAACCCTG
1 AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
*** * * * *
5328006 AATGTTGGCGTGTTATAGATTTCCTCCATGGCATGT--CAAACTCTG
1 AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
* * * *
5328051 AACCCTGGCATATCACAGATTCCCTCCATGGCGTGTCACAAACTCTG
1 AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
** * * * * *
5328098 AACCCTAACATGTCATAGATTCCTTTCATGGCATGTCACAAACCTTG
1 AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
* **
5328145 AACCCTGACGTGTCATAGATTCCCTCCATGGCGTGTCACAAACTTTG
1 AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
** * * ** * *
5328192 AACCCTCCCTTGTCACAGATTCCCTCCATGATGTGCCACAAACTCTG
1 AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
* * * * *
5328239 AACCCT-CCTTTATTACAGATTCCCTCCATGGCGTGTCA
1 AACCCTGGC-GTGTCATAGATTCCCTCCATGGCGTGTCA
5328277 TAATTTCTAA
Statistics
Matches: 223, Mismatches: 45, Indels: 6
0.81 0.16 0.02
Matches are distributed among these distances:
45 35 0.16
46 2 0.01
47 186 0.83
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (47 bp):
AACCCTGGCGTGTCATAGATTCCCTCCATGGCGTGTCACAAACCCTG
Found at i:5328259 original size:141 final size:139
Alignment explanation
Indices: 5327971--5328276 Score: 362
Period size: 141 Copynumber: 2.2 Consensus size: 139
5327961 CCCTGGCGTG
*** * * *
5327971 TCACAGATTCCCTCCATGGCGTGTCACAAACCCTGAATGTTGGCGTGTTATAGATTTCCTCCATG
1 TCACAGATTCCCTCCATGGCGTGTCACAAACCCTGAACCCTGACGTGTCATAGATTCCCTCCATG
** * *
5328036 GCATGTCAAACTCTGAACCCTGGCATATCACAGATTCCCTCCATGGCGTGTCACAAACTCTGAAC
66 GCATGTCAAACTCTGAACCCTCCCATATCACAGATTCCCTCCATGACGTGCCACAAACTCTGAAC
*
5328101 CCTAACATG
131 CCTAACATA
* * * * *
5328110 TCATAGATTCCTTTCATGGCATGTCACAAACCTTGAACCCTGACGTGTCATAGATTCCCTCCATG
1 TCACAGATTCCCTCCATGGCGTGTCACAAACCCTGAACCCTGACGTGTCATAGATTCCCTCCATG
* * * * *
5328175 GCGTGTCACAAACTTTGAACCCTCCCTTGTCACAGATTCCCTCCATGATGTGCCACAAACTCTGA
66 GCATGT--CAAACTCTGAACCCTCCCATATCACAGATTCCCTCCATGACGTGCCACAAACTCTGA
* *
5328240 ACCCT-CCTTTA
129 ACCCTAAC-ATA
*
5328251 TTACAGATTCCCTCCATGGCGTGTCA
1 TCACAGATTCCCTCCATGGCGTGTCA
5328277 TAATTTCTAA
Statistics
Matches: 136, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
139 59 0.43
140 1 0.01
141 76 0.56
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (139 bp):
TCACAGATTCCCTCCATGGCGTGTCACAAACCCTGAACCCTGACGTGTCATAGATTCCCTCCATG
GCATGTCAAACTCTGAACCCTCCCATATCACAGATTCCCTCCATGACGTGCCACAAACTCTGAAC
CCTAACATA
Found at i:5328359 original size:23 final size:23
Alignment explanation
Indices: 5328318--5328361 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5328308 GTCACATATG
*
5328318 CTCACCATGGCATGCCACATTCT
1 CTCACCATGGCATACCACATTCT
* *
5328341 CTCACCATGTCATATCACATT
1 CTCACCATGGCATACCACATT
5328362 TTCCCTTCGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.36, G:0.09, T:0.30
Consensus pattern (23 bp):
CTCACCATGGCATACCACATTCT
Found at i:5330721 original size:15 final size:16
Alignment explanation
Indices: 5330703--5330732 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5330693 TTGTTATGTG
5330703 GATTTT-ATTTTTAAT
1 GATTTTAATTTTTAAT
5330718 GATTTTAATTTTTAA
1 GATTTTAATTTTTAA
5330733 AAATTAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (16 bp):
GATTTTAATTTTTAAT
Found at i:5331449 original size:23 final size:23
Alignment explanation
Indices: 5331423--5331472 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
5331413 GTTAGTATAA
5331423 TATAAAAACTCACATCAGACAAG
1 TATAAAAACTCACATCAGACAAG
*** * *
5331446 TATATGCACTCACATCATACTAG
1 TATAAAAACTCACATCAGACAAG
5331469 TATA
1 TATA
5331473 TGCTCTAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (23 bp):
TATAAAAACTCACATCAGACAAG
Found at i:5331473 original size:23 final size:23
Alignment explanation
Indices: 5331430--5331475 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
5331420 TAATATAAAA
5331430 ACTCACATCAGACAAGTATATGC
1 ACTCACATCAGACAAGTATATGC
* *
5331453 ACTCACATCATACTAGTATATGC
1 ACTCACATCAGACAAGTATATGC
5331476 TCTAATACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (23 bp):
ACTCACATCAGACAAGTATATGC
Found at i:5340805 original size:3 final size:3
Alignment explanation
Indices: 5340797--5340824 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5340787 TTACCATTTG
5340797 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5340825 CGTGAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5342380 original size:2 final size:2
Alignment explanation
Indices: 5342375--5342420 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
5342365 AGGAGTGATT
* *
5342375 TA TA TA TA TA TG TA TA TA TA TA TA TA TA TA TC 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
5342417 TA TA
1 TA TA
5342421 GAGTGTGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5342428 original size:2 final size:2
Alignment explanation
Indices: 5342423--5342449 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5342413 TATATATAGA
5342423 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
5342450 AGAAATAGGG
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:5342812 original size:15 final size:15
Alignment explanation
Indices: 5342772--5342806 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5342762 AAGTAATAAC
5342772 AATAAAAAAATGGAA
1 AATAAAAAAATGGAA
5342787 AATAAAAAAAT-GAA
1 AATAAAAAAATGGAA
5342801 AATAAA
1 AATAAA
5342807 TGAAATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (15 bp):
AATAAAAAAATGGAA
Found at i:5362903 original size:67 final size:67
Alignment explanation
Indices: 5362775--5362909 Score: 157
Period size: 67 Copynumber: 2.0 Consensus size: 67
5362765 AAATGTTATA
* * * * ** *
5362775 TTTGGGTTTTGGTTGATTCCATGAAAAACCATTGTCAAAGGTTATGGTTGAGCCTTTGAAAAGCC
1 TTTGGGTTTTGATTGATCCCATGAAAAACCATTGTCAAAGATTATGGCTGAGCCTAAGAAAAACC
5362840 AT
66 AT
* *
5362842 TTTGGGTTTTGATTGATCCCGA-GAAAAATCATTGGT-AAAGATTGTGGCTGAGCCTAAGAAAAA
1 TTTGGGTTTTGATTGATCCC-ATGAAAAACCATT-GTCAAAGATTATGGCTGAGCCTAAGAAAAA
5362905 CCAT
64 CCAT
5362909 T
1 T
5362910 GTAAAGCTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
67 54 0.95
68 3 0.05
ACGTcount: A:0.30, C:0.13, G:0.24, T:0.33
Consensus pattern (67 bp):
TTTGGGTTTTGATTGATCCCATGAAAAACCATTGTCAAAGATTATGGCTGAGCCTAAGAAAAACC
AT
Found at i:5377363 original size:16 final size:17
Alignment explanation
Indices: 5377339--5377373 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
5377329 GTTAGTTAAG
5377339 AGCTCATTACCAGA-AA
1 AGCTCATTACCAGACAA
*
5377355 AGCTGATTACCAGACAA
1 AGCTCATTACCAGACAA
5377372 AG
1 AG
5377374 AAGAATTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (17 bp):
AGCTCATTACCAGACAA
Found at i:5382393 original size:14 final size:14
Alignment explanation
Indices: 5382368--5382405 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
5382358 CCAATACTGT
*
5382368 AACAAATTATCATC
1 AACAAATGATCATC
*
5382382 AACAGATGATCATC
1 AACAAATGATCATC
5382396 AACAAATGAT
1 AACAAATGAT
5382406 ATCTATTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.50, C:0.18, G:0.08, T:0.24
Consensus pattern (14 bp):
AACAAATGATCATC
Found at i:5389902 original size:8 final size:8
Alignment explanation
Indices: 5389891--5389920 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5389881 AATAAAAATA
5389891 AAAAATTC
1 AAAAATTC
5389899 AAAAATTC
1 AAAAATTC
5389907 AAAAATT-
1 AAAAATTC
5389914 AAAAATT
1 AAAAATT
5389921 AAGTAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 7 0.32
8 15 0.68
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (8 bp):
AAAAATTC
Found at i:5389920 original size:7 final size:7
Alignment explanation
Indices: 5389883--5389922 Score: 53
Period size: 7 Copynumber: 5.4 Consensus size: 7
5389873 AAAAAAGTAA
5389883 TAAAAAT
1 TAAAAAT
*
5389890 AAAAAAT
1 TAAAAAT
5389897 TCAAAAAT
1 T-AAAAAT
5389905 TCAAAAAT
1 T-AAAAAT
5389913 TAAAAAT
1 TAAAAAT
5389920 TAA
1 TAA
5389923 GTAAAAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 15 0.50
8 15 0.50
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (7 bp):
TAAAAAT
Found at i:5389920 original size:15 final size:14
Alignment explanation
Indices: 5389883--5389922 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
5389873 AAAAAAGTAA
*
5389883 TAAAAATAAAAAAT
1 TAAAAATTAAAAAT
5389897 TCAAAAATTCAAAAAT
1 T-AAAAATT-AAAAAT
5389913 TAAAAATTAA
1 TAAAAATTAA
5389923 GTAAAAATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 13 0.57
16 7 0.30
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAAAATTAAAAAT
Found at i:5392673 original size:49 final size:49
Alignment explanation
Indices: 5392592--5392748 Score: 174
Period size: 49 Copynumber: 3.2 Consensus size: 49
5392582 CGCTAAGGAA
* * * *
5392592 TATGTTCCACCTGTATATGATTTTGGACGATGATATGATGTGAGATATG
1 TATGTTCCATCTGTAGATGATTTCGGAAGATGATATGATGTGAGATATG
** * * **
5392641 TATGCTTCGTTC-GTAGATGATTTCGGAAGATGATAGGATGTCAGATACA
1 TATG-TTCCATCTGTAGATGATTTCGGAAGATGATATGATGTGAGATATG
* *
5392690 TATGTTCCATCTGTAGATGATTTC-GAACGATGACATGAAGTGAGATATG
1 TATGTTCCATCTGTAGATGATTTCGGAA-GATGATATGATGTGAGATATG
5392739 TATGTTCCAT
1 TATGTTCCAT
5392749 AGGTGGATTG
Statistics
Matches: 87, Mismatches: 18, Indels: 6
0.78 0.16 0.05
Matches are distributed among these distances:
48 8 0.09
49 75 0.86
50 4 0.05
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.36
Consensus pattern (49 bp):
TATGTTCCATCTGTAGATGATTTCGGAAGATGATATGATGTGAGATATG
Found at i:5393389 original size:5 final size:5
Alignment explanation
Indices: 5393379--5393414 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
5393369 AGGACCACTT
*
5393379 TATGA TATGA TATGA TATGA TATAA TATGA TATGA T
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA T
5393415 GACCACGTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:5402962 original size:25 final size:25
Alignment explanation
Indices: 5402925--5402972 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5402915 ACGGTCGTAA
* **
5402925 TCGCATATCACAACTTGTGGCCTAG
1 TCGCATATAACAACCCGTGGCCTAG
5402950 TCGCATATAACAACCCGTGGCCT
1 TCGCATATAACAACCCGTGGCCT
5402973 TGCCACATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (25 bp):
TCGCATATAACAACCCGTGGCCTAG
Found at i:5429601 original size:3 final size:3
Alignment explanation
Indices: 5429593--5429624 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
5429583 TTGAAATTAC
5429593 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5429625 TCTAAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.