Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 16 of 170
Found at i:4473718 original size:22 final size:23
Alignment explanation
Indices: 4473683--4473726 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
4473673 TTCCCTTTAC
4473683 TCTTTTGTTATTC-AATTTTTGT
1 TCTTTTGTTATTCAAATTTTTGT
4473705 TCTTTT-TTATTTCAAATTTTTG
1 TCTTTTGTTA-TTCAAATTTTTG
4473727 CAAATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 9 0.45
23 8 0.40
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.68
Consensus pattern (23 bp):
TCTTTTGTTATTCAAATTTTTGT
Found at i:4474368 original size:18 final size:18
Alignment explanation
Indices: 4474345--4474387 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
4474335 ACCCAATCTA
**
4474345 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
4474363 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
4474381 AACCCAA
1 AACCCAA
4474388 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:4474512 original size:9 final size:9
Alignment explanation
Indices: 4474495--4474561 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
4474485 GTAGTGATTC
*
4474495 AATTTGGTT
1 AATTCGGTT
4474504 AATTCGGTT
1 AATTCGGTT
* *
4474513 AATTTGGGT
1 AATTCGGTT
4474522 AATTCGGTT
1 AATTCGGTT
*
4474531 AATTCGGGT
1 AATTCGGTT
4474540 AATTCGGTT
1 AATTCGGTT
4474549 AATTCGGTT
1 AATTCGGTT
4474558 AATT
1 AATT
4474562 TGTTTAATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:4474518 original size:18 final size:18
Alignment explanation
Indices: 4474495--4474571 Score: 100
Period size: 18 Copynumber: 4.3 Consensus size: 18
4474485 GTAGTGATTC
*
4474495 AATTTGGTTAATTCGGTT
1 AATTTGGGTAATTCGGTT
4474513 AATTTGGGTAATTCGGTT
1 AATTTGGGTAATTCGGTT
*
4474531 AATTCGGGTAATTCGGTT
1 AATTTGGGTAATTCGGTT
* * * *
4474549 AATTCGGTTAATTTGTTT
1 AATTTGGGTAATTCGGTT
4474567 AATTT
1 AATTT
4474572 TTAACCAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 53 1.00
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (18 bp):
AATTTGGGTAATTCGGTT
Found at i:4474530 original size:27 final size:27
Alignment explanation
Indices: 4474495--4474571 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
4474485 GTAGTGATTC
*
4474495 AATTTGGTTAATTCGGTTAATTTGGGT
1 AATTCGGTTAATTCGGTTAATTTGGGT
* * *
4474522 AATTCGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGGTTAATTTGGGT
* *
4474549 AATTCGGTTAATTTGTTTAATTT
1 AATTCGGTTAATTCGGTTAATTT
4474572 TTAACCAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.48
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTTGGGT
Found at i:4481094 original size:18 final size:18
Alignment explanation
Indices: 4481068--4481103 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4481058 TTCTTTAAAA
* *
4481068 ATTATAATGATATAATTT
1 ATTAAAATGATAAAATTT
4481086 ATTAAAATGATAAAATTT
1 ATTAAAATGATAAAATTT
4481104 TATTTTTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
ATTAAAATGATAAAATTT
Found at i:4481433 original size:20 final size:20
Alignment explanation
Indices: 4481406--4481456 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
4481396 AAAATAAAAT
**
4481406 ATTTTTATTTATTTTGAAG-
1 ATTTTTATTTATTTACAAGA
4481425 ATGTTTTATTT-TTTACAAGA
1 AT-TTTTATTTATTTACAAGA
4481445 ATTTTTATTTAT
1 ATTTTTATTTAT
4481457 ATTTCTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.59
20 11 0.41
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (20 bp):
ATTTTTATTTATTTACAAGA
Found at i:4488956 original size:16 final size:18
Alignment explanation
Indices: 4488925--4488957 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
4488915 GTTAATAGAA
4488925 TAAATTTAGTTTTAATTG
1 TAAATTTAGTTTTAATTG
4488943 TAAATTT-G-TTTAATT
1 TAAATTTAGTTTTAATT
4488958 TTTCATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (18 bp):
TAAATTTAGTTTTAATTG
Found at i:4489969 original size:308 final size:307
Alignment explanation
Indices: 4489278--4490119 Score: 897
Period size: 308 Copynumber: 2.7 Consensus size: 307
4489268 GAAAATTACA
* * * * * *
4489278 GGAACGCACATCCATAATTAAAATAAAGAATATTTTTTGAGTGTATTTTAGTCTTTTCACTTTAA
1 GGAATGCACATCCGTAATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
* * * * ** ** * *
4489343 AAATCAATAAAAAGCAAGGATATGATAGGATTCAAACCCATGCCAAGTGCATTAATAAAATATTT
66 AAATCAATAAAAA-TATGCATATGGTA-GATTTGAACCCACACCAATTGCATTAATAAAACATTT
* *
4489408 AATTTACCACTCAACTAAAGCTTCATTTTAATATTTTTATACATTTTAGTTTTATTATGCACATT
129 AATTTACCACTCAACTAAA-CTTAATTTTAATATTTTTATACATTTTAATTTTATTATGCACATT
* * * * *
4489473 CTATTATCTC-C--ATTA-A-ATGTATA-TTTATATCTATCTATACTATTGTTTAAAATCTTGAC
193 TTATTACCTCACTAATTATATATCTATACTTTATATCTATCTATACTATTATTTAAAATCCTGAC
* * * *
4489532 TGAGTTGGTGTCGCAAGTCAACCGAGCACGAACTAATTGGTTAGGAAATTATG
258 TGAGTTGATGTCACAACTCAACCGAGCACCAACTAA---GTTAGGAAATTATG
* * * * *
4489585 GGAATGCACATCCTTAATTAAAATAAGTAATATTATTC-AGGGTATTTTAGTCTTTTTAATTTAA
1 GGAATGCACATCCGTAATTAAAATAAATAATATTATTCGAGTGTATTTTAGTC-TTTTCACTTAA
* * * * *
4489649 AAAATGAATAAAAATATGTATATGGTGAGATTTGAATCTACACCAATTGCATT-ATAAAACCTTT
65 AAAATCAATAAAAATATGCATATGGT-AGATTTGAACCCACACCAATTGCATTAATAAAACATTT
*
4489713 AATTTACCACTCAACTAAACATTAATTTTAATATTTTTATAAATTTTAATTTTATTATGCACATT
129 AATTTACCACTCAACTAAAC-TTAATTTTAATATTTTTATACATTTTAATTTTATTATGCACATT
* * **
4489778 TTATTACCTCCACTAATTATATATCTATACTTGTATAT-TATTTATACTATTATTTCAGCTCCTG
193 TTATTACCT-CACTAATTATATATCTATACTT-TATATCTATCTATACTATTATTTAAAATCCTG
* * *
4489842 -CTGAGTTGATGTCAC-CCTCAACCGGGTCACCAACTCAA-TTAGGAAGTTATG
256 ACTGAGTTGATGTCACAACTCAACCGAG-CACCAACT-AAGTTAGGAAATTATG
* *
4489893 GGAATGCACTTTCGTAATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
1 GGAATGCACATCCGTAATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
* * *
4489958 AAACCAATAAAAATATACATATGGTAAAATTTGAACCCACACCAATTGCATTAATAAAACATTTA
66 AAATCAATAAAAATATGCATATGGT-AGATTTGAACCCACACCAATTGCATTAATAAAACATTTA
* * * * *
4490023 ATTTACC-GTGCAACTAAAGTTTA-TAT-ATATTTTTATACATTTTAATTTTATTATGCACACTT
130 ATTTACCACT-CAACTAAACTTAATTTTAATATTTTTATACATTTTAATTTTATTATGCACATTT
* *
4490085 TATTACCTTCA-TCAGTTGTATATCTATACTATTAT
194 TATTACC-TCACT-AATTATATATCTATACT-TTAT
4490120 TTAAATTCCT
Statistics
Matches: 449, Mismatches: 67, Indels: 39
0.81 0.12 0.07
Matches are distributed among these distances:
304 1 0.00
305 77 0.17
306 101 0.22
307 59 0.13
308 104 0.23
309 43 0.10
310 9 0.02
311 26 0.06
312 24 0.05
313 5 0.01
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.39
Consensus pattern (307 bp):
GGAATGCACATCCGTAATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAA
AAATCAATAAAAATATGCATATGGTAGATTTGAACCCACACCAATTGCATTAATAAAACATTTAA
TTTACCACTCAACTAAACTTAATTTTAATATTTTTATACATTTTAATTTTATTATGCACATTTTA
TTACCTCACTAATTATATATCTATACTTTATATCTATCTATACTATTATTTAAAATCCTGACTGA
GTTGATGTCACAACTCAACCGAGCACCAACTAAGTTAGGAAATTATG
Found at i:4499779 original size:19 final size:19
Alignment explanation
Indices: 4499757--4499793 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4499747 CTTGCATGCT
4499757 AATATACAAATAACATATA
1 AATATACAAATAACATATA
* *
4499776 AATATATACATAACATAT
1 AATATACAAATAACATAT
4499794 TAGTTAGGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.11, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATACAAATAACATATA
Found at i:4502961 original size:16 final size:17
Alignment explanation
Indices: 4502940--4502972 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4502930 CTTTCATTTA
4502940 TTTAAATAT-ATTTAAT
1 TTTAAATATAATTTAAT
*
4502956 TTTAAATCTAATTTAAT
1 TTTAAATATAATTTAAT
4502973 GATTAAGCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAATATAATTTAAT
Found at i:4517740 original size:9 final size:9
Alignment explanation
Indices: 4517684--4517779 Score: 74
Period size: 9 Copynumber: 11.0 Consensus size: 9
4517674 TAAGTATAAT
4517684 TAAGTTATG
1 TAAGTTATG
*
4517693 TAACTTATG
1 TAAGTTATG
* * *
4517702 ATATGATATA
1 -TAAGTTATG
*
4517712 T-ATTTATG
1 TAAGTTATG
4517720 T-A-TTATG
1 TAAGTTATG
*
4517727 CAAGTTATG
1 TAAGTTATG
4517736 TAAGTTATG
1 TAAGTTATG
4517745 TAAGTTATG
1 TAAGTTATG
*
4517754 TGAG-TATG
1 TAAGTTATG
* *
4517762 CAAATTATG
1 TAAGTTATG
4517771 TAAGTTATG
1 TAAGTTATG
4517780 ATATATATTT
Statistics
Matches: 66, Mismatches: 17, Indels: 8
0.73 0.19 0.09
Matches are distributed among these distances:
7 5 0.08
8 11 0.17
9 45 0.68
10 5 0.08
ACGTcount: A:0.34, C:0.03, G:0.19, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:4518233 original size:33 final size:33
Alignment explanation
Indices: 4518191--4518256 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
4518181 TAAAAAAGAG
4518191 TTGTTTTTGCAGCAATTTTAAAATGAAAATTAA
1 TTGTTTTTGCAGCAATTTTAAAATGAAAATTAA
* *
4518224 TTGTTTTTGCTGCAATTTTAAAATGGAAATTAA
1 TTGTTTTTGCAGCAATTTTAAAATGAAAATTAA
4518257 AAAAATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (33 bp):
TTGTTTTTGCAGCAATTTTAAAATGAAAATTAA
Found at i:4518935 original size:22 final size:22
Alignment explanation
Indices: 4518907--4518968 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
4518897 GGAGCAAAAA
4518907 AGAACTTGCAACAACATTAACC
1 AGAACTTGCAACAACATTAACC
4518929 AGAACTTGCAACAA-A--AA--
1 AGAACTTGCAACAACATTAACC
*
4518946 AGAACTTGCAGCAACATTAACC
1 AGAACTTGCAACAACATTAACC
4518968 A
1 A
4518969 AATTCCTAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 13 0.38
18 1 0.03
19 2 0.06
20 2 0.06
21 1 0.03
22 15 0.44
ACGTcount: A:0.48, C:0.24, G:0.11, T:0.16
Consensus pattern (22 bp):
AGAACTTGCAACAACATTAACC
Found at i:4518951 original size:17 final size:17
Alignment explanation
Indices: 4518901--4518955 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 17
4518891 CAAAATGGAG
4518901 CAAAAAAGAACTTGCAA
1 CAAAAAAGAACTTGCAA
4518918 CAACATTAACCAGAACTTGCAA
1 CAA-A--AA--AGAACTTGCAA
4518940 CAAAAAAGAACTTGCA
1 CAAAAAAGAACTTGCA
4518956 GCAACATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 13 0.39
18 1 0.03
19 2 0.06
20 2 0.06
21 1 0.03
22 14 0.42
ACGTcount: A:0.53, C:0.22, G:0.11, T:0.15
Consensus pattern (17 bp):
CAAAAAAGAACTTGCAA
Found at i:4520345 original size:124 final size:125
Alignment explanation
Indices: 4520056--4520352 Score: 343
Period size: 126 Copynumber: 2.4 Consensus size: 125
4520046 ATTGTTCTGA
* * * * *
4520056 ACAATTTTTAATACATTGTTGCGGCGTTTTTAGACAAAACGTCACTAATGCTTACCTTTTGCGGT
1 ACAATTTTTAATACATTGTTGCGGCGTTTTT-GTCCAAACGCCACTAATGCATACCTTTTGCGGC
* * *
4520121 GATTCTGAGAAAAATGCTACTAAAAAGTTAAAATCTTGTAAGCAAACGATGCCGTTTTTGT
65 GATTCTGAGAAAAATGCTACTAAAAAGTCAAAATCCTGTAACCAAACGATGCCGTTTTTGT
* * * * *
4520182 ACACTTTTTAATACATTGTTGCGGCGTTTTTATAACAAACGCCGCTATTGCATACCTTTTGCGGC
1 ACAATTTTTAATACATTGTTGCGGCGTTTTTGT-CCAAACGCCACTAATGCATACCTTTTGCGGC
* *
4520247 G-TTGTGGAGAAAAATGGC-ACTAAAAA-TCAAATTCCTGTAACCAAAC-AGTGCCG-TTTTGT
65 GATTCT-GAGAAAAAT-GCTACTAAAAAGTCAAAATCCTGTAACCAAACGA-TGCCGTTTTTGT
* * *
4520306 ACAATTTTTAAGACATTGTTGTGACGTTTTTGGTCCAAACGCCACTA
1 ACAATTTTTAATACATTGTTGCGGCGTTTTT-GTCCAAACGCCACTA
4520353 CTATTAAAAA
Statistics
Matches: 144, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
124 45 0.31
125 25 0.17
126 72 0.50
127 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (125 bp):
ACAATTTTTAATACATTGTTGCGGCGTTTTTGTCCAAACGCCACTAATGCATACCTTTTGCGGCG
ATTCTGAGAAAAATGCTACTAAAAAGTCAAAATCCTGTAACCAAACGATGCCGTTTTTGT
Found at i:4520652 original size:7 final size:7
Alignment explanation
Indices: 4520642--4520876 Score: 84
Period size: 7 Copynumber: 32.4 Consensus size: 7
4520632 TTAGACAAAA
4520642 AAACCCT
1 AAACCCT
4520649 AAA-CCT
1 AAACCCT
4520655 AAGACCCT
1 AA-ACCCT
4520663 AAACACCT
1 AAAC-CCT
4520671 GAAAACACCT
1 --AAAC-CCT
*
4520681 AAATCCT
1 AAACCCT
4520688 AAAACCCCT
1 -AAA-CCCT
*
4520697 AAACCAT
1 AAACCCT
***
4520704 AAAATTT
1 AAACCCT
4520711 AAACCCT
1 AAACCCT
* *
4520718 AATCTCT
1 AAACCCT
*
4520725 ATACCCT
1 AAACCCT
4520732 AAACCCTT
1 AAACCC-T
4520740 AAACCCT
1 AAACCCT
**
4520747 AGTCCCT
1 AAACCCT
*
4520754 AAATTACCAT
1 -AA--ACCCT
*
4520764 AAACCCA
1 AAACCCT
*
4520771 AAACCTT
1 AAACCCT
*
4520778 AAACCAT
1 AAACCCT
4520785 AAA-CCT
1 AAACCCT
** *
4520791 CCACCAT
1 AAACCCT
4520798 ATTAA--CT
1 A--AACCCT
**
4520805 AAACTTT
1 AAACCCT
*
4520812 AAACCTT
1 AAACCCT
4520819 AAACCCT
1 AAACCCT
4520826 AAACCCT
1 AAACCCT
*
4520833 AAACCTT
1 AAACCCT
*
4520840 AAACCCC
1 AAACCCT
*
4520847 AAACCAT
1 AAACCCT
*
4520854 AAA-CAT
1 AAACCCT
*
4520860 ACACCCT
1 AAACCCT
*
4520867 AAACCAT
1 AAACCCT
4520874 AAA
1 AAA
4520877 TATAGATATT
Statistics
Matches: 167, Mismatches: 44, Indels: 34
0.68 0.18 0.14
Matches are distributed among these distances:
5 2 0.01
6 13 0.08
7 110 0.66
8 25 0.15
9 6 0.04
10 11 0.07
ACGTcount: A:0.45, C:0.34, G:0.01, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:4520934 original size:7 final size:7
Alignment explanation
Indices: 4520924--4520971 Score: 60
Period size: 7 Copynumber: 6.9 Consensus size: 7
4520914 ATCTTAAATA
4520924 CTAAACC
1 CTAAACC
4520931 CTAAACC
1 CTAAACC
4520938 CTAAACC
1 CTAAACC
*
4520945 CCAAACC
1 CTAAACC
* *
4520952 CTAGACT
1 CTAAACC
4520959 CTAAACC
1 CTAAACC
*
4520966 ATAAAC
1 CTAAAC
4520972 GCAAAACTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.44, C:0.40, G:0.02, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:4521028 original size:7 final size:7
Alignment explanation
Indices: 4521016--4521082 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
4521006 CATTTTATCA
4521016 TAAACCT
1 TAAACCT
*
4521023 TAAACCA
1 TAAACCT
* *
4521030 TAGACAT
1 TAAACCT
4521037 TAAACCT
1 TAAACCT
*
4521044 TAAATAC-
1 TAAA-CCT
**
4521051 TACCCCT
1 TAAACCT
*
4521058 TAAACCC
1 TAAACCT
4521065 TAAACCT
1 TAAACCT
4521072 TAAACCT
1 TAAACCT
4521079 TAAA
1 TAAA
4521083 ACCATAAAGT
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
6 1 0.02
7 42 0.95
8 1 0.02
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.25
Consensus pattern (7 bp):
TAAACCT
Found at i:4523126 original size:315 final size:315
Alignment explanation
Indices: 4522554--4523183 Score: 1224
Period size: 315 Copynumber: 2.0 Consensus size: 315
4522544 AGATGTCAAC
*
4522554 TATCTTATATGAAGATAACACAAAATGTATAGGAAGAGAAGTCGACTATCTTATTTGAAGATAAT
1 TATCTTATATGAAGATAACACAAAATGTATAGGAAGAGAAGTCAACTATCTTATTTGAAGATAAT
4522619 GCAGCATGTATAGCTCAGTTGAAGGGTGATTACATCAAAGGACATAGAACGAAACATATTTCACC
66 GCAGCATGTATAGCTCAGTTGAAGGGTGATTACATCAAAGGACATAGAACGAAACATATTTCACC
4522684 AAAATTATTCTTCACCCGTGATTTTGAGAAAAGAAGTGATATAAATGTTCAACAAATTCGTTCTA
131 AAAATTATTCTTCACCCGTGATTTTGAGAAAAGAAGTGATATAAATGTTCAACAAATTCGTTCTA
*
4522749 GTGATAATTTATCAGATCTTTTTGTAAGGCATTGCCGACTTCAACATTTGAAAGACTACTACATA
196 GTGATAATTTATCAGATCTTTTTGTAAGGCATTGCCAACTTCAACATTTGAAAGACTACTACATA
4522814 AGATTGGAATGCATCAACTAAAAAATGTAATGTAGTGTTGCCATTAGGGGGAGTT
261 AGATTGGAATGCATCAACTAAAAAATGTAATGTAGTGTTGCCATTAGGGGGAGTT
4522869 TATCTTATATGAAGATAACACAAAATGTATAGGAAGAGAAGTCAACTATCTTATTTGAAGATAAT
1 TATCTTATATGAAGATAACACAAAATGTATAGGAAGAGAAGTCAACTATCTTATTTGAAGATAAT
*
4522934 GCAGCATGTATAGCTCAGTTGAAGGGTGATTACATCAAAGGAGATAGAACGAAACATATTTCACC
66 GCAGCATGTATAGCTCAGTTGAAGGGTGATTACATCAAAGGACATAGAACGAAACATATTTCACC
4522999 AAAATTATTCTTCACCCGTGATTTTGAGAAAAGAAGTGATATAAATGTTCAACAAATTCGTTCTA
131 AAAATTATTCTTCACCCGTGATTTTGAGAAAAGAAGTGATATAAATGTTCAACAAATTCGTTCTA
4523064 GTGATAATTTATCAGATCTTTTTGTAAGGCATTGCCAACTTCAACATTTGAAAGACTACTACATA
196 GTGATAATTTATCAGATCTTTTTGTAAGGCATTGCCAACTTCAACATTTGAAAGACTACTACATA
*
4523129 AGATTGGAATGCGTCAACTAAAAAATGTAATGTAGTGTTGCCATTAGGGGGAGTT
261 AGATTGGAATGCATCAACTAAAAAATGTAATGTAGTGTTGCCATTAGGGGGAGTT
4523184 CAAAATAAGT
Statistics
Matches: 311, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
315 311 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.30
Consensus pattern (315 bp):
TATCTTATATGAAGATAACACAAAATGTATAGGAAGAGAAGTCAACTATCTTATTTGAAGATAAT
GCAGCATGTATAGCTCAGTTGAAGGGTGATTACATCAAAGGACATAGAACGAAACATATTTCACC
AAAATTATTCTTCACCCGTGATTTTGAGAAAAGAAGTGATATAAATGTTCAACAAATTCGTTCTA
GTGATAATTTATCAGATCTTTTTGTAAGGCATTGCCAACTTCAACATTTGAAAGACTACTACATA
AGATTGGAATGCATCAACTAAAAAATGTAATGTAGTGTTGCCATTAGGGGGAGTT
Found at i:4523572 original size:8 final size:8
Alignment explanation
Indices: 4523559--4523586 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
4523549 TATTTATTGC
4523559 TTTCATAT
1 TTTCATAT
4523567 TTTCATAT
1 TTTCATAT
4523575 TTTCATAT
1 TTTCATAT
4523583 TTTC
1 TTTC
4523587 TTTTTTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (8 bp):
TTTCATAT
Found at i:4523806 original size:13 final size:13
Alignment explanation
Indices: 4523782--4523815 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4523772 ACTTTTTTAT
*
4523782 TATTTTTAATTAA
1 TATTTATAATTAA
*
4523795 TGTTTATAATTAA
1 TATTTATAATTAA
4523808 TATTTATA
1 TATTTATA
4523816 TTGTTTTCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (13 bp):
TATTTATAATTAA
Found at i:4529744 original size:17 final size:18
Alignment explanation
Indices: 4529719--4529758 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
4529709 ATTGCCTCGC
*
4529719 CTTTATTTT-TAATTTTT
1 CTTTTTTTTCTAATTTTT
*
4529736 CTTTTTTTTCTAGTTTTT
1 CTTTTTTTTCTAATTTTT
4529754 CTTTT
1 CTTTT
4529759 GGTTCAAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.78
Consensus pattern (18 bp):
CTTTTTTTTCTAATTTTT
Found at i:4530342 original size:14 final size:15
Alignment explanation
Indices: 4530325--4530357 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4530315 AAATTTTAAG
4530325 AAAAAAATAAAA-AT
1 AAAAAAATAAAACAT
*
4530339 AAAAATATAAAACAT
1 AAAAAAATAAAACAT
4530354 AAAA
1 AAAA
4530358 CTTTTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (15 bp):
AAAAAAATAAAACAT
Found at i:4530917 original size:21 final size:21
Alignment explanation
Indices: 4530876--4530917 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4530866 GGTTGTAAGT
* *
4530876 AGTAATATTAATTATTGTAAC
1 AGTAATATTAATTACTATAAC
*
4530897 AGTAATATTAGTTACTATAAC
1 AGTAATATTAATTACTATAAC
4530918 GGTGATGATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.10, T:0.40
Consensus pattern (21 bp):
AGTAATATTAATTACTATAAC
Found at i:4534826 original size:13 final size:13
Alignment explanation
Indices: 4534803--4534836 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4534793 AATTCTGATG
*
4534803 TCAACTTTCTTCT
1 TCAATTTTCTTCT
*
4534816 TCACTTTTCTTCT
1 TCAATTTTCTTCT
4534829 TCAATTTT
1 TCAATTTT
4534837 TTGCGTCTTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.26, G:0.00, T:0.59
Consensus pattern (13 bp):
TCAATTTTCTTCT
Found at i:4539513 original size:23 final size:23
Alignment explanation
Indices: 4539296--4539658 Score: 214
Period size: 23 Copynumber: 16.1 Consensus size: 23
4539286 CTATTTAAGT
* *
4539296 ATTGAAGTGTTT-AGTAGTTGGAA
1 ATTGAAGTGTTTAAAT-GTTGTAA
* * *
4539319 ATTG-AGATGTTTTATTGCTGT-A
1 ATTGAAG-TGTTTAAATGTTGTAA
* * *
4539341 ATTGAGGTGTATAAATGTTGTTA
1 ATTGAAGTGTTTAAATGTTGTAA
* * *
4539364 ATAG-AGATG-TTAAAGTGCTGCAA
1 ATTGAAG-TGTTTAAA-TGTTGTAA
*
4539387 ATTGAAGTGTTTAAATGATGTAA
1 ATTGAAGTGTTTAAATGTTGTAA
* * *
4539410 ATTAAAGTGTTAAAATGTTGCAA
1 ATTGAAGTGTTTAAATGTTGTAA
* * *
4539433 ATTGAAGTATTTAAATGCTGTGA
1 ATTGAAGTGTTTAAATGTTGTAA
* *
4539456 ATTGAAGTG-TTAAAGTGCTGCAA
1 ATTGAAGTGTTTAAA-TGTTGTAA
4539479 ATTGAAGTGTTTAAATGTTGTAA
1 ATTGAAGTGTTTAAATGTTGTAA
*
4539502 ATTGAAGTGTTTTAA----GT--
1 ATTGAAGTGTTTAAATGTTGTAA
* * * *
4539519 ACTGAGGTGTATAAATGTTGTTA
1 ATTGAAGTGTTTAAATGTTGTAA
* *
4539542 ATTG-GGATG-TTAAAGTGTTGTGA
1 ATTGAAG-TGTTTAAA-TGTTGTAA
* * *
4539565 GTTGAGGTGTTTAAATGCTGTAA
1 ATTGAAGTGTTTAAATGTTGTAA
* *
4539588 ATTGAAGTATTTAATTGTTGTAA
1 ATTGAAGTGTTTAAATGTTGTAA
* * * *
4539611 ATTGAGGTGCTGAAATGATGTAA
1 ATTGAAGTGTTTAAATGTTGTAA
* * *
4539634 ATCGAAGTGTTTAAGTGTTGCAA
1 ATTGAAGTGTTTAAATGTTGTAA
4539657 AT
1 AT
4539659 AATATATGAT
Statistics
Matches: 259, Mismatches: 61, Indels: 40
0.72 0.17 0.11
Matches are distributed among these distances:
17 11 0.04
19 2 0.01
21 2 0.01
22 33 0.13
23 190 0.73
24 21 0.08
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.39
Consensus pattern (23 bp):
ATTGAAGTGTTTAAATGTTGTAA
Found at i:4541221 original size:28 final size:27
Alignment explanation
Indices: 4541140--4541223 Score: 105
Period size: 28 Copynumber: 3.0 Consensus size: 27
4541130 CATGCAGTAG
* * **
4541140 CAGTTTGGGCCTAAGCCCTATACAGCAA
1 CAGTGTGGGCCT-AGCCCAATACAATAA
4541168 CAGTGTGGGCCTTAGCCCAATACAATAA
1 CAGTGTGGGCC-TAGCCCAATACAATAA
4541196 CAGTGTGGGCCATAGCCCAATACAATAA
1 CAGTGTGGGCC-TAGCCCAATACAATAA
4541224 TAGTATAATG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 49 0.98
29 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (27 bp):
CAGTGTGGGCCTAGCCCAATACAATAA
Found at i:4541363 original size:26 final size:26
Alignment explanation
Indices: 4541334--4541430 Score: 122
Period size: 26 Copynumber: 3.7 Consensus size: 26
4541324 CACCAATATC
4541334 GCAGCAAAGCTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAATAGTGAT
*
4541360 GCAGTAAAGCTGCCAGTAATAGTGAT
1 GCAGCAAAGCTGCCAGTAATAGTGAT
* * * *
4541386 GCAGCAAAGTTGCTAGTAACAGTGAC
1 GCAGCAAAGCTGCCAGTAATAGTGAT
* * *
4541412 GCAGTAAAGTTACCAGTAA
1 GCAGCAAAGCTGCCAGTAA
4541431 CAGTATATGT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 62 1.00
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.21
Consensus pattern (26 bp):
GCAGCAAAGCTGCCAGTAATAGTGAT
Found at i:4541366 original size:14 final size:13
Alignment explanation
Indices: 4541347--4541421 Score: 50
Period size: 14 Copynumber: 5.7 Consensus size: 13
4541337 GCAAAGCTGC
4541347 CAGTAATAGTGATG
1 CAGTAA-AGTGATG
*
4541361 CAGTAAAGCTG--C
1 CAGTAAAG-TGATG
4541373 CAGTAATAGTGATG
1 CAGTAA-AGTGATG
*
4541387 CAGCAAAGT--TG
1 CAGTAAAGTGATG
*
4541398 CTAGTAACAGTGACG
1 C-AGTAA-AGTGATG
4541413 CAGTAAAGT
1 CAGTAAAGT
4541422 TACCAGTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 17
0.69 0.07 0.24
Matches are distributed among these distances:
11 3 0.06
12 12 0.25
13 13 0.27
14 18 0.38
15 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.23
Consensus pattern (13 bp):
CAGTAAAGTGATG
Found at i:4541630 original size:27 final size:27
Alignment explanation
Indices: 4541599--4541878 Score: 244
Period size: 27 Copynumber: 10.4 Consensus size: 27
4541589 TCAACTCCTA
**
4541599 AGGGTATAGCAGTCATTTTACCCTTTG
1 AGGGTATTTCAGTCATTTTACCCTTTG
* *
4541626 GGGGTATTTCGGTCATTTTA-CC-TTG
1 AGGGTATTTCAGTCATTTTACCCTTTG
* * **
4541651 CCAGGGTATTTCAGTAATTCTACCCTGCG
1 --AGGGTATTTCAGTCATTTTACCCTTTG
* * **
4541680 AGGGTATTTTAGTTATTTTACCAGTTG
1 AGGGTATTTCAGTCATTTTACCCTTTG
* ** *
4541707 GGGGTATTTTGGTCATTTTACCCTTTA
1 AGGGTATTTCAGTCATTTTACCCTTTG
*
4541734 AGGGTATTTCAGTCATTTTACCTTTTG
1 AGGGTATTTCAGTCATTTTACCCTTTG
* *
4541761 AGGATATTTCAGTCATTTTACCCTTCG
1 AGGGTATTTCAGTCATTTTACCCTTTG
** * *
4541788 AGGGTATTTTGGTTATTTTACCCTTCG
1 AGGGTATTTCAGTCATTTTACCCTTTG
* *
4541815 AGGGTATTTC-GATCATTTTACCTTTTA
1 AGGGTATTTCAG-TCATTTTACCCTTTG
* *
4541842 AGGGTATTTC-GATCATTTTATCCTTCG
1 AGGGTATTTCAG-TCATTTTACCCTTTG
*
4541869 AGGGTTTTTC
1 AGGGTATTTC
4541879 TATTATTTTA
Statistics
Matches: 203, Mismatches: 45, Indels: 10
0.79 0.17 0.04
Matches are distributed among these distances:
25 3 0.01
26 3 0.01
27 194 0.96
28 2 0.01
29 1 0.00
ACGTcount: A:0.19, C:0.17, G:0.21, T:0.44
Consensus pattern (27 bp):
AGGGTATTTCAGTCATTTTACCCTTTG
Found at i:4541831 original size:81 final size:81
Alignment explanation
Indices: 4541599--4541877 Score: 298
Period size: 81 Copynumber: 3.5 Consensus size: 81
4541589 TCAACTCCTA
** * * * *
4541599 AGGGTATAGCAGTCATTTTACCCTTTGGGGGTATTTCGGTCATTTTA-CCTTGCCAGGGTATTTC
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTT-CAAGGGTATTTC
* * * **
4541663 AGTAATTCTACCCTGCG
65 AGTCATTTTACCTTTTG
* * * * *
4541680 AGGGTATTTTAGTTATTTTACCAGTT-GGGGGTATTTTGGTCATTTTACCCTTTAAGGGTATTTC
1 AGGGTATTTCAGTCATTTTACC-CTTCGAGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTC
4541744 AGTCATTTTACCTTTTG
65 AGTCATTTTACCTTTTG
* * *
4541761 AGGATATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTTATTTTACCCTTCGAGGGTATTTC-
1 AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCA
*
4541825 GATCATTTTACCTTTTA
66 G-TCATTTTACCTTTTG
*
4541842 AGGGTATTTC-GATCATTTTATCCTTCGAGGGT-TTTT
1 AGGGTATTTCAG-TCATTTTACCCTTCGAGGGTATTTT
4541878 CTATTATTTT
Statistics
Matches: 169, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
80 8 0.05
81 155 0.92
82 6 0.04
ACGTcount: A:0.19, C:0.16, G:0.21, T:0.44
Consensus pattern (81 bp):
AGGGTATTTCAGTCATTTTACCCTTCGAGGGTATTTTGGTCATTTTACCCTTCAAGGGTATTTCA
GTCATTTTACCTTTTG
Found at i:4546220 original size:21 final size:21
Alignment explanation
Indices: 4546179--4546221 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
4546169 AATAAAGTAG
*
4546179 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
4546200 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
4546221 A
1 A
4546222 AATTCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:4546262 original size:38 final size:37
Alignment explanation
Indices: 4546204--4546281 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 37
4546194 TATAGTATTA
*
4546204 TATATTATGATTTTAGTAAATTCATA-ATAATAATAAT
1 TATATTATAATTTTAGTAAATT-ATATATAATAATAAT
* * *
4546241 TATATTCATAATTTTATTAAATTATATTTAATAATTAT
1 TATATT-ATAATTTTAGTAAATTATATATAATAATAAT
4546279 TAT
1 TAT
4546282 GTTAAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
37 9 0.26
38 26 0.74
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (37 bp):
TATATTATAATTTTAGTAAATTATATATAATAATAAT
Found at i:4546532 original size:46 final size:44
Alignment explanation
Indices: 4546440--4546533 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 44
4546430 ATTACAACAT
4546440 CATTCCATTCAACCACACACAAGAATACTATTACAGTTATATTC
1 CATTCCATTCAACCACACACAAGAATACTATTACAGTTATATTC
4546484 CATTCCATTCAACCA-A-ACAATTGAATTACTAATTACAGCTT-TATTC
1 CATTCCATTCAACCACACACAA--GAA-TACT-ATTACAG-TTATATTC
4546530 CATT
1 CATT
4546534 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
42 4 0.09
43 1 0.02
44 18 0.40
45 4 0.09
46 16 0.36
47 2 0.04
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCACACACAAGAATACTATTACAGTTATATTC
Found at i:4546536 original size:16 final size:16
Alignment explanation
Indices: 4546515--4546569 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
4546505 TGAATTACTA
*
4546515 ATTACAGCTTTATTCC
1 ATTACAGCTCTATTCC
*
4546531 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCC
* *
4546547 ATAATAGCTCTATTCC
1 ATTACAGCTCTATTCC
4546563 ATTACAG
1 ATTACAG
4546570 TGAACCAAAC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:4547975 original size:15 final size:15
Alignment explanation
Indices: 4547957--4547985 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4547947 TTATAATTAA
4547957 AAATTTATATTTATC
1 AAATTTATATTTATC
4547972 AAATTTATATTTAT
1 AAATTTATATTTAT
4547986 ATTTAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATTTATATTTATC
Found at i:4548789 original size:11 final size:11
Alignment explanation
Indices: 4548773--4548798 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4548763 TATTTTTTTA
4548773 TTTTAAAATAC
1 TTTTAAAATAC
4548784 TTTTAAAATAC
1 TTTTAAAATAC
4548795 TTTT
1 TTTT
4548799 TTATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:4548825 original size:26 final size:26
Alignment explanation
Indices: 4548784--4548836 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4548774 TTTAAAATAC
** * *
4548784 TTTTAAAATACTTTTTTATTTTTTAT
1 TTTTAAAATAAATTTTTAGTGTTTAT
4548810 TTTTAAAATAAATTTTTAGTGTTTAT
1 TTTTAAAATAAATTTTTAGTGTTTAT
4548836 T
1 T
4548837 AAAAAAATGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (26 bp):
TTTTAAAATAAATTTTTAGTGTTTAT
Found at i:4551120 original size:29 final size:29
Alignment explanation
Indices: 4551078--4551150 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
4551068 CTACACTTGG
*
4551078 AACAAAATGTAAGAAATCTATTTGCATTA
1 AACAAAATGTAAGAAATCTATGTGCATTA
*
4551107 AACAAAATGTAAGAAATCTATGTGTATTA
1 AACAAAATGTAAGAAATCTATGTGCATTA
4551136 AACAAAATGTAAGAA
1 AACAAAATGTAAGAA
4551151 CACATATGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.27
Consensus pattern (29 bp):
AACAAAATGTAAGAAATCTATGTGCATTA
Found at i:4551717 original size:4 final size:4
Alignment explanation
Indices: 4551708--4551733 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
4551698 TTTTAAATAG
4551708 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
4551734 TTAGTTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:4567162 original size:19 final size:20
Alignment explanation
Indices: 4567117--4567166 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
4567107 AAATAAAATA
**
4567117 TTTTTATTTATTTTGAAGAT
1 TTTTTATTTATTTACAAGAT
* *
4567137 GTCTTATTT-TTTACAAGAT
1 TTTTTATTTATTTACAAGAT
4567156 TTTTTATTTAT
1 TTTTTATTTAT
4567167 ATTTCTATTT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.24, C:0.04, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTTTATTTATTTACAAGAT
Found at i:4568688 original size:7 final size:7
Alignment explanation
Indices: 4568673--4568711 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
4568663 TAAACAAATA
*
4568673 AGGGATT
1 AGGGTTT
4568680 AGGGTTT
1 AGGGTTT
4568687 AGGGTTT
1 AGGGTTT
4568694 AGGGTTT
1 AGGGTTT
*
4568701 AGGGTAT
1 AGGGTTT
4568708 AGGG
1 AGGG
4568712 ATTAAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (7 bp):
AGGGTTT
Found at i:4569017 original size:126 final size:126
Alignment explanation
Indices: 4568779--4569224 Score: 641
Period size: 126 Copynumber: 3.6 Consensus size: 126
4568769 AGGATAACGA
4568779 TTCTAGC-AGAATGCTTTATAAGAAGAATTTGTGAAAT--CG-CCATCGTGGACGCGCTTTTGCT
1 TTCTAGCAAG-ATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCA-CGTGGACGCGCTTTTGCT
* * ** * * *
4568840 ACAGTTGGCCCCGAAAAAAAATAATTTCGAGTTGACGTTTCTGAGCGAATAGTATAAAAATGGC
64 ACAGTAGGTCTTG-GAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAATGGC
* * **
4568904 TTCTAGCAAGATGCGTTATGAGAAGAATTTGTGAAATCATGCCCACGTGGACGCGCTTTTGCTAC
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
*
4568969 AGTAGGTCTTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAAAGGC
66 AGTAGGTCTTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAATGGC
* * * *
4569030 TTCTAGCAGGATGCTTTATGAGAAGAATTTGTGAAATTGCGCCCACGTGGATGCGCTTTTGCTAC
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
4569095 AGTAGGTCTTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAAT-GC
66 AGTAGGTCTTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAATGGC
* * * * *
4569155 TTTTAGCAGGATGTTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTAT
1 TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
4569220 AGTAG
66 AGTAG
4569225 CATGTTCGGT
Statistics
Matches: 292, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
125 97 0.33
126 164 0.56
127 28 0.10
128 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.30
Consensus pattern (126 bp):
TTCTAGCAAGATGCTTTATAAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTAC
AGTAGGTCTTGGAAAAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAAATGGC
Found at i:4570511 original size:20 final size:20
Alignment explanation
Indices: 4570486--4570523 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4570476 TTTTTAAAAA
4570486 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
4570506 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
4570524 TACCTCATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:4571516 original size:51 final size:51
Alignment explanation
Indices: 4571455--4571554 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
4571445 AAATTATTTA
* *
4571455 AAATAGGGATTTACGAGAAATTTA-AGAGGAAATTGAGAGTAAATTGAGATT
1 AAATAGGGATTTAAGAGAAATTTAGA-AGGAAATTGAGAGCAAATTGAGATT
* * *
4571506 AAATATGGATTTAAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGA
4571555 GAAAATTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.26, T:0.27
Consensus pattern (51 bp):
AAATAGGGATTTAAGAGAAATTTAGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:4571552 original size:11 final size:11
Alignment explanation
Indices: 4571532--4571588 Score: 69
Period size: 11 Copynumber: 5.1 Consensus size: 11
4571522 GAAATTTGGA
*
4571532 AGGAATTTGAG
1 AGGAAATTGAG
*
4571543 AGCAAATTGAG
1 AGGAAATTGAG
* *
4571554 AGAAAATTTAG
1 AGGAAATTGAG
4571565 AGGAAATTGAG
1 AGGAAATTGAG
4571576 AGGAAATTTGAG
1 AGGAAA-TTGAG
4571588 A
1 A
4571589 AAGGATTAGT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 33 0.85
12 6 0.15
ACGTcount: A:0.46, C:0.02, G:0.30, T:0.23
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:4571569 original size:33 final size:34
Alignment explanation
Indices: 4571514--4571588 Score: 91
Period size: 33 Copynumber: 2.2 Consensus size: 34
4571504 TTAAATATGG
* * *
4571514 ATTTAAGAGAAATTTGGAAGGAATTTGAGAGCAA
1 ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
*
4571548 A-TTGAGAGAAAATTTAG-AGGAAATTGAGAGGAA
1 ATTTGAGAG-AAATTTAGAAGGAAATTGAGAGCAA
4571581 ATTTGAGA
1 ATTTGAGA
4571589 AAGGATTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
33 21 0.60
34 14 0.40
ACGTcount: A:0.45, C:0.01, G:0.28, T:0.25
Consensus pattern (34 bp):
ATTTGAGAGAAATTTAGAAGGAAATTGAGAGCAA
Found at i:4571571 original size:22 final size:23
Alignment explanation
Indices: 4571535--4571588 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 23
4571525 ATTTGGAAGG
4571535 AATTTGAGAGCAAATTGAGAGAA
1 AATTTGAGAGCAAATTGAGAGAA
* *
4571558 AATTT-AGAGGAAATTGAGAGGA
1 AATTTGAGAGCAAATTGAGAGAA
4571580 AATTTGAGA
1 AATTTGAGA
4571589 AAGGATTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.28, T:0.24
Consensus pattern (23 bp):
AATTTGAGAGCAAATTGAGAGAA
Found at i:4571833 original size:39 final size:40
Alignment explanation
Indices: 4571756--4571853 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 40
4571746 GTCTACGTAA
* ** *
4571756 ACGCGCTTTGCTGACGTGGACGCAAGTCGCGCATACGTGG
1 ACGCGATTTGCTGACACGTACGCAAGTCGCGCATACGTGG
* * * * *
4571796 ATGCGATTTGTTGCCACGTACGCAA-TCGTGCTTACGTGG
1 ACGCGATTTGCTGACACGTACGCAAGTCGCGCATACGTGG
4571835 ACGCGATTTGCTGACACGT
1 ACGCGATTTGCTGACACGT
4571854 CCCCTGACAT
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
39 28 0.61
40 18 0.39
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.26
Consensus pattern (40 bp):
ACGCGATTTGCTGACACGTACGCAAGTCGCGCATACGTGG
Found at i:4575032 original size:32 final size:31
Alignment explanation
Indices: 4574996--4575060 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
4574986 AAAATTTCAA
4574996 AATTCAAAAAAGTAGAAG-GACTAAAATTGATC
1 AATTCAAAAAA-TA-AAGAGACTAAAATTGATC
* *
4575028 AATTCAAAAAATATAGATACTAAAATTGATC
1 AATTCAAAAAATAAAGAGACTAAAATTGATC
4575059 AA
1 AA
4575061 ATTAAAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 2 0.07
31 17 0.57
32 11 0.37
ACGTcount: A:0.55, C:0.09, G:0.11, T:0.25
Consensus pattern (31 bp):
AATTCAAAAAATAAAGAGACTAAAATTGATC
Found at i:4575075 original size:31 final size:31
Alignment explanation
Indices: 4575015--4575075 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4575005 AAGTAGAAGG
*
4575015 ACTAAAATTGATCAATTCAAAAAATATAGAT
1 ACTAAAATTGATCAATTCAAAAAACATAGAT
*
4575046 ACTAAAATTGATCAAATT-AAAATACATAGA
1 ACTAAAATTGATC-AATTCAAAAAACATAGA
4575076 CTAATCCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.28
Consensus pattern (31 bp):
ACTAAAATTGATCAATTCAAAAAACATAGAT
Found at i:4577015 original size:308 final size:297
Alignment explanation
Indices: 4576236--4577263 Score: 803
Period size: 308 Copynumber: 3.4 Consensus size: 297
4576226 TACATCCATG
* * * * * ** *
4576236 ATTAGAATAAAGAATATTTTTTGAGTGTATTTTTA-TCTTTTCACTTTAAAAATTAATAAAAAGC
1 ATTAAAATAAATAATATTATTCGAGTGTA-TTTTAGTCTTTTCACTTAAAAAACCAATAAAAA-T
* * ** * ** *
4576300 A-AGGATATGGTAGGATTCAAACTCATGCCAAGTGCATTAGTAAAACATTTAATTTACCACTCAA
64 ATA-CATATGGTAAGATTTGAACCCACACCAATTGCATTA-TAAAACATTTAATTTACCACTCAA
* *
4576364 CTAAAGCTTCATTTTAATATTTTTATACATTTTAGTTTTATTATGCACATTCTATTA--TCTCCA
127 CTAAAG-TTCATTTTAATATTTTTATACATTTTAATTTTATTATGCACATTCTATTACCTCACCA
* * *
4576427 --TA-A-ATGTATA-TT-TATATCTATCTATACTATTGTTTAAACTCTTGACTGAGTTGGTGTCG
191 GTTATATATCTATACTTGTATAT-TATTTA-ACTATT-TTT--ACTC-T-ACTGAGTT-GTGTCA
* * * * * * * *
4576486 CAAGTTAACTGAG-CACGAACTAATTGGTTAGGAAATTACGGGAATGCACATCCTTA
248 CCA-TCAACCG-GTCACCAACTAATT-G---GGAAGTTACGGGAATGC-CTTTCATA
* * * **
4576542 ATTAAAATAAGTAATATTATTCG-GGGTATTTTAGTCTTTTCAATTCAAAAAAATGAATAAAAAT
1 ATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTT--AAAAAACCAATAAAAAT
** * * * * ** *
4576606 ATGTATATGGTGAGATTTGAATCTACACCATTTGCATTATAAAACCCTTAATTTACCACTCAAGT
64 ATACATATGGTAAGATTTGAACCCACACCAATTGCATTATAAAACATTTAATTTACCACTCAACT
* *
4576671 AAACATTCATTTTAATATTTTTATAAATTTTAATTTTATTATGCACATTCTATTACCTCCACCAG
129 AAA-GTTCATTTTAATATTTTTATACATTTTAATTTTATTATGCACATTCTATTACCT-CACCAG
*
4576736 TTATATATCTATACTTGTATATTATTTACACTATTATTTCAGCTCCTACTGAGTTGATGTCACCC
192 TTATATATCTATACTTGTATATTATTTA-ACTATT-TTT-A-CT-CTACTGAGTTG-TGTCACCA
4576801 TCAACCAGGTCACCAACTCAATTGGGAAGTTACGGGAATGCGCTTTCATA
251 TCAACC-GGTCACCAACT-AATTGGGAAGTTACGGGAATGC-CTTTCATA
4576851 ATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAAAAACCAATAAAAATAT
1 ATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAAAAACCAATAAAAATAT
* *
4576916 ACATATGGTAAAATTTGAACCCACGCCAATTGCATTGATAAAACATTTAATTTACCA-TGCAACT
66 ACATATGGTAAGATTTGAACCCACACCAATTGCATT-ATAAAACATTTAATTTACCACT-CAACT
* * **
4576980 AAAGTTTA-TATATATATTTTTATACATTTTAATTTTATTATGCACACTT-TATTACCTTCATTA
129 AAAGTTCATTTTA-ATATTTTTATACATTTTAATTTTATTATGCACA-TTCTATTACC-TCACCA
* * * * *
4577043 GTTGTTTATCTATAC-TG----TTATTTAA--ATTCTTAAT-TACT-CG--GTGTCACCATCAAC
191 GTTATATATCTATACTTGTATATTATTTAACTATTTTTACTCTACTGAGTTGTGTCACCATCAAC
** * ** *
4577097 CGGATCACCAACTGGGTTAGGAAGTTACAAGAATACCTTTCCATA
256 CGG-TCACCAACT-AATTGGGAAGTTACGGGAATGCCTTT-CATA
* * * * *
4577142 ACTAAAATAAGTAATATTATTTGAGTATATTTTAGTCTTTTCACTTTTAAAAAACCAATGAAAAT
1 ATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCAC--TTAAAAAACCAATAAAAAT
* ** * * * *
4577207 ATGCATATCATAGGATTTGAACCCATACTAATTGCATTAATAAAATATTTAATTTAC
64 ATACATATGGTAAGATTTGAACCCACACCAATTGCATT-ATAAAACATTTAATTTAC
4577264 TCTTTACTAT
Statistics
Matches: 596, Mismatches: 96, Indels: 73
0.78 0.13 0.10
Matches are distributed among these distances:
290 6 0.01
291 82 0.14
292 1 0.00
293 65 0.11
294 1 0.00
295 4 0.01
297 1 0.00
298 1 0.00
299 2 0.00
300 3 0.01
302 1 0.00
303 7 0.01
304 5 0.01
305 88 0.15
306 43 0.07
307 20 0.03
308 108 0.18
309 71 0.12
310 22 0.04
311 7 0.01
312 29 0.05
313 23 0.04
314 6 0.01
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.39
Consensus pattern (297 bp):
ATTAAAATAAATAATATTATTCGAGTGTATTTTAGTCTTTTCACTTAAAAAACCAATAAAAATAT
ACATATGGTAAGATTTGAACCCACACCAATTGCATTATAAAACATTTAATTTACCACTCAACTAA
AGTTCATTTTAATATTTTTATACATTTTAATTTTATTATGCACATTCTATTACCTCACCAGTTAT
ATATCTATACTTGTATATTATTTAACTATTTTTACTCTACTGAGTTGTGTCACCATCAACCGGTC
ACCAACTAATTGGGAAGTTACGGGAATGCCTTTCATA
Found at i:4578119 original size:21 final size:21
Alignment explanation
Indices: 4578095--4578135 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
4578085 GTCAATAACC
4578095 AAATGTTCACACAAACAGACA
1 AAATGTTCACACAAACAGACA
**
4578116 AAATGTTCTGACAAACAGAC
1 AAATGTTCACACAAACAGAC
4578136 GTAAATTCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.22, G:0.12, T:0.17
Consensus pattern (21 bp):
AAATGTTCACACAAACAGACA
Found at i:4583512 original size:13 final size:13
Alignment explanation
Indices: 4583481--4583520 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
4583471 CTTTTCAAAT
4583481 ACAGATA-ACAGA
1 ACAGATATACAGA
*
4583493 ATTAGATATACAGA
1 A-CAGATATACAGA
4583507 ACAGATATACAGA
1 ACAGATATACAGA
4583520 A
1 A
4583521 TCCTACCCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 1 0.04
13 17 0.71
14 6 0.25
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (13 bp):
ACAGATATACAGA
Found at i:4587060 original size:17 final size:18
Alignment explanation
Indices: 4587038--4587072 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4587028 ATTTGGGTCA
*
4587038 TGTGGG-CCACATGGGCG
1 TGTGGGCCCACACGGGCG
4587055 TGTGGGCCCACACGGGCG
1 TGTGGGCCCACACGGGCG
4587073 AATAGTATGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.11, C:0.29, G:0.46, T:0.14
Consensus pattern (18 bp):
TGTGGGCCCACACGGGCG
Found at i:4588056 original size:18 final size:18
Alignment explanation
Indices: 4588033--4588072 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
4588023 GTTTTAAAAT
*
4588033 TGAATAACGATTTGTAAA
1 TGAATAACGATTTGGAAA
* *
4588051 TGAATAATGTTTTGGAAA
1 TGAATAACGATTTGGAAA
4588069 TGAA
1 TGAA
4588073 CGACACAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.20, T:0.35
Consensus pattern (18 bp):
TGAATAACGATTTGGAAA
Found at i:4592475 original size:22 final size:21
Alignment explanation
Indices: 4592450--4592521 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 21
4592440 TCAACTATCT
4592450 TATATGAAGATAATACAACATG
1 TATATGAAGATAAT-CAACATG
* * *
4592472 TATAGGAAGAGAAGTCAACTATCT
1 TATATGAAGATAA-TCAAC-AT-G
*
4592496 TATCTGAAGATAATGCAACATG
1 TATATGAAGATAAT-CAACATG
4592518 TATA
1 TATA
4592522 GCTCAATTGC
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 18 0.47
23 6 0.16
24 14 0.37
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (21 bp):
TATATGAAGATAATCAACATG
Found at i:4592478 original size:46 final size:46
Alignment explanation
Indices: 4592426--4592522 Score: 167
Period size: 46 Copynumber: 2.1 Consensus size: 46
4592416 AATTTGTCTT
*
4592426 TATAGGAAGAGATGTCAACTATCTTATATGAAGATAATACAACATG
1 TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
* *
4592472 TATAGGAAGAGAAGTCAACTATCTTATCTGAAGATAATGCAACATG
1 TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
4592518 TATAG
1 TATAG
4592523 CTCAATTGCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (46 bp):
TATAGGAAGAGAAGTCAACTATCTTATATGAAGATAATACAACATG
Found at i:4592504 original size:24 final size:24
Alignment explanation
Indices: 4592425--4592505 Score: 78
Period size: 24 Copynumber: 3.5 Consensus size: 24
4592415 TAATTTGTCT
* *
4592425 TTATAGGAAGAGATGTCAACTATC
1 TTATATGAAGAGAAGTCAACTATC
*
4592449 TTATATGAAGATAA-TACAAC-AT-
1 TTATATGAAGAGAAGT-CAACTATC
* *
4592471 GTATAGGAAGAGAAGTCAACTATC
1 TTATATGAAGAGAAGTCAACTATC
*
4592495 TTATCTGAAGA
1 TTATATGAAGA
4592506 TAATGCAACA
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
22 15 0.34
23 6 0.14
24 23 0.52
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.28
Consensus pattern (24 bp):
TTATATGAAGAGAAGTCAACTATC
Found at i:4592514 original size:24 final size:24
Alignment explanation
Indices: 4592441--4592514 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
4592431 GAAGAGATGT
*
4592441 CAACTATCTTATATGAAGATAATA
1 CAACTATCTTATATGAAGATAATG
* * *
4592465 CAAC-AT-GTATAGGAAGAGAA-G
1 CAACTATCTTATATGAAGATAATG
*
4592486 TCAACTATCTTATCTGAAGATAATG
1 -CAACTATCTTATATGAAGATAATG
4592511 CAAC
1 CAAC
4592515 ATGTATAGCT
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
22 15 0.39
23 4 0.11
24 18 0.47
25 1 0.03
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (24 bp):
CAACTATCTTATATGAAGATAATG
Found at i:4594411 original size:3 final size:3
Alignment explanation
Indices: 4594403--4594437 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
4594393 GCAAAAACAA
4594403 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4594438 GCACGAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4596605 original size:15 final size:15
Alignment explanation
Indices: 4596585--4596616 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4596575 TACTTAAGTG
4596585 ATTTTAAATATCAGT
1 ATTTTAAATATCAGT
*
4596600 ATTTTATATATCAGT
1 ATTTTAAATATCAGT
4596615 AT
1 AT
4596617 GCAAGGTGGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (15 bp):
ATTTTAAATATCAGT
Found at i:4597512 original size:16 final size:17
Alignment explanation
Indices: 4597491--4597525 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
4597481 TGATATTTGG
4597491 ATGATTAAAAT-TTTTT
1 ATGATTAAAATATTTTT
*
4597507 ATGATTAAATTATTTTT
1 ATGATTAAAATATTTTT
4597524 AT
1 AT
4597526 TAAATATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (17 bp):
ATGATTAAAATATTTTT
Found at i:4604009 original size:12 final size:12
Alignment explanation
Indices: 4603994--4604022 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
4603984 TTATATTAAT
4603994 TATATTATTATA
1 TATATTATTATA
4604006 TATATTATTATA
1 TATATTATTATA
4604018 TATAT
1 TATAT
4604023 AAAACAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TATATTATTATA
Found at i:4605630 original size:45 final size:45
Alignment explanation
Indices: 4605561--4605648 Score: 117
Period size: 45 Copynumber: 2.0 Consensus size: 45
4605551 GCCGACTACT
*
4605561 GTTACTGTTACTGATTCGATACTTTGTGTG-TCAAATACTGTTACC
1 GTTACTGTTACAGATTCGATACTTTGTGTGCT-AAATACTGTTACC
* *
4605606 GTTATTGTTACAGATTC-ATCACTTTGTGTGCTGAATACTGTTA
1 GTTACTGTTACAGATTCGAT-ACTTTGTGTGCTAAATACTGTTA
4605649 TTGCTACCGT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
44 2 0.05
45 35 0.92
46 1 0.03
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.43
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGATACTTTGTGTGCTAAATACTGTTACC
Found at i:4606376 original size:17 final size:18
Alignment explanation
Indices: 4606345--4606378 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4606335 ATAAATAGAA
4606345 ATGATAATGAATGAGTTG
1 ATGATAATGAATGAGTTG
*
4606363 ATGA-AATGATTGAGTT
1 ATGATAATGAATGAGTT
4606379 TGTATGGATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.26, T:0.35
Consensus pattern (18 bp):
ATGATAATGAATGAGTTG
Found at i:4612616 original size:21 final size:21
Alignment explanation
Indices: 4612592--4612657 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
4612582 AAACTATTGC
4612592 TTTCCAAAAGAAAACAGAGGA
1 TTTCCAAAAGAAAACAGAGGA
* *
4612613 TTTCCAAAAGAAAATAAAGGA
1 TTTCCAAAAGAAAACAGAGGA
* *
4612634 TTTCCAAAAGAAGACAGAAGA
1 TTTCCAAAAGAAAACAGAGGA
4612655 TTT
1 TTT
4612658 TTAACAGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.52, C:0.12, G:0.17, T:0.20
Consensus pattern (21 bp):
TTTCCAAAAGAAAACAGAGGA
Found at i:4616896 original size:19 final size:19
Alignment explanation
Indices: 4616872--4616918 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4616862 TCTCTTTCTT
4616872 TTTGCATT-CATTCCATGCA
1 TTTGCATTACATTCCAT-CA
*
4616891 TTTGCATTACATTGCATCA
1 TTTGCATTACATTCCATCA
*
4616910 TATGCATTA
1 TTTGCATTA
4616919 GATTTTCACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.21, G:0.11, T:0.43
Consensus pattern (19 bp):
TTTGCATTACATTCCATCA
Found at i:4620094 original size:13 final size:13
Alignment explanation
Indices: 4620076--4620108 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4620066 GGAATGTTTC
4620076 ATAAAAAGAAAAA
1 ATAAAAAGAAAAA
*
4620089 ATAAAAAGAAAGA
1 ATAAAAAGAAAAA
4620102 A-AAAAAG
1 ATAAAAAG
4620109 GAGAGGCCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (13 bp):
ATAAAAAGAAAAA
Found at i:4621161 original size:44 final size:44
Alignment explanation
Indices: 4621092--4621390 Score: 137
Period size: 44 Copynumber: 6.8 Consensus size: 44
4621082 CAAAAACTGG
* * * * *
4621092 TCCTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAGATTACAGA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATCACAGA
* * * **
4621136 TCCTATCTCCCTAAGTAGTAGTGGAGCAGATCGAAGATGGC-GAA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATCACAG-A
* * * * * * * * *
4621180 TCTTATCTTGCC-AAGGTAGTAGAGAAGTAGATTTAAG-CCACTGG
1 TCCTATC-TCCCTAA-GTAGTAGTGGAGTAGGTTGAAGATCACAGA
** * * **
4621224 TCCTATCTCCCTGCGCAGTAATGGAGTAGGTTGAAGATTGCAGA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATCACAGA
* * * ** * **
4621268 TCCTGTCTTCCTAAGTAGTAGTGGAGCAAATCGAAGATGGC-GAA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATCACAG-A
* * *
4621312 TCATATCTTCCTAATGTAGTAG-GGAAGT-GGATTTAAG-TCACTAG-
1 TCCTATCTCCCTAA-GTAGTAGTGG-AGTAGG-TTGAAGATCAC-AGA
*
4621356 TCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAA
4621391 AATCGTAGAT
Statistics
Matches: 182, Mismatches: 59, Indels: 29
0.67 0.22 0.11
Matches are distributed among these distances:
43 35 0.19
44 112 0.62
45 34 0.19
46 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (44 bp):
TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTTGAAGATCACAGA
Found at i:4621255 original size:132 final size:132
Alignment explanation
Indices: 4621087--4621390 Score: 466
Period size: 132 Copynumber: 2.3 Consensus size: 132
4621077 CAGATCAAAA
*
4621087 ACTGGTCCTATCTCCCTGAGCAGCAATGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGT
1 ACTGGTCCTATCTCCCTGAGCAGTAATGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGT
* *
4621152 AGTAGTGGAGCAGATCGAAGATGGCGAATCTTATCTTGCC-AAGGTAGTAGAGAAGTAGATTTAA
66 AGTAGTGGAGCAAATCGAAGATGGCGAATCATATCTT-CCTAAGGTAGTAGAGAAGTAGATTTAA
4621216 GCC
130 GCC
* * * *
4621219 ACTGGTCCTATCTCCCTGCGCAGTAATGGAGTAGGTTGAAGATTGCAGATCCTGTCTTCCTAAGT
1 ACTGGTCCTATCTCCCTGAGCAGTAATGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGT
* * *
4621284 AGTAGTGGAGCAAATCGAAGATGGCGAATCATATCTTCCTAATGTAGTAGGGAAGTGGATTTAAG
66 AGTAGTGGAGCAAATCGAAGATGGCGAATCATATCTTCCTAAGGTAGTAGAGAAGTAGATTTAAG
*
4621349 TC
131 CC
* * *
4621351 ACTAGTCCTATCTCCCTGAGTAGTAGTGGAGTAGGTTGAA
1 ACTGGTCCTATCTCCCTGAGCAGTAATGGAGTAGGTTGAA
4621391 AATCGTAGAT
Statistics
Matches: 156, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
131 2 0.01
132 154 0.99
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (132 bp):
ACTGGTCCTATCTCCCTGAGCAGTAATGGAGTAGGTTGAAGATTACAGATCCTATCTCCCTAAGT
AGTAGTGGAGCAAATCGAAGATGGCGAATCATATCTTCCTAAGGTAGTAGAGAAGTAGATTTAAG
CC
Found at i:4621537 original size:44 final size:44
Alignment explanation
Indices: 4621462--4621556 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 44
4621452 TTGAAATTTT
* *
4621462 AGTGGAGTAGATTGAAGATACAAGTCTTATCTCCCCGAAGTTGC
1 AGTGGAGTAGACTGAAGATACAAGTCCTATCTCCCCGAAGTTGC
* **
4621506 AGTGGAGTAGACTGAAGCTACTAA-TCCTATCTCCTTGAAGTTGC
1 AGTGGAGTAGACTGAAGATAC-AAGTCCTATCTCCCCGAAGTTGC
4621550 AGTGGAG
1 AGTGGAG
4621557 CGGATTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
44 43 0.96
45 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (44 bp):
AGTGGAGTAGACTGAAGATACAAGTCCTATCTCCCCGAAGTTGC
Found at i:4629743 original size:12 final size:12
Alignment explanation
Indices: 4629726--4629758 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
4629716 GAGAGAGATA
4629726 GTTCTTTAACTT
1 GTTCTTTAACTT
4629738 GTTCTTTAACTT
1 GTTCTTTAACTT
4629750 GTTCTTTAA
1 GTTCTTTAA
4629759 GTAACCATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.15, G:0.09, T:0.58
Consensus pattern (12 bp):
GTTCTTTAACTT
Found at i:4630825 original size:23 final size:22
Alignment explanation
Indices: 4630782--4630826 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
4630772 TTTTTTTAAA
**
4630782 AATATTTATATTATTTTAATTT
1 AATATTTATATTATTGAAATTT
*
4630804 AATATTTTTATATATTGAAATTT
1 AATATTTATAT-TATTGAAATTT
4630827 TTATATAGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
AATATTTATATTATTGAAATTT
Found at i:4637057 original size:20 final size:21
Alignment explanation
Indices: 4637032--4637070 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4637022 CTCCTATGAT
*
4637032 CAAGTTGCCTTCG-CTCCAAA
1 CAAGTTGACTTCGACTCCAAA
4637052 CAAGTTGACTTCGACTCCA
1 CAAGTTGACTTCGACTCCA
4637071 TAACGGATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (21 bp):
CAAGTTGACTTCGACTCCAAA
Found at i:4651755 original size:20 final size:20
Alignment explanation
Indices: 4651714--4651750 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4651704 ACAGAAATAA
4651714 TGTCAAGTATATAATATTAT
1 TGTCAAGTATATAATATTAT
4651734 TGTCAAGTA-ATAA-ATTA
1 TGTCAAGTATATAATATTA
4651751 CATTGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 4 0.24
20 9 0.53
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (20 bp):
TGTCAAGTATATAATATTAT
Found at i:4652346 original size:9 final size:9
Alignment explanation
Indices: 4652334--4652363 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
4652324 GTTTTTAAAA
4652334 TTTTTCAAT
1 TTTTTCAAT
4652343 TTTTTCAAT
1 TTTTTCAAT
4652352 TTTTTCAAT
1 TTTTTCAAT
4652361 TTT
1 TTT
4652364 CATCACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTCAAT
Found at i:4654361 original size:57 final size:58
Alignment explanation
Indices: 4654293--4654411 Score: 177
Period size: 57 Copynumber: 2.1 Consensus size: 58
4654283 TTTTTTTTGA
* *
4654293 AATAGAATTAATATTAAATTAAATTTAATACTTATCTTAAT-AGTATTTTATTAATTT
1 AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
* * * *
4654350 AATAGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTT
1 AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
4654408 AATA
1 AATA
4654412 TTAAAGTGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
57 36 0.65
58 19 0.35
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.49
Consensus pattern (58 bp):
AATAGAATTAATATTAAATTAAATCTAATACTTATCTTAATAAGTATTATATTAATTT
Found at i:4654424 original size:58 final size:56
Alignment explanation
Indices: 4654298--4654431 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 56
4654288 TTTGAAATAG
* *
4654298 AATT-AATATTAAATTAAATTTAATACTTATCTTAATAGTATTTTATTAATTTAAT
1 AATTAAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAAT
* * * *
4654353 AGATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAAT
1 A-ATTAAATATTAAATTAAATCTAATACTTATCTTAAT-AGTATTATATTAATTTAAT
*
4654411 -ATTAAAGTGATTAAGTTAAAT
1 AATTAAA-T-ATTAAATTAAAT
4654432 TATAGTTGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.02
56 8 0.12
57 29 0.44
58 28 0.42
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (56 bp):
AATTAAATATTAAATTAAATCTAATACTTATCTTAATAGTATTATATTAATTTAAT
Found at i:4660191 original size:14 final size:15
Alignment explanation
Indices: 4660167--4660195 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4660157 TTTATTTTGG
4660167 TTTCGATTTAATCTT
1 TTTCGATTTAATCTT
4660182 TTTC-ATTTAATCTT
1 TTTCGATTTAATCTT
4660196 GCCTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.21, C:0.14, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTCGATTTAATCTT
Found at i:4660340 original size:14 final size:14
Alignment explanation
Indices: 4660313--4660346 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4660303 TTTTAGTTCA
* *
4660313 TTTTTGTTTTTATT
1 TTTTTATTTATATT
4660327 TTTTTATTTATATT
1 TTTTTATTTATATT
4660341 TTTTTA
1 TTTTTA
4660347 ATGTTGATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:4664211 original size:17 final size:17
Alignment explanation
Indices: 4664191--4664243 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
4664181 ATAGCAAAAA
4664191 AAAAAAGGAGAAGAGAG
1 AAAAAAGGAGAAGAGAG
4664208 AAAAGAA-GAGAA-AGAAG
1 AAAA-AAGGAGAAGAG-AG
4664225 AAAAAAGGAGGAAGA-AG
1 AAAAAAGGA-GAAGAGAG
4664242 AA
1 AA
4664244 TAGGGAGCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
16 4 0.13
17 21 0.68
18 5 0.16
19 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (17 bp):
AAAAAAGGAGAAGAGAG
Found at i:4664333 original size:17 final size:16
Alignment explanation
Indices: 4664323--4664374 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
4664313 AAGAAAAAGG
4664323 AAAGAAAAAG-AAGAA
1 AAAGAAAAAGAAAGAA
4664338 GAAAGGAAAAA-AAAGAA
1 -AAA-GAAAAAGAAAGAA
4664355 AAAGAAAAAGGAAAGAA
1 AAAGAAAAA-GAAAGAA
4664372 AAA
1 AAA
4664375 AACAGTCGGG
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 6 0.19
16 6 0.19
17 20 0.62
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAGAAAGAA
Found at i:4664340 original size:26 final size:25
Alignment explanation
Indices: 4664304--4664376 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 25
4664294 GTTCGGCCCG
4664304 AAGAAGAAG-AAGAAAAAGGAAAGAAA
1 AAGAAGAAGAAAGAAAAA--AAAGAAA
4664330 AAGAAGAAGAAAGGAAAAAAAAGAAA
1 AAGAAGAAGAAA-GAAAAAAAAGAAA
*
4664356 AAGAAAAAGGAAAGAAAAAAA
1 AAGAAGAA-GAAAGAAAAAAA
4664377 CAGTCGGGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
26 31 0.72
27 6 0.14
28 6 0.14
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (25 bp):
AAGAAGAAGAAAGAAAAAAAAGAAA
Found at i:4664466 original size:19 final size:20
Alignment explanation
Indices: 4664442--4664495 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
4664432 GTATCAGCCA
4664442 ACCCAGCAGGCCA-GCCAG-C
1 ACCCAGCAGG-CAGGCCAGAC
*
4664461 ACCCAGCAAGCAGGCCAGAC
1 ACCCAGCAGGCAGGCCAGAC
4664481 AGCCCAGCA-GCAGGC
1 A-CCCAGCAGGCAGGC
4664496 AGCCAAACAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 2 0.06
19 14 0.45
20 8 0.26
21 7 0.23
ACGTcount: A:0.30, C:0.43, G:0.28, T:0.00
Consensus pattern (20 bp):
ACCCAGCAGGCAGGCCAGAC
Found at i:4664472 original size:23 final size:20
Alignment explanation
Indices: 4664445--4664500 Score: 69
Period size: 23 Copynumber: 2.7 Consensus size: 20
4664435 TCAGCCAACC
4664445 CAGCAGGCCAGCCAGCACCCAG
1 CAGCAGGCCAGCCAG--CCCAG
*
4664467 CAAGCAGGCCAGACAGCCCAG
1 C-AGCAGGCCAGCCAGCCCAG
4664488 CAGCAGG-CAGCCA
1 CAGCAGGCCAGCCA
4664501 AACAGCAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 5 0.16
20 6 0.19
21 6 0.19
22 1 0.03
23 13 0.42
ACGTcount: A:0.30, C:0.41, G:0.29, T:0.00
Consensus pattern (20 bp):
CAGCAGGCCAGCCAGCCCAG
Found at i:4667166 original size:22 final size:22
Alignment explanation
Indices: 4667138--4667182 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4667128 AATTTCCTGG
4667138 TACAACATGTTATGATCTTTTA
1 TACAACATGTTATGATCTTTTA
4667160 TACAACATGTTATGATCTTTTA
1 TACAACATGTTATGATCTTTTA
4667182 T
1 T
4667183 CTTTCAAATG
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:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (22 bp):
TACAACATGTTATGATCTTTTA
Found at i:4670126 original size:27 final size:27
Alignment explanation
Indices: 4670088--4670141 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4670078 ATTTAACGAG
4670088 TGGTGGTGGATTTTAAGAAAGTTCTTA
1 TGGTGGTGGATTTTAAGAAAGTTCTTA
4670115 TGGTGGTGGATTTTAAGAAAGTTCTTA
1 TGGTGGTGGATTTTAAGAAAGTTCTTA
4670142 CTGAGCAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.41
Consensus pattern (27 bp):
TGGTGGTGGATTTTAAGAAAGTTCTTA
Found at i:4671955 original size:15 final size:17
Alignment explanation
Indices: 4671918--4671959 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 17
4671908 TGAAAATATC
*
4671918 AAAAATAATAAGAAATA
1 AAAAATAACAAGAAATA
4671935 ATAAAATAACAAG-AATA
1 A-AAAATAACAAGAAATA
4671952 AAAAATAA
1 AAAAATAA
4671960 TAACGATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 7 0.30
17 6 0.26
18 10 0.43
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (17 bp):
AAAAATAACAAGAAATA
Found at i:4671968 original size:16 final size:16
Alignment explanation
Indices: 4671918--4671975 Score: 64
Period size: 16 Copynumber: 3.5 Consensus size: 16
4671908 TGAAAATATC
4671918 AAAAATAATAAGAAATA
1 AAAAATAATAAG-AATA
*
4671935 ATAAAATAACAAGAATA
1 A-AAAATAATAAGAATA
4671952 AAAAATAATAACG-ATA
1 AAAAATAATAA-GAATA
*
4671968 ATAAATAA
1 AAAAATAA
4671976 AAAAATTGTG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 19 0.53
17 7 0.19
18 10 0.28
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.19
Consensus pattern (16 bp):
AAAAATAATAAGAATA
Found at i:4672076 original size:12 final size:12
Alignment explanation
Indices: 4672045--4672088 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
4672035 GTAATACATA
*
4672045 AATATAAATAGAT
1 AATAAAAATA-AT
4672058 AAT-AAAATAAT
1 AATAAAAATAAT
4672069 AATAAAAATAAT
1 AATAAAAATAAT
4672081 AAATAAAA
1 -AATAAAA
4672089 CAAATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 5 0.18
12 13 0.46
13 10 0.36
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (12 bp):
AATAAAAATAAT
Found at i:4672087 original size:13 final size:13
Alignment explanation
Indices: 4672037--4672100 Score: 64
Period size: 13 Copynumber: 5.0 Consensus size: 13
4672027 ATAAAAAAGT
*
4672037 AATACATAAATATA
1 AATA-ATAAATAAA
4672051 AATAGAT-AAT-AA
1 AATA-ATAAATAAA
4672063 AATAAT-AATAAA
1 AATAATAAATAAA
4672075 AATAATAAATAAA
1 AATAATAAATAAA
4672088 ACA-AATAAATAAA
1 A-ATAATAAATAAA
4672101 TGCTCGATGA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
11 5 0.11
12 13 0.29
13 20 0.44
14 7 0.16
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (13 bp):
AATAATAAATAAA
Found at i:4672208 original size:16 final size:15
Alignment explanation
Indices: 4672189--4672227 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
4672179 AAATAAGCAA
4672189 ATAAATAAAATAATAC
1 ATAAA-AAAATAATAC
*
4672205 AT-AAAAAATAATAT
1 ATAAAAAAATAATAC
4672219 ATAAAAAAA
1 ATAAAAAAA
4672228 ATCTATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 11 0.52
15 8 0.38
16 2 0.10
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
ATAAAAAAATAATAC
Found at i:4672234 original size:13 final size:14
Alignment explanation
Indices: 4672195--4672226 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
4672185 GCAAATAAAT
*
4672195 AAAATAATACATAA
1 AAAATAATATATAA
4672209 AAAATAATATATAA
1 AAAATAATATATAA
4672223 AAAA
1 AAAA
4672227 AATCTATACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAATATATAA
Found at i:4676045 original size:14 final size:14
Alignment explanation
Indices: 4676028--4676054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4676018 GATTACTTGT
4676028 TTATGATTTTATGC
1 TTATGATTTTATGC
4676042 TTATGATTTTATG
1 TTATGATTTTATG
4676055 TGCATGGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.04, G:0.15, T:0.59
Consensus pattern (14 bp):
TTATGATTTTATGC
Found at i:4684532 original size:14 final size:14
Alignment explanation
Indices: 4684515--4684541 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4684505 TTGGTCCCAC
4684515 AATTTATTTTTATA
1 AATTTATTTTTATA
4684529 AATTTATTTTTAT
1 AATTTATTTTTAT
4684542 TTATATGAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AATTTATTTTTATA
Found at i:4685833 original size:101 final size:101
Alignment explanation
Indices: 4685653--4685957 Score: 529
Period size: 101 Copynumber: 3.0 Consensus size: 101
4685643 CAACAACATA
4685653 GTTAATAGATGATGAAGTAGGCAACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCAA
1 GTTAATAGATGATGAAGTAGGCAACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCAA
*
4685718 AAATGAAAGATTAGGTGAGATAGAACATGAGGGCAT
66 AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
*
4685754 GTTAATAGATGATGAAGTAGGCAACTGCGACATGACACCTATCATTTCGAATATTATGTGGTCAA
1 GTTAATAGATGATGAAGTAGGCAACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCAA
4685819 AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
66 AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
* * * * * *
4685855 GTTAATAGATGATGAAGTAGGCAACTACGGCATGATACCTACCATTTTGAATATTGTGTAGTCAA
1 GTTAATAGATGATGAAGTAGGCAACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCAA
*
4685920 AAATGAAAGGTTAGGTGTGATAGAACATGAGGGCAT
66 AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
4685956 GT
1 GT
4685958 ATAGTTTTTC
Statistics
Matches: 194, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
101 194 1.00
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.27
Consensus pattern (101 bp):
GTTAATAGATGATGAAGTAGGCAACTGCGACATGACACCTATCATTTCGAATATTGTGTGGTCAA
AAATGAAAGGTTAGGTGAGATAGAACATGAGGGCAT
Found at i:4687750 original size:19 final size:19
Alignment explanation
Indices: 4687726--4687770 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4687716 ATTTATTTTT
*
4687726 TTATTA-ATTGATAATGTAA
1 TTATTATATTCAT-ATGTAA
*
4687745 TTATTATTTTCATATGTAA
1 TTATTATATTCATATGTAA
4687764 TTATTAT
1 TTATTAT
4687771 TTCTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (19 bp):
TTATTATATTCATATGTAA
Found at i:4687803 original size:18 final size:18
Alignment explanation
Indices: 4687776--4687848 Score: 60
Period size: 18 Copynumber: 3.9 Consensus size: 18
4687766 ATTATTTCTT
*
4687776 TTTATATATATATGTATA
1 TTTATGTATATATGTATA
4687794 TTTATGTATATAT-T-TA
1 TTTATGTATATATGTATA
4687810 TTTCCATGTATATATACGTATA
1 TTT--ATGTATATAT--GTATA
* *
4687832 TTTTTGAATATAATGTA
1 TTTATGTATAT-ATGTA
4687849 GTTATTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 13
0.74 0.05 0.21
Matches are distributed among these distances:
16 5 0.11
17 1 0.02
18 22 0.49
19 3 0.07
20 6 0.13
21 3 0.07
22 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.53
Consensus pattern (18 bp):
TTTATGTATATATGTATA
Found at i:4694103 original size:88 final size:88
Alignment explanation
Indices: 4693954--4694366 Score: 673
Period size: 88 Copynumber: 4.7 Consensus size: 88
4693944 AGCAGATCAG
* *
4693954 TAAAAATAACAGATCTTGCCTTCCTTCACCGACAACGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
4694019 CCTTGGGATACAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
4694042 TAAAAATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGTAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
4694107 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
* * * *
4694130 AAAAAACAACAGATCTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCT
1 TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
* * *
4694195 CACTAGGTTGCAGCGGAGTAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
4694218 TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
1 TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
4694283 CCCTGGGTTGCAGCGGAGCAGGT
66 CCCTGGGTTGCAGCGGAGCAGGT
*
4694306 TAAAAATAACAGATCTTGCCTTCCTGCACTGACAGCGAAGCAGATCGAAGACACCAGCCTT
1 TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTT
4694367 ATCTCCTTGA
Statistics
Matches: 297, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 297 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (88 bp):
TAAAAATAACAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCT
CCCTGGGTTGCAGCGGAGCAGGT
Found at i:4694104 original size:44 final size:44
Alignment explanation
Indices: 4693968--4694366 Score: 186
Period size: 44 Copynumber: 9.1 Consensus size: 44
4693958 AATAACAGAT
* * *
4693968 CTTGCCTTCCTTCACCGACAACGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGC
* * * ** * * * *
4694012 CTTGCC-TCCTTGGGAT--ACAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTTCC-T-GCATCGACAGCGAAGCAGATCGAAGACACCAG-C
* *
4694056 CTTGCCTTCCTGCATCGACAGTGAAGTAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGC
* ** * * * ** * * *
4694100 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTAAAAAACAACAGAT
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAG-C
* * *
4694144 CTTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACTAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGC
* * * * * ** * * * *
4694188 CTTGCC-TCACTAG-GTTG-CAGCGGAGTAGGTTAAAAATAACAGAT
1 CTTGCCTTC-CT-GCATCGACAGCGAAGCAGATCGAAGACACCAG-C
*
4694232 CTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGC
* ** * * * ** * * * *
4694276 CTTGCCTCCCTGGGTTG-CAGCGGAGCAGGTTAAAAATAACAGAT
1 CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAG-C
4694320 CTTGCCTTCCTGCA-CTGACAGCGAAGCAGATCGAAGACACCAGC
1 CTTGCCTTCCTGCATC-GACAGCGAAGCAGATCGAAGACACCAGC
4694364 CTT
1 CTT
4694367 ATCTCCTTGA
Statistics
Matches: 237, Mismatches: 101, Indels: 34
0.64 0.27 0.09
Matches are distributed among these distances:
43 78 0.33
44 83 0.35
45 76 0.32
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.19
Consensus pattern (44 bp):
CTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACCAGC
Found at i:4694430 original size:44 final size:44
Alignment explanation
Indices: 4694364--4694606 Score: 181
Period size: 44 Copynumber: 5.6 Consensus size: 44
4694354 AGACACCAGC
* * *
4694364 CTTATCTCCTTGAGCAACAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * * * * ** *
4694408 CTTATCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGTCCCCAG-C
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAAT-TACAGAT
* **
4694451 CTTGTCTCCCTGGGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
* * * * * **
4694495 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-AAGTCCCTAG-T
1 CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTAC-AGAT
* * * * *
4694538 CTTGTCTCCCTGAA-CAGCAATGGAATATGTTGAAAATTACATAT
1 CTTATCTCCCT-AAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
*
4694582 CTTATCTCCCTAAGCAGTAGTGGAG
1 CTTATCTCCCTAAGCAGCAGTGGAG
4694607 CAGATCGAGG
Statistics
Matches: 143, Mismatches: 48, Indels: 16
0.69 0.23 0.08
Matches are distributed among these distances:
43 60 0.42
44 83 0.58
ACGTcount: A:0.28, C:0.22, G:0.23, T:0.27
Consensus pattern (44 bp):
CTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTACAGAT
Found at i:4694459 original size:87 final size:87
Alignment explanation
Indices: 4694344--4694614 Score: 416
Period size: 87 Copynumber: 3.1 Consensus size: 87
4694334 CTGACAGCGA
* * * * *
4694344 AGCAGATCGAAGACACCAGCCTTATCTCCTTGAGCAACAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
4694409 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* *
4694431 AGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGGGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
4694496 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
* * * * * * *
4694518 AGCAGATCGAAGTCCCTAGTCTTGTCTCCCTGAACAGCAATGGAATATGTTGAAAATTACATATC
1 AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
4694583 TTATCTCCCTAAGCAGTAGTGG
66 TTATCTCCCTAAGCAGTAGTGG
4694605 AGCAGATCGA
1 AGCAGATCGA
4694615 GGATGGTAAA
Statistics
Matches: 168, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 168 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (87 bp):
AGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATC
TTATCTCCCTAAGCAGTAGTGG
Found at i:4694461 original size:43 final size:43
Alignment explanation
Indices: 4694407--4694548 Score: 133
Period size: 43 Copynumber: 3.3 Consensus size: 43
4694397 AAATTACAGA
*
4694407 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAG
1 TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAG
* ** * * * * * **
4694450 CCTTGTCTCCCTGGGCAGCAGTGGAGTAGGTTGAAAAT-TACAG
1 TCTTGTCTCCCTAAGCAGTAGTGGAGCA-GATCAAAGTCCCCAG
* * *
4694493 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCTAG
1 -TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAG
4694537 TCTTGTCTCCCT
1 TCTTGTCTCCCT
4694549 GAACAGCAAT
Statistics
Matches: 71, Mismatches: 25, Indels: 6
0.70 0.25 0.06
Matches are distributed among these distances:
43 41 0.58
44 30 0.42
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (43 bp):
TCTTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAG
Found at i:4694720 original size:44 final size:44
Alignment explanation
Indices: 4694623--4694726 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 44
4694613 GAGGATGGTA
* * * *
4694623 AATCTTATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAACCGAT
1 AATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTAAAACCAAC
* * * *
4694667 AATCCTATCTCCCTGAGGTTATAGCGGAGCGGATTAAAA-TAAC
1 AATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTAAAACCAAC
*
4694710 AGATCTTATCTCTCTGA
1 A-ATCTTATCTCCCTGA
4694727 AATTATGGTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
43 2 0.04
44 47 0.96
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTAAAACCAAC
Found at i:4695126 original size:13 final size:14
Alignment explanation
Indices: 4695110--4695143 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4695100 GCCCAATAAG
4695110 GCCCAAAT-TGCTA
1 GCCCAAATCTGCTA
*
4695123 GCCCTAATCTGCTA
1 GCCCAAATCTGCTA
4695137 GCCCAAA
1 GCCCAAA
4695144 AAACACAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.29, C:0.35, G:0.15, T:0.21
Consensus pattern (14 bp):
GCCCAAATCTGCTA
Found at i:4696039 original size:23 final size:24
Alignment explanation
Indices: 4696003--4696047 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
4695993 TACAATTAAG
*
4696003 TTTATTTTATTTTTAAATTTCATC
1 TTTAATTTATTTTTAAATTTCATC
4696027 TTTAATTTATTTTT-AATTTCA
1 TTTAATTTATTTTTAAATTTCA
4696048 ATTTGGTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (24 bp):
TTTAATTTATTTTTAAATTTCATC
Found at i:4696043 original size:11 final size:11
Alignment explanation
Indices: 4696003--4696045 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
4695993 TACAATTAAG
*
4696003 TTTATTTTATT
1 TTTAATTTATT
*
4696014 TTTAAATTTCATC
1 TTT-AATTT-ATT
4696027 TTTAATTTATT
1 TTTAATTTATT
4696038 TTTAATTT
1 TTTAATTT
4696046 CAATTTGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 13 0.48
12 9 0.33
13 5 0.19
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTAATTTATT
Found at i:4696291 original size:26 final size:26
Alignment explanation
Indices: 4696261--4696315 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
4696251 TTTTTCTTTT
* * *
4696261 TTTATATATATGTATATTTATGTATA
1 TTTATATACATGTATATATACGTATA
* *
4696287 TTTATTTCCATGTATATATACGTATA
1 TTTATATACATGTATATATACGTATA
4696313 TTT
1 TTT
4696316 TTGAATATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.31, C:0.05, G:0.07, T:0.56
Consensus pattern (26 bp):
TTTATATACATGTATATATACGTATA
Found at i:4701470 original size:18 final size:19
Alignment explanation
Indices: 4701447--4701485 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
4701437 TAAAATAAAA
4701447 TGAT-AAAATGCCACTATT
1 TGATAAAAATGCCACTATT
*
4701465 TGATAAAAATGCCGCTATT
1 TGATAAAAATGCCACTATT
4701484 TG
1 TG
4701486 CTTACCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TGATAAAAATGCCACTATT
Found at i:4701815 original size:7 final size:7
Alignment explanation
Indices: 4701803--4702087 Score: 95
Period size: 7 Copynumber: 40.9 Consensus size: 7
4701793 TATTAACTGT
4701803 CTAAACC
1 CTAAACC
4701810 CTAAACC
1 CTAAACC
* *
4701817 TTAAACA
1 CTAAACC
* *
4701824 ATAAACT
1 CTAAACC
* *
4701831 TTAATCCC
1 CTAA-ACC
*
4701839 CTAACCC
1 CTAAACC
4701846 CTAAAACC
1 CT-AAACC
*
4701854 CTAACCC
1 CTAAACC
4701861 CT-AACC
1 CTAAACC
*
4701867 CTTAAACA
1 C-TAAACC
4701875 C--AACC
1 CTAAACC
* **
4701880 ATAAATT
1 CTAAACC
* *
4701887 ATAAACA
1 CTAAACC
*
4701894 CTAAACA
1 CTAAACC
4701901 CTAAACC
1 CTAAACC
4701908 CTAAA-C
1 CTAAACC
*
4701914 CTACACC
1 CTAAACC
4701921 CTAAA--
1 CTAAACC
*
4701926 TTATAACC
1 CTA-AACC
* *
4701934 ATTAAACT
1 -CTAAACC
* *
4701942 CTTAACA
1 CTAAACC
4701949 CTAAACC
1 CTAAACC
4701956 CTAAACC
1 CTAAACC
*
4701963 TTAAACC
1 CTAAACC
* *
4701970 CCAACCCC
1 CTAA-ACC
*
4701978 CTAAATC
1 CTAAACC
4701985 CTAAACC
1 CTAAACC
* *
4701992 TTAAA-A
1 CTAAACC
4701998 CTAAACC
1 CTAAACC
* *
4702005 ATAAACT
1 CTAAACC
*
4702012 CTAAATC
1 CTAAACC
*
4702019 CTAAACT
1 CTAAACC
4702026 CT-AACC
1 CTAAACC
4702032 CTTAAACCC
1 C-TAAA-CC
4702041 CT-AACAC
1 CTAAAC-C
4702048 CTAAACC
1 CTAAACC
*
4702055 TTAAACC
1 CTAAACC
*
4702062 ATAAA-C
1 CTAAACC
*
4702068 ATAAACC
1 CTAAACC
*
4702075 ATAAACC
1 CTAAACC
*
4702082 ATAAAC
1 CTAAAC
4702088 ATACACCCGA
Statistics
Matches: 208, Mismatches: 51, Indels: 38
0.70 0.17 0.13
Matches are distributed among these distances:
5 5 0.02
6 26 0.12
7 143 0.69
8 28 0.13
9 6 0.03
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:4701908 original size:41 final size:41
Alignment explanation
Indices: 4701877--4701955 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 41
4701867 CTTAAACACA
4701877 ACCATAAATTATAAACACTAAACACTAAACCCTAAACCTAC
1 ACCATAAATTATAAACACTAAACACTAAACCCTAAACCTAC
* * * * * *
4701918 ACCCTAAATTATAACCATTAAACTCTTAACACTAAACC
1 ACCATAAATTATAAACACTAAACACTAAACCCTAAACC
4701956 CTAAACCTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (41 bp):
ACCATAAATTATAAACACTAAACACTAAACCCTAAACCTAC
Found at i:4702004 original size:29 final size:29
Alignment explanation
Indices: 4701949--4702004 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
4701939 ACTCTTAACA
* *
4701949 CTAAACCCTAAACCTTAAACCCCAACCCC
1 CTAAACCCTAAACCTTAAAACCAAACCCC
* *
4701978 CTAAATCCTAAACCTTAAAACTAAACC
1 CTAAACCCTAAACCTTAAAACCAAACC
4702005 ATAAACTCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (29 bp):
CTAAACCCTAAACCTTAAAACCAAACCCC
Found at i:4702009 original size:20 final size:20
Alignment explanation
Indices: 4701977--4702158 Score: 85
Period size: 20 Copynumber: 8.8 Consensus size: 20
4701967 ACCCCAACCC
4701977 CCTAAATCC-TAAACCTTAAA
1 CCTAAA-CCATAAACCTTAAA
*
4701997 ACTAAACCATAAA-CTCTAAA
1 CCTAAACCATAAACCT-TAAA
*
4702017 TCCTAAACTC-TAACCCTTAAA
1 -CCTAAAC-CATAAACCTTAAA
4702038 CCCCTAACACC-TAAACCTTAAA
1 --CCTAA-ACCATAAACCTTAAA
*
4702060 CCATAAA-CATAAACCATAAA
1 CC-TAAACCATAAACCTTAAA
* **
4702080 CCATAAA-CATACACCCGAAA
1 CC-TAAACCATAAACCTTAAA
*
4702100 TCGT-AACCATTAAACTCTT-AA
1 -CCTAAACCA-TAAAC-CTTAAA
4702121 CACTAAATCC-TAAACCTTAAA
1 C-CTAAA-CCATAAACCTTAAA
* *
4702142 CCCCAAACCATATACCT
1 -CCTAAACCATAAACCT
4702159 ACACCCTAAA
Statistics
Matches: 127, Mismatches: 16, Indels: 37
0.71 0.09 0.21
Matches are distributed among these distances:
19 7 0.06
20 52 0.41
21 41 0.32
22 23 0.18
23 4 0.03
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (20 bp):
CCTAAACCATAAACCTTAAA
Found at i:4702010 original size:70 final size:70
Alignment explanation
Indices: 4701930--4702080 Score: 184
Period size: 70 Copynumber: 2.1 Consensus size: 70
4701920 CCTAAATTAT
* *
4701930 AACCATTAAACTCTTAA-CACTAAACCCTAAACCTTAAACCCC-AACCCCCTAAATCC-TAAACC
1 AACCA-TAAACTCTAAATC-CTAAACCCTAAACCTTAAACCCCTAA-CACCTAAA-CCTTAAACC
*
4701992 TTAAA-ACTA
62 ATAAACA-TA
* *
4702001 AACCATAAACTCTAAATCCTAAACTCTAACCCTTAAACCCCTAACACCTAAACCTTAAACCATAA
1 AACCATAAACTCTAAATCCTAAACCCTAAACCTTAAACCCCTAACACCTAAACCTTAAACCATAA
4702066 ACATA
66 ACATA
4702071 AACCATAAAC
1 AACCATAAAC
4702081 CATAAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 9
0.84 0.06 0.11
Matches are distributed among these distances:
69 2 0.03
70 60 0.85
71 9 0.13
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.21
Consensus pattern (70 bp):
AACCATAAACTCTAAATCCTAAACCCTAAACCTTAAACCCCTAACACCTAAACCTTAAACCATAA
ACATA
Found at i:4702022 original size:63 final size:63
Alignment explanation
Indices: 4701949--4702087 Score: 153
Period size: 63 Copynumber: 2.2 Consensus size: 63
4701939 ACTCTTAACA
*
4701949 CTAAACCCTAAAC-CTTAAACCC-CAACCCCCTAA-ATCCTAAACCTTAAAAC-TAAACCATAAA
1 CTAAACCCTAAACTC-T-AACCCTCAAACCCCTAACA-CCTAAACCTTAAAACATAAA-CATAAA
4702010 CT
62 CT
* * *
4702012 CTAAATCCTAAACTCTAACCCTTAAACCCCTAACACCTAAACCTTAAACCATAAACATAAAC-
1 CTAAACCCTAAACTCTAACCCTCAAACCCCTAACACCTAAACCTTAAAACATAAACATAAACT
*
4702074 CATAAACCATAAAC
1 C-TAAACCCTAAAC
4702088 ATACACCCGA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
62 6 0.09
63 53 0.82
64 6 0.09
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (63 bp):
CTAAACCCTAAACTCTAACCCTCAAACCCCTAACACCTAAACCTTAAAACATAAACATAAACT
Found at i:4702830 original size:50 final size:50
Alignment explanation
Indices: 4702715--4703005 Score: 384
Period size: 50 Copynumber: 5.7 Consensus size: 50
4702705 GATAATAACA
* **
4702715 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * * * *
4702766 TACCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
4702816 TGCCAACGTCATGTCTCAAACATGGTCTTATATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
4702866 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
4702916 TGCCAACGCCATGTCCCAGACATGGTCTTACATGTGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* *
4702971 ATGCCAATGCCATGTCCCAAACATGGTCTTACATG
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATG
4703006 AGATCTCTTT
Statistics
Matches: 213, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
50 142 0.67
51 32 0.15
53 5 0.02
55 2 0.01
56 32 0.15
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:4706749 original size:12 final size:13
Alignment explanation
Indices: 4706734--4706762 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4706724 GTGTGAATTT
4706734 ATTT-GTGTGAAA
1 ATTTCGTGTGAAA
4706746 ATTTCGTGTGAAA
1 ATTTCGTGTGAAA
4706759 ATTT
1 ATTT
4706763 TATCGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.25
13 12 0.75
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.45
Consensus pattern (13 bp):
ATTTCGTGTGAAA
Found at i:4706749 original size:16 final size:15
Alignment explanation
Indices: 4706716--4706744 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
4706706 ATTTTATGTG
4706716 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
4706731 TTTATT-TGTGTGAA
1 TTTATTATGTGTGAA
4706745 AATTTCGTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Done.