Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 9 of 32
Found at i:4551106 original size:20 final size:19
Alignment explanation
Indices: 4551062--4551110 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
4551052 TGCATGGCTA
*
4551062 ATCTATTATTTTTATATTT
1 ATCTTTTATTTTTATATTT
*
4551081 -T-GTTTATTTTTATAATTT
1 ATCTTTTATTTTTAT-ATTT
4551099 ATCTTTTATTTT
1 ATCTTTTATTTT
4551111 CTTCACTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
17 10 0.42
18 5 0.21
19 1 0.04
20 8 0.33
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.71
Consensus pattern (19 bp):
ATCTTTTATTTTTATATTT
Found at i:4561929 original size:21 final size:21
Alignment explanation
Indices: 4561891--4561930 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
4561881 TACTTGCCAA
* *
4561891 TTCTTTCTTCATCGCCTCTAG
1 TTCTTTCTGCAACGCCTCTAG
*
4561912 TTCTTTCTGCAACTCCTCT
1 TTCTTTCTGCAACGCCTCT
4561931 TTCTCCGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.10, C:0.35, G:0.07, T:0.47
Consensus pattern (21 bp):
TTCTTTCTGCAACGCCTCTAG
Found at i:4574768 original size:33 final size:33
Alignment explanation
Indices: 4574696--4574782 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 33
4574686 AAAAGAAATT
* *
4574696 AAAATAAAATATATAATATA-AAAATTATATTAA
1 AAAATAAAA-ATAAAATATATAAAATTATAATAA
*
4574729 AGAAATAAAAATAAAATATATAATATTATAATAA
1 A-AAATAAAAATAAAATATATAAAATTATAATAA
*
4574763 AAAATAAAAATAAAGTATAT
1 AAAATAAAAATAAAATATAT
4574783 GACATTAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
33 28 0.58
34 20 0.42
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (33 bp):
AAAATAAAAATAAAATATATAAAATTATAATAA
Found at i:4575015 original size:15 final size:15
Alignment explanation
Indices: 4574995--4575038 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4574985 TGTTATTTTT
*
4574995 CTTGCAATTACATTA
1 CTTGCAATCACATTA
4575010 CTTGCAATCACATTA
1 CTTGCAATCACATTA
**
4575025 CTTATAATCACATT
1 CTTGCAATCACATT
4575039 GTATTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.39
Consensus pattern (15 bp):
CTTGCAATCACATTA
Found at i:4577474 original size:15 final size:15
Alignment explanation
Indices: 4577450--4577488 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
4577440 TTTATAATGC
*
4577450 AATATGATTATAAAT
1 AATATAATTATAAAT
*
4577465 AATATAATTATAAGT
1 AATATAATTATAAAT
4577480 AATATAATT
1 AATATAATT
4577489 GTAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (15 bp):
AATATAATTATAAAT
Found at i:4582116 original size:2 final size:2
Alignment explanation
Indices: 4582109--4582157 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
4582099 TTTCTTATTG
* * * *
4582109 AT AT AT AT AC GT AT GT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4582151 AT AT AT A
1 AT AT AT A
4582158 ATCAAAATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4594874 original size:30 final size:30
Alignment explanation
Indices: 4594838--4594897 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
4594828 CTACTATAGC
* *
4594838 CATGTATAATTCAAGTTATTCCATCCAGAT
1 CATGTATAATTCAAGTCATCCCATCCAGAT
*
4594868 CATGTATAATTCAAGTCATCCCATGCAGAT
1 CATGTATAATTCAAGTCATCCCATCCAGAT
4594898 ATCATTAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (30 bp):
CATGTATAATTCAAGTCATCCCATCCAGAT
Found at i:4595428 original size:9 final size:9
Alignment explanation
Indices: 4595414--4595453 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
4595404 CCATATCCTT
4595414 CTCCACCAC
1 CTCCACCAC
4595423 CTCCACCA-
1 CTCCACCAC
4595431 CT-C-CCAC
1 CTCCACCAC
4595438 CTCCACCAC
1 CTCCACCAC
*
4595447 CACCACC
1 CTCCACC
4595454 TCCTGAACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
6 3 0.11
7 3 0.11
8 3 0.11
9 18 0.67
ACGTcount: A:0.23, C:0.68, G:0.00, T:0.10
Consensus pattern (9 bp):
CTCCACCAC
Found at i:4595439 original size:15 final size:15
Alignment explanation
Indices: 4595416--4595456 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
4595406 ATATCCTTCT
4595416 CCACCACCTCCACCA
1 CCACCACCTCCACCA
4595431 CTC-CCACCTCCACCA
1 C-CACCACCTCCACCA
4595446 CCACCACCTCC
1 CCACCACCTCC
4595457 TGAACCAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.04
15 22 0.92
16 1 0.04
ACGTcount: A:0.22, C:0.68, G:0.00, T:0.10
Consensus pattern (15 bp):
CCACCACCTCCACCA
Found at i:4611612 original size:17 final size:19
Alignment explanation
Indices: 4611580--4611618 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
4611570 TGGCGTGCTT
*
4611580 AGTGGCTTGTATCTTT-CA
1 AGTGGCATGTATCTTTCCA
4611598 AGTGGCATG-ATCTTTCCA
1 AGTGGCATGTATCTTTCCA
4611616 AGT
1 AGT
4611619 CAAAAAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (19 bp):
AGTGGCATGTATCTTTCCA
Found at i:4634605 original size:20 final size:20
Alignment explanation
Indices: 4634569--4634606 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4634559 GAAGAGCTAG
*
4634569 AAAAGAAAAGAAGGGAAAGA
1 AAAAGAAAAGAAAGGAAAGA
4634589 AAAAGAAGAA-AAAGGAAA
1 AAAAGAA-AAGAAAGGAAA
4634607 TACCCATTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAGAAAGGAAAGA
Found at i:4653875 original size:3 final size:3
Alignment explanation
Indices: 4653832--4653863 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
4653822 AGCAGCAGCA
4653832 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT CCT CC
4653864 CGATCCTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:4660457 original size:19 final size:19
Alignment explanation
Indices: 4660435--4660478 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4660425 TTAAATATAA
4660435 TAAAATAATAAAAATAATT
1 TAAAATAATAAAAATAATT
** **
4660454 TAAAATTTTGTAAATAATT
1 TAAAATAATAAAAATAATT
4660473 TAAAAT
1 TAAAAT
4660479 TTTTTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAAATAATAAAAATAATT
Found at i:4662417 original size:22 final size:23
Alignment explanation
Indices: 4662373--4662424 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
4662363 GGAATGGTTC
4662373 GTTTGAGGGTTTTGAAAAAAACCG
1 GTTTGAGGGTTTTG-AAAAAACCG
4662397 GTTTGAGGGTTTTG-AAAAACCG
1 GTTTGAGGGTTTTGAAAAAACCG
4662419 GTTTGA
1 GTTTGA
4662425 TTTTTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
22 14 0.50
24 14 0.50
ACGTcount: A:0.29, C:0.08, G:0.31, T:0.33
Consensus pattern (23 bp):
GTTTGAGGGTTTTGAAAAAACCG
Found at i:4662434 original size:20 final size:21
Alignment explanation
Indices: 4662373--4662436 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 21
4662363 GGAATGGTTC
4662373 GTTTGAGGGTTTTGAAAAAAACCG
1 GTTTGA-GGTTTT--AAAAAACCG
*
4662397 GTTTGAGGGTTTTGAAAAACCG
1 GTTTGA-GGTTTTAAAAAACCG
*
4662419 GTTTGA-TTTTTAAAAAAC
1 GTTTGAGGTTTTAAAAAAC
4662437 AGATTTCAGG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 10 0.27
22 14 0.38
24 13 0.35
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (21 bp):
GTTTGAGGTTTTAAAAAACCG
Found at i:4662740 original size:31 final size:31
Alignment explanation
Indices: 4662705--4662768 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
4662695 TCGTAATTTT
4662705 TCTAAAC-CAAATT-AAAAATCAACATTTAATA
1 TCTAAACTCAAATTAAAAAAT-AA-ATTTAATA
*
4662736 TCTAAACTCGAATTAAAAAATAAATTTAATA
1 TCTAAACTCAAATTAAAAAATAAATTTAATA
4662767 TC
1 TC
4662769 AATATTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 17 0.57
32 7 0.23
33 6 0.20
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (31 bp):
TCTAAACTCAAATTAAAAAATAAATTTAATA
Found at i:4665923 original size:102 final size:102
Alignment explanation
Indices: 4665742--4665927 Score: 234
Period size: 102 Copynumber: 1.8 Consensus size: 102
4665732 AATACTCTTT
* * *
4665742 ATTTATTTTTTGCAACTAATTTCTTGTAAAAGAGTAATATTACTTACCCTATGTATCCATACAAT
1 ATTTATTTTTTGCAACTAATCTCTTGTAAAAGAGTAATATTACTTACCCCATGCATCCATACAAT
* *
4665807 GTATACAAGCAAAGTAATACCTCTATTAAGAGTCCTA
66 ATATACAAACAAAGTAATACCTCTATTAAGAGTCCTA
* * *
4665844 ATTTATTTTTTGCAATTAA-CTCTTTGTAAACGAGTAATATTACTT-CTCCCATGCATTCATA-A
1 ATTTATTTTTTGCAACTAATCTC-TTGTAAAAGAGTAATATTACTTAC-CCCATGCATCCATACA
* *
4665906 ACTATATGCAAATAAAGTAATA
64 A-TATATACAAACAAAGTAATA
4665928 TTTCTTTTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
101 5 0.07
102 66 0.93
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (102 bp):
ATTTATTTTTTGCAACTAATCTCTTGTAAAAGAGTAATATTACTTACCCCATGCATCCATACAAT
ATATACAAACAAAGTAATACCTCTATTAAGAGTCCTA
Found at i:4670401 original size:65 final size:65
Alignment explanation
Indices: 4670297--4670437 Score: 273
Period size: 65 Copynumber: 2.2 Consensus size: 65
4670287 CCTTAAACCT
*
4670297 CGAAACTCATGTCTTGAATGCTTATGTTGGAATGCTAGATCACTCTTTTTCAACCATCCCTCAAG
1 CGAAACTCATGTCTTGAATGCTTATGTTGGAACGCTAGATCACTCTTTTTCAACCATCCCTCAAG
4670362 CGAAACTCATGTCTTGAATGCTTATGTTGGAACGCTAGATCACTCTTTTTCAACCATCCCTCAAG
1 CGAAACTCATGTCTTGAATGCTTATGTTGGAACGCTAGATCACTCTTTTTCAACCATCCCTCAAG
4670427 CGAAACTCATG
1 CGAAACTCATG
4670438 GCTTCAGCTG
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 75 1.00
ACGTcount: A:0.27, C:0.26, G:0.16, T:0.32
Consensus pattern (65 bp):
CGAAACTCATGTCTTGAATGCTTATGTTGGAACGCTAGATCACTCTTTTTCAACCATCCCTCAAG
Found at i:4671569 original size:19 final size:20
Alignment explanation
Indices: 4671536--4671573 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4671526 CATTATGTTT
*
4671536 AAATAAAATGCCAAAAAAAA
1 AAATAAAATGACAAAAAAAA
4671556 AAAT-AAATGACAAAAAAA
1 AAATAAAATGACAAAAAAA
4671574 TGGATTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.76, C:0.08, G:0.05, T:0.11
Consensus pattern (20 bp):
AAATAAAATGACAAAAAAAA
Found at i:4675305 original size:33 final size:33
Alignment explanation
Indices: 4675259--4675321 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
4675249 TATTGTCAGT
* * *
4675259 GATAATGATGAAGACCATCAAGCAGAAGAACAA
1 GATAATGAAGAAGAACATCAAGAAGAAGAACAA
*
4675292 GATAATGAAGAAGAAGATCAAGAAGAAGAA
1 GATAATGAAGAAGAACATCAAGAAGAAGAA
4675322 ACAGCTCTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.56, C:0.10, G:0.24, T:0.11
Consensus pattern (33 bp):
GATAATGAAGAAGAACATCAAGAAGAAGAACAA
Found at i:4675319 original size:15 final size:14
Alignment explanation
Indices: 4675282--4675321 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
4675272 ACCATCAAGC
*
4675282 AGAAGAACAAGATA
1 AGAAGAAGAAGATA
4675296 ATGAAGAAGAAGATCA
1 A-GAAGAAGAAGAT-A
4675312 AGAAGAAGAA
1 AGAAGAAGAA
4675322 ACAGCTCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 1 0.04
15 20 0.87
16 2 0.09
ACGTcount: A:0.62, C:0.05, G:0.25, T:0.07
Consensus pattern (14 bp):
AGAAGAAGAAGATA
Found at i:4683801 original size:15 final size:16
Alignment explanation
Indices: 4683764--4683802 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
4683754 TTTAGTCAAA
4683764 AAAATTAATTTTAGAT
1 AAAATTAATTTTAGAT
*
4683780 AAAATTACTTTTA-AT
1 AAAATTAATTTTAGAT
*
4683795 GAAATTAA
1 AAAATTAA
4683803 CTCATATGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (16 bp):
AAAATTAATTTTAGAT
Found at i:4684255 original size:149 final size:145
Alignment explanation
Indices: 4684036--4684311 Score: 354
Period size: 149 Copynumber: 1.9 Consensus size: 145
4684026 TACTTTCTTT
* * * * * * * *
4684036 ATACCAAACTCTACTTAATTTTTTTATCAATAATTACATAAAGATCAAAGGATCTTACTTTATTT
1 ATACCAAACTCTACCTAATTTTTTGATCAATAATTACAAAAAAATCAAAAGATCCTACATCATTT
* *
4684101 TCTCATTATTACATGGAAAAGGCAACGGAGATGAATCCAATGCGAAAAATTTTCAACAAAAAACA
66 TCTCATTATTACATGGAAAAGGCAACGGAGATGAATCAAACGCGAAAAA-TTTCAACAAAAAACA
4684166 ATGTGCTTCACTCCCC
130 ATGTGCTTCACTCCCC
* * *
4684182 ATACCAAATTTTACCTAATTTTCTTGGATCAATAATTATGAAAAAAATCAAAAGATCCTACATCA
1 ATACCAAACTCTACCTAATTTT-TT-GATCAATAATTA-CAAAAAAATCAAAAGATCCTACATCA
* ** * *
4684247 TTTTCTCATTATTACATGGAAAAGGTAGTGGAGATGAATCAAACGTGTAAAATTTCAACAAAAAA
63 TTTTCTCATTATTACATGGAAAAGGCAACGGAGATGAATCAAACGCGAAAAATTTCAACAAAAAA
4684312 TATGTTTTGC
Statistics
Matches: 109, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
146 19 0.17
147 2 0.02
148 24 0.22
149 64 0.59
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (145 bp):
ATACCAAACTCTACCTAATTTTTTGATCAATAATTACAAAAAAATCAAAAGATCCTACATCATTT
TCTCATTATTACATGGAAAAGGCAACGGAGATGAATCAAACGCGAAAAATTTCAACAAAAAACAA
TGTGCTTCACTCCCC
Found at i:4684954 original size:222 final size:224
Alignment explanation
Indices: 4684565--4685023 Score: 845
Period size: 222 Copynumber: 2.1 Consensus size: 224
4684555 TTTAGGTTAA
*
4684565 TTTAATGTAGAAACTGGAATTGTTTCATTTATATATATATATATTGAAAAAGATATTTGCATATT
1 TTTAATGTAGAAACTGGAATTGTTTCATTTATATATACATATATTGAAAAAGATATTTGCATATT
4684630 GACTAAAGGTAAAATAACATAAATACTAAATAAATTTATTTATCATGTATTCAAACTAGCATGAA
66 GACTAAAGGTAAAATAACATAAATACTAAATAAATTTATTTATCATGTATTCAAACTAGCATGAA
4684695 AATTCATATCGATGTTACAACTTTTACTTCAAAAAACTACAT-AAAATATTTAAGAAAAAACTCT
131 AATTCATATCGATGTTACAACTTTTACTTCAAAAAACTACATAAAAATATTTAAGAAAAAACTCT
* *
4684759 AAAACACCCCGTAGAGTTTCTATTTATATT
196 AAAACAACCCATAGAG-TTCTATTTATATT
4684789 TTTAATGTAGAAACTGGAATTGTTTCA-TT-TATATACATATATTGAAAAAGATATTTGCATATT
1 TTTAATGTAGAAACTGGAATTGTTTCATTTATATATACATATATTGAAAAAGATATTTGCATATT
4684852 GACTAAAGGTAAAATAACATAAATACTAAATAAATTTA-TTATCATGTATTCAAACTAGCATGAA
66 GACTAAAGGTAAAATAACATAAATACTAAATAAATTTATTTATCATGTATTCAAACTAGCATGAA
4684916 AATTCATATCGATGTTACAACTTTTACTTCACAAAAACTACATAAAAATATTTAAGAAAAAACTC
131 AATTCATATCGATGTTACAACTTTTACTTCA-AAAAACTACATAAAAATATTTAAGAAAAAACTC
4684981 TAAAACAACCCATAGAGTTCTATTTATATT
195 TAAAACAACCCATAGAGTTCTATTTATATT
4685011 TTTAATGTAGAAA
1 TTTAATGTAGAAA
4685024 TAGTAAAGTA
Statistics
Matches: 230, Mismatches: 3, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
221 57 0.25
222 108 0.47
223 38 0.17
224 27 0.12
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (224 bp):
TTTAATGTAGAAACTGGAATTGTTTCATTTATATATACATATATTGAAAAAGATATTTGCATATT
GACTAAAGGTAAAATAACATAAATACTAAATAAATTTATTTATCATGTATTCAAACTAGCATGAA
AATTCATATCGATGTTACAACTTTTACTTCAAAAAACTACATAAAAATATTTAAGAAAAAACTCT
AAAACAACCCATAGAGTTCTATTTATATT
Found at i:4689028 original size:6 final size:6
Alignment explanation
Indices: 4689019--4689048 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4689009 ACACACACAC
4689019 ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT
4689049 GTATATGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:4690970 original size:2 final size:2
Alignment explanation
Indices: 4690963--4690993 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4690953 GTGTCTGCTT
4690963 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
4690994 GTCTTTGATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4691942 original size:5 final size:5
Alignment explanation
Indices: 4691932--4691956 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
4691922 GATGATCATG
4691932 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
4691957 TGGTATAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:4698086 original size:6 final size:6
Alignment explanation
Indices: 4698075--4698108 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
4698065 GAGAAAAGCC
4698075 AAAAAG AAAAAG AAAAA- AAGAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAAAAG AAAA
4698109 GGGCAAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 2 0.08
6 22 0.85
7 2 0.08
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:4716763 original size:5 final size:5
Alignment explanation
Indices: 4716753--4716778 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4716743 CAACATAGAT
4716753 ATAAA ATAAA ATAAA ATAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA A
4716779 AGGGGAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Found at i:4719856 original size:19 final size:19
Alignment explanation
Indices: 4719811--4719857 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4719801 ATAATTCTCT
*
4719811 TAAAAAAAATACATAATTT
1 TAAAAAAAATACATAATTA
* *
4719830 TAACAAAAAT-TATAACTTA
1 TAAAAAAAATACATAA-TTA
4719849 TAAAAAAAA
1 TAAAAAAAA
4719858 ATTTACCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAAAAATACATAATTA
Found at i:4720033 original size:2 final size:2
Alignment explanation
Indices: 4720026--4720052 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4720016 ACAGTAATCA
4720026 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
4720053 AATAGATTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4732242 original size:35 final size:35
Alignment explanation
Indices: 4732203--4732274 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4732193 TTATGATAGG
4732203 TAATCATATATAATTTGCATATTGCTAAACCAGGT
1 TAATCATATATAATTTGCATATTGCTAAACCAGGT
4732238 TAATCATATATAATTTGCATATTGCTAAACCAGGT
1 TAATCATATATAATTTGCATATTGCTAAACCAGGT
4732273 TA
1 TA
4732275 TCTTTAATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (35 bp):
TAATCATATATAATTTGCATATTGCTAAACCAGGT
Found at i:4741345 original size:59 final size:59
Alignment explanation
Indices: 4741249--4741372 Score: 241
Period size: 59 Copynumber: 2.1 Consensus size: 59
4741239 TCTTCTTACG
4741249 TATA-ACATCACAGAGCTTCAGCATGCATGACAAAGAAAGGATTACTATGAGAAGAATA
1 TATATACATCACAGAGCTTCAGCATGCATGACAAAGAAAGGATTACTATGAGAAGAATA
4741307 TATATACATCACAGAGCTTCAGCATGCATGACAAAGAAAGGATTACTATGAGAAGAATA
1 TATATACATCACAGAGCTTCAGCATGCATGACAAAGAAAGGATTACTATGAGAAGAATA
4741366 TATATAC
1 TATATAC
4741373 TAATATTAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 4 0.06
59 61 0.94
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.23
Consensus pattern (59 bp):
TATATACATCACAGAGCTTCAGCATGCATGACAAAGAAAGGATTACTATGAGAAGAATA
Found at i:4741648 original size:10 final size:11
Alignment explanation
Indices: 4741629--4741657 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4741619 ATCATCATGA
4741629 TATATATCTAT
1 TATATATCTAT
4741640 TAT-TATCTAT
1 TATATATCTAT
4741650 TATATATC
1 TATATATC
4741658 AGCGATCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATATCTAT
Found at i:4744317 original size:22 final size:22
Alignment explanation
Indices: 4744292--4744363 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
4744282 AATTTAATAA
*
4744292 ATATTAATTTTTAACTTAAAAT
1 ATATTAATATTTAACTTAAAAT
4744314 ATATTAATATTTAACTT-AAA-
1 ATATTAATATTTAACTTAAAAT
4744334 AT-TT--T-TTTAACTTAAAA-
1 ATATTAATATTTAACTTAAAAT
4744351 -TATTAATATTTAA
1 ATATTAATATTTAA
4744364 ATTCTTCAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 9 0.20
17 6 0.14
19 3 0.07
20 7 0.16
21 3 0.07
22 16 0.36
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
ATATTAATATTTAACTTAAAAT
Found at i:4746286 original size:21 final size:21
Alignment explanation
Indices: 4746262--4746306 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
4746252 GCGATGAAAT
4746262 GATTAAGGTTATGCAAGGATA
1 GATTAAGGTTATGCAAGGATA
*
4746283 GATTAGGGTTATGCAAGGATA
1 GATTAAGGTTATGCAAGGATA
4746304 GAT
1 GAT
4746307 ATTATGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.31, T:0.29
Consensus pattern (21 bp):
GATTAAGGTTATGCAAGGATA
Found at i:4755848 original size:13 final size:13
Alignment explanation
Indices: 4755830--4755854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4755820 ATCAGAGAAA
4755830 GATCAAGAAAAAG
1 GATCAAGAAAAAG
4755843 GATCAAGAAAAA
1 GATCAAGAAAAA
4755855 ATGAGAGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
GATCAAGAAAAAG
Found at i:4762439 original size:11 final size:11
Alignment explanation
Indices: 4762423--4762447 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
4762413 ATTCTAAGAA
4762423 AATAAGTTACT
1 AATAAGTTACT
4762434 AATAAGTTACT
1 AATAAGTTACT
4762445 AAT
1 AAT
4762448 TGAAAACTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (11 bp):
AATAAGTTACT
Found at i:4779194 original size:96 final size:96
Alignment explanation
Indices: 4779030--4779226 Score: 385
Period size: 96 Copynumber: 2.1 Consensus size: 96
4779020 CTGATAATTA
4779030 AGAAGCCACATAAACTACCAAAAAACATCATTTCTCAGATTATACTCTATGAAATGAGAACCACA
1 AGAAGCCACATAAACTACCAAAAAACATCATTTCTCAGATTATACTCTATGAAATGAGAACCACA
*
4779095 ATACCCATAAGCCAACAAGAAGAGAACCACG
66 ATACCCATAAGCCAACAAGAAGAGAACCAAG
4779126 AGAAGCCACATAAACTACCAAAAAACATCATTTCTCAGATTATACTCTATGAAATGAGAACCACA
1 AGAAGCCACATAAACTACCAAAAAACATCATTTCTCAGATTATACTCTATGAAATGAGAACCACA
4779191 ATACCCATAAGCCAACAAGAAGAGAACCAAG
66 ATACCCATAAGCCAACAAGAAGAGAACCAAG
4779222 AGAAG
1 AGAAG
4779227 GAATTTTTAA
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 100 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (96 bp):
AGAAGCCACATAAACTACCAAAAAACATCATTTCTCAGATTATACTCTATGAAATGAGAACCACA
ATACCCATAAGCCAACAAGAAGAGAACCAAG
Found at i:4784378 original size:22 final size:21
Alignment explanation
Indices: 4784351--4784424 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 21
4784341 TTTTTAATAA
4784351 AATATTAATATTTTAACATATT
1 AATATTAATATTTTAA-ATATT
* *
4784373 AATATTAA-ATTATAAATA-A
1 AATATTAATATTTTAAATATT
4784392 AATATTAATA-TTTAAATTATT
1 AATATTAATATTTTAAA-TATT
4784413 AATTATTAATAT
1 AA-TATTAATAT
4784425 AATAACTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 13 0.30
20 6 0.14
21 8 0.19
22 16 0.37
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (21 bp):
AATATTAATATTTTAAATATT
Found at i:4784407 original size:19 final size:19
Alignment explanation
Indices: 4784346--4784408 Score: 74
Period size: 19 Copynumber: 3.2 Consensus size: 19
4784336 TTCAATTTTT
4784346 AATAAAATATTAATATTTTA
1 AATAAAATATTAATA-TTTA
*
4784366 ACATATTAATATTAA-ATTATA
1 A-ATA-AAATATTAATATT-TA
4784387 AATAAAATATTAATATTTA
1 AATAAAATATTAATATTTA
4784406 AAT
1 AAT
4784409 TATTAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
19 13 0.35
20 9 0.24
21 7 0.19
22 8 0.22
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAAAATATTAATATTTA
Found at i:4784421 original size:15 final size:14
Alignment explanation
Indices: 4784369--4784421 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
4784359 TATTTTAACA
4784369 TATTAATATTAAAT
1 TATTAATATTAAAT
*
4784383 TA-TAA-A-TAAAA
1 TATTAATATTAAAT
4784394 TATTAATATTTAAAT
1 TATTAATA-TTAAAT
4784409 TATTAATTATTAA
1 TATTAA-TATTAA
4784422 TATAATAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
11 6 0.19
12 4 0.12
13 4 0.12
14 2 0.06
15 14 0.44
16 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:4784608 original size:16 final size:16
Alignment explanation
Indices: 4784589--4784639 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
4784579 TTAAATTAAA
*
4784589 TAAAATATCAATATTT
1 TAAAATATTAATATTT
4784605 TAAAATATTAATGA--T
1 TAAAATATTAAT-ATTT
*
4784620 TAAATTATTAATATTT
1 TAAAATATTAATATTT
4784636 TAAA
1 TAAA
4784640 TAAATAATCA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 1 0.03
15 12 0.40
16 16 0.53
17 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:4784635 original size:31 final size:28
Alignment explanation
Indices: 4784587--4784725 Score: 97
Period size: 31 Copynumber: 4.8 Consensus size: 28
4784577 ATTTAAATTA
* *
4784587 AATAAAATATCAATATTTTAAAATATTAAT
1 AATAAATTATTAATATTTTAAAATA--AAT
*
4784617 GATTAAATTATTAATATTTT-AAATAAAT
1 -AATAAATTATTAATATTTTAAAATAAAT
* *
4784645 AATCAATTATTAATATTTAAAAATAAAAT
1 AATAAATTATTAATATTTTAAAAT-AAAT
* *
4784674 AAAGTAATTTATCATAATAATATTTAAATTAAAT
1 -AA-TAAATTAT--TAAT-AT-TTTAAAATAAAT
4784708 -A-AAA-TATTAATATTTTAA
1 AATAAATTATTAATATTTTAA
4784726 TATATTAATG
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
25 5 0.06
26 2 0.02
27 20 0.22
28 7 0.08
29 7 0.08
30 9 0.10
31 22 0.25
32 1 0.01
33 4 0.04
34 6 0.07
35 6 0.07
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (28 bp):
AATAAATTATTAATATTTTAAAATAAAT
Found at i:4784655 original size:127 final size:118
Alignment explanation
Indices: 4784553--4785107 Score: 412
Period size: 118 Copynumber: 4.7 Consensus size: 118
4784543 AAATAAAAAG
*
4784553 AAATAAA-AAATTAATCATAATAATATTTAAATTAAATAAAATATCAATATTTTAAAATATTAAT
1 AAATAAAGTAATTAATCATAATAATATTTAAATTAAATAAAATATCAATATTTTAAAATATTAAT
* * *
4784617 GATTAAATTATTAATATTTTAAATAAATAATCAATTATTAATATTTAAAAATA
66 GACTAAATTATAAATATTTTAAATAAATAAGCAATTATTAATATTTAAAAATA
* * *
4784670 AAATAAAGTAATTTATCATAATAATATTTAAATTAAATAAAATATTAATATTTTAATATATTAAT
1 AAATAAAGTAATTAATCATAATAATATTTAAATTAAATAAAATATCAATATTTTAAAATATTAAT
* * *
4784735 GACTAAATTATAAATAAATATTAATATTTAAAT-GGTCAATTATTAATATTT-TAAAT-
66 GACTAAATTATAAAT--ATTTTAA-A--TAAATAAG-CAATTATTAATATTTAAAAATA
** * * * * ** *
4784791 AAA-CCACT-ATCAAT--TATTAATATTTAAA--AAATAAAATAATTAATCATAATAATAT-TTA
1 AAATAAAGTAATTAATCATAATAATATTTAAATTAAATAAAAT-ATCAAT-ATTTTAAAATATTA
* * * * *
4784849 A--ATTAAAAATATTAATATTTTAAATAAACCACTATCAATTATTAATATTT---AA-A
64 ATGACT-AAATTATAAATATTTTAAATAAA-TA--AGCAATTATTAATATTTAAAAATA
* * *
4784902 AAATAAAATAATTAACCATAATAATATTTAAATT--A-AAAATATTAATATTTTAAAATATTAAT
1 AAATAAAGTAATTAATCATAATAATATTTAAATTAAATAAAATATCAATATTTTAAAATATTAAT
* * * * * *
4784964 TATTAAATTATACATAAAATATTAATATTTAAATTATCAATTATTAATATTTAAAAATA
66 GACTAAATTAT--A-AATATTTTAA-A--TAAATAAGCAATTATTAATATTTAAAAATA
* * * * *
4785023 AAATAAAACAAAATAATTGATCATAATGATGTTTAAATTAAATAAAATATTAATATTTTAAAATA
1 AAAT-----AAAGTAATTAATCATAATAATATTTAAATTAAATAAAATATCAATATTTTAAAATA
*
4785088 TTAATGATTAAATTATAAAT
61 TTAATGACTAAATTATAAAT
4785108 GTAATATTTA
Statistics
Matches: 350, Mismatches: 46, Indels: 75
0.74 0.10 0.16
Matches are distributed among these distances:
110 4 0.01
111 5 0.01
112 10 0.03
113 35 0.10
114 13 0.04
115 35 0.10
116 10 0.03
117 53 0.15
118 67 0.19
119 4 0.01
120 14 0.04
121 9 0.03
122 4 0.01
123 20 0.06
126 28 0.08
127 1 0.00
128 1 0.00
129 37 0.11
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (118 bp):
AAATAAAGTAATTAATCATAATAATATTTAAATTAAATAAAATATCAATATTTTAAAATATTAAT
GACTAAATTATAAATATTTTAAATAAATAAGCAATTATTAATATTTAAAAATA
Found at i:4784790 original size:41 final size:41
Alignment explanation
Indices: 4784702--4784793 Score: 98
Period size: 41 Copynumber: 2.2 Consensus size: 41
4784692 AATATTTAAA
*
4784702 TTAAATAAAATATTAATATTTTAATATATTAATGACTAAATT
1 TTAAAT-AAATATTAATATTTTAATATATCAATGACTAAATT
* * * *
4784744 ATAAATAAATATTAATA-TTTAA-ATGGTCAATTATTAATATT
1 TTAAATAAATATTAATATTTTAATAT-ATCAATGACTAA-ATT
4784785 TTAAATAAA
1 TTAAATAAA
4784794 CCACTATCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
39 2 0.05
40 13 0.31
41 22 0.52
42 5 0.12
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.43
Consensus pattern (41 bp):
TTAAATAAATATTAATATTTTAATATATCAATGACTAAATT
Found at i:4784805 original size:30 final size:29
Alignment explanation
Indices: 4784770--4784898 Score: 89
Period size: 30 Copynumber: 4.6 Consensus size: 29
4784760 ATTTAAATGG
4784770 TCAATTATTAATATTTTAAATAAACCACTA
1 TCAATTATTAATATTTTAAATAAA-CACTA
* **
4784800 TCAATTATTAATA-TTTAAA-AAATAAAA
1 TCAATTATTAATATTTTAAATAAACACTA
*
4784827 T-AATTAATCATAATAATATTTAAAT-TA-A--A
1 TCAATT-AT--TAAT-AT-TTTAAATAAACACTA
4784856 --AA-TATTAATATTTTAAATAAACCACTA
1 TCAATTATTAATATTTTAAATAAA-CACTA
4784883 TCAATTATTAATATTT
1 TCAATTATTAATATTT
4784899 AAAAAATAAA
Statistics
Matches: 79, Mismatches: 5, Indels: 30
0.69 0.04 0.26
Matches are distributed among these distances:
22 7 0.09
23 3 0.04
24 4 0.05
25 1 0.01
26 6 0.08
27 7 0.09
28 5 0.06
29 13 0.16
30 25 0.32
31 1 0.01
32 7 0.09
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (29 bp):
TCAATTATTAATATTTTAAATAAACACTA
Found at i:4784814 original size:83 final size:81
Alignment explanation
Indices: 4784744--4784955 Score: 311
Period size: 83 Copynumber: 2.6 Consensus size: 81
4784734 TGACTAAATT
* * *
4784744 ATAAATAA-ATATTAATATTTAAATGGT-CAATTATTAATATTTTAAATAAACCACTATCAATTA
1 ATAAATAACATAATAATATTTAAAT--TAAAAATATTAATATTTTAAATAAACCACTATCAATTA
4784807 TTAATATTTAAAAAATAAA
64 TTAATA-TTAAAAAATAAA
*
4784826 ATAATTAATCATAATAATATTTAAATTAAAAATATTAATATTTTAAATAAACCACTATCAATTAT
1 ATAAATAA-CATAATAATATTTAAATTAAAAATATTAATATTTTAAATAAACCACTATCAATTAT
4784891 TAATATTTAAAAAATAAA
65 TAATA-TTAAAAAATAAA
*
4784909 ATAATTAACCATAATAATATTTAAATTAAAAATATTAATATTTTAAA
1 ATAAATAA-CATAATAATATTTAAATTAAAAATATTAATATTTTAAA
4784956 ATATTAATTA
Statistics
Matches: 122, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
82 8 0.07
83 99 0.81
84 15 0.12
ACGTcount: A:0.54, C:0.06, G:0.01, T:0.39
Consensus pattern (81 bp):
ATAAATAACATAATAATATTTAAATTAAAAATATTAATATTTTAAATAAACCACTATCAATTATT
AATATTAAAAAATAAA
Found at i:4784852 original size:21 final size:22
Alignment explanation
Indices: 4784836--4784955 Score: 62
Period size: 21 Copynumber: 5.7 Consensus size: 22
4784826 ATAATTAATC
4784836 ATAATAATA-TTTAAATTAAAA
1 ATAATAATATTTTAAATTAAAA
*
4784857 ATATTAATATTTTAAA-TAAACCA
1 ATAATAATATTTTAAATTAAA--A
* * *
4784880 CT-ATCAAT-TATTAATATTTAAA
1 ATAAT-AATATTTTAA-ATTAAAA
* **
4784902 A-AATAA-A--AT-AATTAACC
1 ATAATAATATTTTAAATTAAAA
4784919 ATAATAATA-TTTAAATTAAAA
1 ATAATAATATTTTAAATTAAAA
*
4784940 ATATTAATATTTTAAA
1 ATAATAATATTTTAAA
4784956 ATATTAATTA
Statistics
Matches: 72, Mismatches: 14, Indels: 25
0.65 0.13 0.23
Matches are distributed among these distances:
17 5 0.07
18 6 0.08
19 2 0.03
20 1 0.01
21 28 0.39
22 21 0.29
23 6 0.08
24 3 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATAATATTTTAAATTAAAA
Found at i:4785090 original size:129 final size:126
Alignment explanation
Indices: 4784901--4785144 Score: 353
Period size: 129 Copynumber: 1.9 Consensus size: 126
4784891 TAATATTTAA
* *
4784901 AAAATAAAATAATTAACCATAATAATATTTAAATTAAAAATATTAATATTTTAAAATATTAATTA
1 AAAACAAAATAATTAACCATAATAATATTTAAATTAAAAATATTAATATTTTAAAATATTAATGA
* *
4784966 TTAAATTATACATAAAATATTAATATTTAAATTATCAATTATTAATATTTAAAAATAAAAT
66 TTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAATATTTAAAAATAAAAT
* * * *
4785027 AAAACAAAATAATTGATCATAATGATGTTTAAATTAAATAAAATATTAATATTTTAAAATATTAA
1 AAAACAAAATAATTAACCATAATAATATTTAAATT--A-AAAATATTAATATTTTAAAATATTAA
** * *
4785092 TGATTAAATTATAAATGTAATATTTATATTTAAATAATTAATTATTAATATTT
63 TGATTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAATATTT
4785145 TAATTAAATT
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
126 30 0.29
128 1 0.01
129 72 0.70
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (126 bp):
AAAACAAAATAATTAACCATAATAATATTTAAATTAAAAATATTAATATTTTAAAATATTAATGA
TTAAATTATAAATAAAATATTAATATTTAAATAATCAATTATTAATATTTAAAAATAAAAT
Found at i:4785174 original size:15 final size:15
Alignment explanation
Indices: 4785065--4785174 Score: 54
Period size: 15 Copynumber: 7.3 Consensus size: 15
4785055 TTAAATTAAA
*
4785065 TAAAATATTAATATTT
1 TAAATTATTAATA-TT
*
4785081 TAAAATATTAATGA-T
1 TAAATTATTAAT-ATT
*
4785096 TAAATTA-TAA-ATG
1 TAAATTATTAATATT
*
4785109 T-AA-TATTTATATT
1 TAAATTATTAATATT
*
4785122 TAAATAATTAAT-TAT
1 TAAATTATTAATAT-T
4785137 TAATATT-TTAATTAAATT
1 TAA-ATTATTAA-T--ATT
4785155 CTAAATTATTAATATT
1 -TAAATTATTAATATT
4785171 TAAA
1 TAAA
4785175 AAATCTAATA
Statistics
Matches: 73, Mismatches: 7, Indels: 29
0.67 0.06 0.27
Matches are distributed among these distances:
11 2 0.03
12 5 0.07
13 4 0.05
14 6 0.08
15 24 0.33
16 18 0.25
17 1 0.01
18 5 0.07
19 8 0.11
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (15 bp):
TAAATTATTAATATT
Found at i:4785186 original size:27 final size:28
Alignment explanation
Indices: 4785109--4785186 Score: 65
Period size: 27 Copynumber: 2.9 Consensus size: 28
4785099 ATTATAAATG
* * *
4785109 TAATATTTATATTTAAA-TAATTAATTAT
1 TAATATTT-TAATAAAATTAATAAATTAT
* *
4785137 TAATATTTTAATTAAATT-CTAAATTAT
1 TAATATTTTAATAAAATTAATAAATTAT
4785164 TAATA-TTTAA-AAAATCTAATAAA
1 TAATATTTTAATAAAAT-TAATAAA
4785187 AATAAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
25 4 0.10
26 6 0.14
27 23 0.55
28 9 0.21
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATATTTTAATAAAATTAATAAATTAT
Found at i:4785192 original size:18 final size:19
Alignment explanation
Indices: 4785171--4785212 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
4785161 TATTAATATT
4785171 TAAAAAATC-TAATAAA-AA
1 TAAAAAATCAT-ATAAATAA
*
4785189 TAAATAATCATATAAATAA
1 TAAAAAATCATATAAATAA
4785208 TAAAA
1 TAAAA
4785213 GGTGTTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAATCATATAAATAA
Found at i:4785237 original size:15 final size:15
Alignment explanation
Indices: 4785217--4785249 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4785207 ATAAAAGGTG
4785217 TTTTTATCTTTTTAT
1 TTTTTATCTTTTTAT
*
4785232 TTTTTATTTTTTTAT
1 TTTTTATCTTTTTAT
4785247 TTT
1 TTT
4785250 AAAATTATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTATCTTTTTAT
Found at i:4800943 original size:3 final size:3
Alignment explanation
Indices: 4800935--4800960 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4800925 TCTGAATTCC
4800935 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4800961 AAGAATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4805170 original size:43 final size:43
Alignment explanation
Indices: 4805109--4805217 Score: 202
Period size: 43 Copynumber: 2.5 Consensus size: 43
4805099 TTGAGTGTTG
4805109 AATTCAAAACAATTCAAATTAAAAAATAACTCAAAATACCTTT
1 AATTCAAAACAATTCAAATTAAAAAATAACTCAAAATACCTTT
4805152 AATTCAAAACAATTCAAATTAAAAAATAACTCAAAATACCTTT
1 AATTCAAAACAATTCAAATTAAAAAATAACTCAAAATACCTTT
4805195 AATTCAAAACAA-TCAAATCTAAA
1 AATTCAAAACAATTCAAAT-TAAA
4805218 TCTAATCGGA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
42 6 0.09
43 59 0.91
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.27
Consensus pattern (43 bp):
AATTCAAAACAATTCAAATTAAAAAATAACTCAAAATACCTTT
Found at i:4826203 original size:2 final size:2
Alignment explanation
Indices: 4826196--4826220 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4826186 GAATTATGAC
4826196 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4826221 CAAGTTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4832613 original size:2 final size:2
Alignment explanation
Indices: 4832606--4832632 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4832596 AATTAAAAAG
4832606 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 T
4832633 TATGGACAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4833808 original size:25 final size:24
Alignment explanation
Indices: 4833778--4833838 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
4833768 TAATATTATT
*
4833778 TTTAAAAAATTAATATAAATTAATA
1 TTTAAAAAATTAATATAAA-CAATA
* *
4833803 TTTAAAATATATAATATATACAATA
1 TTTAAAAAAT-TAATATAAACAATA
*
4833828 TTTTAAAAATT
1 TTTAAAAAATT
4833839 GTGGAAGGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
24 1 0.03
25 21 0.70
26 8 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAAAAATTAATATAAACAATA
Found at i:4833832 original size:26 final size:26
Alignment explanation
Indices: 4833777--4833836 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
4833767 TTAATATTAT
*
4833777 TTTTAAAAAATTAATATAAATTAATA
1 TTTTAAAAAATTAATATAAATCAATA
* *
4833803 -TTTAAAATATATAATATATA-CAATA
1 TTTTAAAAAAT-TAATATAAATCAATA
4833828 TTTTAAAAA
1 TTTTAAAAA
4833837 TTGTGGAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
25 13 0.46
26 15 0.54
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (26 bp):
TTTTAAAAAATTAATATAAATCAATA
Found at i:4837224 original size:13 final size:14
Alignment explanation
Indices: 4837200--4837229 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
4837190 TTATTTCATT
4837200 AAAACCATATAAAA
1 AAAACCATATAAAA
4837214 AAAACCA-ATAAAA
1 AAAACCATATAAAA
4837227 AAA
1 AAA
4837230 GCCTTAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (14 bp):
AAAACCATATAAAA
Found at i:4841522 original size:27 final size:27
Alignment explanation
Indices: 4841494--4841546 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
4841484 TCAAAGGATA
4841494 AAAG-TATCTATCAACTTTCT-GTGGGT
1 AAAGTTATCTATCAACTTT-TAGTGGGT
*
4841520 AAAGTTATTTATCAACTTTTAGTGGGT
1 AAAGTTATCTATCAACTTTTAGTGGGT
4841547 CTTTCGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (27 bp):
AAAGTTATCTATCAACTTTTAGTGGGT
Found at i:4859332 original size:35 final size:35
Alignment explanation
Indices: 4859288--4859380 Score: 114
Period size: 35 Copynumber: 2.7 Consensus size: 35
4859278 AAAATAATGT
* *
4859288 TTCATTTATTTTAATTGTTTTACGTGAAGTAACGC
1 TTCACTTATTTTAATTGTTTTACGTGAAGTAACAC
* * ** *
4859323 TTCACTTATTATAATTATTTTGTGTGAAGTAATAC
1 TTCACTTATTTTAATTGTTTTACGTGAAGTAACAC
*
4859358 TTCAGTTATTTTAATTGTTTTAC
1 TTCACTTATTTTAATTGTTTTAC
4859381 AAAAAATAAT
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.52
Consensus pattern (35 bp):
TTCACTTATTTTAATTGTTTTACGTGAAGTAACAC
Found at i:4862348 original size:17 final size:17
Alignment explanation
Indices: 4862321--4862360 Score: 71
Period size: 17 Copynumber: 2.3 Consensus size: 17
4862311 TATATATTTG
4862321 TTTACTCTACTCGTGAAT
1 TTTA-TCTACTCGTGAAT
4862339 TTTATCTACTCGTGAAT
1 TTTATCTACTCGTGAAT
4862356 TTTAT
1 TTTAT
4862361 AGAGTTTACG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (17 bp):
TTTATCTACTCGTGAAT
Found at i:4877346 original size:49 final size:49
Alignment explanation
Indices: 4877289--4877394 Score: 212
Period size: 49 Copynumber: 2.2 Consensus size: 49
4877279 ATTATCTTCA
4877289 CCATCATCGTCGCGAGTAACCTGTCCCTTGCTATTAACCTATGCATACC
1 CCATCATCGTCGCGAGTAACCTGTCCCTTGCTATTAACCTATGCATACC
4877338 CCATCATCGTCGCGAGTAACCTGTCCCTTGCTATTAACCTATGCATACC
1 CCATCATCGTCGCGAGTAACCTGTCCCTTGCTATTAACCTATGCATACC
4877387 CCATCATC
1 CCATCATC
4877395 TTTACCTATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 57 1.00
ACGTcount: A:0.23, C:0.36, G:0.13, T:0.28
Consensus pattern (49 bp):
CCATCATCGTCGCGAGTAACCTGTCCCTTGCTATTAACCTATGCATACC
Found at i:4893429 original size:2 final size:2
Alignment explanation
Indices: 4893422--4893451 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4893412 TCTATTGCTA
4893422 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4893452 GTATTCAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4895704 original size:2 final size:2
Alignment explanation
Indices: 4895652--4895694 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
4895642 CAACGGTGGA
*
4895652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4895694 A
1 A
4895695 GGGGTATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4898812 original size:2 final size:2
Alignment explanation
Indices: 4898801--4898830 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
4898791 CGAACAAAAT
4898801 AC AC -C AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
4898831 TATATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:4900090 original size:80 final size:81
Alignment explanation
Indices: 4900006--4900176 Score: 263
Period size: 80 Copynumber: 2.1 Consensus size: 81
4899996 ATTTTAAGAT
* *
4900006 TGATTTTTATACATTACATGACTTAATCATTATTTCTCTGATTTTTAGATA-TGTGTGGCTAGTT
1 TGATTTTTAGACATTACATGACTTAATCATTATTTCTCTGATTTTTAGATATTGCGTGGCTAGTT
*
4900070 TTAGGCATTGTATTAC
66 TTAAGCATTGTATTAC
* * * *
4900086 TGATTTTTAGACATTACGTGACTTAATCATTATTTTTCTGATTTTTAGATATTGCGTGGTTGGTT
1 TGATTTTTAGACATTACATGACTTAATCATTATTTCTCTGATTTTTAGATATTGCGTGGCTAGTT
*
4900151 TTAAGTATTGTATTAC
66 TTAAGCATTGTATTAC
4900167 TGATTTTTAG
1 TGATTTTTAG
4900177 GTATAACCTA
Statistics
Matches: 82, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
80 48 0.59
81 34 0.41
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.50
Consensus pattern (81 bp):
TGATTTTTAGACATTACATGACTTAATCATTATTTCTCTGATTTTTAGATATTGCGTGGCTAGTT
TTAAGCATTGTATTAC
Found at i:4900134 original size:38 final size:38
Alignment explanation
Indices: 4900006--4900143 Score: 105
Period size: 38 Copynumber: 3.5 Consensus size: 38
4899996 ATTTTAAGAT
* * *
4900006 TGATTTTTATACATTACATGACTTAATCATTATTTCTC
1 TGATTTTTAGACATTACGTGACTTAATCATTATTTTTC
* ** ** ** * * *
4900044 TGATTTTTAGATATGTGTGGCTAGTTTTAGGCATTGTATTAC
1 TGATTTTTAGACAT-T-ACG-T-GACTTAATCATTATTTTTC
4900086 TGATTTTTAGACATTACGTGACTTAATCATTATTTTTC
1 TGATTTTTAGACATTACGTGACTTAATCATTATTTTTC
* *
4900124 TGATTTTTAGATATTGCGTG
1 TGATTTTTAGACATTACGTG
4900144 GTTGGTTTTA
Statistics
Matches: 71, Mismatches: 25, Indels: 8
0.68 0.24 0.08
Matches are distributed among these distances:
38 42 0.59
39 2 0.03
40 1 0.01
41 2 0.03
42 24 0.34
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (38 bp):
TGATTTTTAGACATTACGTGACTTAATCATTATTTTTC
Found at i:4900190 original size:22 final size:22
Alignment explanation
Indices: 4900165--4900209 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
4900155 GTATTGTATT
4900165 ACTGATTTTTAGGT-ATAACCTA
1 ACTGATTTTTAGGTAAT-ACCTA
4900187 ACTGATTTTTAGGTAATACCTA
1 ACTGATTTTTAGGTAATACCTA
4900209 A
1 A
4900210 GTCACATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
ACTGATTTTTAGGTAATACCTA
Found at i:4905718 original size:16 final size:16
Alignment explanation
Indices: 4905694--4905727 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4905684 TATTAATAAG
*
4905694 AATTGATAATAAATTT
1 AATTAATAATAAATTT
*
4905710 AATTAATAATATATTT
1 AATTAATAATAAATTT
4905726 AA
1 AA
4905728 AATATATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTAATAATAAATTT
Found at i:4905757 original size:26 final size:27
Alignment explanation
Indices: 4905699--4905757 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
4905689 ATAAGAATTG
*
4905699 ATAATAAATTTAATTAATAATATATTT
1 ATAATAAATTTAATTAATAATATATAT
* * * *
4905726 AAAATATA-TTAATTTATTATATATAT
1 ATAATAAATTTAATTAATAATATATAT
4905752 ATAATA
1 ATAATA
4905758 GTAATCATAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
26 20 0.77
27 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
ATAATAAATTTAATTAATAATATATAT
Found at i:4905827 original size:23 final size:25
Alignment explanation
Indices: 4905782--4905828 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
4905772 TTAATTTTAG
**
4905782 TTATATATATTTATTTAATTATAAA
1 TTATATATATTTAAATAATTATAAA
4905807 TTATATAT-TTTAAATAA-TATAA
1 TTATATATATTTAAATAATTATAA
4905829 CTTACATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTATATATATTTAAATAATTATAAA
Found at i:4906205 original size:21 final size:23
Alignment explanation
Indices: 4906171--4906219 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
4906161 AAGTAATATA
* * *
4906171 TTATATATATGTA-TATT-TAAT
1 TTATACATAAGTATTATTATAAC
4906192 TTATACATAAGTATTATTATAAC
1 TTATACATAAGTATTATTATAAC
4906215 TTATA
1 TTATA
4906220 ATAGACTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 11 0.48
22 4 0.17
23 8 0.35
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (23 bp):
TTATACATAAGTATTATTATAAC
Found at i:4906559 original size:24 final size:26
Alignment explanation
Indices: 4906518--4906580 Score: 85
Period size: 24 Copynumber: 2.5 Consensus size: 26
4906508 GTCAAACTGA
4906518 TTAAATTAATTTTATATTTAATTAA-T
1 TTAAATT-ATTTTATATTTAATTAATT
*
4906544 TTAAATT-TTTTATATTTTATTAATT
1 TTAAATTATTTTATATTTAATTAATT
*
4906569 TTAAATAATTTT
1 TTAAATTATTTT
4906581 TTAAAATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 15 0.45
25 7 0.21
26 11 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
TTAAATTATTTTATATTTAATTAATT
Found at i:4952997 original size:18 final size:17
Alignment explanation
Indices: 4952977--4953016 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
4952967 GCTTTTATCT
4952977 TATTATTT--CTATTTA
1 TATTATTTAACTATTTA
4952992 TATTATTTAACTATTTA
1 TATTATTTAACTATTTA
4953009 TA-TATTTA
1 TATTATTTA
4953017 CTCATTGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.35
16 6 0.26
17 9 0.39
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TATTATTTAACTATTTA
Found at i:4953007 original size:17 final size:16
Alignment explanation
Indices: 4952977--4953018 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
4952967 GCTTTTATCT
4952977 TATTATTT-CTATTTA
1 TATTATTTACTATTTA
4952992 TATTATTTAACTATTTA
1 TATTATTT-ACTATTTA
4953009 TA-TATTTACT
1 TATTATTTACT
4953019 CATTGCGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.44
16 5 0.20
17 9 0.36
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTATTTACTATTTA
Found at i:4953097 original size:20 final size:22
Alignment explanation
Indices: 4953051--4953097 Score: 62
Period size: 20 Copynumber: 2.2 Consensus size: 22
4953041 TTATTTAATC
4953051 ATTTATATTTTATGTATTATAG
1 ATTTATATTTTATGTATTATAG
* *
4953073 TTTTATA-TTTAT-TATTTTAG
1 ATTTATATTTTATGTATTATAG
4953093 ATTTA
1 ATTTA
4953098 AGTAGAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 11 0.50
21 5 0.23
22 6 0.27
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (22 bp):
ATTTATATTTTATGTATTATAG
Found at i:4983356 original size:21 final size:22
Alignment explanation
Indices: 4983313--4983355 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
4983303 TTATAAGAAT
*
4983313 TTATTTAATTTAAAATAAAAAA
1 TTATTTAATTAAAAATAAAAAA
*
4983335 TTATTTGATTAAAAATAAAAA
1 TTATTTAATTAAAAATAAAAA
4983356 TATAAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
TTATTTAATTAAAAATAAAAAA
Found at i:4983363 original size:30 final size:29
Alignment explanation
Indices: 4983327--4983391 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
4983317 TTAATTTAAA
* * *
4983327 ATAAAAAATTATTTGATTAAAAATAAAAAT
1 ATAAAAAATTAATTAAAT-AAAATAAAAAT
* *
4983357 ATAAAAATTTAATTAAATATAATAAAAAT
1 ATAAAAAATTAATTAAATAAAATAAAAAT
4983386 ATAAAA
1 ATAAAA
4983392 TTTTATTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (29 bp):
ATAAAAAATTAATTAAATAAAATAAAAAT
Found at i:4987480 original size:15 final size:17
Alignment explanation
Indices: 4987447--4987488 Score: 61
Period size: 15 Copynumber: 2.5 Consensus size: 17
4987437 TAATAAAATA
4987447 TTTTATTATTCTTTCTCT
1 TTTTATT-TTCTTTCTCT
4987465 TTTTATTTT-TTT-TCT
1 TTTTATTTTCTTTCTCT
4987480 TTTTATTTT
1 TTTTATTTT
4987489 AAGCAGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.50
16 3 0.12
17 2 0.08
18 7 0.29
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTATTTTCTTTCTCT
Found at i:4990608 original size:3 final size:3
Alignment explanation
Indices: 4990600--4990625 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4990590 TTTATATAGT
4990600 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
4990626 CATTAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:5013323 original size:15 final size:16
Alignment explanation
Indices: 5013292--5013326 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5013282 ATAATTTTTT
*
5013292 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
5013308 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
5013323 AATT
1 AATT
5013327 CACATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:5013458 original size:11 final size:11
Alignment explanation
Indices: 5013439--5013482 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
5013429 AAATATATGA
5013439 ATAAATAAAAT
1 ATAAATAAAAT
* *
5013450 ATAATTAAAAA
1 ATAAATAAAAT
*
5013461 ATAACTAATAAT
1 ATAAATAA-AAT
5013473 ATAAATAAAA
1 ATAAATAAAA
5013483 ATTTTATCTC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
ATAAATAAAAT
Found at i:5013474 original size:23 final size:22
Alignment explanation
Indices: 5013438--5013483 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
5013428 AAAATATATG
*
5013438 AATAAATAAAATATAATTAAAA
1 AATAAATAAAATATAAATAAAA
*
5013460 AATAACTAATAATATAAATAAAA
1 AATAAATAA-AATATAAATAAAA
5013483 A
1 A
5013484 TTTTATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAATAAAATATAAATAAAA
Found at i:5014719 original size:2 final size:2
Alignment explanation
Indices: 5014712--5014759 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
5014702 CAGTGATGAA
5014712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5014754 AT AT AT
1 AT AT AT
5014760 TAAAAAGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5023503 original size:62 final size:62
Alignment explanation
Indices: 5023420--5023586 Score: 208
Period size: 62 Copynumber: 2.7 Consensus size: 62
5023410 ATAAATGTGC
* * *
5023420 GGAATACAAGGAACCCTTATGGACGGTTCTTAACTACAATATGCTTGATTATCAAAGGCTCA
1 GGAATACAAGGAATCCTTATGGACGGTTCTTAACTACAATATGCTTCATTAACAAAGGCTCA
* * * * * *
5023482 GGAATACAAAGAATCTTTATGGACGGTTCTTGACTACAATATGCTTCATTAACGAAGGTTTA
1 GGAATACAAGGAATCCTTATGGACGGTTCTTAACTACAATATGCTTCATTAACAAAGGCTCA
* ** * *
5023544 GGAATACAAGGAATCCTTACGGATAGCTCTTAATTACAATATG
1 GGAATACAAGGAATCCTTATGGACGGTTCTTAACTACAATATG
5023587 TTTTTTCCAA
Statistics
Matches: 88, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 88 1.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (62 bp):
GGAATACAAGGAATCCTTATGGACGGTTCTTAACTACAATATGCTTCATTAACAAAGGCTCA
Found at i:5024073 original size:19 final size:20
Alignment explanation
Indices: 5024029--5024073 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
5024019 TATCTATTTA
5024029 AAATAAA-ATTTTGTAATAT
1 AAATAAAGATTTTGTAATAT
5024048 AAA-AAAGATTTT-T-ATAT
1 AAATAAAGATTTTGTAATAT
5024065 AACATAAAG
1 AA-ATAAAG
5024074 TTTATAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 6 0.26
18 5 0.22
19 12 0.52
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
AAATAAAGATTTTGTAATAT
Found at i:5024184 original size:18 final size:18
Alignment explanation
Indices: 5024157--5024205 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5024147 TTTTTTATTG
5024157 AATAATAATAAATAAATAA
1 AATAA-AATAAATAAATAA
* *
5024176 AATAAAATAAGTAAATCA
1 AATAAAATAAATAAATAA
*
5024194 AATAAAAAAAAT
1 AATAAAATAAAT
5024206 GAGAGATGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 21 0.81
19 5 0.19
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (18 bp):
AATAAAATAAATAAATAA
Found at i:5025562 original size:2 final size:2
Alignment explanation
Indices: 5025555--5025581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5025545 GACTCACTAC
5025555 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 T
5025582 TCCTTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5041399 original size:6 final size:6
Alignment explanation
Indices: 5041383--5041417 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
5041373 TTAATGGAAT
5041383 TATAGAC TATAAC TATAAC TATAAC TATAAC TATA
1 TATA-AC TATAAC TATAAC TATAAC TATAAC TATA
5041418 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.49, C:0.14, G:0.03, T:0.34
Consensus pattern (6 bp):
TATAAC
Found at i:5053858 original size:73 final size:73
Alignment explanation
Indices: 5053768--5053911 Score: 227
Period size: 73 Copynumber: 2.0 Consensus size: 73
5053758 CATTTAATTG
* *
5053768 AGTCTTGCTCTAGAAAACATCAGCAAGCAAGAAAGCAAAGTAAAAACCACTCAAAAAAAAATCTT
1 AGTCTTGCTCTACAAAACATCAACAAGCAAGAAAGCAAAGTAAAAACCACTCAAAAAAAAATCTT
5053833 ACTCTAAA
66 ACTCTAAA
* * *
5053841 AGTCTTAG-TCTACAAAACATCAACAAGCAAGAAGGCAAAGTAAAACCCACTCAAAAAAAAGTCT
1 AGTCTT-GCTCTACAAAACATCAACAAGCAAGAAAGCAAAGTAAAAACCACTCAAAAAAAAATCT
5053905 TACTCTA
65 TACTCTA
5053912 GAAAACATCA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 64 0.98
74 1 0.02
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (73 bp):
AGTCTTGCTCTACAAAACATCAACAAGCAAGAAAGCAAAGTAAAAACCACTCAAAAAAAAATCTT
ACTCTAAA
Found at i:5054845 original size:17 final size:16
Alignment explanation
Indices: 5054817--5054858 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
5054807 ACATGGGAAA
*
5054817 ATATTCTTAAAATTATT
1 ATATT-TTAAAATAATT
5054834 GATATTTTAAAATAATT
1 -ATATTTTAAAATAATT
5054851 AT-TTTTAA
1 ATATTTTAA
5054859 TTTATTGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 2 0.09
17 10 0.43
18 5 0.22
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATTTTAAAATAATT
Found at i:5058998 original size:13 final size:13
Alignment explanation
Indices: 5058980--5059008 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5058970 TTGATTTGGT
5058980 GATCCAATGACCA
1 GATCCAATGACCA
5058993 GATCCAATGACCA
1 GATCCAATGACCA
5059006 GAT
1 GAT
5059009 ACTCCATAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (13 bp):
GATCCAATGACCA
Found at i:5059262 original size:23 final size:22
Alignment explanation
Indices: 5059215--5059279 Score: 58
Period size: 27 Copynumber: 2.7 Consensus size: 22
5059205 TGTTTTAATG
*
5059215 ATAAATTATTAATATTTTAAATAAA
1 ATAAATAATT-ATATTTT-AA-AAA
*
5059240 CTATAAATTATTAGTATTTTAAAAA
1 --ATAAATAATTA-TATTTTAAAAA
5059265 ATAAATAATTATATT
1 ATAAATAATTATATT
5059280 AAAGTTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 4 0.11
23 10 0.28
25 3 0.08
26 3 0.08
27 16 0.44
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
ATAAATAATTATATTTTAAAAA
Found at i:5060249 original size:20 final size:20
Alignment explanation
Indices: 5060212--5060249 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5060202 AACCCCCTCA
* *
5060212 CTCTCTTTCTTCCTTCGCAT
1 CTCTCTTTCCTCCCTCGCAT
5060232 CTCTCTTTCCTCCCTCGC
1 CTCTCTTTCCTCCCTCGC
5060250 CACTCCCTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.03, C:0.47, G:0.05, T:0.45
Consensus pattern (20 bp):
CTCTCTTTCCTCCCTCGCAT
Found at i:5072102 original size:16 final size:15
Alignment explanation
Indices: 5072077--5072112 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5072067 AATAATTTTT
*
5072077 AAATTTTTAAAAATTA
1 AAATTATTAAAAA-TA
5072093 AAATTATTAAAAATA
1 AAATTATTAAAAATA
5072108 AAATT
1 AAATT
5072113 CACATAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAATTATTAAAAATA
Found at i:5072112 original size:21 final size:21
Alignment explanation
Indices: 5072086--5072131 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5072076 TAAATTTTTA
* *
5072086 AAAATTAAAATTATTAAAAAT
1 AAAATTAAAATAATAAAAAAT
* *
5072107 AAAATTCACATAATAAAAAAT
1 AAAATTAAAATAATAAAAAAT
5072128 AAAA
1 AAAA
5072132 AATCATGACA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAATTAAAATAATAAAAAAT
Found at i:5072263 original size:4 final size:4
Alignment explanation
Indices: 5072256--5072296 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
5072246 GAATTAAAAA
5072256 AAAT AAAT --AT AAAT -AAT AATAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAA
5072297 AAACTTTACT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 2 0.06
3 3 0.09
4 24 0.73
5 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:5077517 original size:15 final size:16
Alignment explanation
Indices: 5077481--5077515 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5077471 TGAGAAAATA
5077481 TTTTAAAATATTAATT
1 TTTTAAAATATTAATT
5077497 TTTTAAAATAATT-ATT
1 TTTTAAAAT-ATTAATT
5077513 TTT
1 TTT
5077516 AATTTATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTTAAAATATTAATT
Found at i:5078370 original size:9 final size:9
Alignment explanation
Indices: 5078358--5078406 Score: 71
Period size: 9 Copynumber: 5.4 Consensus size: 9
5078348 CCATGACGAT
5078358 GACGATGAC
1 GACGATGAC
5078367 GACGATGAC
1 GACGATGAC
5078376 GACGATGAC
1 GACGATGAC
*
5078385 GACGACGAC
1 GACGATGAC
* *
5078394 GAGGACGAC
1 GACGATGAC
5078403 GACG
1 GACG
5078407 CCGCCCTTGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.37, T:0.06
Consensus pattern (9 bp):
GACGATGAC
Found at i:5078370 original size:15 final size:15
Alignment explanation
Indices: 5078350--5078406 Score: 69
Period size: 15 Copynumber: 3.8 Consensus size: 15
5078340 GATGATGGCC
* *
5078350 ATGACGATGACGATG
1 ATGACGACGACGACG
* *
5078365 ACGACGATGACGACG
1 ATGACGACGACGACG
5078380 ATGACGACGACGACG
1 ATGACGACGACGACG
*
5078395 AGGACGACGACG
1 ATGACGACGACG
5078407 CCGCCCTTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.33, C:0.23, G:0.35, T:0.09
Consensus pattern (15 bp):
ATGACGACGACGACG
Found at i:5078393 original size:6 final size:6
Alignment explanation
Indices: 5078352--5078406 Score: 65
Period size: 6 Copynumber: 9.2 Consensus size: 6
5078342 TGATGGCCAT
* * * * *
5078352 GACGAT GACGAT GACGAC GATGAC GACGAT GACGAC GACGAC GAGGAC
1 GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC GACGAC
5078400 GACGAC G
1 GACGAC G
5078407 CCGCCCTTGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.33, C:0.24, G:0.36, T:0.07
Consensus pattern (6 bp):
GACGAC
Found at i:5080277 original size:33 final size:34
Alignment explanation
Indices: 5080231--5080302 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
5080221 ATAATATATA
* * *
5080231 ATATAAGAAATTATATTAAGAATTGAAAATAAAAT
1 ATATAAG-AATTATAATAAGAAATAAAAATAAAAT
5080266 ATATAAG-ATTATAATAAGAAATAAAAATAAAAT
1 ATATAAGAATTATAATAAGAAATAAAAATAAAAT
5080299 ATAT
1 ATAT
5080303 GACATTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 27 0.79
35 7 0.21
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (34 bp):
ATATAAGAATTATAATAAGAAATAAAAATAAAAT
Found at i:5080537 original size:15 final size:15
Alignment explanation
Indices: 5080517--5080546 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5080507 TATTATCTTT
5080517 CTTACAATCATATTA
1 CTTACAATCATATTA
5080532 CTTACAATCATATTA
1 CTTACAATCATATTA
5080547 TCACATTGCA
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:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (15 bp):
CTTACAATCATATTA
Found at i:5082590 original size:14 final size:15
Alignment explanation
Indices: 5082560--5082592 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5082550 AAACATTAAT
5082560 ATTTTTTATATATTA
1 ATTTTTTATATATTA
*
5082575 ATTTTTTATTTA-TA
1 ATTTTTTATATATTA
5082589 ATTT
1 ATTT
5082593 CAACAAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTTTATATATTA
Found at i:5083511 original size:10 final size:11
Alignment explanation
Indices: 5083489--5083526 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5083479 CAGGGTATGG
5083489 TGTTTTTTGTT
1 TGTTTTTTGTT
5083500 TGTTTTTT-TT
1 TGTTTTTTGTT
**
5083510 TGTTTTCGGTT
1 TGTTTTTTGTT
5083521 TGTTTT
1 TGTTTT
5083527 GTGGATGTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (11 bp):
TGTTTTTTGTT
Found at i:5084186 original size:3 final size:3
Alignment explanation
Indices: 5084180--5084209 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
5084170 AGAAATAATA
5084180 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
5084210 GTATATAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:5092147 original size:24 final size:22
Alignment explanation
Indices: 5092103--5092147 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5092093 GTATAATAAT
* *
5092103 TTTTAAAAATTGAATTTTTATA
1 TTTTAAAAATTGAAATATTATA
5092125 TTTTATAAAATTGATAATATTAT
1 TTTTA-AAAATTGA-AATATTAT
5092148 CTTAATGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 8 0.42
24 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTTAAAAATTGAAATATTATA
Found at i:5098708 original size:6 final size:6
Alignment explanation
Indices: 5098697--5098730 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
5098687 CAGGCCCACA
*
5098697 AATGGG AATGGG AATGGG AATGGG ACTGGG AATG
1 AATGGG AATGGG AATGGG AATGGG AATGGG AATG
5098731 ATGGAGTGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.32, C:0.03, G:0.47, T:0.18
Consensus pattern (6 bp):
AATGGG
Found at i:5102184 original size:3 final size:3
Alignment explanation
Indices: 5102176--5102200 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5102166 AGGAAATTAA
5102176 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5102201 GGTGGAGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5103065 original size:2 final size:2
Alignment explanation
Indices: 5103058--5103083 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5103048 GAAAGAAAGG
5103058 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5103084 CAGCTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5105731 original size:2 final size:2
Alignment explanation
Indices: 5105724--5105749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5105714 TTTTATTTCT
5105724 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
5105750 AATCCCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5113323 original size:29 final size:30
Alignment explanation
Indices: 5113268--5113327 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
5113258 TTTAAAAAAA
*
5113268 TTATTTTTTATTACATTCAATTAAAATTTT
1 TTATTTTTTATTAAATTCAATTAAAATTTT
*
5113298 TTATTTTTATCTTAAATT-AATT-AAATTTT
1 TTATTTTT-TATTAAATTCAATTAAAATTTT
5113327 T
1 T
5113328 ATTAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 12 0.44
31 7 0.26
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (30 bp):
TTATTTTTTATTAAATTCAATTAAAATTTT
Found at i:5113333 original size:15 final size:15
Alignment explanation
Indices: 5113313--5113348 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
5113303 TTTATCTTAA
5113313 ATTAATTAAATTTTT
1 ATTAATTAAATTTTT
5113328 ATTAATTAAATTTTT
1 ATTAATTAAATTTTT
5113343 ATTAAT
1 ATTAAT
5113349 ATTTTAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTAATTAAATTTTT
Found at i:5113560 original size:16 final size:18
Alignment explanation
Indices: 5113536--5113590 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
5113526 TTTTAAAATA
*
5113536 TTATGACTTT-TTTATT-
1 TTATAACTTTCTTTATTC
*
5113552 TTATAACTTTCTTTGTTC
1 TTATAACTTTCTTTATTC
5113570 TTATACACTTTCATTT-TTC
1 TTATA-ACTTTC-TTTATTC
5113589 TT
1 TT
5113591 TATTACATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 9 0.27
17 5 0.15
18 5 0.15
19 11 0.33
20 3 0.09
ACGTcount: A:0.18, C:0.15, G:0.04, T:0.64
Consensus pattern (18 bp):
TTATAACTTTCTTTATTC
Found at i:5115522 original size:22 final size:22
Alignment explanation
Indices: 5115475--5115522 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
5115465 AAAATTTTAT
* * *
5115475 CTTTCTTCTTATTCCTTTGTTC
1 CTTTCTTCTGATGCCTTTGTAC
5115497 CTTTCTTCTGATGCCTTT-TAC
1 CTTTCTTCTGATGCCTTTGTAC
5115518 GCTTT
1 -CTTT
5115523 ATGCAGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 2 0.09
22 20 0.91
ACGTcount: A:0.06, C:0.27, G:0.08, T:0.58
Consensus pattern (22 bp):
CTTTCTTCTGATGCCTTTGTAC
Found at i:5121802 original size:3 final size:3
Alignment explanation
Indices: 5121794--5121824 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5121784 AAGTTTAAAT
5121794 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
5121825 ATTTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5137526 original size:87 final size:85
Alignment explanation
Indices: 5137355--5137643 Score: 326
Period size: 87 Copynumber: 3.3 Consensus size: 85
5137345 ATAAAAAAAT
* *
5137355 TTGAGAAAAAACCTAGTTATACTCAATATGTTGTGATTGAGGTAAGAATAAGAAGGCTATATTTA
1 TTGAGAAAAAACCTAATTATACTCAGTATGTTGTGATTGA-G---G--TAAGAAGGCTATATTTA
*
5137420 TAAGTAGAGGACCAAAATAAAGGGAG
60 TAAGCAGAGGACCAAAATAAAGGGAG
** * *
5137446 TTGAGAAAAAGGCTAGTTATACTCAGTGTATGTTGTGATTGAGGTAAGAAGGCTATATTTATAAA
1 TTGAGAAAAAACCTAATTATACTCA--GTATGTTGTGATTGAGGTAAGAAGGCTATATTTATAAG
* ***
5137511 CAGATGACCAAAATAAAAAAAG
64 CAGAGGACCAAAATAAAGGGAG
* * * *
5137533 TTAAGAAAAAACTTAATTATACTCAACGTATGTTGTGGTTGAGGTAAGAAGACTATATTTATAAG
1 TTGAGAAAAAACCTAATTATACTC-A-GTATGTTGTGATTGAGGTAAGAAGGCTATATTTATAAG
* *
5137598 CAGAGGATCAAAATCAAGGGAG
64 CAGAGGACCAAAATAAAGGGAG
*
5137620 TTGAAAAAAAACCTAATTATACTC
1 TTGAGAAAAAACCTAATTATACTC
5137644 TGTAAGGTAC
Statistics
Matches: 168, Mismatches: 27, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
87 128 0.76
88 1 0.01
89 1 0.01
91 23 0.14
92 1 0.01
93 14 0.08
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (85 bp):
TTGAGAAAAAACCTAATTATACTCAGTATGTTGTGATTGAGGTAAGAAGGCTATATTTATAAGCA
GAGGACCAAAATAAAGGGAG
Done.