Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 30 of 31
Found at i:13691750 original size:28 final size:28
Alignment explanation
Indices: 13691710--13691876 Score: 147
Period size: 28 Copynumber: 5.7 Consensus size: 28
13691700 CAGCTTTAAC
13691710 ATGTTTGTCTTAATTTAGACAA-AAAAA
1 ATGTTTGTCTTAATTTAGACAAGAAAAA
* *
13691737 ATGTTTGGTCTTAATTTAGATAAGAAAAT
1 ATGTTT-GTCTTAATTTAGACAAGAAAAA
13691766 ATGTTTGTCTTAATTTAAGACAAGAAAAA
1 ATGTTTGTCTTAATTT-AGACAAGAAAAA
* * * * * *
13691795 TATTTTTTGTCTGAATCTAAATAAGAAAAC
1 -A-TGTTTGTCTTAATTTAGACAAGAAAAA
* *
13691825 ATATTTGTCTTAATTTAGATACAATAAAATA
1 ATGTTTGTCTTAATTTAG--ACAAGAAAA-A
* *
13691856 TTTTTTGTCTTAATTATAGAC
1 ATGTTTGTCTTAATT-TAGAC
13691877 GAGAGTTGTC
Statistics
Matches: 112, Mismatches: 19, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
27 6 0.05
28 38 0.34
29 21 0.19
30 19 0.17
31 25 0.22
32 3 0.03
ACGTcount: A:0.40, C:0.07, G:0.11, T:0.41
Consensus pattern (28 bp):
ATGTTTGTCTTAATTTAGACAAGAAAAA
Found at i:13691829 original size:31 final size:31
Alignment explanation
Indices: 13691761--13691830 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
13691751 TTTAGATAAG
* * *
13691761 AAAATA-TGTTTGTCTTAATTTAAGACAAGA
1 AAAATATTTTTTGTCTGAATCTAAGACAAGA
*
13691791 AAAATATTTTTTGTCTGAATCTAA-ATAAGA
1 AAAATATTTTTTGTCTGAATCTAAGACAAGA
13691821 AAACATATTT
1 AAA-ATATTT
13691831 GTCTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.39
Consensus pattern (31 bp):
AAAATATTTTTTGTCTGAATCTAAGACAAGA
Found at i:13691832 original size:59 final size:58
Alignment explanation
Indices: 13691707--13691865 Score: 205
Period size: 59 Copynumber: 2.7 Consensus size: 58
13691697 TAACAGCTTT
* * * * *
13691707 AACATGTTTGTCTTAATTT-AGACAAAAAAA-ATGTTTGGTCTTAATTTAGATAAGAA
1 AACATGTTTGTCTTAATTTAAGACAAAAAAATATTTTTTGTCTGAATCTAAATAAGAA
*
13691763 AATATGTTTGTCTTAATTTAAGACAAGAAAAATATTTTTTGTCTGAATCTAAATAAGAA
1 AACATGTTTGTCTTAATTTAAGACAA-AAAAATATTTTTTGTCTGAATCTAAATAAGAA
* * *
13691822 AACATATTTGTCTTAATTTAGATACAATAAAATATTTTTTGTCT
1 AACATGTTTGTCTTAATTTA-AGACAAAAAAATATTTTTTGTCT
13691866 TAATTATAGA
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
56 18 0.20
57 6 0.07
58 5 0.06
59 55 0.62
60 5 0.06
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (58 bp):
AACATGTTTGTCTTAATTTAAGACAAAAAAATATTTTTTGTCTGAATCTAAATAAGAA
Found at i:13692044 original size:17 final size:17
Alignment explanation
Indices: 13692022--13692054 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13692012 ATAATAATAA
13692022 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
13692039 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
13692055 TTATCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:13695283 original size:19 final size:21
Alignment explanation
Indices: 13695261--13695302 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 21
13695251 ATAAGTGAAA
13695261 ATTTTTA-AAATAAAAT-AAT
1 ATTTTTATAAATAAAATAAAT
*
13695280 A-TTTTATTAATAAAATAAAT
1 ATTTTTATAAATAAAATAAAT
13695300 ATT
1 ATT
13695303 AAAATATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 4 0.21
21 1 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATTTTTATAAATAAAATAAAT
Found at i:13710216 original size:25 final size:25
Alignment explanation
Indices: 13710188--13710237 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
13710178 TAGTTAAAGC
*
13710188 TTATAAATGTGTCAATTGATCACAA
1 TTATAAATGTGCCAATTGATCACAA
* *
13710213 TTATGAATGTGCCACTTGATCACAA
1 TTATAAATGTGCCAATTGATCACAA
13710238 ACTAATCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (25 bp):
TTATAAATGTGCCAATTGATCACAA
Found at i:13722115 original size:23 final size:22
Alignment explanation
Indices: 13722070--13722115 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
13722060 TAATGAGTTA
* * *
13722070 TTGTGATGGAATTGTGATGATT
1 TTGTGATAGAATTATGATAATT
13722092 TTGTGATAGAATTAATGATAATT
1 TTGTGATAGAATT-ATGATAATT
13722115 T
1 T
13722116 GTTTTTGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.46
Consensus pattern (22 bp):
TTGTGATAGAATTATGATAATT
Found at i:13746362 original size:39 final size:40
Alignment explanation
Indices: 13746318--13746400 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
13746308 GCATTATGAA
*
13746318 AACACCAATCATGG-AGAGGCT-AG-AAATCCCATTAAGGTG
1 AACACCAATCATGGCA-AGG-TAAGAAAACCCCATTAAGGTG
* *
13746357 AACACCAATCTTGGCAATGTAAGAAAACCCCATTAAGGTG
1 AACACCAATCATGGCAAGGTAAGAAAACCCCATTAAGGTG
13746397 AACA
1 AACA
13746401 GTAGCCAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
38 1 0.03
39 17 0.45
40 20 0.53
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (40 bp):
AACACCAATCATGGCAAGGTAAGAAAACCCCATTAAGGTG
Found at i:13753890 original size:73 final size:73
Alignment explanation
Indices: 13753739--13753893 Score: 188
Period size: 73 Copynumber: 2.1 Consensus size: 73
13753729 CAGACAAAAT
* * * * * * *
13753739 GCTCTTAGTCGACTAACATGCTTCTTAGTCGATTAAGTCATTTTTGTTTTCTGATCTCAGCTTTT
1 GCTCTTAGTCGACTAAAATGCTTCTTAGTCGATTAAGTCATCTTTGTTCTCTAAACCCAGATTTT
*
13753804 AGCAATGA
66 AGCAATAA
* *
13753812 CCTCTTAGTCGACTAATAATGCTTCTTAGTCGATTAAGTCGTCTTTG-TCTCTAAACCCA-ATTT
1 GCTCTTAGTCGACTAA-AATGCTTCTTAGTCGATTAAGTCATCTTTGTTCTCTAAACCCAGATTT
13753875 CTAGCAATAA
65 -TAGCAATAA
13753885 GCTCTTAGT
1 GCTCTTAGT
13753894 TAACTAACAA
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
72 3 0.04
73 39 0.57
74 27 0.39
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (73 bp):
GCTCTTAGTCGACTAAAATGCTTCTTAGTCGATTAAGTCATCTTTGTTCTCTAAACCCAGATTTT
AGCAATAA
Found at i:13775068 original size:2 final size:2
Alignment explanation
Indices: 13775063--13775092 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13775053 TCTTTATATA
13775063 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
13775093 GCATTCTTGA
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:13776976 original size:13 final size:13
Alignment explanation
Indices: 13776960--13776984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13776950 TCTAATATGG
13776960 ATTTAATTAAATT
1 ATTTAATTAAATT
13776973 ATTTAATTAAAT
1 ATTTAATTAAAT
13776985 GAAAAGATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAATTAAATT
Found at i:13784606 original size:7 final size:7
Alignment explanation
Indices: 13784594--13784618 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
13784584 AGTGCCTAAG
13784594 TGCCGAC
1 TGCCGAC
13784601 TGCCGAC
1 TGCCGAC
13784608 TGCCGAC
1 TGCCGAC
13784615 TGCC
1 TGCC
13784619 AAACCCAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.44, G:0.28, T:0.16
Consensus pattern (7 bp):
TGCCGAC
Found at i:13785643 original size:14 final size:14
Alignment explanation
Indices: 13785619--13785650 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
13785609 TATATATAAT
13785619 ATAATTAT-TTTT-
1 ATAATTATATTTTA
13785631 ATAATTATATTTTA
1 ATAATTATATTTTA
13785645 ATAATT
1 ATAATT
13785651 TTTCAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 4 0.22
14 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATAATTATATTTTA
Found at i:13787552 original size:27 final size:27
Alignment explanation
Indices: 13787482--13787725 Score: 150
Period size: 27 Copynumber: 9.4 Consensus size: 27
13787472 GCTATGTTTT
*
13787482 AAAATTTAGTTGTTACACGTTATGTTAA
1 AAAATTTAGTTATTACACGTTATGTT-A
* * * *
13787510 AAAATATAATTGTTACATGTTATGTTA
1 AAAATTTAGTTATTACACGTTATGTTA
* * *
13787537 AAAGTTTAGTTATTACATGTCATGTTA
1 AAAATTTAGTTATTACACGTTATGTTA
* * * *
13787564 AAGATTCAGTTATTATACGCTATGTTA
1 AAAATTTAGTTATTACACGTTATGTTA
* * *
13787591 AAAATTTAGTTGTTATA--TAATG-T-
1 AAAATTTAGTTATTACACGTTATGTTA
* * *
13787614 --AA-TT-GTT-GTACA--TCATGTTG
1 AAAATTTAGTTATTACACGTTATGTTA
* *
13787634 AAAATTTAGTTATTACAAGTCATGTTA
1 AAAATTTAGTTATTACACGTTATGTTA
** *
13787661 AAAATTTAGTTATTACATATCATGTTA
1 AAAATTTAGTTATTACACGTTATGTTA
* * * *
13787688 AAAATATAGCTGTTACACGCTATGTTA
1 AAAATTTAGTTATTACACGTTATGTTA
*
13787715 AAGATTTAGTT
1 AAAATTTAGTT
13787726 TAAAATTTTA
Statistics
Matches: 170, Mismatches: 37, Indels: 19
0.75 0.16 0.08
Matches are distributed among these distances:
18 7 0.04
19 4 0.02
20 2 0.01
21 2 0.01
22 2 0.01
23 2 0.01
24 4 0.02
25 7 0.04
27 117 0.69
28 23 0.14
ACGTcount: A:0.36, C:0.07, G:0.14, T:0.43
Consensus pattern (27 bp):
AAAATTTAGTTATTACACGTTATGTTA
Found at i:13787795 original size:27 final size:27
Alignment explanation
Indices: 13787749--13787840 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
13787739 GCTATACGTT
* *
13787749 ATGTTAAAAAATATAGTTGTTACATGTC
1 ATGTT-AAAAATTTAGTTGTTACATATC
* * *
13787777 ATGTTGAAGATTTAGTTGTTACATATT
1 ATGTTAAAAATTTAGTTGTTACATATC
* *
13787804 ATGTTAAAAATTTAGTTATTATATA-C
1 ATGTTAAAAATTTAGTTGTTACATATC
13787830 GATGTTAAAAA
1 -ATGTTAAAAA
13787841 ATGCAGTTAT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
27 48 0.91
28 5 0.09
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.42
Consensus pattern (27 bp):
ATGTTAAAAATTTAGTTGTTACATATC
Found at i:13791708 original size:27 final size:27
Alignment explanation
Indices: 13791671--13791728 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
13791661 CTTTTGGCAG
* *
13791671 TAAC-AAATGAACTATGTATCATCACA
1 TAACAAAATGAACCATATATCATCACA
13791697 TAACAAAATGAACCATATATCATCACA
1 TAACAAAATGAACCATATATCATCACA
13791724 TAACA
1 TAACA
13791729 TAGAGGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (27 bp):
TAACAAAATGAACCATATATCATCACA
Found at i:13792019 original size:357 final size:359
Alignment explanation
Indices: 13791358--13792059 Score: 1192
Period size: 357 Copynumber: 1.9 Consensus size: 359
13791348 GCTCCCACCA
* * * *
13791358 ACATAACATAGAGGGTAACTCCACAGGACCATACATCTGCCAACTGTAAAAGAAAAGACATCACT
1 ACATAACATAGAGGGTAACTCCACAGGACCATAAATCTCCCAACCGTAAAAGAAAAGACATAACT
* * *
13791423 TGAGGTCAACAAACTTTTATATGTTACAAATTAGATCTAATTAATTTTGGAATTTATACATCAAA
66 TGAGGTCAACAAACTTTTACATGTTACAAATTAGATCTAATTAATTTTCGAATATATACATCAAA
** *
13791488 TTAGAAGGAAAAGTGGTTAGGGCGGGGAGGGTTTAGGGTTGACAATTTATTGTATAATTTAAGTA
131 TTAGAAGGAAAAGTGG-T-CCGAGGGGAGGG--TAGGGTTGACAATTTATTGTATAATTTAAGTA
* * * *
13791553 AAAAACATTTGATGGAATGATATTCATGGTCAGAAAGAAGGTGACTTCACCATAAAAGTGGAAGC
192 AAAAACATTTGATGGAATGATATTAATGGTCAGAAACAAGATGACTTCACCATAAAAGCGGAAGC
13791618 AGATCCCAAAAGACAAAGGTGTTTGACAAGCAAATGTCAAATACTTTTGGCAGTAACAAATGAAC
257 AGATCCCAAAAGACAAAGGTGTTTGACAAGCAAATGTCAAATACTTTTGGCAGTAACAAATGAAC
*
13791683 TATGTATCATCACATAACAAAATGAACCATATATCATC
322 TATATATCATCACATAACAAAATGAACCATATATCATC
13791721 ACATAACATAGAGGGTAACTCCACAGGACCATAAATCTCCCAACCGTAAAAGAAAAGACATAACT
1 ACATAACATAGAGGGTAACTCCACAGGACCATAAATCTCCCAACCGTAAAAGAAAAGACATAACT
13791786 TGAGGTCAACAAACTTTTACATGTTACAAATTAGATCTAATTAATTTTCGAATATATACATCAAA
66 TGAGGTCAACAAACTTTTACATGTTACAAATTAGATCTAATTAATTTTCGAATATATACATCAAA
** *
13791851 TTAGAAGTTAAAGTGG-CCGAGGGGAGGG-GGGGTTGACAATTTATTGTATAATTTAAGTAAAAA
131 TTAGAAGGAAAAGTGGTCCGAGGGGAGGGTAGGGTTGACAATTTATTGTATAATTTAAGTAAAAA
13791914 ACATTTGATGGAATGATATTAATGGTCAGAAACAAGATGACTTCACCATAAAAGCGGAAGCAGAT
196 ACATTTGATGGAATGATATTAATGGTCAGAAACAAGATGACTTCACCATAAAAGCGGAAGCAGAT
13791979 CCCAAAAGACAAAGGTGTTTGACAAGCAAATGTCAAATACTTTTGGCAGTAACAAATGAACTATA
261 CCCAAAAGACAAAGGTGTTTGACAAGCAAATGTCAAATACTTTTGGCAGTAACAAATGAACTATA
13792044 TATCATCACATAACAA
326 TATCATCACATAACAA
13792060 GACGCAGCCA
Statistics
Matches: 321, Mismatches: 18, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
357 175 0.55
360 9 0.03
363 137 0.43
ACGTcount: A:0.41, C:0.15, G:0.18, T:0.26
Consensus pattern (359 bp):
ACATAACATAGAGGGTAACTCCACAGGACCATAAATCTCCCAACCGTAAAAGAAAAGACATAACT
TGAGGTCAACAAACTTTTACATGTTACAAATTAGATCTAATTAATTTTCGAATATATACATCAAA
TTAGAAGGAAAAGTGGTCCGAGGGGAGGGTAGGGTTGACAATTTATTGTATAATTTAAGTAAAAA
ACATTTGATGGAATGATATTAATGGTCAGAAACAAGATGACTTCACCATAAAAGCGGAAGCAGAT
CCCAAAAGACAAAGGTGTTTGACAAGCAAATGTCAAATACTTTTGGCAGTAACAAATGAACTATA
TATCATCACATAACAAAATGAACCATATATCATC
Found at i:13796308 original size:167 final size:166
Alignment explanation
Indices: 13796006--13796332 Score: 537
Period size: 167 Copynumber: 2.0 Consensus size: 166
13795996 AAGGTAAAAA
* * * *
13796006 TTTGGGAGCAACTGGAGTTGGTTTTGGTTGTTTAATCTTGGTGCAAAGTTCATATAAAAATTTAG
1 TTTGGGAGCAACTGGAATTGGTCTTAGTTGTTTAATCTTGGTGCAAAGTTCAGATAAAAATTTAG
* *
13796071 AAAACTTATTTCAGCATTCTAGATAGCAGCTTCTTCATGTAATTGGTACATGTTAGAGGACTCCA
66 AAAACTTATTTCAGCATTCTAAATAGCAACTTCTTCATGTAATTGGTACATGTTAGAGGACTCCA
13796136 ATGGCTATGAAATAAAACTAGTGAATGTTCTTAATT
131 ATGGCTATGAAATAAAACTAGTGAATGTTCTTAATT
*
13796172 TTTGGAGAGCAATTGGAATTGGTCTTAGTTGTTTAATCTTGGTGCAAAGTTCAGATAAAAATTTA
1 TTTGG-GAGCAACTGGAATTGGTCTTAGTTGTTTAATCTTGGTGCAAAGTTCAGATAAAAATTTA
* * *
13796237 GAAAATTTATTTCAGCATTCTAAATAGCAACTTCTTTATGTAATTGTTACATGTTAGAGGACTCC
65 GAAAACTTATTTCAGCATTCTAAATAGCAACTTCTTCATGTAATTGGTACATGTTAGAGGACTCC
* *
13796302 AATGGCTATGAAATTAAACTAGTGGATGTTC
130 AATGGCTATGAAATAAAACTAGTGAATGTTC
13796333 CTAACATTTA
Statistics
Matches: 148, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
166 5 0.03
167 143 0.97
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (166 bp):
TTTGGGAGCAACTGGAATTGGTCTTAGTTGTTTAATCTTGGTGCAAAGTTCAGATAAAAATTTAG
AAAACTTATTTCAGCATTCTAAATAGCAACTTCTTCATGTAATTGGTACATGTTAGAGGACTCCA
ATGGCTATGAAATAAAACTAGTGAATGTTCTTAATT
Found at i:13797684 original size:23 final size:24
Alignment explanation
Indices: 13797639--13797684 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
13797629 TTTGTCTTTC
13797639 TTTTCTTCTTTAAAATTAATAGCTA
1 TTTTCTTCTTTAAAATT-ATAGCTA
13797664 TTTTCTT-TTATAAAATT-TAGC
1 TTTTCTTCTT-TAAAATTATAGC
13797685 CAAGAACGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 2 0.10
25 14 0.70
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTTCTTCTTTAAAATTATAGCTA
Found at i:13798195 original size:28 final size:27
Alignment explanation
Indices: 13798163--13798313 Score: 126
Period size: 28 Copynumber: 5.3 Consensus size: 27
13798153 ATTAAGACAA
*
13798163 AAATAT-TTTATCTTATCTAAATTGAAGC
1 AAATATGTTT-TCTTGTCTAAATT-AAGC
*
13798191 AAATATGTTTTCTTGTCTAGATTAAGAC
1 AAATATGTTTTCTTGTCTAAATTAAG-C
* *
13798219 AAAATAT-TTTTTTTGTCTTAAATTAAGA
1 -AAATATGTTTTCTTGTC-TAAATTAAGC
* *
13798247 AACACATATTTTCTTGTCTAAATTAAGAC
1 AA-ATATGTTTTCTTGTCTAAATTAAG-C
* * *
13798276 AAAAAATGTTTTCTTATCTAAATTAAAAC
1 -AAATATGTTTTCTTGTCTAAATT-AAGC
13798305 AAATATGTT
1 AAATATGTT
13798314 AAAGCTTCCA
Statistics
Matches: 101, Mismatches: 13, Indels: 18
0.77 0.10 0.14
Matches are distributed among these distances:
27 5 0.05
28 47 0.47
29 45 0.45
30 4 0.04
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (27 bp):
AAATATGTTTTCTTGTCTAAATTAAGC
Found at i:13798241 original size:57 final size:55
Alignment explanation
Indices: 13798141--13798313 Score: 193
Period size: 57 Copynumber: 3.0 Consensus size: 55
13798131 TTTAAGATAA
*
13798141 TTCTTGTCTTTAATTAAGACAAAAATATTTTATCTTATCTAAATTGAAGCAAATATGTT
1 TTCTTGTC-TAAATTAAGAC-AAAATATTTT-TCTTATCTAAATT-AAGCAAATATGTT
* * * * * *
13798200 TTCTTGTCTAGATTAAGACAAAATATTTTTTTTGTCTTAAATTAAGAAACACATATT
1 TTCTTGTCTAAATTAAGACAAAATATTTTTCTTATC-TAAATTAAGCAA-ATATGTT
* *
13798257 TTCTTGTCTAAATTAAGACAAAAAATGTTTTCTTATCTAAATTAAAACAAATATGTT
1 TTCTTGTCTAAATTAAGACAAAATAT-TTTTCTTATCTAAATT-AAGCAAATATGTT
13798314 AAAGCTTCCA
Statistics
Matches: 95, Mismatches: 15, Indels: 10
0.79 0.12 0.08
Matches are distributed among these distances:
56 10 0.11
57 56 0.59
58 21 0.22
59 8 0.08
ACGTcount: A:0.39, C:0.10, G:0.08, T:0.43
Consensus pattern (55 bp):
TTCTTGTCTAAATTAAGACAAAATATTTTTCTTATCTAAATTAAGCAAATATGTT
Found at i:13798243 original size:29 final size:28
Alignment explanation
Indices: 13798141--13798307 Score: 162
Period size: 29 Copynumber: 5.8 Consensus size: 28
13798131 TTTAAGATAA
*
13798141 TTCTTGTCTTTAATTAAGACAAAAATATTT
1 TTCTTGTC-TAAATTAAGAC-AAAATATTT
*
13798171 TATCTTATCTAAATTGAAG-C-AAATATGTT
1 T-TCTTGTCTAAATT-AAGACAAAATAT-TT
*
13798200 TTCTTGTCTAGATTAAGACAAAATATTT
1 TTCTTGTCTAAATTAAGACAAAATATTT
*
13798228 TTTTTGTCTTAAATTAAGA-AACACATA-TT
1 TTCTTGTC-TAAATTAAGACAA-A-ATATTT
*
13798257 TTCTTGTCTAAATTAAGACAAAAAATGTT
1 TTCTTGTCTAAATTAAGACAAAATAT-TT
* *
13798286 TTCTTATCTAAATTAAAACAAA
1 TTCTTGTCTAAATTAAGACAAA
13798308 TATGTTAAAG
Statistics
Matches: 116, Mismatches: 10, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.04
28 40 0.34
29 52 0.45
30 10 0.09
31 9 0.08
ACGTcount: A:0.40, C:0.11, G:0.08, T:0.42
Consensus pattern (28 bp):
TTCTTGTCTAAATTAAGACAAAATATTT
Found at i:13803392 original size:37 final size:37
Alignment explanation
Indices: 13803309--13803395 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
13803299 GGCTGTTCAA
*
13803309 CAGAGTCAAATCATGCACGGTCTCGAAGCAACTAGTG
1 CAGAGTCAAATCATGCACGATCTCGAAGCAACTAGTG
* * * * *
13803346 GAGAGTCAAATCATGCATGATGTCGAAGCAATTGGTG
1 CAGAGTCAAATCATGCACGATCTCGAAGCAACTAGTG
13803383 CAG-GTTCAAATCA
1 CAGAG-TCAAATCA
13803396 CGCTAAGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
36 1 0.02
37 41 0.98
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (37 bp):
CAGAGTCAAATCATGCACGATCTCGAAGCAACTAGTG
Found at i:13805008 original size:71 final size:72
Alignment explanation
Indices: 13804921--13805057 Score: 195
Period size: 71 Copynumber: 1.9 Consensus size: 72
13804911 TGTTCCAATG
* * *
13804921 CTTCCTTTTAGCTCACGGGTGGACATTTATCAATAGTTATCATGAATCTATTGATAGATGTTCTT
1 CTTCCTTTTAGCTCACGGGTAGACATTTATCAATAGTTACCATGAATCTATTGATAAATGTTCTT
13804986 TAGTTGC
66 TAGTTGC
* * * * *
13804993 CTTCCTTTTA-TTCACGTGTAGACATTTATCTATCGTTGCCATGAATCTATTGATAAATGTTCTT
1 CTTCCTTTTAGCTCACGGGTAGACATTTATCAATAGTTACCATGAATCTATTGATAAATGTTCTT
13805057 T
66 T
13805058 GATTGGTACC
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
71 47 0.82
72 10 0.18
ACGTcount: A:0.23, C:0.18, G:0.15, T:0.44
Consensus pattern (72 bp):
CTTCCTTTTAGCTCACGGGTAGACATTTATCAATAGTTACCATGAATCTATTGATAAATGTTCTT
TAGTTGC
Found at i:13811490 original size:4 final size:4
Alignment explanation
Indices: 13811483--13811509 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13811473 TATTAATATA
13811483 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
13811510 AATGTTAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:13813818 original size:22 final size:22
Alignment explanation
Indices: 13813790--13813831 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
13813780 TAAATAAATA
13813790 AATAAAAACATAACTCAAAAGG
1 AATAAAAACATAACTCAAAAGG
* *
13813812 AATAAAACCATAGCTCAAAA
1 AATAAAAACATAACTCAAAA
13813832 AAAATTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.17, G:0.07, T:0.14
Consensus pattern (22 bp):
AATAAAAACATAACTCAAAAGG
Found at i:13819846 original size:66 final size:67
Alignment explanation
Indices: 13819766--13819895 Score: 192
Period size: 67 Copynumber: 2.0 Consensus size: 67
13819756 TTACAATAGC
* *
13819766 TTTTCACAAGCTCAACCATAACCTTTAA-CATGGTTTGTCACGGGATCAACCAAAACCCAAAATG
1 TTTTCACAAGCTCAACCACAACCTTTAATAATGGTTTGTCACGGGATCAACCAAAACCCAAAATG
13819830 GT
66 GT
* * *
13819832 TTTTCA-AAGGCTCAACCACAACCTTTAATAATGGTTTTTCATGGGATCAACCAAAACTCAAAAT
1 TTTTCACAA-GCTCAACCACAACCTTTAATAATGGTTTGTCACGGGATCAACCAAAACCCAAAAT
13819896 CTAACTTTTC
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
65 2 0.04
66 24 0.42
67 31 0.54
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (67 bp):
TTTTCACAAGCTCAACCACAACCTTTAATAATGGTTTGTCACGGGATCAACCAAAACCCAAAATG
GT
Found at i:13819882 original size:35 final size:34
Alignment explanation
Indices: 13819777--13819888 Score: 120
Period size: 32 Copynumber: 3.3 Consensus size: 34
13819767 TTTCACAAGC
* * * *
13819777 TCAACCATAACCTTTAACATGGTTTGTCACGGGA
1 TCAACCAAAACCTTTAAAATGGTTTTTCAAGGGA
* * *
13819811 TCAACCAAAACC--CAAAATGGTTTTTCAAAGGC
1 TCAACCAAAACCTTTAAAATGGTTTTTCAAGGGA
* *
13819843 TCAACCACAACCTTTAATAATGGTTTTTCATGGGA
1 TCAACCAAAACCTTTAA-AATGGTTTTTCAAGGGA
13819878 TCAACCAAAAC
1 TCAACCAAAAC
13819889 TCAAAATCTA
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
32 25 0.40
34 13 0.21
35 24 0.39
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (34 bp):
TCAACCAAAACCTTTAAAATGGTTTTTCAAGGGA
Found at i:13820406 original size:74 final size:74
Alignment explanation
Indices: 13820302--13820465 Score: 238
Period size: 74 Copynumber: 2.2 Consensus size: 74
13820292 CAGACAGAGT
* * *
13820302 GCTCTTAGTTGACTAACAATACTTCTTAGTCGATTAAGTTTTCTCTGTCTTGTAATTAAATTCTC
1 GCTCTTAGTTGACTAACAATACTTCTTAGTCCATTAAGTTCTCTCTGTCTTGTAATTAAAGTCTC
13820367 TAGTAGTAA
66 TAGTAGTAA
* * * * *
13820376 GCTCTTAGTTGATTAACTATGCTTCTTAGTCCATTAAGTTCTCTTTGTCTTGTAATTGAAGTCTC
1 GCTCTTAGTTGACTAACAATACTTCTTAGTCCATTAAGTTCTCTCTGTCTTGTAATTAAAGTCTC
* *
13820441 TGGTAGTGA
66 TAGTAGTAA
13820450 GCTCTTAGTTGACTAA
1 GCTCTTAGTTGACTAA
13820466 GTCTTTTCTG
Statistics
Matches: 79, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
74 79 1.00
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (74 bp):
GCTCTTAGTTGACTAACAATACTTCTTAGTCCATTAAGTTCTCTCTGTCTTGTAATTAAAGTCTC
TAGTAGTAA
Found at i:13821123 original size:15 final size:15
Alignment explanation
Indices: 13821103--13821135 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
13821093 GATTCGATAC
13821103 AATGATAAAAAGCTA
1 AATGATAAAAAGCTA
13821118 AATGATAAAAAGCTA
1 AATGATAAAAAGCTA
13821133 AAT
1 AAT
13821136 AAGGAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.12, T:0.21
Consensus pattern (15 bp):
AATGATAAAAAGCTA
Found at i:13823273 original size:20 final size:20
Alignment explanation
Indices: 13823245--13823293 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
13823235 TTATAATTAG
*
13823245 TTTATTTTTAAGTGAGTTAT
1 TTTAATTTTAAGTGAGTTAT
* * * *
13823265 TTTAATTTTATGTTATTTTT
1 TTTAATTTTAAGTGAGTTAT
13823285 TTTAATTTT
1 TTTAATTTT
13823294 GTTATTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (20 bp):
TTTAATTTTAAGTGAGTTAT
Found at i:13823296 original size:18 final size:18
Alignment explanation
Indices: 13823264--13823322 Score: 57
Period size: 18 Copynumber: 3.1 Consensus size: 18
13823254 AAGTGAGTTA
13823264 TTTTAATTTTATGTTATTTT
1 TTTTAA-TTT-TGTTATTTT
13823284 TTTTAATTTTGTTATTATT
1 TTTTAATTTTGTTATT-TT
* *
13823303 TATTAGTTTT-TTATATTT
1 TTTTAATTTTGTTAT-TTT
13823321 TT
1 TT
13823323 GTAGGAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 14 0.41
19 14 0.41
20 6 0.18
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTAATTTTGTTATTTT
Found at i:13823303 original size:21 final size:20
Alignment explanation
Indices: 13823264--13823303 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13823254 AAGTGAGTTA
*
13823264 TTTTAATTTTATGTTATTTT
1 TTTTAATTTTATATTATTTT
*
13823284 TTTTAATTTTGTTATTATTT
1 TTTTAATTTT-ATATTATTT
13823304 ATTAGTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (20 bp):
TTTTAATTTTATATTATTTT
Found at i:13823913 original size:29 final size:29
Alignment explanation
Indices: 13823880--13823936 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
13823870 CTAGGATTGC
13823880 AATTGAACTCACATATAATCTAAATTTTT
1 AATTGAACTCACATATAATCTAAATTTTT
13823909 AATTGAACTCACATATAATCTAAATTTT
1 AATTGAACTCACATATAATCTAAATTTT
13823937 CAATCTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (29 bp):
AATTGAACTCACATATAATCTAAATTTTT
Found at i:13841838 original size:12 final size:11
Alignment explanation
Indices: 13841821--13841860 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
13841811 AGGAGGTAGA
13841821 AAGAAAGAAACG
1 AAGAAAGAAA-G
13841833 AAGAAAGAAAG
1 AAGAAAGAAAG
13841844 AA-AAGAGAAAG
1 AAGAA-AGAAAG
13841855 AAGAAA
1 AAGAAA
13841861 AAGCTAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.08
11 12 0.46
12 12 0.46
ACGTcount: A:0.72, C:0.03, G:0.25, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:13841863 original size:15 final size:15
Alignment explanation
Indices: 13841818--13841861 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
13841808 GAAAGGAGGT
*
13841818 AGAAAGAAAGAAACG
1 AGAAAGAAAGAAAAG
13841833 AAGAAAGAAAGAAAAG
1 -AGAAAGAAAGAAAAG
13841849 AGAAAG-AAGAAAA
1 AGAAAGAAAGAAAA
13841862 AGCTAAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 7 0.26
15 6 0.22
16 14 0.52
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAGAAAAG
Found at i:13850670 original size:19 final size:18
Alignment explanation
Indices: 13850647--13850690 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
13850637 AAAGAAGAAG
*
13850647 GAAGAAAGTAAGGAGGAA
1 GAAGAAAGAAAGGAGGAA
*
13850665 GAAAGAAAGAAAGGAGAAA
1 G-AAGAAAGAAAGGAGGAA
13850684 GAAGAAA
1 GAAGAAA
13850691 AAGCTAAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (18 bp):
GAAGAAAGAAAGGAGGAA
Found at i:13853039 original size:9 final size:8
Alignment explanation
Indices: 13853025--13853106 Score: 51
Period size: 8 Copynumber: 9.8 Consensus size: 8
13853015 AGATTCAGCT
13853025 AGGAAGCAA
1 AGGAAG-AA
13853034 AGGAAGAA
1 AGGAAGAA
13853042 ATGAAGAAAGAA
1 A-G--G-AAGAA
*
13853054 AGAAAGAA
1 AGGAAGAA
13853062 AGG-AGAA
1 AGGAAGAA
*
13853069 AGAAAGAA
1 AGGAAGAA
*
13853077 AGGATGAA
1 AGGAAGAA
*
13853085 AGGGAGAA
1 AGGAAGAA
*
13853093 AAG-AGAA
1 AGGAAGAA
13853100 AGTGAAG
1 AG-GAAG
13853107 GTTTGGCCTA
Statistics
Matches: 57, Mismatches: 9, Indels: 14
0.71 0.11 0.17
Matches are distributed among these distances:
7 11 0.19
8 29 0.51
9 9 0.16
11 2 0.04
12 6 0.11
ACGTcount: A:0.61, C:0.01, G:0.34, T:0.04
Consensus pattern (8 bp):
AGGAAGAA
Found at i:13853054 original size:4 final size:4
Alignment explanation
Indices: 13853032--13853078 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
13853022 GCTAGGAAGC
* *
13853032 AAAG GAAG AAATG -AAG AAAG AAAG AAAG AAAG -GAG AAAG AAAG AAAG
1 AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
13853079 GATGAAAGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
4 32 0.89
5 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:13853075 original size:23 final size:24
Alignment explanation
Indices: 13853045--13853101 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
13853035 GGAAGAAATG
13853045 AAGAAAGAAAGAAAGAAA-GGAGA
1 AAGAAAGAAAGAAAGAAAGGGAGA
* *
13853068 AAGAAAGAAAGGATGAAAGGGAGA
1 AAGAAAGAAAGAAAGAAAGGGAGA
*
13853092 AA-AGAGAAAG
1 AAGAAAGAAAG
13853102 TGAAGGTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 23 0.77
24 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.02
Consensus pattern (24 bp):
AAGAAAGAAAGAAAGAAAGGGAGA
Found at i:13853092 original size:16 final size:15
Alignment explanation
Indices: 13853050--13853101 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
13853040 AAATGAAGAA
13853050 AGAAAGAAAGAAAGG
1 AGAAAGAAAGAAAGG
13853065 AGAAAGAAAGAAAGG
1 AGAAAGAAAGAAAGG
** *
13853080 ATGAAAGGGAGAAAAG
1 A-GAAAGAAAGAAAGG
13853096 AGAAAG
1 AGAAAG
13853102 TGAAGGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
15 21 0.64
16 12 0.36
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (15 bp):
AGAAAGAAAGAAAGG
Found at i:13861701 original size:80 final size:80
Alignment explanation
Indices: 13861558--13861753 Score: 261
Period size: 80 Copynumber: 2.5 Consensus size: 80
13861548 CATGAGTTCC
* * * * *
13861558 ATTTAAGAGATTATAACATGCATGCGATGAGATGTATGTGTTAAGCATATCATGTACTATATGGG
1 ATTTAGGAGGTTATAAAATGCATGCCATGAGATGTATGTGTTAAGCATATCATATACTATATGGG
13861623 CTAAGCATGTGAATG
66 CTAAGCATGTGAATG
** *
13861638 ATTTATTAGGTTATAAAATGCATGCCATGAGATGTATGTGTTGAG-ATAGTCATATAC-ACTATG
1 ATTTAGGAGGTTATAAAATGCATGCCATGAGATGTATGTGTTAAGCATA-TCATATACTA-TATG
13861701 GGCTAAGCATGTGAATG
64 GGCTAAGCATGTGAATG
* **
13861718 ATTTAGGAGGTTATGAAATATATGCCATGAGATGTA
1 ATTTAGGAGGTTATAAAATGCATGCCATGAGATGTA
13861754 CATGTTGTGA
Statistics
Matches: 102, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
79 4 0.04
80 98 0.96
ACGTcount: A:0.34, C:0.09, G:0.24, T:0.33
Consensus pattern (80 bp):
ATTTAGGAGGTTATAAAATGCATGCCATGAGATGTATGTGTTAAGCATATCATATACTATATGGG
CTAAGCATGTGAATG
Found at i:13864921 original size:21 final size:22
Alignment explanation
Indices: 13864892--13864935 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13864882 GAGTAGCTAA
13864892 TTTAAGTTATTTTA-GTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
* *
13864913 TTTATGTTATTTTATTTTAAAT
1 TTTAAGTTATTTTATGTTAAAT
13864935 T
1 T
13864936 ACTTTAANNN
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTAAGTTATTTTATGTTAAAT
Found at i:13869191 original size:68 final size:64
Alignment explanation
Indices: 13869105--13869276 Score: 186
Period size: 65 Copynumber: 2.6 Consensus size: 64
13869095 TTGTATGAAA
*
13869105 TATGCTATGTTGTAATGTATGTGATGTTG-TTCC-CATATACTATGTGAGATAAAAATGAGCACA
1 TATGCTATGTTGT-ATGTATGTGATGTTGCTTCCACATA-A--A--TGAGATAAAAATAAGCACA
13869168 TGATG
60 TGATG
* *
13869173 TATGCCATGTTGCTATGTATGTGATGTTGCTTCCACATAAATGAGATAAGAATAAGCACATGATG
1 TATGCTATGTTG-TATGTATGTGATGTTGCTTCCACATAAATGAGATAAAAATAAGCACATGATG
* * * *
13869238 AATGCTATGTGTGAAATGTATGTGATGATGATTCCACAT
1 TATGCTATGT-TG-TATGTATGTGATGTTGCTTCCACAT
13869277 GCTATATGAC
Statistics
Matches: 91, Mismatches: 9, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
65 30 0.33
66 24 0.26
67 1 0.01
68 26 0.29
69 6 0.07
70 4 0.04
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (64 bp):
TATGCTATGTTGTATGTATGTGATGTTGCTTCCACATAAATGAGATAAAAATAAGCACATGATG
Found at i:13869192 original size:17 final size:17
Alignment explanation
Indices: 13869170--13869203 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13869160 TGAGCACATG
13869170 ATGTATGCCATGTTGCT
1 ATGTATGCCATGTTGCT
**
13869187 ATGTATGTGATGTTGCT
1 ATGTATGCCATGTTGCT
13869204 TCCACATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.18, C:0.12, G:0.26, T:0.44
Consensus pattern (17 bp):
ATGTATGCCATGTTGCT
Found at i:13870670 original size:11 final size:11
Alignment explanation
Indices: 13870654--13870683 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
13870644 TAGCCCACAT
13870654 ATGAATGAATG
1 ATGAATGAATG
13870665 ATGAATGAATG
1 ATGAATGAATG
13870676 ATG-ATGAA
1 ATGAATGAA
13870684 AAGGCTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (11 bp):
ATGAATGAATG
Found at i:13883004 original size:19 final size:20
Alignment explanation
Indices: 13882982--13883020 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
13882972 AAAAAAACTA
13882982 AAAAATTAA-AAAA-GATGGG
1 AAAAA-TAAGAAAATGATGGG
13883001 AAAAATAAGAAAATGATGGG
1 AAAAATAAGAAAATGATGGG
13883021 CTTTTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 9 0.50
20 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (20 bp):
AAAAATAAGAAAATGATGGG
Found at i:13902192 original size:36 final size:36
Alignment explanation
Indices: 13902145--13902250 Score: 151
Period size: 35 Copynumber: 3.0 Consensus size: 36
13902135 NNNNNNNNNN
*
13902145 GTTTAATCAAGTTATTGGGCCTAATTGATTAAATTT
1 GTTTAATCAAGTTATTGGGCTTAATTGATTAAATTT
* * *
13902181 GTTTAATCAAGTTATTGGACTTGATTGATCAAA-TT
1 GTTTAATCAAGTTATTGGGCTTAATTGATTAAATTT
* *
13902216 ATTTAATTAAGTTATTGGGCTTAATTGATTAAATT
1 GTTTAATCAAGTTATTGGGCTTAATTGATTAAATT
13902251 AAATAATTAA
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
35 30 0.50
36 30 0.50
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (36 bp):
GTTTAATCAAGTTATTGGGCTTAATTGATTAAATTT
Found at i:13910936 original size:13 final size:14
Alignment explanation
Indices: 13910909--13910941 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
13910899 CAAATGTCGA
13910909 AAAAAATAACACAT
1 AAAAAATAACACAT
*
13910923 AAAAAATCAC-CAT
1 AAAAAATAACACAT
13910936 AAAAAA
1 AAAAAA
13910942 GTACATCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAAATAACACAT
Found at i:13916128 original size:14 final size:15
Alignment explanation
Indices: 13916109--13916138 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13916099 AATCATAAAC
13916109 AAAAG-AAGAAAAAA
1 AAAAGAAAGAAAAAA
13916123 AAAAGAAAGAAAAAA
1 AAAAGAAAGAAAAAA
13916138 A
1 A
13916139 GGAAGATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAAAAA
Found at i:13916964 original size:2 final size:2
Alignment explanation
Indices: 13916953--13916981 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13916943 TTGTACCTAG
13916953 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13916982 GAATTCTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:13919271 original size:34 final size:35
Alignment explanation
Indices: 13919183--13919279 Score: 110
Period size: 34 Copynumber: 2.8 Consensus size: 35
13919173 GTTAGTGTTT
* *
13919183 TGGTAG-AGGTTACGCTTGATCTTACAAAAGACAAG
1 TGGTAGAAGGTTACGCTTGATCCTAC-AAAGACAAA
* *
13919218 TGGTAGAA-GTTACACTTGATCCTACAAAGGCAAA
1 TGGTAGAAGGTTACGCTTGATCCTACAAAGACAAA
* *
13919252 TTGT-GAAGGTTACGTTTGATCCTACAAA
1 TGGTAGAAGGTTACGCTTGATCCTACAAA
13919280 AAAACATGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
33 3 0.06
34 28 0.53
35 21 0.40
36 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (35 bp):
TGGTAGAAGGTTACGCTTGATCCTACAAAGACAAA
Found at i:13925150 original size:23 final size:23
Alignment explanation
Indices: 13925105--13925151 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
13925095 TAGGCCATCC
* ***
13925105 CAAAGGTTGATAAGTGGTTGCTT
1 CAAAGGTTGACAAGTGCCAGCTT
13925128 CAAAGGTTGACAAGTGCCAGCTT
1 CAAAGGTTGACAAGTGCCAGCTT
13925151 C
1 C
13925152 TTATACTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (23 bp):
CAAAGGTTGACAAGTGCCAGCTT
Found at i:13930415 original size:19 final size:20
Alignment explanation
Indices: 13930379--13930417 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13930369 CATAATTTTT
*
13930379 TATTTTTTCAAATATAATAA
1 TATTTTTTAAAATATAATAA
13930399 TATTTTTTAAAAT-TAATAA
1 TATTTTTTAAAATATAATAA
13930418 AAAAAGAGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TATTTTTTAAAATATAATAA
Found at i:13932012 original size:104 final size:104
Alignment explanation
Indices: 13931832--13932024 Score: 271
Period size: 104 Copynumber: 1.9 Consensus size: 104
13931822 TTTAGAGTTA
* * *
13931832 TATCTTCGTCTATATCTTCTATTAAGCCACATGCTTTTGTCTTAATGTTTAATCCATTTGGTCTT
1 TATCTTCGTATATATCTTCTATTAAGCCACATGCTTTTGTCTTAATGCTTAATCCATTTGGTCTA
*
13931897 TGTTTGTTATTTGAGTTTAGATATCAAGCATCTTTGTTG
66 TGTTTGTTATTTGAGTTTACATATCAAGCATCTTTGTTG
* * * * *
13931936 TATCTTTGTATATATCTTCTGTTAAGCCACATGTTTTTGTGTTAATGCTT-ATGTCATTTGGTCT
1 TATCTTCGTATATATCTTCTATTAAGCCACATGCTTTTGTCTTAATGCTTAAT-CCATTTGGTCT
* *
13932000 ATGTTTTTTATTTTAGTTTACATAT
65 ATGTTTGTTATTTGAGTTTACATAT
13932025 GAAATTTTTT
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
103 2 0.03
104 75 0.97
ACGTcount: A:0.20, C:0.13, G:0.14, T:0.52
Consensus pattern (104 bp):
TATCTTCGTATATATCTTCTATTAAGCCACATGCTTTTGTCTTAATGCTTAATCCATTTGGTCTA
TGTTTGTTATTTGAGTTTACATATCAAGCATCTTTGTTG
Found at i:13933951 original size:8 final size:9
Alignment explanation
Indices: 13933938--13933999 Score: 59
Period size: 8 Copynumber: 7.7 Consensus size: 9
13933928 CTCTCTCCCC
13933938 TTCTTCT-T
1 TTCTTCTCT
13933946 TTCTTC-CT
1 TTCTTCTCT
13933954 TTC-TC-CT
1 TTCTTCTCT
13933961 TTCTT-TCT
1 TTCTTCTCT
13933969 TTCTT-TCT
1 TTCTTCTCT
13933977 TTCTT-TCT
1 TTCTTCTCT
13933985 TTCTTC-CT
1 TTCTTCTCT
13933993 TTGCTTC
1 TT-CTTC
13934000 CTAGCTAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.14
8 38 0.78
9 4 0.08
ACGTcount: A:0.00, C:0.31, G:0.02, T:0.68
Consensus pattern (9 bp):
TTCTTCTCT
Found at i:13933962 original size:16 final size:16
Alignment explanation
Indices: 13933902--13934001 Score: 57
Period size: 16 Copynumber: 6.4 Consensus size: 16
13933892 TAGGCCAAAC
13933902 CTTCACTTTCT-CTTTT
1 CTTC-CTTTCTCCTTTT
* *
13933918 CTT-CTTTGTCC-TCT
1 CTTCCTTTCTCCTTTT
* * *
13933932 CTCCCCTTCTTCTTTT
1 CTTCCTTTCTCCTTTT
13933948 CTTCCTTTCTCC-TTT
1 CTTCCTTTCTCCTTTT
* *
13933963 CTTTCTTTCT-TTCTTT
1 CTTCCTTTCTCCT-TTT
* *
13933979 CTTTCTTTCTTCCTTTG
1 CTTCCTTTC-TCCTTTT
13933996 CTTCCT
1 CTTCCT
13934002 AGCTAAATCT
Statistics
Matches: 62, Mismatches: 15, Indels: 13
0.69 0.17 0.14
Matches are distributed among these distances:
14 9 0.15
15 18 0.29
16 26 0.42
17 8 0.13
18 1 0.02
ACGTcount: A:0.01, C:0.35, G:0.02, T:0.62
Consensus pattern (16 bp):
CTTCCTTTCTCCTTTT
Found at i:13933968 original size:4 final size:4
Alignment explanation
Indices: 13933945--13933994 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
13933935 CCCTTCTTCT
* * *
13933945 TTTC TTCC TTTC -TCC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTCC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
13933992 TTT
1 TTT
13933995 GCTTCCTAGC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 2 0.05
4 37 0.95
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:13934448 original size:16 final size:16
Alignment explanation
Indices: 13934427--13934460 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
13934417 TCTCTCTTGA
*
13934427 TTTATTTCACATGCAT
1 TTTATTCCACATGCAT
*
13934443 TTTATTCCACATGTAT
1 TTTATTCCACATGCAT
13934459 TT
1 TT
13934461 CTATGCATTT
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:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (16 bp):
TTTATTCCACATGCAT
Found at i:13935535 original size:77 final size:77
Alignment explanation
Indices: 13935442--13935596 Score: 310
Period size: 77 Copynumber: 2.0 Consensus size: 77
13935432 AATATTATCA
13935442 TGCATTTGTATTACAAAATCACACTAATGTATTTAAGCTGGCTAGTTTATATTCATTTTTCTGCA
1 TGCATTTGTATTACAAAATCACACTAATGTATTTAAGCTGGCTAGTTTATATTCATTTTTCTGCA
13935507 ATCCAGTCTCTG
66 ATCCAGTCTCTG
13935519 TGCATTTGTATTACAAAATCACACTAATGTATTTAAGCTGGCTAGTTTATATTCATTTTTCTGCA
1 TGCATTTGTATTACAAAATCACACTAATGTATTTAAGCTGGCTAGTTTATATTCATTTTTCTGCA
13935584 ATCCAGTCTCTG
66 ATCCAGTCTCTG
13935596 T
1 T
13935597 TGATTGTATT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 78 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (77 bp):
TGCATTTGTATTACAAAATCACACTAATGTATTTAAGCTGGCTAGTTTATATTCATTTTTCTGCA
ATCCAGTCTCTG
Found at i:13958822 original size:31 final size:31
Alignment explanation
Indices: 13958784--13958845 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
13958774 TAGGTAGCCA
* * *
13958784 ACTAGTTGATATTAAGAAATCTTAGAACATT
1 ACTAGTTGATAATAAGAAATCTAAAAACATT
*
13958815 ACTAGTTGGTAATAAGAAATCTAAAAACATT
1 ACTAGTTGATAATAAGAAATCTAAAAACATT
13958846 CTTTTATAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (31 bp):
ACTAGTTGATAATAAGAAATCTAAAAACATT
Found at i:13975003 original size:28 final size:28
Alignment explanation
Indices: 13974971--13975061 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
13974961 ATCAAGTGAT
13974971 AACCCATGGTTTTAATGGGTTCACCACA
1 AACCCATGGTTTTAATGGGTTCACCACA
** * * *
13974999 AACCCATGGTTTTTCTGAGCTCATCACA
1 AACCCATGGTTTTAATGGGTTCACCACA
* *
13975027 AACTCATGGTTTTAACGGGATT-ACCACA
1 AACCCATGGTTTTAATGGG-TTCACCACA
*
13975055 AGCCCAT
1 AACCCAT
13975062 ACACTAACTT
Statistics
Matches: 48, Mismatches: 14, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
28 47 0.98
29 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (28 bp):
AACCCATGGTTTTAATGGGTTCACCACA
Found at i:13976402 original size:242 final size:242
Alignment explanation
Indices: 13975963--13976454 Score: 690
Period size: 242 Copynumber: 2.0 Consensus size: 242
13975953 GAGCTTCATG
*
13975963 GCTTG-AAAGTAACCTTGGTGTTGTGAAGATCAAGAATTGAGTGATGACTAAGTTTCTTGACTTG
1 GCTTGTAAAGTAACCTTGGTGTTATGAAGATCAAGAATTGAGTGATGACTAAGTTTCTTGACTTG
* * * *
13976027 CGACAAGCTCGATGAAGTGTAGATTGATGATCTTTGAATGCTTTGAGATAAATTCCACCACTTGT
66 AGACAAGCTCGATGAAGTATAGATTGATGATCTTTGAATGCTTTAAGATAAACTCCACCACTTGT
* * *
13976092 AATCTTATCTTGCAACCTCAACCTCTCAAAAATGAATGTTAGAGTGATCCTAAACTGATACAACT
131 AATCTTATCTTGCAACCTCAACATCTCAAAAATGAATGTTAAAGTGATCATAAACTGATACAACT
* *
13976157 AAAACTTATACAAGCTTAT-ATATAGTTCAATAACTTTAAGAATCAA
196 AAAACTTATACAAGCTTATAATATAGTTCAAAAACTTCAAGAATCAA
* * *
13976203 GCTTGTAAGAGTAACTTTGGTGTTATGAAGATCAA-ATATTGAGTGATGATTAAGTTTTTTGACT
1 GCTTGTAA-AGTAACCTTGGTGTTATGAAGATCAAGA-ATTGAGTGATGACTAAGTTTCTTGACT
* * **
13976267 TGTAG-CAAGCTTGGTGAAGTATAGATTGATGATCTTTGAATGCTTTAAGATAAACTGTACCACT
64 TG-AGACAAGCTCGATGAAGTATAGATTGATGATCTTTGAATGCTTTAAGATAAACTCCACCACT
* * * *
13976331 TGTGATCTTATCTTGCAACTTCAATATCTCAAAAATGAATGTTAAAG-GAATCATATACTTG-TA
128 TGTAATCTTATCTTGCAACCTCAACATCTCAAAAATGAATGTTAAAGTG-ATCATAAAC-TGATA
*
13976394 CAACTAAAACTTATACAAGCTTATAGATGTAGTTCAAAAACTTCAAGAATCAA
191 CAACTAAAACTTATACAAGCTTATA-ATATAGTTCAAAAACTTCAAGAATCAA
13976447 GCTTGTAA
1 GCTTGTAA
13976455 TTATGTAAGA
Statistics
Matches: 222, Mismatches: 22, Indels: 12
0.87 0.09 0.05
Matches are distributed among these distances:
240 5 0.02
241 4 0.02
242 178 0.80
243 3 0.01
244 32 0.14
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (242 bp):
GCTTGTAAAGTAACCTTGGTGTTATGAAGATCAAGAATTGAGTGATGACTAAGTTTCTTGACTTG
AGACAAGCTCGATGAAGTATAGATTGATGATCTTTGAATGCTTTAAGATAAACTCCACCACTTGT
AATCTTATCTTGCAACCTCAACATCTCAAAAATGAATGTTAAAGTGATCATAAACTGATACAACT
AAAACTTATACAAGCTTATAATATAGTTCAAAAACTTCAAGAATCAA
Found at i:13991244 original size:249 final size:248
Alignment explanation
Indices: 13990769--13991418 Score: 731
Period size: 249 Copynumber: 2.6 Consensus size: 248
13990759 GTAAAGATAG
* * * *
13990769 AATAACTAAATTTAAAATCTTAACATAAATGA-GTAAAAGTTAACATAACAGGTCAATTAA--AA
1 AATAACTAAATTTTAAATCTTAACGTAAAT-ATGTGAAAGTTAACATAACAAGTCAATTAAGTAA
* * * * * * *
13990831 AATATTTAATTTTAATAAAAAATAAATATTTAAATTTATATTGTC-GAACAAAAATTGTTT-ACT
65 AAAATCTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTCAG-ACTAAAAGTGTTTAAC-
* **
13990894 GATATACAAATTTTAATTTTTAAATAAAAATAAAAATAATAAGAATAATTATAATTCAAAATTGG
128 GATATACAAATTTTAA-TTTTAAATAAAAATAAAAATAATAAAAATAATTATAATTCAAAATTAA
* *
13990959 CATAAATAAGCTTTAACGTAAAACTGTAACAATTGACATAAAAACTTATAAAAGTGA
192 CATAAATAAGCCTTAACGTAAAACTATAACAATTGACATAAAAACTTATAAAAGTGA
* *
13991016 AATAACTGAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACATAACAAGTCAACTAAGTAAA
1 AATAACTAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACATAACAAGTCAATTAAGTAAA
* * * *
13991081 AAACTCTAATTTTAGTGAAAAATAAACATTTATATTTATATTCTCAGA-TTAAAGTGTTTAACAA
66 AAA-TCTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACGA
* * *
13991145 TATATAAATTTTAATTTTAAATAAAAAATAATAAA-GATAAAAATAATTATAGTTCAAAATTAAC
130 TATACAAATTTTAATTTTAAAT-AAAAATAA-AAATAATAAAAATAATTATAATTCAAAATTAAC
* * * * * * * *
13991209 ATGCAA-AAGCCTTGACGTTAAACTATGAGAATTGACGTAAAAACTTATAAAGGTGG
193 AT-AAATAAGCCTTAACGTAAAACTATAACAATTGACATAAAAACTTATAAAAGTGA
* * * ** * *
13991265 AATAACTAAATTTTAAGTATTAATGTAAACGTGTGAAAGTTAACGTAACAAGTTAATTAAGTAAA
1 AATAACTAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACATAACAAGTCAATTAAGT---
* * * *
13991330 AAAAAATCTAACTTTAGTGAAAAATAAATATTTAAATTTATACTTTTGAAACTAAAAGTGTTTAA
63 AAAAAATCTAATTTTAGTGAAAAATAAATATTTAAATTTATA-TTCTCAGACTAAAAGTGTTTAA
13991395 CGATATACAAATTTTAAATTTTAA
127 CGATATACAAATTTT-AATTTTAA
13991419 GTTTTGACGT
Statistics
Matches: 337, Mismatches: 51, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
246 1 0.00
247 52 0.15
248 8 0.02
249 155 0.46
250 43 0.13
251 34 0.10
252 11 0.03
253 25 0.07
254 8 0.02
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.34
Consensus pattern (248 bp):
AATAACTAAATTTTAAATCTTAACGTAAATATGTGAAAGTTAACATAACAAGTCAATTAAGTAAA
AAATCTAATTTTAGTGAAAAATAAATATTTAAATTTATATTCTCAGACTAAAAGTGTTTAACGAT
ATACAAATTTTAATTTTAAATAAAAATAAAAATAATAAAAATAATTATAATTCAAAATTAACATA
AATAAGCCTTAACGTAAAACTATAACAATTGACATAAAAACTTATAAAAGTGA
Found at i:13991550 original size:21 final size:19
Alignment explanation
Indices: 13991526--13991582 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
13991516 AAGTCAATTA
13991526 AATAAAAAAAACTCTAATTTT
1 AATAAAAAAAA-T-TAATTTT
* *
13991547 AATAAAAAATATTTATTTT
1 AATAAAAAAAATTAATTTT
13991566 AATAAATAAAAA-TAATT
1 AATAAA-AAAAATTAATT
13991583 ATAGTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 16 0.52
20 5 0.16
21 10 0.32
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
AATAAAAAAAATTAATTTT
Found at i:13992284 original size:250 final size:249
Alignment explanation
Indices: 13991773--13992707 Score: 984
Period size: 251 Copynumber: 3.8 Consensus size: 249
13991763 TAAACCATAA
* * * * * *
13991773 ATTATTTTCATTTAAAAATTAAAA-TTATTGTATTGTTACATACTTTTAGCTAGATAGTAAAAAT
1 ATTATTTTTATTTAAAAATTAAAATTTA-TATATTATTACATACTTTTAGCCAGATAATATAAAT
* * * *
13991837 ATAAATGCTTATTTTTTATTAAAATGAAACTTTTTTACTTATTTAACTTATTACGCTAACTCTCA
65 ATAAATGCTTATTTTTCATTAAAATTAAAC-TTTTTACTTAATTAACTTATTACGTTAACTCTCA
* * *
13991902 CATATTTATGTTAAGATTTAAAATTTAGTTAATCCATCGTTATAAGTTTTTATATTAATTCTTAT
129 CACATTTATGTTAAGATTTAAAATTTAGTTAATCCACCGTTATAAGTTTTTACATTAATTCTTAT
* * * *
13991967 AGTTTTATGTCGAA-ACTTATCTATGTTAATTTTAAACTATAAATTAGTTTTATTTTT
194 AGTTTTATGTC-AAGGCTTATCTATGTCAATTTTGAACTAT-AATTATTTTTATTTTT
*
13992024 ATTATTTTTATTTAAAAATTAAAA-TTATTATATTGTTACATACTTTTAGCCAGATAATATAAAT
1 ATTATTTTTATTTAAAAATTAAAATTTA-TATATTATTACATACTTTTAGCCAGATAATATAAAT
*
13992088 ATAAATGCTTATTTTTCATTAAAATTAAACTTTTTACTTAATTAACTTATTACGTTAACTCTTAC
65 ATAAATGCTTATTTTTCATTAAAATTAAACTTTTTACTTAATTAACTTATTACGTTAACTCTCAC
* * *
13992153 ACATTTACGTTGAA-ATTTAAAATTTAGTTAATCCACCGTTATAAGTTTTTACATTAATGCTTAC
130 ACATTTATGTT-AAGATTTAAAATTTAGTTAATCCACCGTTATAAGTTTTTACATTAATTCTTAT
* * * *
13992217 AGTTTTATGTTAAGGCTTTTTTATGTCAGTTTTGAA-TGATAATTATTTTTATTTTT
194 AGTTTTATGTCAAGGCTTATCTATGTCAATTTTGAACT-ATAATTATTTTTATTTTT
* * * * *
13992273 ATTATTTTTTATTTAAAAGTAAAAATTTGA-ATATCATTACATACTTTCAGCCCGATAATATAAA
1 ATTA-TTTTTATTTAAAAATTAAAATTT-ATATATTATTACATACTTTTAGCCAGATAATATAAA
* * * * * *
13992337 TACAAATGCTTATTGTTCATTAAAATTAAATTTTTTTACTTAATTAATTTATTACGTTAACTTTT
64 TATAAATGCTTATTTTTCATTAAAATTAAA-CTTTTTACTTAATTAACTTATTACGTTAACTCTC
* * * * * ** * *
13992402 AAATATTTATGTTAAGATTTAAAATTTAATTATTTCACTTTTATAAGTTTTTACATCAATTTTTA
128 ACACATTTATGTTAAGATTTAAAATTTAGTTAATCCACCGTTATAAGTTTTTACATTAATTCTTA
* *
13992467 TAATTTTACT-TCAAGGCTTATCTATGTCAATATTGAACTATAATT-TTTTTCA---TT
193 TAGTTTTA-TGTCAAGGCTTATCTATGTCAATTTTGAACTATAATTATTTTT-ATTTTT
* * *
13992521 ATTATTCTTTATTTAAAAATTAAAATTTATATATAATTA-ACCACTTTTAG-CTGA-AATATAAA
1 ATTATT-TTTATTTAAAAATTAAAATTTATATATTATTACA-TACTTTTAGCCAGATAATATAAA
* ** * *
13992583 TTTAAA----TATTTTT-ATTAAAATTAGATTTTTTTAC-TAATTGACTTGTTACGTTAACTCTC
64 TATAAATGCTTATTTTTCATTAAAATTA-AACTTTTTACTTAATTAACTTATTACGTTAACTCTC
* * * * * * * *
13992642 ACACA-TTAT-AT-AGATTTAAAATTTA-ATATTTCATC-TTATAAGTTTTTACGTCAATTATTA
128 ACACATTTATGTTAAGATTTAAAATTTAGTTAATCCACCGTTATAAGTTTTTACATTAATTCTTA
13992702 TAGTTT
193 TAGTTT
13992708 ACGTCAAAAC
Statistics
Matches: 592, Mismatches: 77, Indels: 46
0.83 0.11 0.06
Matches are distributed among these distances:
235 28 0.05
236 7 0.01
237 14 0.02
238 1 0.00
239 4 0.01
240 23 0.04
241 18 0.03
242 7 0.01
246 12 0.02
247 7 0.01
248 40 0.07
249 22 0.04
250 198 0.33
251 208 0.35
252 3 0.01
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (249 bp):
ATTATTTTTATTTAAAAATTAAAATTTATATATTATTACATACTTTTAGCCAGATAATATAAATA
TAAATGCTTATTTTTCATTAAAATTAAACTTTTTACTTAATTAACTTATTACGTTAACTCTCACA
CATTTATGTTAAGATTTAAAATTTAGTTAATCCACCGTTATAAGTTTTTACATTAATTCTTATAG
TTTTATGTCAAGGCTTATCTATGTCAATTTTGAACTATAATTATTTTTATTTTT
Found at i:13992475 original size:20 final size:21
Alignment explanation
Indices: 13992440--13992480 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
13992430 ATTATTTCAC
13992440 TTTTATAAGTTTTTACATCAAT
1 TTTTATAAG-TTTTACATCAAT
*
13992462 TTTTATAA-TTTTACTTCAA
1 TTTTATAAGTTTTACATCAA
13992481 GGCTTATCTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTATAAGTTTTACATCAAT
Found at i:13992726 original size:184 final size:196
Alignment explanation
Indices: 13992536--13992908 Score: 491
Period size: 184 Copynumber: 1.9 Consensus size: 196
13992526 TCTTTATTTA
*
13992536 AAAATTAAAATTTATATATAATTAACCACTTTTAGCT-GA-AATATAAATTTAAATATTT-TTAT
1 AAAATTAAAATTTATATATAATTAAACACTTTTAGCTCGAGAATATAAATTTAAATATTTATTAT
13992598 T-A-AAATTAGA-TTTTTTTAC-TAATTGACTTGTTACGTTAACTCTCACAC-ATTAT-AT-AGA
66 TCACAAATTAGATTTTTTTTACTTAATTGACTTGTTACGTTAACTCTCACACGATTATGATAAGA
* * *
13992656 TTTAAAATTTA-ATATTTCATC-TTATAAGTTTTTACGTCAATTATTATAGTTTACGTCAAAACT
131 TTTAAAATTTAGATATTCCACCTTTATAAGTTTTTACGTCAATTATCATAGTTTACGTCAAAACT
13992719 T
196 T
* ** * *
13992720 AAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTATTTT
1 AAAATTAAAATTTATATATAATTAAACACTTTTAGCTCGAGAATATAAATTTAAATATTTATTAT
* * * *
13992785 TCACTGAAGTTAGATTTTTTTTTTACTTAATTGACTTGTTACGTTAACTTTCACACGTTTATGTT
66 TCAC--AAATTAGA--TTTTTTTTACTTAATTGACTTGTTACGTTAACTCTCACACGATTATGAT
* *
13992850 AAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAATTCTCATAGTTTA
127 AAGATTTAAAATTTAGATATTCCACCTTTATAAGTTTTTACGTCAATTATCATAGTTTA
13992909 ACGTTAAAGA
Statistics
Matches: 158, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
184 32 0.20
185 2 0.01
186 19 0.12
187 4 0.03
188 1 0.01
191 7 0.04
194 9 0.06
195 28 0.18
196 4 0.03
197 1 0.01
198 14 0.09
199 7 0.04
200 30 0.19
ACGTcount: A:0.35, C:0.11, G:0.08, T:0.46
Consensus pattern (196 bp):
AAAATTAAAATTTATATATAATTAAACACTTTTAGCTCGAGAATATAAATTTAAATATTTATTAT
TCACAAATTAGATTTTTTTTACTTAATTGACTTGTTACGTTAACTCTCACACGATTATGATAAGA
TTTAAAATTTAGATATTCCACCTTTATAAGTTTTTACGTCAATTATCATAGTTTACGTCAAAACT
T
Found at i:13993296 original size:249 final size:248
Alignment explanation
Indices: 13992720--13993391 Score: 637
Period size: 249 Copynumber: 2.7 Consensus size: 248
13992710 GTCAAAACTT
*
13992720 AAAATTAAAATTTGTATATCGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTATTTT
1 AAAATTAAAATTTGTATATTGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTATTTT
* * * *
13992785 TCACTGAAGTTAGATTTTTTTTTTACTTAATTGACTTGTTACGTTAACTTTCACACGTTTATGTT
66 TCACTAAAATTAGA----TTTTTTACTTAATTAACTTGTTACGTTAACTTTCACACATTTATGTT
* *
13992850 AAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAATTCTCATAGTTTAACGTTA
127 AAGATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAATTCTCACAGTTTAAC-TAA
* * *
13992915 AAGATTTTTTATGTTAATTTTGAACTATAATTATTTTTATCTTTATTATTCTTTATTA
191 AAGATTATTTATATCAATTTTGAACTATAATTATTTTTATCTTTATTATTCTTTATTA
* * * * *** * * * *
13992973 AAAGTTAAAAGTTATATATTGTTAAACACTTTAAACCCAAGAATATATATATAAATGTTTA-TTT
1 AAAATTAAAATTTGTATATTGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTATTTT
* *
13993037 TCACTAAAATTAGAGTTTTTTACTTAATTAACTTGTTATGTTAACTTTCACATATTTATGTTAAG
66 TCACTAAAATTAGA-TTTTTTACTTAATTAACTTGTTACGTTAACTTTCACACATTTATGTTAAG
* ** ********** * * *
13993102 ATTTAAAATTTAGTTATTTCATTTTTATAAGTTNNNNNNNNNNTTGTTACAGTTTTA-TAACAAG
130 ATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAATTCTCACAGTTTAACTAA-AA-
* *
13993166 GCTTATTTATATCAATTTTGAATTATAATTATTTTTAT-TATTATTA-T-TTTATTTA
193 GATTATTTATATCAATTTTGAACTATAATTATTTTTATCT-TTATTATTCTTTA-TTA
* * *
13993221 AAAATTAAAATTTGTATATTGTTAAATAATTTTAGTTTGAGAATATAAATTTAAATATTTATTTT
1 AAAATTAAAATTTGTATATTGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTATTTT
* * * * * * *
13993286 TTATTAAAATTA-A--TTTT--TT-AGTGACTTGTTACGTTAACTTTTACTCATTTCTTGTTAAG
66 TCACTAAAATTAGATTTTTTACTTAATTAACTTGTTACGTTAACTTTCACACATTT-ATGTTAAG
* * * * ** **
13993345 ATTTTAAATTTAGGTATTCTATCTTTACGAGTTTTTATATCAATTCT
130 ATTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAATTCT
13993392 TATTGCTTTA
Statistics
Matches: 330, Mismatches: 83, Indels: 22
0.76 0.19 0.05
Matches are distributed among these distances:
242 25 0.08
243 38 0.12
245 4 0.01
247 6 0.02
248 55 0.17
249 138 0.42
252 15 0.05
253 49 0.15
ACGTcount: A:0.33, C:0.08, G:0.08, T:0.49
Consensus pattern (248 bp):
AAAATTAAAATTTGTATATTGTTAAACACTTTTAGTTCGAGAATATAAATTTAAATATTTATTTT
TCACTAAAATTAGATTTTTTACTTAATTAACTTGTTACGTTAACTTTCACACATTTATGTTAAGA
TTTAAAATTTAGTTATTCCACCTTTATAAGTTTTTACGTCAATTCTCACAGTTTAACTAAAAGAT
TATTTATATCAATTTTGAACTATAATTATTTTTATCTTTATTATTCTTTATTA
Found at i:13993303 original size:17 final size:18
Alignment explanation
Indices: 13993271--13993305 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
13993261 GAATATAAAT
*
13993271 TTAAATATTTATTTTTTA
1 TTAAATATTAATTTTTTA
13993289 TTAAA-ATTAATTTTTTA
1 TTAAATATTAATTTTTTA
13993306 GTGACTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTAAATATTAATTTTTTA
Found at i:13997075 original size:19 final size:19
Alignment explanation
Indices: 13997051--13997088 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
13997041 TGACACCGGG
13997051 GCATTGT-AAATGACACCAA
1 GCATTGTGAAA-GACACCAA
13997070 GCATTGTGAAAGACACCAA
1 GCATTGTGAAAGACACCAA
13997089 TCGTGGTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.42, C:0.21, G:0.18, T:0.18
Consensus pattern (19 bp):
GCATTGTGAAAGACACCAA
Found at i:13999694 original size:19 final size:19
Alignment explanation
Indices: 13999667--13999705 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
13999657 ATTGATGTTG
13999667 AGGCATTGTAAAAGACACC
1 AGGCATTGTAAAAGACACC
* * *
13999686 AGGCGTTGTGAAAGGCACC
1 AGGCATTGTAAAAGACACC
13999705 A
1 A
13999706 ATCGTGGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.28, T:0.15
Consensus pattern (19 bp):
AGGCATTGTAAAAGACACC
Found at i:14000106 original size:15 final size:17
Alignment explanation
Indices: 14000083--14000115 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
14000073 ATCCTAAATC
14000083 AACTAAAATTAAA-AAA
1 AACTAAAATTAAATAAA
14000099 AACT-AAATTAAATAAA
1 AACTAAAATTAAATAAA
14000115 A
1 A
14000116 TATAATCCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
AACTAAAATTAAATAAA
Found at i:14003978 original size:6 final size:6
Alignment explanation
Indices: 14003967--14003991 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14003957 TGTATACATG
14003967 TGTATA TGTATA TGTATA TGTATA T
1 TGTATA TGTATA TGTATA TGTATA T
14003992 ACGTATACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (6 bp):
TGTATA
Found at i:14004096 original size:9 final size:9
Alignment explanation
Indices: 14004076--14004114 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
14004066 GGAAATACTC
14004076 AATATG-AA
1 AATATGAAA
14004084 AATATGAAA
1 AATATGAAA
14004093 AATATG---
1 AATATGAAA
14004099 AATATGAAA
1 AATATGAAA
14004108 AATATGA
1 AATATGA
14004115 TCAAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
6 6 0.22
8 6 0.22
9 15 0.56
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (9 bp):
AATATGAAA
Found at i:14004098 original size:17 final size:16
Alignment explanation
Indices: 14004076--14004114 Score: 62
Period size: 15 Copynumber: 2.4 Consensus size: 16
14004066 GGAAATACTC
14004076 AATATGAAAATATGAAA
1 AATATG-AAATATGAAA
14004093 AATATG-AATATGAAA
1 AATATGAAATATGAAA
14004108 AATATGA
1 AATATGA
14004115 TCAAAAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.71
17 6 0.29
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.26
Consensus pattern (16 bp):
AATATGAAATATGAAA
Found at i:14004487 original size:53 final size:53
Alignment explanation
Indices: 14004378--14004484 Score: 132
Period size: 52 Copynumber: 2.0 Consensus size: 53
14004368 TTTTGAGGGC
*
14004378 TGCATTTGTTTTTGTCAGCTGACTGGAAGCGCGATGCTTTTGCTGCTTTTGCTT
1 TGCATTTGTTTTTGTCAGCTGACTGGAAGCGCCATGC-TTTGCTGCTTTTGCTT
*
14004432 TGCA-TTGTTTTTTGTC-GCTGACT-GAATGCTGCCATG-TTTGCTGCTTTTTCTT
1 TGCATTTG-TTTTTGTCAGCTGACTGGAA-GC-GCCATGCTTTGCTGCTTTTGCTT
14004484 T
1 T
14004485 TGCTTTGAGC
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
52 19 0.40
53 12 0.25
54 17 0.35
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (53 bp):
TGCATTTGTTTTTGTCAGCTGACTGGAAGCGCCATGCTTTGCTGCTTTTGCTT
Found at i:14008637 original size:12 final size:12
Alignment explanation
Indices: 14008601--14008631 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
14008591 CATTTGAAGA
14008601 TTCTGTTGATGT
1 TTCTGTTGATGT
14008613 TTCTGTTGATGT
1 TTCTGTTGATGT
14008625 TTCTGTT
1 TTCTGTT
14008632 TCTGTTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.10, G:0.23, T:0.61
Consensus pattern (12 bp):
TTCTGTTGATGT
Found at i:14010987 original size:49 final size:49
Alignment explanation
Indices: 14010912--14011051 Score: 156
Period size: 49 Copynumber: 2.9 Consensus size: 49
14010902 GAATATGTTT
* * ** *
14010912 CATCCGTGGATGGTTCTAGACAATGATATGATGTGCGATATTTATATTC
1 CATCCGTGGATGGTTTTAGACGATGATATGATGTGAAATATGTATATTC
*
14010961 CATCCGTGGATGGTTTTAGACGATGATATGATGTGAAATATGTATGTTC
1 CATCCGTGGATGGTTTTAGACGATGATATGATGTGAAATATGTATATTC
* * * * * *
14011010 CATTCGTAGAT-GTTTTCGGATGATGATATGATGGGAGATATG
1 CATCCGTGGATGGTTTT-AGACGATGATATGATGTGAAATATG
14011052 CATGTGCCAT
Statistics
Matches: 78, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 5 0.06
49 73 0.94
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.36
Consensus pattern (49 bp):
CATCCGTGGATGGTTTTAGACGATGATATGATGTGAAATATGTATATTC
Found at i:14017119 original size:16 final size:18
Alignment explanation
Indices: 14017090--14017127 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
14017080 AGCTATATCA
14017090 TTTTAAGTTGAGTTGT-T
1 TTTTAAGTTGAGTTGTGT
*
14017107 TTTTTAGTT-AGTTGTGT
1 TTTTAAGTTGAGTTGTGT
14017124 TTTT
1 TTTT
14017128 CTATTTACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.13, C:0.00, G:0.21, T:0.66
Consensus pattern (18 bp):
TTTTAAGTTGAGTTGTGT
Found at i:14021519 original size:14 final size:15
Alignment explanation
Indices: 14021492--14021520 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
14021482 ATATGTTAAT
14021492 TTTATATAGTATATA
1 TTTATATAGTATATA
14021507 TTTATAT-GTATATA
1 TTTATATAGTATATA
14021521 ATTAGCTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (15 bp):
TTTATATAGTATATA
Found at i:14027528 original size:6 final size:6
Alignment explanation
Indices: 14027517--14027541 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
14027507 GCTCATGATT
14027517 TATAAA TATAAA TATAAA TATAAA T
1 TATAAA TATAAA TATAAA TATAAA T
14027542 TCTTAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
TATAAA
Found at i:14048273 original size:36 final size:37
Alignment explanation
Indices: 14048233--14048326 Score: 104
Period size: 36 Copynumber: 2.6 Consensus size: 37
14048223 CTTTTTCACA
* *
14048233 GGATCAAGCAATAACCCTTACAT-TTTCATTTTAATG
1 GGATCAAGCAATAACCCTTACATATTGCATTTTAAGG
* * *
14048269 GGATCAAACAATAA-CCTTA-ATACTTGCTTTTTCAGG
1 GGATCAAGCAATAACCCTTACATA-TTGCATTTTAAGG
*
14048305 GGATCAAGCGATAACCCTTACA
1 GGATCAAGCAATAACCCTTACA
14048327 CCAGTTTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
34 2 0.04
35 5 0.11
36 34 0.72
37 5 0.11
38 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (37 bp):
GGATCAAGCAATAACCCTTACATATTGCATTTTAAGG
Found at i:14051556 original size:26 final size:26
Alignment explanation
Indices: 14051520--14051571 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
14051510 GAATGCTATT
14051520 TCATGCCATTGTCACATATGTGGTAG
1 TCATGCCATTGTCACATATGTGGTAG
14051546 TCATGCCATTGTCACATATGTGGTAG
1 TCATGCCATTGTCACATATGTGGTAG
14051572 GAAAGGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (26 bp):
TCATGCCATTGTCACATATGTGGTAG
Found at i:14064012 original size:26 final size:26
Alignment explanation
Indices: 14063983--14064058 Score: 152
Period size: 26 Copynumber: 2.9 Consensus size: 26
14063973 TTGAAGTATG
14063983 TGAGATATTTGGGGATAGTATGTGTC
1 TGAGATATTTGGGGATAGTATGTGTC
14064009 TGAGATATTTGGGGATAGTATGTGTC
1 TGAGATATTTGGGGATAGTATGTGTC
14064035 TGAGATATTTGGGGATAGTATGTG
1 TGAGATATTTGGGGATAGTATGTG
14064059 GGTGCTTGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 50 1.00
ACGTcount: A:0.24, C:0.03, G:0.36, T:0.38
Consensus pattern (26 bp):
TGAGATATTTGGGGATAGTATGTGTC
Found at i:14074305 original size:83 final size:83
Alignment explanation
Indices: 14074203--14074368 Score: 287
Period size: 83 Copynumber: 2.0 Consensus size: 83
14074193 CAGTTAAGTA
* * *
14074203 AGACTTTAATCGATTAAGAGCATACTGTTTTTGGAACAACCAGCTTCACCAACTTTGCTTTGTTT
1 AGACTTTAATCGATTAAGAGCATACTATTTCTAGAACAACCAGCTTCACCAACTTTGCTTTGTTT
14074268 GAATAATTCTTCTCTTAG
66 GAATAATTCTTCTCTTAG
*
14074286 AGACTTTAATCGATTAAGAGCTTACTATTTCTAGAACAACCAGCTTCACCAACTTTGCTTTGTTT
1 AGACTTTAATCGATTAAGAGCATACTATTTCTAGAACAACCAGCTTCACCAACTTTGCTTTGTTT
*
14074351 GAATACTTCTTCTCTTAG
66 GAATAATTCTTCTCTTAG
14074369 CTTGGTAACA
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (83 bp):
AGACTTTAATCGATTAAGAGCATACTATTTCTAGAACAACCAGCTTCACCAACTTTGCTTTGTTT
GAATAATTCTTCTCTTAG
Found at i:14081801 original size:25 final size:25
Alignment explanation
Indices: 14081767--14081816 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
14081757 CAATAGGAAT
*
14081767 AACACGTTACTTAAAGTTAGAGTCA
1 AACACGTTACTTAAAGTTAAAGTCA
* *
14081792 AACATGTTACTTAGAGTTAAAGTCA
1 AACACGTTACTTAAAGTTAAAGTCA
14081817 TCCTAGCCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (25 bp):
AACACGTTACTTAAAGTTAAAGTCA
Found at i:14083486 original size:28 final size:27
Alignment explanation
Indices: 14083439--14083537 Score: 126
Period size: 28 Copynumber: 3.6 Consensus size: 27
14083429 AAACTATTGT
* *
14083439 ATGGGTTTGTGGTGATCTCATTAAAACC
1 ATGGGTTTGTGGTGAGCTCA-AAAAACC
*
14083467 ATGAGTTTGTGGTGAGCTCAAAAAAACC
1 ATGGGTTTGTGGTGAGCTC-AAAAAACC
*
14083495 ATGGGTTTGTGGTGAGCCCGAAAAAACC
1 ATGGGTTTGTGGTGAGCTC-AAAAAACC
*
14083523 ATGGGTTTATGGTGA
1 ATGGGTTTGTGGTGA
14083538 ACGTGTTAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
28 62 0.98
29 1 0.02
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (27 bp):
ATGGGTTTGTGGTGAGCTCAAAAAACC
Found at i:14091932 original size:21 final size:20
Alignment explanation
Indices: 14091892--14091943 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
14091882 TGATCTATAG
14091892 AATTGAATTAATTAATTTAA
1 AATTGAATTAATTAATTTAA
* *
14091912 AATTGAATATGATTCATTT-A
1 AATTGAAT-TAATTAATTTAA
14091932 AATT-AATTAATT
1 AATTGAATTAATT
14091944 TATAAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 4 0.14
19 3 0.11
20 13 0.46
21 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (20 bp):
AATTGAATTAATTAATTTAA
Found at i:14096328 original size:22 final size:22
Alignment explanation
Indices: 14096298--14096343 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
14096288 TTAGCTTGAG
14096298 TTCCCCACAT-ATAGTTCACCAT
1 TTCCCCACATCATAG-TCACCAT
*
14096320 TTCCTCACATCCATAGTCACCAT
1 TTCCCCACAT-CATAGTCACCAT
14096343 T
1 T
14096344 GTTGCCACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 8 0.38
24 4 0.19
ACGTcount: A:0.26, C:0.37, G:0.04, T:0.33
Consensus pattern (22 bp):
TTCCCCACATCATAGTCACCAT
Found at i:14096658 original size:24 final size:23
Alignment explanation
Indices: 14096624--14096676 Score: 63
Period size: 24 Copynumber: 2.3 Consensus size: 23
14096614 TCCTTTCCAT
* *
14096624 TTTC-TTCTTCCTCCTTTCTTCC
1 TTTCTTTCTTCCCCCTCTCTTCC
14096646 TTTCTTTCTTTCCCCCTCTCTTCC
1 TTTCTTTC-TTCCCCCTCTCTTCC
*
14096670 TCTCTTT
1 TTTCTTT
14096677 GTTATGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 4 0.15
23 3 0.12
24 19 0.73
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTCTTTCTTCCCCCTCTCTTCC
Found at i:14106216 original size:21 final size:19
Alignment explanation
Indices: 14106175--14106222 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
14106165 TTTAAGTTTT
* *
14106175 TTAATTTTAGTTACTTTGG
1 TTAATTTTAGTTAATTAGG
14106194 TTAAGTTTTATGTTAATTAGG
1 TTAA-TTTTA-GTTAATTAGG
14106215 TTCAATTT
1 TT-AATTT
14106223 CTTATGTGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 4 0.17
20 5 0.21
21 13 0.54
22 2 0.08
ACGTcount: A:0.25, C:0.04, G:0.15, T:0.56
Consensus pattern (19 bp):
TTAATTTTAGTTAATTAGG
Found at i:14109935 original size:24 final size:22
Alignment explanation
Indices: 14109882--14109937 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 22
14109872 GCCATGGTTT
* *
14109882 GTGATATATGTGGTAGGCCACA
1 GTGATATTTGTGGTAGGCCAAA
*
14109904 GTGTTATTTGTGGGTAGGCCATAA
1 GTGATATTTGT-GGTAGGCCA-AA
14109928 GTGATATTTG
1 GTGATATTTG
14109938 CAGTTGCGAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 9 0.32
23 9 0.32
24 10 0.36
ACGTcount: A:0.23, C:0.09, G:0.32, T:0.36
Consensus pattern (22 bp):
GTGATATTTGTGGTAGGCCAAA
Found at i:14113178 original size:59 final size:59
Alignment explanation
Indices: 14113072--14113184 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
14113062 GCCATGTGTA
* * ** *
14113072 ACTAGTTTTAGGCATTAAGTTTAAGGGCTTTAGGCATTGTGTGACTTAGGGTTTACGTG
1 ACTAATTTTAGGCATTAAGTTTAAGGGCTTTAGGCATTATGCAACTTAAGGTTTACGTG
** * *
14113131 ACTAATTTTAGGCATTGGGTTTAGGGGTTTTAGGCATTATGCAACTTAAGGTTT
1 ACTAATTTTAGGCATTAAGTTTAAGGGCTTTAGGCATTATGCAACTTAAGGTTT
14113185 GCATGGCTAG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.23, C:0.10, G:0.27, T:0.40
Consensus pattern (59 bp):
ACTAATTTTAGGCATTAAGTTTAAGGGCTTTAGGCATTATGCAACTTAAGGTTTACGTG
Found at i:14113296 original size:23 final size:22
Alignment explanation
Indices: 14113270--14113340 Score: 63
Period size: 23 Copynumber: 3.1 Consensus size: 22
14113260 GACTGGTGGA
*
14113270 TAAGGGATTGCGTGATCAGTTTT
1 TAAGGTATTGCGTGAT-AGTTTT
* * *
14113293 TAA-GTATTGCATGATTGTTTGA
1 TAAGGTATTGCGTGATAGTTT-T
*
14113315 TAAGGTATTGTGTGATTAGTTTT
1 TAAGGTATTGCGTGA-TAGTTTT
14113338 TAA
1 TAA
14113341 TCATTACGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
21 4 0.11
22 13 0.35
23 15 0.41
24 5 0.14
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.45
Consensus pattern (22 bp):
TAAGGTATTGCGTGATAGTTTT
Found at i:14113356 original size:22 final size:22
Alignment explanation
Indices: 14113326--14113402 Score: 64
Period size: 22 Copynumber: 3.5 Consensus size: 22
14113316 AAGGTATTGT
* *
14113326 GTGATTAGTTTTTAATCATTAC
1 GTGACTAGTTTTTAGTCATTAC
** * **
14113348 GTGACTAGTTAATAGGGCATTGT
1 GTGACTAGTTTTTA-GTCATTAC
* *
14113371 GTGATTGGTTTTTAGTCATTAC
1 GTGACTAGTTTTTAGTCATTAC
14113393 GTGACTAGTT
1 GTGACTAGTT
14113403 GATAGTGTTA
Statistics
Matches: 38, Mismatches: 16, Indels: 2
0.68 0.29 0.04
Matches are distributed among these distances:
22 24 0.63
23 14 0.37
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.44
Consensus pattern (22 bp):
GTGACTAGTTTTTAGTCATTAC
Found at i:14113370 original size:45 final size:45
Alignment explanation
Indices: 14113321--14113407 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
14113311 TTGATAAGGT
14113321 ATTGTGTGATTAGTTTTTAATCATTACGTGACTAGTTAATAGGGC
1 ATTGTGTGATTAGTTTTTAATCATTACGTGACTAGTTAATAGGGC
* * *
14113366 ATTGTGTGATTGGTTTTTAGTCATTACGTGACTAGTTGATAG
1 ATTGTGTGATTAGTTTTTAATCATTACGTGACTAGTTAATAG
14113408 TGTTAGTATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.24, C:0.08, G:0.24, T:0.44
Consensus pattern (45 bp):
ATTGTGTGATTAGTTTTTAATCATTACGTGACTAGTTAATAGGGC
Found at i:14114350 original size:21 final size:21
Alignment explanation
Indices: 14114320--14114370 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
14114310 CAATTGTGTG
*
14114320 GCCATGATGCATT-GCTAGAT
1 GCCATCATGCATTGGCTAGAT
14114340 GCCAATCATGCATTGGCTAGAT
1 GCC-ATCATGCATTGGCTAGAT
14114362 GCCATCATG
1 GCCATCATG
14114371 ATCCATGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 3 0.11
21 15 0.54
22 10 0.36
ACGTcount: A:0.25, C:0.24, G:0.24, T:0.27
Consensus pattern (21 bp):
GCCATCATGCATTGGCTAGAT
Found at i:14115286 original size:22 final size:23
Alignment explanation
Indices: 14115261--14115342 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 23
14115251 AGGGCATTGC
* *
14115261 ATGACTTA-TTTTTAGTCATTTT
1 ATGACTTAGTTTTTAGGCATTAT
* *
14115283 ATGAC-TAGTTTATAGGGCATTGT
1 ATGACTTAGTTTTTA-GGCATTAT
*
14115306 ATGACTGA-TTTTTAGGCATTAT
1 ATGACTTAGTTTTTAGGCATTAT
*
14115328 GTGA-TTAGTTTTTAG
1 ATGACTTAGTTTTTAG
14115343 ATTTTTCATG
Statistics
Matches: 48, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
21 4 0.08
22 27 0.56
23 16 0.33
24 1 0.02
ACGTcount: A:0.24, C:0.07, G:0.20, T:0.49
Consensus pattern (23 bp):
ATGACTTAGTTTTTAGGCATTAT
Found at i:14115288 original size:45 final size:45
Alignment explanation
Indices: 14115156--14115325 Score: 139
Period size: 45 Copynumber: 3.8 Consensus size: 45
14115146 TGCATGAATG
* * * * *
14115156 GTTGATA-GGCATTACATGACT-AGCTTTTAGTCATTGTATGAATA
1 GTTGATAGGGCATTGCATGACTGA-TTTTTAGGCATTTTATGACTA
* * * * * * * * *
14115200 GTTTG-TAAGGTATTGCATAATTGGTTTTGAGGCATTGTGTGACTG
1 G-TTGATAGGGCATTGCATGACTGATTTTTAGGCATTTTATGACTA
* *
14115245 GTTGATAGGGCATTGCATGACTTATTTTTAGTCATTTTATGACTA
1 GTTGATAGGGCATTGCATGACTGATTTTTAGGCATTTTATGACTA
* *
14115290 GTTTATAGGGCATTGTATGACTGATTTTTAGGCATT
1 GTTGATAGGGCATTGCATGACTGATTTTTAGGCATT
14115326 ATGTGATTAG
Statistics
Matches: 96, Mismatches: 26, Indels: 7
0.74 0.20 0.05
Matches are distributed among these distances:
44 6 0.06
45 90 0.94
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (45 bp):
GTTGATAGGGCATTGCATGACTGATTTTTAGGCATTTTATGACTA
Found at i:14115321 original size:23 final size:22
Alignment explanation
Indices: 14115229--14115325 Score: 79
Period size: 23 Copynumber: 4.3 Consensus size: 22
14115219 ATTGGTTTTG
* * *
14115229 AGGCATTGTGTGACTGGTTGAT
1 AGGCATTGTATGACTGATTTAT
* * *
14115251 AGGGCATTGCATGACTTATTTTT
1 A-GGCATTGTATGACTGATTTAT
* *
14115274 AGTCATTTTATGACT-AGTTTAT
1 AGGCATTGTATGACTGA-TTTAT
*
14115296 AGGGCATTGTATGACTGATTTTT
1 A-GGCATTGTATGACTGATTTAT
14115319 AGGCATT
1 AGGCATT
14115326 ATGTGATTAG
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
21 1 0.02
22 23 0.40
23 33 0.57
24 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (22 bp):
AGGCATTGTATGACTGATTTAT
Found at i:14115323 original size:90 final size:89
Alignment explanation
Indices: 14115140--14115331 Score: 215
Period size: 90 Copynumber: 2.1 Consensus size: 89
14115130 CTAGCAGATA
** *
14115140 AGGCATTGCATGAATGGTTGATAGGCATTACATGACTAGCTTTTAGTCATTGTATGAATAGTTTG
1 AGGCATTGTGTGAATGGTTGATAGGCATTACATGACTAGCTTTTAGTCATTGTATGAATAGTTTA
* * *
14115205 TAAGGTATTGCATAATTGGTTTTG
66 TAAGGCATTGCATAACTGATTTTG
* * * * *
14115229 AGGCATTGTGTGACTGGTTGATAGGGCATTGCATGACTTA-TTTTTAGTCATTTTATGACTAGTT
1 AGGCATTGTGTGAATGGTTGATA-GGCATTACATGAC-TAGCTTTTAGTCATTGTATGAATAGTT
* * * *
14115293 TATAGGGCATTGTATGACTGATTTTT
64 TATAAGGCATTGCATAACTGATTTTG
*
14115319 AGGCATTATGTGA
1 AGGCATTGTGTGA
14115332 TTAGTTTTTA
Statistics
Matches: 85, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
89 20 0.24
90 63 0.74
91 2 0.02
ACGTcount: A:0.25, C:0.09, G:0.25, T:0.41
Consensus pattern (89 bp):
AGGCATTGTGTGAATGGTTGATAGGCATTACATGACTAGCTTTTAGTCATTGTATGAATAGTTTA
TAAGGCATTGCATAACTGATTTTG
Found at i:14115337 original size:45 final size:45
Alignment explanation
Indices: 14115224--14115338 Score: 140
Period size: 45 Copynumber: 2.6 Consensus size: 45
14115214 GCATAATTGG
* * * * *
14115224 TTTTGAGGCATTGTGTGACTGGTTGATAGGGCATTGCATGACTTA
1 TTTTTAGGCATTATGTGACTAGTTTATAGGGCATTGCATGACTGA
* * * *
14115269 TTTTTAGTCATTTTATGACTAGTTTATAGGGCATTGTATGACTGA
1 TTTTTAGGCATTATGTGACTAGTTTATAGGGCATTGCATGACTGA
*
14115314 TTTTTAGGCATTATGTGATTAGTTT
1 TTTTTAGGCATTATGTGACTAGTTT
14115339 TTAGATTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 58 1.00
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (45 bp):
TTTTTAGGCATTATGTGACTAGTTTATAGGGCATTGCATGACTGA
Found at i:14118859 original size:43 final size:43
Alignment explanation
Indices: 14118784--14118874 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
14118774 GCATTAATAA
* * * *
14118784 GCATTGTGTGACCCCATATCCGAGATTACATTACGTGACTTAG
1 GCATTCTGTGACCCCACATCCGACATTACATTACGAGACTTAG
** *
14118827 GCATTCTGTGACCCCACATTTGACATTGCATTACGAGACTTAG
1 GCATTCTGTGACCCCACATCCGACATTACATTACGAGACTTAG
14118870 GCATT
1 GCATT
14118875 GCGTGATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (43 bp):
GCATTCTGTGACCCCACATCCGACATTACATTACGAGACTTAG
Found at i:14118901 original size:22 final size:22
Alignment explanation
Indices: 14118870--14118926 Score: 80
Period size: 22 Copynumber: 2.6 Consensus size: 22
14118860 CGAGACTTAG
*
14118870 GCATTGCGTGA-TAATTTTTTAT
1 GCATTGCGTGACT-ATTTTTTAA
*
14118892 GCATTCCGTGACTATTTTTTAA
1 GCATTGCGTGACTATTTTTTAA
14118914 GCATTGCGTGACT
1 GCATTGCGTGACT
14118927 GAAAAGCATG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 30 0.97
23 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (22 bp):
GCATTGCGTGACTATTTTTTAA
Found at i:14125510 original size:22 final size:22
Alignment explanation
Indices: 14125482--14125538 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
14125472 ACAATGCCTA
14125482 AGTCATGCAATGCCTAAAAACT
1 AGTCATGCAATGCCTAAAAACT
* *
14125504 AGTCATGCAATGCCTATAACCT
1 AGTCATGCAATGCCTAAAAACT
**
14125526 AGTCGCGCAATGC
1 AGTCATGCAATGC
14125539 TTCAGTCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (22 bp):
AGTCATGCAATGCCTAAAAACT
Found at i:14125537 original size:60 final size:60
Alignment explanation
Indices: 14125436--14125560 Score: 160
Period size: 60 Copynumber: 2.1 Consensus size: 60
14125426 ACATAATACT
* ** *
14125436 TAAAAACTAGTCATGCAATACTTAAAAGGTAGCCTCACAATGCCTAAGTCATGCAATGCC
1 TAAAAACTAGTCATGCAATACCTAAAACCTAGCCGCACAATGCCTAAGTCATGCAATGCC
* * * * * *
14125496 TAAAAACTAGTCATGCAATGCCTATAACCTAGTCGCGCAATGCTTCAGTCATGCAATGCC
1 TAAAAACTAGTCATGCAATACCTAAAACCTAGCCGCACAATGCCTAAGTCATGCAATGCC
14125556 TAAAA
1 TAAAA
14125561 TCAATCACGT
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (60 bp):
TAAAAACTAGTCATGCAATACCTAAAACCTAGCCGCACAATGCCTAAGTCATGCAATGCC
Found at i:14125590 original size:37 final size:37
Alignment explanation
Indices: 14125534--14125612 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
14125524 CTAGTCGCGC
* ** * *
14125534 AATGCTTCAGTCATGCAATGCCTAAAATCAATCACGT
1 AATGCTTCAATCAAACAATGCCTAAAACCAATCACAT
14125571 AATGCTTCAATCAAACAATGCCTAAAACCAATCACAT
1 AATGCTTCAATCAAACAATGCCTAAAACCAATCACAT
14125608 AATGC
1 AATGC
14125613 CTAAGTTTCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.24
Consensus pattern (37 bp):
AATGCTTCAATCAAACAATGCCTAAAACCAATCACAT
Found at i:14125678 original size:38 final size:36
Alignment explanation
Indices: 14125636--14125712 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
14125626 ATGTAATGAT
*
14125636 TAAGTCACAAAATGCCTAAAAGCCAGTCTCACAATGCC
1 TAAGTCACAAAATGCC-AAAA-CCAATCTCACAATGCC
** **
14125674 TAAGTCACGTAATGCCAAAACCAATCTTGCAATGCC
1 TAAGTCACAAAATGCCAAAACCAATCTCACAATGCC
14125710 TAA
1 TAA
14125713 AAACCAGTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 16 0.47
37 4 0.12
38 14 0.41
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (36 bp):
TAAGTCACAAAATGCCAAAACCAATCTCACAATGCC
Found at i:14125717 original size:22 final size:22
Alignment explanation
Indices: 14125690--14125734 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
14125680 ACGTAATGCC
**
14125690 AAAACCAATCTTGCAATGCCTA
1 AAAACCAATAATGCAATGCCTA
*
14125712 AAAACCAGTAATGCAATGCCTA
1 AAAACCAATAATGCAATGCCTA
14125734 A
1 A
14125735 TAACTAATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.20
Consensus pattern (22 bp):
AAAACCAATAATGCAATGCCTA
Found at i:14127075 original size:22 final size:23
Alignment explanation
Indices: 14127023--14127077 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
14127013 TTCTTATTGG
14127023 AATTATTATTTCATATATAAATTA
1 AATTATTA-TTCATATATAAATTA
* ** *
14127047 AAATATTATT-ATATATTCATTT
1 AATTATTATTCATATATAAATTA
14127069 AATTATTAT
1 AATTATTAT
14127078 ATGAATTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
22 17 0.65
23 2 0.08
24 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTATTATTCATATATAAATTA
Found at i:14148264 original size:18 final size:18
Alignment explanation
Indices: 14148231--14148270 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
14148221 AGTTTCACAA
**
14148231 ATAATTCATAGGTAACAC
1 ATAATTCATAAATAACAC
*
14148249 ATAATTCATAAATAACTC
1 ATAATTCATAAATAACAC
14148267 ATAA
1 ATAA
14148271 ATTAACGATT
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:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (18 bp):
ATAATTCATAAATAACAC
Found at i:14154369 original size:28 final size:28
Alignment explanation
Indices: 14154337--14154393 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
14154327 AACTTTATCA
14154337 TGCACACTTAAATACTGAAGTTAGACAT
1 TGCACACTTAAATACTGAAGTTAGACAT
* *
14154365 TGCACATTTAAATAGTGAAGTTAGACAT
1 TGCACACTTAAATACTGAAGTTAGACAT
14154393 T
1 T
14154394 AATGAATGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (28 bp):
TGCACACTTAAATACTGAAGTTAGACAT
Found at i:14169614 original size:15 final size:15
Alignment explanation
Indices: 14169592--14169647 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
14169582 TCCTTAGCTT
14169592 TTTC-TTCTTTCTCC
1 TTTCTTTCTTTCTCC
*
14169606 TTTCTTTCTTGCTTCC
1 TTTCTTTCTTTC-TCC
* *
14169622 TTTCTTTCTTCCTCT
1 TTTCTTTCTTTCTCC
14169637 TTTCTTTCTTT
1 TTTCTTTCTTT
14169648 TCATCTTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
14 4 0.11
15 18 0.50
16 14 0.39
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (15 bp):
TTTCTTTCTTTCTCC
Found at i:14179852 original size:2 final size:2
Alignment explanation
Indices: 14179845--14179869 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
14179835 AGTTTATACC
14179845 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
14179870 CTTACCCTCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:14184074 original size:234 final size:234
Alignment explanation
Indices: 14183653--14184077 Score: 640
Period size: 234 Copynumber: 1.8 Consensus size: 234
14183643 TTTACCCTTG
14183653 TTATTGTTTACTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTCCGAAAATATATATT
1 TTATTGTTTACTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTCCGAAAATATATATT
* * * *
14183718 TAAATATTTATTTTTGTTAAAATTAATTTTTTTACTTCATTGACTAATTACGTTAACTCTCACAC
66 TAAATATTTATTTTTATTAAAATTAATTTTTTTACTTAATTAACTAACTACGTTAACTCTCACAC
* * * * *
14183783 GTTTACGTTAATATTTAAAATTTAGTTATTCTACTTTTATAAGCTTTTACGTCAATTCTTACAGT
131 ATTTACATTAAGATTTAAAATTTAGTTATTCCACTTTTATAAGCTTTTACATCAATTCTTACAGT
14183848 TTTACGTCAAAGTTTTTTAATGTCAATTTTATACTATAA
196 TTTACGTCAAAGTTTTTTAATGTCAATTTTATACTATAA
* * * * *
14183887 TTATT-TTTATTTAAAAATTAAAATTTATATCTCGTTACATACTTTTAG-CTCGATAATATA-AT
1 TTATTGTTTACTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTC-CGAAAATATATAT
**
14183949 TTAAATATTTATTTTTCATTAAAATTAAATTTTTTTACTTAATTAACTTGCTACGTTAACTCTCA
65 TTAAATATTTATTTTT-ATTAAAATT-AATTTTTTTACTTAATTAACTAACTACGTTAACTCTCA
* *
14184014 TACATTTACATTAAGATTTAAAATTTAGTTATTCCACTTTTATAAGTTTTTACATCAATTCTTA
128 CACATTTACATTAAGATTTAAAATTTAGTTATTCCACTTTTATAAGCTTTTACATCAATTCTTA
14184078 NNNNNNNNNN
Statistics
Matches: 170, Mismatches: 18, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
232 19 0.11
233 56 0.33
234 95 0.56
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.48
Consensus pattern (234 bp):
TTATTGTTTACTTAAAAATTAAAATTTATATATCGTTAAACACTTTTAGTCCGAAAATATATATT
TAAATATTTATTTTTATTAAAATTAATTTTTTTACTTAATTAACTAACTACGTTAACTCTCACAC
ATTTACATTAAGATTTAAAATTTAGTTATTCCACTTTTATAAGCTTTTACATCAATTCTTACAGT
TTTACGTCAAAGTTTTTTAATGTCAATTTTATACTATAA
Found at i:14184333 original size:23 final size:23
Alignment explanation
Indices: 14184307--14184350 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
14184297 TCTCACACAT
14184307 TTATATTAAAATTTA-AAATTTAA
1 TTAT-TTAAAATTTATAAATTTAA
* *
14184330 TTATTTCACATTTATAAATTT
1 TTATTTAAAATTTATAAATTT
14184351 TTACTTCAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATTTAAAATTTATAAATTTAA
Found at i:14184531 original size:18 final size:18
Alignment explanation
Indices: 14184499--14184536 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
14184489 TAAATATTTA
14184499 TTTTTTACTAAAATTAGAT
1 TTTTTTACTAAAATTA-AT
*
14184518 TTTTTTACT-TAATTAAT
1 TTTTTTACTAAAATTAAT
14184535 TT
1 TT
14184537 GTTACGNNNN
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 5 0.28
19 9 0.50
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTTTACTAAAATTAAT
Found at i:14186078 original size:249 final size:248
Alignment explanation
Indices: 14185595--14186052 Score: 634
Period size: 248 Copynumber: 1.8 Consensus size: 248
14185585 NNNNNNNNNN
* * * *
14185595 TTTATGTCAATTCTTACAATTTTACGTCAAGATTTTCTATGTCCATTTTAAACTCTAATTATTTT
1 TTTATGTCAATTCTTACAATTCTACGTCAAGATTATCTATGTCAATTTTAAACTATAATTATTTT
* **
14185660 AATTCTTATTATTTTTTATTAAAAAATTAAAATTTATATATTGTTAAACACTTTTAATCTGAAAA
66 AATTCTTATTA-TTTTTATTAAAAAATAAAAATTTATATATCCTTAAACACTTTTAATCTGAAAA
* *
14185725 TACAAATTTAAATATTTATTTTTCACTAAAATTAATTTTTTTACTTAATTGACTTGTTACGTTAA
130 TACAAATTTAAATATTTATTTTTCAATAAAATTAATTTTTTTACTTAATTAACTTGTTACGTTAA
* *
14185790 CTCTTACACGTTTATGTTAAAATTTAAAATTTAGTTATTCTACTTTTATAAGAT
195 CTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCTACTTTTATAAGAT
* * * * *
14185844 TTTATGTCAATTCTTATAGTTCTATGTTAAGACTTATCTATGAT-AATTTTATACTATAATTATT
1 TTTATGTCAATTCTTACAATTCTACGTCAAGA-TTATCTATG-TCAATTTTAAACTATAATTATT
* * * * * *
14185908 TTTATTCTTATTA-TTTTATTTAAAAATAAAAATTTATATCTCCTTACATACTTTTAA-CTCGAT
64 TTAATTCTTATTATTTTTATTAAAAAATAAAAATTTATATATCCTTAAACACTTTTAATCT-GAA
* *
14185971 AATATAAATTTAAATATTTATTTTTCAATCAAATTAAATTTTTTTACTTAATTAACTTGTTACGT
128 AATACAAATTTAAATATTTATTTTTCAATAAAATT-AATTTTTTTACTTAATTAACTTGTTACGT
14186036 TAACTCTCACACATTTA
192 TAACTCTCACACATTTA
14186053 NNNNNNNNNN
Statistics
Matches: 181, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
247 2 0.01
248 71 0.39
249 70 0.39
250 37 0.20
251 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.50
Consensus pattern (248 bp):
TTTATGTCAATTCTTACAATTCTACGTCAAGATTATCTATGTCAATTTTAAACTATAATTATTTT
AATTCTTATTATTTTTATTAAAAAATAAAAATTTATATATCCTTAAACACTTTTAATCTGAAAAT
ACAAATTTAAATATTTATTTTTCAATAAAATTAATTTTTTTACTTAATTAACTTGTTACGTTAAC
TCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCTACTTTTATAAGAT
Found at i:14186089 original size:249 final size:249
Alignment explanation
Indices: 14185595--14186162 Score: 691
Period size: 249 Copynumber: 2.3 Consensus size: 249
14185585 NNNNNNNNNN
*
14185595 TTTATGTCAATTCTTACAATTTTACGTCAAGA-TTTTCTATG-TCCATTTTAAACTCTAATTATT
1 TTTATGTCAATTCTTACAGTTTTACGTCAAGACTTTTCTATGATCCATTTT-AACTCTAATTATT
* * **
14185658 TTAATTCTTATTATTTTTTATTAAAAAATTAAAATTTATATATTGTTAAACACTTTTAATCTGAA
65 TTTATTCTTATTA-TTTTTATTAAAAAATAAAAATTTATATATCCTTAAACACTTTTAATCTGAA
* *
14185723 AATACAAATTTAAATATTTATTTTTCACTAAAATTAATTTTTTTACTTAATTGACTTGTTACGTT
129 AATACAAATTTAAATATTTATTTTTCAATAAAATTAATTTTTTTACTTAATTAACTTGTTACGTT
* * * *
14185788 AACTCTTACACGTTTATGTTAAAATTTAAAATTTAGTTATTCTACTTTTATAAGA-T
194 AACTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCCACCTTTATAA-ATT
* * * * * * *
14185844 TTTATGTCAATTCTTATAGTTCTATGTTAAGACTTATCTATGAT-AATTTTATACTATAATTATT
1 TTTATGTCAATTCTTACAGTTTTACGTCAAGACTTTTCTATGATCCATTTTA-ACTCTAATTATT
* * * * *
14185908 TTTATTCTTATTA-TTTTATTTAAAAATAAAAATTTATATCTCCTTACATACTTTTAA-CTCGAT
65 TTTATTCTTATTATTTTTATTAAAAAATAAAAATTTATATATCCTTAAACACTTTTAATCT-GAA
* *
14185971 AATATAAATTTAAATATTTATTTTTCAATCAAATTAAATTTTTTTACTTAATTAACTTGTTACGT
129 AATACAAATTTAAATATTTATTTTTCAATAAAATT-AATTTTTTTACTTAATTAACTTGTTACGT
**********
14186036 TAACTCTCACACATTTANNNNNNNNNNTAAAATTTAGTTATTCCACCTTTATAAATT
193 TAACTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCCACCTTTATAAATT
* *
14186093 TTTATGTCAATTTTTACAGTTTTACGTCAAGGCTTTTCTAT-ATCCATTTTAAGCTCTAATTATT
1 TTTATGTCAATTCTTACAGTTTTACGTCAAGACTTTTCTATGATCCATTTTAA-CTCTAATTATT
14186157 TTTATT
65 TTTATT
14186163 TAAAAAATAA
Statistics
Matches: 267, Mismatches: 44, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
247 2 0.01
248 75 0.28
249 153 0.57
250 36 0.13
251 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.49
Consensus pattern (249 bp):
TTTATGTCAATTCTTACAGTTTTACGTCAAGACTTTTCTATGATCCATTTTAACTCTAATTATTT
TTATTCTTATTATTTTTATTAAAAAATAAAAATTTATATATCCTTAAACACTTTTAATCTGAAAA
TACAAATTTAAATATTTATTTTTCAATAAAATTAATTTTTTTACTTAATTAACTTGTTACGTTAA
CTCTCACACATTTATGTTAAAATTTAAAATTTAGTTATTCCACCTTTATAAATT
Done.