Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 64 of 210
Found at i:19237316 original size:21 final size:22
Alignment explanation
Indices: 19237273--19237316 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
19237263 ATGTTTAATA
*
19237273 ATATTGAAAATTATAATATTTT
1 ATATTGAAAATTATAATACTTT
19237295 ATATT-AAAATTA-AATACCTTT
1 ATATTGAAAATTATAATA-CTTT
19237316 A
1 A
19237317 AAAATAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATTGAAAATTATAATACTTT
Found at i:19241870 original size:8 final size:8
Alignment explanation
Indices: 19241853--19241893 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
19241843 TTGTATAAGC
19241853 ATATAT-T
1 ATATATGT
19241860 ATATATGT
1 ATATATGT
19241868 ATATATGT
1 ATATATGT
19241876 ATATATGT
1 ATATATGT
*
19241884 ATATCTGT
1 ATATATGT
19241892 AT
1 AT
19241894 TTTGTATCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 6 0.19
8 26 0.81
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (8 bp):
ATATATGT
Found at i:19245568 original size:16 final size:16
Alignment explanation
Indices: 19245549--19245579 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19245539 AAAAGAAGTT
19245549 GTTAAGGTTGTTAGCA
1 GTTAAGGTTGTTAGCA
*
19245565 GTTAGGGTTGTTAGC
1 GTTAAGGTTGTTAGC
19245580 TGCAGCTAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.35, T:0.39
Consensus pattern (16 bp):
GTTAAGGTTGTTAGCA
Found at i:19245795 original size:6 final size:6
Alignment explanation
Indices: 19245784--19245820 Score: 56
Period size: 6 Copynumber: 6.0 Consensus size: 6
19245774 TCTTTTACTC
*
19245784 ATATTT ATATTT TTATTT CATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT -ATATTT ATATTT ATATTT
19245821 TTTTATTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (6 bp):
ATATTT
Found at i:19245806 original size:19 final size:19
Alignment explanation
Indices: 19245782--19245820 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
19245772 CCTCTTTTAC
*
19245782 TCATATTTATATTTTTATT
1 TCATATTTATATTTATATT
19245801 TCATATTTATATTTATATT
1 TCATATTTATATTTATATT
19245820 T
1 T
19245821 TTTTATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TCATATTTATATTTATATT
Found at i:19245831 original size:27 final size:25
Alignment explanation
Indices: 19245784--19245834 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
19245774 TCTTTTACTC
19245784 ATATTTATATTTTTATTTCATATTT
1 ATATTTATATTTTTATTTCATATTT
19245809 ATATTTATATTTTTTTATTTCATATT
1 ATATTTATA--TTTTTATTTCATATT
19245835 GTTTTAAGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 9 0.38
27 15 0.62
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (25 bp):
ATATTTATATTTTTATTTCATATTT
Found at i:19247862 original size:24 final size:24
Alignment explanation
Indices: 19247830--19247891 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
19247820 GCAACATTTA
* *
19247830 ATTACAAGCCTAAACTCATCGTTTC
1 ATTA-AAGCATAAACTCACCGTTTC
* *
19247855 ATTTAAGCATAAACTCACCGTTTT
1 ATTAAAGCATAAACTCACCGTTTC
*
19247879 ATTAAAGCTTAAA
1 ATTAAAGCATAAA
19247892 ACCAATTACT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
24 28 0.90
25 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (24 bp):
ATTAAAGCATAAACTCACCGTTTC
Found at i:19253915 original size:27 final size:25
Alignment explanation
Indices: 19253870--19253921 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 25
19253860 GTAACCAAAA
19253870 CTCTCTCCTCTCCTTCTTTTCTTTT
1 CTCTCTCCTCTCCTTCTTTTCTTTT
*
19253895 CTCTCTCGTTCTCCTTACTTTTCTTTT
1 CTCTCTC-CTCTCCTT-CTTTTCTTTT
19253922 TTGTAACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.29
26 7 0.29
27 10 0.42
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (25 bp):
CTCTCTCCTCTCCTTCTTTTCTTTT
Found at i:19254173 original size:21 final size:21
Alignment explanation
Indices: 19254142--19254206 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
19254132 AAGAGAAGCG
19254142 GAAAAAGGAAAGAAAAAAAATA
1 GAAAAA-GAAAGAAAAAAAATA
**
19254164 GAAAAAGAAAGGAAAAAGCATA
1 GAAAAAGAAA-GAAAAAAAATA
* * *
19254186 -AATATGAAAGAATAAAAATA
1 GAAAAAGAAAGAAAAAAAATA
19254206 G
1 G
19254207 GTTAAAAATC
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 8 0.24
21 11 0.32
22 15 0.44
ACGTcount: A:0.71, C:0.02, G:0.18, T:0.09
Consensus pattern (21 bp):
GAAAAAGAAAGAAAAAAAATA
Found at i:19258439 original size:12 final size:12
Alignment explanation
Indices: 19258422--19258446 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19258412 ATTGATTTTC
19258422 TCATAATCATAG
1 TCATAATCATAG
19258434 TCATAATCATAG
1 TCATAATCATAG
19258446 T
1 T
19258447 AATGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATAATCATAG
Found at i:19264764 original size:12 final size:12
Alignment explanation
Indices: 19264747--19264771 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
19264737 ATTGATTTAC
19264747 TCATAATCATAG
1 TCATAATCATAG
19264759 TCATAATCATAG
1 TCATAATCATAG
19264771 T
1 T
19264772 AATGTTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TCATAATCATAG
Found at i:19265108 original size:13 final size:13
Alignment explanation
Indices: 19265090--19265116 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19265080 TTATTATTTC
19265090 ATTATTTATTCTA
1 ATTATTTATTCTA
19265103 ATTATTTATTCTA
1 ATTATTTATTCTA
19265116 A
1 A
19265117 CATGATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTATTTATTCTA
Found at i:19280899 original size:14 final size:14
Alignment explanation
Indices: 19280880--19280919 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
19280870 ACAAGTTCCC
19280880 AGAAGAGTCACTAA
1 AGAAGAGTCACTAA
19280894 AGAAGAGTCACTAA
1 AGAAGAGTCACTAA
*
19280908 AGAAGAGCCACT
1 AGAAGAGTCACT
19280920 TTATAACTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.12
Consensus pattern (14 bp):
AGAAGAGTCACTAA
Found at i:19288305 original size:21 final size:20
Alignment explanation
Indices: 19288277--19288320 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
19288267 GATGAAAAAA
*
19288277 AAATTTAAA-AGTTGTATTAT
1 AAATTTAAACA-TTATATTAT
19288297 AAATCTTAAACATTATATTAT
1 AAAT-TTAAACATTATATTAT
19288318 AAA
1 AAA
19288321 AATAATTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 16 0.76
22 1 0.05
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (20 bp):
AAATTTAAACATTATATTAT
Found at i:19289945 original size:24 final size:24
Alignment explanation
Indices: 19289891--19289941 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
19289881 AATCATGGTG
*
19289891 TATTATTATTTCAAAGTTACTATG
1 TATTATTATTTCAAAGTTACTATA
19289915 TATTATTATTT-AAAGTTATCT-TA
1 TATTATTATTTCAAAGTTA-CTATA
19289938 TATT
1 TATT
19289942 TATTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
TATTATTATTTCAAAGTTACTATA
Found at i:19293581 original size:27 final size:27
Alignment explanation
Indices: 19293541--19293620 Score: 83
Period size: 27 Copynumber: 3.0 Consensus size: 27
19293531 AACAAGTCGA
* *
19293541 GAAAGAAAAGCCTTTGTGGCGAAATGT
1 GAAAGAAAATCCTTTGTGGCGAAATAT
* *
19293568 GAAAGAAAATCCTTTTTGGTGAAATAT
1 GAAAGAAAATCCTTTGTGGCGAAATAT
* *
19293595 GAAAG-GAATGCCTTTGTGTC-AAATAT
1 GAAAGAAAAT-CCTTTGTGGCGAAATAT
19293621 TGAATGGATC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
26 9 0.20
27 35 0.80
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (27 bp):
GAAAGAAAATCCTTTGTGGCGAAATAT
Found at i:19294625 original size:19 final size:19
Alignment explanation
Indices: 19294601--19294638 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
19294591 TATCAGATGT
19294601 GTGGTAATAAGTTGTTTAA
1 GTGGTAATAAGTTGTTTAA
19294620 GTGGTAATAAGTTGTTTAA
1 GTGGTAATAAGTTGTTTAA
19294639 CATATATTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
GTGGTAATAAGTTGTTTAA
Found at i:19295846 original size:23 final size:22
Alignment explanation
Indices: 19295820--19295899 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
19295810 AACACTCCAC
*
19295820 GCTAGAATGAAATGCACATAAGT
1 GCTAGAATGAATTGCACA-AAGT
*
19295843 GCTA-AAGTGATTTGCATCAAAGT
1 GCTAGAA-TGAATTGCA-CAAAGT
* *
19295866 GCCTAGAATTAATTGCAAACAAGT
1 G-CTAGAATGAATTGCACA-AAGT
19295890 GCTAGAATGA
1 GCTAGAATGA
19295900 TTTGTATTGA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
22 2 0.04
23 25 0.54
24 17 0.37
25 2 0.04
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (22 bp):
GCTAGAATGAATTGCACAAAGT
Found at i:19302237 original size:13 final size:13
Alignment explanation
Indices: 19302219--19302248 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
19302209 AAACTAGATT
*
19302219 TTAACTAAGTAAA
1 TTAACTAAGAAAA
19302232 TTAACTAAGAAAA
1 TTAACTAAGAAAA
19302245 TTAA
1 TTAA
19302249 AAGATAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
TTAACTAAGAAAA
Found at i:19304085 original size:16 final size:16
Alignment explanation
Indices: 19304064--19304097 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19304054 TTACCAATGA
* *
19304064 AATTCTTTTATTTCTC
1 AATTCTTTCACTTCTC
19304080 AATTCTTTCACTTCTC
1 AATTCTTTCACTTCTC
19304096 AA
1 AA
19304098 GCTAAGATAC
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:0.24, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTCTTTCACTTCTC
Found at i:19306484 original size:29 final size:29
Alignment explanation
Indices: 19306451--19306585 Score: 144
Period size: 29 Copynumber: 4.7 Consensus size: 29
19306441 CAGAGTCTCA
* *
19306451 CCACAAAGGCATCTTTTTAACAGAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * **
19306480 CCACAAAGGTTTCCTTTTAACATAGACCG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
** * *
19306509 CCACAAATTCTTCCTTTTAATAGAGAAAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
* * *
19306538 CTACAAAGGCTTCCTTGTAACAAAGATAG
1 CCACAAAGGCTTCCTTTTAACAGAGATAG
*
19306567 CCACAAAGGCATCCTTTTA
1 CCACAAAGGCTTCCTTTTA
19306586 TGAAATTTGG
Statistics
Matches: 83, Mismatches: 23, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
29 83 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (29 bp):
CCACAAAGGCTTCCTTTTAACAGAGATAG
Found at i:19306582 original size:58 final size:58
Alignment explanation
Indices: 19306451--19306585 Score: 162
Period size: 58 Copynumber: 2.3 Consensus size: 58
19306441 CAGAGTCTCA
* * * * * *
19306451 CCACAAAGGCATCTTTTTAACAGAGATAGCCACAAAGGTTTCCTTTTAACATAGACCG
1 CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
** * * * *
19306509 CCACAAATTCTTCCTTTTAATAGAGAAAGCTACAAAGGCTTCCTTGTAACAAAGATAG
1 CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
19306567 CCACAAAGGCATCCTTTTA
1 CCACAAAGGCATCCTTTTA
19306586 TGAAATTTGG
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.27
Consensus pattern (58 bp):
CCACAAAGGCATCCTTTTAACAGAGAAAGCCACAAAGGCTTCCTTGTAACAAAGACAG
Found at i:19309621 original size:31 final size:30
Alignment explanation
Indices: 19309584--19309733 Score: 99
Period size: 31 Copynumber: 4.8 Consensus size: 30
19309574 TATATGGTTG
19309584 AACATTGCTGAAAATAATTTTTATGTAGTT
1 AACATTGCTGAAAATAATTTTTATGTAGTT
* * * *
19309614 ATTCATTGTTGAAATTGAATTGTATATGTA-TAT
1 A-ACATTGCTGAAAAT-AATT-TTTATGTAGT-T
* * * * *
19309647 AA-GTTGCTG-AAATGATTTGTATATGGTT
1 AACATTGCTGAAAATAATTTTTATGTAGTT
*
19309675 GAACATTGCTGAAAATAATTTTTATATAGTT
1 -AACATTGCTGAAAATAATTTTTATGTAGTT
* *
19309706 ATACATTGTTGAAATTAAATTGTTTATG
1 A-ACATTGCTGAAAAT-AATT-TTTATG
19309734 AATATAGGAT
Statistics
Matches: 90, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
28 6 0.07
29 6 0.07
30 11 0.12
31 44 0.49
32 9 0.10
33 14 0.16
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.45
Consensus pattern (30 bp):
AACATTGCTGAAAATAATTTTTATGTAGTT
Found at i:19309676 original size:92 final size:92
Alignment explanation
Indices: 19309520--19309739 Score: 343
Period size: 92 Copynumber: 2.4 Consensus size: 92
19309510 ATTGTTTTTG
* * *
19309520 GTTATACATTGCTGATATTGAATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGTTG
1 GTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGTTG
*
19309584 AACATTGCTGAAAATAATTTTTATGTA
66 AACATTGCTGAAAATAATTTTTATATA
* * *
19309611 GTTATTCATTGTTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTTGTATATGGTTG
1 GTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGTTG
19309676 AACATTGCTGAAAATAATTTTTATATA
66 AACATTGCTGAAAATAATTTTTATATA
* * *
19309703 GTTATACATTGTTGAAATTAAATTGTTTATGAATATA
1 GTTATACATTGTTGAAATTGAATTGTATATGTATATA
19309740 GGATGTCGAA
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
91 27 0.23
92 90 0.77
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (92 bp):
GTTATACATTGTTGAAATTGAATTGTATATGTATATAAGTTGCCGAAATGATTCGTATATGGTTG
AACATTGCTGAAAATAATTTTTATATA
Found at i:19309783 original size:31 final size:31
Alignment explanation
Indices: 19309748--19309813 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
19309738 TAGGATGTCG
19309748 AATTTGATT-TGTATAT-GATTATACATTGCCA
1 AATTTGATTCT-TATATAG-TTATACATTGCCA
* *
19309779 AATTTGATTCTTATATAGTTATATATTGCCG
1 AATTTGATTCTTATATAGTTATACATTGCCA
19309810 AATT
1 AATT
19309814 GCTTGGCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.09, G:0.12, T:0.47
Consensus pattern (31 bp):
AATTTGATTCTTATATAGTTATACATTGCCA
Found at i:19309799 original size:93 final size:92
Alignment explanation
Indices: 19309520--19309806 Score: 285
Period size: 92 Copynumber: 3.1 Consensus size: 92
19309510 ATTGTTTTTG
* * * * * * * * *
19309520 GTTATACATTGCTGATATTGAATTGTATAT-TACATAAGTTGCCGAAATGATTCGTATATGGTTG
1 GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCTGAAATGATTTGTATATGATTG
* * *
19309584 AACATTGCTGAAAATAATTTTTATGTA
66 AACATTGCTCAAAATAATTCTTATATA
* * * * *
19309611 GTTATTCATTGTTGAAATTGAATTGTATATGTATATAAGTTGCTGAAATGATTTGTATATGGTTG
1 GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCTGAAATGATTTGTATATGATTG
* *
19309676 AACATTGCTGAAAATAATTTTTATATA
66 AACATTGCTCAAAATAATTCTTATATA
* * *
19309703 GTTATACATTGTTGAAATTAAATTGTTTATGAATATAGGATG-TCGAATTTGATTTGTATATGAT
1 GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCT-GAA-ATGATTTGTATATGAT
* *
19309767 T-ATACATTGC-CAAATTTGATTCTTATATA
64 TGA-ACATTGCTCAAA-ATAATTCTTATATA
*
19309796 GTTATATATTG
1 GTTATACATTG
19309807 CCGAATTGCT
Statistics
Matches: 171, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
91 28 0.16
92 100 0.58
93 43 0.25
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (92 bp):
GTTATACATTGTTGAAATTAAATTGTATATGAATATAAGATGCTGAAATGATTTGTATATGATTG
AACATTGCTCAAAATAATTCTTATATA
Found at i:19313972 original size:20 final size:21
Alignment explanation
Indices: 19313947--19313996 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
19313937 AAGCTTACGC
19313947 TAAGTAAATGA-AATGGA-AAG
1 TAAGTAAATGAGAAT-GATAAG
19313967 TAAGTAAAT-AGAATGATAAG
1 TAAGTAAATGAGAATGATAAG
19313987 TAAGTAAATG
1 TAAGTAAATG
19313997 GAGTGGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 3 0.11
20 24 0.89
ACGTcount: A:0.54, C:0.00, G:0.22, T:0.24
Consensus pattern (21 bp):
TAAGTAAATGAGAATGATAAG
Found at i:19323602 original size:12 final size:12
Alignment explanation
Indices: 19323584--19323613 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
19323574 AGGTAGGCAA
19323584 CTTTTTTTTGCG
1 CTTTTTTTTGCG
*
19323596 GTTTTTTTTGCG
1 CTTTTTTTTGCG
19323608 CTTTTT
1 CTTTTT
19323614 GCTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.13, G:0.17, T:0.70
Consensus pattern (12 bp):
CTTTTTTTTGCG
Found at i:19326363 original size:22 final size:22
Alignment explanation
Indices: 19326335--19326377 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
19326325 GCCGTGGCTA
19326335 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
19326357 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
19326378 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:19333571 original size:27 final size:30
Alignment explanation
Indices: 19333541--19333598 Score: 68
Period size: 31 Copynumber: 2.0 Consensus size: 30
19333531 GTTTCTCTTC
19333541 TCTCAC-CACTTTT-TTCTT-TTGGCCGAA
1 TCTCACTCACTTTTCTTCTTGTTGGCCGAA
* *
19333568 TCTCTCTTCCCTTTTCTTCTTGTTGGCCGAA
1 TCTCAC-TCACTTTTCTTCTTGTTGGCCGAA
19333599 CCTTTTCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
27 5 0.20
29 6 0.24
30 5 0.20
31 9 0.36
ACGTcount: A:0.10, C:0.31, G:0.12, T:0.47
Consensus pattern (30 bp):
TCTCACTCACTTTTCTTCTTGTTGGCCGAA
Found at i:19334325 original size:27 final size:27
Alignment explanation
Indices: 19334286--19334619 Score: 323
Period size: 27 Copynumber: 12.4 Consensus size: 27
19334276 AAATTGTGGG
* * *
19334286 AAAATGTCTGAAATACTCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
19334313 AAAATGACCGAAATATCCC-CGAATGGT
1 AAAATGACCGAAATA-CCCTCGAAGGGT
* * *
19334340 AAAATAACTGAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
19334367 AAAATGACCGAAATACTCC-CGAAAGGT
1 AAAATGACCGAAATAC-CCTCGAAGGGT
** *
19334394 AAAATGACTAAAATA-CCTCCGAAGTGT
1 AAAATGACCGAAATACCCT-CGAAGGGT
* **
19334421 AAAATAACTAAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
*
19334448 AAAATGACCGAAATACCCTCGAAAGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
19334475 AAAATGACCAAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* ** * *
19334502 AAAATAATTGAAATACCCTAGAAAGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * *
19334529 CAAATAACTGAAATACCCTAGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* *
19334556 AAAATGATCGAAATACCCCCGAAGGGT
1 AAAATGACCGAAATACCCTCGAAGGGT
* * * * *
19334583 AAAATGACCAAAATAACTTCGAAAGTT
1 AAAATGACCGAAATACCCTCGAAGGGT
19334610 AAAATGACCG
1 AAAATGACCG
19334620 TTATACCCCT
Statistics
Matches: 254, Mismatches: 47, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
25 2 0.01
26 3 0.01
27 242 0.95
28 7 0.03
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCGAAGGGT
Found at i:19334627 original size:81 final size:81
Alignment explanation
Indices: 19334286--19334619 Score: 391
Period size: 81 Copynumber: 4.1 Consensus size: 81
19334276 AAATTGTGGG
* * * * * * * *
19334286 AAAATGTCTGAAATACTCTCGAAGGGTAAAATGACCGAAATATCCCCGAATGGTAAAATAACTGA
1 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
* *
19334351 AATACCCCCGAAGGGT
66 AATACCCTCGAAAGGT
* * *
19334367 AAAATGACCGAAATACTCC-CGAAAGGTAAAATGACTAAAATACCTCCGAAGTGTAAAATAACTA
1 AAAATGACCGAAATAC-CCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTA
*
19334431 AAATACCCTCGAAGGGT
65 AAATACCCTCGAAAGGT
* *
19334448 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAATTGA
1 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
*
19334513 AATACCCTAGAAAGGT
66 AATACCCTCGAAAGGT
* * * * * * * * *
19334529 CAAATAACTGAAATACCCTAGAAGGGTAAAATGATCGAAATACCCCCGAAGGGTAAAATGACCAA
1 AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
* * *
19334594 AATAACTTCGAAAGTT
66 AATACCCTCGAAAGGT
19334610 AAAATGACCG
1 AAAATGACCG
19334620 TTATACCCCT
Statistics
Matches: 214, Mismatches: 37, Indels: 4
0.84 0.15 0.02
Matches are distributed among these distances:
80 2 0.01
81 211 0.99
82 1 0.00
ACGTcount: A:0.45, C:0.19, G:0.18, T:0.18
Consensus pattern (81 bp):
AAAATGACCGAAATACCCTCGAAAGGTAAAATGACCAAAATACCCCCGAAGGGTAAAATAACTAA
AATACCCTCGAAAGGT
Found at i:19335015 original size:28 final size:28
Alignment explanation
Indices: 19334975--19335059 Score: 116
Period size: 28 Copynumber: 3.0 Consensus size: 28
19334965 ATTGTACTAA
* * *
19334975 TTACTGTATTGGGCTAAGGGCCATATTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
*
19335003 TTACTTTATTGGGCTAAGGCCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
* *
19335031 TTACTGTAATGGGCTAAGACCCACACTG
1 TTACTGTATTGGGCTAAGGCCCACACTG
19335059 T
1 T
19335060 ACTTTTACTG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 50 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTG
Found at i:19351844 original size:35 final size:35
Alignment explanation
Indices: 19351785--19351901 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
19351775 ACTCTCTGTT
* ** *
19351785 TTGGTGTATTTCGGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* *
19351820 TTAGTGTGTTTTGGAGGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * **
19351855 TTGGTGTGTTTCGGATGGATTTGCTCTTACAAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
19351890 TCTGGTGTGTTT
1 T-TGGTGTGTTT
19351902 GGGTGGTTTG
Statistics
Matches: 69, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
35 59 0.86
36 10 0.14
ACGTcount: A:0.16, C:0.12, G:0.30, T:0.42
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
Found at i:19354425 original size:109 final size:110
Alignment explanation
Indices: 19354256--19354453 Score: 344
Period size: 109 Copynumber: 1.8 Consensus size: 110
19354246 AGACATATTT
*
19354256 ATGAAAATGTTGTGTGTAAAATGCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
1 ATGAAAATGTTGTGTGTAAAATCCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
*
19354321 AATACGTTATTTTGTCTTAATGAAATATCATTAATAGATTAATAC
66 AATACGTTATTTTGGCTTAATGAAATATCATTAATAGATTAATAC
*
19354366 ATGAAAATGTTGTGTGT-AAATCCATATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
1 ATGAAAATGTTGTGTGTAAAATCCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
* *
19354430 AATACGTTGTTTTGGCTTGATGAA
66 AATACGTTATTTTGGCTTAATGAA
19354454 TTATTGTTAA
Statistics
Matches: 83, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
109 66 0.80
110 17 0.20
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (110 bp):
ATGAAAATGTTGTGTGTAAAATCCAAATGAATATATAAGCTAGACTTGTGGGTCATTAAAGCATG
AATACGTTATTTTGGCTTAATGAAATATCATTAATAGATTAATAC
Found at i:19356406 original size:15 final size:15
Alignment explanation
Indices: 19356386--19356422 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
19356376 TACCTACGCA
19356386 TTAAAATTAAACGTG
1 TTAAAATTAAACGTG
19356401 TTAAAATTAAACGTG
1 TTAAAATTAAACGTG
*
19356416 TCAAAAT
1 TTAAAAT
19356423 ATGGTACCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (15 bp):
TTAAAATTAAACGTG
Found at i:19356722 original size:22 final size:23
Alignment explanation
Indices: 19356690--19356746 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
19356680 TGCACTAATG
*
19356690 AACAGATAGCACTA-AAGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
* *
19356712 CACAGAGAGCAC-AGATGTGCTA
1 AACAGAGAGCACTAGAAGTGCTA
19356734 AACAGAGAGCACT
1 AACAGAGAGCACT
19356747 GACATGCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.42, C:0.21, G:0.23, T:0.14
Consensus pattern (23 bp):
AACAGAGAGCACTAGAAGTGCTA
Found at i:19356754 original size:22 final size:22
Alignment explanation
Indices: 19356690--19356757 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
19356680 TGCACTAATG
*
19356690 AACAGATAGCACT-AAAGTGCTA
1 AACAGAGAGCACTGAAA-TGCTA
* * **
19356712 CACAGAGAGCACAGATGTGCTA
1 AACAGAGAGCACTGAAATGCTA
*
19356734 AACAGAGAGCACTGACATGCTA
1 AACAGAGAGCACTGAAATGCTA
19356756 AA
1 AA
19356758 TATCAGAGAG
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
22 35 0.97
23 1 0.03
ACGTcount: A:0.43, C:0.21, G:0.22, T:0.15
Consensus pattern (22 bp):
AACAGAGAGCACTGAAATGCTA
Found at i:19356767 original size:25 final size:25
Alignment explanation
Indices: 19356736--19356818 Score: 105
Period size: 25 Copynumber: 3.3 Consensus size: 25
19356726 ATGTGCTAAA
**
19356736 CAGAGAGCACTGACATGCTAA-ATAT
1 CAGAGAGCACCAACATGCTAATA-AT
*
19356761 CAGAGAGCACCAACGTGCTAATAAT
1 CAGAGAGCACCAACATGCTAATAAT
**
19356786 CAGAGAGCACCAATGTGCTAATAAT
1 CAGAGAGCACCAACATGCTAATAAT
19356811 CAGAGAGC
1 CAGAGAGC
19356819 GCGCTAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
25 52 0.98
26 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.17
Consensus pattern (25 bp):
CAGAGAGCACCAACATGCTAATAAT
Found at i:19357112 original size:41 final size:40
Alignment explanation
Indices: 19357037--19357122 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 40
19357027 TAAAAAATTT
*
19357037 TAAAACAAATATTAAAACAAAAAACAAATAAAAAATAATAC
1 TAAAACAAATATTAAAACAAAAAACAAATAAAAAAT-ATAA
* * * * * *
19357078 TAAAACAATTCTTAAAACAATACATAAATTAAAAATATAA
1 TAAAACAAATATTAAAACAAAAAACAAATAAAAAATATAA
19357118 TAAAA
1 TAAAA
19357123 AGTAATTATA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.22
Consensus pattern (40 bp):
TAAAACAAATATTAAAACAAAAAACAAATAAAAAATATAA
Found at i:19357219 original size:25 final size:27
Alignment explanation
Indices: 19357171--19357221 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
19357161 TAATAGTCAA
*
19357171 ATTAATAATAAAACAAAAGTATATTTG
1 ATTAAAAATAAAACAAAAGTATATTTG
19357198 ATTAAAAATAAAA-AAAA-TATATTT
1 ATTAAAAATAAAACAAAAGTATATTT
19357222 AATATATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (27 bp):
ATTAAAAATAAAACAAAAGTATATTTG
Found at i:19357712 original size:14 final size:14
Alignment explanation
Indices: 19357695--19357724 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
19357685 TAATATAGGC
*
19357695 ATTTAAATAAAATA
1 ATTTAAAAAAAATA
19357709 ATTTAAAAAAAATA
1 ATTTAAAAAAAATA
19357723 AT
1 AT
19357725 CTTGTAGTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTTAAAAAAAATA
Found at i:19358437 original size:5 final size:5
Alignment explanation
Indices: 19358413--19358484 Score: 117
Period size: 5 Copynumber: 14.0 Consensus size: 5
19358403 TTCTTTTGTT
*
19358413 TTATA TATATAA TAATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA T-TAT-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
19358465 TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA
19358485 AAATAACATA
Statistics
Matches: 63, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
5 56 0.89
6 5 0.08
7 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (5 bp):
TTATA
Found at i:19361074 original size:21 final size:22
Alignment explanation
Indices: 19361050--19361091 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
19361040 TTATTAAATA
*
19361050 AAAATAAAAAAAT-ATTTTTCG
1 AAAACAAAAAAATAATTTTTCG
*
19361071 AAAACAAAATAATAATTTTTC
1 AAAACAAAAAAATAATTTTTC
19361092 AAAGTGGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAACAAAAAAATAATTTTTCG
Found at i:19361898 original size:19 final size:19
Alignment explanation
Indices: 19361861--19361947 Score: 99
Period size: 19 Copynumber: 4.5 Consensus size: 19
19361851 ATATGTTTAA
*
19361861 TTTT-TAATTTATTTCTA-
1 TTTTATAATTTATTTATAT
19361878 TTTTATAATTTAATTTATATT
1 TTTTATAATTT-ATTTATA-T
*
19361899 TTTTATATATTT-TTTAGAT
1 TTTTATA-ATTTATTTATAT
19361918 TTTTATACATTTATTTATAT
1 TTTTATA-ATTTATTTATAT
19361938 TTTTATAATT
1 TTTTATAATT
19361948 CTTTAAAGTT
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
17 4 0.07
18 6 0.10
19 21 0.35
20 18 0.30
21 7 0.12
22 4 0.07
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.68
Consensus pattern (19 bp):
TTTTATAATTTATTTATAT
Found at i:19362968 original size:14 final size:13
Alignment explanation
Indices: 19362937--19362975 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 13
19362927 TTCAACTAGT
19362937 ATAATA-ATAATC
1 ATAATATATAATC
19362949 ATTAATATATAATAC
1 A-TAATATATAAT-C
19362964 ATAATATATAAT
1 ATAATATATAAT
19362976 GTACTACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 5 0.21
14 16 0.67
15 2 0.08
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (13 bp):
ATAATATATAATC
Found at i:19362992 original size:20 final size:20
Alignment explanation
Indices: 19362967--19363007 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
19362957 ATAATACATA
19362967 ATATATA-ATGTACTACTATT
1 ATATATATATG-ACTACTATT
*
19362987 ATATATATATGACTATTATT
1 ATATATATATGACTACTATT
19363007 A
1 A
19363008 CAATATAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATATATATGACTACTATT
Found at i:19370393 original size:21 final size:21
Alignment explanation
Indices: 19370369--19370518 Score: 110
Period size: 21 Copynumber: 7.2 Consensus size: 21
19370359 TTACTTTTCA
* *
19370369 TTTAGCTCTTACGAGCTTCTG
1 TTTAACTCTTATGAGCTTCTG
* * *
19370390 TTTAACTCATATGAGTTTCCG
1 TTTAACTCTTATGAGCTTCTG
* *
19370411 TTCAACTC-TATTGAGCTTCTA
1 TTTAACTCTTA-TGAGCTTCTG
* *
19370432 TTTAACTCTTATG-GGTTTTCG
1 TTTAACTCTTATGAGCTTCT-G
* *
19370453 TTTAGCTCTTATGAGCTTCCG
1 TTTAACTCTTATGAGCTTCTG
* *
19370474 TTCAAAC-CTTATGGGCTTCTG
1 TT-TAACTCTTATGAGCTTCTG
* *
19370495 TTTAGCTC-AATGAGCTTCTG
1 TTTAACTCTTATGAGCTTCTG
19370515 TTTA
1 TTTA
19370519 GCCTTCGAGC
Statistics
Matches: 98, Mismatches: 25, Indels: 13
0.72 0.18 0.10
Matches are distributed among these distances:
20 22 0.22
21 69 0.70
22 7 0.07
ACGTcount: A:0.19, C:0.21, G:0.17, T:0.44
Consensus pattern (21 bp):
TTTAACTCTTATGAGCTTCTG
Found at i:19370468 original size:42 final size:41
Alignment explanation
Indices: 19370363--19370518 Score: 145
Period size: 42 Copynumber: 3.7 Consensus size: 41
19370353 TTGTGTTTAC
* * * *
19370363 TTTTCATTTAGCTCTTACGAGCTTCTGTTTAACTCATATGAG
1 TTTTCGTTTAGCTC-TATGAGCTTCTGTTTAACTCTTATGGG
* * * *
19370405 TTTCCGTTCAACTCTATTGAGCTTCTATTTAACTCTTATGGG
1 TTTTCGTTTAGCTCTA-TGAGCTTCTGTTTAACTCTTATGGG
* *
19370447 TTTTCGTTTAGCTCTTATGAGCTTCCGTTCAAAC-CTTATGGG
1 TTTTCGTTTAGCTC-TATGAGCTTCTGTT-TAACTCTTATGGG
* *
19370489 -CTTCTGTTTAGCTCAATGAGCTTCTGTTTA
1 TTTTC-GTTTAGCTCTATGAGCTTCTGTTTA
19370519 GCCTTCGAGC
Statistics
Matches: 92, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
40 1 0.01
41 17 0.18
42 69 0.75
43 5 0.05
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.45
Consensus pattern (41 bp):
TTTTCGTTTAGCTCTATGAGCTTCTGTTTAACTCTTATGGG
Found at i:19374146 original size:51 final size:49
Alignment explanation
Indices: 19374014--19374209 Score: 196
Period size: 51 Copynumber: 3.9 Consensus size: 49
19374004 GTGAAAGTGA
* *
19374014 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGAT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATA-G-T
* * * * *
19374064 AGGTCGCATGTGTAATACTATGTGCAAGCTACTATGTGTACCGGATAGCT
1 TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-T
* * * * *
19374114 TCGATCACATGTGTAGTACTATATGTAGGCTACGACGTGTATCGGATAGT
1 T-GGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
* * *
19374164 GATGGTCACATGTGTAGTACTATGTGTAGGCTACTATGTGAACCGG
1 --TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
19374210 TATCATTAAT
Statistics
Matches: 118, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
50 41 0.35
51 76 0.64
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.31
Consensus pattern (49 bp):
TGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT
Found at i:19374296 original size:46 final size:43
Alignment explanation
Indices: 19374205--19374303 Score: 110
Period size: 46 Copynumber: 2.2 Consensus size: 43
19374195 TACTATGTGA
* *
19374205 ACCGGTATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCC
1 ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCC
* *
19374248 ACCGGATATCATTGATTAGAAAGGGTGGTTGCTGTGTGCTAAAT-CC
1 ACCGG-TATCATTAATTA-AAA-GGTGGTTGCTATGTGCT-AATCCC
19374294 ACCGTGTATC
1 ACCG-GTATC
19374304 TGTTATTATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
43 5 0.11
44 11 0.23
45 2 0.04
46 26 0.55
47 3 0.06
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.32
Consensus pattern (43 bp):
ACCGGTATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCC
Found at i:19380986 original size:42 final size:41
Alignment explanation
Indices: 19380931--19381074 Score: 139
Period size: 42 Copynumber: 3.4 Consensus size: 41
19380921 TAGCTCTCAC
* * * *
19380931 GAGCTTATATTTAACTCATATGAGTTTCTGTTCAGCTCTATT
1 GAGCTTCTGTTTAAC-CTTATGGGTTTCTGTTCAGCTCTATT
**
19380973 GAGCTTCTGTTTAACCCTTATGGGTTTCCATTCAGCTCT-TAT
1 GAGCTTCTGTTTAA-CCTTATGGGTTTCTGTTCAGCTCTAT-T
* * *
19381015 GAGCTTCCGTTCAACCTTTATGGGTTTCTGTTTAGCTCTCA-T
1 GAGCTTCTGTTTAACC-TTATGGGTTTCTGTTCAGCTCT-ATT
*
19381057 GAGCTTCTGTTTAGCCTT
1 GAGCTTCTGTTTAACCTT
19381075 CAGGCTTCTG
Statistics
Matches: 83, Mismatches: 14, Indels: 11
0.77 0.13 0.10
Matches are distributed among these distances:
41 5 0.06
42 77 0.93
43 1 0.01
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (41 bp):
GAGCTTCTGTTTAACCTTATGGGTTTCTGTTCAGCTCTATT
Found at i:19381066 original size:21 final size:21
Alignment explanation
Indices: 19380917--19381071 Score: 89
Period size: 21 Copynumber: 7.4 Consensus size: 21
19380907 GTTTACTTTT
* * *
19380917 TGTTTAGCTCTCACGAGCTTA
1 TGTTTAGCTCTTATGAGCTTC
* * * *
19380938 TATTTAACTCATATGAGTTTC
1 TGTTTAGCTCTTATGAGCTTC
*
19380959 TGTTCAGCTC-TATTGAGCTTC
1 TGTTTAGCTCTTA-TGAGCTTC
* * * *
19380980 TGTTTAACCCTTATGGGTTTC
1 TGTTTAGCTCTTATGAGCTTC
** *
19381001 CATTCAGCTCTTATGAGCTTC
1 TGTTTAGCTCTTATGAGCTTC
* * * * *
19381022 CGTTCAAC-CTTTATGGGTTTC
1 TGTTTAGCTC-TTATGAGCTTC
*
19381043 TGTTTAGCTCTCATGAGCTTC
1 TGTTTAGCTCTTATGAGCTTC
19381064 TGTTTAGC
1 TGTTTAGC
19381072 CTTCAGGCTT
Statistics
Matches: 97, Mismatches: 33, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
20 3 0.03
21 91 0.94
22 3 0.03
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.43
Consensus pattern (21 bp):
TGTTTAGCTCTTATGAGCTTC
Found at i:19382538 original size:19 final size:18
Alignment explanation
Indices: 19382499--19382540 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
19382489 ACACTTGCCG
* *
19382499 ATCA-CAACAATCTCCAC
1 ATCATCAACAATCTCAAA
19382516 ATCATCAACAATTCTCAAA
1 ATCATCAACAA-TCTCAAA
19382535 ATCATC
1 ATCATC
19382541 CTCTTAGTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 4 0.19
18 6 0.29
19 11 0.52
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.24
Consensus pattern (18 bp):
ATCATCAACAATCTCAAA
Found at i:19384152 original size:37 final size:37
Alignment explanation
Indices: 19384102--19384172 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
19384092 GTTTACAGAT
19384102 CAAATATAATTAAATCGTATCATTTACTATTCATATC
1 CAAATATAATTAAATCGTATCATTTACTATTCATATC
*
19384139 CAAATATAATTAAATTGTATCATTTACTATTCAT
1 CAAATATAATTAAATCGTATCATTTACTATTCAT
19384173 GCATATTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.42
Consensus pattern (37 bp):
CAAATATAATTAAATCGTATCATTTACTATTCATATC
Found at i:19385451 original size:27 final size:25
Alignment explanation
Indices: 19385421--19385476 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
19385411 CATAATTGGA
19385421 AAGCACACTCTCGAGCCATATAACAAG
1 AAGCACA-TCT-GAGCCATATAACAAG
* * * *
19385448 AAGCTCATGTGAGCCATGTAACAGG
1 AAGCACATCTGAGCCATATAACAAG
19385473 AAGC
1 AAGC
19385477 TTATCCAGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 17 0.68
26 2 0.08
27 6 0.24
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.16
Consensus pattern (25 bp):
AAGCACATCTGAGCCATATAACAAG
Found at i:19385551 original size:25 final size:25
Alignment explanation
Indices: 19385489--19385553 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 25
19385479 ATCCAGGTCA
*
19385489 TATAACGGGAAGCT-CATGCGAGCC
1 TATAACGGGAAGCTCCATGAGAGCC
*
19385513 TATAACGGGTAGCTCCAT-AGAGCC
1 TATAACGGGAAGCTCCATGAGAGCC
19385537 -ATCAATCGGGAAGCTCC
1 TAT-AA-CGGGAAGCTCC
19385554 GGATAGCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
23 2 0.06
24 20 0.57
25 13 0.37
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (25 bp):
TATAACGGGAAGCTCCATGAGAGCC
Found at i:19389271 original size:45 final size:45
Alignment explanation
Indices: 19389207--19389295 Score: 178
Period size: 45 Copynumber: 2.0 Consensus size: 45
19389197 CTGAACTTGC
19389207 GCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAAGA
1 GCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAAGA
19389252 GCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAAG
1 GCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAAG
19389296 TCCCCAATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.27
Consensus pattern (45 bp):
GCAAGGAGTGTTGGCGATATGGTTGTAGCTTCAAGTAAACTAAGA
Found at i:19395090 original size:20 final size:20
Alignment explanation
Indices: 19395053--19395090 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19395043 ATAGTGACTG
*
19395053 ATTAAATTAGTCACTTTACT
1 ATTAAATTAGTCAATTTACT
19395073 ATTAAA-TAGATCAATTTA
1 ATTAAATTAG-TCAATTTA
19395091 GTTTTTATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.42, C:0.11, G:0.05, T:0.42
Consensus pattern (20 bp):
ATTAAATTAGTCAATTTACT
Found at i:19396446 original size:21 final size:20
Alignment explanation
Indices: 19396413--19396452 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19396403 CCTTTTTAAT
19396413 ATAAAACCAAATAGAAACCA
1 ATAAAACCAAATAGAAACCA
* *
19396433 ATAAATCCTAAATATAAACC
1 ATAAAACC-AAATAGAAACC
19396453 CACAAAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (20 bp):
ATAAAACCAAATAGAAACCA
Found at i:19403416 original size:221 final size:219
Alignment explanation
Indices: 19403008--19403451 Score: 601
Period size: 218 Copynumber: 2.0 Consensus size: 219
19402998 AGTGTAAATC
* * **
19403008 CCTTAGGACTCTCATCTTGCAGATAGGCACTAATCTCAGCCACTGATGTAATTCAATCTGTACCG
1 CCTTAGGAATCTCATATTGCAGATAAACACTAATCTCAGCCACTGATGTAATTCAATCTGTACCG
* * * * *
19403073 TTGGATTTGGGGGAGCTCAACTAAATAGAGGTCTTCCCCCTCATTTGTAATCACTTAGTTATTCC
66 TTGGATCTGGGAGAGATCAACTAAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAGTTAATCC
* * *
19403138 TTCTAAGTAATAGAATATTTTTTAGAACATTTACTCAAACACTTGGTGTGTTATTATTCTCTTTT
131 TTCTAAGTAATAGAACATCTTTTAGAACATTTACTCAAACACTTGGTGTGATATTATTCTCTTTT
19403203 GGC-TTTTCTGTTCAATACAAGTT
196 GGCTTTTTCTGTTCAATACAAGTT
* * * *
19403226 CCTTAGGAATCTCATATTGTAGATAAACACTAATC-CTAGTCATTGATGTAATTCAATTTGTACC
1 CCTTAGGAATCTCATATTGCAGATAAACACTAATCTC-AGCCACTGATGTAATTCAATCTGTACC
19403290 GTTGGATCT-GGAGAGATCAACTATAAATAGA-GTCATTCCCCCTCATTTGTAATCACTCAGTTG
65 GTTGGATCTGGGAGAGATCAAC--TAAATAGAGGTC-TTCCCCCTCATTTGTAATCACTCAG-T-
**
19403353 TAATCCTTC-ATAGTAATAGAACATCTTTTAGAGTATTTACTCAAACACTTGGTGTGATATTATT
125 TAATCCTTCTA-AGTAATAGAACATCTTTTAGAACATTTACTCAAACACTTGGTGTGATATTATT
* * *
19403417 TTCTTTTGGCTTTTTTTGTTCAATATAAGTT
189 CTCTTTTGGCTTTTTCTGTTCAATACAAGTT
19403448 CCTT
1 CCTT
19403452 TGTATTTTCG
Statistics
Matches: 197, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
217 11 0.06
218 65 0.33
219 32 0.16
220 2 0.01
221 65 0.33
222 22 0.11
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.39
Consensus pattern (219 bp):
CCTTAGGAATCTCATATTGCAGATAAACACTAATCTCAGCCACTGATGTAATTCAATCTGTACCG
TTGGATCTGGGAGAGATCAACTAAATAGAGGTCTTCCCCCTCATTTGTAATCACTCAGTTAATCC
TTCTAAGTAATAGAACATCTTTTAGAACATTTACTCAAACACTTGGTGTGATATTATTCTCTTTT
GGCTTTTTCTGTTCAATACAAGTT
Found at i:19411969 original size:32 final size:32
Alignment explanation
Indices: 19411915--19411975 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
19411905 AAATTAACAC
19411915 ATAATTATTCATTTAATATTATAACTATTGAA
1 ATAATTATTCATTTAATATTATAACTATTGAA
*
19411947 ATAA-TATT-ATTTAAATAGTTATAATTATT
1 ATAATTATTCATTT-AATA-TTATAACTATT
19411976 TTTCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 8 0.31
32 14 0.54
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (32 bp):
ATAATTATTCATTTAATATTATAACTATTGAA
Found at i:19412999 original size:20 final size:20
Alignment explanation
Indices: 19412965--19413006 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
19412955 AACTATTTAA
** *
19412965 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
19412985 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
19413005 AT
1 AT
19413007 GTGTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:19434436 original size:27 final size:27
Alignment explanation
Indices: 19434396--19434461 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
19434386 CAGCAGAGCT
19434396 ACCAGT-ACAGTATATGTGGCAAAGCC
1 ACCAGTAACAGTATATGTGGCAAAGCC
* *
19434422 ACGAGTAACAGTATATGTGGCAGAGCC
1 ACCAGTAACAGTATATGTGGCAAAGCC
*
19434449 ACCCGTAACAGTA
1 ACCAGTAACAGTA
19434462 CTTCCTCCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
26 5 0.14
27 30 0.86
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
ACCAGTAACAGTATATGTGGCAAAGCC
Found at i:19434714 original size:27 final size:27
Alignment explanation
Indices: 19434663--19434714 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
19434653 ATGGTCATTT
* * **
19434663 TACCCTATAAGGGTATTTCGGTAATCC
1 TACCCTACAAAGGTATTTCAATAATCC
19434690 TACCCTACAAAGGTATTTCAATAAT
1 TACCCTACAAAGGTATTTCAATAAT
19434715 TTCACAAACC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (27 bp):
TACCCTACAAAGGTATTTCAATAATCC
Found at i:19434731 original size:27 final size:27
Alignment explanation
Indices: 19434701--19434830 Score: 102
Period size: 27 Copynumber: 4.8 Consensus size: 27
19434691 ACCCTACAAA
*
19434701 GGTATTTCAATAATTTCACAAACCAAG
1 GGTATTTCGATAATTTCACAAACCAAG
**
19434728 GGTATTTCGATAATTTCACAAATTAAG
1 GGTATTTCGATAATTTCACAAACCAAG
* * * * ** *
19434755 GGTGTTTTGGTAATTTTACAAATTAGG
1 GGTATTTCGATAATTTCACAAACCAAG
* * *
19434782 GGTATTTC-AGTAATTTTACACACC-GG
1 GGTATTTCGA-TAATTTCACAAACCAAG
*
19434808 AGGTATTTTGATAATTTCACAAA
1 -GGTATTTCGATAATTTCACAAA
19434831 TCGGGGGTCT
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 80 0.96
28 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (27 bp):
GGTATTTCGATAATTTCACAAACCAAG
Found at i:19439925 original size:34 final size:34
Alignment explanation
Indices: 19439881--19439946 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
19439871 CATGATTAAT
19439881 ATGACAAAGACCGTTTTGATCCCATATGGATAAA
1 ATGACAAAGACCGTTTTGATCCCATATGGATAAA
*
19439915 ATGACTAAGACCGTTTTGATCCCATATGGATA
1 ATGACAAAGACCGTTTTGATCCCATATGGATA
19439947 TAGTTGGTGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (34 bp):
ATGACAAAGACCGTTTTGATCCCATATGGATAAA
Found at i:19443135 original size:14 final size:14
Alignment explanation
Indices: 19443116--19443151 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
19443106 ATTACGTTAG
19443116 AAATTAAAGTATAT
1 AAATTAAAGTATAT
19443130 AAATTAAAGTATAT
1 AAATTAAAGTATAT
19443144 AAATTAAA
1 AAATTAAA
19443152 TCAGAAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (14 bp):
AAATTAAAGTATAT
Found at i:19444948 original size:18 final size:17
Alignment explanation
Indices: 19444916--19445014 Score: 67
Period size: 17 Copynumber: 5.7 Consensus size: 17
19444906 AGGCCAGATC
19444916 GGGCATGTGGGCCACAA
1 GGGCATGTGGGCCACAA
*
19444933 GGGCGTGTGGGCCCACACA
1 GGGCATGTGGG-CCACA-A
* * * *
19444952 -AGCATATGGGCCAGAC
1 GGGCATGTGGGCCACAA
* *
19444968 GGGCATGTGAGCCAGACA
1 GGGCATGTGGGCCACA-A
* *
19444986 -GGCGTGTGGGCCCACAC
1 GGGCATGTGGG-CCACAA
19445003 GGGCATGTGGGC
1 GGGCATGTGGGC
19445015 TCATAATTCT
Statistics
Matches: 61, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
17 35 0.57
18 25 0.41
19 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.41, T:0.12
Consensus pattern (17 bp):
GGGCATGTGGGCCACAA
Found at i:19445014 original size:52 final size:53
Alignment explanation
Indices: 19444887--19445002 Score: 154
Period size: 52 Copynumber: 2.3 Consensus size: 53
19444877 TGAGTGTGGT
* *
19444887 CGTGTGGG-CCACACGAGC-TA--GGCCAGATCGGGCATGTGGGCCACAAGGG
1 CGTGTGGGCCCACACAAGCATATGGGCCAGATCGGGCATGTGAGCCACAAGGG
*
19444936 CGTGTGGGCCCACACAAGCATATGGGCCAGA-CGGGCATGTGAGCCAGACA-GG
1 CGTGTGGGCCCACACAAGCATATGGGCCAGATCGGGCATGTGAGCCACA-AGGG
19444988 CGTGTGGGCCCACAC
1 CGTGTGGGCCCACAC
19445003 GGGCATGTGG
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 8 0.14
50 9 0.15
51 2 0.03
52 32 0.54
53 8 0.14
ACGTcount: A:0.22, C:0.28, G:0.38, T:0.12
Consensus pattern (53 bp):
CGTGTGGGCCCACACAAGCATATGGGCCAGATCGGGCATGTGAGCCACAAGGG
Found at i:19450999 original size:16 final size:16
Alignment explanation
Indices: 19450978--19451008 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19450968 TAGTAGGTAA
*
19450978 TCTAAAAGGTCTATTG
1 TCTAAAAGGACTATTG
19450994 TCTAAAAGGACTATT
1 TCTAAAAGGACTATT
19451009 ATGTCGTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (16 bp):
TCTAAAAGGACTATTG
Found at i:19451362 original size:296 final size:296
Alignment explanation
Indices: 19450828--19451418 Score: 1094
Period size: 296 Copynumber: 2.0 Consensus size: 296
19450818 ATTCACATTA
19450828 ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
1 ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
19450893 ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
66 ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
*
19450958 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATTGTCTAAAAGGACTATTATGTCGTCTATCAA
131 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
*
19451023 GTCCAAATAGGGGGATACCTTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACATA
196 GTCCAAATAGGGGGATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACATA
19451088 AATATTATTTTCTAGACTAACAATACATTAGACATG
261 AATATTATTTTCTAGACTAACAATACATTAGACATG
* *
19451124 ATATCATTTGTATTTGTCCTTGATGGTTTTTGCACTCAAAACAAAATTTAAGCAAATATTTGCTC
1 ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
* * *
19451189 ATTGATTACCTAAATTTTAACTAATATTAAGTTGTATTACGTTGTCTGATCGGAATGTAAGAAGA
66 ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
19451254 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
131 CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
19451319 GTCCAAAT-GGGGAGATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACAT
196 GTCCAAATAGGGG-GATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACAT
*
19451383 AAATGTTATTTTCTAGACTAACAATACATTAGACAT
260 AAATATTATTTTCTAGACTAACAATACATTAGACAT
19451419 AACCCAAGTT
Statistics
Matches: 286, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
295 4 0.01
296 282 0.99
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (296 bp):
ATATCATTTGTATTTGTCCTTAATGGTTTTTGCACTCAAAACAAAATGTAAGCAAATATTTGCTC
ATTGATTACCTAAATTTTAACTAATACTAAGTTGTATTACGTTGTCGGATCGGAATGTAAAAAGA
CAACTTGTATTAGTAGGTAATCTAAAAGGTCTATAGTCTAAAAGGACTATTATGTCGTCTATCAA
GTCCAAATAGGGGGATACATTATCTTGGATATTAGAGTGATTTACTCCCAGAAGATAGAGACATA
AATATTATTTTCTAGACTAACAATACATTAGACATG
Found at i:19452113 original size:13 final size:13
Alignment explanation
Indices: 19452081--19452113 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
19452071 CTGGGCATTT
*
19452081 CCACACAGGATGG
1 CCACACGGGATGG
19452094 CCACACGGGATGG
1 CCACACGGGATGG
19452107 CCACACG
1 CCACACG
19452114 CCCATGTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.27, C:0.36, G:0.30, T:0.06
Consensus pattern (13 bp):
CCACACGGGATGG
Found at i:19453270 original size:18 final size:17
Alignment explanation
Indices: 19453247--19453280 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19453237 ATTGCTTTTT
19453247 ATTTTTGGTTTTAGTTTA
1 ATTTTT-GTTTTAGTTTA
*
19453265 ATTTTTGTTTTTGTTT
1 ATTTTTGTTTTAGTTT
19453281 TCTAATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.12, C:0.00, G:0.15, T:0.74
Consensus pattern (17 bp):
ATTTTTGTTTTAGTTTA
Found at i:19457196 original size:20 final size:20
Alignment explanation
Indices: 19457154--19457196 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
19457144 ATTTTCTTTG
* * *
19457154 TTTTTATTTTATTTATTTAT
1 TTTTTAATTTAGTTACTTAT
*
19457174 TTTTTAATTTAGTTACTTCT
1 TTTTTAATTTAGTTACTTAT
19457194 TTT
1 TTT
19457197 CTTGGTGTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTAATTTAGTTACTTAT
Found at i:19458939 original size:19 final size:19
Alignment explanation
Indices: 19458912--19458971 Score: 52
Period size: 19 Copynumber: 3.1 Consensus size: 19
19458902 ATGAGGACCA
*
19458912 TTAAGTTTATTTCTTTATT
1 TTAATTTTATTTCTTTATT
*
19458931 TTAATTTTAATT-TTTATGT
1 TTAATTTTATTTCTTTAT-T
19458950 TT-ATTGTTATTTTCTTATATT
1 TTAATT-TTA-TTTCTT-TATT
19458971 T
1 T
19458972 ATTTTGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
18 8 0.24
19 16 0.48
20 2 0.06
21 4 0.12
22 3 0.09
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (19 bp):
TTAATTTTATTTCTTTATT
Found at i:19461704 original size:14 final size:14
Alignment explanation
Indices: 19461681--19461711 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
19461671 TATTGCGTTC
*
19461681 TTAGTTAATTTAGA
1 TTAGTAAATTTAGA
19461695 TTAGTAAATTTAGA
1 TTAGTAAATTTAGA
19461709 TTA
1 TTA
19461712 AAAATAATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
TTAGTAAATTTAGA
Found at i:19462668 original size:29 final size:29
Alignment explanation
Indices: 19462627--19462688 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
19462617 TTTAACAAAA
*
19462627 TTGT-CAATATGGTACATGTACTTTAATT
1 TTGTCCAATATGGTACATGAACTTTAATT
* * *
19462655 TTGTCCAATGTGGTACCTGAACTTTTATT
1 TTGTCCAATATGGTACATGAACTTTAATT
19462684 TTGTC
1 TTGTC
19462689 TACCGATATG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.47
Consensus pattern (29 bp):
TTGTCCAATATGGTACATGAACTTTAATT
Found at i:19474013 original size:21 final size:20
Alignment explanation
Indices: 19473976--19474015 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
19473966 TATAAAATTT
*
19473976 TATAAATAACATTTTTATAA
1 TATAAATAACATATTTATAA
*
19473996 TATAATATAATATATTTATA
1 TATAA-ATAACATATTTATA
19474016 TTAATTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TATAAATAACATATTTATAA
Found at i:19479224 original size:3 final size:3
Alignment explanation
Indices: 19479218--19479246 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
19479208 TTCCTCTTCT
19479218 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
19479247 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:19482378 original size:133 final size:134
Alignment explanation
Indices: 19482139--19482400 Score: 314
Period size: 133 Copynumber: 2.0 Consensus size: 134
19482129 GTGTTTACTT
* ** ** *
19482139 CTTGTCTTACTACACCTATCAAAATGGCATTGAGATGGTAAAACTTTTAGCCATATATTTAGGAT
1 CTTGTCTTACTACACCTATCAAAATGACATCAAGATGGTAAAACTTCAAGCCATATAATTAGGAT
* * * * ** * *
19482204 GACTTGTATTTTTCATTTGGGAAATGTTCTCCTTTTTGGTATCCATGCTGTATATAAATCATGAC
66 CACTTGTATTTTTCATTTGGGAAATATTCGCCTTCTTGGTATCCACACTCTAGATAAATCATGAC
19482269 ATGA
131 ATGA
* * * *
19482273 CTTGTCTTACTA-ACCTATCAAGATGACATCAAGGTGGTAAAACTTCAAGCCTTGTAATTAGGAT
1 CTTGTCTTACTACACCTATCAAAATGACATCAAGATGGTAAAACTTCAAGCCATATAATTAGGAT
*
19482337 CA-TGTGTAGTTTTT-ATTTGGGAAATATTGGCCTTCTTGGTATCCACACTCTAGATAAATCATG
66 CACT-TGTA-TTTTTCATTTGGGAAATATTCGCCTTCTTGGTATCCACACTCTAGATAAATCATG
19482400 A
129 A
19482401 GAATGCATCT
Statistics
Matches: 107, Mismatches: 19, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
132 1 0.01
133 89 0.83
134 17 0.16
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (134 bp):
CTTGTCTTACTACACCTATCAAAATGACATCAAGATGGTAAAACTTCAAGCCATATAATTAGGAT
CACTTGTATTTTTCATTTGGGAAATATTCGCCTTCTTGGTATCCACACTCTAGATAAATCATGAC
ATGA
Found at i:19487226 original size:11 final size:10
Alignment explanation
Indices: 19487210--19487239 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
19487200 TTTTTTCTCC
19487210 CCCCACCCCA
1 CCCCACCCCA
19487220 GCCCCACCCCA
1 -CCCCACCCCA
19487231 CCCCACCCC
1 CCCCACCCC
19487240 TTCTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.17, C:0.80, G:0.03, T:0.00
Consensus pattern (10 bp):
CCCCACCCCA
Found at i:19487229 original size:5 final size:5
Alignment explanation
Indices: 19487210--19487239 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
19487200 TTTTTTCTCC
19487210 CCCCA CCCCA GCCCCA CCCCA CCCCA CCCC
1 CCCCA CCCCA -CCCCA CCCCA CCCCA CCCC
19487240 TTCTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.80, G:0.03, T:0.00
Consensus pattern (5 bp):
CCCCA
Found at i:19487231 original size:16 final size:15
Alignment explanation
Indices: 19487210--19487239 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
19487200 TTTTTTCTCC
19487210 CCCCACCCCAGCCCCA
1 CCCCACCCCA-CCCCA
19487226 CCCCACCCCACCCC
1 CCCCACCCCACCCC
19487240 TTCTATTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.17, C:0.80, G:0.03, T:0.00
Consensus pattern (15 bp):
CCCCACCCCACCCCA
Found at i:19487749 original size:11 final size:12
Alignment explanation
Indices: 19487732--19487760 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
19487722 ATGGTGGTGG
19487732 GTTTTTTTTTCT
1 GTTTTTTTTTCT
19487744 -TTTTTTTTTCT
1 GTTTTTTTTTCT
19487755 GTTTTT
1 GTTTTT
19487761 GTAAAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (12 bp):
GTTTTTTTTTCT
Found at i:19493079 original size:85 final size:85
Alignment explanation
Indices: 19492934--19493104 Score: 218
Period size: 85 Copynumber: 2.0 Consensus size: 85
19492924 AACGCTCCAC
* * * * * *
19492934 ATACTTGTGTTGTTGCAAGTATGTTACAGGATCATCTGGAATTGGATTTTGACCTAATCTCTAAC
1 ATACTTGTGTTGTTGCAAGTATGTCACAAGATCATCTGAAATTGGATTCTAACATAATCTCTAAC
* * *
19492999 ATTGTCTTACTTATTTTGAA
66 ATTATCTTACCTATGTTGAA
* * *
19493019 ATACTTGTGTTGTTGCAGGTATGTCACAAGATCA-CTCGAAATTGGATTCTAAGATGATCTCTAA
1 ATACTTGTGTTGTTGCAAGTATGTCACAAGATCATCT-GAAATTGGATTCTAACATAATCTCTAA
19493083 CATTATCTTACCTATGTTGAA
65 CATTATCTTACCTATGTTGAA
19493104 A
1 A
19493105 GCGAGTCCTA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
84 2 0.03
85 71 0.97
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (85 bp):
ATACTTGTGTTGTTGCAAGTATGTCACAAGATCATCTGAAATTGGATTCTAACATAATCTCTAAC
ATTATCTTACCTATGTTGAA
Found at i:19494248 original size:5 final size:5
Alignment explanation
Indices: 19494240--19494290 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
19494230 CCTAATCTAA
* *
19494240 AAAAG AAAAG AAAAAG AAAAAG AGAAG AGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG -AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
19494291 AAGCCCTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
5 32 0.74
6 11 0.26
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:19498638 original size:25 final size:26
Alignment explanation
Indices: 19498610--19498658 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19498600 CAACAAAACT
*
19498610 AAAATCTAACCT-AAAAAGAAAAGAG
1 AAAACCTAACCTAAAAAAGAAAAGAG
*
19498635 AAAACCTAATCTAAAAAAGAAAAG
1 AAAACCTAACCTAAAAAAGAAAAG
19498659 TAAAAGAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (26 bp):
AAAACCTAACCTAAAAAAGAAAAGAG
Found at i:19498663 original size:25 final size:24
Alignment explanation
Indices: 19498604--19498663 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
19498594 AGGAAACAAC
* *
19498604 AAAACTAAAATCTAACCTAAAAAG
1 AAAAGTAAAACCTAACCTAAAAAG
* *
19498628 AAAAGAGAAAACCTAATCTAAAAAAG
1 AAAAG-TAAAACCTAACCT-AAAAAG
19498654 AAAAGTAAAA
1 AAAAGTAAAA
19498664 GAAAAGAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
24 4 0.14
25 14 0.48
26 11 0.38
ACGTcount: A:0.67, C:0.12, G:0.08, T:0.13
Consensus pattern (24 bp):
AAAAGTAAAACCTAACCTAAAAAG
Found at i:19500824 original size:79 final size:76
Alignment explanation
Indices: 19500725--19501009 Score: 355
Period size: 75 Copynumber: 3.8 Consensus size: 76
19500715 TTTTCATTGC
* * * * * *
19500725 TTTTA-TTTTTTGGTAAATTGTAAATAAGTATATATTATTGATGTAAAATATAGTAGAATATAAT
1 TTTTATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAAT
* *
19500789 ATAAACAATTTTT
66 ACAAATAA--TTT
* *
19500802 TTTTCATTTTTTTCGTATATTGTAAATAAGTATATATTATTGATATAAAATACAATAAAATACAA
1 TTTT-ATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAA
*
19500867 GACAAATAA-TT
65 TACAAATAATTT
** *
19500878 TTTTAAATTTTTCGTAGATTGTAAATAAATATATATTATTGATATAAAATACAATAGAATACAAT
1 TTTTATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAAT
19500943 ACAAATAATTT
66 ACAAATAATTT
* *
19500954 TTCTATTGTTTTT-GTAGATTGTAAATAA--ATATATTATTGATGTAAAATACAATAGA
1 TTTTATT-TTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGA
19501010 TAAACTTTTT
Statistics
Matches: 184, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
74 27 0.15
75 63 0.34
76 27 0.15
77 9 0.05
78 1 0.01
79 57 0.31
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (76 bp):
TTTTATTTTTTTCGTAGATTGTAAATAAGTATATATTATTGATATAAAATACAATAGAATACAAT
ACAAATAATTT
Found at i:19505855 original size:16 final size:16
Alignment explanation
Indices: 19505834--19505864 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19505824 TGGCAGTTTG
19505834 ATAGTTAATTGAAATT
1 ATAGTTAATTGAAATT
*
19505850 ATAGTTGATTGAAAT
1 ATAGTTAATTGAAAT
19505865 GGATTGAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (16 bp):
ATAGTTAATTGAAATT
Found at i:19505941 original size:16 final size:16
Alignment explanation
Indices: 19505922--19505955 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19505912 AAATGAATAT
* *
19505922 ATGTGTAAATGTGATA
1 ATGTGCAAATATGATA
19505938 ATGTGCAAATATGATA
1 ATGTGCAAATATGATA
19505954 AT
1 AT
19505956 TGGATATTGT
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:0.41, C:0.03, G:0.21, T:0.35
Consensus pattern (16 bp):
ATGTGCAAATATGATA
Found at i:19511608 original size:18 final size:17
Alignment explanation
Indices: 19511595--19511631 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
19511585 GAATTATTAT
19511595 TATTAGTATTATTATTTA
1 TATTAGT-TTATTATTTA
19511613 TATTAGTTTATATATTTA
1 TATTAGTTTAT-TATTTA
19511631 T
1 T
19511632 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (17 bp):
TATTAGTTTATTATTTA
Found at i:19511912 original size:12 final size:13
Alignment explanation
Indices: 19511872--19511913 Score: 68
Period size: 14 Copynumber: 3.2 Consensus size: 13
19511862 ATTTCAACTT
19511872 TTATATATTATTA
1 TTATATATTATTA
19511885 TGTATATATTATTA
1 T-TATATATTATTA
19511899 TT-TATATTATTA
1 TTATATATTATTA
19511911 TTA
1 TTA
19511914 AGTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.44
13 2 0.07
14 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:19516592 original size:19 final size:19
Alignment explanation
Indices: 19516570--19516612 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
19516560 AATCCAAATC
19516570 AAAAACAAAAAAAAAAGAA
1 AAAAACAAAAAAAAAAGAA
* ***
19516589 AAAATCAAAGTCAAAAGAA
1 AAAAACAAAAAAAAAAGAA
19516608 AAAAA
1 AAAAA
19516613 AGAGAAATCA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.81, C:0.07, G:0.07, T:0.05
Consensus pattern (19 bp):
AAAAACAAAAAAAAAAGAA
Found at i:19516610 original size:30 final size:30
Alignment explanation
Indices: 19516556--19516641 Score: 93
Period size: 31 Copynumber: 2.8 Consensus size: 30
19516546 TCAGATTAAA
19516556 AAAAAATCCAAA-TCAAAAACAAAAAAAAAAG
1 AAAAAAT-CAAAGTC-AAAACAAAAAAAAAAG
* *
19516587 AAAAAATCAAAGTCAAAAGAAAAAAAAGAG
1 AAAAAATCAAAGTCAAAACAAAAAAAAAAG
* * *
19516617 AAATCAATTAAAGTCAAAATAAAAA
1 AAA-AAATCAAAGTCAAAACAAAAA
19516642 TATGAAAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 21 0.44
31 27 0.56
ACGTcount: A:0.73, C:0.09, G:0.07, T:0.10
Consensus pattern (30 bp):
AAAAAATCAAAGTCAAAACAAAAAAAAAAG
Found at i:19518688 original size:50 final size:50
Alignment explanation
Indices: 19518630--19519188 Score: 352
Period size: 50 Copynumber: 11.2 Consensus size: 50
19518620 GTGGTGGAAC
* *
19518630 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* ** * * ** ** *
19518680 AGATTAAAGCTACAATAGCGAATCTTAC-TCCCC-AGGTGATGCAGCGGAACA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACAT--TGCAG-TTAAAA
19518731 A-ATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * * * *** *
19518780 AGATTAAAGCTACAGCAGCGAATCTTACCTCTCAGGCAGTGCAGCGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * **
19518830 AGATTAAAGCCACAACGTTGAATCTTGCCTCCATGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* ** * * * * *** *
19518880 AGATTAAAGCTACAATAGTGAATCTTACTTCCCAGGCGA-TGTAGCGGAAC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGAC-ATTGCAGTTAAAA
*
19518930 AGATTAAAGCCACAACGGTGAAACTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * *** * **
19518980 AGACTAAAGCCACATCGGCGAGTGTTACTTCCCTGGCAACACAGTGAAGC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * *
19519030 AGACTAAAGCCACAACGTTGAATCTTGCTTCCCCGACATTGTAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * * * * * * * ** * **
19519080 ATACTAAAGCCACAGCGGCGAGTGTTACTTCCCTGGCAACGCAGTGAAGC
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
* * * *
19519130 AGACTAAAGCCACAACGGTGAATTTTGCTTTCTCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
*
19519180 GGATTAAAG
1 AGATTAAAG
19519189 TCAAAATGAT
Statistics
Matches: 362, Mismatches: 139, Indels: 16
0.70 0.27 0.03
Matches are distributed among these distances:
48 2 0.01
49 10 0.03
50 338 0.93
51 10 0.03
52 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (50 bp):
AGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
Found at i:19518776 original size:100 final size:100
Alignment explanation
Indices: 19518625--19519188 Score: 657
Period size: 100 Copynumber: 5.6 Consensus size: 100
19518615 GTGATGTGGT
* *
19518625 GGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* **
19518690 TACAATAGCGAATCTTACTCCCCAGGTGATGCAGC
66 TACAATAGCGAATCTTACTTCCCAGGCAATGCAGC
*
19518725 GGAACAAATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
** * * *
19518790 TACAGCAGCGAATCTTACCTCTCAGGCAGTGCAGC
66 TACAATAGCGAATCTTACTTCCCAGGCAATGCAGC
* * **
19518825 GGAACAGATTAAAGCCACAACGTTGAATCTTGCCTCCATGACATTGCAGTTAAAAAGATTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* * *
19518890 TACAATAGTGAATCTTACTTCCCAGGCGATGTAGC
66 TACAATAGCGAATCTTACTTCCCAGGCAATGCAGC
* *
19518925 GGAACAGATTAAAGCCACAACGGTGAAACTTGCTTCCCCGACATTGCAGTTAAAAAGACTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* * * * * **
19518990 CAC-ATCGGCGAGTGTTACTTCCCTGGCAACACAG-
66 TACAAT-AGCGAATCTTACTTCCCAGGCAATGCAGC
* * * * * *
19519024 TGAAGCAGACTAAAGCCACAACGTTGAATCTTGCTTCCCCGACATTGTAGTTAAAAATACTAAAG
1 GGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
* *** * * * *
19519089 CCACAGCGGCGAGTGTTACTTCCCTGGCAACGCAG-
65 CTACAATAGCGAATCTTACTTCCCAGGCAATGCAGC
* * * * * *
19519124 TGAAGCAGACTAAAGCCACAACGGTGAATTTTGCTTTCTCGACATTGCAGTTAAAAGGATTAAAG
1 GGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
19519189 TCAAAATGAT
Statistics
Matches: 404, Mismatches: 57, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
99 5 0.01
100 399 0.99
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.23
Consensus pattern (100 bp):
GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
TACAATAGCGAATCTTACTTCCCAGGCAATGCAGC
Found at i:19519208 original size:100 final size:100
Alignment explanation
Indices: 19518625--19519289 Score: 601
Period size: 100 Copynumber: 6.6 Consensus size: 100
19518615 GTGATGTGGT
* *
19518625 GGAACAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGTAGTTAAAAAGATTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* * **
19518690 TACAAT-AGCGAATCTTACTCCCCAGGTGATGCAGC
66 -AAAATGAGCGAATCTTACTTCCCAGGCAATGCAGC
*
19518725 GGAACAAATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* * * * *
19518790 TACA-GCAGCGAATCTTACCTCTCAGGCAGTGCAGC
66 AAAATG-AGCGAATCTTACTTCCCAGGCAATGCAGC
* * **
19518825 GGAACAGATTAAAGCCACAACGTTGAATCTTGCCTCCATGACATTGCAGTTAAAAAGATTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* * * *
19518890 TACAAT-AGTGAATCTTACTTCCCAGGCGATGTAGC
66 -AAAATGAGCGAATCTTACTTCCCAGGCAATGCAGC
* *
19518925 GGAACAGATTAAAGCCACAACGGTGAAACTTGCTTCCCCGACATTGCAGTTAAAAAGACTAAAGC
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
* * * * * **
19518990 CACATCG-GCGAGTGTTACTTCCCTGGCAACACAG-
66 AAAAT-GAGCGAATCTTACTTCCCAGGCAATGCAGC
* * * * * *
19519024 TGAAGCAGACTAAAGCCACAACGTTGAATCTTGCTTCCCCGACATTGTAGTTAAAAATACTAAAG
1 GGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
* * * * * * *
19519089 CCACA-GCGGCGAGTGTTACTTCCCTGGCAACGCAG-
65 CAAAATG-AGCGAATCTTACTTCCCAGGCAATGCAGC
* * * * * *
19519124 TGAAGCAGACTAAAGCCACAACGGTGAATTTTGCTTTCTCGACATTGCAGTTAAAAGGATTAAAG
1 GGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
* * * **
19519189 TCAAAATGA-TGAATCTTACTCTCTCA-GCTAGTGCATT
65 -CAAAATGAGCGAATCTTACT-TCCCAGGC-AATGCAGC
* * * * * ** * ** *
19519226 AGAGCAGATTGAAGCTACAATGGTGAATCTTAATTCCTCGACATCACAGTTAAACAGATTAAAG
1 GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAG
19519290 TAACGTGTTA
Statistics
Matches: 468, Mismatches: 83, Indels: 27
0.81 0.14 0.05
Matches are distributed among these distances:
98 1 0.00
99 6 0.01
100 399 0.85
101 59 0.13
102 3 0.01
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (100 bp):
GGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAAAGATTAAAGC
AAAATGAGCGAATCTTACTTCCCAGGCAATGCAGC
Found at i:19522024 original size:5 final size:6
Alignment explanation
Indices: 19521973--19522029 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
19521963 ACCAATTTAG
* ** * *
19521973 TTTATC TTTATT TTTCCT TTTATT TCTATT TGTAGTGT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT
19522023 TTTATT T
1 TTTATT T
19522030 GAATTCCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 35 0.85
7 2 0.05
8 4 0.10
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:19522063 original size:3 final size:3
Alignment explanation
Indices: 19522055--19522093 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
19522045 TTTTAATCCC
19522055 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19522094 TCTTCTTTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19526564 original size:6 final size:6
Alignment explanation
Indices: 19526555--19526613 Score: 64
Period size: 6 Copynumber: 9.3 Consensus size: 6
19526545 AACAAAAAAG
* * *
19526555 AAGAAA AAGAAA AAGAAA AAGAAA AATCAAA ATGAAA AAGAAAA AAGAGAG
1 AAGAAA AAGAAA AAGAAA AAGAAA AA-GAAA AAGAAA AAG-AAA AAGA-AA
19526606 AAGAAA AA
1 AAGAAA AA
19526614 AGGAGAGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
6 29 0.66
7 15 0.34
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:19526572 original size:12 final size:12
Alignment explanation
Indices: 19526555--19526613 Score: 64
Period size: 13 Copynumber: 4.7 Consensus size: 12
19526545 AACAAAAAAG
19526555 AAGAAAAAGAAA
1 AAGAAAAAGAAA
19526567 AAGAAAAAGAAA
1 AAGAAAAAGAAA
* *
19526579 AATCAAAATGAAA
1 AA-GAAAAAGAAA
*
19526592 AAGAAAAAAGAGAG
1 AAG-AAAAAGA-AA
19526606 AAGAAAAA
1 AAGAAAAA
19526614 AGGAGAGGCC
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
12 14 0.36
13 21 0.54
14 4 0.10
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:19526586 original size:19 final size:18
Alignment explanation
Indices: 19526542--19526599 Score: 66
Period size: 19 Copynumber: 3.3 Consensus size: 18
19526532 AATCCAAATC
*
19526542 AAAAAC-AAAA-AAGAAG
1 AAAAACAAAAAGAAAAAG
*
19526558 AAAAAGAAAAAGAAAAAG
1 AAAAACAAAAAGAAAAAG
*
19526576 AAAAATCAAAATGAAAAAG
1 AAAAA-CAAAAAGAAAAAG
19526595 AAAAA
1 AAAAA
19526600 AGAGAGAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 10 0.29
19 16 0.46
ACGTcount: A:0.81, C:0.03, G:0.12, T:0.03
Consensus pattern (18 bp):
AAAAACAAAAAGAAAAAG
Found at i:19527460 original size:14 final size:15
Alignment explanation
Indices: 19527440--19527483 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
19527430 TAAAAGAAGA
*
19527440 GAAAAATGGAAAAAT
1 GAAAAATGAAAAAAT
19527455 -AAAAATGAAAAAAT
1 GAAAAATGAAAAAAT
*
19527469 GAAAAA-GTAAAAAT
1 GAAAAATGAAAAAAT
19527483 G
1 G
19527484 GAGAGGCTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.70, C:0.00, G:0.16, T:0.14
Consensus pattern (15 bp):
GAAAAATGAAAAAAT
Found at i:19527469 original size:22 final size:22
Alignment explanation
Indices: 19527425--19527483 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 22
19527415 GACTTTGAAA
*
19527425 AAAAATAAAAGAAGAGAAAAATGG
1 AAAAATAAAA-ATGAGAAAAAT-G
19527449 AAAAATAAAAATGA-AAAAATG
1 AAAAATAAAAATGAGAAAAATG
19527470 AAAAAGTAAAAATG
1 AAAAA-TAAAAATG
19527484 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
21 6 0.18
22 14 0.42
23 3 0.09
24 10 0.30
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (22 bp):
AAAAATAAAAATGAGAAAAATG
Found at i:19528859 original size:44 final size:44
Alignment explanation
Indices: 19528786--19528887 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 44
19528776 CCTTCAAGTT
* *
19528786 GGAGCAGATTGAAAGCCAAAAATCTTATCTCCTTGAGATCACAGC
1 GGAGCAGATT-AAAGCCAAAAATCCTATCTCCCTGAGATCACAGC
* ** * *
19528831 GGAGCAGATTAAAGCTAGTAATCCTATCTCCCTGAGATTACAGT
1 GGAGCAGATTAAAGCCAAAAATCCTATCTCCCTGAGATCACAGC
*
19528875 GGAGCGGATTAAA
1 GGAGCAGATTAAA
19528888 ATAAAGGATC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 39 0.80
45 10 0.20
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.24
Consensus pattern (44 bp):
GGAGCAGATTAAAGCCAAAAATCCTATCTCCCTGAGATCACAGC
Found at i:19528903 original size:44 final size:44
Alignment explanation
Indices: 19528806--19529246 Score: 152
Period size: 44 Copynumber: 9.6 Consensus size: 44
19528796 GAAAGCCAAA
* * * *
19528806 AATCTTATCTCCTTGAGATCACAGCGGAGCAGATTAAAGCT--AG
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAA-ATAAAG
* *
19528849 TAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAG
1 -AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAG
* * * * * * *
19528894 GATCTTATCTCTCT-AAAGTTACAGTAGAGTAGATGGCATCAGATTGAAGCCAG
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGAT----T-AAAAT-AA---AG
* * **
19528947 AAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCT--AG
1 -AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAAG
* * *
19528991 TAATCCTATCTCCCTGAGATTACAGTGGATCGGATTAAAATAAAG
1 -AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAG
* * * * * *
19529036 GATCTTATCTCTCTGA-AGTTACAGTAGAGTAGATCACATCAGATTGAAGCCAAA
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTA-A--A-A-T--A---AAG
* **
19529090 AATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCT--AG
1 AATCTTATCTCCCTGAGATTACAGTGGAGCAGATT-AAAATAAAG
* ***
19529133 TAATCCTATCTCCCTGAGATTACAGTGGAATGGATTAAAATAAATG
1 -AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAA-G
* * * ***
19529179 -ATCTTATCTCTCTGA-AGTTACAGTAGAGTAGA-TCGCAT-AAG
1 AATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTAAAATAAAG
* *
19529220 -GTCTTATCTCCCTGAGATTACGGTGGA
1 AATCTTATCTCCCTGAGATTACAGTGGA
19529247 ATAAACCAAA
Statistics
Matches: 292, Mismatches: 70, Indels: 73
0.67 0.16 0.17
Matches are distributed among these distances:
41 22 0.08
42 3 0.01
43 15 0.05
44 170 0.58
45 6 0.02
46 1 0.00
47 1 0.00
48 2 0.01
49 4 0.01
50 6 0.02
51 1 0.00
53 2 0.01
54 55 0.19
55 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAG
Found at i:19529055 original size:142 final size:142
Alignment explanation
Indices: 19528790--19529216 Score: 739
Period size: 142 Copynumber: 3.0 Consensus size: 142
19528780 CAAGTTGGAG
* * *
19528790 CAGATTGAAAGCCAAAAATCTTATCTCCTTGAGATCACAGCGGAGCAGATTAAAGCTAGTAATCC
1 CAGATTG-AAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCC
* *
19528855 TATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTA
65 TATCTCCCTGAGATTACAGTGGATCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
*
19528920 GAGTAGATGGCAT
130 GAGTAGATCGCAT
* *
19528933 CAGATTGAAGCCAGAAATCTTATCTCCCTAAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
19528998 ATCTCCCTGAGATTACAGTGGATCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGATCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
19529063 AGTAGATCACAT
131 AGTAGATCGCAT
19529075 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
19529140 ATCTCCCTGAGATTACAGTGGAAT-GGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTA
66 ATCTCCCTGAGATTACAGTGG-ATCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTA
19529204 GAGTAGATCGCAT
130 GAGTAGATCGCAT
19529217 AAGGTCTTAT
Statistics
Matches: 270, Mismatches: 13, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
142 261 0.97
143 9 0.03
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (142 bp):
CAGATTGAAGCCAAAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGATCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
AGTAGATCGCAT
Found at i:19529378 original size:50 final size:50
Alignment explanation
Indices: 19529324--19529947 Score: 306
Period size: 50 Copynumber: 12.6 Consensus size: 50
19529314 AAATTTTGCA
* *
19529324 TCCCTGACATTGCAATTAAAAAGATTAAAGCTACAGCAGCGAATCTTACC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
** * ** * * *
19529374 TCCCTGGTAGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTACC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
*
19529424 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTACGC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTAC-C
* * *** * * * *
19529475 -CCCAGGCGA-TGCAGCGGAATAGATTAAAGCCACA-TAGGTGAATCTTGCC
1 TCCCTGAC-ATTGCAGTTAAAAAGATTAAAGCTACAGCA-GTGAATCTTACC
* * *
19529524 TCCCTAACATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATCTTACT
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
* * ** *** ** * * * * *
19529574 TCTC-AAGCGGTGCAGCGGAGCAGATTAAAGCCACATCGGTGAATCTTGCT
1 TCCCTGA-CATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
* * * * * *
19529624 TCCCCGACATTGC-------AA-ATTAAAGCCACAGCGGCGAATCCTACT
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
* * * ** * * * * *
19529666 TCCTTGGCGA-TGCCGTGGAACAGATTAAAG-TCACAACGGTGAATCTTGCT
1 TCCCTGAC-ATTGCAGTTAAAAAGATTAAAGCT-ACAGCAGTGAATCTTACC
* * * *
19529716 TCCCTGGCGTTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
* * * * ** * * * * *
19529766 TCCCAGGCAGTGTAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
* * * * *
19529816 TCCATGACATTGCAGTTAAAATGATTAAAGCTATAACGGTGAATCTTACGC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTAC-C
* * * * ** * * * * *
19529867 TCCCAGGCAGTGCAGTGAAGCATATTAAAGCCACAAC-GATGAATCTTGCT
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAG-TGAATCTTACC
*
19529917 TCCCCGACATTGCAGTTAAAAAGATTAAAGC
1 TCCCTGACATTGCAGTTAAAAAGATTAAAGC
19529948 CACAATGGCG
Statistics
Matches: 429, Mismatches: 123, Indels: 44
0.72 0.21 0.07
Matches are distributed among these distances:
42 31 0.07
43 2 0.00
49 6 0.01
50 349 0.81
51 41 0.10
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (50 bp):
TCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGAATCTTACC
Found at i:19529443 original size:100 final size:100
Alignment explanation
Indices: 19529269--19529965 Score: 781
Period size: 100 Copynumber: 7.0 Consensus size: 100
19529259 ATTACAGATT
* * * * * *
19529269 TTACCACCCAGGCGGTGCAGTGGAACAGATTAAAGCCACAACGATAAATTTTGCATCCCTGACAT
1 TTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACAT
* *
19529334 TGCAATTAAAAAGATTAAAGCTACAGCAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * * *
19529369 TTACCTCCCTGGTAGTGCAGTGGAACAGATTAAAGCCACATCAGTGAATCTTACCTCCCTGACAT
1 TTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACAT
*
19529434 TGCAGTTAAAAAGATTAAAGCTACAGCAGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * *
19529469 TTACGC-CCCAGGC-GATGCAGCGGAATAGATTAAAGCCACATA-GGTGAATCTTGCCTCCCTAA
1 TTAC-CTCCCAGGCAG-TGCAGTGGAACAGATTAAAGCCACA-ACGGTGAATCTTGCCTCCCTGA
*
19529531 CATTGCAGTTAAAAAGATTAAAGCTACAACAGTGAATC
63 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * * * * * * *
19529569 TTACTTCTCAAGCGGTGCAGCGGAGCAGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACAT
1 TTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACAT
* * *
19529634 TGC-------AA-ATTAAAGCCACAGCGGCGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * ** * * * * *
19529661 CTACTTCCTTGGC-GATGCCGTGGAACAGATTAAAGTCACAACGGTGAATCTTGCTTCCCTGGCG
1 TTACCTCCCAGGCAG-TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACA
19529725 TTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
65 TTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* *
19529761 TTACCTCCCAGGCAGTGTAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCATGACAT
1 TTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACAT
* * * *
19529826 TGCAGTTAAAATGATTAAAGCTATAACGGTGAATC
66 TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
* * * *
19529861 TTACGCTCCCAGGCAGTGCAGT-GAAGCATATTAAAGCCACAACGATGAATCTTGCTTCCCCGAC
1 TTAC-CTCCCAGGCAGTGCAGTGGAA-CAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGAC
* **
19529925 ATTGCAGTTAAAAAGATTAAAGCCACAATGGCGAATC
64 ATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
19529962 TTAC
1 TTAC
19529966 TTTCCAAAAG
Statistics
Matches: 502, Mismatches: 77, Indels: 35
0.82 0.13 0.06
Matches are distributed among these distances:
91 1 0.00
92 71 0.14
93 2 0.00
99 3 0.01
100 337 0.67
101 88 0.18
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (100 bp):
TTACCTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCCTCCCTGACAT
TGCAGTTAAAAAGATTAAAGCTACAACAGCGAATC
Found at i:19529812 original size:292 final size:293
Alignment explanation
Indices: 19529347--19529930 Score: 809
Period size: 292 Copynumber: 2.0 Consensus size: 293
19529337 AATTAAAAAG
* * * *
19529347 ATTAAAGCTACAGCAGCGAATCTTACCTCCCTGGTAGTGCAGTGGAACAGATTAAAGCCACATCA
1 ATTAAAGCCACAGCAGCGAATCCTACCTCCCTGGGAGTGCAGTGGAACAGATTAAAGCCACAACA
*
19529412 GTGAATCTTACCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGAATCTTACGCCC
66 GTGAATCTTACCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACGCCC
* *
19529477 CAGGCGATGCAGCGGAATAGATTAAAGCCACATAGGTGAATCTTGCCTCCCTAACATTGCAGTTA
131 CAGGCGATGCAGCGGAACAGATTAAAGCCACATAGGTGAATCTTGCCTCCATAACATTGCAGTTA
* * * *
19529542 AAAAGATTAAAGCTACAACAGTGAATCTTAC-TTCTCAAGCGGTGCAGCGGAGCAGATTAAAGCC
196 AAAAGATTAAAGCTACAACAGTGAATCTTACGCTCCCAAGCAGTGCAGCGAAGCAGATTAAAGCC
* *
19529606 ACATCGGTGAATCTTGCTTCCCCGACATTGCAA
261 ACAACGATGAATCTTGCTTCCCCGACATTGCAA
* * * * *
19529639 ATTAAAGCCACAGCGGCGAATCCTACTTCCTTGGCGA-TGCCGTGGAACAGATTAAAGTCACAAC
1 ATTAAAGCCACAGCAGCGAATCCTACCTCCCTGG-GAGTGCAGTGGAACAGATTAAAGCCACAAC
* * * * *
19529703 GGTGAATCTTGCTTCCCTGGCGTTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTAC-CT
65 AGTGAATCTTACCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACGC-
* * *
19529767 CCCAGGC-AGTGTAGTGGAACAGATTAAAGCCACA-ACGGTGAATCTTGCCTCCATGACATTGCA
129 CCCAGGCGA-TGCAGCGGAACAGATTAAAGCCACATA-GGTGAATCTTGCCTCCATAACATTGCA
* * * * * *
19529830 GTTAAAATGATTAAAGCTATAACGGTGAATCTTACGCTCCCAGGCAGTGCAGTGAAGCATATTAA
192 GTTAAAAAGATTAAAGCTACAACAGTGAATCTTACGCTCCCAAGCAGTGCAGCGAAGCAGATTAA
19529895 AGCCACAACGATGAATCTTGCTTCCCCGACATTGCA
257 AGCCACAACGATGAATCTTGCTTCCCCGACATTGCA
19529931 GTTAAAAAGA
Statistics
Matches: 255, Mismatches: 32, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
291 3 0.01
292 195 0.76
293 57 0.22
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (293 bp):
ATTAAAGCCACAGCAGCGAATCCTACCTCCCTGGGAGTGCAGTGGAACAGATTAAAGCCACAACA
GTGAATCTTACCTCCCTGACATTGCAGTTAAAAAGATTAAAGCTACAACAGCGAATCTTACGCCC
CAGGCGATGCAGCGGAACAGATTAAAGCCACATAGGTGAATCTTGCCTCCATAACATTGCAGTTA
AAAAGATTAAAGCTACAACAGTGAATCTTACGCTCCCAAGCAGTGCAGCGAAGCAGATTAAAGCC
ACAACGATGAATCTTGCTTCCCCGACATTGCAA
Found at i:19531408 original size:7 final size:6
Alignment explanation
Indices: 19531356--19531412 Score: 51
Period size: 6 Copynumber: 9.2 Consensus size: 6
19531346 ACCAATTTAG
* * * * *
19531356 TTTATC TTTATT TTTCTT TTTATT TCTATT TGTAGTGT TTAATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-T-T TTTATT TTTATT
19531406 TTTATT T
1 TTTATT T
19531413 GAATTCCAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 36 0.88
7 2 0.05
8 3 0.07
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.74
Consensus pattern (6 bp):
TTTATT
Found at i:19531446 original size:3 final size:3
Alignment explanation
Indices: 19531438--19531482 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
19531428 TTTTAATCCC
19531438 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
19531483 TCTTCTTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:19532911 original size:18 final size:18
Alignment explanation
Indices: 19532890--19532924 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
19532880 ATTATTATTG
19532890 TTAGTATTAT-TATTTATA
1 TTAGT-TTATATATTTATA
19532908 TTAGTTTATATATTTAT
1 TTAGTTTATATATTTAT
19532925 CTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
TTAGTTTATATATTTATA
Found at i:19533206 original size:12 final size:13
Alignment explanation
Indices: 19533166--19533207 Score: 68
Period size: 14 Copynumber: 3.2 Consensus size: 13
19533156 ATTTCAACTT
19533166 TTATATATTATTA
1 TTATATATTATTA
19533179 TGTATATATTATTA
1 T-TATATATTATTA
19533193 TT-TATATTATTA
1 TTATATATTATTA
19533205 TTA
1 TTA
19533208 AGTTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.44
13 2 0.07
14 13 0.48
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:19547243 original size:20 final size:20
Alignment explanation
Indices: 19547218--19547258 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
19547208 GTAAGCATGA
19547218 ACCTAAGTAAATTTGAAGCT
1 ACCTAAGTAAATTTGAAGCT
19547238 ACCTAAGTAAATTTGAAGCT
1 ACCTAAGTAAATTTGAAGCT
19547258 A
1 A
19547259 TCTTCTCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (20 bp):
ACCTAAGTAAATTTGAAGCT
Found at i:19547726 original size:56 final size:56
Alignment explanation
Indices: 19547614--19547727 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
19547604 TTACAAGCTC
* ** * *
19547614 AATCTTTGGTTTTGAGGAGATTGTTAGCCTCTACACAAATGGTGAGAACTTCGAAG
1 AATCTTTGGTTTTGAGGAGATTATTAGCCTCTACACAAATGACGAGAACATAGAAG
* *
19547670 AATCTTTGGTTTTGAGGATATTATTAGCCTCTACACAAATGACGAGGACATAGAAG
1 AATCTTTGGTTTTGAGGAGATTATTAGCCTCTACACAAATGACGAGAACATAGAAG
19547726 AA
1 AA
19547728 ATAAAGAAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (56 bp):
AATCTTTGGTTTTGAGGAGATTATTAGCCTCTACACAAATGACGAGAACATAGAAG
Found at i:19548132 original size:42 final size:42
Alignment explanation
Indices: 19548075--19548209 Score: 243
Period size: 42 Copynumber: 3.2 Consensus size: 42
19548065 GTTTACAAAC
19548075 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* *
19548117 AAAAATGCCTCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
*
19548159 AAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCGCTTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
19548201 AAAAACGCC
1 AAAAACGCC
19548210 ACTATTTTTG
Statistics
Matches: 88, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 88 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:19548541 original size:21 final size:21
Alignment explanation
Indices: 19548514--19548563 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
19548504 TTTTGGCCTG
*
19548514 CTCTGCTTCTCTAGCTGCAGC
1 CTCTGCTTCCCTAGCTGCAGC
* * *
19548535 TTCTGCTTCCCTCGCTGCCGC
1 CTCTGCTTCCCTAGCTGCAGC
19548556 CTCTGCTT
1 CTCTGCTT
19548564 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTAGCTGCAGC
Done.