Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 149 of 196
Found at i:44134822 original size:30 final size:29
Alignment explanation
Indices: 44134788--44134854 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
44134778 ACCAAAAAAA
**
44134788 GCCGATTTTTTTCTAAATTTACCGAAATGG
1 GCCGATTTTTTAAT-AATTTACCGAAATGG
* * *
44134818 GCCGACTTTTTAATTATTTACCGGAATGG
1 GCCGATTTTTTAATAATTTACCGAAATGG
44134847 GCC-ATTTT
1 GCCGATTTT
44134855 CCGCGAAATG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 4 0.13
29 16 0.52
30 11 0.35
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (29 bp):
GCCGATTTTTTAATAATTTACCGAAATGG
Found at i:44135218 original size:126 final size:125
Alignment explanation
Indices: 44135028--44135269 Score: 412
Period size: 126 Copynumber: 1.9 Consensus size: 125
44135018 CCTCTAGCAG
* ** *
44135028 GATGCTATTTGAGAAGAAATTGTGAAATCATGCCCTCGTGGACGCGATTTCGCTATAGTTGGTCA
1 GATGCTATATGAGAAGAAATTGTGAAATCACACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
44135093 TGTAGGAAATAATTATTTTTTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAA
66 TGTAGGAAATAATTATTTTTTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAA
*
44135154 GATGCTATATGAGAAGAAATTGTGAAATCGCACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
1 GATGCTATATGAGAAGAAATTGTGAAATCACACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
* *
44135219 TGTAGGAAATAATTATTTTTTGACGTTTCTGAGCAAATAGTGTCAAATCGC
66 TGTAGGAAATAATTATTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGC
44135270 GCCGTCGTGG
Statistics
Matches: 109, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
125 24 0.22
126 85 0.78
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (125 bp):
GATGCTATATGAGAAGAAATTGTGAAATCACACCCTCGTGGACGCGATTTCGCTACAGTTGGTCA
TGTAGGAAATAATTATTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAA
Found at i:44136755 original size:7 final size:7
Alignment explanation
Indices: 44136745--44136781 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
44136735 AATTAAAAAT
44136745 AATAATA
1 AATAATA
44136752 AATAATA
1 AATAATA
44136759 AATAATA
1 AATAATA
44136766 AAT--TA
1 AATAATA
44136771 AATATATA
1 AATA-ATA
44136779 AAT
1 AAT
44136782 TATTGGTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.19
7 17 0.63
8 5 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATAATA
Found at i:44139082 original size:20 final size:20
Alignment explanation
Indices: 44139065--44139104 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
44139055 ATATATATAC
44139065 ATATATATAATAAGATATAAAG
1 ATATATA-AATAA-ATATAAAG
44139087 ATATATAAATAAATATAA
1 ATATATAAATAAATATAA
44139105 TAGTAAAAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 5 0.28
22 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
ATATATAAATAAATATAAAG
Found at i:44140861 original size:46 final size:46
Alignment explanation
Indices: 44140805--44141362 Score: 628
Period size: 46 Copynumber: 12.2 Consensus size: 46
44140795 AAGATTCACC
* * * *
44140805 ATCTTCGATCTCCTTTGCTGCTAGATACAGGAAGAAAAGATCTTG-T
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATC-TGCT
* *
44140851 ATCTTTGATCTCCTCCGCTGCCAAATACAGGAAGACAAGATCTTG-T
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATC-TGCT
* * * *
44140897 CTCTTCGATCTCCTTCGTTGCCAAATACAGGAAGACAAGTTCTGCC
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
44140943 ATCTTCGATCTCTTTCGCTGCCAAATACAGGAAGACAAGATCTG-T
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
44140988 CATCTTCGATCT-CTTCCACTGCCAAATACAGGAAGACAAGTTCTGTT
1 -ATCTTCGATCTCCTT-CGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * ** *
44141035 ATCTTTGATCT-CTCCCGCTG-TATTTACATGAAGACAAGATCTGCT
1 ATCTTCGATCTCCT-TCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
44141080 ATCTTCGATCTCCTCCGCTGCCAGATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
** ** * *
44141126 ATCTTCGATCTCCCCCATTGCTAAATATAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
* * *
44141172 ATCTTCGATCT-TTTCCACTGCCAAATACAAGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTT-CGCTGCCAAATACAGGAAGACAAGATCTGCT
* * * *
44141218 ATCTTCGATCT-TTTCCACTACCAAATACAAGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTT-CGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
44141264 ATCTTCGATCTTCTTCACTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
* *
44141310 ATCTTCGATCTCCTCCGTTGCCAAATACAGGAAGACAAGATCTGCT
1 ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
*
44141356 ATATTCG
1 ATCTTCG
44141363 TTGATCTGTT
Statistics
Matches: 447, Mismatches: 56, Indels: 18
0.86 0.11 0.03
Matches are distributed among these distances:
45 39 0.09
46 405 0.91
47 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (46 bp):
ATCTTCGATCTCCTTCGCTGCCAAATACAGGAAGACAAGATCTGCT
Found at i:44142521 original size:44 final size:43
Alignment explanation
Indices: 44142456--44142569 Score: 115
Period size: 43 Copynumber: 2.6 Consensus size: 43
44142446 AGATCATCAT
* *
44142456 ATGCCCCGATCTGATCAAAATTTGAGCT-GCTCTGATCACCACC
1 ATGCCCCAATTTGATCAAAATTTGAGCTCGCTCTGATCA-CACC
* **
44142499 ATGCCCCAATTTGATACAAAATTTAAG-TCGCTCTGATCACTTC
1 ATGCCCCAATTTGAT-CAAAATTTGAGCTCGCTCTGATCACACC
* * *
44142542 GTGCCCCATTTTGTTCCAAAATTTGAGC
1 ATGCCCCAATTTGAT-CAAAATTTGAGC
44142570 CGCCCATTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
43 38 0.66
44 20 0.34
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (43 bp):
ATGCCCCAATTTGATCAAAATTTGAGCTCGCTCTGATCACACC
Found at i:44142547 original size:43 final size:43
Alignment explanation
Indices: 44142456--44142538 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 43
44142446 AGATCATCAT
* * *
44142456 ATGCCCCGATCTGATCAAAATTTGAGCTGCTCTGATCACCACC
1 ATGCCCCAATTTGATCAAAATTTAAGCTGCTCTGATCACCACC
44142499 ATGCCCCAATTTGATACAAAATTTAAG-TCGCTCTGATCAC
1 ATGCCCCAATTTGAT-CAAAATTTAAGCT-GCTCTGATCAC
44142539 TTCGTGCCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
43 14 0.40
44 21 0.60
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.28
Consensus pattern (43 bp):
ATGCCCCAATTTGATCAAAATTTAAGCTGCTCTGATCACCACC
Found at i:44144510 original size:17 final size:18
Alignment explanation
Indices: 44144478--44144514 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
44144468 TCTGCACAGT
44144478 ATGATTATGAATGAAAGA
1 ATGATTATGAATGAAAGA
*
44144496 ATGATT-TGGATGAAAGA
1 ATGATTATGAATGAAAGA
44144513 AT
1 AT
44144515 AAAAGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.30
Consensus pattern (18 bp):
ATGATTATGAATGAAAGA
Found at i:44144521 original size:8 final size:8
Alignment explanation
Indices: 44144508--44144542 Score: 70
Period size: 8 Copynumber: 4.4 Consensus size: 8
44144498 GATTTGGATG
44144508 AAAGAATA
1 AAAGAATA
44144516 AAAGAATA
1 AAAGAATA
44144524 AAAGAATA
1 AAAGAATA
44144532 AAAGAATA
1 AAAGAATA
44144540 AAA
1 AAA
44144543 ATAATCATTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAGAATA
Found at i:44148613 original size:4 final size:4
Alignment explanation
Indices: 44148604--44148630 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
44148594 ATAAAAAATA
44148604 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
44148631 ATAAGCTAAA
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:44151877 original size:13 final size:11
Alignment explanation
Indices: 44151845--44151901 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 11
44151835 CCATTTTTTA
*
44151845 AATAAAATAAT
1 AATAAAATATT
44151856 AAT-AAATATCT
1 AATAAAATAT-T
44151867 AAGTAAAATATT
1 AA-TAAAATATT
44151879 AATAAAATAATATT
1 AAT--AA-AATATT
44151893 AATAAAATA
1 AATAAAATA
44151902 ATATTTAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
10 5 0.13
11 11 0.28
12 6 0.15
13 8 0.21
14 9 0.23
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (11 bp):
AATAAAATATT
Found at i:44151892 original size:14 final size:14
Alignment explanation
Indices: 44151873--44151906 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
44151863 ATCTAAGTAA
44151873 AATATTAATAAAAT
1 AATATTAATAAAAT
44151887 AATATTAATAAAAT
1 AATATTAATAAAAT
44151901 AATATT
1 AATATT
44151907 TAACTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AATATTAATAAAAT
Found at i:44152811 original size:19 final size:20
Alignment explanation
Indices: 44152776--44152816 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
44152766 AAAAGTATTT
*
44152776 AAAAATTATTAAGAATTATA
1 AAAAATTACTAAGAATTATA
*
44152796 AAAAATTACTAA-AATTTTA
1 AAAAATTACTAAGAATTATA
44152815 AA
1 AA
44152817 TTAATGATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATTACTAAGAATTATA
Found at i:44156416 original size:30 final size:29
Alignment explanation
Indices: 44156382--44156441 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
44156372 ACAATTTTCC
* *
44156382 CAAGTTGGTGCTGAAACTTTTTCTT-GGTTA
1 CAAG-TGGTACTGAAAC-TATTCTTCGGTTA
*
44156412 CAAGTGGTACTTAAACTATTCTTCGGTTA
1 CAAGTGGTACTGAAACTATTCTTCGGTTA
44156441 C
1 C
44156442 TCATTTTATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
28 6 0.23
29 16 0.62
30 4 0.15
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.40
Consensus pattern (29 bp):
CAAGTGGTACTGAAACTATTCTTCGGTTA
Found at i:44157681 original size:28 final size:28
Alignment explanation
Indices: 44157619--44157682 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
44157609 CAAAAAAAGC
44157619 CCATTTTTTAAAAAATTACCGAAATGGG
1 CCATTTTTTAAAAAATTACCGAAATGGG
** * *
44157647 CCGATTTTTTAATTATTTACCGGAATGGG
1 CC-ATTTTTTAAAAAATTACCGAAATGGG
44157676 CCATTTT
1 CCATTTT
44157683 CCGCGAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 24 0.77
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (28 bp):
CCATTTTTTAAAAAATTACCGAAATGGG
Found at i:44161459 original size:28 final size:28
Alignment explanation
Indices: 44161442--44162123 Score: 741
Period size: 28 Copynumber: 24.4 Consensus size: 28
44161432 GGTTTTTACA
**
44161442 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
44161471 TTAATTAAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATT-AA--A--TTA-GGTTAGGGTTT
44161505 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* ** *
44161533 TTAACTAAATTATGTTAGGTTAGGGTAT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
44161561 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
44161589 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
**
44161618 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
* **
44161647 TTAACTAAATT--A-T--GTTATAGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
44161670 TTAATTAAATTAAATTAGGTTAGGG-TT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
44161697 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* *
44161725 TTAATTAAATTAGATTATGGTTAGAG-TT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
* * **
44161753 TTCATGTAAAATATGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAATTA-GGTTAGGGTTT
*
44161783 TAAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
44161811 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
* **
44161840 TT-ATGTAAAATAGGTTAGGGTTAGGGTTT
1 TTAAT-TAAATTAAATTA-GGTTAGGGTTT
*
44161869 TTAACTAAATT--A-T--GTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
44161892 TTAATTAAATTAAATTAGGTTAGAGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
44161920 TTAATTAAATTAGGTTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
44161948 TTAATTAAATTAAATTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
* **
44161976 TTAACTAAATTATGTTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
44162004 TTAATTAAATTAGGTTAGGGTTAGGGTTT
1 TTAATTAAATTAAATTA-GGTTAGGGTTT
*
44162033 TCAATGTAAA-T---TTAGGTTAGGGTTT
1 TTAAT-TAAATTAAATTAGGTTAGGGTTT
*
44162058 TTAATTAAATTAAATTATGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
**
44162086 TTAATTAAATTAGGTTAGGTTAGGGTTT
1 TTAATTAAATTAAATTAGGTTAGGGTTT
*
44162114 TTAATCAAAT
1 TTAATTAAAT
44162124 AATGTCAAAA
Statistics
Matches: 566, Mismatches: 58, Indels: 59
0.83 0.08 0.09
Matches are distributed among these distances:
23 38 0.07
24 4 0.01
25 18 0.03
26 7 0.01
27 27 0.05
28 277 0.49
29 155 0.27
30 11 0.02
31 1 0.00
33 2 0.00
34 26 0.05
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (28 bp):
TTAATTAAATTAAATTAGGTTAGGGTTT
Found at i:44162110 original size:222 final size:221
Alignment explanation
Indices: 44161478--44162123 Score: 902
Period size: 222 Copynumber: 2.9 Consensus size: 221
44161468 TTTTTAATTA
44161478 AATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAAT
1 AATTAAATTAGGTTA-GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAAT
*
44161543 TATGTTAGGTTAGGGTATTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGG
65 TATGTTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATT--GTTAGG
44161608 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAATTATGTTA--TA--GTT
128 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAATTA-GTTAGTTAGGGTT
44161669 TTTAATTAAATTAAATTAGGTTAGGGTTTT
192 TTTAATTAAATTAAATTAGGTTAGGGTTTT
** * * * ** *
44161699 AATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGATTATGGTTAGAGTTTTCATGTAAAA
1 AATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAACTAAAT
*
44161764 TATGTTAGGGTTAGGGTTTTAAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAG
65 TATGTTA-GGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATT--GTTAG
*
44161829 GGTTAGGGTTTTT-ATGTAAAATAGGTTAGGGTTAGGGTTTTTAACTAAATTA--T-GTTAGGGT
127 GGTTAGGGTTTTTAAT-TAAATTAGGTTAGGGTTAGGGTTTTTAACTAAATTAGTTAGTTAGGGT
*
44161890 TTTTAATTAAATTAAATTAGGTTAGAGTTTTT
191 TTTTAATTAAATTAAATTAGGTTAG-GGTTTT
44161922 AATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAATT
1 AATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAATT
** *
44161987 ATGTTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTCAATGTAAA-T-TTA-GG
66 ATGTTAGGTTAGGGTTTTTAATTAAATTAAATTA-GGTTAGGGTTTTTAAT-TAAATTGTTAGGG
** * *
44162049 TTAGGGTTTTTAATTAAATTAAATTA-TGTTAGGGTTTTTAATTAAATTAGGTTAGGTTAGGGTT
129 TTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAATTA-GTTA-GTTAGGGTT
*
44162113 TTTAATCAAAT
192 TTTAATTAAAT
44162124 AATGTCAAAA
Statistics
Matches: 379, Mismatches: 30, Indels: 31
0.86 0.07 0.07
Matches are distributed among these distances:
217 21 0.06
218 22 0.06
219 6 0.02
220 30 0.08
221 63 0.17
222 188 0.50
223 49 0.13
ACGTcount: A:0.32, C:0.01, G:0.21, T:0.45
Consensus pattern (221 bp):
AATTAAATTAGGTTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAACTAAATT
ATGTTAGGTTAGGGTTTTTAATTAAATTAAATTAGGTTAGGGTTTTTAATTAAATTGTTAGGGTT
AGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAACTAAATTAGTTAGTTAGGGTTTTTA
ATTAAATTAAATTAGGTTAGGGTTTT
Found at i:44164284 original size:14 final size:15
Alignment explanation
Indices: 44164267--44164300 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
44164257 AATAAATATC
44164267 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
44164281 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
44164296 TAAAA
1 TAAAA
44164301 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:44164524 original size:11 final size:10
Alignment explanation
Indices: 44164507--44164574 Score: 61
Period size: 11 Copynumber: 6.6 Consensus size: 10
44164497 TTTTTTGAAG
44164507 GAATTTGAGA
1 GAATTTGAGA
44164517 GAATTTTG-GAA
1 GAA-TTTGAG-A
44164528 GGAATTTGAGA
1 -GAATTTGAGA
44164539 G--TTTGAGA
1 GAATTTGAGA
*
44164547 GAATTTTGAAA
1 GAA-TTTGAGA
44164558 GGAATTTGAGA
1 -GAATTTGAGA
44164569 GAATTT
1 GAATTT
44164575 TTGAAGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
8 8 0.17
10 11 0.23
11 22 0.46
12 7 0.15
ACGTcount: A:0.37, C:0.00, G:0.29, T:0.34
Consensus pattern (10 bp):
GAATTTGAGA
Found at i:44164528 original size:22 final size:22
Alignment explanation
Indices: 44164488--44164539 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
44164478 TTTAATATGG
* *
44164488 ATTTGA-AGATTTTTTGAAGGA
1 ATTTGAGAGAATTTTGGAAGGA
44164509 ATTTGAGAGAATTTTGGAAGGA
1 ATTTGAGAGAATTTTGGAAGGA
44164531 ATTTGAGAG
1 ATTTGAGAG
44164540 TTTGAGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.37
Consensus pattern (22 bp):
ATTTGAGAGAATTTTGGAAGGA
Found at i:44164544 original size:30 final size:30
Alignment explanation
Indices: 44164510--44164569 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
44164500 TTTGAAGGAA
*
44164510 TTTGAGAGAATTTTGGAAGGAATTTGAGAG
1 TTTGAGAGAATTTTGAAAGGAATTTGAGAG
44164540 TTTGAGAGAATTTTGAAAGGAATTTGAGAG
1 TTTGAGAGAATTTTGAAAGGAATTTGAGAG
44164570 AATTTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.33
Consensus pattern (30 bp):
TTTGAGAGAATTTTGAAAGGAATTTGAGAG
Found at i:44164566 original size:22 final size:22
Alignment explanation
Indices: 44164540--44164588 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
44164530 AATTTGAGAG
44164540 TTTGAGAGAA-TTTTGAAAGGAA
1 TTTGAGAGAATTTTTG-AAGGAA
44164562 TTTGAGAGAATTTTTGAAGGAA
1 TTTGAGAGAATTTTTGAAGGAA
*
44164584 ATTGA
1 TTTGA
44164589 TATTGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.35
Consensus pattern (22 bp):
TTTGAGAGAATTTTTGAAGGAA
Found at i:44175737 original size:9 final size:9
Alignment explanation
Indices: 44175723--44175756 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
44175713 TATTTTTTGG
44175723 TAATTCAGT
1 TAATTCAGT
*
44175732 TAATTCGGT
1 TAATTCAGT
*
44175741 TAATTCAGG
1 TAATTCAGT
44175750 TAATTCA
1 TAATTCA
44175757 AGTAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (9 bp):
TAATTCAGT
Found at i:44179211 original size:91 final size:90
Alignment explanation
Indices: 44179056--44179253 Score: 369
Period size: 91 Copynumber: 2.2 Consensus size: 90
44179046 ATAAATCATA
**
44179056 ATATAAAATTATATAAATTATATTAATCTTGATAAATCTAAAAAGAATTAGCTAAATACTGATAA
1 ATATAAAAAAATATAAATTATATTAATCTTGATAAATCTAAAAAGAATTAGCTAAATACTGAT-A
44179121 AAAAATATAGACCGTATTAACAAAGT
65 AAAAATATAGACCGTATTAACAAAGT
44179147 ATATAAAAAAATATAAATTATATTAATCTTGATAAATCTAAAAAGAATTAGCTAAATACTGATAA
1 ATATAAAAAAATATAAATTATATTAATCTTGATAAATCTAAAAAGAATTAGCTAAATACTGATAA
44179212 AAAATATAGACCGTATTAACAAAGT
66 AAAATATAGACCGTATTAACAAAGT
44179237 ATATAAAAAAATATAAA
1 ATATAAAAAAATATAAA
44179254 ACTTATAAGA
Statistics
Matches: 105, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
90 44 0.42
91 61 0.58
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (90 bp):
ATATAAAAAAATATAAATTATATTAATCTTGATAAATCTAAAAAGAATTAGCTAAATACTGATAA
AAAATATAGACCGTATTAACAAAGT
Found at i:44189843 original size:3 final size:3
Alignment explanation
Indices: 44189835--44189866 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
44189825 TCCAAACAAA
44189835 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
44189867 AATAAGCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:44191067 original size:26 final size:29
Alignment explanation
Indices: 44191011--44191074 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
44191001 AAATTAAAAG
* *
44191011 AAAATATATAAAAATATATAT-AATTTTT
1 AAAATATATAAAAATATATATAAATTATA
44191039 AAAATATA-AAAGAA-AT-TATAAATTATA
1 AAAATATATAAA-AATATATATAAATTATA
44191066 AAAATATAT
1 AAAATATAT
44191075 GTGTCTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 3 0.10
27 18 0.58
28 10 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATATATAAAAATATATATAAATTATA
Found at i:44194326 original size:21 final size:23
Alignment explanation
Indices: 44194300--44194343 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
44194290 AATAAAGTAG
44194300 ATTATATA-TAT-ATTTTATAAT
1 ATTATATATTATGATTTTATAAT
*
44194321 ATTATATATTATGATTTTTTAAT
1 ATTATATATTATGATTTTATAAT
44194344 TCATATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 8 0.40
22 3 0.15
23 9 0.45
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (23 bp):
ATTATATATTATGATTTTATAAT
Found at i:44194483 original size:25 final size:26
Alignment explanation
Indices: 44194434--44194483 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
44194424 ATTTTTATTT
*
44194434 TTATTAAAATATATTTAATAATAACC
1 TTATTAAAATATATATAATAATAACC
*
44194460 TTATTAAAATTTA-ATAATAATAAC
1 TTATTAAAATATATATAATAATAAC
44194484 AATAATCATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (26 bp):
TTATTAAAATATATATAATAATAACC
Found at i:44197294 original size:26 final size:25
Alignment explanation
Indices: 44197254--44197302 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
44197244 ATGAACGCCC
44197254 TTCTTTGCTCTCTGCTCTCTGCTGG
1 TTCTTTGCTCTCTGCTCTCTGCTGG
*
44197279 TTCTTTGTTTCTCTGCTCTCTGCT
1 TTCTTTG-CTCTCTGCTCTCTGCT
44197303 ACGCTGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.00, C:0.31, G:0.16, T:0.53
Consensus pattern (25 bp):
TTCTTTGCTCTCTGCTCTCTGCTGG
Found at i:44197312 original size:31 final size:33
Alignment explanation
Indices: 44197254--44197316 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
44197244 ATGAACGCCC
* *
44197254 TTCTTTGCTCTCTGCTCTCTGCTGGTTCTTTGT
1 TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTGT
44197287 TTCTCTGCTCTCTGCT-AC-GCTGGTTCTTTG
1 TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTG
44197317 CCCTCATCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 12 0.43
32 1 0.04
33 15 0.54
ACGTcount: A:0.02, C:0.29, G:0.19, T:0.51
Consensus pattern (33 bp):
TTCTCTGCTCTCTGCTCACTGCTGGTTCTTTGT
Found at i:44197412 original size:8 final size:8
Alignment explanation
Indices: 44197399--44197429 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
44197389 GTTTATCTTT
44197399 TTCTTCTC
1 TTCTTCTC
44197407 TTCTTCTC
1 TTCTTCTC
44197415 TTCTTCTC
1 TTCTTCTC
44197423 TTCTTCT
1 TTCTTCT
44197430 GTATATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (8 bp):
TTCTTCTC
Found at i:44200320 original size:3 final size:3
Alignment explanation
Indices: 44200312--44200340 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44200302 CTTAAAATGA
44200312 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
44200341 AGTTTAACAA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:44201558 original size:19 final size:21
Alignment explanation
Indices: 44201520--44201559 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44201510 TTTATAAATC
*
44201520 TATAAATTTTTAGTTCTTTTA
1 TATAAATTTTTAGATCTTTTA
44201541 TATAAATTTTTA-AT-TTTTA
1 TATAAATTTTTAGATCTTTTA
44201560 ATTTTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 1 0.06
21 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (21 bp):
TATAAATTTTTAGATCTTTTA
Found at i:44201564 original size:6 final size:7
Alignment explanation
Indices: 44201545--44201572 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
44201535 CTTTTATATA
44201545 AATTTTT
1 AATTTTT
44201552 AATTTTT
1 AATTTTT
44201559 AATTTTT
1 AATTTTT
44201566 AATTTTT
1 AATTTTT
44201573 GATAAATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
AATTTTT
Found at i:44205284 original size:2 final size:2
Alignment explanation
Indices: 44205277--44205325 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
44205267 TTAGAACAAA
44205277 AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
44205318 AG AG AG AG
1 AG AG AG AG
44205326 TAGTGTATCC
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44208142 original size:42 final size:42
Alignment explanation
Indices: 44208078--44208207 Score: 217
Period size: 42 Copynumber: 3.1 Consensus size: 42
44208068 ACAAAAACGC
*
44208078 CGCCGCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTTTAAG
1 CGCCTCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTTTAAG
44208120 CGCCTCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTTTAAG
1 CGCCTCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTTTAAG
* *
44208162 CGCCTCTAAAGAACATGGTCTTTAACGGCGTTTTT-TTCTAAG
1 CGCCTCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTT-TAAG
44208204 CGCC
1 CGCC
44208208 GGCACTTTTA
Statistics
Matches: 84, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
41 2 0.02
42 82 0.98
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (42 bp):
CGCCTCTAAAGAACATGGTTTTTAGCGGCGTTTTTGTTTAAG
Found at i:44208556 original size:21 final size:21
Alignment explanation
Indices: 44208530--44208600 Score: 88
Period size: 21 Copynumber: 3.4 Consensus size: 21
44208520 TTTTGCTCTG
*
44208530 CTTTGCTTCTCTCGCTGCAGC
1 CTTTGCTTCCCTCGCTGCAGC
*
44208551 TTTTGCTTCCCTCGCTGCAGC
1 CTTTGCTTCCCTCGCTGCAGC
** *
44208572 CACTGCTTCCCTCGCTGCCGC
1 CTTTGCTTCCCTCGCTGCAGC
*
44208593 CTCTGCTT
1 CTTTGCTT
44208601 TAAGTTGTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.04, C:0.42, G:0.18, T:0.35
Consensus pattern (21 bp):
CTTTGCTTCCCTCGCTGCAGC
Found at i:44209325 original size:16 final size:17
Alignment explanation
Indices: 44209289--44209324 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
44209279 TGAATTTTTG
*
44209289 TTTCTGCCTGCTGCTTT
1 TTTCTGCATGCTGCTTT
44209306 TTTCTGCATGCTGCTTT
1 TTTCTGCATGCTGCTTT
44209323 TT
1 TT
44209325 CCAACTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.25, G:0.17, T:0.56
Consensus pattern (17 bp):
TTTCTGCATGCTGCTTT
Found at i:44213998 original size:9 final size:9
Alignment explanation
Indices: 44213981--44214262 Score: 243
Period size: 9 Copynumber: 32.4 Consensus size: 9
44213971 TATGTATTAA
*
44213981 GTAAATTAT
1 GTAAGTTAT
44213990 GTAAGTTAT
1 GTAAGTTAT
*
44213999 GTACGTGTA-
1 GTAAGT-TAT
44214008 -TAAGTTAT
1 GTAAGTTAT
44214016 GTAAGTTAT
1 GTAAGTTAT
*
44214025 GT-A-TTAA
1 GTAAGTTAT
*
44214032 GTAAGCTAT
1 GTAAGTTAT
*
44214041 GTAAGTTGT
1 GTAAGTTAT
44214050 GT-A-TTAT
1 GTAAGTTAT
44214057 GTAAGTTAT
1 GTAAGTTAT
44214066 GTAAGTTAT
1 GTAAGTTAT
** *
44214075 CAAAGTAAT
1 GTAAGTTAT
*
44214084 GTATGTTAT
1 GTAAGTTAT
44214093 GTAAG-T-T
1 GTAAGTTAT
44214100 GTAAGTTAT
1 GTAAGTTAT
*
44214109 -TATGTATTAT
1 GTAAG--TTAT
44214119 GTAAGTTAT
1 GTAAGTTAT
44214128 GTAAGTTAAAT
1 GTAAGTT--AT
44214139 GT-A-TTAT
1 GTAAGTTAT
*
44214146 GTAGGTTAT
1 GTAAGTTAT
*
44214155 GTAAGTTGT
1 GTAAGTTAT
*
44214164 GTAAGATAT
1 GTAAGTTAT
*
44214173 TTAAGTTAT
1 GTAAGTTAT
* *
44214182 GTGAGTTTT
1 GTAAGTTAT
44214191 GT-A-TTAT
1 GTAAGTTAT
44214198 GTAAGTTAT
1 GTAAGTTAT
44214207 GTAAGTTAT
1 GTAAGTTAT
*
44214216 GTAAGTTTT
1 GTAAGTTAT
44214225 GT-A-TTAT
1 GTAAGTTAT
44214232 GTAAGTTAT
1 GTAAGTTAT
*
44214241 GTAGGTTAT
1 GTAAGTTAT
*
44214250 GTAAGTTTT
1 GTAAGTTAT
44214259 GTAA
1 GTAA
44214263 TGTACAAGTG
Statistics
Matches: 218, Mismatches: 35, Indels: 40
0.74 0.12 0.14
Matches are distributed among these distances:
7 32 0.15
8 17 0.08
9 155 0.71
10 7 0.03
11 7 0.03
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:44214070 original size:34 final size:34
Alignment explanation
Indices: 44213985--44214261 Score: 221
Period size: 34 Copynumber: 8.0 Consensus size: 34
44213975 TATTAAGTAA
*
44213985 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGT
1 ATTATGTAAGTTATGTAAGT-TATGTAAGTTATGT
* * *
44214018 AAGTTATGT-A-TTAAGTAAGCTATGTAAGTTGTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
** *
44214052 ATTATGTAAGTTATGTAAGTTATCAAAGTAATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
*
44214086 ATGTTATGTAAG-T-TGTAAGTTAT-TATGTATTATGT
1 A--TTATGTAAGTTATGTAAGTTATGTAAG--TTATGT
*
44214121 AAGTTATGTAAGTTAAATGT-A-TTATGTAGGTTATGT
1 -A-TTATGTAAGTT--ATGTAAGTTATGTAAGTTATGT
* * * * *
44214157 AAGTTGTGTAAGATATTTAAGTTATGTGAGTTTTGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGTTATGT
*
44214193 ATTATGTAAGTTATGTAAGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
* *
44214227 ATTATGTAAGTTATGTAGGTTATGTAAGTTTTGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
44214261 A
1 A
44214262 ATGTACAAGT
Statistics
Matches: 201, Mismatches: 25, Indels: 34
0.77 0.10 0.13
Matches are distributed among these distances:
32 8 0.04
33 11 0.05
34 106 0.53
35 24 0.12
36 41 0.20
37 4 0.02
38 4 0.02
39 3 0.01
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (34 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGTTATGT
Found at i:44214113 original size:19 final size:19
Alignment explanation
Indices: 44214089--44214127 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
44214079 GTAATGTATG
44214089 TTATGTAAGT-TGTAAGTTA
1 TTATGT-AGTATGTAAGTTA
*
44214108 TTATGTATTATGTAAGTTA
1 TTATGTAGTATGTAAGTTA
44214127 T
1 T
44214128 GTAAGTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (19 bp):
TTATGTAGTATGTAAGTTA
Found at i:44214147 original size:27 final size:25
Alignment explanation
Indices: 44213985--44214262 Score: 178
Period size: 25 Copynumber: 10.7 Consensus size: 25
44213975 TATTAAGTAA
* *
44213985 ATTATGTAAGTTATGTACGTGTAT-A
1 ATTATGTAAGTTATGTAAGT-TATGT
*
44214010 AGTTATGTAAGTTATGT-A-TTAAGT
1 A-TTATGTAAGTTATGTAAGTTATGT
* *
44214034 AAGCTATGTAAGTTGTGT-A-TTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
** *
44214059 AAGTTATGTAAGTTATCAAAGTAATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
44214086 ATGTTATGTAAG-T-TGTAAGTTATTATGT
1 A--TTATGTAAGTTATGTAAG---TTATGT
44214114 ATTATGTAAGTTATGTAAGTTAAATGT
1 ATTATGTAAGTTATGTAAGTT--ATGT
* *
44214141 ATTATGTAGGTTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTAAGTTATGT
* * * *
44214166 AAGATATTTAAGTTATGTGAGTTTTGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
44214193 ATTATGTAAGTTATGTAAGTTATGT
1 ATTATGTAAGTTATGTAAGTTATGT
*
44214218 AAGTTTTGT-A-TTATGTAAGTTATGT
1 -A-TTATGTAAGTTATGTAAGTTATGT
*
44214243 AGGTTATGTAAGTTTTGTAA
1 A--TTATGTAAGTTATGTAA
44214263 TGTACAAGTG
Statistics
Matches: 205, Mismatches: 28, Indels: 38
0.76 0.10 0.14
Matches are distributed among these distances:
23 2 0.01
24 2 0.01
25 86 0.42
26 32 0.16
27 71 0.35
28 12 0.06
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (25 bp):
ATTATGTAAGTTATGTAAGTTATGT
Found at i:44214199 original size:52 final size:53
Alignment explanation
Indices: 44213985--44214262 Score: 192
Period size: 52 Copynumber: 5.3 Consensus size: 53
44213975 TATTAAGTAA
* * *
44213985 ATTATGTAAGTTATGTACGTGTA--TAAGTTATGTAAGTTATGT-A-TTAA-GT
1 ATTATGTAAGTTATGTAAGT-TATGTAAGATATTTAAGTTATGTAAGTTAATGT
* * * * **
44214034 AAGCTATGTAAGTTGTGT-A-TTATGTAAGTTATGTAAGTTATCAAAG-TAATGT
1 -A-TTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTTAATGT
* *
44214086 ATGTTATGTAAG-T-TGTAAGTTAT-TATGTATTATGTAAGTTATGTAAGTTAAATGT
1 A--TTATGTAAGTTATGTAAGTTATGTAAG-A-TATTTAAGTTATGTAAGTT-AATGT
* * * *
44214141 ATTATGTAGGTTATGTAAGTTGTGTAAGATATTTAAGTTATGTGAGTT-TTGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTTAATGT
*
44214193 ATTATGTAAGTTATGTAAGTTATGTAAG-T-TTTGTA-TTATGTAAGTT-ATGT
1 ATTATGTAAGTTATGTAAGTTATGTAAGATATTT-AAGTTATGTAAGTTAATGT
*
44214243 AGGTTATGTAAGTTTTGTAA
1 A--TTATGTAAGTTATGTAA
44214263 TGTACAAGTG
Statistics
Matches: 187, Mismatches: 22, Indels: 36
0.76 0.09 0.15
Matches are distributed among these distances:
48 2 0.01
49 1 0.01
50 38 0.20
51 25 0.13
52 60 0.32
53 23 0.12
54 19 0.10
55 16 0.09
56 3 0.02
ACGTcount: A:0.31, C:0.01, G:0.22, T:0.46
Consensus pattern (53 bp):
ATTATGTAAGTTATGTAAGTTATGTAAGATATTTAAGTTATGTAAGTTAATGT
Found at i:44214241 original size:43 final size:43
Alignment explanation
Indices: 44213981--44214262 Score: 254
Period size: 43 Copynumber: 6.5 Consensus size: 43
44213971 TATGTATTAA
* * *
44213981 GTAAATTATGTAAGTTATGTACGTGTAT-AAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGT-TATGTA-TTATGTAAGTTAT
* * *
44214025 GT-A-TTAAGTAAGCTATGTAAGTTGTGTATTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
** * * *
44214066 GTAAGTTATCAAAGTAATGTATGTTATGTAAGT-TGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGT-ATTATGTAAGTTAT
* *
44214109 -TATGTATTATGTAAGTTATGTAAGTTAAATGTATTATGTAGGTTAT
1 GTAAG--TTATGTAAGTTATGTAAGTT--ATGTATTATGTAAGTTAT
* * * *
44214155 GTAAGTTGTGTAAGATATTTAAGTTATGTGAGTTTTGT-A-TTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGTTAT
*
44214198 GTAAGTTATGTAAGTTATGTAAGTTTTGTATTATGTAAGTTAT
1 GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
* *
44214241 GTAGGTTATGTAAGTTTTGTAA
1 GTAAGTTATGTAAGTTATGTAA
44214263 TGTACAAGTG
Statistics
Matches: 191, Mismatches: 33, Indels: 29
0.75 0.13 0.11
Matches are distributed among these distances:
41 22 0.12
42 23 0.12
43 85 0.45
44 21 0.11
45 24 0.13
46 13 0.07
47 3 0.02
ACGTcount: A:0.32, C:0.01, G:0.22, T:0.46
Consensus pattern (43 bp):
GTAAGTTATGTAAGTTATGTAAGTTATGTATTATGTAAGTTAT
Found at i:44214306 original size:25 final size:26
Alignment explanation
Indices: 44214278--44214326 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
44214268 AAGTGTCAGG
*
44214278 TTATTGTT-ATTAAATTTTAATAAGA
1 TTATTGTTAACTAAATTTTAATAAGA
*
44214303 TTATTGTTAACTATATTTTAATAA
1 TTATTGTTAACTAAATTTTAATAA
44214327 AAATAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
TTATTGTTAACTAAATTTTAATAAGA
Found at i:44214450 original size:13 final size:13
Alignment explanation
Indices: 44214432--44214465 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
44214422 ATATAATTAT
44214432 TAATAATATTTAA
1 TAATAATATTTAA
44214445 TAATAAT-TTTAA
1 TAATAATATTTAA
44214457 T-ATAATATT
1 TAATAATATT
44214466 ATTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.25
12 8 0.40
13 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATAATATTTAA
Found at i:44215316 original size:31 final size:31
Alignment explanation
Indices: 44215274--44215357 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
44215264 GAGCTCTTAG
* * *
44215274 CCAT-TTAGCAGCAGAAATCAATATAAGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
44215304 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
1 CCATCTTAGCAGCAAAAACCAATAGAAGGTA
*
44215335 CCATCTTAGCTGCAAAAACCAAT
1 CCATCTTAGCAGCAAAAACCAAT
44215358 TAAAATCCAA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.43, C:0.23, G:0.14, T:0.20
Consensus pattern (31 bp):
CCATCTTAGCAGCAAAAACCAATAGAAGGTA
Found at i:44217664 original size:38 final size:38
Alignment explanation
Indices: 44217609--44217693 Score: 111
Period size: 38 Copynumber: 2.2 Consensus size: 38
44217599 CCAAATCCCT
*
44217609 AACCCATAACCCTTAAATC-CTCTTAACCCTTAAAGCATA
1 AACCC-TAACCCTTAAATCTCTC-TAACCCCTAAAGCATA
44217648 AACCCTAA-CCTCTAAATCTCTCTAACCCCTAAAGCATA
1 AACCCTAACCCT-TAAATCTCTCTAACCCCTAAAGCATA
*
44217686 ACCCCTAA
1 AACCCTAA
44217694 AAATTTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
37 3 0.07
38 31 0.74
39 8 0.19
ACGTcount: A:0.38, C:0.36, G:0.02, T:0.24
Consensus pattern (38 bp):
AACCCTAACCCTTAAATCTCTCTAACCCCTAAAGCATA
Found at i:44217859 original size:21 final size:21
Alignment explanation
Indices: 44217833--44217877 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
44217823 AAATCCTCCT
*
44217833 TAACCCTTAAAGCATAAACCC
1 TAACCCCTAAAGCATAAACCC
*
44217854 TAACCCCTAAAGCATAACCCC
1 TAACCCCTAAAGCATAAACCC
44217875 TAA
1 TAA
44217878 AAATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.42, C:0.36, G:0.04, T:0.18
Consensus pattern (21 bp):
TAACCCCTAAAGCATAAACCC
Found at i:44218172 original size:15 final size:16
Alignment explanation
Indices: 44218152--44218197 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
44218142 ACCGTTGAAA
*
44218152 CCCTAAACCCTAAA-C
1 CCCTAACCCCTAAATC
44218167 CCCTAACCCCTAAATC
1 CCCTAACCCCTAAATC
44218183 CTCCTAACCCCTAAA
1 C-CCTAACCCCTAAA
44218198 GCATAACCCC
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 13 0.46
16 2 0.07
17 13 0.46
ACGTcount: A:0.35, C:0.48, G:0.00, T:0.17
Consensus pattern (16 bp):
CCCTAACCCCTAAATC
Found at i:44218190 original size:17 final size:15
Alignment explanation
Indices: 44218152--44218210 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
44218142 ACCGTTGAAA
*
44218152 CCCTAAACCCTAAAC
1 CCCTAACCCCTAAAC
44218167 CCCTAACCCCTAAATC
1 CCCTAACCCCTAAA-C
44218183 CTCCTAACCCCTAAA-
1 C-CCTAACCCCTAAAC
* *
44218198 GCATAACCCCTAA
1 CCCTAACCCCTAA
44218211 CCCTTAAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
14 11 0.28
15 13 0.33
16 2 0.05
17 13 0.33
ACGTcount: A:0.36, C:0.46, G:0.02, T:0.17
Consensus pattern (15 bp):
CCCTAACCCCTAAAC
Found at i:44218195 original size:7 final size:7
Alignment explanation
Indices: 44218152--44218213 Score: 52
Period size: 7 Copynumber: 8.3 Consensus size: 7
44218142 ACCGTTGAAA
*
44218152 CCCTAAA
1 CCCTAAC
44218159 CCCTAAAC
1 CCCT-AAC
44218167 CCCTAAC
1 CCCTAAC
44218174 CCCTAAATC
1 CCCT-AA-C
44218183 CTCCTAAC
1 C-CCTAAC
*
44218191 CCCTAAA
1 CCCTAAC
* *
44218198 GCATAAC
1 CCCTAAC
44218205 CCCTAAC
1 CCCTAAC
44218212 CC
1 CC
44218214 TTAAACATTA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
7 27 0.61
8 10 0.23
9 4 0.09
10 3 0.07
ACGTcount: A:0.34, C:0.48, G:0.02, T:0.16
Consensus pattern (7 bp):
CCCTAAC
Found at i:44218602 original size:73 final size:71
Alignment explanation
Indices: 44218484--44218623 Score: 167
Period size: 73 Copynumber: 1.9 Consensus size: 71
44218474 CGCTTTCCTA
* * *
44218484 AAAACGCCGCTAAATCCCCGAAAGCACAGAAAATGGCACCGTTGGGCTTAGTTTTTTTTGCGGCG
1 AAAACGCCGCAAAATCCCCGAAAGCACAGAAAATGGCA-C-TTGGGCTTAGGTTTTCTTGCGGCG
44218549 CTACACCT
64 CTACACCT
* *
44218557 AAAACGCCGCAAAATCCCCGAAAGGCTA-AGAAACAGTGTCA-TTGGGCTTAGGTTTTCTTGTGG
1 AAAACGCCGCAAAATCCCCGAAA-GC-ACAGAAA-A-TGGCACTTGGGCTTAGGTTTTCTTGCGG
44218620 CGCT
62 CGCT
44218624 TTTTTAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
73 45 0.78
74 7 0.12
75 2 0.03
76 4 0.07
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.24
Consensus pattern (71 bp):
AAAACGCCGCAAAATCCCCGAAAGCACAGAAAATGGCACTTGGGCTTAGGTTTTCTTGCGGCGCT
ACACCT
Found at i:44218844 original size:112 final size:114
Alignment explanation
Indices: 44218557--44218868 Score: 330
Period size: 112 Copynumber: 2.8 Consensus size: 114
44218547 CGCTACACCT
* * * * * *
44218557 AAAACGCCGCAAAATCCCCGAAAGGCTAAGAAACAGTGTCATTGGGCTTAGGTTTTCTTGTGGCG
1 AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
*
44218622 CTTTTTTAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
66 CTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
* * * * * *
44218671 AAAACGCCG-TAAAAT-CCTG-AAAGCACAAAAAACGGTGCCGTTGGGCTTAGTTTTTTTTTGCG
1 AAAACGCCGCT-AAATCCCCGAAAAGCTC-AGAAACGGTGTCGTTGGGCTTAG-GTTTTCTTGCG
* * * * *
44218733 GCGCTATTCCAAAAACGCCGCTAAATC-CT-TGCATTAGCGGCGCTTCTT-TA
63 GCGCTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTT-TTAAA
* * * * *
44218783 GAAACGCCGCTAAATCCCCGAAAAGCTCTGAAATGGTGTCGTTGTGCTTTGGTTTTCTTGCGGCG
1 AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
*
44218848 CTTTTTCAAAAACGCCACTAA
66 CTTTTTCAAAAACGCCGCTAA
44218869 TGACTCGAAA
Statistics
Matches: 159, Mismatches: 32, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
112 62 0.39
113 47 0.30
114 50 0.31
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (114 bp):
AAAACGCCGCTAAATCCCCGAAAAGCTCAGAAACGGTGTCGTTGGGCTTAGGTTTTCTTGCGGCG
CTTTTTCAAAAACGCCGCTAAAGCGCTGAGCATTAGCGGCGCTTTTAAA
Found at i:44218891 original size:186 final size:184
Alignment explanation
Indices: 44218689--44219054 Score: 449
Period size: 186 Copynumber: 2.0 Consensus size: 184
44218679 GTAAAATCCT
* * *
44218689 GAAAGCACAAAAAACGGTGCCGTTGGGCTTAGTTTTTTTTTGCGGCGCTATTC-CAAAAACGCCG
1 GAAAGCACAAAAAACGGCGCCGTTGGGATTAG--GTTTTTTGCGGCGCT-TTCTCAAAAACGCCG
* * *
44218753 CTAAA-TCCTTG-CATTAGCGGCGCTTCT-TTAGAAACGCCGCTAAATCCCCGAAAAGCTCTG-A
63 CTAAAGGCC-TGACATTAGCGGCGCTT-TATTAAAAACGCCGCTAAATCCCCG-AAAGCTCGGTA
* ** * *
44218814 AATGGTGTCGTT-GTGCTTTGGTTTTCTTGCGGCGCTTTTTCA-AAAACGCCACTAATGACTC
125 AACGACGTCGTTCG-GCTTAGGTTTT-TTGCGGCGCTTTCT-ATAAAACGCCACTAATGACTC
* * * *
44218875 GAAAGCTCAGAAAACGGCGTCGTTGGGATTAGGTTTTTTGCGGCGCTTTCTCAAAAACGTCGCTA
1 GAAAGCACAAAAAACGGCGCCGTTGGGATTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTA
44218940 AAGGCCTGAACATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCGGTAAACGA
66 AAGGCCTG-ACATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCGGTAAACGA
*
44219005 CGTCGTTCGGCTTAGGTTTTTTGCGGCGCTTTCTATAAAACGCCGCTAAT
130 CGTCGTTCGGCTTAGGTTTTTTGCGGCGCTTTCTATAAAACGCCACTAAT
44219055 TCTTATTTTC
Statistics
Matches: 156, Mismatches: 16, Indels: 17
0.83 0.08 0.09
Matches are distributed among these distances:
183 3 0.02
184 32 0.21
185 37 0.24
186 83 0.53
187 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (184 bp):
GAAAGCACAAAAAACGGCGCCGTTGGGATTAGGTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTA
AAGGCCTGACATTAGCGGCGCTTTATTAAAAACGCCGCTAAATCCCCGAAAGCTCGGTAAACGAC
GTCGTTCGGCTTAGGTTTTTTGCGGCGCTTTCTATAAAACGCCACTAATGACTC
Found at i:44219045 original size:113 final size:113
Alignment explanation
Indices: 44218842--44219053 Score: 295
Period size: 113 Copynumber: 1.9 Consensus size: 113
44218832 TGGTTTTCTT
* * *
44218842 GCGGCGCTTTTTCAAAAACGCCACTAATGACTCGAAAGCTCAGAAAACGGCGTCGTTGGGATTAG
1 GCGGCGCTTTTTCAAAAACGCCACTAATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATTAG
*
44218907 GTTTTTTGCGGCGCTTTCTCAAAAACGTCGCTAAAGGCCTGAACATTA
66 GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCTGAACATTA
* * * * *
44218955 GCGGCGCTTTATT-AAAAACGCCGCTAAAT-CCCCGAAAGCTCGGTAAACGACGTCGTTCGGCTT
1 GCGGCGCTTT-TTCAAAAACGCCACT-AATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATT
44219018 AGGTTTTTTGCGGCGCTTTCT-ATAAAACGCCGCTAA
64 AGGTTTTTTGCGGCGCTTTCTCA-AAAACGCCGCTAA
44219054 TTCTTATTTT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
112 1 0.01
113 81 0.93
114 5 0.06
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.26
Consensus pattern (113 bp):
GCGGCGCTTTTTCAAAAACGCCACTAATGACCCGAAAGCTCAGAAAACGACGTCGTTCGGATTAG
GTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCTGAACATTA
Found at i:44220208 original size:20 final size:21
Alignment explanation
Indices: 44220168--44220208 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
44220158 AAGTGTTGAA
*
44220168 TGGATTAAAAATTATTTTAAT
1 TGGATTAAAAATTAATTTAAT
*
44220189 TGGATT-AAAGTTAATTTAAT
1 TGGATTAAAAATTAATTTAAT
44220209 CATCTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (21 bp):
TGGATTAAAAATTAATTTAAT
Found at i:44232359 original size:18 final size:19
Alignment explanation
Indices: 44232331--44232375 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
44232321 CCCCCCCCCC
* *
44232331 AAAAAAAAAGGAA-AAATG
1 AAAAGAAAAGGAATAAAAG
*
44232349 AAATGAAAAGGAATAAAAG
1 AAAAGAAAAGGAATAAAAG
44232368 AAAAGAAA
1 AAAAGAAA
44232376 CTACAAATCC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.07
Consensus pattern (19 bp):
AAAAGAAAAGGAATAAAAG
Found at i:44232994 original size:25 final size:25
Alignment explanation
Indices: 44232960--44233012 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
44232950 TAGAGCACTT
*
44232960 AGTGCCTTTAGGTCAGTACATC-CA
1 AGTGCCTTTAAGTCAGTACATCTCA
44232984 AGTGCTCTTTAAGTCAGTACATCTCA
1 AGTGC-CTTTAAGTCAGTACATCTCA
44233010 AGT
1 AGT
44233013 TGCAAAGGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
AGTGCCTTTAAGTCAGTACATCTCA
Found at i:44240452 original size:199 final size:199
Alignment explanation
Indices: 44240110--44240472 Score: 521
Period size: 199 Copynumber: 1.8 Consensus size: 199
44240100 CCCTTGGCAC
*
44240110 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTATTGATCTAGTCAATG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
* * * * *
44240175 ATTAGTATAATGATGATGGGCCACTTCAAACTTTAGTAAGAGTTTGAAAGAATAACTCACCTACT
66 ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTGGAAAGAATAACTCACCTACT
* *
44240240 GATATACTTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
131 GACATAATTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
44240305 ACAT
196 ACAT
* * *
44240309 TGCTAAGTCTAAAGAAAAGTTAGAAGTAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAGTG
1 TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
* * * * * * *
44240374 ATCAGTCTAATAATGATGGACCACTTTAACCTTTAGCAAGAGTTAGGAAA-AATCACTTATCTAT
66 ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTT-GGAAAGAATAACTCACCTAC
** *
44240438 TGACATAATTGGTGATGTTCATGATGGGATCAAAA
130 TGACATAATTGGTGATAATCATGATAGGATCAAAA
44240473 TAAGGGGTAG
Statistics
Matches: 142, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
199 138 0.97
200 4 0.03
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (199 bp):
TGCTAAGTCTAAAGAAAAATTAGAAGCAGAAAGTCAAGATGTTCAAGTTACTGATCTAGTCAATG
ATCAGTATAATAATGATGGACCACTTCAAACTTTAGCAAGAGTTGGAAAGAATAACTCACCTACT
GACATAATTGGTGATAATCATGATAGGATCAAAACAAGAGGCAGAGGGAGTGCCCTCTCTCCTTA
ACAT
Found at i:44242792 original size:29 final size:31
Alignment explanation
Indices: 44242736--44242793 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
44242726 GGGTTGGGAG
*
44242736 GGGAGAGGAATAAAAGTTTTTGGGGGAAAGT
1 GGGAGAGGAATAAAAGTTTTTGAGGGAAAGT
*
44242767 GGGA-AGGAGTAAAAG-TTTTGAGGGAAA
1 GGGAGAGGAATAAAAGTTTTTGAGGGAAA
44242794 AGTAAAAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 11 0.44
30 10 0.40
31 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (31 bp):
GGGAGAGGAATAAAAGTTTTTGAGGGAAAGT
Found at i:44242796 original size:30 final size:31
Alignment explanation
Indices: 44242736--44242796 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
44242726 GGGTTGGGAG
*
44242736 GGGAGAGGAATAAAAGTTTTTGGGGGAAAGT
1 GGGAGAGGAATAAAAGTTTTTGGGGAAAAGT
*
44242767 GGGA-AGGAGTAAAAG-TTTTGAGGGAAAAGT
1 GGGAGAGGAATAAAAGTTTTTG-GGGAAAAGT
44242797 AAAAAGGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 5 0.19
30 18 0.67
31 4 0.15
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.21
Consensus pattern (31 bp):
GGGAGAGGAATAAAAGTTTTTGGGGAAAAGT
Found at i:44242862 original size:9 final size:9
Alignment explanation
Indices: 44242845--44242881 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
44242835 TATAGTTTGA
44242845 TATTCGAAT
1 TATTCGAAT
*
44242854 TATTTGAAT
1 TATTCGAAT
*
44242863 TATTCGAGT
1 TATTCGAAT
44242872 TATTCGAAT
1 TATTCGAAT
44242881 T
1 T
44242882 CGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:44242951 original size:9 final size:9
Alignment explanation
Indices: 44242934--44242964 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
44242924 TCGAATTGAT
44242934 TCGAATAAC
1 TCGAATAAC
*
44242943 TCGATTAAC
1 TCGAATAAC
44242952 TCGAATAAC
1 TCGAATAAC
44242961 TCGA
1 TCGA
44242965 TTCGTTTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:44247076 original size:16 final size:16
Alignment explanation
Indices: 44247042--44247094 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
44247032 ATAGCATTAG
44247042 TCATGCAATACTCAAT
1 TCATGCAATACTCAAT
*
44247058 TCATG-AATACATCATT
1 TCATGCAATAC-TCAAT
* *
44247074 TCATACCATACTCAAT
1 TCATGCAATACTCAAT
44247090 TCATG
1 TCATG
44247095 AGTATATAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 5 0.17
16 21 0.70
17 4 0.13
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
TCATGCAATACTCAAT
Found at i:44249862 original size:3 final size:3
Alignment explanation
Indices: 44249856--44249912 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
44249846 GACGACCACG
44249856 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
44249904 ATA ATA ATA
1 ATA ATA ATA
44249913 GAAACTATTA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44264101 original size:73 final size:73
Alignment explanation
Indices: 44264020--44264161 Score: 284
Period size: 73 Copynumber: 1.9 Consensus size: 73
44264010 TGACAAATAT
44264020 AATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTGTGTA
1 AATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTGTGTA
44264085 AAACATAG
66 AAACATAG
44264093 AATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTGTGTA
1 AATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTGTGTA
44264158 AAAC
66 AAAC
44264162 TTATTATCTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 69 1.00
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.37
Consensus pattern (73 bp):
AATTTATACTTAGAAATAAATTCTCACTATTTTTTAGTAGAATAACAATATCTCAAAGTTGTGTA
AAACATAG
Found at i:44275052 original size:7 final size:7
Alignment explanation
Indices: 44275037--44275070 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
44275027 ATGTATATAT
*
44275037 TGCACAC
1 TGCAAAC
44275044 TGCAAAC
1 TGCAAAC
44275051 TGCAAAC
1 TGCAAAC
44275058 TGCAAAC
1 TGCAAAC
44275065 TGCAAA
1 TGCAAA
44275071 GCATAATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.41, C:0.29, G:0.15, T:0.15
Consensus pattern (7 bp):
TGCAAAC
Found at i:44280286 original size:3 final size:3
Alignment explanation
Indices: 44280278--44280304 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44280268 TAGTAGATGA
44280278 AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG
44280305 GGCCTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:44285452 original size:37 final size:37
Alignment explanation
Indices: 44285404--44285506 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
44285394 TTAATGAATG
*
44285404 CATGATTAAGCATGCCATTGAGATTGTTAAACCAG-AAC
1 CATGA-TAAGCATGCCATTGAAATTGTTAAA-CAGAAAC
* * *
44285442 CATGATAAGCATGCCACTGAAATTGTTAAACTGAAAG
1 CATGATAAGCATGCCATTGAAATTGTTAAACAGAAAC
* *
44285479 CATGATAAACATGCCATTGATATTGTTA
1 CATGATAAGCATGCCATTGAAATTGTTA
44285507 CTATTACCGA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
36 2 0.04
37 50 0.88
38 5 0.09
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (37 bp):
CATGATAAGCATGCCATTGAAATTGTTAAACAGAAAC
Found at i:44286320 original size:72 final size:68
Alignment explanation
Indices: 44286244--44286381 Score: 188
Period size: 72 Copynumber: 2.0 Consensus size: 68
44286234 TGATTAAACT
* * *
44286244 TAATCACTTTAATATTAAATTAATAGAATATTTATCTACAAAATAATTATTAAAATT-AATTTAA
1 TAATCACTTTAATAGTAAATTAATAAAATA-TTAT-T--AAAATAAGTATT-AAATTAAATTTAA
44286308 TATTAAGC
61 TATTAAGC
*
44286316 TAATCACTTTAATAGTAAATTAATAAAATATTATTAAGATAAGTATTAAATTAAATTTAATATTA
1 TAATCACTTTAATAGTAAATTAATAAAATATTATTAAAATAAGTATTAAATTAAATTTAATATTA
44286381 A
66 A
44286382 ATCTATTAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
67 5 0.08
68 23 0.38
70 1 0.02
71 4 0.07
72 28 0.46
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.41
Consensus pattern (68 bp):
TAATCACTTTAATAGTAAATTAATAAAATATTATTAAAATAAGTATTAAATTAAATTTAATATTA
AGC
Found at i:44291122 original size:21 final size:21
Alignment explanation
Indices: 44291096--44291207 Score: 109
Period size: 21 Copynumber: 5.3 Consensus size: 21
44291086 GTGTTTTACT
*
44291096 TTCTGTTTAGCTCTTTCGAGC
1 TTCTGTTCAGCTCTTTCGAGC
44291117 TTCTGTTCAGCTCTTTCGAGC
1 TTCTGTTCAGCTCTTTCGAGC
* *
44291138 TTTTGTTCAGCTCTTACGAGC
1 TTCTGTTCAGCTCTTTCGAGC
* ** * *
44291159 TTCTATTCAATTCTAAT-GAGT
1 TTCTGTTCAGCTCT-TTCGAGC
* **
44291180 TTTTGTTCAGCTCTCACGAGC
1 TTCTGTTCAGCTCTTTCGAGC
44291201 TTCTGTT
1 TTCTGTT
44291208 GGCGTGTTCA
Statistics
Matches: 71, Mismatches: 18, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAGCTCTTTCGAGC
Found at i:44294173 original size:51 final size:52
Alignment explanation
Indices: 44294083--44294201 Score: 165
Period size: 52 Copynumber: 2.3 Consensus size: 52
44294073 GTAGAAATTG
* *
44294083 TGAAAATGGAGAAATGAGAAACATTTGGAAATGATTGTGG-TTTTCTCCAAAA
1 TGAAAATGGAGAAATGAG-AACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
*
44294135 TGAAAATGGAGAAATGTAG-TCATTTGGAAATGAATGTGGTTTTTCTCAAAAA
1 TGAAAATGGAGAAATG-AGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
44294187 TGAAAAT-GA-AAATGA
1 TGAAAATGGAGAAATGA
44294202 CTTGGAAATG
Statistics
Matches: 62, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
49 1 0.02
50 5 0.08
51 20 0.32
52 34 0.55
53 2 0.03
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.29
Consensus pattern (52 bp):
TGAAAATGGAGAAATGAGAACATTTGGAAATGAATGTGGTTTTTCTCAAAAA
Found at i:44295133 original size:22 final size:22
Alignment explanation
Indices: 44295108--44295154 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
44295098 ATGATTTTTT
*
44295108 AAAAAAAA-AAGTTACTCTCTTG
1 AAAAAAAATAAATTAC-CTCTTG
*
44295130 AAAAAAAATAAATTTCCTCTTG
1 AAAAAAAATAAATTACCTCTTG
44295152 AAA
1 AAA
44295155 GTTATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (22 bp):
AAAAAAAATAAATTACCTCTTG
Found at i:44297605 original size:18 final size:18
Alignment explanation
Indices: 44297559--44297607 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
44297549 TAGAGTTATG
44297559 GGCCCACATGCCCGTGTA
1 GGCCCACATGCCCGTGTA
* *
44297577 GGCCTATATGCCCGTGTA
1 GGCCCACATGCCCGTGTA
44297595 GGCCCACATGCCC
1 GGCCCACATGCCC
44297608 ATATTGGCCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.16, C:0.39, G:0.27, T:0.18
Consensus pattern (18 bp):
GGCCCACATGCCCGTGTA
Found at i:44297606 original size:36 final size:32
Alignment explanation
Indices: 44297559--44297643 Score: 98
Period size: 36 Copynumber: 2.5 Consensus size: 32
44297549 TAGAGTTATG
44297559 GGCCCACATGCCCGTGTAGGCCTATATGCCCGTGT
1 GGCCCACATGCCCGTGTAGGCC--T-TGCCCGTGT
* * * *
44297594 AGGCCCACATGCCCATATTGGCCTTGCTCGTGT
1 -GGCCCACATGCCCGTGTAGGCCTTGCCCGTGT
44297627 GGCCCACATGCCCGTGT
1 GGCCCACATGCCCGTGT
44297644 GGCATGCTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
32 15 0.35
33 8 0.19
34 1 0.02
36 19 0.44
ACGTcount: A:0.14, C:0.35, G:0.27, T:0.24
Consensus pattern (32 bp):
GGCCCACATGCCCGTGTAGGCCTTGCCCGTGT
Found at i:44301812 original size:20 final size:20
Alignment explanation
Indices: 44301787--44301825 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
44301777 TACTCGCTTC
44301787 TTTACTTACTCGCTTACTTG
1 TTTACTTACTCGCTTACTTG
*
44301807 TTTACTTACTTGCTTACTT
1 TTTACTTACTCGCTTACTT
44301826 AAATAACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.23, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTACTTACTCGCTTACTTG
Found at i:44304276 original size:22 final size:22
Alignment explanation
Indices: 44304246--44304288 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
44304236 ACACCGAAAC
*
44304246 AGGCTTTTAGCGGCGTTTTTTT
1 AGGCCTTTAGCGGCGTTTTTTT
44304268 AGGCCTTTAGCGGCGTTTTTT
1 AGGCCTTTAGCGGCGTTTTTT
44304289 AGCGCCGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.16, G:0.28, T:0.47
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGTTTTTTT
Found at i:44304512 original size:42 final size:43
Alignment explanation
Indices: 44304447--44304627 Score: 165
Period size: 44 Copynumber: 4.2 Consensus size: 43
44304437 AGATGGAAAG
* *
44304447 CGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTACAAAAA
1 CGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTACAAAAA
* *
44304489 CGCCGCTAAAGATCACAAGCTTTAGCGGCACTTTTTATCACAAA
1 CGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTA-CAAAAA
* * * * * *
44304533 CGCCGCTAAAGGTCATAATCTTTAGCGACGCTTTTTGCCACAAA
1 CGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTT-ACAAAAA
* * **
44304577 CGCCGCTATAA-A--ACAAGCCTTTAGC-TCGCTTCTCGCAAAAA
1 CGCCGCTA-AAGATCACAAG-CTTTAGCGGCGCTTTTTACAAAAA
44304618 CGCCGCTAAA
1 CGCCGCTAAA
44304628 AACATAACAT
Statistics
Matches: 116, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
40 2 0.02
41 13 0.11
42 37 0.32
43 12 0.10
44 50 0.43
45 2 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.23
Consensus pattern (43 bp):
CGCCGCTAAAGATCACAAGCTTTAGCGGCGCTTTTTACAAAAA
Found at i:44304556 original size:44 final size:43
Alignment explanation
Indices: 44304447--44304584 Score: 170
Period size: 44 Copynumber: 3.2 Consensus size: 43
44304437 AGATGGAAAG
* *
44304447 CGCCGCTAAAGATCACGACCTTTAGCGGCGC-TTTTACAAAAA
1 CGCCGCTAAAGATCACAACCTTTAGCGGCGCTTTTTACACAAA
* *
44304489 CGCCGCTAAAGATCACAAGCTTTAGCGGCACTTTTTATCACAAA
1 CGCCGCTAAAGATCACAACCTTTAGCGGCGCTTTTTA-CACAAA
* * * * *
44304533 CGCCGCTAAAGGTCATAATCTTTAGCGACGCTTTTTGCCACAAA
1 CGCCGCTAAAGATCACAACCTTTAGCGGCGCTTTTT-ACACAAA
44304577 CGCCGCTA
1 CGCCGCTA
44304585 TAAAACAAGC
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
42 28 0.34
43 5 0.06
44 50 0.60
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (43 bp):
CGCCGCTAAAGATCACAACCTTTAGCGGCGCTTTTTACACAAA
Found at i:44304674 original size:18 final size:19
Alignment explanation
Indices: 44304648--44304683 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44304638 TTAAAAAAAA
*
44304648 TTATTTAAATATT-TATTT
1 TTATATAAATATTATATTT
44304666 TTATATAAATATTATATT
1 TTATATAAATATTATATT
44304684 ATGTTTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATATAAATATTATATTT
Found at i:44305680 original size:16 final size:16
Alignment explanation
Indices: 44305659--44305689 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
44305649 AGTCCCAAAC
44305659 TATTGTAAACATCAGT
1 TATTGTAAACATCAGT
44305675 TATTGTAAACATCAG
1 TATTGTAAACATCAG
44305690 ATAGGTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (16 bp):
TATTGTAAACATCAGT
Found at i:44308861 original size:41 final size:41
Alignment explanation
Indices: 44308812--44309088 Score: 337
Period size: 41 Copynumber: 6.8 Consensus size: 41
44308802 TTGTGGCCTT
*
44308812 TGAGCATTAGCGGCG-TTTTTGAAAAAGCGCCGCTAAAGACCC
1 TGAGCATTAGCGGCGCTTTTT-AAAAAACGCCGCTAAA-ACCC
* * * * *
44308854 -GATCATTAGTGGCGCTTTCTAAAAAATGCCGCTAATACCC
1 TGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCC
*
44308894 TGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGA-CC
1 TGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAA-ACCC
* *
44308935 TGATCATTAGTGGCGCTTTTTAAAAAACGCCGCTAAAACCC
1 TGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCC
* * * *
44308976 TGAGCACTAGCTGCGCATTTTAAAAAACGCCGATAAATA-CC
1 TGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAA-ACCC
**
44309017 TGAGCATTAGCGGCGCTTTACAAAAAACGCCGCTAAAACCC
1 TGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCC
* *
44309058 TGAGCATTAGCGACGCATTTTAAAAAACGCC
1 TGAGCATTAGCGGCGCTTTTTAAAAAACGCC
44309089 ACAAAATCCC
Statistics
Matches: 198, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
40 6 0.03
41 186 0.94
42 6 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (41 bp):
TGAGCATTAGCGGCGCTTTTTAAAAAACGCCGCTAAAACCC
Found at i:44308949 original size:82 final size:82
Alignment explanation
Indices: 44308812--44309088 Score: 387
Period size: 82 Copynumber: 3.4 Consensus size: 82
44308802 TTGTGGCCTT
* * *
44308812 TGAGCATTAGCGGCG-TTTTTGAAAAAGCGCCGCTAAAGACCCGATCATTAGTGGCGCTTTCTAA
1 TGAGCATTAGCGGCGCATTTT-AAAAAACGCCGCTAAAGACCTGATCATTAGTGGCGCTTTCTAA
* *
44308876 AAAATGCCGCTAATACCC
65 AAAACGCCGCTAAAACCC
* * *
44308894 TGAGCATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGACCTGATCATTAGTGGCGCTTTTTAAA
1 TGAGCATTAGCGGCGCATTTTAAAAAACGCCGCTAAAGACCTGATCATTAGTGGCGCTTTCTAAA
44308959 AAACGCCGCTAAAACCC
66 AAACGCCGCTAAAACCC
* * * * * *
44308976 TGAGCACTAGCTGCGCATTTTAAAAAACGCCGATAAATACCTGAGCATTAGCGGCGCTTTAC-AA
1 TGAGCATTAGCGGCGCATTTTAAAAAACGCCGCTAAAGACCTGATCATTAGTGGCGCTTT-CTAA
44309040 AAAACGCCGCTAAAACCC
65 AAAACGCCGCTAAAACCC
*
44309058 TGAGCATTAGCGACGCATTTTAAAAAACGCC
1 TGAGCATTAGCGGCGCATTTTAAAAAACGCC
44309089 ACAAAATCCC
Statistics
Matches: 175, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
82 170 0.97
83 5 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (82 bp):
TGAGCATTAGCGGCGCATTTTAAAAAACGCCGCTAAAGACCTGATCATTAGTGGCGCTTTCTAAA
AAACGCCGCTAAAACCC
Found at i:44309181 original size:39 final size:38
Alignment explanation
Indices: 44309132--44309266 Score: 135
Period size: 39 Copynumber: 3.4 Consensus size: 38
44309122 AAGGCTTAGG
* * *
44309132 TTTTTTGCGGCGCTTTTTGAAAAACGCCGCTAGTGCTCA
1 TTTTTAGCGGCG-TTTTTCAAAAACGCCGCTAATGCTCA
* *
44309171 TTTTTAGCGGCGTTTTCCAAAAAGCGCCGCTAATACTCAA
1 TTTTTAGCGGCGTTTTTCAAAAA-CGCCGCTAATGCTC-A
* ** * *
44309211 TCTTTAGCGGCGTTTTTTTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGTTTTTCAAAAACGCCGCTAATGC-TCA
*
44309250 TTTTTAGCGGTGTTTTT
1 TTTTTAGCGGCGTTTTT
44309267 TATCCAAACG
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 9 0.11
39 50 0.63
40 20 0.25
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (38 bp):
TTTTTAGCGGCGTTTTTCAAAAACGCCGCTAATGCTCA
Found at i:44315765 original size:22 final size:21
Alignment explanation
Indices: 44315740--44315783 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
44315730 TGATAAACTT
44315740 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
44315762 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
44315783 T
1 T
44315784 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:44320530 original size:33 final size:33
Alignment explanation
Indices: 44320493--44320561 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
44320483 TAAATAAAAT
44320493 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
1 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
44320526 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
1 AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
44320559 AGT
1 AGT
44320562 CAAATTCTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.42, C:0.06, G:0.16, T:0.36
Consensus pattern (33 bp):
AGTTTAAATTTTTGTAGAACAATTAAATGAAGC
Found at i:44321153 original size:23 final size:23
Alignment explanation
Indices: 44321127--44321180 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
44321117 GTTACTAAGC
* * *
44321127 ATATATTAATAATTAATATAATA
1 ATATAATAATAATTAAAATAAAA
*
44321150 ATATAATAATATTTAAAATAAAA
1 ATATAATAATAATTAAAATAAAA
*
44321173 ATAAAATA
1 ATATAATA
44321181 TAAATAATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (23 bp):
ATATAATAATAATTAAAATAAAA
Found at i:44321439 original size:15 final size:16
Alignment explanation
Indices: 44321416--44321462 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 16
44321406 TTAATGATTA
44321416 TATAAAATATAA-AAT
1 TATAAAATATAATAAT
*
44321431 TATATAATATAATAAT
1 TATAAAATATAATAAT
*
44321447 T-TAATATATAATAAT
1 TATAAAATATAATAAT
44321462 T
1 T
44321463 GAAGAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 24 0.86
16 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATAAAATATAATAAT
Found at i:44334181 original size:14 final size:15
Alignment explanation
Indices: 44334162--44334194 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44334152 GGTATAAAAT
*
44334162 AAAT-AAAGTAATAA
1 AAATAAAAGAAATAA
44334176 AAATAAAAGAAATAA
1 AAATAAAAGAAATAA
44334191 AAAT
1 AAAT
44334195 GCTAGATGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAATAAAAGAAATAA
Found at i:44336548 original size:33 final size:33
Alignment explanation
Indices: 44336488--44336557 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
44336478 CACAAAGATC
* *
44336488 CAAATGTTTATATGCTCATCAAATACATATAAA
1 CAAATGTTCATATACTCATCAAATACATATAAA
* * * *
44336521 CAAATGTTCATATACTTATCCATTACATATAAC
1 CAAATGTTCATATACTCATCAAATACATATAAA
44336554 CAAA
1 CAAA
44336558 ATCATATATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (33 bp):
CAAATGTTCATATACTCATCAAATACATATAAA
Found at i:44336674 original size:41 final size:42
Alignment explanation
Indices: 44336599--44336679 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 42
44336589 CTTAATTTAA
* * * *
44336599 CAGATTCACCGGCACTTAGCTTGTTAGGCTTATAGCCTGATT
1 CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATT
*
44336641 CAGA-TCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
1 CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGA
44336680 ATAATTTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
41 30 0.88
42 4 0.12
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (42 bp):
CAGATTCACCGGCACTTAGCCTGCTAGACGTATAGCCTGATT
Found at i:44338443 original size:51 final size:49
Alignment explanation
Indices: 44338388--44338845 Score: 294
Period size: 51 Copynumber: 9.8 Consensus size: 49
44338378 GAATTGTAAT
*
44338388 TTTAATCTACTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
** * * * *
44338439 TTTAATCTATTCCACTGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
* * * * *
44338490 TTTAATCTGTTCCACTGCAAATT-TAGAGAAATAAGA-TT-T-GCG-ATC
1 TTTAATCTGCTCCACTGCAACTTCAAG-GAGATAAGATTTGTAGCGTAGC
* * * * *
44338535 TTCAATCTGCTCCACTGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGC--GTAGC
* * * *
44338586 TTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TT-T-GC-TATC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* * * **
44338631 TTCAATCTACTTCGTTGCAACTTC-AGGTAGATAAGATTTGTA---T--C
1 TTTAATCTGCTCCACTGCAACTTCAAGG-AGATAAGATTTGTAGCGTAGC
*
44338675 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-TT-TA-C-TATC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
* * *
44338720 TTCAATCTGCTCCACTTCAACCTT-AGGGAGA-AGAGATTTGTA--GT---
1 TTTAATCTGCTCCACTGCAA-CTTCAAGGAGATA-AGATTTGTAGCGTAGC
* * * *
44338764 TTTAATCTGCTCTATTGCAACTTCAGGGGGATAAGATTTGT---G--GC
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
*
44338808 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATT
44338846 CTCCACGATG
Statistics
Matches: 328, Mismatches: 54, Indels: 57
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.01
43 7 0.02
44 96 0.29
45 89 0.27
46 11 0.03
47 5 0.02
48 3 0.01
49 2 0.01
50 5 0.02
51 108 0.33
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (49 bp):
TTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTGTAGCGTAGC
Found at i:44338569 original size:45 final size:45
Alignment explanation
Indices: 44338359--44338845 Score: 371
Period size: 44 Copynumber: 10.5 Consensus size: 45
44338349 TGCAACCCAT
* * *
44338359 TGCAACTTCAGGG-GTATAGGAATTG-TAAT-TTTAATCTACTCCAC
1 TGCAACTTCAGGGAG-ATAAGATTTGCT-ATCTTTAATCTGCTCCAC
* * **
44338403 TGCAACTTCAAGGAGATAAGATTTGTAGCTTGTAGCTTTAATCTATTCCAC
1 TGCAACTTCAGGGAGATAAGA-TT-T-GC---TATCTTTAATCTGCTCCAC
* * * *
44338454 TGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGATTTG---C---TATCTTTAATCTGCTCCAC
* * * * * *
44338505 TGCAAATTTAGAGAAATAAGATTTGCGATCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * * *
44338550 TGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGCTTTAATCTGTTCCAC
1 TGCAACTTCAGGGAGATAAGATT--T-GC---TATCTTTAATCTGCTCCAC
* * * * **
44338601 TGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTACTTCGT
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
*
44338646 TGCAACTTCAGGTAGATAAGATTTG-TATCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * *
44338690 TGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
* * *
44338735 TTCAACCTT-AGGGAGA-AGAGATTTG-TAGT-TTTAATCTGCTCTAT
1 TGCAA-CTTCAGGGAGATA-AGATTTGCTA-TCTTTAATCTGCTCCAC
* **
44338779 TGCAACTTCAGGGGGATAAGATTTG-TGGCTTTAATCTGCTCCAC
1 TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
44338823 TGCAACTTCAGGGAGATAAGATT
1 TGCAACTTCAGGGAGATAAGATT
44338846 CTCCACGATG
Statistics
Matches: 357, Mismatches: 61, Indels: 50
0.76 0.13 0.11
Matches are distributed among these distances:
43 3 0.01
44 121 0.34
45 106 0.30
46 4 0.01
47 2 0.01
48 4 0.01
49 2 0.01
50 3 0.01
51 112 0.31
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
TGCAACTTCAGGGAGATAAGATTTGCTATCTTTAATCTGCTCCAC
Found at i:44338579 original size:96 final size:94
Alignment explanation
Indices: 44338449--44338845 Score: 388
Period size: 96 Copynumber: 4.3 Consensus size: 94
44338439 TTTAATCTAT
* * * * *
44338449 TCCACTGCAACTTTAGGGAGATAAAATTTGTAACTTGTAGCTTTAATCTGTTCCACTGCAAATTT
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGT-ACTTGTAGCTTTAATCTGCTCCACTGCAACTTC
44338514 AGAGAAATAAGATTTGCGATCTTCAATCTGC
64 AGAGAAATAAGATTTGCGATCTTCAATCTGC
* *
44338545 TCCACTGTAACTTCAGGGAGATAAGATTCGTAACTTGTAGCTTTAATCTGTTCCACTGCAACTTC
1 TCCACTGCAACTTCAGGGAGATAAGATT-GT-ACTTGTAGCTTTAATCTGCTCCACTGCAACTTC
* * *
44338610 AGGGAAATAAGATTTGCTATCTTCAATCTAC
64 AGAGAAATAAGATTTGCGATCTTCAATCTGC
* ** * *
44338641 TTCGTTGCAACTTCAGGTAGATAAGA---T--TTGTATCTTTAATCTGCTCCACTGCAACTTCA-
1 TCCACTGCAACTTCAGGGAGATAAGATTGTACTTGTAGCTTTAATCTGCTCCACTGCAACTTCAG
* * *
44338700 AGGAGATAAGATTTACTATCTTCAATCTGC
66 A-GAAATAAGATTTGCGATCTTCAATCTGC
* * * * *
44338730 TCCACTTCAACCTT-AGGGAG--AAGA--G-ATTTGTAGTTTTAATCTGCTCTATTGCAACTTCA
1 TCCACTGCAA-CTTCAGGGAGATAAGATTGTACTTGTAGCTTTAATCTGCTCCACTGCAACTTCA
* ** * * *
44338789 GGGGGATAAGATTTGTG-GCTTTAATCTGC
65 GAGAAATAAGATTTGCGATCTTCAATCTGC
44338818 TCCACTGCAACTTCAGGGAGATAAGATT
1 TCCACTGCAACTTCAGGGAGATAAGATT
44338846 CTCCACGATG
Statistics
Matches: 253, Mismatches: 36, Indels: 28
0.80 0.11 0.09
Matches are distributed among these distances:
87 7 0.03
88 25 0.10
89 105 0.42
90 7 0.03
92 1 0.00
95 2 0.01
96 106 0.42
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (94 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGTACTTGTAGCTTTAATCTGCTCCACTGCAACTTCAG
AGAAATAAGATTTGCGATCTTCAATCTGC
Found at i:44338757 original size:89 final size:88
Alignment explanation
Indices: 44338483--44338845 Score: 349
Period size: 89 Copynumber: 4.0 Consensus size: 88
44338473 AATTTGTAAC
* * * * * * *
44338483 TTGTAGCTTTAATCTGTTCCACTGCAAATTTAGAGAAATAAGATTTGCGATCTTCAATCTGCTCC
1 TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGCTCC
44338548 ACTGT-AACTTCAGGGAGATAAGATTCGT
65 ACT-TCAACTTCAGGGAGATAAGA----T
* * * *
44338576 AACTTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCTTCAATCTAC
1 ---TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGC
* * *
44338641 TTC-GTTGCAACTTCAGGTAGATAAGAT
62 TCCACTT-CAACTTCAGGGAGATAAGAT
*
44338668 TTGTATCTTTAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTTACTATCTTCAATCTGCTCC
1 TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-CTATCTTCAATCTGCTCC
44338733 ACTTCAACCTT-AGGGAGA-AGAGAT
65 ACTTCAA-CTTCAGGGAGATA-AGAT
* * * * ** *
44338757 TTGTAGT-TTTAATCTGCTCTATTGCAACTTCAGGGGGATAAGATTTGTGGCTTTAATCTGCTCC
1 TTGTA-TCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAATCTGCTCC
*
44338821 ACTGCAACTTCAGGGAGATAAGAT
65 ACTTCAACTTCAGGGAGATAAGAT
44338845 T
1 T
44338846 CTCCACGATG
Statistics
Matches: 233, Mismatches: 26, Indels: 24
0.82 0.09 0.08
Matches are distributed among these distances:
87 3 0.01
88 33 0.14
89 112 0.48
90 6 0.03
92 1 0.00
94 1 0.00
95 1 0.00
96 76 0.33
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (88 bp):
TTGTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTCTATCTTCAATCTGCTCCA
CTTCAACTTCAGGGAGATAAGAT
Found at i:44339433 original size:11 final size:11
Alignment explanation
Indices: 44339403--44339463 Score: 56
Period size: 11 Copynumber: 5.7 Consensus size: 11
44339393 CCGGCCCATT
44339403 TTTTAATAAATA
1 TTTTAA-AAATA
**
44339415 TTAAAAAAATA
1 TTTTAAAAATA
44339426 TTTTAAAAATA
1 TTTTAAAAATA
*
44339437 ---AAAAAATA
1 TTTTAAAAATA
*
44339445 TTTTAAAAGTA
1 TTTTAAAAATA
44339456 TTTTAAAA
1 TTTTAAAA
44339464 TTAAAAAATA
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.18
11 28 0.72
12 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TTTTAAAAATA
Found at i:44339446 original size:30 final size:30
Alignment explanation
Indices: 44339410--44339488 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
44339400 ATTTTTTAAT
44339410 AAATATTAAAAAAATATTTTAAAAATAAAA
1 AAATATTAAAAAAATATTTTAAAAATAAAA
** * *
44339440 AAATATTTTAAAAGTATTTT-AAAATTAAA
1 AAATATTAAAAAAATATTTTAAAAATAAAA
44339469 AAATA--AAAAAAATATATTTA
1 AAATATTAAAAAAATAT-TTTA
44339489 TTATATTCGA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
27 7 0.17
28 3 0.08
29 13 0.32
30 17 0.43
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (30 bp):
AAATATTAAAAAAATATTTTAAAAATAAAA
Found at i:44339471 original size:19 final size:19
Alignment explanation
Indices: 44339416--44339452 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
44339406 TAATAAATAT
44339416 TAAAAAAATATTTTAAAAA
1 TAAAAAAATATTTTAAAAA
44339435 TAAAAAAATATTTTAAAA
1 TAAAAAAATATTTTAAAA
44339453 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAAAATATTTTAAAAA
Found at i:44343669 original size:25 final size:23
Alignment explanation
Indices: 44343596--44343673 Score: 72
Period size: 25 Copynumber: 3.3 Consensus size: 23
44343586 AGCCCGGGCC
44343596 CCCAAATTAAACCTAACCCATCAGA
1 CCCAAA-TAAACCTAA-CCATCAGA
* * *
44343621 CCCAAATAAATCAAACC--CA-C
1 CCCAAATAAACCTAACCATCAGA
44343641 CCCAAACTAAACCTAACCTATCAGA
1 CCCAAA-TAAACCTAACC-ATCAGA
44343666 CCCAAATA
1 CCCAAATA
44343674 CAACTAGGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
20 6 0.14
21 11 0.26
23 2 0.05
24 11 0.26
25 12 0.29
ACGTcount: A:0.46, C:0.37, G:0.03, T:0.14
Consensus pattern (23 bp):
CCCAAATAAACCTAACCATCAGA
Found at i:44343789 original size:85 final size:85
Alignment explanation
Indices: 44343644--44343815 Score: 299
Period size: 85 Copynumber: 2.0 Consensus size: 85
44343634 AACCCACCCC
* * * *
44343644 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTGTGCATAATTCGGGTAAAATCGAA
1 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGGGGAAAATCAAA
44343709 AAAATTTGGTTAACAGACCG
66 AAAATTTGGTTAACAGACCG
44343729 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGGGGAAAATCAAA
1 AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGGGGAAAATCAAA
*
44343794 AAAATTTGGTTAACCGACCG
66 AAAATTTGGTTAACAGACCG
44343814 AA
1 AA
44343816 TTCGGTTAAT
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 82 1.00
ACGTcount: A:0.42, C:0.21, G:0.17, T:0.20
Consensus pattern (85 bp):
AAACTAAACCTAACCTATCAGACCCAAATACAACTAGGGGTATGCACAATTCGGGGAAAATCAAA
AAAATTTGGTTAACAGACCG
Found at i:44343997 original size:13 final size:13
Alignment explanation
Indices: 44343979--44344008 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
44343969 AGCCCAAACT
44343979 CAATTACCCAACC
1 CAATTACCCAACC
44343992 CAATTACCCAACC
1 CAATTACCCAACC
44344005 CAAT
1 CAAT
44344009 AAAACTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.43, G:0.00, T:0.17
Consensus pattern (13 bp):
CAATTACCCAACC
Found at i:44344191 original size:9 final size:9
Alignment explanation
Indices: 44344156--44344217 Score: 81
Period size: 9 Copynumber: 6.8 Consensus size: 9
44344146 AAAAAGTTCA
44344156 GGTAATTCG
1 GGTAATTCG
*
44344165 GGTATTTTTC-
1 GGTA--ATTCG
44344175 GGTAATTCG
1 GGTAATTCG
*
44344184 GTTAATTCG
1 GGTAATTCG
44344193 GGTAATTCG
1 GGTAATTCG
44344202 GGTAATTCG
1 GGTAATTCG
44344211 GGTAATT
1 GGTAATT
44344218 TTTAACCAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
8 3 0.07
9 36 0.78
10 4 0.09
11 3 0.07
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (9 bp):
GGTAATTCG
Found at i:44344394 original size:12 final size:12
Alignment explanation
Indices: 44344377--44344401 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44344367 AGTAATTTCG
44344377 GGTCGGTTAACC
1 GGTCGGTTAACC
44344389 GGTCGGTTAACC
1 GGTCGGTTAACC
44344401 G
1 G
44344402 AATGAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:44353384 original size:17 final size:19
Alignment explanation
Indices: 44353364--44353404 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
44353354 ATACTTCTTA
*
44353364 AAAAATAAAA-A-ATGTAT
1 AAAAATAAAATATATATAT
*
44353381 AAAAGTAAAATATATATAT
1 AAAAATAAAATATATATAT
44353400 AAAAA
1 AAAAA
44353405 ATTGATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (19 bp):
AAAAATAAAATATATATAT
Found at i:44358053 original size:20 final size:20
Alignment explanation
Indices: 44358027--44358078 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
44358017 ATTATATTCT
44358027 CAATATATTATAGATAAATC
1 CAATATATTATAGATAAATC
* * *
44358047 GAATATATTAGAGATAAGTC
1 CAATATATTATAGATAAATC
*
44358067 CAATACATTATA
1 CAATATATTATA
44358079 TAAGCCCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (20 bp):
CAATATATTATAGATAAATC
Found at i:44358165 original size:18 final size:18
Alignment explanation
Indices: 44358131--44358164 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
44358121 AGAATGGGCT
44358131 TAAAAATATTATGAAAAC
1 TAAAAATATTATGAAAAC
44358149 TAAAAATATT-TGAAAA
1 TAAAAATATTATGAAAA
44358165 AAACTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (18 bp):
TAAAAATATTATGAAAAC
Found at i:44359172 original size:27 final size:27
Alignment explanation
Indices: 44359131--44359189 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
44359121 TGTTCAATAT
*
44359131 TATTAAATATATTAATTGAATTATTT-A
1 TATTAAATATATTAA-TAAATTATTTAA
* *
44359158 TATTTAATATTTTAATAAATTATTTAA
1 TATTAAATATATTAATAAATTATTTAA
44359185 TATTA
1 TATTA
44359190 CAATTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 9 0.33
27 18 0.67
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (27 bp):
TATTAAATATATTAATAAATTATTTAA
Found at i:44359521 original size:17 final size:18
Alignment explanation
Indices: 44359501--44359538 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
44359491 TTTATATATT
*
44359501 ATATTAT-TTATTATAAA
1 ATATTATCTTACTATAAA
*
44359518 ATATTTTCTTACTATAAA
1 ATATTATCTTACTATAAA
44359536 ATA
1 ATA
44359539 AATTTTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
ATATTATCTTACTATAAA
Found at i:44360665 original size:12 final size:12
Alignment explanation
Indices: 44360645--44360675 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
44360635 AAAGGAAGAA
44360645 AGAAAAAAAAAG
1 AGAAAAAAAAAG
*
44360657 AGAAGAAAAAAG
1 AGAAAAAAAAAG
44360669 AGAAAAA
1 AGAAAAA
44360676 TAATGTAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAAAG
Found at i:44364304 original size:21 final size:21
Alignment explanation
Indices: 44364278--44364317 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
44364268 TAATGTCATA
44364278 TCAGTATTTTCATCTTGAATT
1 TCAGTATTTTCATCTTGAATT
*
44364299 TCAGTATTTTCATTTTGAA
1 TCAGTATTTTCATCTTGAA
44364318 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (21 bp):
TCAGTATTTTCATCTTGAATT
Found at i:44368172 original size:24 final size:24
Alignment explanation
Indices: 44368145--44368196 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
44368135 AATCAAAGTC
* *
44368145 AAATATATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
* *
44368169 AAATATGTTATACTCATAAATACT
1 AAATATATTATACTAATAAATACT
44368193 AAAT
1 AAAT
44368197 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:44372554 original size:24 final size:24
Alignment explanation
Indices: 44372527--44372573 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44372517 AAACCTAATT
44372527 CTAATCAAA-GTAAAATATATTATG
1 CTAAT-AAATGTAAAATATATTATG
*
44372551 CTAATAAATGTTAAATATATTAT
1 CTAATAAATGTAAAATATATTAT
44372574 ATTCATAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAATAAATGTAAAATATATTATG
Found at i:44372589 original size:24 final size:24
Alignment explanation
Indices: 44372539--44372590 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
44372529 AATCAAAGTA
* **
44372539 AAATATATTATGCTAATAAATGTT
1 AAATATATTATACTAATAAATACT
* *
44372563 AAATATATTATATTCATAAATACT
1 AAATATATTATACTAATAAATACT
44372587 AAAT
1 AAAT
44372591 CTTCTAGAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:44374732 original size:22 final size:24
Alignment explanation
Indices: 44374707--44374772 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
44374697 TTGACATCCT
44374707 TTCTTGTTCTG-GTT-GAAATAGA
1 TTCTTGTTCTGTGTTAGAAATAGA
* *
44374729 TTCTTTTTGTGTGTTAGAAATAGA
1 TTCTTGTTCTGTGTTAGAAATAGA
* * *
44374753 TTCTTTTTGTGGGTTAGAAA
1 TTCTTGTTCTGTGTTAGAAA
44374773 AGTATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
22 9 0.23
23 3 0.08
24 27 0.69
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (24 bp):
TTCTTGTTCTGTGTTAGAAATAGA
Found at i:44374749 original size:24 final size:24
Alignment explanation
Indices: 44374717--44374772 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
44374707 TTCTTGTTCT
44374717 GGTT-GAAATAGATTCTTTTTGTG
1 GGTTAGAAATAGATTCTTTTTGTG
*
44374740 TGTTAGAAATAGATTCTTTTTGTG
1 GGTTAGAAATAGATTCTTTTTGTG
44374764 GGTTAGAAA
1 GGTTAGAAA
44374773 AGTATTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 3 0.10
24 27 0.90
ACGTcount: A:0.27, C:0.04, G:0.25, T:0.45
Consensus pattern (24 bp):
GGTTAGAAATAGATTCTTTTTGTG
Found at i:44385037 original size:25 final size:25
Alignment explanation
Indices: 44385003--44385052 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
44384993 AAATGAACTG
*
44385003 TTGAACAATTTGTTCGATCTTTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
44385028 TTGAACAATTTGTTCGATCTCTGCA
1 TTGAACAATTTGTTCGATCTCTGCA
44385053 CAAACTCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
TTGAACAATTTGTTCGATCTCTGCA
Found at i:44390391 original size:19 final size:19
Alignment explanation
Indices: 44390367--44390404 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
44390357 TCTAGTTTCA
*
44390367 GATAAAATTTATGGATCTT
1 GATAAAATTTACGGATCTT
44390386 GATAAAATTTACGGATCTT
1 GATAAAATTTACGGATCTT
44390405 AATTTGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (19 bp):
GATAAAATTTACGGATCTT
Found at i:44403474 original size:15 final size:15
Alignment explanation
Indices: 44403454--44403485 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
44403444 CTATGAACCT
44403454 TAGTAAAATTCGGCC
1 TAGTAAAATTCGGCC
44403469 TAGTAAAATTCGGCC
1 TAGTAAAATTCGGCC
44403484 TA
1 TA
44403486 ACTATAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (15 bp):
TAGTAAAATTCGGCC
Found at i:44417548 original size:20 final size:20
Alignment explanation
Indices: 44417525--44417564 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
44417515 TAACGGGACC
44417525 GCTGATGTGG-CAAGTTAACT
1 GCTGATGTGGCCAA-TTAACT
44417545 GCTGATGTGGCCAATTAACT
1 GCTGATGTGGCCAATTAACT
44417565 TGCCACGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
GCTGATGTGGCCAATTAACT
Done.