Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
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: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 128 of 221
Found at i:39445206 original size:12 final size:12
Alignment explanation
Indices: 39445191--39445217 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39445181 ATAATAATAA
39445191 TAATAATTTAAT
1 TAATAATTTAAT
39445203 TAATAATTTAAT
1 TAATAATTTAAT
39445215 TAA
1 TAA
39445218 AAAAACAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
TAATAATTTAAT
Found at i:39450495 original size:21 final size:22
Alignment explanation
Indices: 39450452--39450498 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
39450442 AAATTTAGTA
*
39450452 TATTTTAAATTTATTACCATAT
1 TATTTTAAATTTATTAACATAT
39450474 TATTTT-AATATTA-TAACATAT
1 TATTTTAAAT-TTATTAACATAT
39450495 TATT
1 TATT
39450499 GTTCTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTTAAATTTATTAACATAT
Found at i:39452274 original size:52 final size:52
Alignment explanation
Indices: 39452202--39452306 Score: 120
Period size: 52 Copynumber: 2.0 Consensus size: 52
39452192 AAATATTTAG
* * * * **
39452202 AATTAGAACTAAATTGACAAAATTTGTAAATGTTGAGGGCTAAATTTATTAA
1 AATTAGAACTAAAATAACAAAATTTATAAATATTGAAAGCTAAATTTATTAA
* * * *
39452254 AATTTGAACTAAAATAACAAATTTTATCAATATTGAAAGCTAAATTTGTTAA
1 AATTAGAACTAAAATAACAAAATTTATAAATATTGAAAGCTAAATTTATTAA
39452306 A
1 A
39452307 TTTTTATATT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.47, C:0.07, G:0.11, T:0.35
Consensus pattern (52 bp):
AATTAGAACTAAAATAACAAAATTTATAAATATTGAAAGCTAAATTTATTAA
Found at i:39452766 original size:15 final size:15
Alignment explanation
Indices: 39452746--39452801 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
39452736 TAAAATATAA
39452746 AATATTATAATTTTT
1 AATATTATAATTTTT
* **
39452761 AATATTATTAAACTATAA
1 AATATTA-T-AA-TTTTT
39452779 AATATTATAATTTTT
1 AATATTATAATTTTT
39452794 AATATTAT
1 AATATTAT
39452802 TAAACATACA
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
15 17 0.53
16 3 0.09
17 3 0.09
18 9 0.28
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATTATAATTTTT
Found at i:39452822 original size:36 final size:33
Alignment explanation
Indices: 39452727--39452806 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
39452717 ATTTTTTAAA
* *
39452727 TTAATAATA-TAAAATATAAAATATTATAATTT
1 TTAATATTATTAAACTATAAAATATTATAATTT
39452759 TTAATATTATTAAACTATAAAATATTATAATTT
1 TTAATATTATTAAACTATAAAATATTATAATTT
39452792 TTAATATTATTAAAC
1 TTAATATTATTAAAC
39452807 ATACATATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 8 0.18
33 37 0.82
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (33 bp):
TTAATATTATTAAACTATAAAATATTATAATTT
Found at i:39452926 original size:15 final size:16
Alignment explanation
Indices: 39452899--39452929 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
39452889 ACTTTATTCT
39452899 AATAATAAATTTTAAA
1 AATAATAAATTTTAAA
39452915 AATAAT-AATTTTAAA
1 AATAATAAATTTTAAA
39452930 TTATATTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAATAAATTTTAAA
Found at i:39452990 original size:15 final size:15
Alignment explanation
Indices: 39452966--39452998 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
39452956 ATTTGATATT
*
39452966 AATATTTTAATAATA
1 AATATATTAATAATA
39452981 AATATATTAATAATA
1 AATATATTAATAATA
39452996 AAT
1 AAT
39452999 GTTCTGTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
AATATATTAATAATA
Found at i:39476447 original size:42 final size:42
Alignment explanation
Indices: 39476410--39476566 Score: 113
Period size: 42 Copynumber: 3.8 Consensus size: 42
39476400 AGGCTGCAGA
*
39476410 GAAGCACATAAGTGCTAAACAGAAACCCATAAGGGCTGAATG
1 GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAATG
* * * * * *
39476452 GAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGTTAAACT-
1 GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAA-TG
** * * ** *
39476494 GAAGCTTAAAAG-GCTAAACGGAAACCCATAAGGATTAAACT-
1 GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAA-TG
* * * *
39476535 GAAGCTCAAAAGAGCTGAACAAAAACCCATAA
1 GAAGCACATAAGAGCTAAACAGAAACCCATAA
39476567 AGGTTAAACT
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
41 38 0.39
42 58 0.60
43 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.15
Consensus pattern (42 bp):
GAAGCACATAAGAGCTAAACAGAAACCCATAAGGGCTGAATG
Found at i:39476484 original size:21 final size:21
Alignment explanation
Indices: 39476416--39476484 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
39476406 CAGAGAAGCA
* * *
39476416 CATAAGTGCTAAACAGAAACC
1 CATAAGAGCTGAACGGAAACC
* * * *
39476437 CATAAGGGCTGAATGGAAGCT
1 CATAAGAGCTGAACGGAAACC
*
39476458 CGTAAGAGCTGAACGGAAACC
1 CATAAGAGCTGAACGGAAACC
39476479 CATAAG
1 CATAAG
39476485 GGTTAAACTG
Statistics
Matches: 36, Mismatches: 12, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.25, T:0.14
Consensus pattern (21 bp):
CATAAGAGCTGAACGGAAACC
Found at i:39476532 original size:21 final size:20
Alignment explanation
Indices: 39476469--39476533 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
39476459 GTAAGAGCTG
39476469 AACGGAAACCCATAAGGGTTA
1 AACGGAAACCCATAA-GGTTA
* * ** * *
39476490 AACTGAAGCTTAAAAGGCTA
1 AACGGAAACCCATAAGGTTA
39476510 AACGGAAACCCATAAGGATTA
1 AACGGAAACCCATAAGG-TTA
39476531 AAC
1 AAC
39476534 TGAAGCTCAA
Statistics
Matches: 31, Mismatches: 12, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (20 bp):
AACGGAAACCCATAAGGTTA
Found at i:39476539 original size:83 final size:83
Alignment explanation
Indices: 39476423--39476579 Score: 217
Period size: 83 Copynumber: 1.9 Consensus size: 83
39476413 GCACATAAGT
* * ** ** *
39476423 GCTAAACAGAAACCCATAAGGGCTGAATGGAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGT
1 GCTAAACAGAAACCCATAAGGACTAAATGGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGT
39476488 TAAACTGAAGCTTAAAAG
66 TAAACTGAAGCTTAAAAG
* *
39476506 GCTAAACGGAAACCCATAAGGATTAAACT-GAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGG
1 GCTAAACAGAAACCCATAAGGACTAAA-TGGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGG
39476570 TTAAACTGAA
65 TTAAACTGAA
39476580 ACTCATATGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
83 63 0.98
84 1 0.02
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (83 bp):
GCTAAACAGAAACCCATAAGGACTAAATGGAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGT
TAAACTGAAGCTTAAAAG
Found at i:39476574 original size:42 final size:42
Alignment explanation
Indices: 39476452--39476584 Score: 171
Period size: 42 Copynumber: 3.2 Consensus size: 42
39476442 GGGCTGAATG
** *
39476452 GAAGCTCGTAAGAGCTGAACGGAAACCCATAAGGGTTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAAGGTTAAACT
* *
39476494 GAAGCTTAAAAG-GCTAAACGGAAACCCAT-AAGGATTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAAGG-TTAAACT
**
39476535 GAAGCTCAAAAGAGCTGAACAAAAACCCATAAAGGTTAAACT
1 GAAGCTCAAAAGAGCTGAACGGAAACCCATAAAGGTTAAACT
*
39476577 GAAACTCA
1 GAAGCTCA
39476585 TATGAGTTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 3 0.04
41 34 0.44
42 37 0.47
43 4 0.05
ACGTcount: A:0.45, C:0.19, G:0.20, T:0.16
Consensus pattern (42 bp):
GAAGCTCAAAAGAGCTGAACGGAAACCCATAAAGGTTAAACT
Found at i:39476581 original size:21 final size:21
Alignment explanation
Indices: 39476473--39476586 Score: 72
Period size: 21 Copynumber: 5.5 Consensus size: 21
39476463 GAGCTGAACG
*
39476473 GAAACCCATAAGGGTTAAACT
1 GAAACCCATAAAGGTTAAACT
* ** * *
39476494 GAAGCTTA-AAAGGCTAAACG
1 GAAACCCATAAAGGTTAAACT
39476514 GAAACCCAT-AAGGATTAAACT
1 GAAACCCATAAAGG-TTAAACT
* * * * *
39476535 GAAGCTCA-AAAGAGCTGAACA
1 GAAACCCATAAAG-GTTAAACT
*
39476556 AAAACCCATAAAGGTTAAACT
1 GAAACCCATAAAGGTTAAACT
*
39476577 GAAACTCATA
1 GAAACCCATA
39476587 TGAGTTAATA
Statistics
Matches: 64, Mismatches: 24, Indels: 10
0.65 0.24 0.10
Matches are distributed among these distances:
20 18 0.28
21 41 0.64
22 5 0.08
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.17
Consensus pattern (21 bp):
GAAACCCATAAAGGTTAAACT
Found at i:39476703 original size:24 final size:24
Alignment explanation
Indices: 39476671--39476718 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
39476661 TACTTGGGTA
39476671 ATTTGCCGTCAATTCATCCTTTGC
1 ATTTGCCGTCAATTCATCCTTTGC
*
39476695 ATTTTCCGTCAATTCATCCTTTGC
1 ATTTGCCGTCAATTCATCCTTTGC
39476719 CATAGAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.29, G:0.10, T:0.44
Consensus pattern (24 bp):
ATTTGCCGTCAATTCATCCTTTGC
Found at i:39476827 original size:45 final size:45
Alignment explanation
Indices: 39476777--39476863 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
39476767 TTTTCAATTC
* * * * *
39476777 ATAATTTAACAATATTTCATTTTTTAACAATATGCTAAATACATA
1 ATAATTTAACAACATTCCATTTTTCAAAAATATACTAAATACATA
*
39476822 ATAATTTAACAACATTCCATTTTTCAAAAATATATTAAATAC
1 ATAATTTAACAACATTCCATTTTTCAAAAATATACTAAATAC
39476864 GTAACATCAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (45 bp):
ATAATTTAACAACATTCCATTTTTCAAAAATATACTAAATACATA
Found at i:39478987 original size:17 final size:18
Alignment explanation
Indices: 39478950--39478988 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
39478940 TAAATCTAAA
39478950 TAAAACTATTAAGTATAC
1 TAAAACTATTAAGTATAC
* *
39478968 TAAAACT-TTAATTATCC
1 TAAAACTATTAAGTATAC
39478985 TAAA
1 TAAA
39478989 CAAAAAGTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.49, C:0.13, G:0.03, T:0.36
Consensus pattern (18 bp):
TAAAACTATTAAGTATAC
Found at i:39496111 original size:50 final size:50
Alignment explanation
Indices: 39495996--39496188 Score: 271
Period size: 50 Copynumber: 3.8 Consensus size: 50
39495986 AATAATAACA
** * *
39495996 TGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCAG
1 TGCCAATA-CCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
39496047 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
39496097 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGACTTCTCATCTCGG
1 TGCCAATACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
39496147 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATACCATGTCCCAGACATGGTCTTACATGGGACCTCT
39496189 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
50 93 0.74
51 33 0.26
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:39496174 original size:100 final size:101
Alignment explanation
Indices: 39495996--39496188 Score: 318
Period size: 100 Copynumber: 1.9 Consensus size: 101
39495986 AATAATAACA
* * *
39495996 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTCAGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTTCTCATCTCAGTGCCAATGCCATGT
39496061 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
66 CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
*
39496097 TGCCAACA-CCATGTCCCAGACATGGTCTTACATGGGA-CTTCTCATCTCGGTGCCAATGCCATG
1 TGCCAA-AGCCATGTCCCAGACATGGTCTTACATGGGATCTTCTCATCTCAGTGCCAATGCCATG
*
39496160 TCCCAGACATGGTCTTACATGGGACCTCT
65 TCCCAGACATGGTCTTACAGGGGACCTCT
39496189 TTACCCAAAT
Statistics
Matches: 86, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
100 50 0.58
101 35 0.41
102 1 0.01
ACGTcount: A:0.21, C:0.31, G:0.22, T:0.26
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTTCTCATCTCAGTGCCAATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:39505353 original size:30 final size:30
Alignment explanation
Indices: 39505317--39505377 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
39505307 ACTGTAGGGG
39505317 TCACACGGCAATGTGGCCAGGCCGTGTGAC
1 TCACACGGCAATGTGGCCAGGCCGTGTGAC
*
39505347 TCACACGGCAATGTGGCCAGGCTGTGTGAC
1 TCACACGGCAATGTGGCCAGGCCGTGTGAC
39505377 T
1 T
39505378 TACGCGGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.20, C:0.28, G:0.33, T:0.20
Consensus pattern (30 bp):
TCACACGGCAATGTGGCCAGGCCGTGTGAC
Found at i:39523617 original size:39 final size:39
Alignment explanation
Indices: 39523577--39523753 Score: 246
Period size: 39 Copynumber: 4.5 Consensus size: 39
39523567 ATTCACTTTT
* * *
39523577 AAGCATATATCACATTACACATATAATCACATAACATTT
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
39523616 AAGCATATATCACAATACTCATATAATTACATAACGTTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* * * *
39523655 AAGCATATGTCGCAATACTCATATGATTACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
* *
39523694 AAGCATATATCGCAATACTTATATAATCACATAACATTC
1 AAGCATATATCACAATACTCATATAATCACATAACATTC
*
39523733 AAGCATATGTCACAATACTCA
1 AAGCATATATCACAATACTCA
39523754 AAAACATGTT
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 122 1.00
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.30
Consensus pattern (39 bp):
AAGCATATATCACAATACTCATATAATCACATAACATTC
Found at i:39545914 original size:10 final size:10
Alignment explanation
Indices: 39545898--39545945 Score: 60
Period size: 10 Copynumber: 4.8 Consensus size: 10
39545888 ATAGATATCT
39545898 TAAAAAATTA
1 TAAAAAATTA
*
39545908 TAGAAAATTA
1 TAAAAAATTA
* *
39545918 TTAAAAATCA
1 TAAAAAATTA
*
39545928 TAAAAAAGTA
1 TAAAAAATTA
39545938 TAAAAAAT
1 TAAAAAAT
39545946 AGTAAAATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:39545951 original size:20 final size:19
Alignment explanation
Indices: 39545898--39545952 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 19
39545888 ATAGATATCT
* *
39545898 TAAAAAATTATAGAAAATTA
1 TAAAAAA-TATAAAAAAGTA
*
39545918 TTAAAAATCATAAAAAAGTA
1 TAAAAAAT-ATAAAAAAGTA
39545938 TAAAAAATAGTAAAA
1 TAAAAAATA-TAAAA
39545953 TTGTTCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 27 0.93
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
TAAAAAATATAAAAAAGTA
Found at i:39553102 original size:20 final size:19
Alignment explanation
Indices: 39553077--39553131 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
39553067 AGATTATTTG
39553077 CACTTCTGTGTCTCTTCTTA
1 CACTTC-GTGTCTCTTCTTA
*
39553097 CACTTCGATGCCTCTTCTTA
1 CACTTCG-TGTCTCTTCTTA
39553117 CACTTCGGTGTCTCT
1 CACTTC-GTGTCTCT
39553132 GTTAAAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.11, C:0.33, G:0.13, T:0.44
Consensus pattern (19 bp):
CACTTCGTGTCTCTTCTTA
Found at i:39553182 original size:40 final size:40
Alignment explanation
Indices: 39553070--39553221 Score: 114
Period size: 40 Copynumber: 3.8 Consensus size: 40
39553060 TTACGATAGA
* * *
39553070 TTATTTGCACTTCTGTGTCTCTT-CTTACACTTCGATGCCT
1 TTATTTGCACTTCGGTGCCT-TTGCTTACACTTTGATGCCT
* * * * *
39553110 CTT-CTTACACTTCGGTGTCTCTG-TTAAAACTTTGATGCCT
1 -TTATTTGCACTTCGGTGCCTTTGCTT-ACACTTTGATGCCT
* * *
39553150 TTATTTGCACTTCAGTGCCTTTGCTTACACTTTGGTGTCT
1 TTATTTGCACTTCGGTGCCTTTGCTTACACTTTGATGCCT
* **
39553190 TTGATTT-CACTTTGGTGCCTTTATTTACACTT
1 TT-ATTTGCACTTCGGTGCCTTTGCTTACACTT
39553222 CGGTGCATCT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
39 5 0.06
40 75 0.85
41 8 0.09
ACGTcount: A:0.14, C:0.24, G:0.14, T:0.47
Consensus pattern (40 bp):
TTATTTGCACTTCGGTGCCTTTGCTTACACTTTGATGCCT
Found at i:39553256 original size:60 final size:60
Alignment explanation
Indices: 39553094--39553274 Score: 229
Period size: 60 Copynumber: 3.0 Consensus size: 60
39553084 GTGTCTCTTC
* * * ** *
39553094 TTACACTTCGATGCCTCTTCTTACACTTCGGTGTCTCTG-TTAAAACTTTGATGCCTTTAT
1 TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATT-TCACTTTGGTGCCTTTAT
* * * *
39553154 TTGCACTTCAGTGCCTTTGCTTACACTTTGGTGTCTTTGATTTCACTTTGGTGCCTTTAT
1 TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
* * *
39553214 TTACACTTCGGTGCATCTGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTAT
1 TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
39553274 T
1 T
39553275 AGCACTAAGG
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
60 101 0.98
61 2 0.02
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (60 bp):
TTACACTTCGGTGCCTCTGCTTACACTTTGGTGTCTCTGATTTCACTTTGGTGCCTTTAT
Found at i:39553280 original size:20 final size:20
Alignment explanation
Indices: 39553094--39553290 Score: 105
Period size: 20 Copynumber: 9.8 Consensus size: 20
39553084 GTGTCTCTTC
* **
39553094 TTACACTTCGATGCCTCTTC
1 TTACACTTCGGTGCCTCTGA
*
39553114 TTACACTTCGGTGTCTCTG-
1 TTACACTTCGGTGCCTCTGA
* * * *
39553133 TTAAAACTTTGATGCCT-TTA
1 TT-ACACTTCGGTGCCTCTGA
* * * *
39553153 TTTGCACTTCAGTGCCTTTGC
1 -TTACACTTCGGTGCCTCTGA
* * *
39553174 TTACACTTTGGTGTCTTTGA
1 TTACACTTCGGTGCCTCTGA
* * *
39553194 TTTCACTTTGGTGCCT-TTA
1 TTACACTTCGGTGCCTCTGA
* *
39553213 TTTACACTTCGGTGCATCTGC
1 -TTACACTTCGGTGCCTCTGA
* *
39553234 TTACACTTTGGTGTCTCTGA
1 TTACACTTCGGTGCCTCTGA
*
39553254 TTTCACTTCGGTGCCTCT-A
1 TTACACTTCGGTGCCTCTGA
**
39553273 TTAGCACTAAGGTGCCTC
1 TTA-CACTTCGGTGCCTC
39553291 CGTATAGCAT
Statistics
Matches: 132, Mismatches: 38, Indels: 14
0.72 0.21 0.08
Matches are distributed among these distances:
19 8 0.06
20 120 0.91
21 4 0.03
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.43
Consensus pattern (20 bp):
TTACACTTCGGTGCCTCTGA
Found at i:39553287 original size:60 final size:60
Alignment explanation
Indices: 39553171--39553287 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
39553161 TCAGTGCCTT
* * * **
39553171 TGCTTACACTTTGGTGTCTTTGATTTCACTTTGGTGCCTTTATTTACACTTCGGTGCATC
1 TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTATTTACACTAAGGTGCATC
39553231 TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTA-TTAGCACTAAGGTGC
1 TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTATTTA-CACTAAGGTGC
39553288 CTCCGTATAG
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
59 3 0.06
60 48 0.94
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (60 bp):
TGCTTACACTTTGGTGTCTCTGATTTCACTTCGGTGCCTCTATTTACACTAAGGTGCATC
Found at i:39556436 original size:11 final size:11
Alignment explanation
Indices: 39556422--39556463 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
39556412 TAAATATTAC
39556422 TTTATTAATAT
1 TTTATTAATAT
*
39556433 TTTAATGAGATAT
1 TTT-ATTA-ATAT
39556446 TTTATTAATAT
1 TTTATTAATAT
39556457 TTTATTA
1 TTTATTA
39556464 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:39556512 original size:15 final size:15
Alignment explanation
Indices: 39556488--39556517 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39556478 AAAAGGAGAG
*
39556488 AAAGATGAAGAAAGA
1 AAAGAAGAAGAAAGA
39556503 AAAGAAGAAGAAAGA
1 AAAGAAGAAGAAAGA
39556518 TGATCCTCCC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (15 bp):
AAAGAAGAAGAAAGA
Found at i:39559998 original size:22 final size:22
Alignment explanation
Indices: 39559968--39560009 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
39559958 ACAGCAGAAC
*
39559968 AGGCTTTTAGCAGCACTTTTTT
1 AGGCCTTTAGCAGCACTTTTTT
* *
39559990 AGGCCTTTAGCGGCGCTTTT
1 AGGCCTTTAGCAGCACTTTT
39560010 AAGCGCCGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (22 bp):
AGGCCTTTAGCAGCACTTTTTT
Found at i:39560241 original size:43 final size:42
Alignment explanation
Indices: 39560169--39560266 Score: 124
Period size: 43 Copynumber: 2.3 Consensus size: 42
39560159 AGACAAATAC
* *
39560169 CTTTAGCGGCGCTTTAGTGGAAGCGCCGCTAAAGATCAGGGT
1 CTTTAGCAGCGCTTTAGTGGAAACGCCGCTAAAGATCAGGGT
* * **
39560211 CTTTAGCAGCGTTTTTGTGGGAAACGCCGCTAAAGATTGGGGT
1 CTTTAGCAGCGCTTTAGT-GGAAACGCCGCTAAAGATCAGGGT
*
39560254 CTTTAGCGGCGCT
1 CTTTAGCAGCGCT
39560267 CTTACTACAA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 15 0.32
43 32 0.68
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (42 bp):
CTTTAGCAGCGCTTTAGTGGAAACGCCGCTAAAGATCAGGGT
Found at i:39560484 original size:43 final size:43
Alignment explanation
Indices: 39560253--39560546 Score: 206
Period size: 43 Copynumber: 6.8 Consensus size: 43
39560243 AAGATTGGGG
* * * *
39560253 TCTTTAGCGGCGCTCTTACTACAAACGCCGC-AATAGACCCTGA
1 TCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAA-AGACCATGA
* * * *
39560296 TCTATAGCGGCGCATTTT-CTAAAAATGCCG-TAATAGA-CACCGA
1 TCTTTAGCGGCGC-TTTTACCAAAAACGCCGCTAA-AGACCA-TGA
* * * *
39560339 TCTATAGCGGCGCTTTTACAAAAAACGCCGC-AGTAGACCCTGA
1 TCTTTAGCGGCGCTTTTACCAAAAACGCCGCTA-AAGACCATGA
* ** * * * *
39560382 TCTATAGCGGCGCTTCGGA-TAAAAACGCCACTAAAGATCATGG
1 TCTTTAGCGGCGCTT-TTACCAAAAACGCCGCTAAAGACCATGA
*
39560425 TCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCATGA
1 TCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGACCATGA
* * * * * **
39560468 TCTTTAGTGGCGCTTTTTCCACAAACGCCGGTAAATAACC-TTC
1 TCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAA-GACCATGA
* * *
39560511 TCTTTAGCTGCACTTTTACCAAAAACGCCACTAAAG
1 TCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAG
39560547 GCCAACACCT
Statistics
Matches: 198, Mismatches: 42, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
42 5 0.03
43 184 0.93
44 9 0.05
ACGTcount: A:0.29, C:0.28, G:0.18, T:0.25
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTTACCAAAAACGCCGCTAAAGACCATGA
Found at i:39560494 original size:86 final size:85
Alignment explanation
Indices: 39560232--39560539 Score: 260
Period size: 86 Copynumber: 3.6 Consensus size: 85
39560222 TTTTTGTGGG
*** * * * *
39560232 AAACGCCGCTAAAGATTGGGGTCTTTAGCGGCGCTCTTACTACAAACGCCGCAATAGACCCTGAT
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAACGCCGCAA-AGACCATGAT
*
39560297 CTATAGCGGCGCATTTTCTAA
65 CTATAGCGGCGCTTTTTCTAA
* * * * * * *
39560318 AAATGCCG-TAATAGA-CACCGATCTATAGCGGCGCTTTTACAAAAAACGCCGCAGTAGACCCTG
1 AAACGCCGCTAA-AGATCA-TGGTCTTTAGCGGCGCTTTTACCAAAAACGCCGCA-AAGACCATG
****
39560381 ATCTATAGCGGCGCTTCGGATAA
63 ATCTATAGCGGCGCTTTTTCTAA
* *
39560404 AAACGCCACTAAAGATCATGGTCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAGACCATGAT
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAACGCCGC-AAAGACCATGAT
* * * *
39560469 CTTTAGTGGCGCTTTTTCCAC
65 CTATAGCGGCGCTTTTTCTAA
* * * * ** * *
39560490 AAACGCCGGTAAATAACCTTCTCTTTAGCTGCACTTTTACCAAAAACGCC
1 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAACGCC
39560540 ACTAAAGGCC
Statistics
Matches: 174, Mismatches: 42, Indels: 12
0.76 0.18 0.05
Matches are distributed among these distances:
85 3 0.02
86 165 0.95
87 6 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.24
Consensus pattern (85 bp):
AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTACCAAAAACGCCGCAAAGACCATGATC
TATAGCGGCGCTTTTTCTAA
Found at i:39560968 original size:21 final size:21
Alignment explanation
Indices: 39560897--39560977 Score: 90
Period size: 21 Copynumber: 3.9 Consensus size: 21
39560887 TTTGACGCTG
* *
39560897 CTCTGCTTACCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* *
39560918 CTCTACTTGCCTCGCTACAGC
1 CTCTACTTCCCTCGCTGCAGC
*
39560939 CTCTGCTTCCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
* * *
39560960 CTGTACTTCTCTCACTGC
1 CTCTACTTCCCTCGCTGC
39560978 CGCATCTGCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.10, C:0.43, G:0.16, T:0.31
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:39560986 original size:42 final size:42
Alignment explanation
Indices: 39560898--39560989 Score: 114
Period size: 42 Copynumber: 2.2 Consensus size: 42
39560888 TTGACGCTGC
* * *
39560898 TCTGCTTACCTCGCTGCAGCCTCTACTTGCCTCGCTACAGCC
1 TCTGCTTCCCTCGCTGCAGCCTCTACTTGCCTCACTACAGCA
* * *
39560940 TCTGCTTCCCTCGCTGCAGCCTGTACTT-CTCTCACTGCCGCA
1 TCTGCTTCCCTCGCTGCAGCCTCTACTTGC-CTCACTACAGCA
39560982 TCTGCTTC
1 TCTGCTTC
39560990 TCTTACTGCC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.10, C:0.42, G:0.16, T:0.32
Consensus pattern (42 bp):
TCTGCTTCCCTCGCTGCAGCCTCTACTTGCCTCACTACAGCA
Found at i:39560989 original size:21 final size:21
Alignment explanation
Indices: 39560965--39561008 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
39560955 GCAGCCTGTA
39560965 CTTCTCTCACTGCCGCATCTG
1 CTTCTCTCACTGCCGCATCTG
*
39560986 CTTCTCTTACTGCCGCATCTG
1 CTTCTCTCACTGCCGCATCTG
39561007 CT
1 CT
39561009 CTAAGCTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.41, G:0.14, T:0.36
Consensus pattern (21 bp):
CTTCTCTCACTGCCGCATCTG
Found at i:39561074 original size:66 final size:66
Alignment explanation
Indices: 39561000--39561126 Score: 220
Period size: 66 Copynumber: 1.9 Consensus size: 66
39560990 TCTTACTGCC
*
39561000 GCATCTGCTCTAAGCTGTTGCTGGAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGTTG
1 GCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTT-GTTGAACCTCAGCTTCTCTCGTTG
39561064 CT
65 CT
*
39561066 GCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCG
1 GCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCG
39561127 ATGTTGCCTC
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
66 54 0.93
67 4 0.07
ACGTcount: A:0.14, C:0.28, G:0.19, T:0.39
Consensus pattern (66 bp):
GCATCTGCTCTAAGCTGCTGCTGGAGTTCTTCATATCTTTGTTGAACCTCAGCTTCTCTCGTTGC
T
Found at i:39566601 original size:18 final size:18
Alignment explanation
Indices: 39566578--39566613 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
39566568 ATAGTTAAGC
39566578 TATGTAAGTTATGTATTA
1 TATGTAAGTTATGTATTA
*
39566596 TATGTAAGTTATTTATTA
1 TATGTAAGTTATGTATTA
39566614 CCCAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (18 bp):
TATGTAAGTTATGTATTA
Found at i:39566663 original size:9 final size:9
Alignment explanation
Indices: 39566651--39566892 Score: 91
Period size: 9 Copynumber: 27.7 Consensus size: 9
39566641 AAAATTATGC
39566651 TATGTAAGT
1 TATGTAAGT
39566660 TATGTAAGT
1 TATGTAAGT
* ** *
39566669 CACATAAGC
1 TATGTAAGT
39566678 TATGTAAG-
1 TATGTAAGT
*
39566686 AAGTTGTAAGT
1 TA--TGTAAGT
39566697 TATGTAAGT
1 TATGTAAGT
*
39566706 TAT-TTA-T
1 TATGTAAGT
* *
39566713 TATGAAAAT
1 TATGTAAGT
*
39566722 TAAGTAAGT
1 TATGTAAGT
**
39566731 TATGTACTT
1 TATGTAAGT
*
39566740 TACG-AA-T
1 TATGTAAGT
* **
39566747 AAT-TAAAA
1 TATGTAAGT
*
39566755 AAATGTAAGT
1 TA-TGTAAGT
*
39566765 TATGT-AGA
1 TATGTAAGT
39566773 T-TGTAAGT
1 TATGTAAGT
39566781 TATGTAAG-
1 TATGTAAGT
39566789 T-TGTAAGT
1 TATGTAAGT
39566797 TATGTAAGT
1 TATGTAAGT
*
39566806 TATGTATA-A
1 TATGTA-AGT
39566815 TAT-TAA-T
1 TATGTAAGT
** *
39566822 TAACTAACT
1 TATGTAAGT
*
39566831 TATGTAATT
1 TATGTAAGT
* *
39566840 TAAGTATAATAT
1 T-A-TGTAA-GT
39566852 TAATGTAAGT
1 T-ATGTAAGT
39566862 TATGTAAG-
1 TATGTAAGT
39566870 T-TGTAAGT
1 TATGTAAGT
39566878 TATGTAAGT
1 TATGTAAGT
39566887 TATGTA
1 TATGTA
39566893 TAATATTAAT
Statistics
Matches: 174, Mismatches: 38, Indels: 42
0.69 0.15 0.17
Matches are distributed among these distances:
7 26 0.15
8 22 0.13
9 99 0.57
10 14 0.08
11 9 0.05
12 4 0.02
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (9 bp):
TATGTAAGT
Found at i:39566779 original size:16 final size:16
Alignment explanation
Indices: 39566758--39566887 Score: 87
Period size: 16 Copynumber: 8.1 Consensus size: 16
39566748 ATTAAAAAAA
39566758 TGTAAGTTATGT-AGAT
1 TGTAAGTTATGTAAG-T
39566774 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
39566790 TGTAAGTTATGTAAGTT
1 TGTAAGTTATGTAAG-T
*
39566807 ATGTATA-ATAT-TAA-T
1 -TGTA-AGTTATGTAAGT
* *
39566822 TAACTAACTTATGTAA-T
1 T--GTAAGTTATGTAAGT
*
39566839 T-TAAGTATAATATTAA--
1 TGTAAGT-T-AT-GTAAGT
39566855 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
39566871 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
39566887 T
1 T
39566888 ATGTATAATA
Statistics
Matches: 94, Mismatches: 6, Indels: 28
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.09
15 5 0.05
16 54 0.57
17 19 0.20
18 7 0.07
19 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:39566785 original size:25 final size:25
Alignment explanation
Indices: 39566757--39566811 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
39566747 AATTAAAAAA
39566757 ATGTAAGTTATGT-AGAT-TGTAAGTT
1 ATGTAAG-T-TGTAAGATATGTAAGTT
*
39566782 ATGTAAGTTGTAAGTTATGTAAGTT
1 ATGTAAGTTGTAAGATATGTAAGTT
39566807 ATGTA
1 ATGTA
39566812 TAATATTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 3 0.11
24 4 0.15
25 20 0.74
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.44
Consensus pattern (25 bp):
ATGTAAGTTGTAAGATATGTAAGTT
Found at i:39566874 original size:81 final size:81
Alignment explanation
Indices: 39566774--39566949 Score: 352
Period size: 81 Copynumber: 2.2 Consensus size: 81
39566764 TTATGTAGAT
39566774 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
1 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
39566839 TTAAGTATAATATTAA
66 TTAAGTATAATATTAA
39566855 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
1 TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
39566920 TTAAGTATAATATTAA
66 TTAAGTATAATATTAA
39566936 TGTAAGTTATGTAA
1 TGTAAGTTATGTAA
39566950 TTAATGTATA
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 95 1.00
ACGTcount: A:0.39, C:0.02, G:0.14, T:0.44
Consensus pattern (81 bp):
TGTAAGTTATGTAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAAT
TTAAGTATAATATTAA
Found at i:39566915 original size:34 final size:34
Alignment explanation
Indices: 39566873--39567081 Score: 252
Period size: 34 Copynumber: 6.3 Consensus size: 34
39566863 ATGTAAGTTG
*
39566873 TAAGTTATGTAAGTTATGTATAATATTAATTAAC
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* * *
39566907 TAACTTATGTAATTTAAGTATAATATTAA-T--G
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
39566938 TAAGTTATGTAATTAATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
39566972 TAAGTCATGTAATTTATGTATAATATTAA-T-GC
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
39567004 -AAGTTATGTAATATATGTATAATATTAATTAAT
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
* *
39567037 TAAGTTATGTAATTTATGTATAATACTAAATAA-
1 TAAGTTATGTAATTTATGTATAATATTAATTAAC
39567070 TCAAGTTATGTA
1 T-AAGTTATGTA
39567082 TAATATTAAT
Statistics
Matches: 149, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
31 52 0.35
32 2 0.01
33 3 0.02
34 92 0.62
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (34 bp):
TAAGTTATGTAATTTATGTATAATATTAATTAAC
Found at i:39566947 original size:65 final size:64
Alignment explanation
Indices: 39566871--39567061 Score: 310
Period size: 65 Copynumber: 2.9 Consensus size: 64
39566861 TTATGTAAGT
* * *
39566871 TGTAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA
1 TGTAAGTTATGTAA-TTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
39566936 TGTAAGTTATGTAATTAATGTATAATATTAATTAATTAAGTCATGTAATTTATGTATAATATTAA
1 TGTAAGTTATGTAATT-ATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
*
39567001 TGCAAGTTATGTAATATATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
1 TGTAAGTTATGTAAT-TATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATA
39567062 CTAAATAATC
Statistics
Matches: 118, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
64 2 0.02
65 115 0.97
66 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.11, T:0.46
Consensus pattern (64 bp):
TGTAAGTTATGTAATTATGTATAATATTAATTAATTAAGTTATGTAATTTATGTATAATATTAA
Found at i:39566989 original size:99 final size:98
Alignment explanation
Indices: 39566873--39567081 Score: 269
Period size: 99 Copynumber: 2.1 Consensus size: 98
39566863 ATGTAAGTTG
*
39566873 TAAGTTATGTAAGTTATGTATAATATTAATTAACTAACTTATGTAATTTAAGTATAATATTAA-T
1 TAAGTTATGTAAGTTATGTATAATATTAA-T-AC-AACTTATGTAATATAAGTATAATATTAATT
* *
39566937 -GTAAGTTATGTAATTAATGTATAATATTAATTAAT
63 AGTAAGTTATGTAATTAATGTATAATACTAAATAAT
* * * * * *
39566972 TAAGTCATGTAATTTATGTATAATATTAATGCAAGTTATGTAATATATGTATAATATTAATTAAT
1 TAAGTTATGTAAGTTATGTATAATATTAATACAACTTATGTAATATAAGTATAATATTAATT-AG
*
39567037 TAAGTTATGTAATTTATGTATAATACTAAATAAT
65 TAAGTTATGTAATTAATGTATAATACTAAATAAT
*
39567071 CAAGTTATGTA
1 TAAGTTATGTA
39567082 TAATATTAAT
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
96 25 0.26
97 2 0.02
98 1 0.01
99 67 0.71
ACGTcount: A:0.42, C:0.03, G:0.11, T:0.44
Consensus pattern (98 bp):
TAAGTTATGTAAGTTATGTATAATATTAATACAACTTATGTAATATAAGTATAATATTAATTAGT
AAGTTATGTAATTAATGTATAATACTAAATAAT
Found at i:39567995 original size:18 final size:19
Alignment explanation
Indices: 39567957--39568001 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
39567947 AGAAATTGGG
*
39567957 AACCCCTAGCTAAATCCTA
1 AACCCCTAGCTAAACCCTA
39567976 AACCCCTAGCT-AACCCTA
1 AACCCCTAGCTAAACCCTA
*
39567994 AATCCCTA
1 AACCCCTA
39568002 ACCCCTAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.36, C:0.40, G:0.04, T:0.20
Consensus pattern (19 bp):
AACCCCTAGCTAAACCCTA
Found at i:39568750 original size:113 final size:113
Alignment explanation
Indices: 39568551--39569261 Score: 911
Period size: 113 Copynumber: 6.3 Consensus size: 113
39568541 AGATAAAATG
* * * * * *
39568551 TTTTTGCGGCGCTTTATAAAAAACGCCGCTAAAGGCATCAGCATTAGCGGCGCTTATTCA-GAAA
1 TTTTTGCGGCGCTTT-TAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTT-TACATAAAA
*
39568615 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGTCGTTGGGCTTAGGC
64 CGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
*
39568665 -TTTTGCGGCGCATTTTAAAAAACTCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
1 TTTTTGCGGCGC-TTTTAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
* *
39568729 GCCACTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGTTTAGGC
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * **
39568778 TTTTTGCGGCGCTTTTGAAAAAACGCCGCTAAAGACCTCAACATTAGCGACGCTTT--ATAGATG
1 TTTTTGCGGCGCTTTT-AAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATA-AAA
* *
39568841 CACCGCTAAAGACCCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGT
64 CGCCGCTAAAGA-CCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
** ** *
39568892 TTTTTGCGGCGCAATTAAAAAACATCGCTAAAGACCTGAACATTAGCGGCGCTTTACAT-AAACA
1 TTTTTGCGGCGCTTTTAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAACG
* * *
39568956 CCGCGAAAGACCCCAAAAACTCAAAAAACGGTGCCGTTGAGCTTAGGC
66 CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
* * * *
39569004 TTTTTGC-GCGCTTTAAAAAAAACGCCGCTAAAGACATGAGCATTAGCGGCACTTTACATAAAAC
1 TTTTTGCGGCGCTTT-TAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAAC
* * * * *
39569068 GCCACTAAAGACCCC-AAAACTTAGAAAACGGTGTCGTTGGGTTTAGAC
65 GCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
*
39569116 TTTTTGCGGCGCTTTTAAAACAACGCCGCTAAAGACCT-AAGCATTAGCGGCGCTTTTACA-GAA
1 TTTTTGCGGCGCTTTTAAAA-AACGCCGCTAAAGACCTGAA-CATTAGCGGCGC-TTTACATAAA
* * *
39569179 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGTCGTTTGTCTTTA-GC
63 ACGCCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGC-TTAGGC
39569230 TTTTTGCGGCGCTTTTATAAAAACGCCGCTAA
1 TTTTTGCGGCGCTTTTA-AAAAACGCCGCTAA
39569262 TGCTTATTTT
Statistics
Matches: 521, Mismatches: 59, Indels: 34
0.85 0.10 0.06
Matches are distributed among these distances:
111 5 0.01
112 125 0.24
113 225 0.43
114 158 0.30
115 8 0.02
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (113 bp):
TTTTTGCGGCGCTTTTAAAAAACGCCGCTAAAGACCTGAACATTAGCGGCGCTTTACATAAAACG
CCGCTAAAGACCCCAAAAACTCAGAAAACGGTGCCGTTGGGCTTAGGC
Found at i:39577246 original size:6 final size:6
Alignment explanation
Indices: 39577235--39577286 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
39577225 GCTGTCACCT
39577235 GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG
1 GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG GCTCGG
39577283 GCTC
1 GCTC
39577287 CGACCCCTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.00, C:0.35, G:0.48, T:0.17
Consensus pattern (6 bp):
GCTCGG
Found at i:39577478 original size:25 final size:25
Alignment explanation
Indices: 39577449--39577498 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39577439 TTTAAAAAAA
* *
39577449 TAAATATAT-TAATTTATTTTTATAT
1 TAAATAAATATAA-TTATTTATATAT
39577474 TAAATAAATATAATTATTTATATAT
1 TAAATAAATATAATTATTTATATAT
39577499 CTAATATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TAAATAAATATAATTATTTATATAT
Found at i:39581519 original size:21 final size:20
Alignment explanation
Indices: 39581495--39581545 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 20
39581485 ATTCATAACA
*
39581495 TATTCAATTCTCATCACTTGC
1 TATTCAAATCTCAT-ACTTGC
*
39581516 TATTTCAAATCTCATATTTGC
1 TA-TTCAAATCTCATACTTGC
39581537 TATTCAAAT
1 TATTCAAAT
39581546 AGTTTTTCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (20 bp):
TATTCAAATCTCATACTTGC
Found at i:39582736 original size:17 final size:18
Alignment explanation
Indices: 39582704--39582739 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
39582694 GAAACCCTGG
39582704 CTTTTTCTCCTTTCTTTCT
1 CTTTTTCT-CTTTCTTTCT
39582723 CTTTTTCT-TTTCTTTCT
1 CTTTTTCTCTTTCTTTCT
39582740 TTCCTTCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTTTTCTCTTTCTTTCT
Found at i:39582845 original size:21 final size:22
Alignment explanation
Indices: 39582793--39582845 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
39582783 TTCTATTTCT
*
39582793 TTATTTGTTTTGTTTTAATTAC
1 TTATTTATTTTGTTTTAATTAC
39582815 TTATTTATTTTGTTTT-ATTA-
1 TTATTTATTTTGTTTTAATTAC
39582835 TTATTTCATTT
1 TTATTT-ATTT
39582846 ACTTTGTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 6 0.21
21 8 0.28
22 15 0.52
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (22 bp):
TTATTTATTTTGTTTTAATTAC
Found at i:39585322 original size:98 final size:99
Alignment explanation
Indices: 39585196--39585390 Score: 320
Period size: 98 Copynumber: 2.0 Consensus size: 99
39585186 TAAGTAAAGA
* * *
39585196 ATTTGAGATGAAAGGTTTGGGACCAGCAAAGAAGATACTTAGTATGAAGATTCTCAGAGATAGAA
1 ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTAGTATAAAGATTCTCAGAGATAGAA
* *
39585261 AAGAAAGTAAATTGTACCTAAGTCA-AAAGGGGT
66 AAGAAAGCAAATTGCACCTAAGTCAGAAAGGGGT
*
39585294 ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTGGTATAAAGATTCTCAGAGATAGAA
1 ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTAGTATAAAGATTCTCAGAGATAGAA
*
39585359 AAGTAAGCAAATTGCACCTAAGTCAGAAAGGG
66 AAGAAAGCAAATTGCACCTAAGTCAGAAAGGG
39585391 TACATTGAGA
Statistics
Matches: 89, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
98 83 0.93
99 6 0.07
ACGTcount: A:0.43, C:0.10, G:0.25, T:0.23
Consensus pattern (99 bp):
ATTTGAGATAAAAGATTTGGGACCAGCAAAGAAGATACTTAGTATAAAGATTCTCAGAGATAGAA
AAGAAAGCAAATTGCACCTAAGTCAGAAAGGGGT
Found at i:39592871 original size:24 final size:24
Alignment explanation
Indices: 39592839--39592886 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39592829 GAGTATAACC
39592839 CAATCTACCAAGGATAAAGCTAGG
1 CAATCTACCAAGGATAAAGCTAGG
39592863 CAATCTACCAAGGATAAAGCTAGG
1 CAATCTACCAAGGATAAAGCTAGG
39592887 ATTAGAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.21, T:0.17
Consensus pattern (24 bp):
CAATCTACCAAGGATAAAGCTAGG
Found at i:39594908 original size:29 final size:29
Alignment explanation
Indices: 39594813--39594909 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 29
39594803 AAACTACTCC
*
39594813 ACACTAGGTTGCTCGTCCAAGCTAAAATT
1 ACACTAGGTTGCTAGTCCAAGCTAAAATT
* * * *
39594842 TCA-TAAGGTTGCTAGTCTAGGCTAAAAGT
1 ACACT-AGGTTGCTAGTCCAAGCTAAAATT
* * *
39594871 ATACAAGGTTGCTTGTCCAAGCTAAAATT
1 ACACTAGGTTGCTAGTCCAAGCTAAAATT
39594900 ACACTAGGTT
1 ACACTAGGTT
39594910 AGGTTACTAA
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
28 1 0.02
29 51 0.98
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.30
Consensus pattern (29 bp):
ACACTAGGTTGCTAGTCCAAGCTAAAATT
Found at i:39603890 original size:3 final size:3
Alignment explanation
Indices: 39603882--39603915 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
39603872 ATGAAAGACC
39603882 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
39603916 GAAAATATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39610347 original size:16 final size:15
Alignment explanation
Indices: 39610326--39610355 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
39610316 AAGATATTAG
39610326 AAGTTGAAAGTGAAAA
1 AAGTTGAAAG-GAAAA
39610342 AAGTTGAAAGGAAA
1 AAGTTGAAAGGAAA
39610356 GTGAAAGGAA
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:0.57, C:0.00, G:0.27, T:0.17
Consensus pattern (15 bp):
AAGTTGAAAGGAAAA
Found at i:39612623 original size:27 final size:26
Alignment explanation
Indices: 39612592--39612649 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
39612582 AATTCATACA
* *
39612592 TTTTTCATGCACATTAATTTATTTAG
1 TTTTTCATGAACATTAAATTATTTAG
* * *
39612618 TGTTTTTATGAACTTTAAATTCTTTAG
1 T-TTTTCATGAACATTAAATTATTTAG
39612645 TTTTT
1 TTTTT
39612650 AAGTGTTAAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (26 bp):
TTTTTCATGAACATTAAATTATTTAG
Found at i:39614744 original size:26 final size:27
Alignment explanation
Indices: 39614701--39614751 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
39614691 GACCAAAATT
*
39614701 AAATATAAAATAAATTAAAGATATAGA
1 AAATATAAAATAAATTAAAAATATAGA
**
39614728 AAATA-AAAATAGTTTAAAAATATA
1 AAATATAAAATAAATTAAAAATATA
39614752 TTAAAAGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 16 0.76
27 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (27 bp):
AAATATAAAATAAATTAAAAATATAGA
Found at i:39617438 original size:16 final size:16
Alignment explanation
Indices: 39617417--39617451 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39617407 AGTTAAAAAT
*
39617417 TATTTAAATTATATAA
1 TATTTAAATAATATAA
*
39617433 TATTTAAATAATTTAA
1 TATTTAAATAATATAA
39617449 TAT
1 TAT
39617452 AATGATACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTTAAATAATATAA
Found at i:39620235 original size:35 final size:34
Alignment explanation
Indices: 39620196--39620283 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 34
39620186 TATTCATTAG
*
39620196 AAAAAAT-ATATAAATATATACATGTACATATATAA
1 AAAAAATAAT-TAAATATATACATATACAT-TATAA
* * *
39620231 AAAAAATAATTATATATATATATATAGATTAT-A
1 AAAAAATAATTAAATATATACATATACATTATAA
*
39620264 AAAAAATAATTACATATATA
1 AAAAAATAATTAAATATATA
39620284 TAAAAATAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 20 0.43
34 3 0.06
35 22 0.47
36 2 0.04
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.34
Consensus pattern (34 bp):
AAAAAATAATTAAATATATACATATACATTATAA
Found at i:39620247 original size:33 final size:33
Alignment explanation
Indices: 39620209--39620281 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
39620199 AAATATATAA
* *
39620209 ATATATACATGTACATA-TATAAAAAAAATAATT
1 ATATATACATATACAGATTAT-AAAAAAATAATT
* *
39620242 ATATATATATATATAGATTATAAAAAAATAATT
1 ATATATACATATACAGATTATAAAAAAATAATT
*
39620275 ACATATA
1 ATATATA
39620282 TATAAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 31 0.91
34 3 0.09
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.36
Consensus pattern (33 bp):
ATATATACATATACAGATTATAAAAAAATAATT
Found at i:39620322 original size:26 final size:26
Alignment explanation
Indices: 39620220--39620308 Score: 85
Period size: 26 Copynumber: 3.3 Consensus size: 26
39620210 TATATACATG
*
39620220 TACATATATA-AAAAA-AATAATTAT
1 TACATATATATAAAAATAATAATAAT
* *
39620244 ATATATATATATAGATTATAA-AAAAATAAT
1 -TACATATATATA-A--A-AATAATAATAAT
39620274 TACATATATATAAAAATAATAATAAT
1 TACATATATATAAAAATAATAATAAT
39620300 TACATATAT
1 TACATATAT
39620309 TGAAATTAAT
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
25 11 0.21
26 19 0.36
27 1 0.02
28 1 0.02
29 12 0.23
30 9 0.17
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (26 bp):
TACATATATATAAAAATAATAATAAT
Found at i:39620666 original size:3 final size:3
Alignment explanation
Indices: 39620660--39620692 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39620650 GTAGTAGTAG
39620660 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39620693 CTTAATAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39621292 original size:10 final size:9
Alignment explanation
Indices: 39621266--39621306 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
39621256 TTCTTGTTAC
39621266 AAAAT-AAA
1 AAAATAAAA
*
39621274 ATAATAAAA
1 AAAATAAAA
39621283 AAAATAAAA
1 AAAATAAAA
39621292 AAAATAAAA
1 AAAATAAAA
39621301 AAAATA
1 AAAATA
39621307 GACGCGATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
8 4 0.13
9 26 0.87
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (9 bp):
AAAATAAAA
Found at i:39622318 original size:44 final size:43
Alignment explanation
Indices: 39622259--39622375 Score: 137
Period size: 43 Copynumber: 2.7 Consensus size: 43
39622249 GATGTGATCT
* * * * *
39622259 ACTCTACTACAACTTTAGAGAGGTAAGA-TATTTGGTTTTAATCC
1 ACTCCACTGCAACTTTAGGGAGATAAGATTA-TTGGCTTT-ATCC
* *
39622303 ACTCCACTGCAACTTTAGGGAGATAGGATTATTGGCTTTATCT
1 ACTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTTATCC
*
39622346 ACTCCACTGCAACTTCAGGGAGATAAGATT
1 ACTCCACTGCAACTTTAGGGAGATAAGATT
39622376 TGCCATCTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
43 31 0.49
44 30 0.48
45 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (43 bp):
ACTCCACTGCAACTTTAGGGAGATAAGATTATTGGCTTTATCC
Found at i:39622354 original size:43 final size:45
Alignment explanation
Indices: 39622255--39622375 Score: 149
Period size: 44 Copynumber: 2.8 Consensus size: 45
39622245 ACCCGATGTG
* * * * *
39622255 ATCTACTCTACTACAACTTTAGAGAGGTAAGA-TATTTGGTTTTA
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTATTTGGCTTTA
* *
39622299 ATCCACTCCACTGCAACTTTAGGGAGATAGGATTA-TTGGCTTT-
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATTATTTGGCTTTA
*
39622342 ATCTACTCCACTGCAACTTCAGGGAGATAAGATT
1 ATCTACTCCACTGCAACTTTAGGGAGATAAGATT
39622376 TGCCATCTTC
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
43 31 0.47
44 33 0.50
45 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (45 bp):
ATCTACTCCACTGCAACTTTAGGGAGATAAGATTATTTGGCTTTA
Found at i:39622462 original size:50 final size:50
Alignment explanation
Indices: 39622408--39622597 Score: 152
Period size: 50 Copynumber: 3.8 Consensus size: 50
39622398 TGCAATGTTG
*
39622408 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACATCGCCA
1 GGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGTTCCACTACATCGCCA
** * * * ** * * **
39622458 GGGAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTGCAAT-G-TG
1 GGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGTTCCACTAC-ATCGCCA
* * * *
39622507 GGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCCACTACACCGCCA
1 GGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGTTCCACTACATCGCCA
** * * *
39622557 -GGAGAGTAAGATTCGCCGTTGCGGCTTTAATCTGTTCCACT
1 GGGA-AACAAGATTCGCCGTCGCAGCTTCAATCTGTTCCACT
39622598 GTAATGCAAA
Statistics
Matches: 101, Mismatches: 35, Indels: 8
0.70 0.24 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.35
50 63 0.62
51 2 0.02
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (50 bp):
GGGAAACAAGATTCGCCGTCGCAGCTTCAATCTGTTCCACTACATCGCCA
Found at i:39622528 original size:99 final size:100
Alignment explanation
Indices: 39622382--39622589 Score: 339
Period size: 99 Copynumber: 2.1 Consensus size: 100
39622372 GATTTGCCAT
* *
39622382 CTTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
*
39622447 CTACATCGCCAGG-GAAGTAAGATTCGCCGTTGCGG
66 CTACACCGCCAGGAG-AGTAAGATTCGCCGTTGCGG
* *
39622482 CTTCAATCTTTTTAATTGCAATG-TGGGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
39622546 CTACACCGCCAGGAGAGTAAGATTCGCCGTTGCGG
66 CTACACCGCCAGGAGAGTAAGATTCGCCGTTGCGG
*
39622581 CTTTAATCT
1 CTTCAATCT
39622590 GTTCCACTGT
Statistics
Matches: 101, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
99 79 0.78
100 22 0.22
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTTGGGGAAACAAGATTCACCGTCGTAGCTTCAATCTGTTCCA
CTACACCGCCAGGAGAGTAAGATTCGCCGTTGCGG
Found at i:39622534 original size:49 final size:50
Alignment explanation
Indices: 39622382--39622539 Score: 140
Period size: 50 Copynumber: 3.2 Consensus size: 50
39622372 GATTTGCCAT
* *
39622382 CTTCAGTCTTTTAAATTGCAATGTTGGGGAAACAAGATTCGCCGTCGTAG
1 CTTCAATCTTTTAAATTGCAATGCTGGGGAAACAAGATTCGCCGTCGTAG
* ** * * ** ** * **
39622432 CTTCAATCTGTTCCACTAC-ATCGCCAGGGAAGTAAGATTCGCCGTTGCGG
1 CTTCAATCTTTTAAATTGCAAT-GCTGGGGAAACAAGATTCGCCGTCGTAG
* * *
39622482 CTTCAATCTTTTTAATTGCAATG-TGGGGAAACGAGATTCACCGTCGTAG
1 CTTCAATCTTTTAAATTGCAATGCTGGGGAAACAAGATTCGCCGTCGTAG
39622531 CTTCAATCT
1 CTTCAATCT
39622540 GTTCCACTAC
Statistics
Matches: 78, Mismatches: 28, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
49 28 0.36
50 48 0.62
51 2 0.03
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (50 bp):
CTTCAATCTTTTAAATTGCAATGCTGGGGAAACAAGATTCGCCGTCGTAG
Found at i:39622885 original size:44 final size:44
Alignment explanation
Indices: 39622792--39622949 Score: 207
Period size: 44 Copynumber: 3.7 Consensus size: 44
39622782 TGCTACTTTT
* * *
39622792 AACCTACTCCACTGCT-ACTCACGGAGATATGATT---AATCTTC
1 AACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTC
39622833 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
39622877 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
* * * * *
39622921 AGCCTATTCCATTGTTGTCTAGGGAGATA
1 AACCTATTCCACTGCTGACCAGGGAGATA
39622950 TGGCTGGGGT
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
41 28 0.27
42 2 0.02
44 75 0.71
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTC
Found at i:39625359 original size:25 final size:25
Alignment explanation
Indices: 39625309--39625368 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
39625299 AAGAAAATCC
* *
39625309 AAAAGAATGAAAGAATAATTATTAA
1 AAAAGAATGAAAAAATAATTACTAA
*
39625334 AAAAGAATGAAAAAAT-ATTGGCTAA
1 AAAAGAATGAAAAAATAATT-ACTAA
39625359 AAAATGAATG
1 AAAA-GAATG
39625369 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.10
25 22 0.73
26 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.15, T:0.22
Consensus pattern (25 bp):
AAAAGAATGAAAAAATAATTACTAA
Found at i:39629791 original size:17 final size:17
Alignment explanation
Indices: 39629771--39629805 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
39629761 GAAATAAAAA
*
39629771 AAAATGTATATGTATAT
1 AAAATGTAAATGTATAT
39629788 AAAATGTAAATGTATAT
1 AAAATGTAAATGTATAT
39629805 A
1 A
39629806 TATGTATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.37
Consensus pattern (17 bp):
AAAATGTAAATGTATAT
Found at i:39629943 original size:3 final size:3
Alignment explanation
Indices: 39629937--39629993 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
39629927 TATGCGTATG
39629937 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39629985 TAA TAA TAA
1 TAA TAA TAA
39629994 AAAATTGGGA
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):
TAA
Found at i:39634373 original size:16 final size:16
Alignment explanation
Indices: 39634354--39634401 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 16
39634344 TGATTACGAT
* *
39634354 TTTATTCGATTACAGC
1 TTTATTCAATTACAAC
39634370 TTTATTCAATTACAAC
1 TTTATTCAATTACAAC
* *
39634386 TCTATTCCATTACAAC
1 TTTATTCAATTACAAC
39634402 CCTATCTCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.31, C:0.23, G:0.04, T:0.42
Consensus pattern (16 bp):
TTTATTCAATTACAAC
Found at i:39634412 original size:16 final size:16
Alignment explanation
Indices: 39634372--39634406 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39634362 ATTACAGCTT
* *
39634372 TATTCAATTACAACTC
1 TATTCCATTACAACCC
39634388 TATTCCATTACAACCC
1 TATTCCATTACAACCC
39634404 TAT
1 TAT
39634407 CTCATTTCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTCCATTACAACCC
Found at i:39638206 original size:17 final size:17
Alignment explanation
Indices: 39638181--39638219 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
39638171 ATTAATAATT
* *
39638181 TAAATTTTATATTTGCA
1 TAAAATTTACATTTGCA
*
39638198 TAAAATTTACATTTTCA
1 TAAAATTTACATTTGCA
39638215 TAAAA
1 TAAAA
39638220 ATATATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (17 bp):
TAAAATTTACATTTGCA
Found at i:39639007 original size:25 final size:27
Alignment explanation
Indices: 39638976--39639033 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
39638966 TTAAGTTAAT
39638976 ATTATAA-T-TATATATAATTGTCTTA
1 ATTATAATTATATATATAATTGTCTTA
39639001 ATTATAATTAAATATATATAATTGTCTTA
1 ATTATAATT--ATATATATAATTGTCTTA
39639030 ATTA
1 ATTA
39639034 AGTTAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.24
26 1 0.03
29 21 0.72
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (27 bp):
ATTATAATTATATATATAATTGTCTTA
Found at i:39639421 original size:20 final size:20
Alignment explanation
Indices: 39639379--39639414 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39639369 AGGTAAAATA
39639379 AATCAAAGATTAAGTTAATT
1 AATCAAAGATTAAGTTAATT
39639399 AATCAAAG-TTAA-TTAA
1 AATCAAAGATTAAGTTAA
39639415 GATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 4 0.25
20 8 0.50
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (20 bp):
AATCAAAGATTAAGTTAATT
Found at i:39642154 original size:26 final size:26
Alignment explanation
Indices: 39642125--39642183 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
39642115 TACCCCTAGC
*
39642125 AAAATTTTGATGATTTTACCTC-TGGT
1 AAAATTTTGATCATTTT-CCTCTTGGT
*
39642151 AAAATTTTGATCATTTTGCTCTTGGT
1 AAAATTTTGATCATTTTCCTCTTGGT
39642177 AAAATTT
1 AAAATTT
39642184 CAAAAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 3 0.10
26 27 0.90
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (26 bp):
AAAATTTTGATCATTTTCCTCTTGGT
Found at i:39642346 original size:6 final size:6
Alignment explanation
Indices: 39642331--39642378 Score: 69
Period size: 6 Copynumber: 8.0 Consensus size: 6
39642321 GCAAATGGAT
* * *
39642331 CATTTC CATTTT CATTTT CATTTC CATTTC CATTTT CATTTC CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
39642379 TAGAAACCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.17, C:0.27, G:0.00, T:0.56
Consensus pattern (6 bp):
CATTTC
Found at i:39642347 original size:12 final size:12
Alignment explanation
Indices: 39642330--39642377 Score: 78
Period size: 12 Copynumber: 4.0 Consensus size: 12
39642320 TGCAAATGGA
39642330 TCATTTCCATTT
1 TCATTTCCATTT
*
39642342 TCATTTTCATTT
1 TCATTTCCATTT
*
39642354 CCATTTCCATTT
1 TCATTTCCATTT
39642366 TCATTTCCATTT
1 TCATTTCCATTT
39642378 CTAGAAACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:39642353 original size:18 final size:18
Alignment explanation
Indices: 39642330--39642378 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
39642320 TGCAAATGGA
*
39642330 TCATTTCCATTTTCATTT
1 TCATTTCCATTTCCATTT
39642348 TCATTTCCATTTCCATTT
1 TCATTTCCATTTCCATTT
39642366 TCATTTCCATTTC
1 TCATTTCCATTTC
39642379 TAGAAACCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.16, C:0.27, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTTCCATTTCCATTT
Found at i:39645821 original size:24 final size:25
Alignment explanation
Indices: 39645775--39645821 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
39645765 TGGCTATTAT
* * *
39645775 GAGCTTTCCGTTATATGGTTCTTGC
1 GAGCTTCCCGTTATATAGCTCTTGC
39645800 GAGCTTCCCGTTA-ATAGCTCTT
1 GAGCTTCCCGTTATATAGCTCTT
39645822 CGGAACATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GAGCTTCCCGTTATATAGCTCTTGC
Found at i:39646010 original size:24 final size:24
Alignment explanation
Indices: 39645927--39646035 Score: 71
Period size: 24 Copynumber: 4.5 Consensus size: 24
39645917 TAAAGGCTAT
* *
39645927 TTATGAGCTTTTTGATTAATGGCTC
1 TTATGAGCTTCTCGATT-ATGGCTC
*
39645952 TTCA-GAGCTTCCCGA-TATTGGCTC
1 TT-ATGAGCTTCTCGATTA-TGGCTC
* *
39645976 GTT-TGAACTTCTCGATTATGGTTC
1 -TTATGAGCTTCTCGATTATGGCTC
* *
39646000 TTATGAGCTTCCCGTTATATGGCTC
1 TTATGAGCTTCTCGAT-TATGGCTC
**
39646025 ACATGAGCTTC
1 TTATGAGCTTC
39646036 CAGATTACCT
Statistics
Matches: 65, Mismatches: 12, Indels: 14
0.71 0.13 0.15
Matches are distributed among these distances:
23 3 0.05
24 31 0.48
25 30 0.46
26 1 0.02
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.40
Consensus pattern (24 bp):
TTATGAGCTTCTCGATTATGGCTC
Found at i:39653198 original size:27 final size:27
Alignment explanation
Indices: 39653148--39653214 Score: 63
Period size: 27 Copynumber: 2.6 Consensus size: 27
39653138 CCCGTTATAT
*
39653148 GGCT-TTTCAGAGCTTCTCGGTTAA-A
1 GGCTCTTTCAGAGCTTCTCGATTAATA
39653173 GGCTCTTTCATGAGCTTC-CTGATTAATA
1 GGCTCTTTCA-GAGCTTCTC-GATTAATA
*
39653201 -GCTC-TTCGGAGCTT
1 GGCTCTTTCAGAGCTT
39653215 GCCAATATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
25 10 0.28
26 9 0.25
27 16 0.44
28 1 0.03
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.37
Consensus pattern (27 bp):
GGCTCTTTCAGAGCTTCTCGATTAATA
Found at i:39653276 original size:25 final size:25
Alignment explanation
Indices: 39653246--39653293 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
39653236 CATCCCGATT
* *
39653246 ATGGCTCTCATGAGCTTTCCATTAC
1 ATGGCTCACATGAGCTTCCCATTAC
39653271 ATGGCTCACATGAGCTTCCCATT
1 ATGGCTCACATGAGCTTCCCATT
39653294 TATGTGCTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.17, T:0.33
Consensus pattern (25 bp):
ATGGCTCACATGAGCTTCCCATTAC
Found at i:39653302 original size:25 final size:24
Alignment explanation
Indices: 39653244--39653302 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 24
39653234 AACATCCCGA
* *
39653244 TTATGGCTCTCATGAGCTTTCCAT
1 TTATGGCTCACATGAGCTTCCCAT
*
39653268 TACATGGCTCACATGAGCTTCCCAT
1 T-TATGGCTCACATGAGCTTCCCAT
39653293 TTATGTGCTC
1 TTATG-GCTC
39653303 GTATGAGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (24 bp):
TTATGGCTCACATGAGCTTCCCAT
Found at i:39659318 original size:38 final size:38
Alignment explanation
Indices: 39659267--39659373 Score: 126
Period size: 38 Copynumber: 2.8 Consensus size: 38
39659257 GTTTACACGA
* *
39659267 TGTCACCCTGAATGACTAGTAGATAACCGTTGTCACAG
1 TGTCACCCTGAATGACCAGTAGATAACCATTGTCACAG
*
39659305 TGTCA-CCTCGAATGACCAGTAGATAACCATTGTCACGG
1 TGTCACCCT-GAATGACCAGTAGATAACCATTGTCACAG
** * * *
39659343 TGTTGCCCTGAAAGACCAGAAGATAATCATT
1 TGTCACCCTGAATGACCAGTAGATAACCATT
39659374 CCACAATGCT
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
37 3 0.05
38 53 0.90
39 3 0.05
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (38 bp):
TGTCACCCTGAATGACCAGTAGATAACCATTGTCACAG
Found at i:39669699 original size:30 final size:30
Alignment explanation
Indices: 39669663--39669765 Score: 172
Period size: 30 Copynumber: 3.4 Consensus size: 30
39669653 ATTGTATAAA
39669663 GTATGATATGTAATTGAAAATGATTAGAAG
1 GTATGATATGTAATTGAAAATGATTAGAAG
*
39669693 GTATGATATGTAATTGGAAATGATTAGAAG
1 GTATGATATGTAATTGAAAATGATTAGAAG
*
39669723 GTATGATATGTAATT-AGAAATTATTAGAAG
1 GTATGATATGTAATTGA-AAATGATTAGAAG
39669753 GTATGATATGTAA
1 GTATGATATGTAA
39669766 CTATGAATGA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.42, C:0.00, G:0.23, T:0.35
Consensus pattern (30 bp):
GTATGATATGTAATTGAAAATGATTAGAAG
Found at i:39670307 original size:2 final size:2
Alignment explanation
Indices: 39670300--39670324 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39670290 TGATACTCTT
39670300 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
39670325 GTTATAATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39671361 original size:14 final size:14
Alignment explanation
Indices: 39671342--39671381 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
39671332 TTGATTGCCA
39671342 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
39671356 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
39671370 GGAAAATGTTTT
1 GTAAAATGTTTT
39671382 ACTTTTCTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:39672580 original size:30 final size:30
Alignment explanation
Indices: 39672544--39672601 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
39672534 GACCATGCCA
39672544 GTCATAGCAAATTGGTACTTATGGTCTTAT
1 GTCATAGCAAATTGGTACTTATGGTCTTAT
39672574 GTCATAGCAAATTGGTACTTATGGTCTT
1 GTCATAGCAAATTGGTACTTATGGTCTT
39672602 GTACAAATGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.40
Consensus pattern (30 bp):
GTCATAGCAAATTGGTACTTATGGTCTTAT
Found at i:39674074 original size:13 final size:13
Alignment explanation
Indices: 39674058--39674103 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
39674048 GGGGTAGAGA
*
39674058 AAAGGGGTAGGGG
1 AAAGGGGAAGGGG
*
39674071 AAA-GGGAAGGAG
1 AAAGGGGAAGGGG
39674083 -AAGGGGAAAGGGG
1 AAAGGGG-AAGGGG
39674096 AAAGGGGA
1 AAAGGGGA
39674104 GAAGAATGGG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
11 2 0.07
12 10 0.37
13 9 0.33
14 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.57, T:0.02
Consensus pattern (13 bp):
AAAGGGGAAGGGG
Found at i:39674093 original size:31 final size:31
Alignment explanation
Indices: 39674037--39674095 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
39674027 GCTTCGAAAC
* *
39674037 GGGAAAGGGAAGGGGTAGAGAAAAGGGGTAG
1 GGGAAAGGGAAGGAGAAGAGAAAAGGGGTAG
* *
39674068 GGGAAAGGGAAGGAGAAGGGGAAAGGGG
1 GGGAAAGGGAAGGAGAAGAGAAAAGGGG
39674096 AAAGGGGAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.58, T:0.03
Consensus pattern (31 bp):
GGGAAAGGGAAGGAGAAGAGAAAAGGGGTAG
Found at i:39674109 original size:25 final size:25
Alignment explanation
Indices: 39674037--39674109 Score: 71
Period size: 25 Copynumber: 3.0 Consensus size: 25
39674027 GCTTCGAAAC
*
39674037 GGGAAA-GGG-AAGGGGTAGAGAAAAG
1 GGGAAAGGGGAAAGGGG-AGA-AGAAG
* * *
39674062 GGG-TAGGGGAAAGGGAAGGAGAAG
1 GGGAAAGGGGAAAGGGGAGAAGAAG
39674086 GGGAAAGGGGAAAGGGGAGAAGAA
1 GGGAAAGGGGAAAGGGGAGAAGAA
39674110 TGGGTCATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
24 8 0.21
25 25 0.66
26 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.55, T:0.03
Consensus pattern (25 bp):
GGGAAAGGGGAAAGGGGAGAAGAAG
Found at i:39677668 original size:28 final size:28
Alignment explanation
Indices: 39677626--39677689 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
39677616 TTTTATCCTG
* * * *
39677626 AACCCTAAATCTAGAATCCCATACCCTA
1 AACCCAAAATCTAGAACCCCAAACCATA
*
39677654 AACCCAAAATTTAGAACCCCAAACCATA
1 AACCCAAAATCTAGAACCCCAAACCATA
39677682 AA-CCAAAA
1 AACCCAAAA
39677690 CCCGTAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.48, C:0.33, G:0.03, T:0.16
Consensus pattern (28 bp):
AACCCAAAATCTAGAACCCCAAACCATA
Found at i:39677754 original size:21 final size:21
Alignment explanation
Indices: 39677709--39677756 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
39677699 ATGAATCCTT
39677709 AAACCC-AAACTTAAAACCTC
1 AAACCCTAAACTTAAAACCTC
* *
39677729 GAACCCTAAACCTT-AAATCTC
1 AAACCCTAAA-CTTAAAACCTC
39677750 AAACCCT
1 AAACCCT
39677757 GAATCTCGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 15 0.65
22 3 0.13
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (21 bp):
AAACCCTAAACTTAAAACCTC
Found at i:39683469 original size:20 final size:19
Alignment explanation
Indices: 39683444--39683489 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
39683434 ATAAAAATAG
*
39683444 TAAAAATAGTAAATATTATT
1 TAAAAATAAT-AATATTATT
* *
39683464 TAAAAATAATATTTTTATT
1 TAAAAATAATAATATTATT
39683483 TAAAAAT
1 TAAAAAT
39683490 TAATTAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAAATAATAATATTATT
Found at i:39683527 original size:29 final size:31
Alignment explanation
Indices: 39683453--39683531 Score: 110
Period size: 30 Copynumber: 2.6 Consensus size: 31
39683443 GTAAAAATAG
* *
39683453 TAAATATTATTTAA-AAATAATATTTTTATT
1 TAAAAATTATTTAATAATTAATATTTTTATT
*
39683483 TAAAAATTAATTAATAATTAATATTTTTA-T
1 TAAAAATTATTTAATAATTAATATTTTTATT
39683513 TAAAAA-TATTTAATAATTA
1 TAAAAATTATTTAATAATTA
39683532 TTGTAAACTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
29 12 0.27
30 19 0.43
31 13 0.30
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TAAAAATTATTTAATAATTAATATTTTTATT
Found at i:39683567 original size:29 final size:29
Alignment explanation
Indices: 39683478--39683567 Score: 67
Period size: 32 Copynumber: 3.0 Consensus size: 29
39683468 AATAATATTT
* * *
39683478 TTATTTAAAAATTAAT-TAATAATTAATAT
1 TTATTTAAAAATTAATAAAATTATTAA-AC
* *
39683507 TTTTATTAAAAA-TATTTAATAATTATTGTAAAC
1 TTAT-TTAAAAATTA-ATAA-AATTA-T-TAAAC
39683540 TTATTTAAAAATTAATAAAATTATTAAA
1 TTATTTAAAAATTAATAAAATTATTAAA
39683568 AAGTTGTAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
29 9 0.19
30 9 0.19
31 5 0.11
32 14 0.30
33 7 0.15
34 3 0.06
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (29 bp):
TTATTTAAAAATTAATAAAATTATTAAAC
Found at i:39684655 original size:5 final size:5
Alignment explanation
Indices: 39684645--39684675 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
39684635 TTTTCTTCAA
39684645 TCTGC TCTGC TCTGC TCTGC TCTGC TCTGC T
1 TCTGC TCTGC TCTGC TCTGC TCTGC TCTGC T
39684676 TTATGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.39, G:0.19, T:0.42
Consensus pattern (5 bp):
TCTGC
Found at i:39685641 original size:23 final size:24
Alignment explanation
Indices: 39685605--39685649 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
39685595 ATATATTACT
*
39685605 ATTTTGAAATAAAAAATATGTAAA
1 ATTTTCAAATAAAAAATATGTAAA
*
39685629 ATTTTCAAA-AAAAAATTTGTA
1 ATTTTCAAATAAAAAATATGTA
39685650 GATTACTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 11 0.58
24 8 0.42
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (24 bp):
ATTTTCAAATAAAAAATATGTAAA
Found at i:39685806 original size:19 final size:19
Alignment explanation
Indices: 39685767--39685839 Score: 67
Period size: 19 Copynumber: 3.8 Consensus size: 19
39685757 TTTTTAGTTC
* **
39685767 TTTTATATATTTATATTTT
1 TTTTATAAATTTATAAATT
39685786 TTTTATAAATTTATAAA-T
1 TTTTATAAATTTATAAATT
***
39685804 TTTTAGTTCTTTTATAATATT
1 TTTTA-TAAATTTATAA-ATT
39685825 TTTTATAAATTTATA
1 TTTTATAAATTTATA
39685840 TTTTATAGAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 6 0.14
19 22 0.52
20 8 0.19
21 6 0.14
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (19 bp):
TTTTATAAATTTATAAATT
Found at i:39685845 original size:15 final size:16
Alignment explanation
Indices: 39685820--39685857 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
39685810 TTCTTTTATA
*
39685820 ATATTTTTTATAAATT
1 ATATATTTTATAAATT
*
39685836 -TATATTTTATAGATT
1 ATATATTTTATAAATT
39685851 ATATATT
1 ATATATT
39685858 ACAACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATATTTTATAAATT
Found at i:39685928 original size:16 final size:16
Alignment explanation
Indices: 39685898--39685978 Score: 69
Period size: 16 Copynumber: 5.0 Consensus size: 16
39685888 ACTATAGGCT
**
39685898 TTTTATATAAGTTTAA
1 TTTTATATATTTTTAA
*
39685914 TTTTATATACTTTTATA
1 TTTTATATATTTTTA-A
39685931 TTTT-TATATTTTTATAA
1 TTTTATATA-TTTT-TAA
*
39685948 ATTTATA-A-TTTTATA
1 TTTTATATATTTTTA-A
39685963 TTTTATATATTTTTAA
1 TTTTATATATTTTTAA
39685979 AATAATAATA
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.04
15 10 0.19
16 19 0.36
17 18 0.34
18 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (16 bp):
TTTTATATATTTTTAA
Found at i:39685935 original size:8 final size:8
Alignment explanation
Indices: 39685909--39685977 Score: 77
Period size: 8 Copynumber: 8.5 Consensus size: 8
39685899 TTTATATAAG
39685909 TTTA-ATT
1 TTTATATT
*
39685916 TTATATACT
1 TT-TATATT
39685925 TTTATATT
1 TTTATATT
39685933 TTTATATT
1 TTTATATT
**
39685941 TTTATAAA
1 TTTATATT
*
39685949 TTTATAAT
1 TTTATATT
39685957 TTTATATT
1 TTTATATT
39685965 TTATATATT
1 TT-TATATT
39685974 TTTA
1 TTTA
39685978 AAATAATAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
7 2 0.04
8 39 0.74
9 12 0.23
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTATATT
Found at i:39685936 original size:24 final size:25
Alignment explanation
Indices: 39685903--39685977 Score: 91
Period size: 24 Copynumber: 3.1 Consensus size: 25
39685893 AGGCTTTTTA
* *
39685903 TATAAGTTTA-ATTTTATATACTTT
1 TATAATTTTATATTTTATATAATTT
* *
39685927 TATATTTTTATATTTT-TATAAATT
1 TATAATTTTATATTTTATATAATTT
*
39685951 TATAATTTTATATTTTATATATTTT
1 TATAATTTTATATTTTATATAATTT
39685976 TA
1 TA
39685978 AAATAATAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
24 29 0.69
25 13 0.31
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (25 bp):
TATAATTTTATATTTTATATAATTT
Found at i:39685965 original size:32 final size:32
Alignment explanation
Indices: 39685919--39685981 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
39685909 TTTAATTTTA
*
39685919 TATACTTTTATATTTT-TATATTTTTATAAATT
1 TATAATTTTATATTTTATATATTTTTA-AAATT
39685951 TATAATTTTATATTTTATATATTTTTAAAAT
1 TATAATTTTATATTTTATATATTTTTAAAAT
39685982 AATAATAACC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 19 0.66
33 10 0.34
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (32 bp):
TATAATTTTATATTTTATATATTTTTAAAATT
Found at i:39686876 original size:91 final size:91
Alignment explanation
Indices: 39686713--39686889 Score: 228
Period size: 91 Copynumber: 1.9 Consensus size: 91
39686703 TGGGATGGGA
** * *
39686713 CACACGGCCGTGTAAGCAAGCTGTGCAATAGATTGATCTCATGTGGAGTTGGAGTCACAAGACTG
1 CACACGGCCGTGTAAGCAAGCCATGCAACAGATTGATCTCATGTGGAGTTGGAGTCACAAGACCG
39686778 TGCGAACAACCATGTACACTCGGGGT
66 TGCGAACAACCATGTACACTCGGGGT
* * * * * * *
39686804 CACACGGTCGTGTAGGCAAGCCATGCAACAGATTGATGTCGTGTGGGGTTGGAGTCACATGGCCG
1 CACACGGCCGTGTAAGCAAGCCATGCAACAGATTGATCTCATGTGGAGTTGGAGTCACAAGACCG
* * *
39686869 TGTGAACAATCGTGTACACTC
66 TGCGAACAACCATGTACACTC
39686890 ACCAAGGCCG
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (91 bp):
CACACGGCCGTGTAAGCAAGCCATGCAACAGATTGATCTCATGTGGAGTTGGAGTCACAAGACCG
TGCGAACAACCATGTACACTCGGGGT
Found at i:39689287 original size:307 final size:307
Alignment explanation
Indices: 39688733--39689345 Score: 1181
Period size: 307 Copynumber: 2.0 Consensus size: 307
39688723 GCTCATATGA
*
39688733 GTATTCAAAATAAGGTTTCACGGCTGTGTCGCAGACTTTGTACCAGACCATACGTGTATTCGAAA
1 GTATTCAAAATAAGGTTTCACGGCTGTGTCGCAGACTATGTACCAGACCATACGTGTATTCGAAA
39688798 TAAAGTTACACGACCGTATAACACAACCTTATGCCGTGTGAAAAATCTTGGACTTAAAATCAAGA
66 TAAAGTTACACGACCGTATAACACAACCTTATGCCGTGTGAAAAATCTTGGACTTAAAATCAAGA
39688863 AAACACACAACCGTGTAAGGAGGCCGTGTGTGGCACACGGCCAGGTGACAGCCTATGTCCCAGGC
131 AAACACACAACCGTGTAAGGAGGCCGTGTGTGGCACACGGCCAGGTGACAGCCTATGTCCCAGGC
39688928 CGTGTACACCTTAAAAGGCTTTCAAAACAAGGCAAATTTTTAATCAAACCTTAGGTACCAAGCTA
196 CGTGTACACCTTAAAAGGCTTTCAAAACAAGGCAAATTTTTAATCAAACCTTAGGTACCAAGCTA
39688993 ACTTAAAATCAAACATTTCCATATCTTAAAAACATATTCAAATAGGT
261 ACTTAAAATCAAACATTTCCATATCTTAAAAACATATTCAAATAGGT
*
39689040 GTATTCAAAATAATGTTTCACGGCTGTGTCGCAGACTATGTACCAGACCATACGTGTATTCGAAA
1 GTATTCAAAATAAGGTTTCACGGCTGTGTCGCAGACTATGTACCAGACCATACGTGTATTCGAAA
*
39689105 TAAAGTTACATGACCGTATAACACAACCTTATGCCGTGTGAAAAATCTTGGACTTAAAATCAAGA
66 TAAAGTTACACGACCGTATAACACAACCTTATGCCGTGTGAAAAATCTTGGACTTAAAATCAAGA
* *
39689170 AAACACACAACCGTGTGAGGAGGCCGTGTGTGGCACACGGCCGGGTGACAGCCTATGTCCCAGGC
131 AAACACACAACCGTGTAAGGAGGCCGTGTGTGGCACACGGCCAGGTGACAGCCTATGTCCCAGGC
39689235 CGTGTACACCTTAAAAGGCTTTCAAAACAAGGCAAATTTTTAATCAAACCTTAGGTACCAAGCTA
196 CGTGTACACCTTAAAAGGCTTTCAAAACAAGGCAAATTTTTAATCAAACCTTAGGTACCAAGCTA
39689300 ACTTAAAATCAAACATTTCCATATCTTAAAAACATATTCAAATAGG
261 ACTTAAAATCAAACATTTCCATATCTTAAAAACATATTCAAATAGG
39689346 CTTAAAACAT
Statistics
Matches: 301, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
307 301 1.00
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (307 bp):
GTATTCAAAATAAGGTTTCACGGCTGTGTCGCAGACTATGTACCAGACCATACGTGTATTCGAAA
TAAAGTTACACGACCGTATAACACAACCTTATGCCGTGTGAAAAATCTTGGACTTAAAATCAAGA
AAACACACAACCGTGTAAGGAGGCCGTGTGTGGCACACGGCCAGGTGACAGCCTATGTCCCAGGC
CGTGTACACCTTAAAAGGCTTTCAAAACAAGGCAAATTTTTAATCAAACCTTAGGTACCAAGCTA
ACTTAAAATCAAACATTTCCATATCTTAAAAACATATTCAAATAGGT
Found at i:39697573 original size:51 final size:51
Alignment explanation
Indices: 39697497--39697766 Score: 477
Period size: 51 Copynumber: 5.3 Consensus size: 51
39697487 ACTTCTGATC
*
39697497 AGTGACAAGTGATAAGTAGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
39697548 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * *
39697599 AATAACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
39697650 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
* * *
39697701 AGTAACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATCAGGGACA
1 AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
39697752 AGTGACAAGTGATAA
1 AGTGACAAGTGATAA
39697767 ATGTGATCTG
Statistics
Matches: 208, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 208 1.00
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (51 bp):
AGTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
Found at i:39699227 original size:19 final size:20
Alignment explanation
Indices: 39699203--39699252 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
39699193 GATACTTTTT
39699203 TATCGATATT-TTTAAAAAA
1 TATCGATATTATTTAAAAAA
*
39699222 TATCGATACTTATTTAAAAAT
1 TATCGATA-TTATTTAAAAAA
*
39699243 TATTGATATT
1 TATCGATATT
39699253 CATCTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 8 0.30
20 4 0.15
21 15 0.56
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (20 bp):
TATCGATATTATTTAAAAAA
Found at i:39702801 original size:15 final size:15
Alignment explanation
Indices: 39702781--39702815 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
39702771 TATATATGCC
39702781 ACAATAATAAATACA
1 ACAATAATAAATACA
*
39702796 ACAATAATAAATATA
1 ACAATAATAAATACA
39702811 ACAAT
1 ACAAT
39702816 GGCATAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (15 bp):
ACAATAATAAATACA
Found at i:39703076 original size:18 final size:19
Alignment explanation
Indices: 39703055--39703092 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
39703045 ATGTGGAAAG
*
39703055 TGTATATGTGT-TATAAAA
1 TGTATATGTATATATAAAA
39703073 TGTATATGTATATATAAAA
1 TGTATATGTATATATAAAA
39703092 T
1 T
39703093 ATAAAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (19 bp):
TGTATATGTATATATAAAA
Found at i:39703201 original size:22 final size:21
Alignment explanation
Indices: 39703173--39703215 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
39703163 GAGTTAAAAT
39703173 ATATATATTATATAAAAAATGC
1 ATATATATTATA-AAAAAATGC
39703195 ATATATATTATAAAAAAATGC
1 ATATATATTATAAAAAAATGC
39703216 TTGTATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (21 bp):
ATATATATTATAAAAAAATGC
Found at i:39703228 original size:22 final size:21
Alignment explanation
Indices: 39703173--39703229 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
39703163 GAGTTAAAAT
*
39703173 ATATATATTATATAAAAAATGC
1 ATATATAATATA-AAAAAATGC
*
39703195 ATATATATTATAAAAAAATGC
1 ATATATAATATAAAAAAATGC
* *
39703216 TTGTATAAATATAA
1 ATATAT-AATATAA
39703230 TAATAACAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 13 0.42
22 18 0.58
ACGTcount: A:0.54, C:0.04, G:0.05, T:0.37
Consensus pattern (21 bp):
ATATATAATATAAAAAAATGC
Found at i:39703247 original size:21 final size:21
Alignment explanation
Indices: 39703222--39703266 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
39703212 ATGCTTGTAT
39703222 AAAT-ATAATAATAAC-AACAAA
1 AAATAATAA-AATAACTAA-AAA
39703243 AAATAATAAAATAACTAAAAA
1 AAATAATAAAATAACTAAAAA
39703264 AAA
1 AAA
39703267 GGACTAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 16 0.73
22 6 0.27
ACGTcount: A:0.76, C:0.07, G:0.00, T:0.18
Consensus pattern (21 bp):
AAATAATAAAATAACTAAAAA
Found at i:39703250 original size:19 final size:19
Alignment explanation
Indices: 39703226--39703264 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
39703216 TTGTATAAAT
39703226 ATAATAATAACAAC-AAAAA
1 ATAATAA-AACAACTAAAAA
*
39703245 ATAATAAAATAACTAAAAA
1 ATAATAAAACAACTAAAAA
39703264 A
1 A
39703265 AAGGACTAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (19 bp):
ATAATAAAACAACTAAAAA
Found at i:39705695 original size:35 final size:35
Alignment explanation
Indices: 39705656--39705724 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
39705646 ACACTATCAT
* *
39705656 AAATATAATAAATGTTTTATTATATTAAAAATAAA
1 AAATATAAAAAATATTTTATTATATTAAAAATAAA
* *
39705691 AAATATAAAAAATATTTTATTGTATTAAATATAA
1 AAATATAAAAAATATTTTATTATATTAAAAATAA
39705725 TTTTTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.41
Consensus pattern (35 bp):
AAATATAAAAAATATTTTATTATATTAAAAATAAA
Done.