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 127 of 196
Found at i:38130598 original size:18 final size:17
Alignment explanation
Indices: 38130570--38130604 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38130560 ATTATTAAGA
*
38130570 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
38130587 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
38130605 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:38130785 original size:239 final size:240
Alignment explanation
Indices: 38130430--38130864 Score: 836
Period size: 239 Copynumber: 1.8 Consensus size: 240
38130420 TTTTTGTTAT
38130430 AAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAA
1 AAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAA
*
38130495 TTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTATTAAATTTATATAAGAATATTG
66 TTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG
38130560 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
131 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
38130625 TTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATAA
196 TTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATAA
38130670 AAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATA-TTTTAATAATAA
1 AAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAA
38130734 TTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG
66 TTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG
* *
38130799 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAATAATTATGTTAAA
131 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
38130864 T
196 T
38130865 ATGATTAAAT
Statistics
Matches: 192, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
239 140 0.73
240 52 0.27
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (240 bp):
AAGAATATTGATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATTTTTAATAATAA
TTATGTTAAATTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATATAAGAATATTG
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
TTATATTTTATAGTATCATATATTATGATTTTAGTAAATTTATAA
Found at i:38130959 original size:156 final size:157
Alignment explanation
Indices: 38130799--38131105 Score: 562
Period size: 157 Copynumber: 2.0 Consensus size: 157
38130789 AAGAATATTG
* *
38130799 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATGTTTTTAATAATAATTATG-TTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
* *
38130863 ATATGATTAAATTATTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
38130928 ATAATTTACCAAAACAAATTTCTAGTA
131 ATAATTTACCAAAACAAATTTCTAGTA
38130955 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
1 ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
38131020 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
66 ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
*
38131085 ATCATTTACCAAAACAAATTT
131 ATAATTTACCAAAACAAATTT
38131106 ATGCTAAGGG
Statistics
Matches: 145, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
156 58 0.40
157 87 0.60
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
ATTATTAAGAATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAA
ATATGATTAAAATATTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATA
ATAATTTACCAAAACAAATTTCTAGTA
Found at i:38130993 original size:18 final size:17
Alignment explanation
Indices: 38130965--38130999 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
38130955 ATTATTAAGA
*
38130965 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
38130982 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
38131000 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:38131256 original size:16 final size:16
Alignment explanation
Indices: 38131235--38131286 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
38131225 GATTTGCTAT
38131235 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
38131251 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
38131267 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
38131283 TACA
1 TACA
38131287 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:38131332 original size:16 final size:16
Alignment explanation
Indices: 38131311--38131344 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
38131301 CCCTAAGAGA
38131311 TGTCCCCTCCGGTCAT
1 TGTCCCCTCCGGTCAT
38131327 TGTCCCCTCCGGTCAT
1 TGTCCCCTCCGGTCAT
38131343 TG
1 TG
38131345 GCACTGTCGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.41, G:0.21, T:0.32
Consensus pattern (16 bp):
TGTCCCCTCCGGTCAT
Found at i:38132112 original size:28 final size:29
Alignment explanation
Indices: 38132080--38132138 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
38132070 TAAATAGATA
*
38132080 GACAAAATGAAAGTA-AGGTACCACATTG
1 GACAAAATGAAAGTATAGATACCACATTG
* *
38132108 GACAAATTGAAATTATAGATACCACATTG
1 GACAAAATGAAAGTATAGATACCACATTG
38132137 GA
1 GA
38132139 AATTTTGCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 13 0.48
29 14 0.52
ACGTcount: A:0.46, C:0.14, G:0.19, T:0.22
Consensus pattern (29 bp):
GACAAAATGAAAGTATAGATACCACATTG
Found at i:38134748 original size:14 final size:15
Alignment explanation
Indices: 38134726--38134802 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
38134716 CAATCAAACA
38134726 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
38134740 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
38134755 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
38134775 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
38134789 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
38134803 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:38134767 original size:20 final size:20
Alignment explanation
Indices: 38134742--38134781 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
38134732 AATATTTTCC
*
38134742 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
38134762 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
38134782 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:38134787 original size:34 final size:35
Alignment explanation
Indices: 38134730--38134796 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
38134720 CAAACACCAG
*
38134730 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
38134765 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
38134797 TATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:38136965 original size:104 final size:104
Alignment explanation
Indices: 38136773--38137135 Score: 386
Period size: 104 Copynumber: 3.5 Consensus size: 104
38136763 TAATACGAAA
* * * * * * *
38136773 AATCGGAGGCTACGATTTTAAATTAGCTAGCCTTAATAAAATTAACTGTGAATGTAGGTCAGCGA
1 AATCAGAGGCTGCGATCTTAAATTAGCTAGCCTTAGTAAAATTAGCTGTGAACGTAGGTCAACGA
* *
38136838 GTTGTTAGGAGTTGCAATATTAAATCAGCTAACTCAAAT
66 GCTGTTAGGAGTTGCAATCTTAAATCAGCTAACTCAAAT
* * * *
38136877 TATCAGAGGCTGCGATCTTAAATTAGCTAG-CTTCAGTAAAATTAGCTGTTAGCGTAGTTCAACG
1 AATCAGAGGCTGCGATCTTAAATTAGCTAGCCTT-AGTAAAATTAGCTGTGAACGTAGGTCAACG
* * ** *
38136941 AGCTATTAAGAGTTGCGGTCTTAAATCAGCTAACTCGAAT
65 AGCTGTTAGGAGTTGCAATCTTAAATCAGCTAACTCAAAT
* * * * **
38136981 AATCGGAGGTTGCGATCTTAAATCAGCTAGCCTTAGTAAAATTAGTTGTGAACGTAGGTCAATAA
1 AATCAGAGGCTGCGATCTTAAATTAGCTAGCCTTAGTAAAATTAGCTGTGAACGTAGGTCAACGA
* * * *
38137046 GCTGTTAGGAGTTGTAATCTTAAATTAACTAACTCACAT
66 GCTGTTAGGAGTTGCAATCTTAAATCAGCTAACTCAAAT
* * * * * * * *
38137085 GATCAGAGACTGCGATTTTAAATAAGCTAACCTTAATAAAATCAGTTGTGA
1 AATCAGAGGCTGCGATCTTAAATTAGCTAGCCTTAGTAAAATTAGCTGTGA
38137136 GAATCGAACG
Statistics
Matches: 211, Mismatches: 46, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
103 3 0.01
104 205 0.97
105 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (104 bp):
AATCAGAGGCTGCGATCTTAAATTAGCTAGCCTTAGTAAAATTAGCTGTGAACGTAGGTCAACGA
GCTGTTAGGAGTTGCAATCTTAAATCAGCTAACTCAAAT
Found at i:38143728 original size:16 final size:16
Alignment explanation
Indices: 38143702--38143748 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
38143692 GCTATGCTGC
38143702 TGCTGGGGCTGCCTGGG
1 TGCTGGGGCTG-CTGGG
38143719 TGCT-GGGCTGCTGGG
1 TGCTGGGGCTGCTGGG
* *
38143734 AGCGTGGGCCTGCTG
1 TGC-TGGGGCTGCTG
38143749 TTTTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.02, C:0.23, G:0.51, T:0.23
Consensus pattern (16 bp):
TGCTGGGGCTGCTGGG
Found at i:38143896 original size:9 final size:9
Alignment explanation
Indices: 38143882--38143950 Score: 62
Period size: 9 Copynumber: 8.2 Consensus size: 9
38143872 GTTATGTTTT
38143882 TTTTTCTTC
1 TTTTTCTTC
38143891 TTTTTC--C
1 TTTTTCTTC
38143898 TTTTTC--C
1 TTTTTCTTC
38143905 TATTTTCTT-
1 T-TTTTCTTC
38143914 TTTTTCTTC
1 TTTTTCTTC
*
38143923 TTCTTCTTC
1 TTTTTCTTC
38143932 -TTTTCTT-
1 TTTTTCTTC
38143939 TCTTTTCTTC
1 T-TTTTCTTC
38143949 TT
1 TT
38143951 CTTTTCAAAC
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
7 9 0.18
8 18 0.35
9 23 0.45
10 1 0.02
ACGTcount: A:0.01, C:0.23, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:38143923 original size:3 final size:3
Alignment explanation
Indices: 38143917--38143953 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
38143907 TTTTCTTTTT
38143917 TTC TTC TTC TTC TTC TT- TTC TTTC TT- TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TT
38143954 TTCAAACCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:38143932 original size:20 final size:20
Alignment explanation
Indices: 38143909--38143956 Score: 80
Period size: 20 Copynumber: 2.4 Consensus size: 20
38143899 TTTTCCTATT
38143909 TTCTTTT-TTTCTTCTTCTTC
1 TTCTTTTCTTTCTT-TTCTTC
38143929 TTCTTTTCTTTCTTTTCTTC
1 TTCTTTTCTTTCTTTTCTTC
38143949 TTCTTTTC
1 TTCTTTTC
38143957 AAACCCTAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 21 0.78
21 6 0.22
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (20 bp):
TTCTTTTCTTTCTTTTCTTC
Found at i:38144060 original size:28 final size:29
Alignment explanation
Indices: 38144025--38144102 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 29
38144015 TCTTTCTCTG
38144025 TCTTCTTTCTCTCCTTT-TCTT-TTTTTTC
1 TCTTCTTTCTCT-CTTTCTCTTCTTTTTTC
*
38144053 TCTTCTTTCT-TCTTTCCCTTCTTTTTTC
1 TCTTCTTTCTCTCTTTCTCTTCTTTTTTC
*
38144081 T-TTCCTTCTCTCTTTCTCTTCT
1 TCTTCTTTCTCTCTTTCTCTTCT
38144103 ATTTCGACAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
26 4 0.09
27 11 0.25
28 29 0.66
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (29 bp):
TCTTCTTTCTCTCTTTCTCTTCTTTTTTC
Found at i:38144073 original size:16 final size:16
Alignment explanation
Indices: 38144041--38144094 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
38144031 TTCTCTCCTT
*
38144041 TTCTTT-TT-TTTCTC
1 TTCTTTCTTCTTTCCC
38144055 TTCTTTCTTCTTTCCC
1 TTCTTTCTTCTTTCCC
*
38144071 TTCTTTTTTCTTT-CC
1 TTCTTTCTTCTTTCCC
*
38144086 TTCTCTCTT
1 TTCTTTCTT
38144095 TCTCTTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
14 6 0.18
15 11 0.32
16 17 0.50
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTTTCTTCTTTCCC
Found at i:38144095 original size:35 final size:34
Alignment explanation
Indices: 38144014--38144097 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 34
38144004 CGCTCCTCCC
* *
38144014 TTCTT-TCTCTGTCTTCTTTCTCTCCTTTTCTTT
1 TTCTTCTCTCTTTCTTCTTTCCCTCCTTTTCTTT
* *
38144047 TTTTTCTCTTCTTTCTTCTTTCCCTTCTTTT-TTCT
1 TTCTTCTC-TCTTTCTTCTTTCCCTCCTTTTCTT-T
38144082 TTCCTTCTCTCTTTCT
1 TT-CTTCTCTCTTTCT
38144098 CTTCTATTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
33 4 0.10
34 4 0.10
35 29 0.69
36 5 0.12
ACGTcount: A:0.00, C:0.31, G:0.01, T:0.68
Consensus pattern (34 bp):
TTCTTCTCTCTTTCTTCTTTCCCTCCTTTTCTTT
Found at i:38144307 original size:26 final size:26
Alignment explanation
Indices: 38144278--38144329 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
38144268 TTGGCTTTTA
* * *
38144278 GGTGGTGGTGCGACGGTTGCGGTGGC
1 GGTGGTGGCGCGACGGTGGCGATGGC
*
38144304 GGTGGTTGCGCGACGGTGGCGATGGC
1 GGTGGTGGCGCGACGGTGGCGATGGC
38144330 CTTTGGCTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.06, C:0.17, G:0.56, T:0.21
Consensus pattern (26 bp):
GGTGGTGGCGCGACGGTGGCGATGGC
Found at i:38146675 original size:12 final size:13
Alignment explanation
Indices: 38146646--38146679 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
38146636 AATTGCACAA
38146646 AAAAATAAAAGGGC
1 AAAAATAAAA-GGC
38146660 AAAAATAAAA-GC
1 AAAAATAAAAGGC
38146672 AAAAATAA
1 AAAAATAA
38146680 TCAGCAGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.50
14 10 0.50
ACGTcount: A:0.74, C:0.06, G:0.12, T:0.09
Consensus pattern (13 bp):
AAAAATAAAAGGC
Found at i:38151886 original size:17 final size:17
Alignment explanation
Indices: 38151856--38151897 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
38151846 GCATCACAAT
38151856 TTTTATTT-TGTCATCTA
1 TTTTATTTATGTCAT-TA
38151873 TTTTATTTAT-TCATTA
1 TTTTATTTATGTCATTA
38151889 -TTTATTTAT
1 TTTTATTTAT
38151898 CTATCGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.38
16 2 0.08
17 12 0.50
18 1 0.04
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTATTTATGTCATTA
Found at i:38164167 original size:44 final size:44
Alignment explanation
Indices: 38164119--38164267 Score: 133
Period size: 44 Copynumber: 3.2 Consensus size: 44
38164109 TGGAGCAGAT
*
38164119 TGAAGCTACAATTTCTATACCCCTGAAGTTGCAGTGGGTTAGAA
1 TGAAGCTACAATTTCTATACCCCTGAAGTTGCAGTGAGTTAGAA
* * * **
38164163 TGAAGCTACAACAACGAATCCTAT-CTCCATGAAGTTGCAGTAGAGCAAG-A
1 TGAAGCT---AC-A--ATTTCTATAC-CCCTGAAGTTGCAGT-GAGTTAGAA
*
38164213 TGAAGCTAC-ATTTCCTATACCCCTGAAGTTGCAGTGAGTTCGAA
1 TGAAGCTACAATTT-CTATACCCCTGAAGTTGCAGTGAGTTAGAA
38164257 TGAAGCTACAA
1 TGAAGCTACAA
38164268 CTACAAATCC
Statistics
Matches: 81, Mismatches: 12, Indels: 23
0.70 0.10 0.20
Matches are distributed among these distances:
43 6 0.07
44 35 0.43
45 2 0.02
47 4 0.05
48 1 0.01
49 1 0.01
50 28 0.35
51 4 0.05
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (44 bp):
TGAAGCTACAATTTCTATACCCCTGAAGTTGCAGTGAGTTAGAA
Found at i:38164209 original size:94 final size:94
Alignment explanation
Indices: 38164082--38164293 Score: 286
Period size: 94 Copynumber: 2.3 Consensus size: 94
38164072 GGTTGAAGTT
* * * *
38164082 ACGAATCTTATCTCTTTGAAGTTGTAATGGAGC-AGATTGAAGCTACAATTT-CTATACCCCTGA
1 ACGAATCCTATCTCCTTGAAGTTGCAATAGAGCAAGA-TGAAGCTAC-ATTTCCTATACCCCTGA
*
38164145 AGTTGCAGTGGGTTAGAATGAAGCTACAACA
64 AGTTGCAGTGAGTTAGAATGAAGCTACAACA
* *
38164176 ACGAATCCTATCTCCATGAAGTTGCAGTAGAGCAAGATGAAGCTACATTTCCTATACCCCTGAAG
1 ACGAATCCTATCTCCTTGAAGTTGCAATAGAGCAAGATGAAGCTACATTTCCTATACCCCTGAAG
* *
38164241 TTGCAGTGAGTTCGAATGAAGCTACAACT
66 TTGCAGTGAGTTAGAATGAAGCTACAACA
*
38164270 ACAAATCCTATAC-CCTTGAAGTTG
1 ACGAATCCTAT-CTCCTTGAAGTTG
38164294 TAGTGGGTTG
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
93 4 0.04
94 96 0.92
95 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (94 bp):
ACGAATCCTATCTCCTTGAAGTTGCAATAGAGCAAGATGAAGCTACATTTCCTATACCCCTGAAG
TTGCAGTGAGTTAGAATGAAGCTACAACA
Found at i:38164293 original size:50 final size:50
Alignment explanation
Indices: 38164124--38164298 Score: 161
Period size: 50 Copynumber: 3.6 Consensus size: 50
38164114 CAGATTGAAG
* * * *
38164124 CTACAATTTCTATACCCCTGAAGTTGCAGTGGGTTAGAATGAAGCTACAA
1 CTACAAATCCTATACCCCTGAAGTTGCAGTGAGTTCGAATGAAGCTACAA
* * * *
38164174 CAACGAATCCTAT-CTCCATGAAGTTGCAGTAGAG--CAAGATGAAGCTAC-A
1 CTACAAATCCTATAC-CCCTGAAGTTGCAGT-GAGTTCGA-ATGAAGCTACAA
*
38164223 -T----TTCCTATACCCCTGAAGTTGCAGTGAGTTCGAATGAAGCTACAA
1 CTACAAATCCTATACCCCTGAAGTTGCAGTGAGTTCGAATGAAGCTACAA
* *
38164268 CTACAAATCCTATACCCTTGAAGTTGTAGTG
1 CTACAAATCCTATACCCCTGAAGTTGCAGTG
38164299 GGTTGGATTG
Statistics
Matches: 98, Mismatches: 15, Indels: 24
0.72 0.11 0.18
Matches are distributed among these distances:
43 3 0.03
44 30 0.31
45 4 0.04
46 1 0.01
49 3 0.03
50 55 0.56
51 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (50 bp):
CTACAAATCCTATACCCCTGAAGTTGCAGTGAGTTCGAATGAAGCTACAA
Found at i:38164450 original size:44 final size:44
Alignment explanation
Indices: 38164326--38164479 Score: 148
Period size: 44 Copynumber: 3.5 Consensus size: 44
38164316 CATAGCGAAC
* * * * * * *
38164326 CTTATCTCCCTGAAGCTACAGTGAAGCAGATTAAAACTACGAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
* * * * *
38164370 CTTATCTCTCTAAAGTTGTAGTGGAGTAGATCGAAGCTGCAAAT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
* * *
38164414 CTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAATT
1 CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
*
38164458 CCTATAC-CCCTAAAGTTGCAGT
1 CTTAT-CTCCCTAAAGTTGCAGT
38164480 AGGTTAGAAT
Statistics
Matches: 87, Mismatches: 22, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 86 0.99
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (44 bp):
CTTATCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGCTACAAAT
Found at i:38167833 original size:63 final size:63
Alignment explanation
Indices: 38167734--38167886 Score: 252
Period size: 63 Copynumber: 2.4 Consensus size: 63
38167724 GCGAGCATCC
* * * *
38167734 TGATCGGTAGTGATCTTGCATGTATTGCGGACTACCGCAACTCTTTGTGAGCGTCCTGTTATA
1 TGATCGGTTGTGATCCTGCATATATTGCGGACTACCGCAACTCTTTGTGAGCGTCCAGTTATA
* *
38167797 TGATCGGTTGTGATCCTGCATATATTGCGGACTACCGCAGCTCTTTGTGAGTGTCCAGTTATA
1 TGATCGGTTGTGATCCTGCATATATTGCGGACTACCGCAACTCTTTGTGAGCGTCCAGTTATA
38167860 TGATCGGTTGTGATCCTGCATATATTG
1 TGATCGGTTGTGATCCTGCATATATTG
38167887 TAAACACAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 84 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (63 bp):
TGATCGGTTGTGATCCTGCATATATTGCGGACTACCGCAACTCTTTGTGAGCGTCCAGTTATA
Found at i:38167924 original size:63 final size:61
Alignment explanation
Indices: 38167734--38167925 Score: 197
Period size: 63 Copynumber: 3.0 Consensus size: 61
38167724 GCGAGCATCC
* * * ** *
38167734 TGATCGGTAGTGATCTTGCATGTATTGCGGACTACCGCAACTCTTTGTGAGCGTCCTGTTATA
1 TGATCGGTTGTGATCCTGCATATATTGCAAACTACCGCAGCTCTTTGTGAGCGTCCTG--ATA
** * *
38167797 TGATCGGTTGTGATCCTGCATATATTGCGGACTACCGCAGCTCTTTGTGAGTGTCCAGTTATA
1 TGATCGGTTGTGATCCTGCATATATTGCAAACTACCGCAGCTCTTTGTGAGCGTCC--TGATA
* * *
38167860 TGATCGGTTGTGATCCTGCATATATTGTAAAC-ACAAATGCAGCTCTTTGTAAGCGTCCTGATA
1 TGATCGGTTGTGATCCTGCATATATTGCAAACTAC---CGCAGCTCTTTGTGAGCGTCCTGATA
38167923 TGA
1 TGA
38167926 CTCGCTTGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
62 2 0.02
63 90 0.81
65 19 0.17
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
TGATCGGTTGTGATCCTGCATATATTGCAAACTACCGCAGCTCTTTGTGAGCGTCCTGATA
Found at i:38168049 original size:25 final size:26
Alignment explanation
Indices: 38168021--38168126 Score: 80
Period size: 26 Copynumber: 4.3 Consensus size: 26
38168011 ACTTCTTGAT
38168021 TATGGCTC-TTATGAGCTTCCTGTTA
1 TATGGCTCTTTATGAGCTTCCTGTTA
*** *
38168046 TATGGC-CCAGATAAGCTTCCTG--A
1 TATGGCTCTTTATGAGCTTCCTGTTA
* *
38168069 TA-GGCTCTTTGTGAGCTTCCCGATTA
1 TATGGCTCTTTATGAGCTTCCTG-TTA
* *
38168095 -ATGGCTCTTTGTGAGCTTCATGTTA
1 TATGGCTCTTTATGAGCTTCCTGTTA
*
38168120 TCTGGCT
1 TATGGCT
38168127 TGAGAAAGGA
Statistics
Matches: 62, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
22 3 0.05
23 13 0.21
24 1 0.02
25 21 0.34
26 24 0.39
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (26 bp):
TATGGCTCTTTATGAGCTTCCTGTTA
Found at i:38168581 original size:16 final size:17
Alignment explanation
Indices: 38168544--38168591 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 17
38168534 GATATGATTT
38168544 GTATATGTTATAT-G-AA
1 GTATATG-TATATGGAAA
*
38168560 -TATATG-ATGTGGAAA
1 GTATATGTATATGGAAA
38168575 GTATATGTATATGGAAA
1 GTATATGTATATGGAAA
38168592 TCTAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.12
14 1 0.04
15 8 0.31
16 6 0.23
17 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (17 bp):
GTATATGTATATGGAAA
Found at i:38170908 original size:19 final size:19
Alignment explanation
Indices: 38170880--38170923 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
38170870 TTTCTTTCAA
* *
38170880 TTTC-TTTTCTCGATTTTT
1 TTTCTTTTTCTCGACTGTT
*
38170898 TTTCTTTTTCTCTACTGTT
1 TTTCTTTTTCTCGACTGTT
38170917 TTTCTTT
1 TTTCTTT
38170924 AAAAAAAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTCTTTTTCTCGACTGTT
Found at i:38177709 original size:17 final size:17
Alignment explanation
Indices: 38177687--38177725 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
38177677 ACGATTTCTT
38177687 ATTCTATTGAAATCAAA
1 ATTCTATTGAAATCAAA
*
38177704 ATTCTATTGAAATCGAA
1 ATTCTATTGAAATCAAA
38177721 ATTCT
1 ATTCT
38177726 TTCTCTCCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (17 bp):
ATTCTATTGAAATCAAA
Found at i:38178136 original size:21 final size:21
Alignment explanation
Indices: 38178112--38178151 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38178102 AAAAATGGTG
* *
38178112 AAATTGAAAATGAAAAATGAA
1 AAATGGAAAAAGAAAAATGAA
*
38178133 AAATGGAAAAAGTAAAATG
1 AAATGGAAAAAGAAAAATG
38178152 GAGAGGCTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.17, T:0.17
Consensus pattern (21 bp):
AAATGGAAAAAGAAAAATGAA
Found at i:38179408 original size:44 final size:44
Alignment explanation
Indices: 38178963--38179399 Score: 700
Period size: 44 Copynumber: 9.9 Consensus size: 44
38178953 AAAAGTAGCA
* *
38178963 GATCTTGTCTTCATGTATTGACATGAAATAGATCGAGGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
*
38179007 GATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAATG
*
38179051 GATCTTATCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
* *
38179095 GATCTTGTCTTCATGTATTGACATGAAATAGATCAGAA-ATAGTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATC-GAAGATAATG
*
38179139 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGACAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
* * *
38179183 GATCTTGTCTTCATGTATTGACATGAAGTAAAT-TAGAGATAGTG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGA-AGATAATG
38179227 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
*
38179271 GATCTTGTCTTCATGTATTGACATGAAGTAAATCGAAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
* *
38179315 GATCTTGTCTTCATGTTTTGACATGAAGTAAATCGAAGATAATG
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
*
38179359 GATCTTGTCTTCATGTATTGACATGAAGTAGATCAAAGATA
1 GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATA
38179400 GCAAATCTTT
Statistics
Matches: 364, Mismatches: 23, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
43 5 0.01
44 354 0.97
45 5 0.01
ACGTcount: A:0.32, C:0.11, G:0.22, T:0.34
Consensus pattern (44 bp):
GATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAATG
Found at i:38180262 original size:20 final size:20
Alignment explanation
Indices: 38180239--38180276 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38180229 TTTCAATTTC
*
38180239 TTTTCTCGATTTTTTTTCCT
1 TTTTCTCGATTGTTTTTCCT
*
38180259 TTTTCTCTATTGTTTTTC
1 TTTTCTCGATTGTTTTTC
38180277 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.71
Consensus pattern (20 bp):
TTTTCTCGATTGTTTTTCCT
Found at i:38182852 original size:210 final size:208
Alignment explanation
Indices: 38182613--38183095 Score: 580
Period size: 210 Copynumber: 2.3 Consensus size: 208
38182603 TCTACAATAA
* * *
38182613 AAAATTATCTTTTTACTTTTGATGTGTCAATGGCCGACACCAGTATGCGAAAAAAGTTAAAAAAA
1 AAAATT-T-TTTTTACTTTTGGTGTGTCAATGGCCGACACCAGTATACGAAAAAAGTAAAAAAAA
* * * ******* *
38182678 AATTTTAGGGGGTGGCCTGGCAATGGCCGGCA-CCCCTTTATACACTTTTTTTTACTTTTGATTT
64 AATTTAAGGGGGTGGCCAGACAATGGCCGGCACCCCCTTTATACAAAAAAAATTACTTTTGATGT
* * * ** * *
38182742 GTCAATGTCTAGCACTAGTATACGAAAAAAGTAAAAAAAAAAAATTTGGTGGCC-TGTCAATGGT
129 GTCAATGGCTAGCACCAATATACGAAAAAAGTAAAAAAAAAAAA-GGGGTGGCCAAG-CAATGGC
38182806 TGGCACCCCCTTTATAC
192 TGGCACCCCCTTTATAC
38182823 AAAATTTTTTTTCTACTTTTGGTGTGTCAATGGCCGACACCAGTATACGAAAAAAGTAAAAAAAA
1 AAAA-TTTTTTT-TACTTTTGGTGTGTCAATGGCCGACACCAGTATACGAAAAAAGTAAAAAAAA
* * *
38182888 AATTTAAGGGGGTGGCCAGACAATGGCTGTCACCCCCTTTATACAAAAAAAATTACTTTTGGTGT
64 AATTTAAGGGGGTGGCCAGACAATGGCCGGCACCCCCTTTATACAAAAAAAATTACTTTTGATGT
* * **
38182953 GTTAATGGCTGGCACCAATATACGAAAAAAGTAAAAAAAAATTAGGGGTGGCCAAGCAATGGCTG
129 GTCAATGGCTAGCACCAATATACGAAAAAAGTAAAAAAAAAAAAGGGGTGGCCAAGCAATGGCTG
38183018 GCACCCCCTTTATAC
194 GCACCCCCTTTATAC
*** * *
38183033 AAAA---AAATTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAA
1 AAAATTTTTTTTACTTTTGGTGTGTCAATGGCCGACACCAGTATACGAAAAAAGTAAAAAAAAAA
38183095 T
66 T
38183096 ACTTTTTGTG
Statistics
Matches: 236, Mismatches: 33, Indels: 13
0.84 0.12 0.05
Matches are distributed among these distances:
205 53 0.22
206 1 0.00
209 4 0.02
210 115 0.49
211 63 0.27
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (208 bp):
AAAATTTTTTTTACTTTTGGTGTGTCAATGGCCGACACCAGTATACGAAAAAAGTAAAAAAAAAA
TTTAAGGGGGTGGCCAGACAATGGCCGGCACCCCCTTTATACAAAAAAAATTACTTTTGATGTGT
CAATGGCTAGCACCAATATACGAAAAAAGTAAAAAAAAAAAAGGGGTGGCCAAGCAATGGCTGGC
ACCCCCTTTATAC
Found at i:38182992 original size:54 final size:54
Alignment explanation
Indices: 38182932--38183146 Score: 171
Period size: 54 Copynumber: 4.1 Consensus size: 54
38182922 CCCTTTATAC
* *
38182932 AAAAAAAATTACTTTTGGTGTGTTAATGGCTGGCACCAATATACGAAAAAAGTA
1 AAAAAAAATTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTA
**** *** ** * * *
38182986 AAAAAAAATTAGGGGTGGCCAAG-CAATGGCTGGCACCCCCT-T-----TATA-CA
1 AAAAAAAATTACTTTTGG-TGTGTCAATGGCTGGCA-CCAGTATACGAAAAAAGTA
38183034 AA-AAAA-TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTA
1 AAAAAAAATTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTA
* * * * *
38183086 AAAAAAAAATACTTTTTGTGTGTCAATGGCCGACACCAGTATACGAAACAAGTA
1 AAAAAAAATTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTA
38183140 AAAAAAA
1 AAAAAAA
38183147 TTGTATAAAG
Statistics
Matches: 119, Mismatches: 30, Indels: 24
0.69 0.17 0.14
Matches are distributed among these distances:
45 4 0.03
46 19 0.16
47 4 0.03
48 3 0.03
49 2 0.02
51 2 0.02
52 3 0.03
53 4 0.03
54 74 0.62
55 4 0.03
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (54 bp):
AAAAAAAATTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTA
Found at i:38183094 original size:101 final size:102
Alignment explanation
Indices: 38182625--38183095 Score: 493
Period size: 101 Copynumber: 4.5 Consensus size: 102
38182615 AATTATCTTT
* * * * *
38182625 TTACTTTTGATGTGTCAATGGCCGACACCAGTATGCGAAAAAAGTTAAAAAAAAATTTTAGGGGG
1 TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAG-TAAAAAAAAA-ATTAGGGGG
* * * ******
38182690 TGGCCTGGCAATGGCCGGCA-CCCCTTTATACACTTTTTT
64 TGGCCAGACAATGGCTGGCACCCCCTTTATACA-AAAAAA
* * * * * * ***
38182729 TTACTTTTGATTTGTCAATGTCTAGCACTAGTATACGAAAAAAGTAAAAAAAAAA-AATTTGGTG
1 TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAATTAGGGGGTG
* * * ***
38182793 GCCTGTCAATGGTTGGCACCCCCTTTATACAAAATTTTTTT
66 GCCAGACAATGGCTGGCACCCCCTTTATACAAAA----AAA
* *
38182834 TCTACTTTTGGTGTGTCAATGGCCGACACCAGTATACGAAAAAAGTAAAAAAAAAATTTAAGGGG
1 T-TACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAA-TT-AGGGG
*
38182899 GTGGCCAGACAATGGCTGTCACCCCCTTTATACAAAAAAAA
63 GTGGCCAGACAATGGCTGGCACCCCCTTTATAC-AAAAAAA
* *
38182940 TTACTTTTGGTGTGTTAATGGCTGGCACCAATATACGAAAAAAGT-AAAAAAAAATTA-GGGGTG
1 TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAATTAGGGGGTG
38183003 GCCA-AGCAATGGCTGGCACCCCCTTTATACAAAAAAA
66 GCCAGA-CAATGGCTGGCACCCCCTTTATACAAAAAAA
38183040 TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAAT
1 TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAAT
38183096 ACTTTTTGTG
Statistics
Matches: 312, Mismatches: 43, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
100 51 0.16
101 63 0.20
102 13 0.04
103 12 0.04
104 46 0.15
105 44 0.14
106 48 0.15
109 31 0.10
110 4 0.01
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.28
Consensus pattern (102 bp):
TTACTTTTGGTGTGTCAATGGCTGGCACCAGTATACGAAAAAAGTAAAAAAAAAATTAGGGGGTG
GCCAGACAATGGCTGGCACCCCCTTTATACAAAAAAA
Found at i:38184946 original size:19 final size:19
Alignment explanation
Indices: 38184882--38184978 Score: 62
Period size: 19 Copynumber: 5.3 Consensus size: 19
38184872 CCAAAATTAT
38184882 TATTTTAAACTTTTT-T-TA
1 TATTTTAAA-TTTTTATATA
*
38184900 AATTTTAAATTTTTATATA
1 TATTTTAAATTTTTATATA
**
38184919 TATACTAAATTTTTATA-A
1 TATTTTAAATTTTTATATA
* **
38184937 TTTTTTTAAAAATTTA-A-A
1 -TATTTTAAATTTTTATATA
* *
38184955 -ATTTAAAATTTTTATAAA
1 TATTTTAAATTTTTATATA
38184973 TATTTT
1 TATTTT
38184979 GAATCTTAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
16 10 0.17
17 6 0.10
18 13 0.22
19 30 0.51
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTAAATTTTTATATA
Found at i:38187416 original size:3 final size:3
Alignment explanation
Indices: 38187402--38187447 Score: 74
Period size: 3 Copynumber: 15.3 Consensus size: 3
38187392 CAAATGAGTA
* *
38187402 AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38187448 CAAAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:38190414 original size:12 final size:12
Alignment explanation
Indices: 38190377--38190418 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 12
38190367 AATTTTTTAA
*
38190377 TTTTAAAA-TAT
1 TTTTAAAATTTT
38190388 TTTTAAAATACTTT
1 TTTTAAAAT--TTT
38190402 TTTTAAAATTTT
1 TTTTAAAATTTT
38190414 TTTTA
1 TTTTA
38190419 TTTTTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 8 0.30
12 8 0.30
14 11 0.41
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
TTTTAAAATTTT
Found at i:38197176 original size:32 final size:32
Alignment explanation
Indices: 38197139--38197203 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
38197129 TTTAAATATA
* *
38197139 GTTACTAGGTATGGAACAACTTTAAAACTTAT
1 GTTACTAAGTATGAAACAACTTTAAAACTTAT
*
38197171 GTTACTAAGTATGAAACAATTTTAAAACTTAT
1 GTTACTAAGTATGAAACAACTTTAAAACTTAT
38197203 G
1 G
38197204 GCCAGCATCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (32 bp):
GTTACTAAGTATGAAACAACTTTAAAACTTAT
Found at i:38197234 original size:45 final size:45
Alignment explanation
Indices: 38197168--38197260 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 45
38197158 CTTTAAAACT
*
38197168 TATGTTACTAAGTATGAAACAATTTTAAAACTTATGGCCAGCATC
1 TATGTTACTAAGTATGAAACAACTTTAAAACTTATGGCCAGCATC
* *
38197213 TATGTTACTGAGTATGGAACAACTTTAAAACTTATGGCCAGCATC
1 TATGTTACTAAGTATGAAACAACTTTAAAACTTATGGCCAGCATC
38197258 TAT
1 TAT
38197261 CCCTAACCTA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (45 bp):
TATGTTACTAAGTATGAAACAACTTTAAAACTTATGGCCAGCATC
Found at i:38202122 original size:16 final size:16
Alignment explanation
Indices: 38202101--38202171 Score: 88
Period size: 16 Copynumber: 4.4 Consensus size: 16
38202091 GTTTGGTTCA
38202101 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
**
38202117 CTGTAATTAAATAGAG
1 CTGTAATGGAATAGAG
* *
38202133 TTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
*
38202149 CTGTAATGGAATAAAG
1 CTGTAATGGAATAGAG
*
38202165 TTGTAAT
1 CTGTAAT
38202172 CAGTAATTCA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:38202145 original size:32 final size:32
Alignment explanation
Indices: 38202102--38202171 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
38202092 TTTGGTTCAC
* *
38202102 TGTAATGGAATAGAGCTGTAATTAAATAGAGT
1 TGTAATGGAATAGAGCTGTAATGAAATAAAGT
* *
38202134 TGTAATTGAATAGAGCTGTAATGGAATAAAGT
1 TGTAATGGAATAGAGCTGTAATGAAATAAAGT
38202166 TGTAAT
1 TGTAAT
38202172 CAGTAATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (32 bp):
TGTAATGGAATAGAGCTGTAATGAAATAAAGT
Found at i:38202255 original size:39 final size:40
Alignment explanation
Indices: 38202153--38202258 Score: 99
Period size: 44 Copynumber: 2.5 Consensus size: 40
38202143 ATAGAGCTGT
* *
38202153 AATGGAATAAAGTTGTAATCAGTAATTCAATTGTTTGGTTG
1 AATGGAATGATGTTGTAAT-AGTAATTCAATTGTTTGGTTG
* *
38202194 AATGGAATGGAATAGAACTGTAATAGT-ATTC-TTGTGTTTGGTTG
1 AATGGAAT-G-AT-G--TTGTAATAGTAATTCAAT-TGTTTGGTTG
38202238 AATGGAATGATGTTGTAATAG
1 AATGGAATGATGTTGTAATAG
38202259 CATAAGGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
39 8 0.15
41 9 0.17
42 2 0.04
43 3 0.06
44 23 0.43
45 3 0.06
46 6 0.11
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (40 bp):
AATGGAATGATGTTGTAATAGTAATTCAATTGTTTGGTTG
Found at i:38202467 original size:58 final size:58
Alignment explanation
Indices: 38202333--38202471 Score: 174
Period size: 58 Copynumber: 2.4 Consensus size: 58
38202323 TGTTATTATT
* *
38202333 AAATTTTAAGA-AGATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATC
1 AAATTTTAACATA-ATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATA
* * *
38202391 ATATTTTAACATAATTATTATTAAATATAATTTAAT-AAAATAATATATAATTTAATA
1 AAATTTTAACATAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATA
** *
38202448 AAATTCTTAATGTATTTATTATTA
1 AAATT-TTAACATAATTATTATTA
38202472 TATGAATTAA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
57 23 0.33
58 46 0.66
59 1 0.01
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (58 bp):
AAATTTTAACATAATTATTATTAAAAATAATTTAATAAAAATAATAAATAATTTAATA
Found at i:38210916 original size:23 final size:24
Alignment explanation
Indices: 38210880--38210935 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 24
38210870 TTTTTTTGAG
*
38210880 TAATTTGTGAGTTTAGATTTAAA-TAA
1 TAATTT-T-AGTTT-GAATTAAATTAA
38210906 -AATTTTAGTTTGAATTAAATTAA
1 TAATTTTAGTTTGAATTAAATTAA
38210929 TAATTTT
1 TAATTTT
38210936 TCAATTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.26
23 8 0.30
24 7 0.26
25 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (24 bp):
TAATTTTAGTTTGAATTAAATTAA
Found at i:38213316 original size:18 final size:18
Alignment explanation
Indices: 38213281--38213314 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
38213271 TAATAATTAA
38213281 ATTTAAAATTTTATAAAT
1 ATTTAAAATTTTATAAAT
38213299 ATTTAAAA-TTTATAAA
1 ATTTAAAATTTTATAAA
38213315 ATCAATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATTTAAAATTTTATAAAT
Found at i:38215201 original size:45 final size:45
Alignment explanation
Indices: 38215150--38215246 Score: 106
Period size: 45 Copynumber: 2.1 Consensus size: 45
38215140 CCTGCAAATA
* * **
38215150 TGTTGTGCA-TCTATAGCCTAGTAGAAAATTTTATCTTTGATATTT
1 TGTTGTGCATTC-ACAGCCCAGTAGAAAATTTTATCTGCGATATTT
* * *
38215195 TGTTGTGTATTCACAGCCCAGTGGAAGATTTTATCTGCGATATTT
1 TGTTGTGCATTCACAGCCCAGTAGAAAATTTTATCTGCGATATTT
38215240 TGCTTGT
1 TG-TTGT
38215247 TGACACCATT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
45 37 0.86
46 6 0.14
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (45 bp):
TGTTGTGCATTCACAGCCCAGTAGAAAATTTTATCTGCGATATTT
Found at i:38216552 original size:3 final size:3
Alignment explanation
Indices: 38216499--38216532 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
38216489 CAAGACATAG
*
38216499 ATA ATA ATA ATA ATA ATA ATC ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38216533 GTTATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38218195 original size:49 final size:48
Alignment explanation
Indices: 38218120--38218382 Score: 202
Period size: 49 Copynumber: 5.6 Consensus size: 48
38218110 GCAATGTCGG
* * *
38218120 GGAAGTGAGACTCGCTGTTGTAGCTTCAATCTGTTCTGCTGCATCGCCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCG-CT
* * * * * *
38218169 GGAATTAAGATTCGCCATTGTGGCTTCGAT-T-TAT-TGC--AAT-G-G
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGT-TCTGCTGCATCGCT
* * *
38218211 GGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCGC-T
* * * * **** *
38218260 GGAAGTAAGATTCACCGTTGTGGCTTCGATCTTTTAAATTGCAAT-G-G
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGC-ATCGCT
* *
38218307 GGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCGCCT
1 GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCG-CT
*
38218356 GGAAGTAAGATTCGCCATTGTAGCTTC
1 GGAAGTAAGATTCGCCGTTGTAGCTTC
38218383 GATATTTTAA
Statistics
Matches: 158, Mismatches: 43, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
42 24 0.15
43 2 0.01
44 4 0.03
45 2 0.01
46 4 0.03
47 38 0.24
48 2 0.01
49 80 0.51
50 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.26, T:0.32
Consensus pattern (48 bp):
GGAAGTAAGATTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCGCT
Found at i:38218337 original size:96 final size:95
Alignment explanation
Indices: 38218019--38218400 Score: 484
Period size: 96 Copynumber: 4.0 Consensus size: 95
38218009 ACTGCAATGT
* * * * * * * ** * *
38218019 TGGGGAAGCGAGATTCGCCATCGTAGCTTCAATCTGTTCCACTACACCGCAAGGAAATGAGATTC
1 TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTC
* * *
38218084 GCCGTTATGGCTTCAATCTTTTAATTGCAA
66 GCCATTGTGGCTTCGATCTTTTAATTGCAA
* * *
38218114 TGTCGGGGAAGTGAGACTCGCTGTTGTAGCTTCAATCTGTTCTGCTGCATCGCCTGGAATTAAGA
1 --T-GGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGA
38218179 TTCGCCATTGTGGCTTCGA---TTT-ATTGCAA
63 TTCGCCATTGTGGCTTCGATCTTTTAATTGCAA
*
38218208 TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGATTC
1 TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTC
* *
38218273 ACCGTTGTGGCTTCGATCTTTTAAATTGCAA
66 GCCATTGTGGCTTCGATCTTTT-AATTGCAA
*
38218304 TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCTGCTGCATCGCCTGGAAGTAAGATTC
1 TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTC
* *
38218369 GCCATTGTAGCTTCGATATTTTAAATTGCAA
66 GCCATTGTGGCTTCGATCTTTT-AATTGCAA
38218400 T
1 T
38218401 CTATGGTTAC
Statistics
Matches: 251, Mismatches: 28, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
91 74 0.29
92 1 0.00
94 10 0.04
95 3 0.01
96 98 0.39
97 1 0.00
98 64 0.25
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (95 bp):
TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCCTGGAAGTAAGATTC
GCCATTGTGGCTTCGATCTTTTAATTGCAA
Found at i:38218347 original size:187 final size:188
Alignment explanation
Indices: 38218019--38218385 Score: 549
Period size: 187 Copynumber: 2.0 Consensus size: 188
38218009 ACTGCAATGT
* *
38218019 TGGGGAAGCGAGATTCGCCATCGTAGCTTCAATCTGTTCCACTACACCGCAAGGAAATGAGATTC
1 TGGGGAAGCGAGACTCGCCATCGTAGCTTCAATCTGTTCCACTACACCGCAAGGAAATAAGATTC
* *
38218084 GCCGTTATGGCTTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGACTCGCTGTTGTAGCTTCAA
66 ACCGTTATGGCTTCAATCTTTTAATTGCAA-GTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAA
* *
38218149 TCTGTTCTGCTGCATCGCCTGGAATTAAGATTCGCCATTGTGGCTTCGATTTATTGCAA
130 TCTGTTCTGCTGCATCGCCTGGAAGTAAGATTCGCCATTGTAGCTTCGATTTATTGCAA
* * * * * * ** *
38218208 TGGGGAAGTGAGACTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCATCGCTTGGAAGTAAGATTC
1 TGGGGAAGCGAGACTCGCCATCGTAGCTTCAATCTGTTCCACTACACCGCAAGGAAATAAGATTC
* *
38218273 ACCGTTGTGGCTTCGATCTTTTAAATTGCAA-T-GGGGAAGTGAGACTCGCCGTTGTAGCTTCAA
66 ACCGTTATGGCTTCAATCTTTT-AATTGCAAGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAA
38218336 TCTGTTCTGCTGCATCGCCTGGAAGTAAGATTCGCCATTGTAGCTTCGAT
130 TCTGTTCTGCTGCATCGCCTGGAAGTAAGATTCGCCATTGTAGCTTCGAT
38218386 ATTTTAAATT
Statistics
Matches: 160, Mismatches: 17, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
187 78 0.49
188 1 0.01
189 73 0.46
190 8 0.05
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (188 bp):
TGGGGAAGCGAGACTCGCCATCGTAGCTTCAATCTGTTCCACTACACCGCAAGGAAATAAGATTC
ACCGTTATGGCTTCAATCTTTTAATTGCAAGTCGGGGAAGTGAGACTCGCCGTTGTAGCTTCAAT
CTGTTCTGCTGCATCGCCTGGAAGTAAGATTCGCCATTGTAGCTTCGATTTATTGCAA
Found at i:38231079 original size:3 final size:3
Alignment explanation
Indices: 38231026--38231059 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
38231016 CAAGACATAG
*
38231026 ATA ATA ATA ATA ATC ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
38231060 CTTATTAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:38231858 original size:5 final size:5
Alignment explanation
Indices: 38231850--38231881 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
38231840 GTAAAAGAAA
38231850 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
38231882 CAAGAAACGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:38234459 original size:23 final size:23
Alignment explanation
Indices: 38234419--38234466 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
38234409 ATCAAAGTCA
*
38234419 AATATATTATGCTAATAAATGCT
1 AATATATTATGCTAATAAATACT
*
38234442 AATATATTAT-CTTCATAAATACT
1 AATATATTATGC-TAATAAATACT
38234465 AA
1 AA
38234467 ATCTTCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (23 bp):
AATATATTATGCTAATAAATACT
Found at i:38238657 original size:24 final size:25
Alignment explanation
Indices: 38238605--38238657 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
38238595 CTTGAAAACT
* *
38238605 TAATCTTTTTAAAAATATTTATGAA
1 TAATGTTTTTAAAAATATTTATAAA
38238630 -AATGTTTTT-AAAAT-TTTATCAAA
1 TAATGTTTTTAAAAATATTTAT-AAA
38238653 TAATG
1 TAATG
38238658 CTGAAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 5 0.21
23 7 0.29
24 12 0.50
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (25 bp):
TAATGTTTTTAAAAATATTTATAAA
Found at i:38240048 original size:21 final size:22
Alignment explanation
Indices: 38240012--38240052 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38240002 TAGTTTTTAA
38240012 TAATAAAAATTGATAAATTTTT
1 TAATAAAAATTGATAAATTTTT
*
38240034 TAATAGAAA-TGATAAATTT
1 TAATAAAAATTGATAAATTT
38240053 ACTCTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (22 bp):
TAATAAAAATTGATAAATTTTT
Found at i:38241018 original size:22 final size:22
Alignment explanation
Indices: 38240990--38241035 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
38240980 TTTTTACGTT
*
38240990 AAAAAATAATTA-AATATCGTAA
1 AAAAAATAATAAGAATAT-GTAA
*
38241012 AAAAAATGATAAGAATATGTAA
1 AAAAAATAATAAGAATATGTAA
38241034 AA
1 AA
38241036 CTACTATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (22 bp):
AAAAAATAATAAGAATATGTAA
Found at i:38242844 original size:20 final size:20
Alignment explanation
Indices: 38242821--38242867 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
38242811 ACATACTATT
*
38242821 ACTGTTCACAACATGGCCCC
1 ACTGTTCACAACATGACCCC
** *
38242841 ACTGTTCATGACTTGACCCC
1 ACTGTTCACAACATGACCCC
38242861 ACTGTTC
1 ACTGTTC
38242868 CTAGGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (20 bp):
ACTGTTCACAACATGACCCC
Found at i:38256060 original size:7 final size:7
Alignment explanation
Indices: 38256048--38256074 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
38256038 GAACTAGTTG
38256048 GATCACC
1 GATCACC
38256055 GATCACC
1 GATCACC
38256062 GATCACC
1 GATCACC
38256069 GATCAC
1 GATCAC
38256075 TGATTCTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.41, G:0.15, T:0.15
Consensus pattern (7 bp):
GATCACC
Found at i:38258217 original size:33 final size:31
Alignment explanation
Indices: 38258154--38258217 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
38258144 AAATGTTACG
* *
38258154 TTTTAGTCACTTACGTTAATGTGTTGTAACA
1 TTTTAGTCACTAACGTTAATGTATTGTAACA
38258185 TTTTAGTCACTAAGCCGTTAAT-TATTGTTAACA
1 TTTTAGTCACTAA--CGTTAATGTATTG-TAACA
38258218 ATGTAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 12 0.43
32 4 0.14
33 12 0.43
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (31 bp):
TTTTAGTCACTAACGTTAATGTATTGTAACA
Found at i:38258608 original size:8 final size:9
Alignment explanation
Indices: 38258594--38258641 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
38258584 AAGAGAATGA
38258594 AAAAAAAAG
1 AAAAAAAAG
38258603 AAAAAAAAG
1 AAAAAAAAG
38258612 AAAAGCTAAAAG
1 AAAA---AAAAG
*
38258624 AACATAAAAG
1 AA-AAAAAAG
38258634 AAAAAAAA
1 AAAAAAAA
38258642 TTACTCAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 18 0.55
10 7 0.21
12 7 0.21
13 1 0.03
ACGTcount: A:0.81, C:0.04, G:0.10, T:0.04
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:38260337 original size:20 final size:20
Alignment explanation
Indices: 38260312--38260357 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
38260302 TAGTAAAGCT
* *
38260312 TAACAATCTATTTAAATAAG
1 TAACAACCTATTTAAATAAA
*
38260332 TAACAACCTATTTGAATAAA
1 TAACAACCTATTTAAATAAA
38260352 TAACAA
1 TAACAA
38260358 AATATTAGCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (20 bp):
TAACAACCTATTTAAATAAA
Found at i:38260363 original size:20 final size:20
Alignment explanation
Indices: 38260320--38260363 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
38260310 CTTAACAATC
* **
38260320 TATTTAAATAAGTAACAACC
1 TATTTAAATAAATAACAAAA
*
38260340 TATTTGAATAAATAACAAAA
1 TATTTAAATAAATAACAAAA
38260360 TATT
1 TATT
38260364 AGCAGATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (20 bp):
TATTTAAATAAATAACAAAA
Found at i:38264229 original size:20 final size:20
Alignment explanation
Indices: 38264204--38264249 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
38264194 TAGTAAAGCT
*
38264204 TAACAACCTATTTAAATAAG
1 TAACAACCTATTTAAATAAA
*
38264224 TAACAACCTATTTGAATAAA
1 TAACAACCTATTTAAATAAA
38264244 TAACAA
1 TAACAA
38264250 AATATTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.52, C:0.15, G:0.04, T:0.28
Consensus pattern (20 bp):
TAACAACCTATTTAAATAAA
Found at i:38264255 original size:20 final size:20
Alignment explanation
Indices: 38264212--38264255 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
38264202 CTTAACAACC
* **
38264212 TATTTAAATAAGTAACAACC
1 TATTTAAATAAATAACAAAA
*
38264232 TATTTGAATAAATAACAAAA
1 TATTTAAATAAATAACAAAA
38264252 TATT
1 TATT
38264256 AACAGATTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.09, G:0.05, T:0.34
Consensus pattern (20 bp):
TATTTAAATAAATAACAAAA
Found at i:38264918 original size:226 final size:226
Alignment explanation
Indices: 38264524--38264975 Score: 904
Period size: 226 Copynumber: 2.0 Consensus size: 226
38264514 GAGACTTGTC
38264524 GGTGCTTTAAAAGCTTGAACATGAAGAAGAAAAAAGAAGGAACATATACTTTATTGTGTTATATA
1 GGTGCTTTAAAAGCTTGAACATGAAGAAGAAAAAAGAAGGAACATATACTTTATTGTGTTATATA
38264589 TGGTTTTTGTTTAAGGCTAGTGGCATATTTTTTAAGACACCTTAATCATGCTTGTTCAAGTTCAT
66 TGGTTTTTGTTTAAGGCTAGTGGCATATTTTTTAAGACACCTTAATCATGCTTGTTCAAGTTCAT
38264654 TAATTGAATAATAAGGATGATTATTTTTGCTTTAAGCACGTTTATTAATGGATAATGACAAAAAC
131 TAATTGAATAATAAGGATGATTATTTTTGCTTTAAGCACGTTTATTAATGGATAATGACAAAAAC
38264719 CCTTTGCTAAATCAAGTTGGAAAATATAGGA
196 CCTTTGCTAAATCAAGTTGGAAAATATAGGA
38264750 GGTGCTTTAAAAGCTTGAACATGAAGAAGAAAAAAGAAGGAACATATACTTTATTGTGTTATATA
1 GGTGCTTTAAAAGCTTGAACATGAAGAAGAAAAAAGAAGGAACATATACTTTATTGTGTTATATA
38264815 TGGTTTTTGTTTAAGGCTAGTGGCATATTTTTTAAGACACCTTAATCATGCTTGTTCAAGTTCAT
66 TGGTTTTTGTTTAAGGCTAGTGGCATATTTTTTAAGACACCTTAATCATGCTTGTTCAAGTTCAT
38264880 TAATTGAATAATAAGGATGATTATTTTTGCTTTAAGCACGTTTATTAATGGATAATGACAAAAAC
131 TAATTGAATAATAAGGATGATTATTTTTGCTTTAAGCACGTTTATTAATGGATAATGACAAAAAC
38264945 CCTTTGCTAAATCAAGTTGGAAAATATAGGA
196 CCTTTGCTAAATCAAGTTGGAAAATATAGGA
38264976 TTTATTATAA
Statistics
Matches: 226, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
226 226 1.00
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.36
Consensus pattern (226 bp):
GGTGCTTTAAAAGCTTGAACATGAAGAAGAAAAAAGAAGGAACATATACTTTATTGTGTTATATA
TGGTTTTTGTTTAAGGCTAGTGGCATATTTTTTAAGACACCTTAATCATGCTTGTTCAAGTTCAT
TAATTGAATAATAAGGATGATTATTTTTGCTTTAAGCACGTTTATTAATGGATAATGACAAAAAC
CCTTTGCTAAATCAAGTTGGAAAATATAGGA
Found at i:38270126 original size:6 final size:6
Alignment explanation
Indices: 38270115--38270144 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
38270105 TTTTATTTGG
38270115 ATGGCT ATGGCT ATGGCT ATGGCT ATGGCT
1 ATGGCT ATGGCT ATGGCT ATGGCT ATGGCT
38270145 GTAATGGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (6 bp):
ATGGCT
Found at i:38272898 original size:20 final size:19
Alignment explanation
Indices: 38272837--38272901 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
38272827 TATAAAAAAA
*
38272837 TAAAAATCAATAAAATTTA-
1 TAAAAAT-ATTAAAATTTAT
* *
38272856 TAAATATTATTAAATTTTAAT
1 TAAA-AATATTAAAATTT-AT
38272877 TAAAAATATTAAAAATTTAT
1 TAAAAATATT-AAAATTTAT
38272897 TAAAA
1 TAAAA
38272902 GTAGAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 12 0.32
20 15 0.41
21 10 0.27
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
TAAAAATATTAAAATTTAT
Found at i:38272944 original size:9 final size:9
Alignment explanation
Indices: 38272821--38272957 Score: 71
Period size: 9 Copynumber: 14.4 Consensus size: 9
38272811 ACATGTAACA
38272821 AAAAATTAT
1 AAAAATTAT
*
38272830 AAAAA-AAT
1 AAAAATTAT
*
38272838 AAAAATCAAT
1 AAAAAT-TAT
*
38272848 AAAATTTAT
1 AAAAATTAT
*
38272857 AAATATTATT
1 AAAAATTA-T
**
38272867 AAATTTTAATT
1 AAAAATT-A-T
38272878 AAAAA-TATT
1 AAAAATTA-T
38272887 AAAAATTTAT
1 AAAAA-TTAT
* * *
38272897 TAAAAGTAG
1 AAAAATTAT
*
38272906 AAAAAATAT
1 AAAAATTAT
38272915 AAAAATTAT
1 AAAAATTAT
*
38272924 AAAATTTTAT
1 AAAA-ATTAT
*
38272934 AAAAATCATAA
1 AAAAAT--TAT
38272945 AAAAATTAT
1 AAAAATTAT
38272954 AAAA
1 AAAA
38272958 TGCATCAAAA
Statistics
Matches: 100, Mismatches: 19, Indels: 18
0.73 0.14 0.13
Matches are distributed among these distances:
8 7 0.07
9 48 0.48
10 29 0.29
11 16 0.16
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:38272968 original size:20 final size:20
Alignment explanation
Indices: 38272906--38272957 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
38272896 TTAAAAGTAG
*
38272906 AAAAAA-TATAAAAATTAT-
1 AAAAAATTATAAAAATCATA
**
38272924 AAAATTTTATAAAAATCATA
1 AAAAAATTATAAAAATCATA
38272944 AAAAAATTATAAAA
1 AAAAAATTATAAAA
38272958 TGCATCAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 4 0.15
19 11 0.41
20 12 0.44
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAATTATAAAAATCATA
Found at i:38273154 original size:9 final size:9
Alignment explanation
Indices: 38273140--38273322 Score: 52
Period size: 9 Copynumber: 19.0 Consensus size: 9
38273130 TTAGTACAAA
38273140 AATTTTTAT
1 AATTTTTAT
38273149 AATTTTTTTAT
1 AA--TTTTTAT
*
38273160 AAATTTTAT
1 AATTTTTAT
* *
38273169 ATTTCTTTAC
1 AATT-TTTAT
*
38273179 ATTTTTTTAT
1 A-ATTTTTAT
38273189 AATTTTCT-T
1 AATTTT-TAT
**
38273198 ACAACTTTAT
1 A-ATTTTTAT
38273208 GGAA-TTTTAT
1 --AATTTTTAT
*
38273218 AATCTTTTTT
1 AAT-TTTTAT
*
38273228 ATATTTCTAT
1 A-ATTTTTAT
38273238 -ATATTTTAT
1 AAT-TTTTAT
38273247 -ATATTTTAT
1 AAT-TTTTAT
*
38273256 CATTTTTAAT
1 AATTTTT-AT
*
38273266 ATTTTTTAT
1 AATTTTTAT
38273275 -ATATTTTATT
1 AAT-TTTTA-T
* *
38273285 AAAATTTAAT
1 -AATTTTTAT
*
38273295 CATTTTTAT
1 AATTTTTAT
38273304 AATTTTTATT
1 AATTTTTA-T
*
38273314 GATTTTTAT
1 AATTTTTAT
38273323 TTTTTTATCT
Statistics
Matches: 131, Mismatches: 23, Indels: 40
0.68 0.12 0.21
Matches are distributed among these distances:
8 5 0.04
9 56 0.43
10 49 0.37
11 19 0.15
12 2 0.02
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (9 bp):
AATTTTTAT
Found at i:38273164 original size:12 final size:11
Alignment explanation
Indices: 38273142--38273194 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 11
38273132 AGTACAAAAA
38273142 TTTTTATAATT
1 TTTTTATAATT
38273153 TTTTTATAA--
1 TTTTTATAATT
*
38273162 ATTTTAT-ATT
1 TTTTTATAATT
* *
38273172 TCTTTA-CATT
1 TTTTTATAATT
38273182 TTTTTATAATT
1 TTTTTATAATT
38273193 TT
1 TT
38273195 CTTACAACTT
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
8 1 0.03
9 6 0.18
10 12 0.36
11 14 0.42
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:38273233 original size:19 final size:18
Alignment explanation
Indices: 38273211--38273283 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 18
38273201 ACTTTATGGA
* *
38273211 ATTTTATAATCTTTTTTAT
1 ATTTTAT-ATATTTTATAT
38273230 ATTTCTATATATTTTATAT
1 ATTT-TATATATTTTATAT
38273249 ATTTTATCAT-TTTTAATAT
1 ATTTTAT-ATATTTT-ATAT
*
38273268 TTTTTATATATTTTAT
1 ATTTTATATATTTTAT
38273284 TAAAATTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
18 11 0.23
19 33 0.70
20 3 0.06
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTATATATTTTATAT
Found at i:38273272 original size:28 final size:26
Alignment explanation
Indices: 38273224--38273283 Score: 84
Period size: 28 Copynumber: 2.2 Consensus size: 26
38273214 TTATAATCTT
38273224 TTTTATATTTCTATATATTTTATATA
1 TTTTATATTTCTATATATTTTATATA
* *
38273250 TTTTATCATTTTTAATATTTTTTATATA
1 TTTTAT-ATTTCT-ATATATTTTATATA
38273278 TTTTAT
1 TTTTAT
38273284 TAAAATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 6 0.20
27 5 0.17
28 19 0.63
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.68
Consensus pattern (26 bp):
TTTTATATTTCTATATATTTTATATA
Found at i:38273311 original size:19 final size:19
Alignment explanation
Indices: 38273210--38273322 Score: 60
Period size: 19 Copynumber: 6.0 Consensus size: 19
38273200 AACTTTATGG
*
38273210 AATTTTATAATCTTTTTTAT
1 AATTTT-TAATCATTTTTAT
*
38273230 -ATTTCT-AT-ATATTTTAT
1 AATTTTTAATCAT-TTTTAT
38273247 -ATATTTT-ATCATTTTTA-
1 AAT-TTTTAATCATTTTTAT
*
38273264 ATATTTTTTAT-ATATTTTATT
1 A-ATTTTTAATCAT-TTTTA-T
**
38273285 AAAATTTAATCATTTTTAT
1 AATTTTTAATCATTTTTAT
* *
38273304 AATTTTTATTGATTTTTAT
1 AATTTTTAATCATTTTTAT
38273323 TTTTTTATCT
Statistics
Matches: 73, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
16 1 0.01
17 10 0.14
18 17 0.23
19 31 0.42
20 11 0.15
21 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.65
Consensus pattern (19 bp):
AATTTTTAATCATTTTTAT
Found at i:38273323 original size:39 final size:39
Alignment explanation
Indices: 38273217--38273312 Score: 112
Period size: 37 Copynumber: 2.6 Consensus size: 39
38273207 TGGAATTTTA
* * *
38273217 TAATC-TTTTTTAT-ATTTCTATATATTTTA-T-ATATT
1 TAATCATTTTTAATAATTTTTATATATTTTATTAAAATT
* *
38273252 TTATCATTTTTAATATTTTTTATATATTTTATTAAAATT
1 TAATCATTTTTAATAATTTTTATATATTTTATTAAAATT
38273291 TAATCATTTTT-ATAATTTTTAT
1 TAATCATTTTTAATAATTTTTAT
38273313 TGATTTTTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 4 0.08
36 7 0.14
37 14 0.28
38 11 0.22
39 14 0.28
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (39 bp):
TAATCATTTTTAATAATTTTTATATATTTTATTAAAATT
Found at i:38284698 original size:2 final size:2
Alignment explanation
Indices: 38284691--38284721 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38284681 TTGATACATT
38284691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38284722 CAGTGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38286120 original size:19 final size:20
Alignment explanation
Indices: 38286082--38286121 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
38286072 CGATGGTTTA
*
38286082 AATAATTTTTTTGAATAACTT
1 AATAATTATTTT-AATAACTT
38286103 AATAATTATTTT-ATAACTT
1 AATAATTATTTTAATAACTT
38286122 TTTAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (20 bp):
AATAATTATTTTAATAACTT
Found at i:38288791 original size:14 final size:14
Alignment explanation
Indices: 38288772--38288821 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
38288762 TGAATTAAAT
38288772 TAAAATTTCATATA
1 TAAAATTTCATATA
* *
38288786 TAAAATTTCACAAAA
1 TAAAATTTCA-TATA
38288801 TCAAAA-TTCATATA
1 T-AAAATTTCATATA
38288815 TAAAATT
1 TAAAATT
38288822 GAACATTAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 4 0.14
14 14 0.48
15 7 0.24
16 4 0.14
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (14 bp):
TAAAATTTCATATA
Found at i:38289122 original size:26 final size:23
Alignment explanation
Indices: 38289085--38289131 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
38289075 AAAGAAATTG
38289085 CAAAAAATAAATTACAAAAACTTT
1 CAAAAAATAAATT-CAAAAACTTT
*
38289109 CAAAGAAATAAAATTTAAAAACT
1 CAAA-AAAT-AAATTCAAAAACT
38289132 ATTTATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 4 0.20
25 11 0.55
26 5 0.25
ACGTcount: A:0.64, C:0.11, G:0.02, T:0.23
Consensus pattern (23 bp):
CAAAAAATAAATTCAAAAACTTT
Found at i:38290304 original size:20 final size:20
Alignment explanation
Indices: 38290279--38290316 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38290269 AAAGTGAAAT
*
38290279 ATTTAGGATAAATCAATGCA
1 ATTTAGGAGAAATCAATGCA
*
38290299 ATTTAGGAGGAATCAATG
1 ATTTAGGAGAAATCAATG
38290317 AAAGGATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.29
Consensus pattern (20 bp):
ATTTAGGAGAAATCAATGCA
Found at i:38301790 original size:14 final size:14
Alignment explanation
Indices: 38301771--38301801 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38301761 TGATTGTTTT
*
38301771 TAATCTAAATTTAC
1 TAATCTAAATTAAC
38301785 TAATCTAAATTAAC
1 TAATCTAAATTAAC
38301799 TAA
1 TAA
38301802 GAATGCAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATCTAAATTAAC
Found at i:38305725 original size:23 final size:22
Alignment explanation
Indices: 38305692--38305828 Score: 109
Period size: 23 Copynumber: 6.0 Consensus size: 22
38305682 ATATGTTGAA
38305692 AGGTATA-TTGGTTGTGTTTGG
1 AGGTATACTTGGTTGTGTTTGG
* **
38305713 AGGCTAGACTTGGTTGTGTTCAG
1 AGG-TATACTTGGTTGTGTTTGG
38305736 AGGTTATACATATGGTTGTGTTTGG
1 AGG-TATAC-T-TGGTTGTGTTTGG
* *
38305761 AAGGTATATTTGGTTGTGTTCGG
1 -AGGTATACTTGGTTGTGTTTGG
*
38305784 ATGGTACA-TATGGTTGTGTTTGG
1 A-GGTATACT-TGGTTGTGTTTGG
* *
38305807 AGGGTA-AATTGGTTATGTTTGG
1 A-GGTATACTTGGTTGTGTTTGG
38305829 TGGGTGATAG
Statistics
Matches: 95, Mismatches: 13, Indels: 15
0.77 0.11 0.12
Matches are distributed among these distances:
21 3 0.03
22 18 0.19
23 54 0.57
24 2 0.02
25 15 0.16
26 3 0.03
ACGTcount: A:0.18, C:0.04, G:0.35, T:0.42
Consensus pattern (22 bp):
AGGTATACTTGGTTGTGTTTGG
Found at i:38305774 original size:48 final size:45
Alignment explanation
Indices: 38305700--38305825 Score: 139
Period size: 48 Copynumber: 2.7 Consensus size: 45
38305690 AAAGGTATAT
*
38305700 TGGTTGTGTTTGG-AGGCTAGACTTGGTTGTGTTCAGA-GGTTATACATA
1 TGGTTGTGTTTGGAAGG-TA-AATTGGTTGTGTTCAGATGG---TACATA
* *
38305748 TGGTTGTGTTTGGAAGGTATATTTGGTTGTGTTCGGATGGTACATA
1 TGGTTGTGTTTGGAAGGTA-AATTGGTTGTGTTCAGATGGTACATA
* *
38305794 TGGTTGTGTTTGGAGGGTAAATTGGTTATGTT
1 TGGTTGTGTTTGGAAGGTAAATTGGTTGTGTT
38305826 TGGTGGGTGA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
45 11 0.16
46 24 0.34
48 30 0.43
49 5 0.07
ACGTcount: A:0.17, C:0.05, G:0.35, T:0.43
Consensus pattern (45 bp):
TGGTTGTGTTTGGAAGGTAAATTGGTTGTGTTCAGATGGTACATA
Found at i:38308987 original size:4 final size:4
Alignment explanation
Indices: 38308978--38309106 Score: 249
Period size: 4 Copynumber: 32.2 Consensus size: 4
38308968 AGATATTGAG
*
38308978 TACA TACA TACA TACA TACA TACA TATA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
38309026 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
38309074 TACA TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA T
38309107 GACTTCGTTA
Statistics
Matches: 123, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 123 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:38309195 original size:56 final size:56
Alignment explanation
Indices: 38309014--38309202 Score: 213
Period size: 56 Copynumber: 3.4 Consensus size: 56
38309004 TATACATACA
* * * * * *
38309014 TACATACATACATACATACATACATACATACATACAT-ACATAC-ATACATACATACA-
1 TACATACATACACACATACACACATACATACATACATGAC-TTCGTTAGATA-GTA-AG
* * *
38309070 TACATACATACATACATACATACATACATACATACATGACTTCGTTAGATAGTGAG
1 TACATACATACACACATACACACATACATACATACATGACTTCGTTAGATAGTAAG
* *
38309126 TACATACATACACACATACACACATACATATATACATGACTTCGTTAGATATTAAG
1 TACATACATACACACATACACACATACATACATACATGACTTCGTTAGATAGTAAG
* *
38309182 TACATACACACACACACACAC
1 TACATACATACACACATACAC
38309203 CCACACCCAC
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
55 1 0.01
56 110 0.93
57 7 0.06
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.25
Consensus pattern (56 bp):
TACATACATACACACATACACACATACATACATACATGACTTCGTTAGATAGTAAG
Found at i:38313491 original size:17 final size:18
Alignment explanation
Indices: 38313458--38313491 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38313448 AATAAATAAT
*
38313458 TTAAAATATATAAAATAC
1 TTAAAATATAAAAAATAC
38313476 TTAAAA-ATAAAAAATA
1 TTAAAATATAAAAAATA
38313492 AAAAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAATATAAAAAATAC
Found at i:38313971 original size:31 final size:30
Alignment explanation
Indices: 38313909--38313971 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
38313899 AAAAAAAAGC
* * * **
38313909 AATTTGACTTTTTTCAAAGGTTTATGGTCA
1 AATTTGACTTTTTTAAAAAGTTGATAATCA
38313939 AATTTGACTCTTTTTAAAAAGTTGATAATCA
1 AATTTGACT-TTTTTAAAAAGTTGATAATCA
38313970 AA
1 AA
38313972 GTTTAGCTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.43
Consensus pattern (30 bp):
AATTTGACTTTTTTAAAAAGTTGATAATCA
Found at i:38315783 original size:30 final size:32
Alignment explanation
Indices: 38315721--38315786 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
38315711 TACACTTATT
*
38315721 TTCACCTATGTCGAATGCATACACATAAATATA
1 TTCACCTATGCCGAATGCA-ACACATAAATATA
* *
38315754 TTCACCTATGCCGAATGCAACATATATATATA
1 TTCACCTATGCCGAATGCAACACATAAATATA
38315786 T
1 T
38315787 ACATATCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 12 0.40
33 18 0.60
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.32
Consensus pattern (32 bp):
TTCACCTATGCCGAATGCAACACATAAATATA
Found at i:38316144 original size:41 final size:43
Alignment explanation
Indices: 38316001--38316153 Score: 210
Period size: 41 Copynumber: 3.7 Consensus size: 43
38315991 ACCGGCTCTT
*
38316001 AGCCTGCTAGACTTATAGTCCG-A-AATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
*
38316042 AGCCTGCTAGACTTATAGCCTG-A-AATGTGTCACCGGCATTA
1 AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
*
38316083 AGCCTGCTAGACTTATAGTCTGAATAAT-T-TCACCGGCGTTA
1 AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
* * *
38316124 AGCCTGCTAGACGTAAAGTCTGAATTATGT
1 AGCCTGCTAGACTTATAGTCTGAATAATGT
38316154 CACTAACGAT
Statistics
Matches: 102, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
41 96 0.94
42 3 0.03
43 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (43 bp):
AGCCTGCTAGACTTATAGTCTGAATAATGTGTCACCGGCATTA
Found at i:38318453 original size:27 final size:27
Alignment explanation
Indices: 38318423--38318492 Score: 77
Period size: 28 Copynumber: 2.6 Consensus size: 27
38318413 GAGTCTTTTG
*
38318423 GGACAATAAACACGGATAAGTCCATCA
1 GGACAGTAAACACGGATAAGTCCATCA
* * * * *
38318450 GGACAGTTAACACGAGGTATGTTCATTA
1 GGACAGTAAACACG-GATAAGTCCATCA
38318478 GGACAGTAAACACGG
1 GGACAGTAAACACGG
38318493 GGTAAGTCTG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
27 13 0.37
28 22 0.63
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (27 bp):
GGACAGTAAACACGGATAAGTCCATCA
Found at i:38321886 original size:18 final size:18
Alignment explanation
Indices: 38321860--38321897 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
38321850 TAAATTTTAC
*
38321860 AATTTGAATAACTCAAAT
1 AATTCGAATAACTCAAAT
38321878 AATTCGAATAACTCAAAT
1 AATTCGAATAACTCAAAT
38321896 AA
1 AA
38321898 CAAATTGGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.13, G:0.05, T:0.29
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:38322006 original size:20 final size:22
Alignment explanation
Indices: 38321968--38322020 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
38321958 TCTCAGCAAA
*
38321968 AAAAATAT-AAAAATAATTT-T
1 AAAAATTTCAAAAATAATTTAT
38321988 CAAAAA-TTCAAAAAT-ATTTAT
1 -AAAAATTTCAAAAATAATTTAT
38322009 AAAAATTTCAAA
1 AAAAATTTCAAA
38322021 TTTTCATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (22 bp):
AAAAATTTCAAAAATAATTTAT
Found at i:38322930 original size:15 final size:17
Alignment explanation
Indices: 38322899--38322946 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
38322889 AACAAATAAT
38322899 TTAAAAATCATAAAATA
1 TTAAAAATCATAAAATA
38322916 TTAAAAAT-A-AAAATA
1 TTAAAAATCATAAAATA
* * *
38322931 ATAAAATTCAAAAAAT
1 TTAAAAATCATAAAAT
38322947 TATATAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 12 0.44
16 2 0.07
17 13 0.48
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAAAATCATAAAATA
Found at i:38322944 original size:23 final size:23
Alignment explanation
Indices: 38322900--38322946 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
38322890 ACAAATAATT
* *
38322900 TAAAAATCATAAAATATTAAAAA
1 TAAAAATAATAAAATATAAAAAA
38322923 TAAAAATAATAAAAT-TCAAAAAA
1 TAAAAATAATAAAATAT-AAAAAA
38322946 T
1 T
38322947 TATATAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 20 0.95
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (23 bp):
TAAAAATAATAAAATATAAAAAA
Found at i:38322964 original size:19 final size:17
Alignment explanation
Indices: 38322924--38322957 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38322914 TATTAAAAAT
38322924 AAAAATAATAAAATTCA
1 AAAAATAATAAAATTCA
*
38322941 AAAAATTATATAAATTC
1 AAAAATAATA-AAATTC
38322958 CATAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAATAAAATTCA
Found at i:38324523 original size:18 final size:19
Alignment explanation
Indices: 38324480--38324525 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
38324470 ACCTATATTT
38324480 TAAAAAAAAATAATTAAATA
1 TAAAAAAAAATAA-TAAATA
*
38324500 TGAAAAAGAAATAA-AAA-A
1 T-AAAAAAAAATAATAAATA
38324518 TAAAAAAA
1 TAAAAAAA
38324526 CTAATTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 3 0.13
20 1 0.04
21 11 0.48
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.17
Consensus pattern (19 bp):
TAAAAAAAAATAATAAATA
Found at i:38324524 original size:37 final size:38
Alignment explanation
Indices: 38324481--38324560 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
38324471 CCTATATTTT
**
38324481 AAAAAAAAATAATTAAATATGAA-AAAG-AAATAAAAA
1 AAAAAAAAATAATTAAATAAAAATAAAGAAAATAAAAA
* *
38324517 ATAAAAAAACTAATTAATTAAAAATAAAGAAAATAAAAA
1 A-AAAAAAAATAATTAAATAAAAATAAAGAAAATAAAAA
38324556 AAAAA
1 AAAAA
38324561 GCTAATTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
36 1 0.03
37 18 0.49
38 8 0.22
39 10 0.27
ACGTcount: A:0.78, C:0.01, G:0.04, T:0.17
Consensus pattern (38 bp):
AAAAAAAAATAATTAAATAAAAATAAAGAAAATAAAAA
Found at i:38325097 original size:21 final size:21
Alignment explanation
Indices: 38325062--38325135 Score: 111
Period size: 19 Copynumber: 3.7 Consensus size: 21
38325052 AATCACATCT
38325062 TCTAAGATT--ATATATCATA
1 TCTAAGATTGCATATATCATA
38325081 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
38325102 TCTAATATTGC--ATATCATA
1 TCTAAGATTGCATATATCATA
38325121 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
38325136 CCTCGAAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
19 27 0.55
21 22 0.45
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:38329917 original size:42 final size:42
Alignment explanation
Indices: 38329871--38329953 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
38329861 ATAAAAATAT
* *
38329871 ATTTTTA-AAATTTTATGTACTTTTAAT-ATTTTATAATTTTTC
1 ATTTTTATAAAATTTATATA-TTTT-ATGATTTTATAATTTTTC
38329913 ATTTTTATAAAATTTATATATTTTATGATTTTATAATTTTT
1 ATTTTTATAAAATTTATATATTTTATGATTTTATAATTTTT
38329954 TTTTAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 2 0.05
42 25 0.68
43 10 0.27
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (42 bp):
ATTTTTATAAAATTTATATATTTTATGATTTTATAATTTTTC
Found at i:38339929 original size:3 final size:3
Alignment explanation
Indices: 38339923--38339956 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38339913 ATATCAACAA
38339923 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
38339957 ATCATCATCA
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:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:38340572 original size:3 final size:3
Alignment explanation
Indices: 38340566--38340606 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
38340556 GAACTAACAG
38340566 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
38340607 AGGATACATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:38340876 original size:7 final size:7
Alignment explanation
Indices: 38340864--38340888 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
38340854 ATTATTGTTG
38340864 TTGTTCA
1 TTGTTCA
38340871 TTGTTCA
1 TTGTTCA
38340878 TTGTTCA
1 TTGTTCA
38340885 TTGT
1 TTGT
38340889 GGTGATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.60
Consensus pattern (7 bp):
TTGTTCA
Found at i:38340938 original size:2 final size:2
Alignment explanation
Indices: 38340931--38340955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38340921 TTGATTGATC
38340931 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
38340956 TTGATTCTTT
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:38345702 original size:6 final size:6
Alignment explanation
Indices: 38345691--38345715 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38345681 GGCGTTCTAC
38345691 GATGAA GATGAA GATGAA GATGAA G
1 GATGAA GATGAA GATGAA GATGAA G
38345716 TTCTCAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.36, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:38346285 original size:3 final size:3
Alignment explanation
Indices: 38346277--38346306 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
38346267 CCACACATGC
38346277 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38346307 AAGAAGATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38346361 original size:5 final size:5
Alignment explanation
Indices: 38346351--38346381 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
38346341 AATTGTATTT
38346351 TACAA TACAA TACAA TACAA TACAA TACAA T
1 TACAA TACAA TACAA TACAA TACAA TACAA T
38346382 GAATTATATC
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:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (5 bp):
TACAA
Found at i:38349713 original size:119 final size:120
Alignment explanation
Indices: 38349557--38349782 Score: 312
Period size: 121 Copynumber: 1.9 Consensus size: 120
38349547 GTAGTCGGAT
* * * * * *
38349557 TTTCTACATTTTTCATGTTTCGAGGTCATATCCGCATATCGATGT-TATA-TTAAACCTAGTAAC
1 TTTCTACATTTTTCATGTTTCAAAGCCATATCCGCATATCCATGTGTAGACTTAAACCCAGTAAC
* *
38349620 CTACTTGTAACCGTCAGATATGAGTATGGGTCTGAATATCATAATTTTTTCTACA
66 CTACTTGTAACCGTCAGATACGAGTATGGGTCCGAATATCATAATTTTTTCTACA
* *
38349675 TTTCTACATTTTTTCATGTTTCAAAGCCATATCTGCATATCCATGTGTCGACTTAAACCCAGTAA
1 TTTCTACA-TTTTTCATGTTTCAAAGCCATATCCGCATATCCATGTGTAGACTTAAACCCAGTAA
** *
38349740 CCTACTTGTAAGTGTCAGATACGAGTGTGGGTCCGAATATCAT
65 CCTACTTGTAACCGTCAGATACGAGTATGGGTCCGAATATCAT
38349783 CGGATTTTCG
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
118 8 0.09
119 32 0.35
120 2 0.02
121 50 0.54
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (120 bp):
TTTCTACATTTTTCATGTTTCAAAGCCATATCCGCATATCCATGTGTAGACTTAAACCCAGTAAC
CTACTTGTAACCGTCAGATACGAGTATGGGTCCGAATATCATAATTTTTTCTACA
Found at i:38360260 original size:14 final size:14
Alignment explanation
Indices: 38360238--38360267 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38360228 GTTACTCAAT
38360238 GTATAATAATAAGA
1 GTATAATAATAAGA
*
38360252 GTATTATAATAAGA
1 GTATAATAATAAGA
38360266 GT
1 GT
38360268 TAAAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (14 bp):
GTATAATAATAAGA
Found at i:38364871 original size:24 final size:24
Alignment explanation
Indices: 38364844--38364899 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
38364834 CCATATAACG
*
38364844 GGAAGCTCCAGAGAGCTATTAATA
1 GGAAGCTCCAAAGAGCTATTAATA
*
38364868 GGAAGCTCCAAAGAGCTATTAATG
1 GGAAGCTCCAAAGAGCTATTAATA
38364892 GGAAGCTC
1 GGAAGCTC
38364900 ATATGAGCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.20
Consensus pattern (24 bp):
GGAAGCTCCAAAGAGCTATTAATA
Found at i:38366261 original size:14 final size:14
Alignment explanation
Indices: 38366242--38366270 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38366232 TGTACTCGAT
38366242 AAAATTTTCTTCAC
1 AAAATTTTCTTCAC
38366256 AAAATTTTCTTCAC
1 AAAATTTTCTTCAC
38366270 A
1 A
38366271 GAATATACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATTTTCTTCAC
Found at i:38371480 original size:25 final size:25
Alignment explanation
Indices: 38371451--38371542 Score: 89
Period size: 25 Copynumber: 3.7 Consensus size: 25
38371441 TGTATATCGA
38371451 GAAGCTCATAAGAGCCATAAATTGG
1 GAAGCTCATAAGAGCCATAAATTGG
* * * *
38371476 AAAGCTCATACGAGCCA-ATTATCGG
1 GAAGCTCATAAGAGCCATA-AATTGG
*
38371501 GAAGCTCA-AGAGAGCCATTAATTGG
1 GAAGCTCATA-AGAGCCATAAATTGG
* *
38371526 GAAGCTCGTGAGAGCCA
1 GAAGCTCATAAGAGCCA
38371543 AATATCGATA
Statistics
Matches: 52, Mismatches: 11, Indels: 8
0.73 0.15 0.11
Matches are distributed among these distances:
24 2 0.04
25 50 0.96
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.18
Consensus pattern (25 bp):
GAAGCTCATAAGAGCCATAAATTGG
Found at i:38371499 original size:50 final size:50
Alignment explanation
Indices: 38371444--38371563 Score: 145
Period size: 50 Copynumber: 2.4 Consensus size: 50
38371434 ATCAAGTTGT
38371444 ATATCGAGAAGCTCATAAGAGCCATAAATTGGAAAGCTCAT-ACGAGCCAA
1 ATATCGAGAAGCTCATAAGAGCCATAAATTGGAAAGCTCATGA-GAGCCAA
* * * * *
38371494 TTATCGGGAAGCTCA-AGAGAGCCATTAATTGGGAAGCTCGTGAGAGCCAA
1 ATATCGAGAAGCTCATA-AGAGCCATAAATTGGAAAGCTCATGAGAGCCAA
* *
38371544 ATATCGATATGCTCATAAGA
1 ATATCGAGAAGCTCATAAGA
38371564 ACTATGGTGT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
49 1 0.02
50 55 0.95
51 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.21
Consensus pattern (50 bp):
ATATCGAGAAGCTCATAAGAGCCATAAATTGGAAAGCTCATGAGAGCCAA
Found at i:38376458 original size:28 final size:29
Alignment explanation
Indices: 38376393--38376459 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
38376383 CTCATATCAG
*
38376393 CCCAAAATTTTCATCTATTTTAAAATTCAA
1 CCCAAAATTTTCA-CTATTTCAAAATTCAA
* * *
38376423 CCCTAAATTTTCA-TATTTCACAATTTAA
1 CCCAAAATTTTCACTATTTCAAAATTCAA
*
38376451 TCCAAAATT
1 CCCAAAATT
38376460 GACATTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
28 19 0.61
30 12 0.39
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (29 bp):
CCCAAAATTTTCACTATTTCAAAATTCAA
Found at i:38377635 original size:18 final size:18
Alignment explanation
Indices: 38377582--38377635 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
38377572 ATTCACCTAA
* *
38377582 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAATT
*
38377601 ATCCAACCCAACCCAATT
1 ACCCAACCCAACCCAATT
38377619 ACCCAACCCAACCCAAT
1 ACCCAACCCAACCCAAT
38377636 CATAAAAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 26 0.84
19 5 0.16
ACGTcount: A:0.41, C:0.46, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAATT
Found at i:38386104 original size:14 final size:15
Alignment explanation
Indices: 38386072--38386111 Score: 52
Period size: 13 Copynumber: 2.9 Consensus size: 15
38386062 GAAACTCTAA
38386072 TTTCTCCTTTCTTTC
1 TTTCTCCTTTCTTTC
38386087 TTTC-CCTTT-TTTC
1 TTTCTCCTTTCTTTC
38386100 TTT-T-CTTTCTTT
1 TTTCTCCTTTCTTT
38386112 TTCTCCCTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.17
13 10 0.43
14 5 0.22
15 4 0.17
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTCTCCTTTCTTTC
Found at i:38386160 original size:20 final size:20
Alignment explanation
Indices: 38386125--38386168 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
38386115 TCCCTGTTTA
38386125 ATTTCTATTATGTTTCTTTCT
1 ATTTCTATTATGTTTCTTT-T
*
38386146 ATTTCT-TTTTGTTTCTTTT
1 ATTTCTATTATGTTTCTTTT
38386165 ATTT
1 ATTT
38386169 ATTATATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 11 0.50
21 6 0.27
ACGTcount: A:0.11, C:0.11, G:0.05, T:0.73
Consensus pattern (20 bp):
ATTTCTATTATGTTTCTTTT
Found at i:38386192 original size:5 final size:5
Alignment explanation
Indices: 38386184--38386363 Score: 342
Period size: 5 Copynumber: 35.8 Consensus size: 5
38386174 ATTTACTTAT
38386184 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
38386234 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
38386284 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*
38386334 TAAATA TATAA TATAA TATAA TATAA TATA
1 TATA-A TATAA TATAA TATAA TATAA TATA
38386364 TAGTTAATAA
Statistics
Matches: 172, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
5 168 0.98
6 4 0.02
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Done.