Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 165 of 344
Found at i:55194120 original size:42 final size:42
Alignment explanation
Indices: 55194032--55194152 Score: 107
Period size: 42 Copynumber: 2.9 Consensus size: 42
55194022 CAGTGCTAAT
* **** * * *
55194032 GCCATATCCCAGACATGGTCTTATACGGGGCCTCACATTAAT
1 GCCATATCCCAGACATGGTCTTAAACGAAATCTCATATCAAC
* *
55194074 GCCATGTCCCAGACATGGTCTTACACGAAATCTCATATCAAC
1 GCCATATCCCAGACATGGTCTTAAACGAAATCTCATATCAAC
* ** * *
55194116 GCCATATTCCAGGTATGGTCTTAAATGAAATCACATA
1 GCCATATCCCAGACATGGTCTTAAACGAAATCTCATA
55194153 CTGATGTCGA
Statistics
Matches: 63, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (42 bp):
GCCATATCCCAGACATGGTCTTAAACGAAATCTCATATCAAC
Found at i:55194252 original size:48 final size:48
Alignment explanation
Indices: 55194170--55194294 Score: 144
Period size: 48 Copynumber: 2.6 Consensus size: 48
55194160 CGATGCAATA
* * * *
55194170 TCCCAGATATGGTCTTACACTGGAAT-ACATATCAACCCCGATGCCAAG
1 TCCCAGACATGGTCTTACACTGG-CTCTCACATCAACCCCGATGCCAAG
**** *
55194218 TCCCAGACATGGTCTTACACTGGCTCTCACATCAATGTTGATGCCATG
1 TCCCAGACATGGTCTTACACTGGCTCTCACATCAACCCCGATGCCAAG
*
55194266 TCCTAGACATGGTCTTACACTGGCTCTCA
1 TCCCAGACATGGTCTTACACTGGCTCTCA
55194295 TTAATCGTGG
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
47 1 0.02
48 65 0.98
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.27
Consensus pattern (48 bp):
TCCCAGACATGGTCTTACACTGGCTCTCACATCAACCCCGATGCCAAG
Found at i:55209707 original size:47 final size:47
Alignment explanation
Indices: 55209656--55210068 Score: 693
Period size: 47 Copynumber: 8.7 Consensus size: 47
55209646 TTAGGATTCT
* * *
55209656 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCG
55209703 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55209750 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55209797 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCG
55209846 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55209893 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
55209940 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
55209987 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
55210034 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
55210069 TCCCGAAGGG
Statistics
Matches: 350, Mismatches: 13, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 302 0.86
49 47 0.13
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:55209731 original size:25 final size:25
Alignment explanation
Indices: 55209703--55209781 Score: 65
Period size: 25 Copynumber: 3.3 Consensus size: 25
55209693 CTAATGGCCG
55209703 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
* *** ****
55209728 ATGTGAT-AAGGCCTAA-TG-GCCG
1 ATGTGATGAATGTGAAAGTGTATAT
55209750 ATGTGATGAATGTGAAAGTGTATAT
1 ATGTGATGAATGTGAAAGTGTATAT
55209775 ATGTGAT
1 ATGTGAT
55209782 AAGGCCTAAT
Statistics
Matches: 35, Mismatches: 16, Indels: 6
0.61 0.28 0.11
Matches are distributed among these distances:
22 7 0.20
23 7 0.20
24 7 0.20
25 14 0.40
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (25 bp):
ATGTGATGAATGTGAAAGTGTATAT
Found at i:55209836 original size:143 final size:141
Alignment explanation
Indices: 55209656--55210068 Score: 693
Period size: 143 Copynumber: 2.9 Consensus size: 141
55209646 TTAGGATTCT
* * *
55209656 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGAATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
55209720 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
65 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
55209785 GCCTAATGGCCG
130 GCCTAATGGCCG
55209797 ATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 ATGTGATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
55209862 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
64 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAA
55209927 GGCCTAATGGCCG
129 GGCCTAATGGCCG
55209940 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
* * * * * * * *
55210005 TGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
66 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
55210069 TCCCGAAGGG
Statistics
Matches: 258, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
140 1 0.00
141 118 0.46
143 139 0.54
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (141 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCG
Found at i:55209939 original size:190 final size:188
Alignment explanation
Indices: 55209656--55210068 Score: 702
Period size: 190 Copynumber: 2.2 Consensus size: 188
55209646 TTAGGATTCT
* *
55209656 ATGTGATGGATGTGAACA-TGCATATATGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
1 ATGTGATGGATGTGAA-AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAA
55209720 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
65 GTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
* * *
55209785 GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCG
130 GCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATATATGTGACAAGGCCGAATGGCCA
*
55209846 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
55209911 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
66 TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
* *
55209976 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
131 CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCA
* *
55210034 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGGATGTGAAAGTGTATATATGTGATAAG
55210069 TCCCGAAGGG
Statistics
Matches: 211, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
188 54 0.26
189 1 0.00
190 156 0.74
ACGTcount: A:0.32, C:0.09, G:0.30, T:0.29
Consensus pattern (188 bp):
ATGTGATGGATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAG
TGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGG
CCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAAGGCCGAATGGCCA
Found at i:55210244 original size:37 final size:37
Alignment explanation
Indices: 55210187--55210265 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
55210177 CCGAGCTCTA
* * *
55210187 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
** *
55210224 AAGACCCGATAACTTTGTGTGGAGATTATGTTCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
55210261 AAGAC
1 AAGAC
55210266 TTCGTAATAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.28
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:55211910 original size:46 final size:46
Alignment explanation
Indices: 55211835--55212053 Score: 242
Period size: 46 Copynumber: 4.7 Consensus size: 46
55211825 TTATCTTTGA
* * * * *
55211835 CATGATGCCATAGTATCTTTCAACTATGGTTTTACTCGTTTTC-TGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC-ATTTCATGT
* * * **
55211881 CATGTTGCCATGGTATCTTTCAGCCATGGTCTTATTCGTTTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTC-ATTTCATGT
*
55211928 CATGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* ** * * *
55211974 TACATTGCCATGGTATCTTTCAACCATAGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
55212020 CAGGTTGTCATGGTATCTTTCAACCATGGTCTTA
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTA
55212054 TTCAACCATG
Statistics
Matches: 149, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
46 111 0.74
47 38 0.26
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:55212047 original size:16 final size:16
Alignment explanation
Indices: 55212028--55212065 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55212018 ATCAGGTTGT
55212028 CATGGTATCT-TTCAAC
1 CATGGTAT-TATTCAAC
*
55212044 CATGGTCTTATTCAAC
1 CATGGTATTATTCAAC
55212060 CATGGT
1 CATGGT
55212066 CTTACACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (16 bp):
CATGGTATTATTCAAC
Found at i:55212051 original size:92 final size:93
Alignment explanation
Indices: 55211840--55212057 Score: 251
Period size: 93 Copynumber: 2.4 Consensus size: 93
55211830 TTTGACATGA
* * * * * * ** *
55211840 TGCCATAGTATCTTTCAACTATGGTTTTACTCGTTTTC-TGTCATGTTGCCATGGTATCTTTCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTATTC-ATTTCATGTTACATTGCCATGGTATCTTTCAA
* ** * * * *
55211904 CCATGGTCTTATTCGTTTTCCCGTCATGT
65 CCATAGTCTTACACGATTTCACATCAGGT
55211933 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTTACATTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTTACATTGCCATGGTATCTTTCAAC
*
55211998 CATAGTCTTACAC-ATTTCATATCAGGT
66 CATAGTCTTACACGATTTCACATCAGGT
*
55212025 TGTCATGGTATCTTTCAACCATGGTCTTATTCA
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCA
55212058 ACCATGGTCT
Statistics
Matches: 106, Mismatches: 18, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
92 45 0.42
93 61 0.58
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (93 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGTTACATTGCCATGGTATCTTTCAAC
CATAGTCTTACACGATTTCACATCAGGT
Found at i:55212061 original size:62 final size:62
Alignment explanation
Indices: 55211992--55212115 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
55211982 CATGGTATCT
* *
55211992 TTCAACCATAGTCTTACACATTTCATATCAGGTTGTCATGGTATCTTTCAACCATGGTCTTA
1 TTCAACCATAGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTA
*
55212054 TTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTA
1 TTCAACCATAGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTA
55212116 CACATTTCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (62 bp):
TTCAACCATAGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTTCAACCATAGTCTTA
Found at i:55212066 original size:16 final size:16
Alignment explanation
Indices: 55212038--55212069 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55212028 CATGGTATCT
55212038 TTCAACCATGGTCTTA
1 TTCAACCATGGTCTTA
55212054 TTCAACCATGGTCTTA
1 TTCAACCATGGTCTTA
55212070 CACATTTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (16 bp):
TTCAACCATGGTCTTA
Found at i:55217132 original size:26 final size:24
Alignment explanation
Indices: 55217086--55217133 Score: 60
Period size: 26 Copynumber: 1.9 Consensus size: 24
55217076 GAGAGAAATG
*
55217086 AAAGAAAAAGAAATCGAAAAATAA
1 AAAGAAAAAGAAATAGAAAAATAA
*
55217110 AAAGAAAGTAAGAAATAGCAAAAT
1 AAAGAAA--AAGAAATAGAAAAAT
55217134 GAGATTGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
26 13 0.65
ACGTcount: A:0.71, C:0.04, G:0.15, T:0.10
Consensus pattern (24 bp):
AAAGAAAAAGAAATAGAAAAATAA
Found at i:55223801 original size:43 final size:42
Alignment explanation
Indices: 55223753--55223838 Score: 129
Period size: 43 Copynumber: 2.0 Consensus size: 42
55223743 TTAAAGAAAG
* *
55223753 CATGCATGGGACGGTATTAAAGGAGCT-GTTGATTTCTCCTTTT
1 CATGCATAGGACGGTATTAAAGGAG-TAGTTGATTCCT-CTTTT
55223796 CATGCATAGGACGGTATTAAAGGAGTAGTTGATTCCTCTTTT
1 CATGCATAGGACGGTATTAAAGGAGTAGTTGATTCCTCTTTT
55223838 C
1 C
55223839 CATGTGCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
42 7 0.17
43 33 0.82
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.36
Consensus pattern (42 bp):
CATGCATAGGACGGTATTAAAGGAGTAGTTGATTCCTCTTTT
Found at i:55226739 original size:7 final size:7
Alignment explanation
Indices: 55226727--55226751 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
55226717 TAATAAAAAT
55226727 TATTTTA
1 TATTTTA
55226734 TATTTTA
1 TATTTTA
55226741 TATTTTA
1 TATTTTA
55226748 TATT
1 TATT
55226752 AAAACAAATT
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:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTTA
Found at i:55227197 original size:28 final size:26
Alignment explanation
Indices: 55227166--55227224 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 26
55227156 AAAATATTAT
*
55227166 ATTAATGTATTATAATAAATTTATTTTA
1 ATTAATGTATTATAA-AAAATTA-TTTA
* * *
55227194 ATTACTTTTTTATAAAAAATTATTTA
1 ATTAATGTATTATAAAAAATTATTTA
55227220 ATTAA
1 ATTAA
55227225 CCTAAAAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 8 0.31
27 6 0.23
28 12 0.46
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTAATGTATTATAAAAAATTATTTA
Found at i:55228777 original size:17 final size:19
Alignment explanation
Indices: 55228741--55228779 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
55228731 ATTATTTTTT
55228741 AAGAGTATTTTTAGACTAA
1 AAGAGTATTTTTAGACTAA
*
55228760 AAGA-TATTTTT-GAGTAA
1 AAGAGTATTTTTAGACTAA
55228777 AAG
1 AAG
55228780 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 7 0.37
19 4 0.21
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (19 bp):
AAGAGTATTTTTAGACTAA
Found at i:55228910 original size:18 final size:17
Alignment explanation
Indices: 55228871--55228914 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
55228861 CTTATTTAAC
*
55228871 AATTA-TTTTATCTCAA
1 AATTATTTTTTTCTCAA
55228887 AA-TATTTTTTTCTCTAA
1 AATTATTTTTTTCTC-AA
55228904 AATTATTTTTT
1 AATTATTTTTT
55228915 CAAAGTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 2 0.08
16 10 0.42
17 4 0.17
18 8 0.33
ACGTcount: A:0.32, C:0.09, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTATTTTTTTCTCAA
Found at i:55228915 original size:17 final size:16
Alignment explanation
Indices: 55228871--55228915 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
55228861 CTTATTTAAC
*
55228871 AATTATTTTATCTCAA
1 AATTATTTTTTCTCAA
55228887 AA-TATTTTTTTCTCTAA
1 AATTA-TTTTTTCTC-AA
55228904 AATTATTTTTTC
1 AATTATTTTTTC
55228916 AAAGTAATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 10 0.40
17 11 0.44
18 2 0.08
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (16 bp):
AATTATTTTTTCTCAA
Found at i:55229718 original size:12 final size:12
Alignment explanation
Indices: 55229701--55229737 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
55229691 ACTGTTAAAA
55229701 AATAGAATAACT
1 AATAGAATAACT
55229713 AATAGAATAACT
1 AATAGAATAACT
*
55229725 AATAGAACAACT
1 AATAGAATAACT
55229737 A
1 A
55229738 GATACTAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.59, C:0.11, G:0.08, T:0.22
Consensus pattern (12 bp):
AATAGAATAACT
Found at i:55233564 original size:3 final size:3
Alignment explanation
Indices: 55233556--55233603 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
55233546 TTGCAGCACT
* * * *
55233556 GAA GAA GAA GAA GAA GAA GAA GAA AAA GGA GAT TAA GAA TGAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA -GAA GAA
55233602 GA
1 GA
55233604 TTGCCTCGAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:55238516 original size:188 final size:191
Alignment explanation
Indices: 55238131--55238518 Score: 746
Period size: 188 Copynumber: 2.0 Consensus size: 191
55238121 AACCAGATCT
55238131 AAACATAAAACACACAAACATGATTTAGAACCGGTCTTCAACACCCTTATAGGGTTCGGCGAAAA
1 AAACA-AAAACACACAAACATGATTTAGAACCGGTCTTCAACACCCTTATAGGGTTCGGCGAAAA
55238196 CAAGGATTTGCAAAAACTAATCGAATTTGATTTTTCGTATGTTACTTACTCTTCCAAGTATTAAA
65 CAAGGATTTGCAAAAACTAATCGAATTTGATTTTTCGTATGTTACTTACTCTTCCAAGTATTAAA
55238261 AAAGAGATGTGGGTTGTCCTTCAATGCTACTATTGATCTGATACGTTCATATTCGGTCCTTC
130 AAAGAGATGTGGGTTGTCCTTCAATGCTACTATTGATCTGATACGTTCATATTCGGTCCTTC
55238323 AAACAAAAACACACAAACATGATTTAGAA-CGGTCTTCAACACCCTTATAGGGTTCGGCG-AAAC
1 AAACAAAAACACACAAACATGATTTAGAACCGGTCTTCAACACCCTTATAGGGTTCGGCGAAAAC
55238386 AAGGATTTGCAAAAACTAATCGAATTTGATTTTTCGTATGTTACTTACTCTTCCAAGTATT-AAA
66 AAGGATTTGCAAAAACTAATCGAATTTGATTTTTCGTATGTTACTTACTCTTCCAAGTATTAAAA
55238450 AAGAGATGTGGGTTGTCCTTCAATGCTACTATTGATCTGATACGTTCATATTCGGTCCTTC
131 AAGAGATGTGGGTTGTCCTTCAATGCTACTATTGATCTGATACGTTCATATTCGGTCCTTC
55238511 AAACAAAA
1 AAACAAAA
55238519 TTACATATAA
Statistics
Matches: 196, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
188 72 0.37
189 65 0.33
190 30 0.15
191 24 0.12
192 5 0.03
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (191 bp):
AAACAAAAACACACAAACATGATTTAGAACCGGTCTTCAACACCCTTATAGGGTTCGGCGAAAAC
AAGGATTTGCAAAAACTAATCGAATTTGATTTTTCGTATGTTACTTACTCTTCCAAGTATTAAAA
AAGAGATGTGGGTTGTCCTTCAATGCTACTATTGATCTGATACGTTCATATTCGGTCCTTC
Found at i:55238689 original size:3 final size:3
Alignment explanation
Indices: 55238681--55238752 Score: 135
Period size: 3 Copynumber: 23.7 Consensus size: 3
55238671 ACTGGCAACA
55238681 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
55238727 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
55238753 AAGAAGGGTG
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 65 0.96
4 3 0.04
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55239268 original size:9 final size:9
Alignment explanation
Indices: 55239211--55239402 Score: 50
Period size: 9 Copynumber: 21.4 Consensus size: 9
55239201 TATATATACA
*
55239211 AAAACATAT
1 AAAATATAT
55239220 AAAAT-TAT
1 AAAATATAT
*
55239228 AAAAGATA-
1 AAAATATAT
55239236 AAAAT-TAGT
1 AAAATATA-T
* *
55239245 AATAT-TTT
1 AAAATATAT
55239253 AAAAATATAT
1 -AAAATATAT
55239263 AAAATA-AT
1 AAAATATAT
55239271 GAAAATAATAT
1 -AAAAT-ATAT
*
55239282 TAAA-ATA-
1 AAAATATAT
*
55239289 AAAATATCT
1 AAAATATAT
55239298 -AAAT-TAT
1 AAAATATAT
*
55239305 AAAAAACTAT
1 AAAATA-TAT
55239315 ACAAAT-TAT
1 A-AAATATAT
*
55239324 GAAAATACA-
1 -AAAATATAT
*
55239333 AAAAT-TGAA
1 AAAATAT-AT
*
55239342 AAAATATGAA
1 AAAATAT-AT
*
55239352 AAAATATTT
1 AAAATATAT
*
55239361 AAAGCTATAT
1 AAA-ATATAT
*
55239371 -AAATGTATT
1 AAAATATA-T
* *
55239380 AAAATTTAC
1 AAAATATAT
55239389 AAAATATTAT
1 AAAATA-TAT
55239399 AAAA
1 AAAA
55239403 AAACATAAAA
Statistics
Matches: 135, Mismatches: 25, Indels: 45
0.66 0.12 0.22
Matches are distributed among these distances:
7 7 0.05
8 35 0.26
9 49 0.36
10 39 0.29
11 5 0.04
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAATATAT
Found at i:55239441 original size:20 final size:19
Alignment explanation
Indices: 55239389--55239446 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
55239379 TAAAATTTAC
*
55239389 AAAATATTATAAAAAAACATA
1 AAAATA-TATAAAAAAA-TTA
55239410 AAAAT-TATAAAAAAATTA
1 AAAATATATAAAAAAATTA
55239428 AAAATATATGAAAAAAATT
1 AAAATATAT-AAAAAAATT
55239447 TATGAAACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.21
19 13 0.38
20 9 0.26
21 5 0.15
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATATATAAAAAAATTA
Found at i:55240575 original size:61 final size:61
Alignment explanation
Indices: 55240510--55240646 Score: 229
Period size: 61 Copynumber: 2.2 Consensus size: 61
55240500 ACTTACATGA
* * *
55240510 TCTATCAATTTGATCCTAGTTCTAAATAATTCAATAAACGTAACCTTTCATATTTACAAAT
1 TCTATCAATTTGATCCTAATTCTAAATAATTCAATAAACGTAACCATTCACATTTACAAAT
**
55240571 TCTATCAATTTGATCCTAATTCTAAATAATTCAATAAATTTAACCATTCACATTTACAAAT
1 TCTATCAATTTGATCCTAATTCTAAATAATTCAATAAACGTAACCATTCACATTTACAAAT
55240632 TCTATCAATTTGATC
1 TCTATCAATTTGATC
55240647 TTCAAACTTC
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 71 1.00
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (61 bp):
TCTATCAATTTGATCCTAATTCTAAATAATTCAATAAACGTAACCATTCACATTTACAAAT
Found at i:55243229 original size:13 final size:13
Alignment explanation
Indices: 55243208--55243247 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
55243198 GTCAATAAAA
55243208 AAAATAGATAT-C
1 AAAATAGATATAC
*
55243220 AAAATCAGATGTAC
1 AAAAT-AGATATAC
55243234 AAAATAGATATAC
1 AAAATAGATATAC
55243247 A
1 A
55243248 GAATCCTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 5 0.21
13 13 0.54
14 6 0.25
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.23
Consensus pattern (13 bp):
AAAATAGATATAC
Found at i:55243236 original size:14 final size:14
Alignment explanation
Indices: 55243208--55243252 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
55243198 GTCAATAAAA
55243208 AAAAT-AGATAT-C
1 AAAATCAGATATAC
*
55243220 AAAATCAGATGTAC
1 AAAATCAGATATAC
55243234 AAAAT-AGATATAC
1 AAAATCAGATATAC
*
55243247 AGAATC
1 AAAATC
55243253 CTGCCCCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 16 0.59
14 6 0.22
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (14 bp):
AAAATCAGATATAC
Found at i:55267616 original size:217 final size:218
Alignment explanation
Indices: 55267235--55267670 Score: 847
Period size: 217 Copynumber: 2.0 Consensus size: 218
55267225 AAAAAGGTAA
55267235 TAACTGGAATAGTTTTTATTTGACAACTCATTTTTAAACACTCTCCATGTGATATCTTCAGATTC
1 TAACTGGAATAGTTTTTATTTGACAACTCATTTTTAAACACTCTCCATGTGATATCTTCAGATTC
*
55267300 GGCTATAACGTCTACGTCGGGTTTGGGGTGTTACACTTCACTACCAATTTGATGTAATTATTCAT
66 GGCTATAACGTCTACGTCGGGTTTGGGGTGTTACACTTCACTACCAATTTCATGTAATTATTCAT
55267365 ATATACTTATCACGTAACACCCCAATTTTGGCGGGTTCGAGGGTTTGGCGGGTAGTCATAAAATT
131 ATATACTTATCACGTAACACCCCAATTTTGGCGGGTTCGAGGGTTTGGCGGGTAGTCATAAAATT
55267430 ATTTTTTCGTGAACCGTTATCCG
196 ATTTTTTCGTGAACCGTTATCCG
*
55267453 TAACT-GAATAGTTTTTATTTGACAACTCGTTTTTAAACACTCTCCATGTGATATCTTCAGATTC
1 TAACTGGAATAGTTTTTATTTGACAACTCATTTTTAAACACTCTCCATGTGATATCTTCAGATTC
55267517 GGCTATAACGTCTACGTCGGGTTTGGGGTGTTACACTTCACTACCAATTTCATGTAATTATTCAT
66 GGCTATAACGTCTACGTCGGGTTTGGGGTGTTACACTTCACTACCAATTTCATGTAATTATTCAT
55267582 ATATACTTATCACGTAACACCCCAATTTTGGCGGGTTCGAGGGTTTGGCGGGTAGTCATAAAATT
131 ATATACTTATCACGTAACACCCCAATTTTGGCGGGTTCGAGGGTTTGGCGGGTAGTCATAAAATT
55267647 ATTTTTTCGTGAACCGTTATCCG
196 ATTTTTTCGTGAACCGTTATCCG
55267670 T
1 T
55267671 CTAATTCTCT
Statistics
Matches: 216, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
217 211 0.98
218 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (218 bp):
TAACTGGAATAGTTTTTATTTGACAACTCATTTTTAAACACTCTCCATGTGATATCTTCAGATTC
GGCTATAACGTCTACGTCGGGTTTGGGGTGTTACACTTCACTACCAATTTCATGTAATTATTCAT
ATATACTTATCACGTAACACCCCAATTTTGGCGGGTTCGAGGGTTTGGCGGGTAGTCATAAAATT
ATTTTTTCGTGAACCGTTATCCG
Found at i:55268940 original size:27 final size:27
Alignment explanation
Indices: 55268900--55268994 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
55268890 TCCCGATAGT
* *
55268900 CTTTGTGGCATACTTTGGATGGATCAC
1 CTTTGTGGCGTACTTTGAATGGATCAC
* *
55268927 CTTTTTGGCGTACTTTGAATGGATCGC
1 CTTTGTGGCGTACTTTGAATGGATCAC
* ***
55268954 CTATGTGGCGTACTCCAAATGGATCAC
1 CTTTGTGGCGTACTTTGAATGGATCAC
* *
55268981 CTTTATGGTGTACT
1 CTTTGTGGCGTACT
55268995 CTAATTAGAT
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 55 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (27 bp):
CTTTGTGGCGTACTTTGAATGGATCAC
Found at i:55275703 original size:21 final size:21
Alignment explanation
Indices: 55275650--55275704 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
55275640 TATTGTTTTT
* * *
55275650 CACACGGGCGTGTGCCTTGGA
1 CACACAGGCGTGTCCCTTAGA
* * *
55275671 CACGCAGTCGTGTCCCTTAGC
1 CACACAGGCGTGTCCCTTAGA
55275692 CACACAGGCGTGT
1 CACACAGGCGTGT
55275705 AAGATATCCA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.33, G:0.31, T:0.20
Consensus pattern (21 bp):
CACACAGGCGTGTCCCTTAGA
Found at i:55276558 original size:38 final size:37
Alignment explanation
Indices: 55276475--55276566 Score: 105
Period size: 37 Copynumber: 2.5 Consensus size: 37
55276465 GTTCCACAAT
* * *
55276475 TATGGTGTGTAAGGAGGATGGGCCTATCACGGTCATA
1 TATGGTGTGTAAGGTGGATGGGCCTATCAAGCTCATA
*
55276512 TATGGTGTGTAAGGTGGATGGGCTTGAT-ATAGCTCATA
1 TATGGTGTGTAAGGTGGATGGGCCT-ATCA-AGCTCATA
* *
55276550 TGTGGTGTGCAAGGTGG
1 TATGGTGTGTAAGGTGG
55276567 TCGAAGTGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 24 0.51
38 23 0.49
ACGTcount: A:0.22, C:0.10, G:0.38, T:0.30
Consensus pattern (37 bp):
TATGGTGTGTAAGGTGGATGGGCCTATCAAGCTCATA
Found at i:55278141 original size:36 final size:36
Alignment explanation
Indices: 55278099--55278178 Score: 103
Period size: 36 Copynumber: 2.2 Consensus size: 36
55278089 AATATTGTAC
55278099 ATATTTTATGT-GTTATTATTAATT-ATTTTAAATAAT
1 ATATTTTAT-TAGTTATTATTAATTAATTTTAAAT-AT
* *
55278135 ATATTTTATTATTTATTATTTATTAATTTTAAATAT
1 ATATTTTATTAGTTATTATTAATTAATTTTAAATAT
55278171 AT-TTTTAT
1 ATATTTTAT
55278179 ATTCTAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
35 7 0.17
36 24 0.60
37 9 0.22
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (36 bp):
ATATTTTATTAGTTATTATTAATTAATTTTAAATAT
Found at i:55278173 original size:19 final size:19
Alignment explanation
Indices: 55278151--55278188 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
55278141 TATTATTTAT
*
55278151 TATTTATTA-ATTTTAAATA
1 TATTT-TTATATTCTAAATA
55278170 TATTTTTATATTCTAAATA
1 TATTTTTATATTCTAAATA
55278189 AATAATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTTATATTCTAAATA
Found at i:55279026 original size:24 final size:26
Alignment explanation
Indices: 55278998--55279045 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
55278988 AAATCATTTT
55278998 TGAAAAAT-GAAAATAA-AAAATATG
1 TGAAAAATAGAAAATAATAAAATATG
* *
55279022 TGAAAATTAGAATATAATAAAATA
1 TGAAAAATAGAAAATAATAAAATA
55279046 ATGTTTTCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 7 0.35
26 6 0.30
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (26 bp):
TGAAAAATAGAAAATAATAAAATATG
Found at i:55279703 original size:20 final size:20
Alignment explanation
Indices: 55279678--55279718 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
55279668 AAGTAAGTGG
55279678 ATTTTATT-AAATTCAGATTA
1 ATTTTATTCAAATTCA-ATTA
55279698 ATTTTATTCAAATTCAATTA
1 ATTTTATTCAAATTCAATTA
55279718 A
1 A
55279719 CTTATAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.41, C:0.07, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTTTATTCAAATTCAATTA
Found at i:55279763 original size:22 final size:22
Alignment explanation
Indices: 55279738--55279781 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
55279728 TTTCAAACAC
55279738 TTTTGTAAACTATTTAAGTTTA
1 TTTTGTAAACTATTTAAGTTTA
*
55279760 TTTTGTACACTATTTAAGTTTA
1 TTTTGTAAACTATTTAAGTTTA
55279782 AGTTATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.55
Consensus pattern (22 bp):
TTTTGTAAACTATTTAAGTTTA
Found at i:55285875 original size:26 final size:26
Alignment explanation
Indices: 55285839--55285890 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
55285829 AAATGATAAT
55285839 TTCACAAAAAAAAATTTGCTTTTATA
1 TTCACAAAAAAAAATTTGCTTTTATA
*
55285865 TTCACAAAAAAAATTTTGCTTTTATA
1 TTCACAAAAAAAAATTTGCTTTTATA
55285891 GCCTCTTGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.04, T:0.40
Consensus pattern (26 bp):
TTCACAAAAAAAAATTTGCTTTTATA
Found at i:55287076 original size:17 final size:17
Alignment explanation
Indices: 55287054--55287094 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
55287044 TTAATCTGCA
55287054 TCTTTTGTACTCTTCAT
1 TCTTTTGTACTCTTCAT
55287071 TCTTTTGTACTCTTCAT
1 TCTTTTGTACTCTTCAT
55287088 TCTTTTG
1 TCTTTTG
55287095 CCATTATAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.10, C:0.22, G:0.07, T:0.61
Consensus pattern (17 bp):
TCTTTTGTACTCTTCAT
Found at i:55289668 original size:21 final size:21
Alignment explanation
Indices: 55289639--55289678 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
55289629 TAAAATTATT
*
55289639 ATATACTTTTATTATCTTTGC
1 ATATACTTTAATTATCTTTGC
* *
55289660 ATATTCTTTAATTTTCTTT
1 ATATACTTTAATTATCTTT
55289679 TATTATATAT
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:0.23, C:0.12, G:0.03, T:0.62
Consensus pattern (21 bp):
ATATACTTTAATTATCTTTGC
Found at i:55297670 original size:17 final size:17
Alignment explanation
Indices: 55297648--55297682 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55297638 TATATATTAG
*
55297648 TGTATATATTTTTTATA
1 TGTATATATTTTTAATA
*
55297665 TGTATATGTTTTTAATA
1 TGTATATATTTTTAATA
55297682 T
1 T
55297683 ATTTATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.63
Consensus pattern (17 bp):
TGTATATATTTTTAATA
Found at i:55297787 original size:30 final size:30
Alignment explanation
Indices: 55297732--55297806 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
55297722 TTTATCCCTA
*
55297732 ATAT-TTATGTATTATGTAAATA-TTTTAAT
1 ATATATTATGTA-TATCTAAATATTTTTAAT
* **
55297761 ATTATATTATGTATATCTATATATTTTTCGT
1 A-TATATTATGTATATCTAAATATTTTTAAT
55297792 ATATATTATGTATAT
1 ATATATTATGTATAT
55297807 ATGTTTTCAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 1 0.03
30 25 0.64
31 13 0.33
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.56
Consensus pattern (30 bp):
ATATATTATGTATATCTAAATATTTTTAAT
Found at i:55297819 original size:24 final size:25
Alignment explanation
Indices: 55297778--55297833 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
55297768 TATGTATATC
*
55297778 TATATATTTTTCGTATATAT-TATG-
1 TATATATTTTTCGAATAT-TGTATGT
55297802 TATATATGTTTTC-AATATTGTATGT
1 TATATAT-TTTTCGAATATTGTATGT
55297827 TATATAT
1 TATATAT
55297834 ATTATTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 15 0.54
25 12 0.43
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (25 bp):
TATATATTTTTCGAATATTGTATGT
Found at i:55297914 original size:19 final size:19
Alignment explanation
Indices: 55297890--55297926 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55297880 CTATTTTATA
*
55297890 TATATTTCTAATATCATTG
1 TATATTTCTAACATCATTG
55297909 TATATTTCTAACATCATT
1 TATATTTCTAACATCATT
55297927 ATTATTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (19 bp):
TATATTTCTAACATCATTG
Found at i:55298011 original size:9 final size:9
Alignment explanation
Indices: 55297994--55298029 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
55297984 ATCATTTCTA
55297994 ATATATATT
1 ATATATATT
*
55298003 ATATGTATT
1 ATATATATT
*
55298012 TTATATATT
1 ATATATATT
55298021 ATATATATT
1 ATATATATT
55298030 TTAATGTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (9 bp):
ATATATATT
Found at i:55298016 original size:18 final size:18
Alignment explanation
Indices: 55297995--55298032 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55297985 TCATTTCTAA
*
55297995 TATATATTATATGTATTT
1 TATATATTATATATATTT
55298013 TATATATTATATATATTT
1 TATATATTATATATATTT
55298031 TA
1 TA
55298033 ATGTTATTAG
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:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TATATATTATATATATTT
Found at i:55298119 original size:16 final size:15
Alignment explanation
Indices: 55298100--55298135 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
55298090 CTTATGTACA
55298100 TATATAAATATTATGT
1 TATATAAATA-TATGT
55298116 TATATAAATATATGT
1 TATATAAATATATGT
*
55298131 AATAT
1 TATAT
55298136 GCTTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (15 bp):
TATATAAATATATGT
Found at i:55298135 original size:15 final size:16
Alignment explanation
Indices: 55298101--55298135 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
55298091 TTATGTACAT
*
55298101 ATATAAATATTATGTT
1 ATATAAATATTATGTA
55298117 ATATAAATA-TATGTA
1 ATATAAATATTATGTA
55298132 ATAT
1 ATAT
55298136 GCTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (16 bp):
ATATAAATATTATGTA
Found at i:55298319 original size:37 final size:35
Alignment explanation
Indices: 55298254--55298323 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
55298244 TTATATATAG
55298254 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
55298291 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
55298324 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:55298458 original size:25 final size:24
Alignment explanation
Indices: 55298430--55298485 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
55298420 GTTATATTTT
*
55298430 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
55298455 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
55298478 CACTATTA
1 CACTATTA
55298486 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:55311523 original size:25 final size:23
Alignment explanation
Indices: 55311471--55311525 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
55311461 TATAAATAGT
55311471 AATAGTGTTAGAAATATACTATA
1 AATAGTGTTAGAAATATACTATA
* *
55311494 TATAGTGTTTGAAGTATATAC-ATAA
1 AATAGTGTTAGAA--ATATACTAT-A
55311519 AATAGTG
1 AATAGTG
55311526 AAAATATAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 11 0.42
24 2 0.08
25 13 0.50
ACGTcount: A:0.44, C:0.04, G:0.16, T:0.36
Consensus pattern (23 bp):
AATAGTGTTAGAAATATACTATA
Found at i:55313138 original size:93 final size:93
Alignment explanation
Indices: 55313026--55313196 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
55313016 GCCCCTAAGT
*
55313026 GAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 GAACTCGGACTCAACTCAACGAGCTC-GGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
55313090 ACGAGTTCGGATGCCTAGTTACATTTCAC
65 ACGAGTTCAGATGCCTAGTTACATTTCAC
* * *
55313119 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCTTAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
55313184 CGAGTTCAGATGC
66 CGAGTTCAGATGC
55313197 TCAACCATCC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
92 2 0.03
93 70 0.97
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:55313186 original size:46 final size:46
Alignment explanation
Indices: 55313021--55313190 Score: 188
Period size: 46 Copynumber: 3.7 Consensus size: 46
55313011 AACCCGCCCC
* * *
55313021 TAAGTGAACTCGGACTCAACTCAACGAGCTCAGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC-GGACATTCGCATCCT
* *
55313067 TAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCT
* *
55313115 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCT
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCT
55313160 TAAGTGAACTCGGACTCAACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
55313191 AGATGCTCAA
Statistics
Matches: 103, Mismatches: 11, Indels: 20
0.77 0.08 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 5 0.05
46 55 0.53
47 28 0.27
48 2 0.02
49 1 0.01
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCT
Found at i:55314639 original size:19 final size:19
Alignment explanation
Indices: 55314615--55314651 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55314605 TATAAATAAT
*
55314615 AATGATGTTAGAAATATAC
1 AATGATATTAGAAATATAC
55314634 AATGATATTAGAAATATA
1 AATGATATTAGAAATATA
55314652 TATAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (19 bp):
AATGATATTAGAAATATAC
Found at i:55314749 original size:24 final size:24
Alignment explanation
Indices: 55314708--55314763 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
55314698 ACACAATAAT
*
55314708 ATATATAACATACAATAT-TGAAAA
1 ATATAT-ACATACAATATACGAAAA
55314732 CATATATACATA-ATATATACGAAAA
1 -ATATATACATACA-ATATACGAAAA
55314757 ATATATA
1 ATATATA
55314764 GATATACATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 11 0.39
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (24 bp):
ATATATACATACAATATACGAAAA
Found at i:55314788 original size:30 final size:30
Alignment explanation
Indices: 55314735--55314809 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
55314725 TTGAAAACAT
*
55314735 ATATACATAATATATACGAAAAATATATAG
1 ATATACATAATATATACGAAAAATATATAC
** *
55314765 ATATACATAATATAATA-TTAAAATATTTAC
1 ATATACATAATAT-ATACGAAAAATATATAC
55314795 ATAATACATAA-ATAT
1 AT-ATACATAATATAT
55314810 TAGGGATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 2 0.05
30 26 0.67
31 11 0.28
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (30 bp):
ATATACATAATATATACGAAAAATATATAC
Found at i:55319696 original size:35 final size:35
Alignment explanation
Indices: 55319622--55319691 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 35
55319612 TGAATCAAAT
* *
55319622 TTAATTGGTTCATGTAACAAAAAAAAAAGAGTGAA
1 TTAATTGGCTCATGTAACAAAAAAAAAAGAGAGAA
*
55319657 TTAATTGGCTCATGTAACCAAAAAGAAAAAAAGAG
1 TTAATTGGCTCATGTAA-CAAAAA-AAAAAGAGAG
55319692 TTAATGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 16 0.53
36 6 0.20
37 8 0.27
ACGTcount: A:0.51, C:0.09, G:0.17, T:0.23
Consensus pattern (35 bp):
TTAATTGGCTCATGTAACAAAAAAAAAAGAGAGAA
Found at i:55330080 original size:25 final size:25
Alignment explanation
Indices: 55330022--55330107 Score: 84
Period size: 25 Copynumber: 3.5 Consensus size: 25
55330012 TATACATATG
*
55330022 CTCATACGAGCTGTA-AACGGTAAA
1 CTCATACGAGCTGAATAACGGTAAA
* * * *
55330046 CTCCTCCGAGCTGAATAATGGTAAT
1 CTCATACGAGCTGAATAACGGTAAA
* * *
55330071 CTCATACGAGCTGAGTAACGATAAG
1 CTCATACGAGCTGAATAACGGTAAA
*
55330096 CTCATAAGAGCT
1 CTCATACGAGCT
55330108 AAAATCGGTA
Statistics
Matches: 49, Mismatches: 12, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
24 12 0.24
25 37 0.76
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (25 bp):
CTCATACGAGCTGAATAACGGTAAA
Found at i:55343744 original size:23 final size:23
Alignment explanation
Indices: 55343714--55343760 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
55343704 ATGATAAAGT
* *
55343714 AAACCCAATTGGATTTGTTATCA
1 AAACCCAATCGGATTTGTCATCA
55343737 AAACCCAATCGGATTTGTCATCA
1 AAACCCAATCGGATTTGTCATCA
55343760 A
1 A
55343761 CCGCAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (23 bp):
AAACCCAATCGGATTTGTCATCA
Found at i:55346775 original size:4 final size:4
Alignment explanation
Indices: 55346761--55346790 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
55346751 ATAAAGTGAA
55346761 AAAG AAAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG A
55346791 GGATACCCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:55353183 original size:18 final size:19
Alignment explanation
Indices: 55353162--55353202 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
55353152 TTTGAGTTTG
*
55353162 AATCATAGTTGTA-AAAAA
1 AATCATAATTGTACAAAAA
55353180 AATCATAATTGTACAAAAA
1 AATCATAATTGTACAAAAA
55353199 AATC
1 AATC
55353203 CCTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (19 bp):
AATCATAATTGTACAAAAA
Found at i:55353771 original size:26 final size:26
Alignment explanation
Indices: 55353743--55353804 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 26
55353733 AAATTTTCTT
55353743 AAATATTTACCGGGGGTAAAATTGTTA
1 AAAT-TTTACCGGGGGTAAAATTGTTA
* * *
55353770 AAATTTTATCGGGGGTAAAATCGTCA
1 AAATTTTACCGGGGGTAAAATTGTTA
55353796 AAATTTTAC
1 AAATTTTAC
55353805 TGGAGTAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 27 0.87
27 4 0.13
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.34
Consensus pattern (26 bp):
AAATTTTACCGGGGGTAAAATTGTTA
Found at i:55362957 original size:35 final size:34
Alignment explanation
Indices: 55362917--55363002 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
55362907 AATAAATGAA
*
55362917 AAGCATGATT-TTTGGCTACTGAGTTGATCTATTAT
1 AAGCAT-ATTATTT-GCTACTGAGTTGAACTATTAT
* ** *
55362952 AAGCATATTATTTGCTATTGTTTTGAACTGTTAT
1 AAGCATATTATTTGCTACTGAGTTGAACTATTAT
*
55362986 AAGCATATTAATTGCTA
1 AAGCATATTATTTGCTA
55363003 TTGTATTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
34 35 0.80
35 9 0.20
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.44
Consensus pattern (34 bp):
AAGCATATTATTTGCTACTGAGTTGAACTATTAT
Found at i:55362987 original size:34 final size:34
Alignment explanation
Indices: 55362948--55363017 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
55362938 AGTTGATCTA
* *
55362948 TTATAAGCATATTATTTGCTATTGTTTTGAACTG
1 TTATAAGCATATTAATTGCTATTGTATTGAACTG
*
55362982 TTATAAGCATATTAATTGCTATTGTATTGATCTG
1 TTATAAGCATATTAATTGCTATTGTATTGAACTG
55363016 TT
1 TT
55363018 CGAGCTTGCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (34 bp):
TTATAAGCATATTAATTGCTATTGTATTGAACTG
Found at i:55373496 original size:3 final size:3
Alignment explanation
Indices: 55373488--55373557 Score: 58
Period size: 3 Copynumber: 24.0 Consensus size: 3
55373478 ATATATAAAT
* *
55373488 TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA GAA T-A TAA AAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
55373533 CTTAA TAA TAT TAA AAA TAA -AA TAA
1 --TAA TAA TAA TAA TAA TAA TAA TAA
55373558 AATGTGAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
2 8 0.15
3 43 0.80
5 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:55374247 original size:22 final size:24
Alignment explanation
Indices: 55374165--55374247 Score: 68
Period size: 22 Copynumber: 3.5 Consensus size: 24
55374155 TAGTATTAGA
55374165 AATAATATAGTATAAAGATATATA-ACT
1 AATAATATA-TAT-AA-ATATATACA-T
*
55374192 GATAATAT-TA-AAATATATACAT
1 AATAATATATATAAATATATACAT
* *
55374214 AATATTATATATAAAT-TATTCAT
1 AATAATATATATAAATATATACAT
55374237 -ATAATATATAT
1 AATAATATATAT
55374248 TAAAAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
22 24 0.50
23 11 0.23
24 4 0.08
25 2 0.04
27 7 0.15
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
AATAATATATATAAATATATACAT
Found at i:55374494 original size:120 final size:124
Alignment explanation
Indices: 55374353--55374579 Score: 295
Period size: 123 Copynumber: 1.9 Consensus size: 124
55374343 AAAAAGTAAA
* *
55374353 TATAATAAAATGATATTAAAATAAAGTCATTAAAAACAGTAATATATATATACAT-C-TA-AT-A
1 TATAATAAAA-GATATTAAAATAAAGT-AATAAAAACAGTAATACATATATACATACATACATGA
* * * * *
55374414 AGAATATATAGTAATGT-TAATGATGATAATAATAATAATAATATTGAAATACAAAAGCTAT
64 AG-ATATACACTAATGTACAATAATAATAATAATAATAATAATATTGAAATACAAAAGCTAT
* * *
55374475 TATAATAAAA-ATATTAAAATAAAGTAATAAAAACATTACTACATATATATATACATACATGAAG
1 TATAATAAAAGATATTAAAATAAAGTAATAAAAACAGTAATACATATATACATACATACATGAAG
55374539 ATATACACTAATGTACAATAATAATAATAATAATAATAATA
66 ATATACACTAATGTACAATAATAATAATAATAATAATAATA
55374580 ATAATAATAA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
119 22 0.24
120 16 0.18
121 2 0.02
122 24 0.27
123 26 0.29
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (124 bp):
TATAATAAAAGATATTAAAATAAAGTAATAAAAACAGTAATACATATATACATACATACATGAAG
ATATACACTAATGTACAATAATAATAATAATAATAATAATATTGAAATACAAAAGCTAT
Found at i:55374563 original size:3 final size:3
Alignment explanation
Indices: 55374555--55374594 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
55374545 ACTAATGTAC
55374555 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55374595 TTGAAATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55375090 original size:11 final size:11
Alignment explanation
Indices: 55375076--55375110 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
55375066 GAAAAAAAGA
*
55375076 AGAGAGAGGGG
1 AGAGAGAAGGG
55375087 AGAGAGAAGGG
1 AGAGAGAAGGG
55375098 AGAGAGAAGGG
1 AGAGAGAAGGG
55375109 AG
1 AG
55375111 GGGGGAAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (11 bp):
AGAGAGAAGGG
Found at i:55385005 original size:28 final size:26
Alignment explanation
Indices: 55384957--55385059 Score: 84
Period size: 24 Copynumber: 3.9 Consensus size: 26
55384947 TATAAGTAAT
*
55384957 ATATAACTAGTAATATCAAAATATATAC
1 ATATAA-TA-TAATATAAAAATATATAC
**
55384985 ATGATAATATATATATAAAAATATATGT
1 AT-ATAATATA-ATATAAAAATATATAC
* *
55385013 ATATAATGTAATATGAAAATATAT--
1 ATATAATATAATATAAAAATATATAC
* * *
55385037 ATGTAGTATAATATTAAAATATA
1 ATATAATATAATATAAAAATATA
55385060 ATAATACAAC
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
24 19 0.30
26 13 0.20
27 9 0.14
28 19 0.30
29 4 0.06
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (26 bp):
ATATAATATAATATAAAAATATATAC
Found at i:55385037 original size:22 final size:22
Alignment explanation
Indices: 55385012--55385097 Score: 63
Period size: 21 Copynumber: 4.0 Consensus size: 22
55385002 AAAATATATG
*
55385012 TATATAATGTAATATGAAAATA
1 TATATAATATAATATGAAAATA
* *
55385034 TATATGTAGTATAATATTAAAATA
1 TATA--TAATATAATATGAAAATA
* * *
55385058 TA-ATAATACAACATTAAAA-A
1 TATATAATATAATATGAAAATA
*
55385078 TATATGATAT-ATAT-AAAATA
1 TATATAATATAATATGAAAATA
55385098 CAATATTAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
19 4 0.08
20 7 0.14
21 18 0.35
22 4 0.08
23 1 0.02
24 17 0.33
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (22 bp):
TATATAATATAATATGAAAATA
Found at i:55385099 original size:32 final size:32
Alignment explanation
Indices: 55385055--55385119 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
55385045 TAATATTAAA
55385055 ATATAATAATACAACATTAAAAATATATGATAT
1 ATATAATAATACAACATTAAAAATATAT-ATAT
* *
55385088 ATATAA-AATACAATATTAAAAGTATATATAT
1 ATATAATAATACAACATTAAAAATATATATAT
55385119 A
1 A
55385120 ACATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 19 0.63
33 6 0.20
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (32 bp):
ATATAATAATACAACATTAAAAATATATATAT
Found at i:55385103 original size:53 final size:53
Alignment explanation
Indices: 55385046--55385146 Score: 145
Period size: 53 Copynumber: 1.9 Consensus size: 53
55385036 TATGTAGTAT
55385046 AATATTAAAA-TATAATAATACAACAT-TAAAAATATATGATAT-ATATAAAATAC
1 AATATTAAAAGTAT-AT-ATACAACATATAAAAATATAT-ATATAATATAAAATAC
*
55385099 AATATTAAAAGTATATATATAACATATAAAAATATATATATAATATAA
1 AATATTAAAAGTATATATACAACATATAAAAATATATATATAATATAA
55385147 TACTAAGTAT
Statistics
Matches: 44, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
52 12 0.27
53 29 0.66
54 3 0.07
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (53 bp):
AATATTAAAAGTATATATACAACATATAAAAATATATATATAATATAAAATAC
Found at i:55385144 original size:19 final size:20
Alignment explanation
Indices: 55385099--55385146 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
55385089 TATAAAATAC
*
55385099 AATATTAAAAGTATATATATA
1 AATA-TAAAAATATATATATA
55385120 ACATATAAAAATATATATAT-
1 A-ATATAAAAATATATATATA
55385140 AATATAA
1 AATATAA
55385147 TACTAAGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 6 0.24
20 1 0.04
21 15 0.60
22 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AATATAAAAATATATATATA
Found at i:55387667 original size:24 final size:25
Alignment explanation
Indices: 55387616--55387669 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 25
55387606 TGACGAATTT
*
55387616 TTAAAATTTACAATTTCTCAAAATA
1 TTAAAATTTACAATTTCTCAAAAAA
* * *
55387641 TTAAAATTTA-ATTTTTTGAAAAAA
1 TTAAAATTTACAATTTCTCAAAAAA
55387665 TTAAA
1 TTAAA
55387670 TTTGAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (25 bp):
TTAAAATTTACAATTTCTCAAAAAA
Found at i:55388817 original size:55 final size:55
Alignment explanation
Indices: 55388651--55388917 Score: 414
Period size: 55 Copynumber: 4.9 Consensus size: 55
55388641 GTGATCTTGA
* * * *
55388651 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTT-AAAAATAGATATTAAAAG
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAG
* *
55388705 ACTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTAAAAG
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAG
55388759 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAG
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAG
* **
55388814 GCTCAACTCACCTCTCGCAATATGAGTTGACTTTTTGAAAAACCGAAATTAAAAG
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAG
* *
55388869 GCTCAACTCACTTCTCGCAATGTGAGTTGA-TTTTTGAAAAACAGAAATT
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATT
55388918 GAAATTACCT
Statistics
Matches: 197, Mismatches: 14, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
53 4 0.02
54 89 0.45
55 104 0.53
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (55 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAG
Found at i:55388841 original size:109 final size:110
Alignment explanation
Indices: 55388651--55388917 Score: 432
Period size: 109 Copynumber: 2.5 Consensus size: 110
55388641 GTGATCTTGA
* * * *
55388651 GCTCAACTCATTTCTCGCAATATGAATTGACTCTTT-AAAAATAGATATTAAAAGACTCAACTCA
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAGACTCAACTCA
*
55388715 CCTCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTAAAAG
66 CCTCTCGCAATATGAGTTGACTTTTTGAAAAACAGAAATTAAAAG
*
55388759 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAGGCTCAACTCA
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAGACTCAACTCA
*
55388824 CCTCTCGCAATATGAGTTGACTTTTTGAAAAACCGAAATTAAAAG
66 CCTCTCGCAATATGAGTTGACTTTTTGAAAAACAGAAATTAAAAG
* *
55388869 GCTCAACTCACTTCTCGCAATGTGAGTTGA-TTTTTGAAAAACAGAAATT
1 GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATT
55388918 GAAATTACCT
Statistics
Matches: 148, Mismatches: 9, Indels: 3
0.93 0.06 0.02
Matches are distributed among these distances:
108 33 0.22
109 64 0.43
110 51 0.34
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (110 bp):
GCTCAACTCACTTCTCGCAATATGAGTTGACTTTTTGAAAAATAGAAATTAAAAGACTCAACTCA
CCTCTCGCAATATGAGTTGACTTTTTGAAAAACAGAAATTAAAAG
Found at i:55389138 original size:79 final size:79
Alignment explanation
Indices: 55389007--55389159 Score: 288
Period size: 79 Copynumber: 1.9 Consensus size: 79
55388997 AAATTGGAAG
55389007 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
55389072 TTTTGAAAAGCAGA
66 TTTTGAAAAGCAGA
* *
55389086 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
55389151 TTTTGAAAA
66 TTTTGAAAA
55389160 CATGAATTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (79 bp):
AACAGAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTGAAAAGCAGA
Found at i:55389160 original size:178 final size:173
Alignment explanation
Indices: 55388867--55389531 Score: 805
Period size: 178 Copynumber: 3.8 Consensus size: 173
55388857 CGAAATTAAA
* *
55388867 AGGCTCAACTCACTTCTCGCAATGTGAGTTGATTTTTG-A-AAAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTAGAAAACAGAAATTGAAATTACCTCA
*
55388930 GCGTGCCCCGAGGCTCAACTCACCTCTTGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAC
66 GCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAC
*
55388995 AGAAATTGGAAGAACAGAAATTGAAAATACCTCAGCGTGTCCTG
131 AGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGTCC-G
*
55389039 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGCAGAAACAGAAATTGAAATTAC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG--TAG-A-AAACAGAAATTGAAATTAC
* * *
55389104 CTCAGCGTGTCCTGAGGCTTAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTA
62 CTCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTA
* *
55389169 AAACAGAAATTGAAAGAACAGAAACTGAAAATACCTCAGCGTGTGAACCA
127 AAACAGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGT---CCG
* * * *
55389219 AGGTTCAACTCATCTCTCGCAATATGAGTTGATTTTTTTGGAAAACAGAAATTGAAATTACCTCA
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTAGAAAACAGAAATTGAAATTACCTCA
* * *
55389284 GCGTGCCCCAAGGCTCAACTCACCTCTCGCAATATAAGTTGATTTTT-------T---TTTAAAC
66 GCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAC
* * * *
55389339 ATAAATTGAAAGAACAGAAATTGGAAATACCTCAGTATGTGAACCG
131 AGAAATTGAAAGAACAGAAATTGAAAATACCTCAG--CGTG-TCCG
* ** * * * *
55389385 AGGTTCAACTCATTTCTCGCAATGTGAGTTGATTTTTTTTTTGAAAAACAGAAATTAAAATTACC
1 AGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTGTAG-AAAACAGAAATTGAAATTACC
* * *
55389450 TTAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGTATAAATTA
63 TCAGCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA-CATGAATT-
* *
55389515 AAAATAGAAATTAAAAG
126 AAAACAGAAATTGAAAG
55389532 GCTCAACTCA
Statistics
Matches: 429, Mismatches: 37, Indels: 45
0.84 0.07 0.09
Matches are distributed among these distances:
166 70 0.16
168 11 0.03
169 68 0.16
172 36 0.08
175 1 0.00
176 65 0.15
177 3 0.01
178 123 0.29
180 37 0.09
181 15 0.03
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (173 bp):
AGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGTAGAAAACAGAAATTGAAATTACCTCA
GCGTGCCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAACATGAATTAAAAC
AGAAATTGAAAGAACAGAAATTGAAAATACCTCAGCGTGTCCG
Found at i:55389317 original size:75 final size:75
Alignment explanation
Indices: 55389185--55389349 Score: 215
Period size: 75 Copynumber: 2.2 Consensus size: 75
55389175 AAATTGAAAG
* * * *
55389185 AACAGAAACTGAAAATACCTCAGCGTGTGAACCAAGGTTCAACTCATCTCTCGCAATATGAGTTG
1 AACAGAAATTGAAAATACCTCAGCG-GTGAACCAAGGCTCAACTCACCTCTCGCAATATAAGTTG
55389250 ATTTTTTTGGAA
65 ATTTTTTT-GAA
* **
55389262 AACAGAAATTGAAATTACCTCAGC-GTGCCCCAAGGCTCAACTCACCTCTCGCAATATAAGTTGA
1 AACAGAAATTGAAAATACCTCAGCGGTGAACCAAGGCTCAACTCACCTCTCGCAATATAAGTTGA
**
55389326 TTTTTTTTTA
66 TTTTTTTGAA
*
55389336 AACATAAATTGAAA
1 AACAGAAATTGAAA
55389350 GAACAGAAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
74 14 0.18
75 42 0.54
77 22 0.28
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (75 bp):
AACAGAAATTGAAAATACCTCAGCGGTGAACCAAGGCTCAACTCACCTCTCGCAATATAAGTTGA
TTTTTTTGAA
Found at i:55389526 original size:166 final size:165
Alignment explanation
Indices: 55389168--55389530 Score: 500
Period size: 166 Copynumber: 2.2 Consensus size: 165
55389158 AACATGAATT
* * *
55389168 AAAACAGAAATTGAAAGAACAGAAACTGAAAATACCTCAGCGTGTGAACCAAGGTTCAACTCATC
1 AAAACATAAATTGAAAGAACAGAAATTGAAAATACCTCAGCATGTGAACCAAGGTTCAACTCATC
* *
55389233 TCTCGCAATATGAGTTGATTTTTTTGGAAAACAGAAATTGAAATTACCTCAGCGTGCCCCAAGGC
66 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAATTACCTCAGCGTGCCCCAAGGC
*
55389298 TCAACTCACCTCTCGCAATATAAGTTGATTTTTTTT
131 TCAACTCACCTCTCGCAATATAAGTTGA-TTTTTTG
* * * * *
55389334 TAAACATAAATTGAAAGAACAGAAATTGGAAATACCTCAGTATGTGAACCGAGGTTCAACTCATT
1 AAAACATAAATTGAAAGAACAGAAATTGAAAATACCTCAGCATGTGAACCAAGGTTCAACTCATC
* * *
55389399 TCTCGCAATGTGAGTTGATTTTTTTTTTGAAAAACAGAAATTAAAATTACCTTAGCGTGCCCCGA
66 TCTCGCAATATGAGTTGA---TTTTTTTGAAAAACAGAAATTAAAATTACCTCAGCGTGCCCCAA
*
55389464 GGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG
128 GGCTCAACTCACCTCTCGCAATATAAGTTGATTTTTTG
* *
55389501 AAAAGTATAAATT-AAA-AATAGAAATT-AAAA
1 AAAA-CATAAATTGAAAGAACAGAAATTGAAAA
55389531 GGCTCAACTC
Statistics
Matches: 174, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
165 3 0.02
166 83 0.48
167 11 0.06
168 7 0.04
169 70 0.40
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (165 bp):
AAAACATAAATTGAAAGAACAGAAATTGAAAATACCTCAGCATGTGAACCAAGGTTCAACTCATC
TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTAAAATTACCTCAGCGTGCCCCAAGGC
TCAACTCACCTCTCGCAATATAAGTTGATTTTTTG
Found at i:55402158 original size:22 final size:24
Alignment explanation
Indices: 55402099--55402159 Score: 67
Period size: 22 Copynumber: 2.7 Consensus size: 24
55402089 GTATGTACAC
55402099 CAAATAAT-AATAATATATAAGTGA
1 CAAA-AATGAATAATATATAAGTGA
*
55402123 CAATAATGAA-AATA-ATAAGT-A
1 CAAAAATGAATAATATATAAGTGA
*
55402144 TAAAAATGAATAATAT
1 CAAAAATGAATAATAT
55402160 GATATACGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
21 9 0.29
22 10 0.32
23 7 0.23
24 5 0.16
ACGTcount: A:0.61, C:0.03, G:0.08, T:0.28
Consensus pattern (24 bp):
CAAAAATGAATAATATATAAGTGA
Found at i:55402548 original size:26 final size:25
Alignment explanation
Indices: 55402471--55402579 Score: 75
Period size: 26 Copynumber: 4.4 Consensus size: 25
55402461 GGGACAGTAT
55402471 AAAATATATACATGA-AA-ATATATA
1 AAAATATATACAT-ATAATATATATA
* * * *
55402495 AGTAATATATA-A-CTAGTA-ATATC
1 A-AAATATATACATATAATATATATA
55402518 AAAATATATACATGATAATATATATA
1 AAAATATATACAT-ATAATATATATA
** * *
55402544 AAAATATATGTATATAATGTAATATG
1 AAAATATATACATATAATAT-ATATA
55402570 AAAATATATA
1 AAAATATATA
55402580 TGTAGTATAA
Statistics
Matches: 64, Mismatches: 13, Indels: 14
0.70 0.14 0.15
Matches are distributed among these distances:
22 8 0.12
23 7 0.11
24 3 0.05
25 18 0.28
26 28 0.44
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
AAAATATATACATATAATATATATA
Found at i:55402641 original size:32 final size:32
Alignment explanation
Indices: 55402597--55402661 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 32
55402587 TAATATTAAA
55402597 ATATAATAATACAACATTAAAAATATATGATAT
1 ATATAATAATACAACATTAAAAATATAT-ATAT
* *
55402630 ATATAA-AATACAATATTAAAAGTATATATAT
1 ATATAATAATACAACATTAAAAATATATATAT
55402661 A
1 A
55402662 ACATATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 19 0.63
33 6 0.20
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (32 bp):
ATATAATAATACAACATTAAAAATATATATAT
Found at i:55402645 original size:53 final size:51
Alignment explanation
Indices: 55402588--55402686 Score: 139
Period size: 53 Copynumber: 1.9 Consensus size: 51
55402578 TATGTAGTAT
55402588 AATATTAAAA-TATAATAATACAACAT-TAAAAATATATGATATATATAAAATAC
1 AATATTAAAAGTAT-AT-ATACAACATATAAAAATATAT-ATA-ATATAAAATAC
*
55402641 AATATTAAAAGTATATATATAACATATAAAAATATATATAATATAA
1 AATATTAAAAGTATATATACAACATATAAAAATATATATAATATAA
55402687 TACTAAGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
51 6 0.14
52 11 0.26
53 23 0.53
54 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (51 bp):
AATATTAAAAGTATATATACAACATATAAAAATATATATAATATAAAATAC
Found at i:55405200 original size:25 final size:25
Alignment explanation
Indices: 55405153--55405207 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
55405143 TGACGAATTT
*
55405153 TTAAAATTTACAATTTCTCAAAATA
1 TTAAAATTTACAATTTCTCAAAAAA
* *
55405178 TTAAAATTTA-ATTTTTTCAAAAAAA
1 TTAAAATTTACAATTTCTC-AAAAAA
55405203 TTAAA
1 TTAAA
55405208 TTTGAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 6 0.23
25 20 0.77
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (25 bp):
TTAAAATTTACAATTTCTCAAAAAA
Found at i:55407121 original size:18 final size:18
Alignment explanation
Indices: 55407090--55407124 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55407080 AAAATTAAGA
*
55407090 AAAAAAAAGTTTAAAAAG
1 AAAAAAAAGGTTAAAAAG
*
55407108 AAAAATAAGGTTAAAAA
1 AAAAAAAAGGTTAAAAA
55407125 AAGAACCCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AAAAAAAAGGTTAAAAAG
Found at i:55407124 original size:19 final size:19
Alignment explanation
Indices: 55407086--55407125 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
55407076 AAGTAAAATT
*
55407086 AAGAAAAAAAAAGTTTAAA
1 AAGAAAAAAAAAGTTAAAA
* *
55407105 AAGAAAAATAAGGTTAAAA
1 AAGAAAAAAAAAGTTAAAA
55407124 AA
1 AA
55407126 AGAACCCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.15
Consensus pattern (19 bp):
AAGAAAAAAAAAGTTAAAA
Found at i:55409426 original size:26 final size:27
Alignment explanation
Indices: 55409376--55409427 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
55409366 GGATAAGCAT
*
55409376 ATAATATAATATGAAAAATGTATATAC
1 ATAATATAATATGAAAAACGTATATAC
55409403 ATAATAT-ATATG-AAAACGTAATATA
1 ATAATATAATATGAAAAACGT-ATATA
55409428 GTATTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 10 0.43
27 7 0.30
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (27 bp):
ATAATATAATATGAAAAACGTATATAC
Found at i:55409655 original size:12 final size:11
Alignment explanation
Indices: 55409635--55409665 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 11
55409625 AAACATGTTC
55409635 ATAATATACGT
1 ATAATATACGT
55409646 ATATATATACGT
1 ATA-ATATACGT
55409658 ATAATATA
1 ATAATATA
55409666 GTTATACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (11 bp):
ATAATATACGT
Found at i:55409896 original size:15 final size:15
Alignment explanation
Indices: 55409876--55409904 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
55409866 AGACATAATA
55409876 ATACTAAATATATAC
1 ATACTAAATATATAC
55409891 ATACTAAATATATA
1 ATACTAAATATATA
55409905 TATGCATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
ATACTAAATATATAC
Found at i:55412672 original size:26 final size:25
Alignment explanation
Indices: 55412636--55412742 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 25
55412626 GAAATGCCCG
*
55412636 TCATGGAACATTTTCCTAAGCCATTA
1 TCATGGAACATTTACCTAA-CCATTA
55412662 TCATGGAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAA-CCATTA
* *
55412688 TCATGGAATATTTACTTAATCCATTA
1 TCATGGAACATTTACCTAA-CCATTA
55412714 TCATGGAACATTTACCTAACCTATTA
1 TCATGGAACATTTACCTAACC-ATTA
55412740 TCA
1 TCA
55412743 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 7, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
25 2 0.03
26 71 0.97
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (25 bp):
TCATGGAACATTTACCTAACCATTA
Found at i:55412715 original size:52 final size:52
Alignment explanation
Indices: 55412636--55412742 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 52
55412626 GAAATGCCCG
*
55412636 TCATGGAACATTTTCCTAAGCCATTATCATGGAACATTTACCTAACCCATTA
1 TCATGGAACATTTACCTAAGCCATTATCATGGAACATTTACCTAACCCATTA
* * * *
55412688 TCATGGAATATTTACTTAATCCATTATCATGGAACATTTACCTAACCTATTA
1 TCATGGAACATTTACCTAAGCCATTATCATGGAACATTTACCTAACCCATTA
55412740 TCA
1 TCA
55412743 ATTTGTACCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (52 bp):
TCATGGAACATTTACCTAAGCCATTATCATGGAACATTTACCTAACCCATTA
Found at i:55413604 original size:47 final size:48
Alignment explanation
Indices: 55413549--55413659 Score: 151
Period size: 48 Copynumber: 2.4 Consensus size: 48
55413539 TATATATAAG
*
55413549 ATAG-TATAAAAATATATAACT-ATGATA-CTAAAGTATATACACGA-A
1 ATAGATATAAAAATATATAACTAATAATATCTAAA-TATATACACGATA
55413594 ATAGGATATAAAAATATATAACTAATAATATCTAAATATATACACGATA
1 ATA-GATATAAAAATATATAACTAATAATATCTAAATATATACACGATA
*
55413643 ATATATATAAAAA-ATAT
1 ATAGATATAAAAATATAT
55413660 TAGAAAATAT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
45 3 0.05
46 1 0.02
47 21 0.36
48 25 0.42
49 9 0.15
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (48 bp):
ATAGATATAAAAATATATAACTAATAATATCTAAATATATACACGATA
Found at i:55413629 original size:24 final size:24
Alignment explanation
Indices: 55413555--55413635 Score: 60
Period size: 24 Copynumber: 3.4 Consensus size: 24
55413545 TAAGATAGTA
*
55413555 TAAAAATATATAACT-ATGATA-C
1 TAAAAATATATAACTAATAATATC
* * ** *
55413577 T-AAAGTATATACACGAAATAGGATA
1 TAAAAATATATA-AC-TAATAATATC
55413602 TAAAAATATATAACTAATAATATC
1 TAAAAATATATAACTAATAATATC
*
55413626 TAAATATATA
1 TAAAAATATA
55413636 CACGATAATA
Statistics
Matches: 42, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
21 9 0.21
22 3 0.07
24 18 0.43
25 3 0.07
26 9 0.21
ACGTcount: A:0.56, C:0.07, G:0.06, T:0.31
Consensus pattern (24 bp):
TAAAAATATATAACTAATAATATC
Found at i:55413700 original size:24 final size:25
Alignment explanation
Indices: 55413662--55413716 Score: 85
Period size: 24 Copynumber: 2.2 Consensus size: 25
55413652 AAAAATATTA
55413662 GAAAATATATGTACATAATATAATAT
1 GAAAATATA-GTACATAATATAATAT
55413688 GAAAATATA-TACATAATATAATAT
1 GAAAATATAGTACATAATATAATAT
*
55413712 TAAAA
1 GAAAA
55413717 CATAATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 19 0.68
26 9 0.32
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (25 bp):
GAAAATATAGTACATAATATAATAT
Found at i:55413726 original size:21 final size:22
Alignment explanation
Indices: 55413673--55413737 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 22
55413663 AAAATATATG
* *
55413673 TACATAATATAATATGAAAATATA
1 TACATAATATAATAT-TAAA-ACA
55413697 TACATAATATAATATTAAAACA
1 TACATAATATAATATTAAAACA
* *
55413719 TA-ATAATACAACATTAAAA
1 TACATAATATAATATTAAAA
55413738 ATATTTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 15 0.41
22 4 0.11
23 3 0.08
24 15 0.41
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.31
Consensus pattern (22 bp):
TACATAATATAATATTAAAACA
Found at i:55413805 original size:19 final size:18
Alignment explanation
Indices: 55413756--55413807 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 18
55413746 GATATATTTA
*
55413756 ATATATAATATTAAAAGT
1 ATATATAATATAAAAAGT
55413774 ATATATAACATATAAAAAGAT
1 ATATAT-A-ATATAAAAAG-T
55413795 ATATATAATATAA
1 ATATATAATATAA
55413808 TACCTAAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.20
19 7 0.23
20 10 0.33
21 7 0.23
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (18 bp):
ATATATAATATAAAAAGT
Found at i:55413806 original size:55 final size:55
Alignment explanation
Indices: 55413703--55413806 Score: 124
Period size: 55 Copynumber: 1.9 Consensus size: 55
55413693 TATATACATA
* *
55413703 ATATAATATTAAAACATAATAATACAACATTAAAAATATTTATGATATATTTAAT
1 ATATAATATTAAAACATAATAATACAACATTAAAAATATATATAATATATTTAAT
* *
55413758 ATATAATATTAAAA-GT-AT-ATATAACATATAAAAAGATATATATAATATA
1 ATATAATATTAAAACATAATAATACAACAT-T-AAAA-ATATATATAATATA
55413807 ATACCTAAGT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
52 8 0.19
53 3 0.07
54 5 0.12
55 26 0.62
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (55 bp):
ATATAATATTAAAACATAATAATACAACATTAAAAATATATATAATATATTTAAT
Found at i:55415055 original size:54 final size:54
Alignment explanation
Indices: 55415014--55415585 Score: 677
Period size: 54 Copynumber: 10.6 Consensus size: 54
55415004 AAAGTACTCC
*
55415014 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
** * * *
55415068 CGATTTTTAAAATTACCGTTTTACCCTCGATTTATAAAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
*
55415122 C-AGTTTACAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
1 CGA-TTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
** *
55415176 CGATTTTTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* *
55415230 CGATTTACAGAATTACCGTTTTACCCTC-AGTTTATAGAATTACTGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* * * * ** * *
55415284 CAATTTATAGAATTATCATTTTACCCTCGATTTGTAAAATTACCATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* **
55415338 CGATTTATAGAATTACCGTTTTACCCTC-AGTTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* **
55415392 CAATTTACAGAATTACCGTTTTACCCTC-AGTTTACAGAATTACTATTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* * ** * ** *
55415446 CGATTTACAGAATTATCATTTTACCCTCGATTTGTAAAATTACTATTTTACCAT
1 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
* * * * *
55415500 TGATTTACAAAATTACCGGTTTACCCTC-AGTTTACAAAATTATCGTTTTACCCT
1 CGATTTACAGAATTACCGTTTTACCCTCGA-TTTACAGAATTACCGTTTTACCCT
* * * *
55415554 CGATTTATAGAATTGCCATTTTACCCTTGATT
1 CGATTTACAGAATTACCGTTTTACCCTCGATT
55415586 GTGAAATTAC
Statistics
Matches: 451, Mismatches: 59, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
53 4 0.01
54 443 0.98
55 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (54 bp):
CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCT
Found at i:55415109 original size:81 final size:80
Alignment explanation
Indices: 55415014--55415585 Score: 668
Period size: 81 Copynumber: 7.1 Consensus size: 80
55415004 AAAGTACTCC
* * *
55415014 CGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACTGTTTTACCCTCGATTTTTAAA
1 CGATTTATAGAATTACCGTTTTACCCTC-ATTTACAGAATTACTGTTTTACCCTCGATTTATAGA
55415079 ATTACCGTTTTACCCT
65 ATTACCGTTTTACCCT
* * * *
55415095 CGATTTATAAAATTACCGTTTTACCCTCAGTTTACAAAATTACCGTTTTACCCTCGATTTACAGA
1 CGATTTATAGAATTACCGTTTTACCCTCA-TTTACAGAATTACTGTTTTACCCTCGATTTATAGA
55415160 ATTACCGTTTTACCCT
65 ATTACCGTTTTACCCT
* * * *
55415176 CGATTTTTAAAATTACCGTTTTACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGA
1 CGATTTATAGAATTACCGTTTTACCCTC-ATTTACAGAATTACTGTTTTACCCTCGATTTATAGA
55415241 ATTACCGTTTTACCCT
65 ATTACCGTTTTACCCT
* * * *
55415257 C-AGTTTATAGAATTACTGTTTTACCCTCAATTTATAGAATTA-TCATTTTACCCTCGATTTGTA
1 CGA-TTTATAGAATTACCGTTTTACCCTC-ATTTACAGAATTACT-GTTTTACCCTCGATTTATA
* *
55415320 AAATTACCATTTTACCCT
63 GAATTACCGTTTTACCCT
* * *
55415338 CGATTTATAGAATTACCGTTTTACCCTCAGTTTACAGAATTACTATTTTACCCTCAATTTACAGA
1 CGATTTATAGAATTACCGTTTTACCCTCA-TTTACAGAATTACTGTTTTACCCTCGATTTATAGA
55415403 ATTACCGTTTTACCCT
65 ATTACCGTTTTACCCT
* ** * *
55415419 C-AGTTTACAGAATTACTATTTTACCCTCGATTTACAGAATTA-TCATTTTACCCTCGATTTGTA
1 CGA-TTTATAGAATTACCGTTTTACCCTC-ATTTACAGAATTACT-GTTTTACCCTCGATTTATA
* ** *
55415482 AAATTACTATTTTACCAT
63 GAATTACCGTTTTACCCT
* * * * *
55415500 TGATTTACAAAATTACCGGTTTACCCTCAGTTTACAAAATTA-TCGTTTTACCCTCGATTTATAG
1 CGATTTATAGAATTACCGTTTTACCCTCA-TTTACAGAATTACT-GTTTTACCCTCGATTTATAG
* *
55415564 AATTGCCATTTTACCCT
64 AATTACCGTTTTACCCT
*
55415581 TGATT
1 CGATT
55415586 GTGAAATTAC
Statistics
Matches: 430, Mismatches: 49, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
80 6 0.01
81 419 0.97
82 5 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (80 bp):
CGATTTATAGAATTACCGTTTTACCCTCATTTACAGAATTACTGTTTTACCCTCGATTTATAGAA
TTACCGTTTTACCCT
Found at i:55415486 original size:27 final size:27
Alignment explanation
Indices: 55415014--55415585 Score: 605
Period size: 27 Copynumber: 21.2 Consensus size: 27
55415004 AAAGTACTCC
* *
55415014 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* * *
55415041 CGATTTACAGAATTACTGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
*
55415068 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
55415095 CGATTTATAAAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
*
55415122 C-AGTTTACAAAATTACCGTTTTACCCT
1 CGA-TTTATAAAATTACCGTTTTACCCT
* *
55415149 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
*
55415176 CGATTTTTAAAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* *
55415203 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* *
55415230 CGATTTACAGAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* *
55415257 C-AGTTTATAGAATTACTGTTTTACCCT
1 CGA-TTTATAAAATTACCGTTTTACCCT
* * * *
55415284 CAATTTATAGAATTATCATTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* *
55415311 CGATTTGTAAAATTACCATTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
*
55415338 CGATTTATAGAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* * **
55415365 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTATAAAATTACCGTTTTACCCT
* * *
55415392 CAATTTACAGAATTACCGTTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* * **
55415419 C-AGTTTACAGAATTACTATTTTACCCT
1 CGA-TTTATAAAATTACCGTTTTACCCT
* * * *
55415446 CGATTTACAGAATTATCATTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* ** *
55415473 CGATTTGTAAAATTACTATTTTACCAT
1 CGATTTATAAAATTACCGTTTTACCCT
* * *
55415500 TGATTTACAAAATTACCGGTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
* *
55415527 C-AGTTTACAAAATTATCGTTTTACCCT
1 CGA-TTTATAAAATTACCGTTTTACCCT
* * *
55415554 CGATTTATAGAATTGCCATTTTACCCT
1 CGATTTATAAAATTACCGTTTTACCCT
*
55415581 TGATT
1 CGATT
55415586 GTGAAATTAC
Statistics
Matches: 478, Mismatches: 57, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
26 5 0.01
27 468 0.98
28 5 0.01
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (27 bp):
CGATTTATAAAATTACCGTTTTACCCT
Found at i:55415658 original size:54 final size:54
Alignment explanation
Indices: 55415590--55415785 Score: 259
Period size: 54 Copynumber: 3.6 Consensus size: 54
55415580 TTGATTGTGA
* ** *
55415590 AATTACTGAAATACCCCTGTAGGGTAGAATTTTCGAAATACCCCTATAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * *
55415644 AATTACTGAAATACCCTTATAGGATAGAATTACCAAAATACCCCTGTAGGGTAG
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* *
55415698 AATTA-TCGAAATACCCTTGTAGGGTAGAAATACCGAAATACCTCTGTAGGGTAG
1 AATTACT-GAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
* * * *
55415752 AATTACCGAGATACCCTTGTGGGGTAAAATTACC
1 AATTACTGAAATACCCTTGTAGGGTAGAATTACC
55415786 ATTTTGCCCC
Statistics
Matches: 123, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.01
54 122 0.99
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (54 bp):
AATTACTGAAATACCCTTGTAGGGTAGAATTACCGAAATACCCCTGTAGGGTAG
Found at i:55415785 original size:27 final size:27
Alignment explanation
Indices: 55415590--55415785 Score: 232
Period size: 27 Copynumber: 7.3 Consensus size: 27
55415580 TTGATTGTGA
* *
55415590 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
** * *
55415617 AATTTTCGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* * *
55415644 AATTACTGAAATACCCTTATAGGATAG
1 AATTACCGAAATACCCTTGTAGGGTAG
* *
55415671 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
55415698 AATTATCGAAATACCCTTGTAGGGTAG
1 AATTACCGAAATACCCTTGTAGGGTAG
*
55415725 AAATACCGAAATA-CCTCTGTAGGGTAG
1 AATTACCGAAATACCCT-TGTAGGGTAG
* * *
55415752 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCTTGTAGGGTAG
55415779 AATTACC
1 AATTACC
55415786 ATTTTGCCCC
Statistics
Matches: 144, Mismatches: 23, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
26 3 0.02
27 138 0.96
28 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (27 bp):
AATTACCGAAATACCCTTGTAGGGTAG
Found at i:55416027 original size:27 final size:26
Alignment explanation
Indices: 55415985--55416063 Score: 97
Period size: 27 Copynumber: 3.0 Consensus size: 26
55415975 TGAGGAAGCG
*
55415985 TTCTGGTGGCTATGCCACAAATATCTA
1 TTCTGGTGGCTCTGCCAC-AATATCTA
55416012 TTCTGGTGGCTCTGCCACAATATCTGTA
1 TTCTGGTGGCTCTGCCACAATATC--TA
* *
55416040 TT-TGGTGACTCTGTCACAATATCT
1 TTCTGGTGGCTCTGCCACAATATCT
55416064 GTTGACCGAT
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.02
26 6 0.13
27 36 0.77
28 4 0.09
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.37
Consensus pattern (26 bp):
TTCTGGTGGCTCTGCCACAATATCTA
Found at i:55416185 original size:22 final size:22
Alignment explanation
Indices: 55416153--55416211 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
55416143 ACCGTTATTA
*
55416153 ATGGCTCTGTGCCAACCTAAAT
1 ATGGCTTTGTGCCAACCTAAAT
* * * *
55416175 ATGGCTTTGTGCCATCTTGACT
1 ATGGCTTTGTGCCAACCTAAAT
*
55416197 ATGGCTTCGTGCCAA
1 ATGGCTTTGTGCCAA
55416212 ACGTATTTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
ATGGCTTTGTGCCAACCTAAAT
Found at i:55416576 original size:6 final size:6
Alignment explanation
Indices: 55416567--55416768 Score: 166
Period size: 6 Copynumber: 33.3 Consensus size: 6
55416557 TTGCATTCAC
* *
55416567 ATTCTG ATTCTG ATTCTG -TCACGTA ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG AT-TC-TG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
55416616 -TTACTA ATACTG ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTA
1 ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG
* * *
55416664 ATTCTG -TCACCTA ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATAT-TG
1 ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG AT-TCTG
* * * *
55416713 ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCTC ATTTTG GTTCTA
1 ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
55416761 ATTCTG AT
1 ATTCTG AT
55416769 AATGTTTCTT
Statistics
Matches: 156, Mismatches: 24, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
5 11 0.07
6 132 0.85
7 10 0.06
8 3 0.02
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:55416707 original size:85 final size:85
Alignment explanation
Indices: 55416567--55416747 Score: 303
Period size: 85 Copynumber: 2.1 Consensus size: 85
55416557 TTGCATTCAC
* *
55416567 ATTCTGATTCTGATTCTGTCACGTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
1 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
55416632 TGATTCTGATT-CTG-TTACTG
66 TGATTCTG-TTACTGATT-CTG
*
55416652 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATATTGATTC
1 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
55416717 TGATTCTGTTACTGATTCTG
66 TGATTCTGTTACTGATTCTG
55416737 ATTCTGATTCT
1 ATTCTGATTCT
55416748 CATTTTGGTT
Statistics
Matches: 91, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
84 2 0.02
85 87 0.96
86 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (85 bp):
ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTGATTCTGATTCTGTTACTAATACTGATTC
TGATTCTGTTACTGATTCTG
Found at i:55416777 original size:18 final size:17
Alignment explanation
Indices: 55416756--55416789 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55416746 CTCATTTTGG
55416756 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
55416774 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
55416790 GGCTAAGGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:55420152 original size:16 final size:16
Alignment explanation
Indices: 55420131--55420170 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
55420121 CCTTTAGTTC
55420131 GTTGTAATGGAAA-AAA
1 GTTGTAAT-GAAATAAA
*
55420147 GTTGTAATGAAATAGA
1 GTTGTAATGAAATAAA
55420163 GTTGTAAT
1 GTTGTAAT
55420171 CAGTAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (16 bp):
GTTGTAATGAAATAAA
Found at i:55420328 original size:11 final size:11
Alignment explanation
Indices: 55420309--55420363 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
55420299 AGGATTATTA
*
55420309 TTAAAAATAAT
1 TTAATAATAAT
55420320 TTAATAATAA-
1 TTAATAATAAT
*
55420330 ATAATAAATAAT
1 TTAAT-AATAAT
* *
55420342 TTAATCATATT
1 TTAATAATAAT
55420353 TTAAT-ATAAT
1 TTAATAATAAT
55420363 T
1 T
55420364 ATTTTTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 9 0.25
11 23 0.64
12 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAATAATAAT
Found at i:55420409 original size:34 final size:33
Alignment explanation
Indices: 55420366--55420474 Score: 150
Period size: 34 Copynumber: 3.3 Consensus size: 33
55420356 ATATAATTAT
55420366 TTTTATTTTAAATTATATTAAAATATTTAAAATA
1 TTTTATTTTAAATTATATTAAAATATTT-AAATA
**
55420400 TTTTATTTTAAATTATATTTTGAA-A-TTAAATA
1 TTTTATTTTAAATTATA-TTAAAATATTTAAATA
*
55420432 TTTTATATTAAATTATATTAAAATATTTCAAATA
1 TTTTATTTTAAATTATATTAAAATATTT-AAATA
55420466 TTTTATTTT
1 TTTTATTTT
55420475 TATATTTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 4 0.06
32 22 0.34
33 4 0.06
34 31 0.48
35 4 0.06
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (33 bp):
TTTTATTTTAAATTATATTAAAATATTTAAATA
Found at i:55424107 original size:9 final size:9
Alignment explanation
Indices: 55424095--55424209 Score: 51
Period size: 9 Copynumber: 12.6 Consensus size: 9
55424085 AAAAATAGAA
55424095 AAAAATTAT
1 AAAAATTAT
55424104 AAAAA--AT
1 AAAAATTAT
*
55424111 -AAAATCAAT
1 AAAAAT-TAT
**
55424120 AAAAGCTAT
1 AAAAATTAT
*
55424129 AAATATTATT
1 AAAAATTA-T
**
55424139 AAATTTTAAT
1 AAAAATT-AT
55424149 AAAAA-TATT
1 AAAAATTA-T
55424158 AAAATATT-T
1 AAAA-ATTAT
*
55424167 AAAAAATATT
1 AAAAATTA-T
55424177 AAAAATTAT
1 AAAAATTAT
*
55424186 AAAAAAATAT
1 -AAAAATTAT
*
55424196 AAAAATTGT
1 AAAAATTAT
55424205 AAAAA
1 AAAAA
55424210 AAAATATAAA
Statistics
Matches: 80, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
6 4 0.05
7 2 0.03
8 3 0.04
9 38 0.47
10 31 0.39
11 2 0.03
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:55424174 original size:11 final size:10
Alignment explanation
Indices: 55424149--55424200 Score: 63
Period size: 10 Copynumber: 5.4 Consensus size: 10
55424139 AAATTTTAAT
55424149 AAAAATATTA
1 AAAAATATTA
*
55424159 AAATAT-TTA
1 AAAAATATTA
55424168 AAAAATATTA
1 AAAAATATTA
* *
55424178 AAAATTATAA
1 AAAAATATTA
55424188 AAAAATA-TA
1 AAAAATATTA
55424197 AAAA
1 AAAA
55424201 TTGTAAAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
9 13 0.37
10 22 0.63
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (10 bp):
AAAAATATTA
Found at i:55424210 original size:21 final size:19
Alignment explanation
Indices: 55424149--55424220 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 19
55424139 AAATTTTAAT
*
55424149 AAAAATATTAAAATATTTAAA
1 AAAAATA-TAAAA-ATTAAAA
* *
55424170 AAATAT-TAAAAATTATAA
1 AAAAATATAAAAATTAAAA
55424188 AAAAATATAAAAATTGTAAAA
1 AAAAATATAAAAA-T-TAAAA
55424209 AAAAATATAAAA
1 AAAAATATAAAA
55424221 CATATAGAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 10 0.23
19 11 0.26
20 1 0.02
21 21 0.49
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (19 bp):
AAAAATATAAAAATTAAAA
Found at i:55424211 original size:19 final size:19
Alignment explanation
Indices: 55424129--55424211 Score: 89
Period size: 19 Copynumber: 4.2 Consensus size: 19
55424119 TAAAAGCTAT
*
55424129 AAATATTATTAAATTTTAATAA
1 AAATATTA--AAAATTTAA-AA
55424151 AAATATTAAAATATTT-AAA
1 AAATATTAAAA-ATTTAAAA
55424170 AAATATTAAAAATTATAAAA
1 AAATATTAAAAATT-TAAAA
55424190 AAATA-TAAAAATTGTAAAA
1 AAATATTAAAAATT-TAAAA
55424209 AAA
1 AAA
55424212 AATATAAAAC
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.05
19 30 0.54
20 12 0.21
21 3 0.05
22 8 0.14
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (19 bp):
AAATATTAAAAATTTAAAA
Found at i:55424220 original size:9 final size:9
Alignment explanation
Indices: 55424149--55424245 Score: 61
Period size: 9 Copynumber: 10.2 Consensus size: 9
55424139 AAATTTTAAT
55424149 AAAAATATTA
1 AAAAATA-TA
* *
55424159 AAATATTTA
1 AAAAATATA
55424168 AAAAATATTA
1 AAAAATA-TA
*
55424178 AAAATTATAA
1 AAAAATAT-A
55424188 AAAAATATA
1 AAAAATATA
* *
55424197 AAAATTGTAAAA
1 AAAA--AT-ATA
55424209 AAAAATATA
1 AAAAATATA
*
55424218 AAACATAT-
1 AAAAATATA
*
55424226 AGAAATATA
1 AAAAATATA
*
55424235 AAAAACATA
1 AAAAATATA
55424244 AA
1 AA
55424246 TTTATAAATT
Statistics
Matches: 66, Mismatches: 15, Indels: 13
0.70 0.16 0.14
Matches are distributed among these distances:
8 6 0.09
9 31 0.47
10 22 0.33
11 1 0.02
12 6 0.09
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (9 bp):
AAAAATATA
Found at i:55424220 original size:10 final size:10
Alignment explanation
Indices: 55424149--55424220 Score: 56
Period size: 10 Copynumber: 7.2 Consensus size: 10
55424139 AAATTTTAAT
*
55424149 AAAAATATTA
1 AAAAATATAA
* *
55424159 AAATAT-TTA
1 AAAAATATAA
*
55424168 AAAAATATTA
1 AAAAATATAA
*
55424178 AAAATTATAA
1 AAAAATATAA
55424188 AAAAATATAA
1 AAAAATATAA
** *
55424198 AAATTGTAAAA
1 AAA-AATATAA
55424209 AAAAATATAA
1 AAAAATATAA
55424219 AA
1 AA
55424221 CATATAGAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
9 8 0.16
10 34 0.69
11 7 0.14
ACGTcount: A:0.71, C:0.00, G:0.01, T:0.28
Consensus pattern (10 bp):
AAAAATATAA
Found at i:55424573 original size:26 final size:27
Alignment explanation
Indices: 55424540--55424627 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 27
55424530 GAAATTCTAA
55424540 TTTTTATTAAATTTAATTTTT-TAAAT
1 TTTTTATTAAATTTAATTTTTATAAAT
55424566 TTTTTATTAAAATTTAATAATTTTTATAAAAT
1 TTTTTATT-AAA-TT--TAATTTTTAT-AAAT
* *
55424598 TTTTTATT--TTTTATTTTTTATAAAT
1 TTTTTATTAAATTTAATTTTTATAAAT
55424623 TTTTT
1 TTTTT
55424628 CTAATTTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
25 9 0.17
26 17 0.31
27 3 0.06
28 4 0.07
30 8 0.15
31 1 0.02
32 12 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTATTAAATTTAATTTTTATAAAT
Found at i:55424608 original size:19 final size:19
Alignment explanation
Indices: 55424554--55424611 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
55424544 TATTAAATTT
55424554 AATTTTTTAAATTTTTTATTAA
1 AATTTTTT--ATTTTTTA-TAA
** *
55424576 AATTTAATAATTTTTATAA
1 AATTTTTTATTTTTTATAA
55424595 AATTTTTTATTTTTTAT
1 AATTTTTTATTTTTTAT
55424612 TTTTTATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
19 17 0.57
20 7 0.23
22 6 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
AATTTTTTATTTTTTATAA
Done.