Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, whole genome shotgun sequence
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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 175 of 190
Found at i:29083750 original size:18 final size:18
Alignment explanation
Indices: 29083707--29083750 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
29083697 ATTTTAAAAA
29083707 TAAAAAA-TTAATCGAAT
1 TAAAAAATTTAATCGAAT
** *
29083724 TAATCAATTTAATCGATT
1 TAAAAAATTTAATCGAAT
29083742 TAAAAAATT
1 TAAAAAATT
29083751 GATTATAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.52, C:0.07, G:0.05, T:0.36
Consensus pattern (18 bp):
TAAAAAATTTAATCGAAT
Found at i:29084414 original size:19 final size:21
Alignment explanation
Indices: 29084376--29084414 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
29084366 AATTTGTCAT
*
29084376 TATTTTTAATAAAATCATAAA
1 TATTTTTAATAAAATAATAAA
29084397 TATTTTT-AT-AAATAATAA
1 TATTTTTAATAAAATAATAA
29084415 TTAAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 2 0.12
21 7 0.41
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (21 bp):
TATTTTTAATAAAATAATAAA
Found at i:29088969 original size:23 final size:22
Alignment explanation
Indices: 29088942--29088992 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
29088932 TTATATATTA
29088942 AATATT-AAATAAATTTTAAAAT
1 AATATTAAAAT-AATTTTAAAAT
*
29088964 ATATATTAAAATAATTTTAAATT
1 A-ATATTAAAATAATTTTAAAAT
29088987 AATATT
1 AATATT
29088993 TTTATTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 6 0.23
23 16 0.62
24 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATTAAAATAATTTTAAAAT
Found at i:29088972 original size:12 final size:12
Alignment explanation
Indices: 29088940--29088977 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
29088930 TTTTATATAT
29088940 TAAATATT-AAA
1 TAAATATTAAAA
*
29088951 TAAATTTTAAAA
1 TAAATATTAAAA
*
29088963 TATATATTAAAA
1 TAAATATTAAAA
29088975 TAA
1 TAA
29088978 TTTTAAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATATTAAAA
Found at i:29089013 original size:20 final size:21
Alignment explanation
Indices: 29088988--29089026 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
29088978 TTTTAAATTA
29088988 ATATTTTTA-TTGATTATTTT
1 ATATTTTTATTTGATTATTTT
29089008 ATATTTTTATTTGATTATT
1 ATATTTTTATTTGATTATT
29089027 ATCTCTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (21 bp):
ATATTTTTATTTGATTATTTT
Found at i:29089849 original size:23 final size:24
Alignment explanation
Indices: 29089807--29089866 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
29089797 AAAAATAAAT
29089807 TTATTCAAAATAAAACAATTTTAA
1 TTATTCAAAATAAAACAATTTTAA
* *
29089831 TTATTCAAAA-CAAACAATTTTTA
1 TTATTCAAAATAAAACAATTTTAA
29089854 TCTATTCAAAATA
1 T-TATTCAAAATA
29089867 GATAATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.39
24 19 0.61
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (24 bp):
TTATTCAAAATAAAACAATTTTAA
Found at i:29090010 original size:14 final size:13
Alignment explanation
Indices: 29089989--29090029 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
29089979 TCTAGATTTA
29089989 TTTTATAAAAATT
1 TTTTATAAAAATT
**
29090002 TTATTATAAAAAAC
1 TT-TTATAAAAATT
29090016 TTTTATAAAAATT
1 TTTTATAAAAATT
29090029 T
1 T
29090030 AATGATTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTTATAAAAATT
Found at i:29090068 original size:13 final size:13
Alignment explanation
Indices: 29090050--29090074 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29090040 TGATATATCA
29090050 ATGAATGTTTAAG
1 ATGAATGTTTAAG
29090063 ATGAATGTTTAA
1 ATGAATGTTTAA
29090075 TAGACTTATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (13 bp):
ATGAATGTTTAAG
Found at i:29099050 original size:51 final size:51
Alignment explanation
Indices: 29098969--29099069 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
29098959 AAAGCTCTCT
29098969 TGGGCTTTGACATGTAGTGCTTCAACTTACTTTGTAACTCTGCCTTGCTCA
1 TGGGCTTTGACATGTAGTGCTTCAACTTACTTTGTAACTCTGCCTTGCTCA
* * * * *
29099020 TGGGCTTTGTCATGTAGTTCTTGAATTTACTTTGTAACTCTGCTTTGCTC
1 TGGGCTTTGACATGTAGTGCTTCAACTTACTTTGTAACTCTGCCTTGCTC
29099070 CTCATTTCTG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.44
Consensus pattern (51 bp):
TGGGCTTTGACATGTAGTGCTTCAACTTACTTTGTAACTCTGCCTTGCTCA
Found at i:29099216 original size:2 final size:2
Alignment explanation
Indices: 29099198--29099231 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
29099188 TGAAGCTGGG
* *
29099198 TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29099232 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:29099236 original size:2 final size:2
Alignment explanation
Indices: 29099231--29099271 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
29099221 ATATATATAT
29099231 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
29099272 TTGGGTTTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:29103791 original size:35 final size:34
Alignment explanation
Indices: 29103738--29103807 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
29103728 TGTATATGTC
* * *
29103738 AAGTCAGTTATAGGTTTATGCCCAGAAAATATTTG
1 AAGTCAGTTATAGATTTATG-CCAAAAAAAATTTG
* *
29103773 AAGTCAGTTGTATATTTATGCCAAAAAAAATTTG
1 AAGTCAGTTATAGATTTATGCCAAAAAAAATTTG
29103807 A
1 A
29103808 TTTATATATG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
34 13 0.43
35 17 0.57
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (34 bp):
AAGTCAGTTATAGATTTATGCCAAAAAAAATTTG
Found at i:29108117 original size:73 final size:73
Alignment explanation
Indices: 29107976--29108118 Score: 223
Period size: 73 Copynumber: 2.0 Consensus size: 73
29107966 TTAAAATTTG
* ***
29107976 AGTAGTAGAATATTGAAAGCATTTTTTACTAGAAAACGCCTTTAATAATCTTAAAAGTTTTTTTA
1 AGTAGTAGAATATTGAAAGCATTTTTTACTAGAAAACGCCTTTAATAATCTTAAAAATTTTAAAA
29108041 AAAAAATT
66 AAAAAATT
** *
29108049 AGTAGTAGAATATTGAAAGTGTTTTTTACTAGAAAATGCCTTTAATAATCTTAAAAATTTTAAAA
1 AGTAGTAGAATATTGAAAGCATTTTTTACTAGAAAACGCCTTTAATAATCTTAAAAATTTTAAAA
29108114 AAAAA
66 AAAAA
29108119 TTATTGAAGG
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (73 bp):
AGTAGTAGAATATTGAAAGCATTTTTTACTAGAAAACGCCTTTAATAATCTTAAAAATTTTAAAA
AAAAAATT
Found at i:29108421 original size:187 final size:186
Alignment explanation
Indices: 29108049--29108882 Score: 1036
Period size: 185 Copynumber: 4.5 Consensus size: 186
29108039 TAAAAAAATT
* * * **
29108049 AGTAGT-AGAATATTGAAAGTGTTTTTTACTAGAAAATGCCTTTAATAATCTTAAAAATTTTAAA
1 AGTAGTGA-AATATTGAAGGTGTTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAATTTTTTA
* * *
29108113 AAAAAATTATTGAAGGCATTTGTTCTAAAAAAATACCTTCAATAATTTTGTACAAAAATTAAAAA
65 AAAAAATTATTGAAGGCATTTATTCTAAAAAAAGACCTTCAATAATTATGTACAAAAATTAAAAA
*
29108178 GAATTAGTGAAGGTATTTTT-TAGAATAAATGCATTCACTAACCATCTTAAAATTTG
130 GAATTAGTGAAGGTATTTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTG
* * **
29108234 AGTAGT-AAATATTGACGGTGTTTTTTAATAGAAGACACCTTTAATAATCTCAAAAAGTTTTTTA
1 AGTAGTGAAATATTGAAGGTGTTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAA-TTTTTTA
*
29108298 AAAAAATTATTGAAGGCGTTTATTCTAAAAAAAGACCTTCAACTAATTATGTACAAAAATTAAAA
65 AAAAAATTATTGAAGGCATTTATTCTAAAAAAAGACCTTCAA-TAATTATGTACAAAAATTAAAA
* *
29108363 AGAATTAGTGAAGGTATTTTTTTGGAATAAACGCATTCACTAACCATCTTAAAATTTG
129 AGAATTAGTGAAGGTATTTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTG
* * * * * * **
29108421 AGTACTGATATATTGAAGGTATTTTTCACTAGAAGACGCTTTTAATAATCTCAAAAAAATTTTAA
1 AGTAGTGAAATATTGAAGGTGTTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAATTTTTTAA
* * * *
29108486 ATGAAATTATTGAAGGCATTTATTCTCAATAAATG-CCTTCAATAATTATGTACATAAATT-AAA
66 A-AAAATTATTGAAGGCATTTATTCT-AAAAAAAGACCTTCAATAATTATGTACAAAAATTAAAA
* * * * *
29108549 AGAAATCAGTGAAGGTGTTTTTCAAGAATAAACACATTCACTAACCATCTTAAATTTTG
129 AG-AATTAGTGAAGGTATTTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTG
* * * * **
29108608 AGTAGTGAAATATTGAAGCAT-TTTTTCACTAAAAAATGCCTTTAATAATCTCAAAAA-TTTAAA
1 AGTAGTGAAATATTGAAG-GTGTTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAATTTTTTA
** * * * * *
29108671 AAAAAATTATTGAAGGTGTTTATTCTCAAAAAACATCTTTAATAATTATGTACATAAATTAAAAA
65 AAAAAATTATTGAAGGCATTTATTCTAAAAAAAGACCTTCAATAATTATGTACAAAAATTAAAAA
* * * * **
29108736 AAATTATTGAAGGTATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTG
130 GAATTAGTGAAGGTATTTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTG
* *
29108793 AGTAGTGAAATATTGAAGGTTTTTTTTACTAGAAGATGCCTTTAATGATCTCAAAAATTTTTTTA
1 AGTAGTGAAATATTGAAGGTGTTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAA-TTTTTTA
* *
29108858 AAAAAATTATTAAAGGTATTT-TTCT
65 AAAAAATTATTGAAGGCATTTATTCT
29108883 GAAATAAACG
Statistics
Matches: 560, Mismatches: 76, Indels: 25
0.85 0.11 0.04
Matches are distributed among these distances:
184 47 0.08
185 191 0.34
186 60 0.11
187 183 0.33
188 73 0.13
189 6 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.37
Consensus pattern (186 bp):
AGTAGTGAAATATTGAAGGTGTTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAATTTTTTAA
AAAAATTATTGAAGGCATTTATTCTAAAAAAAGACCTTCAATAATTATGTACAAAAATTAAAAAG
AATTAGTGAAGGTATTTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTG
Found at i:29108702 original size:60 final size:59
Alignment explanation
Indices: 29108636--29108771 Score: 134
Period size: 62 Copynumber: 2.2 Consensus size: 59
29108626 CATTTTTTCA
*
29108636 CTAAAAAATGCCTTTAAT-A-ATCT-CAAAAATTTAAAAAAAAATTATTGAAGGTGTTTATT
1 CTAAAAAATGCCTTTAATAATATCTACAAAAA-TT-AAAAAAAATTATTGAAGGTATTT-TT
*** * *
29108695 CTCAAAAAACATCTTTAATAATTATGTACATAAATTAAAAAAAATTATTGAAGGTATTTTT
1 CT-AAAAAATGCCTTTAATAA-TATCTACAAAAATTAAAAAAAATTATTGAAGGTATTTTT
29108756 CTAGAATAAATGCCTT
1 CTA-AA-AAATGCCTT
29108772 CACTAACTGT
Statistics
Matches: 61, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
59 2 0.03
60 14 0.23
61 7 0.11
62 28 0.46
63 5 0.08
64 5 0.08
ACGTcount: A:0.46, C:0.10, G:0.08, T:0.36
Consensus pattern (59 bp):
CTAAAAAATGCCTTTAATAATATCTACAAAAATTAAAAAAAATTATTGAAGGTATTTTT
Found at i:29108754 original size:372 final size:373
Alignment explanation
Indices: 29108057--29108882 Score: 1058
Period size: 372 Copynumber: 2.2 Consensus size: 373
29108047 TTAGTAGTAG
* * * *
29108057 AATATTGAAAGTGTTTTTTACTAGAAAATGCCTTTAATAATCT--TAAAAATTTTAAAAAAAAAT
1 AATATTGAAGGTATTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAAAATTTTAAAAAAAAAT
* * *
29108120 TATTGAAGGCATTTGTTCTAAAAAAATACCTTCAATAATTTTGTACAAAAATTAAAAAGAATTAG
66 TATTGAAGGCATTTATTCTAAAAAAATACCTTCAATAATTATGTACAAAAATTAAAAAGAATCAG
* ** *
29108185 TGAAGGTATTTTTTAGAATAAATGCATTCACTAACCATCTTAAAATTTGAGTAGTAAATATTGAC
131 TGAAGGTATTTTTAAGAATAAACACATTCACTAACCATCTTAAAATTTGAGTAGTAAATATTGAA
* * * * **
29108250 GGTGTTTTTTAATAGAAGACACCTTTAATAATCTCAAAAAGTTTTTTAAAAAAATTATTGAAGGC
196 GATGTTTTTCAATAAAAAACACCTTTAATAATCTCAAAAAG-TTTAAAAAAAAATTATTGAAGGC
* *
29108315 GTTTATTCTAAAAAAAGACCTTCAACTAATTATGTACAAAAATTAAAAAGAATTAGTGAAGGTAT
260 GTTTATTCTAAAAAAACACCTTCAACTAATTATGTACAAAAATTAAAAAAAATTAGTGAAGGTAT
* *
29108380 TTTTTTGGAATAAACGCATTCACTAACCATCTTAAAATTTGAGTACTGA
325 TTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTGAGTACTGA
* * * * **
29108429 TATATTGAAGGTATTTTTCACTAGAAGACGCTTTTAATAATCTCAAAAAAATTTT-AAATGAAAT
1 AATATTGAAGGTATTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAAAATTTTAAAAAAAAAT
* * * *
29108493 TATTGAAGGCATTTATTCTCAATAAATGCCTTCAATAATTATGTACATAAATT-AAAAGAAATCA
66 TATTGAAGGCATTTATTCTAAAAAAATACCTTCAATAATTATGTACAAAAATTAAAAAG-AATCA
* *
29108557 GTGAAGGTGTTTTTCAAGAATAAACACATTCACTAACCATCTTAAATTTTGAGTAGTGAAATATT
130 GTGAAGGTATTTTT-AAGAATAAACACATTCACTAACCATCTTAAAATTTGAGTAGT-AAATATT
* **
29108622 GAAGCAT-TTTTTCACTAAAAAATGCCTTTAATAATCTCAAAAA-TTTAAAAAAAAATTATTGAA
193 GAAG-ATGTTTTTCAATAAAAAACACCTTTAATAATCTCAAAAAGTTTAAAAAAAAATTATTGAA
* * * * * *
29108685 GGTGTTTATTCTCAAAAAACATCTTTAA-TAATTATGTACATAAATTAAAAAAAATTATTGAAGG
257 GGCGTTTATTCTAAAAAAACACCTTCAACTAATTATGTACAAAAATTAAAAAAAATTAGTGAAGG
* * ** *
29108749 TATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTAGTGA
322 TATTTTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTGAGTACTGA
* * * **
29108801 AATATTGAAGGTTTTTTTTACTAGAAGATGCCTTTAATGATCTC-AAAAATTTTTTTAAAAAAAT
1 AATATTGAAGGTATTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAAAATTTTAAAAAAAAAT
* *
29108865 TATTAAAGGTATTT-TTCT
66 TATTGAAGGCATTTATTCT
29108883 GAAATAAACG
Statistics
Matches: 388, Mismatches: 59, Indels: 15
0.84 0.13 0.03
Matches are distributed among these distances:
371 13 0.03
372 175 0.45
373 112 0.29
374 47 0.12
375 40 0.10
376 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.37
Consensus pattern (373 bp):
AATATTGAAGGTATTTTTTACTAGAAGATGCCTTTAATAATCTCAAAAAAATTTTAAAAAAAAAT
TATTGAAGGCATTTATTCTAAAAAAATACCTTCAATAATTATGTACAAAAATTAAAAAGAATCAG
TGAAGGTATTTTTAAGAATAAACACATTCACTAACCATCTTAAAATTTGAGTAGTAAATATTGAA
GATGTTTTTCAATAAAAAACACCTTTAATAATCTCAAAAAGTTTAAAAAAAAATTATTGAAGGCG
TTTATTCTAAAAAAACACCTTCAACTAATTATGTACAAAAATTAAAAAAAATTAGTGAAGGTATT
TTTCTAGAATAAACGCATTCACTAACCATCTTAAAATTTGAGTACTGA
Found at i:29108951 original size:125 final size:125
Alignment explanation
Indices: 29108732--29108956 Score: 319
Period size: 125 Copynumber: 1.8 Consensus size: 125
29108722 ACATAAATTA
* * *
29108732 AAAAAAATTATTGAAGGTATTTTTCTAGAATAAATGCCTTCACTAACTGTCTTAAAATTTGAGTA
1 AAAAAAATTATTAAAGGTATTTTTCTAGAATAAACGCCTTCACTAACTATCTTAAAATTTGAGTA
* ** ** *
29108797 GTGAAATATTGAAGGTTTTTTTTACTAGAAGATGCCTTTAATGATCTCAAAAATTTTTTT
66 GTGAAACATTGAAGGCATTTTACACTAGAAAATGCCTTTAATGATCTCAAAAATTTTTTT
*
29108857 AAAAAAATTATTAAAGGTATTTTTCT-GAAATAAACGCTTTCACTAA-TCATCTTAAAATTTGAG
1 AAAAAAATTATTAAAGGTATTTTTCTAG-AATAAACGCCTTCACTAACT-ATCTTAAAATTTGAG
*
29108920 TAGTGAAACATTGAAGGCATTTTACATTAGAAAATGC
64 TAGTGAAACATTGAAGGCATTTTACACTAGAAAATGC
29108957 ATTCAATAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
124 2 0.02
125 85 0.98
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (125 bp):
AAAAAAATTATTAAAGGTATTTTTCTAGAATAAACGCCTTCACTAACTATCTTAAAATTTGAGTA
GTGAAACATTGAAGGCATTTTACACTAGAAAATGCCTTTAATGATCTCAAAAATTTTTTT
Found at i:29116901 original size:34 final size:34
Alignment explanation
Indices: 29116863--29116927 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
29116853 TAAAATAGCT
* *
29116863 GTATTTTTTATATACAAACGTCACTAATATAACA
1 GTATTTTTCAGATACAAACGTCACTAATATAACA
29116897 GTATTTTTCAGATACAAACGTCACTAATATA
1 GTATTTTTCAGATACAAACGTCACTAATATA
29116928 GTAACGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (34 bp):
GTATTTTTCAGATACAAACGTCACTAATATAACA
Found at i:29122021 original size:26 final size:24
Alignment explanation
Indices: 29121992--29122039 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
29121982 TTTTAATTAA
29121992 TTATTTAAGTATATATATTTATATAT
1 TTATTTAA-T-TATATATTTATATAT
*
29122018 TTATTTAATTTTATATTTATAT
1 TTATTTAATTATATATTTATAT
29122040 TAAAAGTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 1 0.05
26 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTATTTAATTATATATTTATATAT
Found at i:29122071 original size:22 final size:24
Alignment explanation
Indices: 29122025--29122078 Score: 76
Period size: 22 Copynumber: 2.3 Consensus size: 24
29122015 TATTTATTTA
*
29122025 ATTTTATATTTATATTAAAAGTATT
1 ATTTTATATTTATA-TAAAAATATT
29122050 ATTTTATATTT-TA-AAAAATATT
1 ATTTTATATTTATATAAAAATATT
29122072 ATTTTAT
1 ATTTTAT
29122079 TAATTTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
22 15 0.54
24 2 0.07
25 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTTATATTTATATAAAAATATT
Found at i:29123365 original size:21 final size:23
Alignment explanation
Indices: 29123334--29123387 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
29123324 TTATATAATT
29123334 ATATATTTATA-TTT-AAAAAATA
1 ATAT-TTTATATTTTAAAAAAATA
29123356 ATATTTTATATTTTAAAAAAATA
1 ATATTTTATATTTTAAAAAAATA
29123379 ATATTTTAT
1 ATATTTTAT
29123388 TAATTTCGGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.20
22 7 0.23
23 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATTTTATATTTTAAAAAAATA
Found at i:29125791 original size:17 final size:17
Alignment explanation
Indices: 29125769--29125804 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
29125759 GTTTAAAGAA
29125769 AATTCAAATTATTTAAT
1 AATTCAAATTATTTAAT
29125786 AATTCAAATTATTTAAT
1 AATTCAAATTATTTAAT
29125803 AA
1 AA
29125805 AGTCTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTCAAATTATTTAAT
Found at i:29130323 original size:6 final size:6
Alignment explanation
Indices: 29130312--29130336 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
29130302 TTGTTGAATG
29130312 TATGCA TATGCA TATGCA TATGCA T
1 TATGCA TATGCA TATGCA TATGCA T
29130337 TTTCATTTTT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (6 bp):
TATGCA
Found at i:29130893 original size:58 final size:58
Alignment explanation
Indices: 29130831--29130944 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 58
29130821 TGTTAATTAA
* ** * *
29130831 GGTCTAACTTTTTCAACAAAAATTAATATGGCTTTATTATTATTGTTATTAGTTTAGT
1 GGTCTAACTTTTTCAACAAAAAGTAATACAGCTTCATTATTATTGTTATTAATTTAGT
* *
29130889 GGTCTAACTTTTTTAGCAAAAAGTAATACAGCTTCATTATTATTGTTATTAATTTA
1 GGTCTAACTTTTTCAACAAAAAGTAATACAGCTTCATTATTATTGTTATTAATTTA
29130945 TGTTTGTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 49 1.00
ACGTcount: A:0.32, C:0.10, G:0.11, T:0.46
Consensus pattern (58 bp):
GGTCTAACTTTTTCAACAAAAAGTAATACAGCTTCATTATTATTGTTATTAATTTAGT
Found at i:29134086 original size:13 final size:16
Alignment explanation
Indices: 29134056--29134102 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
29134046 CATTTTATTA
29134056 TTATTATTTTATCTTT
1 TTATTATTTTATCTTT
29134072 TTATT-TTTT-TC-TT
1 TTATTATTTTATCTTT
* *
29134085 TTATTCTTTAATCTTT
1 TTATTATTTTATCTTT
29134101 TT
1 TT
29134103 GTCAATTGTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 7 0.26
14 5 0.19
15 6 0.22
16 9 0.33
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTATTATTTTATCTTT
Found at i:29135123 original size:27 final size:28
Alignment explanation
Indices: 29135084--29135142 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
29135074 AAAATTGGTT
* *
29135084 TTTTTTTTCTTTTTTATTATTTATTCTA
1 TTTTTTATCTTTTGTATTATTTATTCTA
* * *
29135112 TTTTTTAT-TTTTGTGTTATTTTTTGTA
1 TTTTTTATCTTTTGTATTATTTATTCTA
29135139 TTTT
1 TTTT
29135143 AATTTATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 19 0.73
28 7 0.27
ACGTcount: A:0.12, C:0.03, G:0.05, T:0.80
Consensus pattern (28 bp):
TTTTTTATCTTTTGTATTATTTATTCTA
Found at i:29135232 original size:17 final size:17
Alignment explanation
Indices: 29135174--29135251 Score: 50
Period size: 17 Copynumber: 4.2 Consensus size: 17
29135164 TAAAATAAAT
*
29135174 ATAATAATAAAAAATAAA
1 ATAATAATGAAAAAT-AA
* *
29135192 ATGATAAATGTAAAATTTATA
1 ATAAT-AATG-AAAA-ATA-A
*
29135213 ATAATGAATGAATAA-AA
1 ATAAT-AATGAAAAATAA
29135230 ATAAATAATGAAAAATAA
1 AT-AATAATGAAAAATAA
29135248 ATAA
1 ATAA
29135252 AATATTATAA
Statistics
Matches: 46, Mismatches: 8, Indels: 13
0.69 0.12 0.19
Matches are distributed among these distances:
17 13 0.28
18 12 0.26
19 3 0.07
20 8 0.17
21 10 0.22
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
ATAATAATGAAAAATAA
Found at i:29135675 original size:119 final size:124
Alignment explanation
Indices: 29135414--29135677 Score: 274
Period size: 119 Copynumber: 2.2 Consensus size: 124
29135404 TGATTTTATT
* * * * *
29135414 TACACAATTAAATTTTTTAAAATATTCTAAAAGTATTAAAAATATTTTATAATTTTTTTCAAACA
1 TACA-AATGAAATTTTCTAAAATATTCTAAAAATATTAAAAATATTTTATAAATTTTTGCAAACA
* **
29135479 TAAAAAACATTATTAATAAAAAAATAAAATCACAAGTGATGATTTTATTAAAAATATTTA
65 TAAAAAACATTATTAATAAAAAAATAAAATCACAAGTGATGATCTTATTAAAAATATGCA
* * * *
29135539 TACAAATG-GATTTTCTAAAATATTCTAAAAATGTTATATATATTTTA-AAATTTTTGCAAA-A-
1 TACAAATGAAATTTTCTAAAATATTCTAAAAATATTAAAAATATTTTATAAATTTTTGCAAACAT
** * * * *
29135600 AAAATCAA-A-TATT-ATTTAAAAATAAAGTCGCAAGTGGTGATCTTATTGAAAATATGCA
66 AAAA--AACATTATTAATAAAAAAATAAAATCACAAGTGATGATCTTATTAAAAATATGCA
*
29135658 TATAAA-GAAATTTTCTAAAA
1 TACAAATGAAATTTTCTAAAA
29135678 AAAAAACTAA
Statistics
Matches: 116, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
118 1 0.01
119 52 0.45
120 8 0.07
121 2 0.02
122 13 0.11
123 33 0.28
124 3 0.03
125 4 0.03
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (124 bp):
TACAAATGAAATTTTCTAAAATATTCTAAAAATATTAAAAATATTTTATAAATTTTTGCAAACAT
AAAAAACATTATTAATAAAAAAATAAAATCACAAGTGATGATCTTATTAAAAATATGCA
Found at i:29135732 original size:119 final size:116
Alignment explanation
Indices: 29135440--29135732 Score: 248
Period size: 119 Copynumber: 2.4 Consensus size: 116
29135430 TTAAAATATT
* *
29135440 CTAAAAGTATTAAAAATATTTTATAATTTTTTTCAAACATAAAAAACATTATTAATAAAAAAATA
1 CTAAAAGTGTTAAAAATATTTTA-AA--ATTTTC-AA-ATAAAAAA-ATTATT-ATAAAAAAATA
* ** * * **
29135505 AAATCACAAGTGATGATTTTATTAAAAATATTTATACAAATGGATTTTCTAAAATATT
59 AAATCACAAGTGATGATCTTATTAAAAATATGCATACAAATGAATTTTCTAAAAAAAA
* * * * ** *
29135563 CTAAAAATGTTATATATATTTTAAAATTTTTGCAAA-AAAAATCAAATATTATTTAAAAATAAAG
1 CTAAAAGTGTTAAAAATATTTTAAAA-TTTT-CAAATAAAAA--AATTATTATAAAAAAATAAAA
* * * *
29135627 TCGCAAGTGGTGATCTTATTGAAAATATGCATATAAA-GAAATTTTCTAAAAAAAAAA
62 TCACAAGTGATGATCTTATTAAAAATATGCATACAAATG-AATTTTCT--AAAAAAAA
*
29135684 CTAAAAGTGTTAGAAATATTTTAGAAATTTTCAAATAAAAAAATTATTA
1 CTAAAAGTGTTAAAAATATTTTA-AAATTTTCAAATAAAAAAATTATTA
29135733 ATGGGGTAAT
Statistics
Matches: 137, Mismatches: 24, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
118 1 0.01
119 60 0.44
120 10 0.07
121 41 0.30
122 6 0.04
123 19 0.14
ACGTcount: A:0.51, C:0.06, G:0.07, T:0.36
Consensus pattern (116 bp):
CTAAAAGTGTTAAAAATATTTTAAAATTTTCAAATAAAAAAATTATTATAAAAAAATAAAATCAC
AAGTGATGATCTTATTAAAAATATGCATACAAATGAATTTTCTAAAAAAAA
Found at i:29136677 original size:132 final size:132
Alignment explanation
Indices: 29136440--29136708 Score: 502
Period size: 132 Copynumber: 2.0 Consensus size: 132
29136430 GTCAAGTCAA
*
29136440 TAAAGCTAGCATTGTTCATGATCTATAAACATAAGATTGGTTAATTGAAGAATTGGTAATGAAGA
1 TAAAGCTAGCATTGTTCATGATCTATAAACATAAGATCGGTTAATTGAAGAATTGGTAATGAAGA
* * *
29136505 CAAAAAGTTTGTTTTATCCATAACCGAATACTAAAACTTATAATGTTTGTGTTTATTACCAACAT
66 CAAAAAGTTTGCTTTATCCATAACCGAATACTAAAACTTATAATGTTTATGTTGATTACCAACAT
29136570 GC
131 GC
29136572 TAAAGCTAGCATTGTTCATGATCTATAAACATAAGATCGGTTAATTGAAGAATTGGTAATGAAGA
1 TAAAGCTAGCATTGTTCATGATCTATAAACATAAGATCGGTTAATTGAAGAATTGGTAATGAAGA
29136637 CAAAAAGTTTGCTTTATCCATAACCGAATACTAAAACTTATAATGTTTATGTTGATTACCAACAT
66 CAAAAAGTTTGCTTTATCCATAACCGAATACTAAAACTTATAATGTTTATGTTGATTACCAACAT
29136702 GC
131 GC
29136704 TAAAG
1 TAAAG
29136709 AATCTAATGG
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
132 133 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (132 bp):
TAAAGCTAGCATTGTTCATGATCTATAAACATAAGATCGGTTAATTGAAGAATTGGTAATGAAGA
CAAAAAGTTTGCTTTATCCATAACCGAATACTAAAACTTATAATGTTTATGTTGATTACCAACAT
GC
Found at i:29138014 original size:18 final size:19
Alignment explanation
Indices: 29137965--29138019 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 19
29137955 TGATATTTAT
29137965 AATTAAAATTATTTTTATATCA
1 AATTAAAA--ATTTTTA-ATCA
*
29137987 AA-TAATAATTTTTAAT-A
1 AATTAAAAATTTTTAATCA
*
29138004 AATTAAAAATTATTAA
1 AATTAAAAATTTTTAA
29138020 AATTATTTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 3 0.10
18 13 0.45
19 7 0.24
21 4 0.14
22 2 0.07
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTAAAAATTTTTAATCA
Found at i:29138687 original size:14 final size:15
Alignment explanation
Indices: 29138663--29138691 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
29138653 GGTGCAATTC
29138663 GAATATTTCAAAAAT
1 GAATATTTCAAAAAT
29138678 GAAT-TTTCAAAAAT
1 GAATATTTCAAAAAT
29138692 TATTAAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
GAATATTTCAAAAAT
Found at i:29139294 original size:34 final size:34
Alignment explanation
Indices: 29139209--29139295 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 34
29139199 TAGTGCTTTG
* * *
29139209 CGAAAATGCATTTTTGGAACATTGAAAAAGTTTC
1 CGAAAATGAATTTTTGGTACAATGAAAAAGTTTC
* *
29139243 CAAAAATGAATTTTTGGTACAATGAAGAAGTTTC
1 CGAAAATGAATTTTTGGTACAATGAAAAAGTTTC
*
29139277 TGAAAATGAATTTTTGGTA
1 CGAAAATGAATTTTTGGTA
29139296 AATTTTTATT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.34
Consensus pattern (34 bp):
CGAAAATGAATTTTTGGTACAATGAAAAAGTTTC
Found at i:29139881 original size:17 final size:17
Alignment explanation
Indices: 29139838--29139881 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
29139828 AAATGTTTAA
* *
29139838 AATATACTAAAAATTTT
1 AATATAATATAAATTTT
* *
29139855 ATTATTATATAAATTTT
1 AATATAATATAAATTTT
29139872 AATATAATAT
1 AATATAATAT
29139882 CTACAATGGT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
AATATAATATAAATTTT
Found at i:29147169 original size:29 final size:30
Alignment explanation
Indices: 29147105--29147173 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
29147095 TGCTTAATTT
* * *
29147105 AAAATTAAATATTTAAATAATTATTTAATTC
1 AAAATTAAATATTTAAAT-ATTATATAAATA
*
29147136 AAAATTAAATATTTTAAT-TTATATAAATA
1 AAAATTAAATATTTAAATATTATATAAATA
29147165 AAAATTAAA
1 AAAATTAAA
29147174 CGTCATCCGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (30 bp):
AAAATTAAATATTTAAATATTATATAAATA
Found at i:29147465 original size:14 final size:15
Alignment explanation
Indices: 29147444--29147473 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29147434 AGGGTTATCT
*
29147444 ATTTTTTTTATTCAA
1 ATTTTTTCTATTCAA
29147459 ATTTTTTCTATTCAA
1 ATTTTTTCTATTCAA
29147474 CTGCTCTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTTCTATTCAA
Found at i:29149826 original size:2 final size:2
Alignment explanation
Indices: 29149821--29149851 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29149811 TAAAAAACAG
29149821 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29149852 GAAAGCTTAC
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29155265 original size:14 final size:14
Alignment explanation
Indices: 29155246--29155272 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29155236 AATTTTTAAA
29155246 TTAAAAAAAAAAAC
1 TTAAAAAAAAAAAC
29155260 TTAAAAAAAAAAA
1 TTAAAAAAAAAAA
29155273 TAATATTGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (14 bp):
TTAAAAAAAAAAAC
Found at i:29156384 original size:23 final size:23
Alignment explanation
Indices: 29156356--29156415 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
29156346 AAAAATCGTG
29156356 TTTTTATTTTTAAAACAC-AT-TT
1 TTTTTATTTTTAAAA-ACTATATT
* *
29156378 TTATTTAATTCTAAAAACTATATT
1 TT-TTTATTTTTAAAAACTATATT
29156402 TTTTATATTTTTAA
1 TTTT-TATTTTTAA
29156416 CAAAGATTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
22 4 0.13
23 15 0.50
24 11 0.37
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (23 bp):
TTTTTATTTTTAAAAACTATATT
Found at i:29156431 original size:71 final size:73
Alignment explanation
Indices: 29156314--29156495 Score: 180
Period size: 71 Copynumber: 2.5 Consensus size: 73
29156304 TCTTTATTAA
* * *
29156314 AATT-TGAAAAATATAATTTTCATGTTTTTAACAAAAATCG--TGTTTTTATTTTTAAAACACAT
1 AATTCTGAAAAATATATTTTTTATATTTTTAACAAAAATCGCAT-TTTTTA-TTTTAAAA-ACAT
29156376 T-TTTAT-TT-
63 TGTTTATGTTG
* * *
29156384 AATTCT-AAAAACTATATTTTTTATATTTTTAACAAAGATTGCATTTTTTATTTTAGAAACATTG
1 AATTCTGAAAAA-TATATTTTTTATATTTTTAACAAAAATCGCATTTTTTATTTTAAAAACATTG
*
29156448 TTTTTGTTG
65 TTTATGTTG
* *
29156457 AATTCTGAAAAATAATTTTTTTTCATATTTTCAACAAAA
1 AATTCTGAAAAAT-ATATTTTTT-ATATTTTTAACAAAA
29156496 GCTAAGTTTT
Statistics
Matches: 92, Mismatches: 10, Indels: 15
0.79 0.09 0.13
Matches are distributed among these distances:
70 14 0.15
71 36 0.39
72 8 0.09
73 8 0.09
74 13 0.14
75 13 0.14
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.49
Consensus pattern (73 bp):
AATTCTGAAAAATATATTTTTTATATTTTTAACAAAAATCGCATTTTTTATTTTAAAAACATTGT
TTATGTTG
Found at i:29156653 original size:40 final size:40
Alignment explanation
Indices: 29156597--29156676 Score: 117
Period size: 41 Copynumber: 2.0 Consensus size: 40
29156587 TTCATGTTTA
*
29156597 TAACAAAAATTATA-TTTTTATCTTAGAAATATTGTCTTTT
1 TAACAAAAATTATATTTTTTATCTTAAAAATATTGT-TTTT
* *
29156637 TAACAAATATTCTATTTTTTATCTTAAAAATATTGTTTTT
1 TAACAAAAATTATATTTTTTATCTTAAAAATATTGTTTTT
29156677 GTTAAATTCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 16 0.44
41 20 0.56
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (40 bp):
TAACAAAAATTATATTTTTTATCTTAAAAATATTGTTTTT
Found at i:29156678 original size:111 final size:110
Alignment explanation
Indices: 29156409--29156710 Score: 351
Period size: 111 Copynumber: 2.7 Consensus size: 110
29156399 ATTTTTTATA
* * *
29156409 TTTTTAACAAAGATTGCATTTTTTATTTTAGAAACATTGTTTTTGTTGAATTCTGAAAAATAATT
1 TTTTTAACAAATATT-CATTTTTTATCTTAGAAACATTGTTTTTGTTAAATTCTG-AAAAT-ATT
*
29156474 TTTTTTCATATTTTCAACAAAAGCTAAGTTTTTATCTTAGAAATTGTC
63 TTTTTTCATATTTTCAACAAAAACTAAGTTTTTATCTTAGAAATTGTC
* * * * *
29156522 TTTTCAATAAAGTTTTCATTTTCTATCTTAGAAACATTGTCTTTGTTAAATTCTG-AAAT-TTTT
1 TTTTTAACAAA-TATTCATTTTTTATCTTAGAAACATTGTTTTTGTTAAATTCTGAAAATATTTT
* *
29156585 TTTTCATGTTTAT-AACAAAAATTATA-TTTTTATCTTAGAAATATTGTC
65 TTTTCATATTT-TCAACAAAAACTA-AGTTTTTATCTTAG-AA-ATTGTC
* * * *
29156633 TTTTTAACAAATATTCTATTTTTTATCTTAAAAATATTGTTTTTGTTAAATTCTAAACAATAATT
1 TTTTTAACAAATATTC-ATTTTTTATCTTAGAAACATTGTTTTTGTTAAATTCTGAA-AATATTT
29156698 TTTTTCATATTTT
64 TTTTTCATATTTT
29156711 TAATAAAGGC
Statistics
Matches: 159, Mismatches: 21, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
109 35 0.22
110 8 0.05
111 52 0.33
112 1 0.01
113 48 0.30
114 15 0.09
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (110 bp):
TTTTTAACAAATATTCATTTTTTATCTTAGAAACATTGTTTTTGTTAAATTCTGAAAATATTTTT
TTTCATATTTTCAACAAAAACTAAGTTTTTATCTTAGAAATTGTC
Found at i:29160753 original size:16 final size:16
Alignment explanation
Indices: 29160709--29160755 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
29160699 ATGTTATAAA
29160709 TAAATATTATATTAAT
1 TAAATATTATATTAAT
* *
29160725 TAATAAATT-TATTACT
1 TAA-ATATTATATTAAT
29160741 TAAATATTATATTAA
1 TAAATATTATATTAA
29160756 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATATTATATTAAT
Found at i:29168704 original size:12 final size:12
Alignment explanation
Indices: 29168671--29168709 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
29168661 AAAAATGACG
29168671 AAAGTAAAAAAA
1 AAAGTAAAAAAA
*
29168683 AAAGGAAAAAAA
1 AAAGTAAAAAAA
29168695 AAAGTCAAAATAAA
1 AAAGT-AAAA-AAA
29168709 A
1 A
29168710 CCACGATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
12 15 0.65
13 4 0.17
14 4 0.17
ACGTcount: A:0.79, C:0.03, G:0.10, T:0.08
Consensus pattern (12 bp):
AAAGTAAAAAAA
Found at i:29170050 original size:2 final size:2
Alignment explanation
Indices: 29170043--29170069 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29170033 CTTATAAATA
29170043 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29170070 GGAGGCTGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29176620 original size:30 final size:30
Alignment explanation
Indices: 29176559--29176631 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
29176549 CATTCAATTG
* *
29176559 AGGGTTTAATTGAGTGAAAATATATATTTA
1 AGGGTTCAATTGAGTGAAAATAAATATTTA
29176589 AGGGTTCAATT-AGATGAAAATAAATGA-TTA
1 AGGGTTCAATTGAG-TGAAAATAAAT-ATTTA
**
29176619 AGAATTCAATTGA
1 AGGGTTCAATTGA
29176632 TTCGAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 2 0.06
30 32 0.89
31 2 0.06
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (30 bp):
AGGGTTCAATTGAGTGAAAATAAATATTTA
Found at i:29177761 original size:13 final size:13
Alignment explanation
Indices: 29177743--29177783 Score: 73
Period size: 13 Copynumber: 3.1 Consensus size: 13
29177733 TTCTAGTCAT
29177743 ATTACATAGAATA
1 ATTACATAGAATA
29177756 ATTACATAGAAATA
1 ATTACATAG-AATA
29177770 ATTACATAGAATA
1 ATTACATAGAATA
29177783 A
1 A
29177784 AAGAACATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 14 0.52
14 13 0.48
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
ATTACATAGAATA
Found at i:29177771 original size:14 final size:14
Alignment explanation
Indices: 29177743--29177780 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
29177733 TTCTAGTCAT
29177743 ATTACATAG-AATA
1 ATTACATAGAAATA
29177756 ATTACATAGAAATA
1 ATTACATAGAAATA
29177770 ATTACATAGAA
1 ATTACATAGAA
29177781 TAAAAGAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.29
Consensus pattern (14 bp):
ATTACATAGAAATA
Found at i:29180536 original size:31 final size:31
Alignment explanation
Indices: 29180491--29180549 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
29180481 TAAAAAAATT
29180491 AATATTATAAATAAT-TCTTAAATTATAATAA
1 AATATTATAAATAATAT-TTAAATTATAATAA
29180522 AATATT-TAATATAATATTTAAATTATAA
1 AATATTATAA-ATAATATTTAAATTATAA
29180550 ATTTATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 3 0.12
31 22 0.85
32 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (31 bp):
AATATTATAAATAATATTTAAATTATAATAA
Found at i:29180669 original size:14 final size:14
Alignment explanation
Indices: 29180645--29180706 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
29180635 TATTAATTAA
29180645 TAAAT-TTATAATT
1 TAAATATTATAATT
*
29180658 TAAATATTATAATA
1 TAAATATTATAATT
* *
29180672 TAAAAATTTAAAATT
1 TAAATA-TTATAATT
*
29180687 TAGATATTA-AA-T
1 TAAATATTATAATT
29180699 TAAATATT
1 TAAATATT
29180707 TCATTATAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.20
13 7 0.17
14 15 0.38
15 10 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
TAAATATTATAATT
Found at i:29180678 original size:29 final size:28
Alignment explanation
Indices: 29180638--29180707 Score: 88
Period size: 29 Copynumber: 2.5 Consensus size: 28
29180628 AATGTTATAT
*
29180638 TAATTAATAAATTTATAATTTAAATATTA
1 TAATTAA-AAATTTAAAATTTAAATATTA
*
29180667 TAATATAAAAATTTAAAATTTAGATATTA
1 TAAT-TAAAAATTTAAAATTTAAATATTA
*
29180696 -AATTAAATATTT
1 TAATTAAAAATTT
29180708 CATTATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 8 0.22
28 3 0.08
29 23 0.62
30 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (28 bp):
TAATTAAAAATTTAAAATTTAAATATTA
Found at i:29181891 original size:2 final size:2
Alignment explanation
Indices: 29181884--29181913 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29181874 TTTTAGTTGT
29181884 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29181914 CTTTAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29185709 original size:20 final size:22
Alignment explanation
Indices: 29185663--29185710 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
29185653 AATTTTCTTT
*
29185663 TGTTATTTGATTGTGTTTGCAAT
1 TGTT-TTTGATTGTGTTTGCAAG
*
29185686 TGTTTTTG-TTGTG-TTGCTAG
1 TGTTTTTGATTGTGTTTGCAAG
29185706 TGTTT
1 TGTTT
29185711 ACCAAACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 10 0.43
21 5 0.22
22 4 0.17
23 4 0.17
ACGTcount: A:0.10, C:0.04, G:0.25, T:0.60
Consensus pattern (22 bp):
TGTTTTTGATTGTGTTTGCAAG
Found at i:29187886 original size:6 final size:6
Alignment explanation
Indices: 29187877--29187904 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
29187867 ACTTTGTTTA
29187877 TGTTCT TGTTCT TGTTCT TGTTCT TGTT
1 TGTTCT TGTTCT TGTTCT TGTTCT TGTT
29187905 TGATTTTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.18, T:0.68
Consensus pattern (6 bp):
TGTTCT
Found at i:29188054 original size:58 final size:58
Alignment explanation
Indices: 29187986--29188109 Score: 203
Period size: 58 Copynumber: 2.1 Consensus size: 58
29187976 TTTTATTTGC
* * * *
29187986 TGTTGGATCATGCTCATAGGTGGTGGAAAAAATTTTCTTTCATTTTTTTTCCTGAGTT
1 TGTTGAATCATGCTCATAGGTGATGGAAAAAAATTGCTTTCATTTTTTTTCCTGAGTT
*
29188044 TGTTGAATCATGCTCATAGGTGATGGAAAAAAATTGCTTTTATTTTTTTTCCTGAGTT
1 TGTTGAATCATGCTCATAGGTGATGGAAAAAAATTGCTTTCATTTTTTTTCCTGAGTT
29188102 TGTTGAAT
1 TGTTGAAT
29188110 TTCTATATAG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 61 1.00
ACGTcount: A:0.23, C:0.10, G:0.20, T:0.46
Consensus pattern (58 bp):
TGTTGAATCATGCTCATAGGTGATGGAAAAAAATTGCTTTCATTTTTTTTCCTGAGTT
Found at i:29190719 original size:58 final size:58
Alignment explanation
Indices: 29190654--29190770 Score: 207
Period size: 58 Copynumber: 2.0 Consensus size: 58
29190644 CATTTTTGCA
* *
29190654 AGCAAGAACATGTATTTTCCCTCAATGGTAGGGAAATCATGCTTTTATCCTGTGAACT
1 AGCAAGAACATGTATTTTACCTCAATGGTAGGGAAATCATGCTTTTATCCTGTAAACT
*
29190712 AGCAAGAACATGTATTTTACCTTAATGGTAGGGAAATCATGCTTTTATCCTGTAAACT
1 AGCAAGAACATGTATTTTACCTCAATGGTAGGGAAATCATGCTTTTATCCTGTAAACT
29190770 A
1 A
29190771 TTTTTTTCTT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (58 bp):
AGCAAGAACATGTATTTTACCTCAATGGTAGGGAAATCATGCTTTTATCCTGTAAACT
Found at i:29196534 original size:27 final size:25
Alignment explanation
Indices: 29196493--29196552 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
29196483 TATAATTTTT
* * * *
29196493 ATATTAAATATAATATAAATATATA
1 ATATAAAAAATAAAATAAAAATATA
* *
29196518 ATTTAAAAAATAAAATAATAATATA
1 ATATAAAAAATAAAATAAAAATATA
29196543 ATATAAAAAA
1 ATATAAAAAA
29196553 ATTATTTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
ATATAAAAAATAAAATAAAAATATA
Found at i:29198879 original size:58 final size:52
Alignment explanation
Indices: 29198757--29198971 Score: 204
Period size: 52 Copynumber: 4.0 Consensus size: 52
29198747 TATAACCATA
* * * * *
29198757 CAAACTTGCCCATTAAGAAT-CTTTCTCCTCTT-AGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAGAATCCTCT-TCCTCTTGA-AATTCTTCTCTTGCAAGT
* * *
29198809 CAAACTTGCCTATTAATAATCCAT-TTCCT-TTTAGAATTCTTCTCTTGACTTTGCAAGT
1 CAAACTTACCTATTAAGAATCC-TCTTCCTCTTGA-AATTC-T-TC-T--C-TTGCAAGT
*
29198867 CAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCTCTTGCAAGT
1 CAAACTTACCTATTAAGAATCCTCTTCCTCTTGAAATTCTTCTCTTGCAAGT
* * *
29198919 CAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCTTTTGTAAGT
1 CAAACTTACCTATTAAGAATCCTCTTCCTCTTGAAATTCTTCTCTTGCAAGT
29198971 C
1 C
29198972 TTCTTGTCCA
Statistics
Matches: 142, Mismatches: 10, Indels: 22
0.82 0.06 0.13
Matches are distributed among these distances:
51 2 0.01
52 88 0.62
53 4 0.03
54 3 0.02
55 2 0.01
56 2 0.01
57 3 0.02
58 35 0.25
59 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTACCTATTAAGAATCCTCTTCCTCTTGAAATTCTTCTCTTGCAAGT
Found at i:29198957 original size:110 final size:110
Alignment explanation
Indices: 29198757--29198961 Score: 258
Period size: 110 Copynumber: 1.9 Consensus size: 110
29198747 TATAACCATA
* * *
29198757 CAAACTTGCCCATTAAGAATCTTTCTCCTCTTAGAATTCTTCTCCTGTAAGTCAAACTTGCCTAT
1 CAAACTTACCCATTAAGAATCTTTCTCCTCTTAGAATTCTTCTCCTGCAAGTCAAACTTACCTAT
* *
29198822 TAATAATCCATTTCCTTTTAGAATTCTTCTCTTGACTTTGCAAGT
66 TAAGAATCCATTTCCTTTGAGAATTCTTCTCTTGACTTTGCAAGT
* *
29198867 CAAACTTACCTATTAAGAATCCTCTT-T-CTCTT-GAAATTCTTCTCTTGCAAGTCAAACTTACC
1 CAAACTTACCCATTAAGAAT-CT-TTCTCCTCTTAG-AATTCTTCTCCTGCAAGTCAAACTTACC
*
29198929 TATTAAGAATCC-TCTTTCTCTTGA-AATTCTTCT
63 TATTAAGAATCCAT-TTCCT-TTGAGAATTCTTCT
29198962 TTTGTAAGTC
Statistics
Matches: 82, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
109 2 0.02
110 72 0.88
111 6 0.07
112 2 0.02
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (110 bp):
CAAACTTACCCATTAAGAATCTTTCTCCTCTTAGAATTCTTCTCCTGCAAGTCAAACTTACCTAT
TAAGAATCCATTTCCTTTGAGAATTCTTCTCTTGACTTTGCAAGT
Found at i:29198971 original size:52 final size:52
Alignment explanation
Indices: 29198858--29198971 Score: 210
Period size: 52 Copynumber: 2.2 Consensus size: 52
29198848 TTCTCTTGAC
29198858 TTTGCAAGTCAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCT
1 TTTGCAAGTCAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCT
*
29198910 CTTGCAAGTCAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCT
1 TTTGCAAGTCAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCT
*
29198962 TTTGTAAGTC
1 TTTGCAAGTC
29198972 TTCTTGTCCA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.42
Consensus pattern (52 bp):
TTTGCAAGTCAAACTTACCTATTAAGAATCCTCTTTCTCTTGAAATTCTTCT
Found at i:29199012 original size:11 final size:11
Alignment explanation
Indices: 29198996--29199027 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29198986 GCAATATCTG
29198996 ACAAATCTCTA
1 ACAAATCTCTA
*
29199007 ACAAATCTCAA
1 ACAAATCTCTA
29199018 ACAAATCTCT
1 ACAAATCTCT
29199028 TATGGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:29199231 original size:18 final size:19
Alignment explanation
Indices: 29199198--29199234 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
29199188 ATCTTCAAAA
29199198 CTCGAACTCGAACTCTTCT
1 CTCGAACTCGAACTCTTCT
*
29199217 CTCGAA-TCGAGCTCTTCT
1 CTCGAACTCGAACTCTTCT
29199235 GAACTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.19, C:0.35, G:0.14, T:0.32
Consensus pattern (19 bp):
CTCGAACTCGAACTCTTCT
Found at i:29199994 original size:52 final size:51
Alignment explanation
Indices: 29199852--29200008 Score: 192
Period size: 52 Copynumber: 3.0 Consensus size: 51
29199842 TATAACCATA
* * *
29199852 CAAACTTGCCCATTAAGAATCT-TTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTT-T-CTCTTAGAATTCTTCTCTTGCAAGT
* *
29199904 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCTCTTT-CTCTTAGAATTCTTCTCTTGCAAGT
* *
29199956 CAAACTTACCTATTAAGAATCATCTTTCTCTT-GAAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-TCTTTCTCTTAG-AATTCTTCTCTTGCAAGT
29200008 C
1 C
29200009 TTCTTGTCCA
Statistics
Matches: 93, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
51 1 0.01
52 86 0.92
53 6 0.06
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCTCTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:29200049 original size:11 final size:11
Alignment explanation
Indices: 29200033--29200064 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
29200023 GCAATATCTG
29200033 ACAAATCTCTA
1 ACAAATCTCTA
*
29200044 ACAAATCTCAA
1 ACAAATCTCTA
29200055 ACAAATCTCT
1 ACAAATCTCT
29200065 TATGGGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.28, G:0.00, T:0.25
Consensus pattern (11 bp):
ACAAATCTCTA
Found at i:29200356 original size:25 final size:25
Alignment explanation
Indices: 29200302--29200356 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
29200292 TCAAACCATG
*
29200302 GCTCTTCCCATATCTCGAACTGTCA
1 GCTCTTCCCACATCTCGAACTGTCA
* * *
29200327 ACTCTTCCCACGTTTCGAACCT-TCA
1 GCTCTTCCCACATCTCGAA-CTGTCA
29200352 GCTCT
1 GCTCT
29200357 GATACCACTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.18, C:0.38, G:0.11, T:0.33
Consensus pattern (25 bp):
GCTCTTCCCACATCTCGAACTGTCA
Found at i:29201033 original size:11 final size:11
Alignment explanation
Indices: 29201017--29201069 Score: 97
Period size: 11 Copynumber: 4.8 Consensus size: 11
29201007 GCAATATCTG
29201017 ACAAATCTCAA
1 ACAAATCTCAA
29201028 ACAAATCTCAA
1 ACAAATCTCAA
*
29201039 ATAAATCTCAA
1 ACAAATCTCAA
29201050 ACAAATCTCAA
1 ACAAATCTCAA
29201061 ACAAATCTC
1 ACAAATCTC
29201070 TTATGGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:29205835 original size:15 final size:15
Alignment explanation
Indices: 29205811--29205841 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29205801 TACTACCAAA
29205811 AAAAAAAAAAAAACC
1 AAAAAAAAAAAAACC
*
29205826 AAAAACAAAAAAACC
1 AAAAAAAAAAAAACC
29205841 A
1 A
29205842 TCTCTATCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAACC
Found at i:29209338 original size:18 final size:18
Alignment explanation
Indices: 29209317--29209365 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
29209307 ATTGGAAATT
29209317 AATAAAATATTAATTTTTA
1 AATAAAATATT-ATTTTTA
29209336 ATATAAAATATTATTTTTA
1 A-ATAAAATATTATTTTTA
29209355 AATATAAATAT
1 AATA-AAATAT
29209366 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAAATATTATTTTTA
Found at i:29209353 original size:19 final size:21
Alignment explanation
Indices: 29209318--29209362 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
29209308 TTGGAAATTA
29209318 ATAAAATATTAATTTTT-AAT
1 ATAAAATATTAATTTTTAAAT
29209338 ATAAAATATT-ATTTTTAAAT
1 ATAAAATATTAATTTTTAAAT
29209358 ATAAA
1 ATAAA
29209363 TATAAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTAATTTTTAAAT
Found at i:29209387 original size:2 final size:2
Alignment explanation
Indices: 29209380--29209404 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29209370 ATAAATAAAT
29209380 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
29209405 CAAAGCGGGT
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:29210431 original size:103 final size:103
Alignment explanation
Indices: 29210252--29210444 Score: 284
Period size: 103 Copynumber: 1.9 Consensus size: 103
29210242 AACCTAAGAT
*
29210252 AAGACAGAAGTAAATTTCATTTGAGATCATGAATGATGATATAGGTTCTATGAAAGCCTATGATA
1 AAGACAGAAGTAAATTTCATTTGAGATCATGAATGATGATATAGGTTCCATGAAAGCCTATGATA
*
29210317 GAAGATTATTTATACTGCAAAGATTAGTAGCCCAAGGC
66 GAAGATCATTTATACTGCAAAGATTAGTAGCCCAAGGC
* *
29210355 AAGACAGACA-TAAA-TTCTATTTGAGATCATGAATGGTGATATAGGTTCCATGGAAGCCTATGA
1 AAGACAGA-AGTAAATTTC-ATTTGAGATCATGAATGATGATATAGGTTCCATGAAAGCCTATGA
* *
29210418 T-GAAAGGTCATTTATACTGTAAAGATT
64 TAG-AAGATCATTTATACTGCAAAGATT
29210445 TGTATGAGCC
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
102 4 0.05
103 76 0.94
104 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (103 bp):
AAGACAGAAGTAAATTTCATTTGAGATCATGAATGATGATATAGGTTCCATGAAAGCCTATGATA
GAAGATCATTTATACTGCAAAGATTAGTAGCCCAAGGC
Found at i:29210699 original size:131 final size:131
Alignment explanation
Indices: 29210465--29210700 Score: 292
Period size: 131 Copynumber: 1.8 Consensus size: 131
29210455 GATATTGGGT
* * * *
29210465 AACTAAAAGAAGTTAGGTAAAAAGACGCTAGCTATAATCAAAAAACGAGTTGATATCAACATGTT
1 AACTAAAAAAAGTTAGATAAAAAGACACTAGCTATAATCAAAAAACAAGTTGATATCAACATGTT
* * ** * * *
29210530 CCATCATGTGACGCAGAAGGTAAATATCCACATTATTTGACTAAACCAATAGATATGAAAGATGA
66 CCATAATGTAAAACAAAAGGCAAATACCCACATTATTTGACTAAACCAATAGATATGAAAGATGA
29210595 A
131 A
* * * ***
29210596 AACTAAAAAAAGTTAGATAGAAAGACACTTGCTATAATCAAAAAATAAGTTGATATCAGTGTGTT
1 AACTAAAAAAAGTTAGATAAAAAGACACTAGCTATAATCAAAAAACAAGTTGATATCAACATGTT
* * *
29210661 TCATAATGTAAAACAAAAGGCAGATGCCCACATTATTTGA
66 CCATAATGTAAAACAAAAGGCAAATACCCACATTATTTGA
29210701 AAAAAATTAA
Statistics
Matches: 85, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
131 85 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (131 bp):
AACTAAAAAAAGTTAGATAAAAAGACACTAGCTATAATCAAAAAACAAGTTGATATCAACATGTT
CCATAATGTAAAACAAAAGGCAAATACCCACATTATTTGACTAAACCAATAGATATGAAAGATGA
A
Found at i:29213416 original size:786 final size:785
Alignment explanation
Indices: 29211940--29213692 Score: 2297
Period size: 786 Copynumber: 2.2 Consensus size: 785
29211930 TAAGGCTCTG
* * *
29211940 TGTAAAAAAAAAGATCAAGC-TCTATGGCCTTTGATTGGTCCAAAATCAATTACATGGGGCTGAA
1 TGTAAAAAAAAAGACCCAGCGGCTATGGCCTTTGATT-GTCCAAAATCAATTACATGGGGCTGAA
** * * * * * *
29212004 GGGAAAAATTGTTAGGAAAATAAGG-TCTAGCCCCATGTAATTGATTTTGGACCAATTAAAAGTC
65 GGGGGAAATTGTTAGGAAAAT-GGGATCCAGCCCCATGTAATTGGTTTTGGACCAATCAAAGGCC
* *
29212068 ATGGGCCTTGGTA-TTTCTTTTTACACAGAACCCTAACTACTTAATAAAAAGAAAGACCAAGGTC
129 ATGGGCCTTAGTATTTTCTTTTTACACAGAACCCTAGCTACTTAATAAAAA-AAAGACCAAGGTC
* * *
29212132 TATGACCTTTGATTGGTCCAAAACCAATTACATGAAGCTAAACTCTATTTGTTTAACAAGCTTTG
193 CATGACCTTTGATTAGTCAAAAACCAATTACATGAAGCTAAACTCTATTTGTTTAACAAGCTTTG
** *
29212197 ACACCACTTGTTGGACTTGAAGCAATAAACACAATAACACAAAAGTAATATATCGTAATAAACTT
258 ACACCACTTGTTGGACTTGAAGCAATAAACACAATAACACAAAAGTAATATATCACAATAAACCT
* **
29212262 ACAGCAATAGACAACAATCAACAAGAAAAAATGTAAGAAAAATAAAGCACGTCAAAATTTATGTG
323 ACAGCAATAGACAACAATCAACAAGAAAAAA-GTAAGAAAAATAAAGCACGGCAAAATTTACATG
* *
29212327 AAAAACCTTCTAGTGTAGAGGAAAAAATCACAGACCATCAGAAAAAACTTCACTATTAAATAATA
387 AAAAACCTTCTAGTGTAGAGGAAAAAATCACAGACCATCAGAAAAAACTTCACTATCAAATAACA
* * * *
29212392 GATATACAAAGTTCTTCTCTAGTTAAAATAAAAGCTAATTAATAACTAAAAAGAGATAATTTGAG
452 GATATACAAAGTTCTTCTCTAGCTAAAATAAAAGCTAATCAACAACTAAAAAGAGACAATTTGAG
* * * *
29212457 AAATCTCACCAAATAGATGACTCAACAAATATACACTGGATTTGTTCCTAGAGAGCTTCACACCT
517 AAATCTCACAAAATAGATGACTCAACAAATACACACTAGATTTGTTCCTAGAGAGCTTCACAACT
* * ** *
29212522 GATCTTCACCGTTCAAAATGTAAAACTATAATCGTAAACTACTGATAAAATTTTAGTTCAATCGG
582 GATCTTCACCGTTCAAAATGTAAAACTATAATCATAAACTACTGATAAAATTTCAACTCAATCGA
* * ** *
29212587 ATTACGGACCGACTTTCATTCAACTAACTCTTTATTCTCCCTATTTTCTCTATTTGTTT-GCTTT
647 ACTACGGACCGACTTTCATTCAACCAACTCTCCATTCTCCCTATTCTCTCTATTTGTTTGGCTTT
* * * *
29212651 TCTTCTTTCTTTTATTGGTTTGTGACACCACCTTAAAACAGTCACACCTCTTTTTATTAAGTAGC
712 T-TTCTTTCTTTTATTGGTTTGCGACACCACCTTAAAACAGCCACACCACTTTTTATTAAATAGC
***
29212716 TAGGGGTTTA
776 TAGGGCCCTA
* * *
29212726 TGTAAAAAAAAAGA-CCAGCGGCCATGGCCTTTGATTAGTCCAAAACCAATTACATGGGGCTGGA
1 TGTAAAAAAAAAGACCCAGCGGCTATGGCCTTTGATT-GTCCAAAATCAATTACATGGGGCTGAA
* * *
29212790 GGGGGAGATTGTTAAGAAAATGGGATCCAACCCCATGTAATTGGTTTTGGACCAATCAAAGGCCA
65 GGGGGAAATTGTTAGGAAAATGGGATCCAGCCCCATGTAATTGGTTTTGGACCAATCAAAGGCCA
* * *
29212855 TGGGCTTTTGTATTTTTTTTTTACACAGAACCCTAGCTACTTAATAAAAAAAATGACCAAGGTCC
130 TGGGCCTTAGTATTTTCTTTTTACACAGAACCCTAGCTACTTAATAAAAAAAA-GACCAAGGTCC
* * *
29212920 ATGGCCTTTGATTAGTCAAAAACCAATTACATG-AGACTAGA-TCTCATTT-TCTTAATAAGCTT
194 ATGACCTTTGATTAGTCAAAAACCAATTACATGAAG-CTAAACTCT-ATTTGT-TTAACAAGCTT
* * *
29212982 TGATATCACTTGTTAGG-CTTGAAGCAATAAAGACAATAACACATAAA-TAATATATCACAATAA
256 TGACACCACTTGTT-GGACTTGAAGCAATAAACACAATAACACA-AAAGTAATATATCACAATAA
* * * * *
29213045 ACCTATAGCAAT-GACAACAATCAACAATAAAAAA-TACAGAAAAAATAGAGCATGGCAAGATTT
319 ACCTACAGCAATAGACAACAATCAACAAGAAAAAAGTA-AG-AAAAATAAAGCACGGCAAAATTT
**
29213108 ACATGAAAAATCCTTC-AGTGTAGAGGAAAAAATCATGGACCATCAGAAAAAAC-TCTACTATCA
382 ACATGAAAAA-CCTTCTAGTGTAGAGGAAAAAATCACAGACCATCAGAAAAAACTTC-ACTATCA
* * *
29213171 AATAACGGATATACAAAGTTCTTTTCTAGCTAAAACT-AAAGCTAATCAACAATTAAAAAGAGAC
445 AATAACAGATATACAAAGTTCTTCTCTAGCTAAAA-TAAAAGCTAATCAACAACTAAAAAGAGAC
* *
29213235 AATTTGAGAAATCTCACAAAATAGGTGA-TGCAACAAATACACACTAGATTTGTTCTTAGAGAGC
509 AATTTGAGAAATCTCACAAAATAGATGACT-CAACAAATACACACTAGATTTGTTCCTAGAGAGC
* **
29213299 TTCA-AACTGATCTTCACCGTGTC-AAATGTAAAACTCTAATCATAAACATGTTGATAAAATTTC
573 TTCACAACTGATCTTCACCGT-TCAAAATGTAAAACTATAATCATAAAC-TACTGATAAAATTTC
* * * *
29213362 AACTCAATCGAACTATGGACTGAC-TTCTATTCAACCAACTCTCCCTTTTCCCTATTCTCTCTAT
636 AACTCAATCGAACTACGGACCGACTTTC-ATTCAACCAACTCTCCATTCTCCCTATTCTCTCTAT
* * * *
29213426 TTTTTTGGCTTTTTTTTTTCTTTTTTTGGTTTGCGACACCACCTTAAAACAGCCCCACCACTTTT
700 TTGTTTGGCTTTTTTCTTTCTTTTATTGGTTTGCGACACCACCTTAAAACAGCCACACCACTTTT
29213491 TATTAAATAGCTAGGGCCCTA
765 TATTAAATAGCTAGGGCCCTA
* *
29213512 TGTAAAAAAAAAAACCCAAG-GGCTATGGCCTTTGATTGATTCAAAATCAATTACATGGGGCTGA
1 TGTAAAAAAAAAGACCC-AGCGGCTATGGCCTTTGATTG-TCCAAAATCAATTACATGGGGCTGA
* *
29213576 AGGGGGACATTGTTAGGAAAATGGGATCCAGCCCCATGTAATTGGTTTTGAACCAATCAAAGGCC
64 AGGGGGAAATTGTTAGGAAAATGGGATCCAGCCCCATGTAATTGGTTTTGGACCAATCAAAGGCC
* * **
29213641 ATAGGCCTTAGT-TTTTCTTTTTACACAGAGCTTTAGCTACTTAATAAAAAAA
129 ATGGGCCTTAGTATTTTCTTTTTACACAGAACCCTAGCTACTTAATAAAAAAA
29213693 GGTGAGGTTG
Statistics
Matches: 843, Mismatches: 102, Indels: 44
0.85 0.10 0.04
Matches are distributed among these distances:
784 2 0.00
785 51 0.06
786 507 0.60
787 276 0.33
788 7 0.01
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (785 bp):
TGTAAAAAAAAAGACCCAGCGGCTATGGCCTTTGATTGTCCAAAATCAATTACATGGGGCTGAAG
GGGGAAATTGTTAGGAAAATGGGATCCAGCCCCATGTAATTGGTTTTGGACCAATCAAAGGCCAT
GGGCCTTAGTATTTTCTTTTTACACAGAACCCTAGCTACTTAATAAAAAAAAGACCAAGGTCCAT
GACCTTTGATTAGTCAAAAACCAATTACATGAAGCTAAACTCTATTTGTTTAACAAGCTTTGACA
CCACTTGTTGGACTTGAAGCAATAAACACAATAACACAAAAGTAATATATCACAATAAACCTACA
GCAATAGACAACAATCAACAAGAAAAAAGTAAGAAAAATAAAGCACGGCAAAATTTACATGAAAA
ACCTTCTAGTGTAGAGGAAAAAATCACAGACCATCAGAAAAAACTTCACTATCAAATAACAGATA
TACAAAGTTCTTCTCTAGCTAAAATAAAAGCTAATCAACAACTAAAAAGAGACAATTTGAGAAAT
CTCACAAAATAGATGACTCAACAAATACACACTAGATTTGTTCCTAGAGAGCTTCACAACTGATC
TTCACCGTTCAAAATGTAAAACTATAATCATAAACTACTGATAAAATTTCAACTCAATCGAACTA
CGGACCGACTTTCATTCAACCAACTCTCCATTCTCCCTATTCTCTCTATTTGTTTGGCTTTTTTC
TTTCTTTTATTGGTTTGCGACACCACCTTAAAACAGCCACACCACTTTTTATTAAATAGCTAGGG
CCCTA
Found at i:29225600 original size:24 final size:24
Alignment explanation
Indices: 29225557--29225618 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
29225547 TATATATAAA
* *
29225557 TTATTTTTTTATTATTTATTTAATT
1 TTATATTTTTA-TATATATTTAATT
29225582 TTATATTTTTATATATATTTAATT
1 TTATATTTTTATATATATTTAATT
29225606 TTATA-TTTTATAT
1 TTATATTTTTATAT
29225619 TAACAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 8 0.23
24 17 0.49
25 10 0.29
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (24 bp):
TTATATTTTTATATATATTTAATT
Found at i:29225610 original size:12 final size:12
Alignment explanation
Indices: 29225573--29225613 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
29225563 TTTTATTATT
29225573 TATTTAATTTTA
1 TATTTAATTTTA
29225585 TATTT--TTATATA
1 TATTTAATT-T-TA
29225597 TATTTAATTTTA
1 TATTTAATTTTA
29225609 TATTT
1 TATTT
29225614 TATATTAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
10 2 0.08
11 1 0.04
12 19 0.76
13 1 0.04
14 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAATTTTA
Found at i:29225633 original size:20 final size:21
Alignment explanation
Indices: 29225608--29225657 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
29225598 ATTTAATTTT
*
29225608 ATATTTTATA-TTAACAAATA
1 ATATTTTATATTTAAAAAATA
29225628 ATATTTTATATTTAAAAAATA
1 ATATTTTATATTTAAAAAATA
29225649 ATATTTTAT
1 ATATTTTAT
29225658 TAATTTCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTTTATATTTAAAAAATA
Found at i:29227322 original size:7 final size:7
Alignment explanation
Indices: 29227310--29227347 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
29227300 TTCCGTCAAT
29227310 CACGGGA
1 CACGGGA
29227317 CACGGGA
1 CACGGGA
29227324 CACGGGA
1 CACGGGA
29227331 CACGGGA
1 CACGGGA
*
29227338 CATGGGA
1 CACGGGA
29227345 CAC
1 CAC
29227348 ATGCTCGATG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.29, C:0.29, G:0.39, T:0.03
Consensus pattern (7 bp):
CACGGGA
Found at i:29231278 original size:25 final size:26
Alignment explanation
Indices: 29231247--29231313 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
29231237 ATTATGTAAC
29231247 ATTAAAATATTAAAAAAAT-TTTATT
1 ATTAAAATATTAAAAAAATATTTATT
***
29231272 ATTAAAATA-TATTGAAATGATTTATT
1 ATTAAAATATTAAAAAAAT-ATTTATT
29231298 ATTAAAATTATTAAAA
1 ATTAAAA-TATTAAAA
29231314 CTAAAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 6 0.19
25 9 0.28
26 13 0.41
27 2 0.06
28 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
ATTAAAATATTAAAAAAATATTTATT
Found at i:29231369 original size:19 final size:19
Alignment explanation
Indices: 29231345--29231411 Score: 73
Period size: 19 Copynumber: 3.3 Consensus size: 19
29231335 AATAATATTT
29231345 AATATTATTAAAATAATAA
1 AATATTATTAAAATAATAA
*
29231364 AATATTATT-TAATATATAA
1 AATATTATTAAAATA-ATAA
29231383 ATATTTATTATTAAAATAATAAA
1 A-A--TATTATTAAAATAAT-AA
29231406 AATATT
1 AATATT
29231412 TTTATTGAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
18 4 0.10
19 14 0.35
20 5 0.12
22 10 0.25
23 7 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATATTATTAAAATAATAA
Found at i:29231372 original size:22 final size:22
Alignment explanation
Indices: 29231347--29231434 Score: 85
Period size: 25 Copynumber: 4.0 Consensus size: 22
29231337 TAATATTTAA
29231347 TATTATTAAAATAATAAAATAT
1 TATTATTAAAATAATAAAATAT
*
29231369 TA-T-TTAATAT-AT-AAATATT
1 TATTATTAAAATAATAAAATA-T
29231388 TATTATTAAAATAATAAAAATAT
1 TATTATTAAAATAAT-AAAATAT
*
29231411 TTTTATTGAATAATATATAAAATA
1 TATTATT-AA-AATA-ATAAAATA
29231435 GAAAGATTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
18 5 0.09
19 5 0.09
20 7 0.13
21 7 0.13
22 4 0.07
23 7 0.13
24 7 0.13
25 10 0.19
26 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (22 bp):
TATTATTAAAATAATAAAATAT
Found at i:29231402 original size:26 final size:24
Alignment explanation
Indices: 29231373--29231431 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
29231363 AAATATTATT
29231373 TAATATATAAATATTTATTATTAAAA
1 TAATATATAAATATTT-TTATT-AAA
*
29231399 TAATA-A-AAATATTTTTATTGAA
1 TAATATATAAATATTTTTATTAAA
29231421 TAATATATAAA
1 TAATATATAAA
29231432 ATAGAAAGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 7 0.23
23 6 0.20
24 11 0.37
25 1 0.03
26 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
TAATATATAAATATTTTTATTAAA
Found at i:29231622 original size:24 final size:24
Alignment explanation
Indices: 29231594--29231639 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
29231584 ACTTGATTAG
* * *
29231594 AATTATATAAATATTTTTTTAAAA
1 AATTAAATAAAAATATTTTTAAAA
29231618 AATTAAATAAAAATATTTTTAA
1 AATTAAATAAAAATATTTTTAA
29231640 TAATATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTAAATAAAAATATTTTTAAAA
Found at i:29236224 original size:20 final size:21
Alignment explanation
Indices: 29236199--29236238 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
29236189 CTATTAAAAA
29236199 TATTTTT-TAAAATAATTTTG
1 TATTTTTCTAAAATAATTTTG
*
29236219 TATTTTTCTAAAATACTTTT
1 TATTTTTCTAAAATAATTTT
29236239 TACTGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.60
Consensus pattern (21 bp):
TATTTTTCTAAAATAATTTTG
Found at i:29236301 original size:8 final size:8
Alignment explanation
Indices: 29236290--29236337 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
29236280 AAATTTTACG
29236290 ATTTATAT
1 ATTTATAT
29236298 ATTTATAT
1 ATTTATAT
*
29236306 -TTTATAAA
1 ATTTAT-AT
29236314 ATATTA-AT
1 AT-TTATAT
29236322 ATTTATAT
1 ATTTATAT
29236330 ATTTATAT
1 ATTTATAT
29236338 TATATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
7 8 0.24
8 22 0.65
9 1 0.03
10 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
ATTTATAT
Found at i:29236365 original size:37 final size:36
Alignment explanation
Indices: 29236295--29236375 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
29236285 TTACGATTTA
29236295 TATATTTATATTTTATAAAATATTAATATTTATATATT
1 TATA-TTATATTTTATAAAATATTAATATTTATA-ATT
*
29236333 TATATTATATTTTAATAAAA-ATT-ATGTATTATAATT
1 TATATTATATTTT-ATAAAATATTAATAT-TTATAATT
*
29236369 TAAATTA
1 TATATTA
29236376 ATATAAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
36 12 0.31
37 17 0.44
38 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
TATATTATATTTTATAAAATATTAATATTTATAATT
Found at i:29236467 original size:27 final size:29
Alignment explanation
Indices: 29236428--29236481 Score: 76
Period size: 27 Copynumber: 1.9 Consensus size: 29
29236418 ATATAATAAT
29236428 TATTATTATTTTAAACTATATTATTTTGA
1 TATTATTATTTTAAACTATATTATTTTGA
* *
29236457 TATT-TTA-TTTATATTATATTATTTT
1 TATTATTATTTTAAACTATATTATTTT
29236482 ATCGTGTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 16 0.70
28 3 0.13
29 4 0.17
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTATTATTTTAAACTATATTATTTTGA
Found at i:29249258 original size:62 final size:62
Alignment explanation
Indices: 29249199--29249316 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 62
29249189 GTCAGAGTCG
* * *
29249199 AGAGTTAATGAGTTACAATAGTGCAGTGGAAGTGGTTGGAGCTATTTGTTGCGCTAGAGTGA
1 AGAGTTAATGAGTTACAATAATGCAGTGGAAGTGGTTGGAGCCATTTGATGCGCTAGAGTGA
* * * *
29249261 AGAGTTACTGAGTTACAATAATTCGGTGGATGTGGTTGGAGCCATTTGATGCGCTA
1 AGAGTTAATGAGTTACAATAATGCAGTGGAAGTGGTTGGAGCCATTTGATGCGCTA
29249317 TGAAGGACGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.26, C:0.10, G:0.32, T:0.31
Consensus pattern (62 bp):
AGAGTTAATGAGTTACAATAATGCAGTGGAAGTGGTTGGAGCCATTTGATGCGCTAGAGTGA
Found at i:29249609 original size:19 final size:18
Alignment explanation
Indices: 29249585--29249620 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29249575 TATAGTATAA
29249585 AATATTAAATTTATATATT
1 AATATTAAATTT-TATATT
*
29249604 AATATTATATTTTATAT
1 AATATTAAATTTTATAT
29249621 AAAAATTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTAAATTTTATATT
Found at i:29249629 original size:18 final size:19
Alignment explanation
Indices: 29249575--29249629 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
29249565 TATATATTTA
*
29249575 TATAGTATAAAATATTAAATT
1 TATA-TATAAAA-ATTATATT
* *
29249596 TATATATTAATATTATATT
1 TATATATAAAAATTATATT
29249615 T-TATATAAAAATTAT
1 TATATATAAAAATTAT
29249630 GTAATAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 12 0.41
19 8 0.28
20 5 0.17
21 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
TATATATAAAAATTATATT
Found at i:29249950 original size:11 final size:11
Alignment explanation
Indices: 29249930--29249965 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
29249920 ATTATTATTT
*
29249930 AAAATTTAATA
1 AAAATATAATA
29249941 AAAATATAATA
1 AAAATATAATA
*
29249952 TAAATATAATA
1 AAAATATAATA
29249963 AAA
1 AAA
29249966 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATATAATA
Found at i:29250030 original size:30 final size:30
Alignment explanation
Indices: 29249940--29250030 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 30
29249930 AAAATTTAAT
29249940 AAAAATATAATATAAATATAATAAAAT-TTA
1 AAAAATATAATATAAATAT-ATAAAATATTA
* * * *
29249970 AAAAATATATTTTATAT-TA-ACACAAAATTA
1 AAAAATATAATATAAATATATA-A-AATATTA
*
29250000 AAAAATATAATATAAATATATAAATTATTA
1 AAAAATATAATATAAATATATAAAATATTA
29250030 A
1 A
29250031 TATTTTATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
27 1 0.02
28 2 0.04
29 3 0.06
30 37 0.79
31 3 0.06
32 1 0.02
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAAATATAATATAAATATATAAAATATTA
Found at i:29254977 original size:17 final size:17
Alignment explanation
Indices: 29254955--29254988 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29254945 ATCGTCTCTT
*
29254955 TTCACTTTGCATGTGAA
1 TTCACTTTGAATGTGAA
29254972 TTCACTTTGAATGTGAA
1 TTCACTTTGAATGTGAA
29254989 ATTGATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (17 bp):
TTCACTTTGAATGTGAA
Found at i:29256124 original size:2 final size:2
Alignment explanation
Indices: 29256112--29256141 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
29256102 AAATAAATAA
29256112 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29256142 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29256822 original size:20 final size:20
Alignment explanation
Indices: 29256797--29256836 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29256787 TTTTCGATAA
* *
29256797 GTTTTGATTTGATTTGATTT
1 GTTTTGATCTGATTCGATTT
29256817 GTTTTGATCTGATTCGATTT
1 GTTTTGATCTGATTCGATTT
29256837 TATGAGATTA
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:0.15, C:0.05, G:0.20, T:0.60
Consensus pattern (20 bp):
GTTTTGATCTGATTCGATTT
Found at i:29257046 original size:20 final size:21
Alignment explanation
Indices: 29257021--29257070 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
29257011 ATATTTTTAG
29257021 ATATTTTATATTAAAAAATA-
1 ATATTTTATATTAAAAAATAT
**
29257041 ATATTTTATATTCTAAAATAT
1 ATATTTTATATTAAAAAATAT
29257062 ATATTTTAT
1 ATATTTTAT
29257071 TAATTTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTTATATTAAAAAATAT
Found at i:29261645 original size:19 final size:19
Alignment explanation
Indices: 29261609--29261647 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29261599 ATTCAATCTA
**
29261609 ATTTTTTATGATCAAATTT
1 ATTTTTTAAAATCAAATTT
*
29261628 ATTTTTTAAAATCGAATTT
1 ATTTTTTAAAATCAAATTT
29261647 A
1 A
29261648 AGATCAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.54
Consensus pattern (19 bp):
ATTTTTTAAAATCAAATTT
Found at i:29261959 original size:17 final size:17
Alignment explanation
Indices: 29261937--29261970 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29261927 TATGTCTCTT
*
29261937 TTCACTTTGCATGTGAA
1 TTCACTTTGAATGTGAA
29261954 TTCACTTTGAATGTGAA
1 TTCACTTTGAATGTGAA
29261971 ATTGATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (17 bp):
TTCACTTTGAATGTGAA
Found at i:29264008 original size:20 final size:21
Alignment explanation
Indices: 29263983--29264032 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
29263973 ATATTTTTAG
29263983 ATATTTTATATTAAAAAATA-
1 ATATTTTATATTAAAAAATAT
**
29264003 ATATTTTATATTCTAAAATAT
1 ATATTTTATATTAAAAAATAT
29264024 ATATTTTAT
1 ATATTTTAT
29264033 TAATTTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 18 0.67
21 9 0.33
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
ATATTTTATATTAAAAAATAT
Found at i:29266057 original size:27 final size:28
Alignment explanation
Indices: 29266008--29266092 Score: 75
Period size: 27 Copynumber: 3.0 Consensus size: 28
29265998 GAGTTACTTC
*
29266008 TAAATTATAATAAAATATTTAATATAATATA
1 TAAATTATAA-ATAA-A-TTAATATAATATA
* *
29266039 TAAATTTTAAA-AAATTAATATAA-ATTT
1 TAAATTATAAATAAATTAATATAATA-TA
**
29266066 TAAATTATAAATTTATTAATATAATAT
1 TAAATTATAAATAAATTAATATAATAT
29266093 TTATTTTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.02
27 20 0.43
28 12 0.26
29 3 0.07
30 1 0.02
31 9 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TAAATTATAAATAAATTAATATAATATA
Found at i:29266088 original size:14 final size:14
Alignment explanation
Indices: 29266052--29266097 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
29266042 ATTTTAAAAA
29266052 ATTAATATAAATTT
1 ATTAATATAAATTT
*
29266066 -TAAATTATAAATTT
1 ATTAA-TATAAATTT
29266080 ATTAATATAATATTT
1 ATTAATATAA-ATTT
29266095 ATT
1 ATT
29266098 TTTAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.11
14 14 0.52
15 10 0.37
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTAATATAAATTT
Found at i:29266262 original size:10 final size:10
Alignment explanation
Indices: 29266247--29266276 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
29266237 ATCAAAATTT
29266247 TATATTTTAA
1 TATATTTTAA
29266257 TATATTTTAA
1 TATATTTTAA
29266267 T-TATTTTAA
1 TATATTTTAA
29266276 T
1 T
29266277 TGATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TATATTTTAA
Found at i:29278452 original size:24 final size:23
Alignment explanation
Indices: 29278425--29278469 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
29278415 AAGCATGAAA
29278425 TTTAAAACAAGCAAGGCTATAATC
1 TTTAAAACAA-CAAGGCTATAATC
* * *
29278449 TTTATAACTACAATGCTATAA
1 TTTAAAACAACAAGGCTATAA
29278470 GTAAAACGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (23 bp):
TTTAAAACAACAAGGCTATAATC
Found at i:29278488 original size:82 final size:83
Alignment explanation
Indices: 29278344--29278514 Score: 308
Period size: 82 Copynumber: 2.1 Consensus size: 83
29278334 AAGAAAAACA
*
29278344 TAAAACAAGCACGGCTATAATCTTTATAACTAACAATGCTATAAGTAAAACGGATTAAAATTAAA
1 TAAAACAAGCAAGGCTATAATCTTTATAACTAACAATGCTATAAGTAAAACGGATTAAAATTAAA
* *
29278409 CCATAAAAGCATGAAATT
66 CAACAAAAGCATGAAATT
29278427 TAAAACAAGCAAGGCTATAATCTTTATAACT-ACAATGCTATAAGTAAAACGGATTAAAATTAAA
1 TAAAACAAGCAAGGCTATAATCTTTATAACTAACAATGCTATAAGTAAAACGGATTAAAATTAAA
29278491 CAACAAAAGCATGAAATT
66 CAACAAAAGCATGAAATT
29278509 TAAAAC
1 TAAAAC
29278515 TCTAAACTAC
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
82 55 0.65
83 30 0.35
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.25
Consensus pattern (83 bp):
TAAAACAAGCAAGGCTATAATCTTTATAACTAACAATGCTATAAGTAAAACGGATTAAAATTAAA
CAACAAAAGCATGAAATT
Found at i:29294044 original size:4 final size:4
Alignment explanation
Indices: 29294035--29294064 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
29294025 TGAGTACCAA
29294035 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
29294065 GAAAATTAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29294774 original size:21 final size:21
Alignment explanation
Indices: 29294750--29294789 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
29294740 TATATTGTAA
* *
29294750 TTTTCAAATAATACAATTTTT
1 TTTTAAAAAAATACAATTTTT
*
29294771 TTTTAAAAAAATACTATTT
1 TTTTAAAAAAATACAATTT
29294790 ATTCCCAGAG
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:0.42, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
TTTTAAAAAAATACAATTTTT
Found at i:29294962 original size:2 final size:2
Alignment explanation
Indices: 29294957--29294983 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29294947 TCCTCATTTA
29294957 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29294984 ACTCCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29299673 original size:2 final size:2
Alignment explanation
Indices: 29299666--29299703 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
29299656 ATTTCTGTGG
29299666 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29299704 ATGGAGAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:29299690 original size:17 final size:17
Alignment explanation
Indices: 29299668--29299701 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29299658 TTCTGTGGAT
29299668 ATATATATATATATATA
1 ATATATATATATATATA
29299685 ATATATATATATATATA
1 ATATATATATATATATA
29299702 TAATGGAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:29299690 original size:19 final size:19
Alignment explanation
Indices: 29299666--29299705 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
29299656 ATTTCTGTGG
29299666 ATATATATATATATATATA
1 ATATATATATATATATATA
29299685 ATATATATATATATATATA
1 ATATATATATATATATATA
29299704 AT
1 AT
29299706 GGAGAAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATATATATATATATATATA
Found at i:29299961 original size:2 final size:2
Alignment explanation
Indices: 29299954--29300006 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
29299944 AAACGTGCTC
* * * *
29299954 AT AT AT AT AA AT AT AT AT AT GT AA AT AT GT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
29299995 AT AC AT AT AT AT
1 AT AT AT AT AT AT
29300007 GTATGTATAG
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:29299961 original size:146 final size:149
Alignment explanation
Indices: 29299690--29299969 Score: 476
Period size: 146 Copynumber: 1.9 Consensus size: 149
29299680 ATATAATATA
* *
29299690 TATATATATATATAATGGAGAAAGTGAATGAAAGTCACTTTTAAAATTTTCTGTGGAGGAACTGC
1 TATATATATATATAATGGAGAAAGGGAATGAAAGTCACCTTTAAAATTTTCTGTGGAGGAACTGC
** * *
29299755 AGACAGAAACTCATATAGAAGTGGATGATGAGAAAACAAAGAGAAACGTGCTCATTTATATATAT
66 AGACAGAAACTCATATAGAAAAGGATGATGAGAAAACAAAGAGAAACGTGCTCATATATATAAAT
29299820 ATATGTGTGTGTGTGTATG
131 ATATGTGTGTGTGTGTATG
*
29299839 TATATATATA-AT-ATGGAGAAAGGGAATGAAAGTCACCTTTAGAATTTTCTGTGGAGGAACTGC
1 TATATATATATATAATGGAGAAAGGGAATGAAAGTCACCTTTAAAATTTTCTGTGGAGGAACTGC
29299902 AGACAG-AACTCATATAGAAAAGGATGATGAGAAAACAAAGAGAAACGTGCTCATATATATAAAT
66 AGACAGAAACTCATATAGAAAAGGATGATGAGAAAACAAAGAGAAACGTGCTCATATATATAAAT
29299966 ATAT
131 ATAT
29299970 ATATGTAAAT
Statistics
Matches: 124, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
146 58 0.47
147 54 0.44
148 2 0.02
149 10 0.08
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.28
Consensus pattern (149 bp):
TATATATATATATAATGGAGAAAGGGAATGAAAGTCACCTTTAAAATTTTCTGTGGAGGAACTGC
AGACAGAAACTCATATAGAAAAGGATGATGAGAAAACAAAGAGAAACGTGCTCATATATATAAAT
ATATGTGTGTGTGTGTATG
Found at i:29299991 original size:147 final size:146
Alignment explanation
Indices: 29299666--29299995 Score: 470
Period size: 147 Copynumber: 2.2 Consensus size: 146
29299656 ATTTCTGTGG
* * * *
29299666 ATATATATATATATATATAATATATATATATATAT-ATAATGGAGAAAGTGAATGAAAGTCACTT
1 ATATATATATATATATGTAATATGTATATATATATAATAATGGAGAAAGGGAATGAAAGTCACCT
**
29299730 TTAAAATTTTCTGTGGAGGAACTGCAGACAGAAACTCATATAGAAGTGGATGATGAGAAAACAAA
66 TTAAAATTTTCTGTGGAGGAACTGCAGACAGAAACTCATATAGAAAAGGATGATGAGAAAACAAA
29299795 GAGAAACGTGCTCATT
131 GAGAAACGTGCTCATT
* ** *
29299811 -TATATATATATATGTGTGTGTGTGTATGTATATATATAAT-ATGGAGAAAGGGAATGAAAGTCA
1 ATATATATATATATATGT-AATATGTA--TATATATATAATAATGGAGAAAGGGAATGAAAGTCA
*
29299874 CCTTTAGAATTTTCTGTGGAGGAACTGCAGACAG-AACTCATATAGAAAAGGATGATGAGAAAAC
63 CCTTTAAAATTTTCTGTGGAGGAACTGCAGACAGAAACTCATATAGAAAAGGATGATGAGAAAAC
29299938 AAAGAGAAACGTGCTCATAT
128 AAAGAGAAACGTGCTCAT-T
*
29299958 ATATAAATATATATATGTAAATATGTATAATATATATA
1 ATATATATATATATATGT-AATATGTAT-ATATATATA
29299996 TACATATATA
Statistics
Matches: 161, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
144 15 0.09
145 4 0.02
146 47 0.29
147 73 0.45
148 22 0.14
ACGTcount: A:0.43, C:0.08, G:0.19, T:0.31
Consensus pattern (146 bp):
ATATATATATATATATGTAATATGTATATATATATAATAATGGAGAAAGGGAATGAAAGTCACCT
TTAAAATTTTCTGTGGAGGAACTGCAGACAGAAACTCATATAGAAAAGGATGATGAGAAAACAAA
GAGAAACGTGCTCATT
Found at i:29302313 original size:205 final size:205
Alignment explanation
Indices: 29302005--29302641 Score: 747
Period size: 205 Copynumber: 3.0 Consensus size: 205
29301995 AAATTAGTGG
* * * *
29302005 TATTTTTATTTTAACATTGTGTGTGTTTTTATTATGAATTATATAAAATTATAAGTTATTTTCTT
1 TATTCTTATTTTAATATTGTGTGTGTTTTTATTATGAATTATAT-ATA-TAT-A--TATATTC--
29302070 TTTTTTTTTCTCCATTTTTATGCAACATTTCATATGAATTCTTTTTTTAATTTTAGATAAGTTAT
59 TTTTTTTTTCTCCATTTTTATGCAACATTTCATATGAATT-TTTTTTTAATTTTAGATAAGTTAT
29302135 ATATTTT-AAAAAAATCTTCTCAAAAGTATGTATGTCATTTAAAAAAAAAATGTCTATGTGCATA
123 ATATTTTAAAAAAAATCTTCTCAAAAGTATGTATGTCATTTAAAAAAAAAATGTCTATGTGCATA
29302199 TATATTTTAAAAAAATTT
188 TATATTTTAAAAAAATTT
29302217 TATTCTTATTTTAATATTGTGTGTGTTTTTATTATGAATTATATATATATATATATTCTTTTTTT
1 TATTCTTATTTTAATATTGTGTGTGTTTTTATTATGAATTATATATATATATATATTCTTTTTTT
*
29302282 TTCTCCATTTTTATGCAACATTTCATATGAATTTTTTTTAAAATTTTAGATAAGTTATATATTTT
66 TTCTCCATTTTTATGCAACATTTCATATGAATTTTTTTT-TAATTTTAGATAAGTTATATATTTT
* *
29302347 CAAAAAAAAAAAACTTCTCAAATGTATGTATGTCATTTAAAATAAAAAAAAAATGTCTATGTGCA
130 ----AAAAAAAATCTTCTCAAAAGTATGTATGTCA-TT----TAAAAAAAAAATGTCTATGTGCA
*
29302412 TATATATTTTTTAAAAAATTT
186 TATATA-TTTTAAAAAAATTT
** **
29302433 TATTCTTATTTTAATATTGTGTGTGTTTTTATTATGAATTATATATA-AT-TATA-AGTTACTTT
1 TATTCTTATTTTAATATTGTGTGTGTTTTTATTATGAATTATATATATATATATATTCTTTTTTT
* * *
29302495 TT-T-CATTTTTATGCAATATTTCATAT--ATATATTTTTAATTTTAGAT-AGCTTATATATTTT
66 TTCTCCATTTTTATGCAACATTTCATATGAATTTTTTTTTAATTTTAGATAAG-TTATATATTTT
* * * * * **
29302555 CAAAAAAAATCATGTCAAAAGTACT-CATATCATTTAAAATAAAAAATATCTTAT-TTTATATAT
130 -AAAAAAAATCTTCTCAAAAGTA-TGTATGTCATTTAAAA-AAAAAATGTC-TATGTGCATATAT
* ***
29302618 ATCTTAAAATTTTTT
191 ATTTTAAAAAAATTT
29302633 TATTCTTAT
1 TATTCTTAT
29302642 ATAAATTTAT
Statistics
Matches: 378, Mismatches: 31, Indels: 44
0.83 0.07 0.10
Matches are distributed among these distances:
200 23 0.06
201 17 0.04
202 3 0.01
204 8 0.02
205 87 0.23
206 1 0.00
207 8 0.02
208 21 0.06
209 8 0.02
210 31 0.08
211 26 0.07
212 43 0.11
213 7 0.02
214 4 0.01
215 31 0.08
216 60 0.16
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (205 bp):
TATTCTTATTTTAATATTGTGTGTGTTTTTATTATGAATTATATATATATATATATTCTTTTTTT
TTCTCCATTTTTATGCAACATTTCATATGAATTTTTTTTTAATTTTAGATAAGTTATATATTTTA
AAAAAAATCTTCTCAAAAGTATGTATGTCATTTAAAAAAAAAATGTCTATGTGCATATATATTTT
AAAAAAATTT
Found at i:29303716 original size:17 final size:18
Alignment explanation
Indices: 29303673--29303718 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
29303663 TATTATATTT
* *
29303673 ATATATTATTAAGATATA
1 ATATTTTATTAAGAAATA
*
29303691 AT-TTATATTAA-AAATA
1 ATATTTTATTAAGAAATA
29303707 ATATTTTATTAA
1 ATATTTTATTAA
29303719 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 6 0.26
17 15 0.65
18 2 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATTTTATTAAGAAATA
Found at i:29306295 original size:24 final size:24
Alignment explanation
Indices: 29306263--29306310 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
29306253 TTCTGGTCAC
29306263 CATGTTATAGGAAGTGAAAGAAGA
1 CATGTTATAGGAAGTGAAAGAAGA
29306287 CATGTTATAGGAAGTGAAAGAAGA
1 CATGTTATAGGAAGTGAAAGAAGA
29306311 GTGGACAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.29, T:0.21
Consensus pattern (24 bp):
CATGTTATAGGAAGTGAAAGAAGA
Found at i:29312223 original size:3 final size:3
Alignment explanation
Indices: 29312215--29312244 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
29312205 AGGACTTTTC
29312215 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
29312245 AGATAAAGCA
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:29316686 original size:17 final size:19
Alignment explanation
Indices: 29316653--29316687 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29316643 TTGATATCTT
29316653 TAGTAATATTATAAATCAA
1 TAGTAATATTATAAATCAA
29316672 TAGTAAT-TT-TAAATCA
1 TAGTAATATTATAAATCA
29316688 CTATATTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 2 0.12
19 7 0.44
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (19 bp):
TAGTAATATTATAAATCAA
Found at i:29324958 original size:25 final size:26
Alignment explanation
Indices: 29324924--29324983 Score: 88
Period size: 25 Copynumber: 2.3 Consensus size: 26
29324914 AAATAATAAT
*
29324924 AAAAA-TTATTATAATTGTTATT-AA
1 AAAAATTTATTATAATTATTATTAAA
29324948 AAAAATTTATTATAATTATTATTGAAA
1 AAAAATTTATTATAATTATTATT-AAA
29324975 AAAAATTTA
1 AAAAATTTA
29324984 ATGAAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
24 5 0.16
25 16 0.50
27 11 0.34
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (26 bp):
AAAAATTTATTATAATTATTATTAAA
Found at i:29325017 original size:27 final size:27
Alignment explanation
Indices: 29324978--29325030 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
29324968 ATTGAAAAAA
*
29324978 AATTTAATGAAAAATTTATA-TTAAATG
1 AATTTAATG-AAAATTAATATTTAAATG
* *
29325005 AATTTTATTAAAATTAATATTTAAAT
1 AATTTAATGAAAATTAATATTTAAAT
29325031 TTAATTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (27 bp):
AATTTAATGAAAATTAATATTTAAATG
Found at i:29331164 original size:2 final size:2
Alignment explanation
Indices: 29331157--29331185 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
29331147 AAGCAAATAC
29331157 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29331186 TTTGCTTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Done.