Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 59 of 202
Found at i:17443336 original size:15 final size:15
Alignment explanation
Indices: 17443324--17443353 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17443314 AATATAATTT
17443324 TGTAATAATTAATAA
1 TGTAATAATTAATAA
*
17443339 TGTTATAATTAATAA
1 TGTAATAATTAATAA
17443354 AAATTAAATG
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:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TGTAATAATTAATAA
Found at i:17448345 original size:19 final size:19
Alignment explanation
Indices: 17448305--17448348 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17448295 TCCTCAACTC
*
17448305 ATTGTGATTCTTTTTTTCT
1 ATTGTGATTCTTTGTTTCT
*
17448324 ATTGTGATTGTTATGTTT-T
1 ATTGTGATTCTT-TGTTTCT
17448343 ATTGTG
1 ATTGTG
17448349 GGATGCATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.14, C:0.05, G:0.18, T:0.64
Consensus pattern (19 bp):
ATTGTGATTCTTTGTTTCT
Found at i:17451490 original size:33 final size:34
Alignment explanation
Indices: 17451432--17451498 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
17451422 ATGAAAGATA
17451432 AATATATTAATTTGAATTTTTTTATAAA-AAAAT
1 AATATATTAATTTGAATTTTTTTATAAATAAAAT
* *
17451465 AATA-ATTTATTTTAATTATTTTTATAAATAAAAT
1 AATATATTAATTTGAATT-TTTTTATAAATAAAAT
17451499 TAACTTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
32 11 0.37
33 14 0.47
34 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (34 bp):
AATATATTAATTTGAATTTTTTTATAAATAAAAT
Found at i:17451852 original size:85 final size:84
Alignment explanation
Indices: 17451727--17451881 Score: 251
Period size: 85 Copynumber: 1.8 Consensus size: 84
17451717 ATGTTTGAGC
*
17451727 AATTAATAATTAATAAATATATTTTTTAATTCATATTTTTAATTAATAACTCTTTTATTTATATA
1 AATTAATAATTAATAAATATATTTTTTAATTAATATTTTTAATTAATAACTCTTTTATTTATATA
17451792 AATAAAATAATAAATATGT
66 AATAAAATAATAAATATGT
17451811 AATTATATAA-TAA-AAATATATTTTTTATATATAATATTTTTAATTAATAACTCTTTTATTTAT
1 AATTA-ATAATTAATAAATATATTTTTTA-AT-TAATATTTTTAATTAATAACTCTTTTATTTAT
*
17451874 ATATATAA
63 ATAAATAA
17451882 TAAAAATTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
83 14 0.21
84 10 0.15
85 42 0.64
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (84 bp):
AATTAATAATTAATAAATATATTTTTTAATTAATATTTTTAATTAATAACTCTTTTATTTATATA
AATAAAATAATAAATATGT
Found at i:17455356 original size:44 final size:44
Alignment explanation
Indices: 17455306--17455402 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 44
17455296 ATGACTTGCA
* * * *
17455306 TATAGTATACATTCTTGAATTGCATAATATACATTCTTGCCTCC
1 TATAGTATACATACTTGAATTGCATAATACACATACTTGACTCC
* * *
17455350 TATAGTACACATACTTGACTTGCATAATACACATACTTGACTCG
1 TATAGTATACATACTTGAATTGCATAATACACATACTTGACTCC
*
17455394 TATAATATA
1 TATAGTATA
17455403 GTGGTTCACA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.09, T:0.37
Consensus pattern (44 bp):
TATAGTATACATACTTGAATTGCATAATACACATACTTGACTCC
Found at i:17455380 original size:22 final size:22
Alignment explanation
Indices: 17455297--17455400 Score: 84
Period size: 22 Copynumber: 4.6 Consensus size: 22
17455287 ATATAATTTA
* *
17455297 TGACTTGCATATAGTATACATTCT
1 TGACTTGCATA-A-TACACATACT
* * *
17455321 TGAATTGCATAATATACATTCT
1 TGACTTGCATAATACACATACT
* * *
17455343 TG-CCTCCTATAGTACACATACT
1 TGACTTGC-ATAATACACATACT
17455365 TGACTTGCATAATACACATACT
1 TGACTTGCATAATACACATACT
* *
17455387 TGACTCGTATAATA
1 TGACTTGCATAATA
17455401 TAGTGGTTCA
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 2 0.03
22 50 0.76
23 4 0.06
24 10 0.15
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (22 bp):
TGACTTGCATAATACACATACT
Found at i:17455450 original size:81 final size:81
Alignment explanation
Indices: 17455363--17455542 Score: 290
Period size: 81 Copynumber: 2.2 Consensus size: 81
17455353 AGTACACATA
*
17455363 CTTGACTTGCATAATACACATACTTGACTCGTATAATATAGTGGTTCACATGTAATTTATGACTT
1 CTTGACTTGCATAATACACATACTTGACTCGTATAATATAGTGGTTCACATGTAATTTATGACTC
*
17455428 GTATGCAATATACGTT
66 GCATGCAATATACGTT
* *
17455444 CTTGACTCT-CATAATACACATGCTTGACTCGTATAATATAGTGGTTCGCATGTAATTTATGACT
1 CTTGACT-TGCATAATACACATACTTGACTCGTATAATATAGTGGTTCACATGTAATTTATGACT
*
17455508 CGCATGCAATATTCGTT
65 CGCATGCAATATACGTT
*
17455525 CTTGACTCGCATAATACA
1 CTTGACTTGCATAATACA
17455543 GTGGTTCGCA
Statistics
Matches: 91, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
81 90 0.99
82 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (81 bp):
CTTGACTTGCATAATACACATACTTGACTCGTATAATATAGTGGTTCACATGTAATTTATGACTC
GCATGCAATATACGTT
Found at i:17455457 original size:125 final size:125
Alignment explanation
Indices: 17455246--17455478 Score: 288
Period size: 125 Copynumber: 1.9 Consensus size: 125
17455236 TTCTTGCCTC
* * * ** * *
17455246 GCATAGTACACTTACTTGACTTGCAAAATATAGTGGTTTGCATATAATTTATGACTTGCATATAG
1 GCATAATACACATACTTGACTCGCAAAATATAGTGGTTCACATATAATTTATGACTTGCATACAA
* * *
17455311 TATACATTCTTGAATTGCATAATATACATTCTTGCCTCCTATAGTACACATACTTGACTT
66 TATACATTCTTGAATTGCATAATACACATGCTTGACTCCTATAGTACACATACTTGACTT
* * * * *
17455371 GCATAATACACATACTTGACTCGTATAATATAGTGGTTCACATGTAATTTATGACTTGTATGCAA
1 GCATAATACACATACTTGACTCGCAAAATATAGTGGTTCACATATAATTTATGACTTGCATACAA
* * *
17455436 TATACGTTCTTGACTCT-CATAATACACATGCTTGACTCGTATA
66 TATACATTCTTGAAT-TGCATAATACACATGCTTGACTCCTATA
17455479 ATATAGTGGT
Statistics
Matches: 89, Mismatches: 18, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
125 88 0.99
126 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.37
Consensus pattern (125 bp):
GCATAATACACATACTTGACTCGCAAAATATAGTGGTTCACATATAATTTATGACTTGCATACAA
TATACATTCTTGAATTGCATAATACACATGCTTGACTCCTATAGTACACATACTTGACTT
Found at i:17455725 original size:29 final size:29
Alignment explanation
Indices: 17455685--17455763 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
17455675 ATGTTCACTT
17455685 ATACTAGGGCTCGCACAACAACTTTACAG
1 ATACTAGGGCTCGCACAACAACTTTACAG
* * * * *
17455714 ATACTAGTGCTCACACAATAGCTTTACAT
1 ATACTAGGGCTCGCACAACAACTTTACAG
17455743 ATACTAGGGCTCGCACAACAA
1 ATACTAGGGCTCGCACAACAA
17455764 GGCTTGCACA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (29 bp):
ATACTAGGGCTCGCACAACAACTTTACAG
Found at i:17455817 original size:43 final size:43
Alignment explanation
Indices: 17455724--17455817 Score: 102
Period size: 43 Copynumber: 2.2 Consensus size: 43
17455714 ATACTAGTGC
* * *
17455724 TCACACAATAGCTTTACATATACTAGGGCTCGCACAACAAGGCT
1 TCACACAACAGCTTCACATATAC-AGGGCTCACACAACAAGGCT
* * *
17455768 T-GCACAACAGGTTCACATATA-AGGGCTCACACAACAAGGGGT
1 TCACACAACAGCTTCACATATACAGGGCTCACACAACAA-GGCT
17455810 TCACACAA
1 TCACACAA
17455818 GGGCTCGCGT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
41 15 0.37
42 4 0.10
43 21 0.51
44 1 0.02
ACGTcount: A:0.36, C:0.27, G:0.18, T:0.19
Consensus pattern (43 bp):
TCACACAACAGCTTCACATATACAGGGCTCACACAACAAGGCT
Found at i:17464869 original size:27 final size:28
Alignment explanation
Indices: 17464830--17464888 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
17464820 TTGTAAATGG
* *
17464830 TTTATTTTAAGTTATTTTGTATATT-AT
1 TTTATTTTAAGTTACTTTATATATTAAT
*
17464857 TTTATTTCT-AGTTGCTTTATATATTAAT
1 TTTATTT-TAAGTTACTTTATATATTAAT
17464885 TTTA
1 TTTA
17464889 AAATTATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 20 0.74
28 7 0.26
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTATTTTAAGTTACTTTATATATTAAT
Found at i:17465319 original size:23 final size:23
Alignment explanation
Indices: 17465293--17465338 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17465283 AATTTATTGT
17465293 TTATATTGATGATTTTAAATTTC
1 TTATATTGATGATTTTAAATTTC
17465316 TTATATTGATGATTTTAAATTTC
1 TTATATTGATGATTTTAAATTTC
17465339 CTTACTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (23 bp):
TTATATTGATGATTTTAAATTTC
Found at i:17470145 original size:20 final size:19
Alignment explanation
Indices: 17470120--17470189 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 19
17470110 TTATAAAAAC
17470120 ATTCAAAATAATTTTCACAA
1 ATTCAAAATAATTTTCA-AA
* *
17470140 ATTCAATATAATTTTTAAA
1 ATTCAAAATAATTTTCAAA
*
17470159 ATTCAAAAT-ATTTATAAAA
1 ATTCAAAATAATTT-TCAAA
*
17470178 ATT-AAAAAAATT
1 ATTCAAAATAATT
17470190 CTAAAGAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.19
19 20 0.47
20 15 0.35
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTCAAAATAATTTTCAAA
Found at i:17470162 original size:19 final size:19
Alignment explanation
Indices: 17470120--17470177 Score: 73
Period size: 20 Copynumber: 3.1 Consensus size: 19
17470110 TTATAAAAAC
*
17470120 ATTCAAAATAATTTTCACAA
1 ATTCAAAATAATTTTTA-AA
*
17470140 ATTCAATATAATTTTTAAA
1 ATTCAAAATAATTTTTAAA
*
17470159 ATTCAAAAT-ATTTATAAA
1 ATTCAAAATAATTTTTAAA
17470177 A
1 A
17470178 ATTAAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.26
19 10 0.29
20 15 0.44
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.40
Consensus pattern (19 bp):
ATTCAAAATAATTTTTAAA
Found at i:17470180 original size:19 final size:20
Alignment explanation
Indices: 17470108--17470178 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
17470098 TCCTAACAAA
*
17470108 AATTATAAAAACATTCAAAAT
1 AATTTTAAAAA-ATTCAAAAT
* * *
17470129 AATTTTCACAAATTCAATAT
1 AATTTTAAAAAATTCAAAAT
*
17470149 AATTTT-TAAAATTCAAAAT
1 AATTTTAAAAAATTCAAAAT
17470168 -ATTTATAAAAA
1 AATTT-TAAAAA
17470179 TTAAAAAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 5
0.75 0.15 0.09
Matches are distributed among these distances:
18 4 0.10
19 11 0.28
20 17 0.43
21 8 0.20
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTTAAAAAATTCAAAAT
Found at i:17471642 original size:144 final size:144
Alignment explanation
Indices: 17471382--17471672 Score: 528
Period size: 144 Copynumber: 2.0 Consensus size: 144
17471372 CAAGTTTTCA
17471382 GTATCAAATGTGTTCCATATGATGACCCAATTACAAAAGATATCCCCTATTCAAGTATATCCAAA
1 GTATCAAATGTGTTCCATATGATGACCCAATTACAAAAGATATCCCCTATTCAAGTATATCCAAA
* * * *
17471447 ATAACACTTTCAGTTTTGCAACTAAATATAAAAAAGTTGTAAAGTAGAAGAAGTTGCAAATGAAA
66 AGAACACTTTCAGTTTTACAACTAAATACAAAAAAGTTGTAAAGTAGAAGAAGCTGCAAATGAAA
17471512 GTGTTCTAAAGTTT
131 GTGTTCTAAAGTTT
17471526 GTATCAAATGTGTTCCATATGATGACCCAATTACAAAAGATATCCCCTATTCAAGTATATCCAAA
1 GTATCAAATGTGTTCCATATGATGACCCAATTACAAAAGATATCCCCTATTCAAGTATATCCAAA
* *
17471591 GGAACACTTTTAGTTTTACAACTAAATACAAAAAAGTTGTAAAGTAGAAGAAGCTGCAAATGAAA
66 AGAACACTTTCAGTTTTACAACTAAATACAAAAAAGTTGTAAAGTAGAAGAAGCTGCAAATGAAA
17471656 GTGTTCTAAAGTTT
131 GTGTTCTAAAGTTT
17471670 GTA
1 GTA
17471673 AAACTTTGTA
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
144 141 1.00
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.30
Consensus pattern (144 bp):
GTATCAAATGTGTTCCATATGATGACCCAATTACAAAAGATATCCCCTATTCAAGTATATCCAAA
AGAACACTTTCAGTTTTACAACTAAATACAAAAAAGTTGTAAAGTAGAAGAAGCTGCAAATGAAA
GTGTTCTAAAGTTT
Found at i:17475747 original size:49 final size:49
Alignment explanation
Indices: 17475588--17475775 Score: 164
Period size: 49 Copynumber: 3.8 Consensus size: 49
17475578 CGGTATCCAG
* * **
17475588 ATATGAATA-GCCACTAGTAGGGCATGTTAGTTGCAAACCAGAATGACA-A
1 ATATG-ATAGGCCACTGGTAGGGCATGTTAGTTGCTAACCAG-ATGGGAGA
* * * * * *
17475637 ATGTGCTAGACTACTGGTAGGGCATGCTAGTTGCTAACCAGGTGGGAGA
1 ATATGATAGGCCACTGGTAGGGCATGTTAGTTGCTAACCAGATGGGAGA
* * * *
17475686 ATATGATAGGCCACTGGTAGGGCATATTAGTTGCTAACCAGATTGGCGT
1 ATATGATAGGCCACTGGTAGGGCATGTTAGTTGCTAACCAGATGGGAGA
* * * * * *
17475735 GTATGTTGGGCCACTAGTAGGACATGTTAGTTGTTAACCAG
1 ATATGATAGGCCACTGGTAGGGCATGTTAGTTGCTAACCAG
17475776 GTTGATGGCC
Statistics
Matches: 110, Mismatches: 27, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
48 5 0.05
49 105 0.95
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (49 bp):
ATATGATAGGCCACTGGTAGGGCATGTTAGTTGCTAACCAGATGGGAGA
Found at i:17476100 original size:48 final size:48
Alignment explanation
Indices: 17476022--17476166 Score: 227
Period size: 48 Copynumber: 3.0 Consensus size: 48
17476012 AAGAAATGAT
* * *
17476022 TTGAAAAGAGTAAGTTAATATCAATTTGTATGTGATATATGTTATGTA
1 TTGAAAAGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTA
* *
17476070 TTGAAAAGGGTAAGTTAATATGACTCTGTATATGATATATGTTATGTA
1 TTGAAAAGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTA
* *
17476118 TTGAAAAGAGTAAGTTAATATGACTCTGTATGTGTTAAATGTTATGTA
1 TTGAAAAGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTA
17476166 T
1 T
17476167 AATTACTGAC
Statistics
Matches: 88, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 88 1.00
ACGTcount: A:0.36, C:0.03, G:0.20, T:0.41
Consensus pattern (48 bp):
TTGAAAAGAGTAAGTTAATATGACTCTGTATGTGATATATGTTATGTA
Found at i:17477322 original size:15 final size:17
Alignment explanation
Indices: 17477292--17477323 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
17477282 TTGGTGTGCA
17477292 TTCTTTCTTGTGTCATT
1 TTCTTTCTTGTGTCATT
17477309 TTCTTT-TTGT-TCATT
1 TTCTTTCTTGTGTCATT
17477324 GCTTATTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 4 0.27
17 6 0.40
ACGTcount: A:0.06, C:0.16, G:0.09, T:0.69
Consensus pattern (17 bp):
TTCTTTCTTGTGTCATT
Found at i:17482025 original size:2 final size:2
Alignment explanation
Indices: 17482018--17482051 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
17482008 ATTATAAACA
17482018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17482052 CTTTGCATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17484554 original size:9 final size:9
Alignment explanation
Indices: 17484525--17484561 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17484515 TGAATTTTTA
17484525 AATTCGAAT
1 AATTCGAAT
*
17484534 AACTCGAAT
1 AATTCGAAT
17484543 AATTCGAAT
1 AATTCGAAT
*
17484552 AATACGAAT
1 AATTCGAAT
17484561 A
1 A
17484562 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.27
Consensus pattern (9 bp):
AATTCGAAT
Found at i:17485098 original size:9 final size:9
Alignment explanation
Indices: 17485084--17485112 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
17485074 AATTTCACAT
17485084 TTTATATTA
1 TTTATATTA
17485093 TTTATATTA
1 TTTATATTA
17485102 TTTATATTA
1 TTTATATTA
17485111 TT
1 TT
17485113 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:17486606 original size:18 final size:17
Alignment explanation
Indices: 17486571--17486603 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17486561 TTCATTCATT
17486571 CATTTTTTTCAGTTTTA
1 CATTTTTTTCAGTTTTA
17486588 CATTATTTTT-AGTTTT
1 CATT-TTTTTCAGTTTT
17486604 TACTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.18, C:0.09, G:0.06, T:0.67
Consensus pattern (17 bp):
CATTTTTTTCAGTTTTA
Found at i:17488041 original size:30 final size:30
Alignment explanation
Indices: 17488007--17488066 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
17487997 TGACTTATAG
17488007 TAATATTATAATTGAGCCGGAACTTGATTA
1 TAATATTATAATTGAGCCGGAACTTGATTA
*
17488037 TAATATTATAATTGAGTCGGAACTTGATTA
1 TAATATTATAATTGAGCCGGAACTTGATTA
17488067 ATGGATGACA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (30 bp):
TAATATTATAATTGAGCCGGAACTTGATTA
Found at i:17490743 original size:6 final size:6
Alignment explanation
Indices: 17490732--17490760 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
17490722 TATATAAAAG
17490732 TATGTA TATGTA TATGTA TATGTA TATGT
1 TATGTA TATGTA TATGTA TATGTA TATGT
17490761 GTTTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
TATGTA
Found at i:17495152 original size:57 final size:58
Alignment explanation
Indices: 17495089--17495207 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 58
17495079 TCATTTTCAT
** * *
17495089 TTTTCATTTTAATTTTGGAGGAAACCACT-TTCATTTCCAAATGATT-CC-ATTTCTCCA
1 TTTTCATTTTAATTTTGGAAAAAACCA-TAATAATTTCCAAATG-TTCCCTATTTCTCCA
*
17495146 TTTTCATTTTTATTTTGGAAAAAACCATAATAATTTCCAAATGTTCCCTATTTCTCCA
1 TTTTCATTTTAATTTTGGAAAAAACCATAATAATTTCCAAATGTTCCCTATTTCTCCA
17495204 TTTT
1 TTTT
17495208 ACCATTTCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
56 3 0.06
57 38 0.70
58 13 0.24
ACGTcount: A:0.28, C:0.19, G:0.07, T:0.46
Consensus pattern (58 bp):
TTTTCATTTTAATTTTGGAAAAAACCATAATAATTTCCAAATGTTCCCTATTTCTCCA
Found at i:17497784 original size:98 final size:98
Alignment explanation
Indices: 17497635--17497824 Score: 265
Period size: 98 Copynumber: 1.9 Consensus size: 98
17497625 AGCTTAGGGT
* *
17497635 CATCCAATATGGTAGAAAATCGAAATACTGAAAGTCATCGTTGTCTAGCCACTTAGGATGGTAGA
1 CATCCAAGATGGTAGAAAATCGAAATACTGAAAGCCATCGTTGTCTAGCCACTTAGGATGGTAGA
* *
17497700 ATATGAAAATAGTGAAAGCCATCGTTGTTGGAC
66 ATATGAAAACAGTAAAAGCCATCGTTGTTGGAC
* * * * * *
17497733 CATCCAAGATGGTGGAGAATTGAAATAGTGAAAGCCATTGTTGTC-AGGCCACTTGGGATGGTAG
1 CATCCAAGATGGTAGAAAATCGAAATACTGAAAGCCATCGTTGTCTA-GCCACTTAGGATGGTAG
*
17497797 AATATGAAAACAGTAAAAGTCATCGTTG
65 AATATGAAAACAGTAAAAGCCATCGTTG
17497825 CTAAGCCACC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
97 1 0.01
98 79 0.99
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (98 bp):
CATCCAAGATGGTAGAAAATCGAAATACTGAAAGCCATCGTTGTCTAGCCACTTAGGATGGTAGA
ATATGAAAACAGTAAAAGCCATCGTTGTTGGAC
Found at i:17497833 original size:49 final size:48
Alignment explanation
Indices: 17497643--17497833 Score: 156
Period size: 49 Copynumber: 3.9 Consensus size: 48
17497633 GTCATCCAAT
* * * *
17497643 ATGGTAGAAAATCG-AAATACTGAAAGTCATCGTTGTCTAGCCACTTAGG
1 ATGGTAGAATAT-GAAAATAGTGAAAGCCATCGTTGT-AAGCCACTTAGG
** * *
17497692 ATGGTAGAATATGAAAATAGTGAAAGCCATCGTTGTTGGACCA-TCCAAG
1 ATGGTAGAATATGAAAATAGTGAAAGCCATCGTTGTAAG-CCACT-TAGG
* * *
17497741 ATGGTGGAGAAT-TG-AAATAGTGAAAGCCATTGTTGTCAGGCCACTTGGG
1 ATGGT--AGAATATGAAAATAGTGAAAGCCATCGTTGT-AAGCCACTTAGG
* * *
17497790 ATGGTAGAATATGAAAACAGTAAAAGTCATCGTTGCTAAGCCAC
1 ATGGTAGAATATGAAAATAGTGAAAGCCATCGTTG-TAAGCCAC
17497834 CCGAGATGAT
Statistics
Matches: 116, Mismatches: 16, Indels: 20
0.76 0.11 0.13
Matches are distributed among these distances:
47 5 0.04
48 6 0.05
49 94 0.81
50 6 0.05
51 5 0.04
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (48 bp):
ATGGTAGAATATGAAAATAGTGAAAGCCATCGTTGTAAGCCACTTAGG
Found at i:17502662 original size:20 final size:20
Alignment explanation
Indices: 17502619--17502663 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
17502609 TTGTTTCATC
* ** *
17502619 TTTTCTTTACCTAATTTTCT
1 TTTTATTTACCTAATTACCA
17502639 TTTTATTTACCTAATTACCA
1 TTTTATTTACCTAATTACCA
17502659 TTTTA
1 TTTTA
17502664 ACCTTATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.22, C:0.18, G:0.00, T:0.60
Consensus pattern (20 bp):
TTTTATTTACCTAATTACCA
Found at i:17507378 original size:26 final size:26
Alignment explanation
Indices: 17507349--17507440 Score: 99
Period size: 23 Copynumber: 3.8 Consensus size: 26
17507339 ATCCTCTTTC
*
17507349 GAGCCATATAACAGGAAACTCACAAA
1 GAGCCATATAACAGGAAGCTCACAAA
*
17507375 GAGCTAT-TAATCAGGAAGCTCACAAA
1 GAGCCATATAA-CAGGAAGCTCACAAA
*
17507401 GAG-CATAT--CGGGAAGCTCACAAA
1 GAGCCATATAACAGGAAGCTCACAAA
17507424 GAGCC-TAT--CAGGAAGCT
1 GAGCCATATAACAGGAAGCT
17507441 TATTCGGGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
23 28 0.48
24 1 0.02
25 5 0.09
26 24 0.41
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (26 bp):
GAGCCATATAACAGGAAGCTCACAAA
Found at i:17507418 original size:23 final size:23
Alignment explanation
Indices: 17507360--17507440 Score: 108
Period size: 23 Copynumber: 3.4 Consensus size: 23
17507350 AGCCATATAA
*
17507360 CAGGAAACTCACAAAGAGCTATTAAT
1 CAGGAAGCTCACAAAGAGC-A-T-AT
17507386 CAGGAAGCTCACAAAGAGCATAT
1 CAGGAAGCTCACAAAGAGCATAT
* *
17507409 CGGGAAGCTCACAAAGAGCCTAT
1 CAGGAAGCTCACAAAGAGCATAT
17507432 CAGGAAGCT
1 CAGGAAGCT
17507441 TATTCGGGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
23 31 0.61
24 1 0.02
25 1 0.02
26 18 0.35
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (23 bp):
CAGGAAGCTCACAAAGAGCATAT
Found at i:17507508 original size:26 final size:26
Alignment explanation
Indices: 17507477--17507567 Score: 96
Period size: 26 Copynumber: 3.5 Consensus size: 26
17507467 ATAAGAGTCA
* *
17507477 TAATCAGGAAGTTCACAAAGAACTTT
1 TAATCAGGAAGCTCACGAAGAACTTT
*
17507503 TAATCAGGAAGCTCACGAAGAGCCTTT
1 TAATCAGGAAGCTCACGAAGA-ACTTT
* * * *
17507530 AAAT-GGGAAGCTCACGAAGAGCCTT
1 TAATCAGGAAGCTCACGAAGAACTTT
17507555 TAATCAGG-AGCTC
1 TAATCAGGAAGCTC
17507568 TGGATAGCCA
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
25 11 0.20
26 36 0.67
27 7 0.13
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
TAATCAGGAAGCTCACGAAGAACTTT
Found at i:17507740 original size:64 final size:64
Alignment explanation
Indices: 17507624--17507753 Score: 161
Period size: 64 Copynumber: 2.0 Consensus size: 64
17507614 TTTGGAGAGC
* * * * * * *
17507624 CATATAACAGGACGCTCATAAAGAGCTGCGGTATGTCTGCAACACATGCAGGATCACTACCGAT
1 CATATAAAAAGACGCTCACAAAGAGCTACGGTATGTCCGCAACACATACAGGATCACAACCGAT
* ** *
17507688 CATATAAAAAGACGCTCACAAAGAGTTACGGTATGTCCGTGACATATACAGGATCACAACCGAT
1 CATATAAAAAGACGCTCACAAAGAGCTACGGTATGTCCGCAACACATACAGGATCACAACCGAT
17507752 CA
1 CA
17507754 GGATGTTCGT
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.36, C:0.24, G:0.20, T:0.20
Consensus pattern (64 bp):
CATATAAAAAGACGCTCACAAAGAGCTACGGTATGTCCGCAACACATACAGGATCACAACCGAT
Found at i:17515000 original size:23 final size:25
Alignment explanation
Indices: 17514956--17515001 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
17514946 TTTGGTGCAA
*
17514956 TTAACTCATTATTTTAATTTAAAAT
1 TTAACTCATTATTTTAAATTAAAAT
17514981 TTAA-TCATT-TTTTAAATTAAA
1 TTAACTCATTATTTTAAATTAAA
17515002 TCGAACTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 5 0.25
25 4 0.20
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAACTCATTATTTTAAATTAAAAT
Found at i:17525596 original size:31 final size:31
Alignment explanation
Indices: 17525561--17525624 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
17525551 ATATTACAAA
* *
17525561 AATTTAAATATAATTA-AAA-TGATATTTAAAT
1 AATTT-AACATAATTATAAACT-ATAGTTAAAT
17525592 AATTTAACATAATTATAAACTATAGTTAAAT
1 AATTTAACATAATTATAAACTATAGTTAAAT
17525623 AA
1 AA
17525625 CTTTTTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 9 0.31
31 19 0.66
32 1 0.03
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (31 bp):
AATTTAACATAATTATAAACTATAGTTAAAT
Found at i:17525708 original size:31 final size:31
Alignment explanation
Indices: 17525642--17525708 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
17525632 ATTGAATAGT
* * * *
17525642 TAAATAATTTAATATAATAATAGATGATATT
1 TAAATAATTTAATATAATAATACATAAAATA
17525673 TAAATAATTTAATATAATGAA-ACATAAAATA
1 TAAATAATTTAATATAAT-AATACATAAAATA
17525704 TAAAT
1 TAAAT
17525709 TAATCTAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (31 bp):
TAAATAATTTAATATAATAATACATAAAATA
Found at i:17527638 original size:46 final size:46
Alignment explanation
Indices: 17527537--17528109 Score: 1005
Period size: 46 Copynumber: 12.6 Consensus size: 46
17527527 TACGTATGAT
* * *
17527537 CACTTATCAC-TTGTC-CCTAATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
17527580 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
17527626 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
17527671 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
17527717 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
17527763 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
17527809 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
17527854 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
17527900 CACTTATCACTTTCTCACTTGATCAGATAAGTGTAGCTAAAGCTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
17527946 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAATCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
17527992 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
17528038 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
17528084 CACTTATCACTTTGTCAC-TGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
17528110 AGTACTCAAA
Statistics
Matches: 506, Mismatches: 19, Indels: 8
0.95 0.04 0.02
Matches are distributed among these distances:
43 10 0.02
44 5 0.01
45 115 0.23
46 376 0.74
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:17527863 original size:183 final size:183
Alignment explanation
Indices: 17527556--17528109 Score: 1022
Period size: 183 Copynumber: 3.0 Consensus size: 183
17527546 CTTGTCCCTA
*
17527556 ATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
17527620 AGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTG
66 AGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTG
17527685 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTG
131 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTG
*
17527738 ATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
17527803 AGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTG
66 AGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTG
17527868 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTG
131 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTG
*
17527921 ATCAGATAAGTGTAGCTAAAGCTAGCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
1 ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
* *
17527986 ATCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTT
66 AGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCT-AGGCTACCACTTATCACTTT
* *
17528051 GTCTCTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCAC-TG
130 GTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTG
17528104 ATCAGA
1 ATCAGA
17528110 AGTACTCAAA
Statistics
Matches: 363, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
182 17 0.05
183 278 0.77
184 68 0.19
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.33
Consensus pattern (183 bp):
ATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAA
AGCTACCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAGGCTACCACTTATCACTTTG
TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTCTCACTTG
Found at i:17532626 original size:17 final size:17
Alignment explanation
Indices: 17532604--17532655 Score: 95
Period size: 17 Copynumber: 3.1 Consensus size: 17
17532594 AAACTACCTA
*
17532604 GCGCCACACGGCTGTGT
1 GCGCCACACGACTGTGT
17532621 GCGCCACACGACTGTGT
1 GCGCCACACGACTGTGT
17532638 GCGCCACACGACTGTGT
1 GCGCCACACGACTGTGT
17532655 G
1 G
17532656 GTTGGCCGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 34 1.00
ACGTcount: A:0.15, C:0.35, G:0.33, T:0.17
Consensus pattern (17 bp):
GCGCCACACGACTGTGT
Found at i:17533352 original size:27 final size:27
Alignment explanation
Indices: 17533322--17533377 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
17533312 GGATATGATC
17533322 TGATATGTTATGGTATAATATGAGATA
1 TGATATGTTATGGTATAATATGAGATA
17533349 TGATATGTTATGGTATAATATGAGATA
1 TGATATGTTATGGTATAATATGAGATA
17533376 TG
1 TG
17533378 GTACAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.41
Consensus pattern (27 bp):
TGATATGTTATGGTATAATATGAGATA
Found at i:17547595 original size:20 final size:20
Alignment explanation
Indices: 17547570--17547608 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
17547560 TACTTTCTTC
17547570 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
17547590 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
17547609 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:17550514 original size:2 final size:2
Alignment explanation
Indices: 17550507--17550533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17550497 AATGAATGTT
17550507 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
17550534 GAAATGTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17577202 original size:30 final size:30
Alignment explanation
Indices: 17577128--17577204 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
17577118 ACACGAGCTA
17577128 TCACACGG-CGGTGTGTCACACACGGTCTCC
1 TCACACGGTC-GTGTGTCACACACGGTCTCC
*
17577158 TCACACGGTTGTGTGTCACACACGGTCTCC
1 TCACACGGTCGTGTGTCACACACGGTCTCC
*
17577188 TCACATGGTCGTGTGTC
1 TCACACGGTCGTGTGTC
17577205 TTTCAATTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.16, C:0.32, G:0.26, T:0.26
Consensus pattern (30 bp):
TCACACGGTCGTGTGTCACACACGGTCTCC
Found at i:17577467 original size:16 final size:16
Alignment explanation
Indices: 17577446--17577476 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
17577436 TGGTTCGCTG
17577446 TATTGGATTAGAGGTA
1 TATTGGATTAGAGGTA
17577462 TATTGGATTAGAGGT
1 TATTGGATTAGAGGT
17577477 GTAATAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (16 bp):
TATTGGATTAGAGGTA
Found at i:17577724 original size:17 final size:18
Alignment explanation
Indices: 17577683--17577718 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17577673 TTATTATTAA
* *
17577683 ATATATTTTAATTAAAAT
1 ATATAATTTAATAAAAAT
17577701 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
17577719 TTTAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:17577857 original size:16 final size:16
Alignment explanation
Indices: 17577820--17577861 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
17577810 TTAATCATAT
*
17577820 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
17577836 TT-AAATATATTATAA
1 TTAAAATATATTATAA
17577851 TTAAAATATAT
1 TTAAAATATAT
17577862 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:17577868 original size:14 final size:15
Alignment explanation
Indices: 17577829--17577870 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
17577819 TTTAAACATA
*
17577829 ATTATTATTAAATAT
1 ATTATAATTAAATAT
17577844 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
17577858 A-TATAATTTAATA
1 ATTATAATTAAATA
17577871 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:17577977 original size:59 final size:59
Alignment explanation
Indices: 17577823--17577994 Score: 156
Period size: 59 Copynumber: 2.9 Consensus size: 59
17577813 ATCATATTTA
* * *
17577823 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATCTAATAAAATTATAAAT
* * * * * * * *
17577882 AA-TTAA-TATTCTTATGAATTTACTCA-AATCATAATATATGATACT-GTAAAA-TATAAATT
1 AACATAATTATTATTA--AATATA-TTATAATTAAAATATATAAT-CTAATAAAATTATAAA-T
*
17577941 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATCTAATAAAATTA
17577995 CTTATAANNN
Statistics
Matches: 83, Mismatches: 20, Indels: 19
0.68 0.16 0.16
Matches are distributed among these distances:
57 7 0.08
58 10 0.12
59 51 0.61
60 8 0.10
61 7 0.08
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATCTAATAAAATTATAAAT
Found at i:17577986 original size:14 final size:15
Alignment explanation
Indices: 17577937--17577988 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
17577927 GTAAAATATA
17577937 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
17577952 TATTAAATATATTAT
1 AATTAAATATATTAT
17577967 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
17577980 AATTTAATA
1 AATTAAATA
17577989 AAATTACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:17578320 original size:101 final size:93
Alignment explanation
Indices: 17578153--17578433 Score: 277
Period size: 91 Copynumber: 3.0 Consensus size: 93
17578143 TATAAAAGAA
* * * *
17578153 AATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATT-TAAAA
1 AATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTCT----
* * * *
17578216 TAATTATAACTAATAAATTATATTTTATGAATTTGTAT
61 T-A--ATAA-T-ATAAATTTTATTATATGAATTTATAC
* *
17578254 AATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTCATAAAATTCTTGAT
1 AATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAAT
*
17578318 -A-ATAAATTTTCTTATATGAATTTATAC
65 AATATAAATTTTATTATATGAATTTATAC
* * *
17578345 AACTTAAAATAATTAATATTAAATATAATTTAATAGTGATATATAATTTCATAAAATTCTTAATA
1 AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
* *
17578410 ATA-AAATGTTCTTATATGAATTTA
66 ATATAAATTTTATTATATGAATTTA
17578434 CTAAAATCAA
Statistics
Matches: 157, Mismatches: 17, Indels: 21
0.81 0.09 0.11
Matches are distributed among these distances:
91 76 0.48
92 24 0.15
93 1 0.01
94 1 0.01
95 2 0.01
98 1 0.01
100 6 0.04
101 45 0.29
102 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (93 bp):
AATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTCTTAATA
ATATAAATTTTATTATATGAATTTATAC
Found at i:17578408 original size:47 final size:46
Alignment explanation
Indices: 17578276--17578414 Score: 117
Period size: 47 Copynumber: 3.0 Consensus size: 46
17578266 TAATTATTAC
* *
17578276 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAAT-ATGATATATAATTTCATAAAATTCTTAATAATAA
* * * * ** *
17578323 AT-T--TTCTTATATGAATTTATACA--ACTTAAAATAATTAATATTAA
1 ATATAATT-TAATATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
17578367 ATATAATTTAATAGTGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATA-TGATATATAATTTCATAAAATTCTTAATAATAA
17578414 A
1 A
17578415 ATGTTCTTAT
Statistics
Matches: 67, Mismatches: 16, Indels: 18
0.66 0.16 0.18
Matches are distributed among these distances:
44 21 0.31
45 11 0.16
46 12 0.18
47 23 0.34
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (46 bp):
ATATAATTTAATATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:17580281 original size:13 final size:13
Alignment explanation
Indices: 17580263--17580288 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17580253 TGCTTTTGGG
17580263 TTCAAAAATAATT
1 TTCAAAAATAATT
17580276 TTCAAAAATAATT
1 TTCAAAAATAATT
17580289 CTGATTTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TTCAAAAATAATT
Found at i:17582074 original size:30 final size:30
Alignment explanation
Indices: 17582038--17582102 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
17582028 ATTAACTCCC
17582038 ACAAATAATGCAATACAGGCAAGAACCGAA
1 ACAAATAATGCAATACAGGCAAGAACCGAA
17582068 ACAAATAATGCAATACAGGCAAGAACCGAA
1 ACAAATAATGCAATACAGGCAAGAACCGAA
17582098 ACAAA
1 ACAAA
17582103 CTATTTAGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.09
Consensus pattern (30 bp):
ACAAATAATGCAATACAGGCAAGAACCGAA
Found at i:17583039 original size:56 final size:56
Alignment explanation
Indices: 17582965--17583077 Score: 190
Period size: 56 Copynumber: 2.0 Consensus size: 56
17582955 AAATATTAGT
* *
17582965 GGCAAGTCGTGAGAACGAAACTAATTAAAGCAATCGGTGTTTTTAATATTGGTGTA
1 GGCAAGTCATGAGAACGAAACTAATTAAAGCAATCGATGTTTTTAATATTGGTGTA
* *
17583021 GGCAAGTCATGAGAACGAAACTAATTACAGTAATCGATGTTTTTAATATTGGTGTA
1 GGCAAGTCATGAGAACGAAACTAATTAAAGCAATCGATGTTTTTAATATTGGTGTA
17583077 G
1 G
17583078 TTTTTATGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.31
Consensus pattern (56 bp):
GGCAAGTCATGAGAACGAAACTAATTAAAGCAATCGATGTTTTTAATATTGGTGTA
Found at i:17585790 original size:18 final size:18
Alignment explanation
Indices: 17585767--17585817 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 18
17585757 GAGATAGAAA
17585767 AGATGAGAAATGAATATG
1 AGATGAGAAATGAATATG
17585785 AGATGAGAAATGAAATATG
1 AGATGAGAAATG-AATATG
17585804 -GAATGATGAAATGA
1 AG-ATGA-GAAATGA
17585818 GATCTGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.43
19 11 0.37
20 6 0.20
ACGTcount: A:0.51, C:0.00, G:0.27, T:0.22
Consensus pattern (18 bp):
AGATGAGAAATGAATATG
Found at i:17586844 original size:54 final size:54
Alignment explanation
Indices: 17586740--17586846 Score: 135
Period size: 54 Copynumber: 2.0 Consensus size: 54
17586730 CGTGAGATCA
* * * *
17586740 AAGTCAGTGAGTTACACAGGCAGAGACACGGGCTGGGGCACAGCCATGTGTCTT
1 AAGTCAGTGAGTTAAACAGGCAGAGACACAGGCTGGGACACAACCATGTGTCTT
* * *
17586794 AAGTTAGTGAGTTAAACAGGCA-AGGACACAGGCTGGGACGCAACCGTGTGTCT
1 AAGTCAGTGAGTTAAACAGGCAGA-GACACAGGCTGGGACACAACCATGTGTCT
17586847 CAACTTTGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
53 1 0.02
54 44 0.98
ACGTcount: A:0.28, C:0.21, G:0.33, T:0.19
Consensus pattern (54 bp):
AAGTCAGTGAGTTAAACAGGCAGAGACACAGGCTGGGACACAACCATGTGTCTT
Found at i:17588639 original size:8 final size:8
Alignment explanation
Indices: 17588626--17588690 Score: 55
Period size: 8 Copynumber: 8.2 Consensus size: 8
17588616 CTAAGCCCTA
17588626 TTTTTATT
1 TTTTTATT
17588634 TTTTTATT
1 TTTTTATT
17588642 TTTTTATT
1 TTTTTATT
*
17588650 TTATGTA--
1 TT-TTTATT
* *
17588657 TTTATATG
1 TTTTTATT
*
17588665 TTTTTA-C
1 TTTTTATT
17588672 TTTTTATTT
1 TTTTTA-TT
17588681 TTTTTATT
1 TTTTTATT
17588689 TT
1 TT
17588691 CTGGATTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
6 3 0.06
7 8 0.17
8 27 0.57
9 9 0.19
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:17588668 original size:22 final size:21
Alignment explanation
Indices: 17588627--17588714 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
17588617 TAAGCCCTAT
* * *
17588627 TTTTATTTTTTTATTTTTTTA
1 TTTTATGTATTTATATTTTTA
17588648 TTTTATGTATTTATATGTTTTTA
1 TTTTATGTATTTATA--TTTTTA
*
17588671 CTTT-T-TA-TT-T-TTTTTA
1 TTTTATGTATTTATATTTTTA
* *
17588687 TTTTCTGGATTTATATCTTTTA
1 TTTTATGTATTTATAT-TTTTA
17588709 TTTTAT
1 TTTTAT
17588715 TATGCATTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
16 9 0.17
17 1 0.02
18 1 0.02
19 3 0.06
20 3 0.06
21 15 0.29
22 11 0.21
23 9 0.17
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTATGTATTTATATTTTTA
Found at i:17588669 original size:31 final size:30
Alignment explanation
Indices: 17588624--17588681 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
17588614 CCCTAAGCCC
* * *
17588624 TATTTTTATTTTTTTATTTTTTTATTTTATG
1 TATTTATATGTTTTTA-CTTTTTATTTTATG
17588655 TATTTATATGTTTTTACTTTTTATTTT
1 TATTTATATGTTTTTACTTTTTATTTT
17588682 TTTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 10 0.42
31 14 0.58
ACGTcount: A:0.17, C:0.02, G:0.03, T:0.78
Consensus pattern (30 bp):
TATTTATATGTTTTTACTTTTTATTTTATG
Found at i:17588683 original size:39 final size:38
Alignment explanation
Indices: 17588634--17588707 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
17588624 TATTTTTATT
* *
17588634 TTTTTATTTTTTTATTTTATGTATTTATATGTTTTTAC
1 TTTTTATTTTTTTATTTTATGGATTTATATCTTTTTAC
*
17588672 TTTTTATTTTTTTTATTTTCTGGATTTATATCTTTT
1 TTTTTA-TTTTTTTATTTTATGGATTTATATCTTTT
17588708 ATTTTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.16, C:0.04, G:0.05, T:0.74
Consensus pattern (38 bp):
TTTTTATTTTTTTATTTTATGGATTTATATCTTTTTAC
Found at i:17599143 original size:42 final size:43
Alignment explanation
Indices: 17599035--17599145 Score: 134
Period size: 43 Copynumber: 2.6 Consensus size: 43
17599025 TATCGTAAAA
** * *
17599035 ATGTCATGTCCCAGACATGGTCTTACATGGAAATCTCATATCG
1 ATGTCATACCCCAGATATGGTCTTACATCGAAATCTCATATCG
* * * *
17599078 ATGCCAATAGCCCAGGTATGGTCTTACA-CGAAGTCTCATATCG
1 ATGTC-ATACCCCAGATATGGTCTTACATCGAAATCTCATATCG
17599121 ATGTCATACCCCAGATATGGTCTTA
1 ATGTCATACCCCAGATATGGTCTTA
17599146 TACGGGATCT
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
42 18 0.32
43 21 0.37
44 18 0.32
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
ATGTCATACCCCAGATATGGTCTTACATCGAAATCTCATATCG
Found at i:17599189 original size:48 final size:47
Alignment explanation
Indices: 17599118--17599255 Score: 195
Period size: 48 Copynumber: 2.9 Consensus size: 47
17599108 AAGTCTCATA
*
17599118 TCGATGTCATACCCCAGATATGGTCTTATACGGGATCTCAAAATAAT
1 TCGATGTCATATCCCAGATATGGTCTTATACGGGATCTCAAAATAAT
* * *
17599165 GTCGATGTCATATCCTAGATATGGTCTTATACGGGATCTCAAATTGAT
1 -TCGATGTCATATCCCAGATATGGTCTTATACGGGATCTCAAAATAAT
* * *
17599213 ACTGATGCCACATCCCAGATATGGTCTTATACGGGATCTCAAA
1 TC-GATGTCATATCCCAGATATGGTCTTATACGGGATCTCAAA
17599256 TCGATTTAGC
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
47 1 0.01
48 80 0.99
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (47 bp):
TCGATGTCATATCCCAGATATGGTCTTATACGGGATCTCAAAATAAT
Found at i:17605430 original size:107 final size:105
Alignment explanation
Indices: 17605244--17605444 Score: 289
Period size: 107 Copynumber: 1.9 Consensus size: 105
17605234 TTATTGATTT
*
17605244 TGAAGACATGTCATGCATGGTATTTATACGCACCATGCATTAGAAAAACATAAATGTTAGTAGGA
1 TGAAGACATGTCATGCATGGTATTTATACGCACCATGCATTAGAAAAACATAAACGTTAGTAGGA
* *
17605309 AGCCTGTTTGACCAAAATAATCTTAAAAAAAATAAAAAAAAA
66 AGCCTATTTAACCAAAAT-AT-TTAAAAAAAATAAAAAAAAA
* * *
17605351 TGAAGAC-TGGTCATGCATGGTATTTATAGGCACCATGTATTAGAAAAACATGAACGTT-GATAG
1 TGAAGACAT-GTCATGCATGGTATTTATACGCACCATGCATTAGAAAAACATAAACGTTAG-TAG
*
17605414 TAAGCCTATTTAACCAAAATATTTAAAAAAA
64 GAAGCCTATTTAACCAAAATATTTAAAAAAA
17605445 GGAGAGAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
105 9 0.11
106 4 0.05
107 72 0.85
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (105 bp):
TGAAGACATGTCATGCATGGTATTTATACGCACCATGCATTAGAAAAACATAAACGTTAGTAGGA
AGCCTATTTAACCAAAATATTTAAAAAAAATAAAAAAAAA
Found at i:17621386 original size:21 final size:21
Alignment explanation
Indices: 17621362--17621408 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
17621352 TGTAAAACTA
* *
17621362 AAAAAACTTC-AAAAATTATTT
1 AAAAAA-TTCTAAAAAATATAT
17621383 AAAAAATTCTAAAAAATATAT
1 AAAAAATTCTAAAAAATATAT
17621404 AAAAA
1 AAAAA
17621409 TTTATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAATTCTAAAAAATATAT
Found at i:17621416 original size:21 final size:21
Alignment explanation
Indices: 17621372--17621416 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
17621362 AAAAAACTTC
* * *
17621372 AAAAATTATTTAAAAAATTCT
1 AAAAAATATATAAAAAATTAT
*
17621393 AAAAAATATATAAAAATTTAT
1 AAAAAATATATAAAAAATTAT
17621414 AAA
1 AAA
17621417 TATGCAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAAAATATATAAAAAATTAT
Found at i:17630086 original size:3 final size:3
Alignment explanation
Indices: 17630078--17630112 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
17630068 AGGCATCAAA
17630078 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
17630113 GTTGCAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17630663 original size:53 final size:53
Alignment explanation
Indices: 17630600--17630704 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
17630590 GAAAAAAAAA
*
17630600 ATAAATTAATTTTTCGTGTAAAACTCAAGTTTTCCTATAAAAACTTAAGTAAG
1 ATAAATTAATTTTTCGTGTAAAACTCAAGTTTTCCTAAAAAAACTTAAGTAAG
*
17630653 ATAAATTAATTTTTCGTGTAAAACTCAAGTTTTCCTAAAAAAAGTTAAGTAA
1 ATAAATTAATTTTTCGTGTAAAACTCAAGTTTTCCTAAAAAAACTTAAGTAA
17630705 TTTATTATAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (53 bp):
ATAAATTAATTTTTCGTGTAAAACTCAAGTTTTCCTAAAAAAACTTAAGTAAG
Found at i:17630985 original size:31 final size:31
Alignment explanation
Indices: 17630950--17631008 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
17630940 ACGTGTGCAA
17630950 TGACTAAAATAATAAAAATATGTAACGAGAG
1 TGACTAAAATAATAAAAATATGTAACGAGAG
* *
17630981 TGACTAAAATGATAAAATTATGTAACGA
1 TGACTAAAATAATAAAAATATGTAACGA
17631009 TAATATCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.53, C:0.07, G:0.15, T:0.25
Consensus pattern (31 bp):
TGACTAAAATAATAAAAATATGTAACGAGAG
Found at i:17635640 original size:24 final size:24
Alignment explanation
Indices: 17635602--17635853 Score: 143
Period size: 24 Copynumber: 10.8 Consensus size: 24
17635592 TGAATTGGAT
* *
17635602 AATTTACAATAAATAATATATAATA
1 AATTTAAAAT-AATAATATATGATA
* *
17635627 AATTTGAAATAATAATAAAT-ATAA
1 AATTTAAAATAATAATATATGAT-A
*
17635651 AATTT-AAA-AAT--TTTGATGAT-
1 AATTTAAAATAATAATAT-ATGATA
* * **
17635671 AATTCTAGAATAATCATACGTGATA
1 AATT-TAAAATAATAATATATGATA
** * *
17635696 AATCCAAAATAATAGTATATAATA
1 AATTTAAAATAATAATATATGATA
*
17635720 AATTT-AAA-AATATTA-ATGATA
1 AATTTAAAATAATAATATATGATA
* *
17635741 AATTTGAAATAGAT-ATACATGATA
1 AATTTAAAATA-ATAATATATGATA
** ** *
17635765 AATTTAAAATAATGTTA-ACAATG
1 AATTTAAAATAATAATATATGATA
17635788 AATTTAAAATAATAATAT-TGATA
1 AATTTAAAATAATAATATATGATA
* *
17635811 AA-TTACAAATAATAAAACATGATA
1 AATTTA-AAATAATAATATATGATA
*
17635835 AATCTAAAATAATAATATA
1 AATTTAAAATAATAATATA
17635854 CAATACACTT
Statistics
Matches: 172, Mismatches: 37, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
20 5 0.03
21 13 0.08
22 19 0.11
23 48 0.28
24 73 0.42
25 14 0.08
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (24 bp):
AATTTAAAATAATAATATATGATA
Found at i:17635653 original size:17 final size:18
Alignment explanation
Indices: 17635616--17635653 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
17635606 TACAATAAAT
* *
17635616 AATATATAATAAATTTGA
1 AATATATAATAAATATAA
17635634 AATA-ATAATAAATATAA
1 AATATATAATAAATATAA
17635651 AAT
1 AAT
17635654 TTAAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
AATATATAATAAATATAA
Found at i:17635697 original size:69 final size:69
Alignment explanation
Indices: 17635624--17635885 Score: 194
Period size: 69 Copynumber: 3.8 Consensus size: 69
17635614 ATAATATATA
* * *
17635624 ATAAATTTGAAATAATAATAAAT-ATAAAATTTAAAAATTTTGATGAT-AATTCT-AGAATA-AT
1 ATAAATTTAAAATAATAATAAATAAT-AAATTTAAAAATATTAATGATAAATT-TGA-AATAGAT
*
17635685 CATACGTG
63 -ATACATG
** * *
17635693 ATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
1 ATAAATTTAAAATAATAATAAATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
17635758 CATG
66 CATG
* * * * * * **
17635762 ATAAATTTAAAATAAT-GTTAACAATGAATTTAAAATAATAATATTGATAAATTACAAATA-ATA
1 ATAAATTTAAAATAATAATAAATAATAAATTT-AAA-AATATTAATGATAAATTTGAAATAGAT-
*
17635825 AAACATG
63 ATACATG
* * * * * * *
17635832 ATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAATTT
1 ATAAATTTAAAATAATAATAAATAATAAATTTA-AAAATATTAATGATAAATTT
17635886 AATAATAAGT
Statistics
Matches: 153, Mismatches: 31, Indels: 17
0.76 0.15 0.08
Matches are distributed among these distances:
68 11 0.07
69 67 0.44
70 65 0.42
71 10 0.07
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.35
Consensus pattern (69 bp):
ATAAATTTAAAATAATAATAAATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATATA
CATG
Found at i:17635870 original size:70 final size:68
Alignment explanation
Indices: 17635691--17635884 Score: 176
Period size: 70 Copynumber: 2.8 Consensus size: 68
17635681 TAATCATACG
* * * * * **
17635691 TGATAAATCCAAAATAATAGTATATAATAAATTTAAAAATATTAATGATAAATTTGAAATAGATA
1 TGATAAATCTAAAATAATAATATACAAT-AATTTAATAATAATAATGATAAATTACAAATAGATA
*
17635756 TACA
65 AACA
* ** *
17635760 TGATAAATTTAAAATAATGTTA-ACAATGAATTTAAAATAATAATATTGATAAATTACAAATA-A
1 TGATAAATCTAAAATAATAATATACAAT-AATTT--AATAATAATAATGATAAATTACAAATAGA
17635823 TAAAACA
63 T-AAACA
* * *
17635830 TGATAAATCTAAAATAATAATATACAATACACTTAGATAATATTAATGATTAATT
1 TGATAAATCTAAAATAATAATATACAATA-ATTTA-ATAATAATAATGATAAATT
17635885 TAATAATAAG
Statistics
Matches: 100, Mismatches: 19, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
68 9 0.09
69 21 0.21
70 62 0.62
71 8 0.08
ACGTcount: A:0.55, C:0.05, G:0.06, T:0.34
Consensus pattern (68 bp):
TGATAAATCTAAAATAATAATATACAATAATTTAATAATAATAATGATAAATTACAAATAGATAA
ACA
Found at i:17637112 original size:12 final size:12
Alignment explanation
Indices: 17637097--17637121 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17637087 ACTTTCCACC
17637097 ACAATCATCAGA
1 ACAATCATCAGA
17637109 ACAATCATCAGA
1 ACAATCATCAGA
17637121 A
1 A
17637122 ACTCCCTCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
ACAATCATCAGA
Found at i:17638204 original size:25 final size:23
Alignment explanation
Indices: 17638160--17638205 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
17638150 AAAAATGATC
17638160 AAACAGATACAGCAAAAGATGGG
1 AAACAGATACAGCAAAAGATGGG
17638183 AAACAAGATATCAG-AAGAAGATG
1 AAAC-AGATA-CAGCAA-AAGATG
17638206 ATATTGAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
25 9 0.45
ACGTcount: A:0.54, C:0.11, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACAGATACAGCAAAAGATGGG
Found at i:17644195 original size:22 final size:22
Alignment explanation
Indices: 17644170--17644218 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
17644160 AATCATGTCA
*
17644170 TTTTGAAGTTGAAACGGTATGG
1 TTTTGAAGTTGAAACGGAATGG
17644192 TTTTGAAGTTGAAACGGAATGG
1 TTTTGAAGTTGAAACGGAATGG
17644214 TTTTG
1 TTTTG
17644219 GCTGGTTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.31, T:0.39
Consensus pattern (22 bp):
TTTTGAAGTTGAAACGGAATGG
Found at i:17654000 original size:19 final size:20
Alignment explanation
Indices: 17653958--17654003 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
17653948 TAAAAAATTA
* *
17653958 AAAATCATAATATATTTTTG
1 AAAATTATAAAATATTTTTG
17653978 AAAATTATAAAATATTTTT-
1 AAAATTATAAAATATTTTTG
17653997 AAAATTA
1 AAAATTA
17654004 CAAGTATGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAATTATAAAATATTTTTG
Found at i:17654107 original size:21 final size:22
Alignment explanation
Indices: 17654083--17654132 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
17654073 AGAAAATCTT
17654083 AAATTTTTTTATGA-TTTTAAA
1 AAATTTTTTTATGATTTTTAAA
**
17654104 AAATAATTTTATGATTTTTAAA
1 AAATTTTTTTATGATTTTTAAA
17654126 AAATTTT
1 AAATTTT
17654133 ATGGGTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (22 bp):
AAATTTTTTTATGATTTTTAAA
Found at i:17654113 original size:22 final size:22
Alignment explanation
Indices: 17654089--17654129 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
17654079 TCTTAAATTT
17654089 TTTTATGA-TTTTAAAAAATAA
1 TTTTATGATTTTTAAAAAATAA
17654110 TTTTATGATTTTTAAAAAAT
1 TTTTATGATTTTTAAAAAAT
17654130 TTTATGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (22 bp):
TTTTATGATTTTTAAAAAATAA
Found at i:17654141 original size:19 final size:20
Alignment explanation
Indices: 17654089--17654143 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 20
17654079 TCTTAAATTT
17654089 TTTTATGA-TTTTAAAAAATAA
1 TTTTATGAGTTTT--AAAATAA
*
17654110 TTTTATGATTTTTAAAA-AA
1 TTTTATGAGTTTTAAAATAA
*
17654129 TTTTATGGGTTTTAA
1 TTTTATGAGTTTTAA
17654144 TTTCATTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 15 0.48
20 4 0.13
21 8 0.26
22 4 0.13
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTTATGAGTTTTAAAATAA
Found at i:17654316 original size:21 final size:20
Alignment explanation
Indices: 17654272--17654317 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
17654262 TTTCGCATGC
17654272 TTATAATTTTAAAAATAGCTT
1 TTATAATTTTAAAAATAGC-T
17654293 TTATAATTTTCAAAAAATAG-T
1 TTATAATTTT--AAAAATAGCT
17654314 TTAT
1 TTAT
17654318 GATTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 15 0.65
23 8 0.35
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (20 bp):
TTATAATTTTAAAAATAGCT
Found at i:17656302 original size:24 final size:24
Alignment explanation
Indices: 17656257--17656307 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
17656247 TGCTTCCTAA
*
17656257 TTAATTGCTCTTCGGAGCTACCCG
1 TTAATTGCTCTTCAGAGCTACCCG
*
17656281 TTAATTGCTC-TCTAGAGTTACCCG
1 TTAATTGCTCTTC-AGAGCTACCCG
17656305 TTA
1 TTA
17656308 TAGTCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (24 bp):
TTAATTGCTCTTCAGAGCTACCCG
Found at i:17662972 original size:223 final size:222
Alignment explanation
Indices: 17662560--17663005 Score: 696
Period size: 223 Copynumber: 2.0 Consensus size: 222
17662550 GCTGTTGATA
* *
17662560 GATAAACAACTTTTGTTAAAGGAATTTTGATGAAAACATGATTTAGGGGCTAAATTGAAAAGTTG
1 GATAAACAACTTTTGTTAAAGGAATTTTGATGAAAACATGATTTAAGGGCTAAATTGAAAAGATG
* * *
17662625 TAAAATTTATGGGAAATTCTAATTTTTCTGAAATACATAGGCTATTATTTTTATAAGTAAAAATT
66 TAAAATTCATGGGAAATTCTAATTTTTCTGAAATACATAGGCTATTATTGTTATAAGTAAAAATC
* * * * *
17662690 GGCTAGGCTTGGAATAAGAATTAAATTGCATGAATTTCATCTTCCGAGCCTAGGGATGAAATCGT
131 GGCTAGGCTTGAAATAAGAATTAAATTGCATGAATTTAATCTTCCAAGCCTAAGGATGAAATCAT
17662755 CATTAATTAAAAGTATAGAGGCAAAAT
196 CATTAATTAAAAGTATAGAGGCAAAAT
17662782 GATAAACAACTTTTGTTAAAGGAATTTTGATGAAAACATGATTTAAGGGCTAAATTGAAAAGATG
1 GATAAACAACTTTTGTTAAAGGAATTTTGATGAAAACATGATTTAAGGGCTAAATTGAAAAGATG
* *
17662847 TAAAATTCAT-GGAAATTTTCTAATTTTTGTGAAATACATGGGCTATTATTGTTATAAGTAAAAA
66 TAAAATTCATGGGAAA--TTCTAATTTTTCTGAAATACATAGGCTATTATTGTTATAAGTAAAAA
* * * *
17662911 TCGGCTAGGCTTGAAATAAGGATTAAATTGCATGCATTTAATTTTTCAAGCCTAAGGATGAAATC
129 TCGGCTAGGCTTGAAATAAGAATTAAATTGCATGAATTTAATCTTCCAAGCCTAAGGATGAAATC
* * *
17662976 ATTATTAATTAAAAGTATAGGGGCTAAAT
194 ATCATTAATTAAAAGTATAGAGGCAAAAT
17663005 G
1 G
17663006 GAAATTTTAT
Statistics
Matches: 203, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
221 5 0.02
222 72 0.35
223 126 0.62
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (222 bp):
GATAAACAACTTTTGTTAAAGGAATTTTGATGAAAACATGATTTAAGGGCTAAATTGAAAAGATG
TAAAATTCATGGGAAATTCTAATTTTTCTGAAATACATAGGCTATTATTGTTATAAGTAAAAATC
GGCTAGGCTTGAAATAAGAATTAAATTGCATGAATTTAATCTTCCAAGCCTAAGGATGAAATCAT
CATTAATTAAAAGTATAGAGGCAAAAT
Found at i:17663526 original size:26 final size:26
Alignment explanation
Indices: 17663496--17663552 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
17663486 GCAACTCTTA
*
17663496 TGAGCGTCCCG-TTATATGGCTCTTCG
1 TGAGCGTCCCGATTA-AAGGCTCTTCG
* * *
17663522 TGAGCTTCTCGATTAAAGGCTCTTTG
1 TGAGCGTCCCGATTAAAGGCTCTTCG
17663548 TGAGC
1 TGAGC
17663553 TTCCTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.16, C:0.23, G:0.26, T:0.35
Consensus pattern (26 bp):
TGAGCGTCCCGATTAAAGGCTCTTCG
Found at i:17663649 original size:24 final size:24
Alignment explanation
Indices: 17663608--17663654 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
17663598 TGCTTATTGA
*
17663608 TTAATTGCTCTTCGGAGCTACCCG
1 TTAATTGCTCTTCAGAGCTACCCG
17663632 TTAATTGCTC-TCTAGAGCTACCC
1 TTAATTGCTCTTC-AGAGCTACCC
17663655 ATTATAGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.19, C:0.30, G:0.17, T:0.34
Consensus pattern (24 bp):
TTAATTGCTCTTCAGAGCTACCCG
Found at i:17676985 original size:24 final size:24
Alignment explanation
Indices: 17676958--17677022 Score: 60
Period size: 25 Copynumber: 2.7 Consensus size: 24
17676948 CGAAAGAGTG
*
17676958 TCCCGTTATTAGCTCTCA-TGAGCT
1 TCCCGTTATTAGCTCT-AGCGAGCT
* *
17676982 TCCCATTATATAGTTCTAGCGAGCT
1 TCCCGTTAT-TAGCTCTAGCGAGCT
* *
17677007 TTCCGTTAATAGCTCT
1 TCCCGTTATTAGCTCT
17677023 TCGGAGCATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
24 15 0.47
25 17 0.53
ACGTcount: A:0.20, C:0.26, G:0.15, T:0.38
Consensus pattern (24 bp):
TCCCGTTATTAGCTCTAGCGAGCT
Found at i:17679929 original size:41 final size:42
Alignment explanation
Indices: 17679872--17680110 Score: 183
Period size: 42 Copynumber: 5.8 Consensus size: 42
17679862 TTACAGAAAT
*
17679872 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGC-TTCAAAA
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCATTCAAAC
* ** *
17679913 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCTCAG
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCATTCAAAC
*
17679955 AAACGCCGCT--A----ATGTTCTTTAGCGGCG-ATTCTACGAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCATTC-A-AAC
** ** * * *
17679992 AAACGCCGCTAAAGAACATGACCTTTAGCAGCGCATACCAAC
1 AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCATTCAAAC
* * * *
17680034 AAACGCCGCTAAAGCTCATGTTCTTTTAGCGGTGCCTTTTC-CAC
1 AAACGCCGCTAAAGGTCATGTTC-TTTAGCGGCG-C-ATTCAAAC
* *
17680078 AAACGCCGCTGCAA-GTAATGTTCTTTAGCGGCG
1 AAACGCCGCT-AAAGGTCATGTTCTTTAGCGGCG
17680111 TTTTTTTCCA
Statistics
Matches: 158, Mismatches: 26, Indels: 26
0.75 0.12 0.12
Matches are distributed among these distances:
35 3 0.02
36 16 0.10
37 11 0.07
39 1 0.01
40 1 0.01
41 34 0.22
42 35 0.22
43 30 0.19
44 23 0.15
45 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (42 bp):
AAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCATTCAAAC
Found at i:17679977 original size:36 final size:37
Alignment explanation
Indices: 17679930--17680003 Score: 107
Period size: 36 Copynumber: 2.0 Consensus size: 37
17679920 GCTAAAGGTC
* *
17679930 ATGTTCTTTAGCGGCGCTTTCT-C-AGAAACGCCGCTA
1 ATGTTCTTTAGCGGCG-ATTCTACGACAAACGCCGCTA
17679966 ATGTTCTTTAGCGGCGATTCTACGACAAACGCCGCTA
1 ATGTTCTTTAGCGGCGATTCTACGACAAACGCCGCTA
17680003 A
1 A
17680004 AGAACATGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 4 0.12
36 17 0.50
37 13 0.38
ACGTcount: A:0.23, C:0.27, G:0.22, T:0.28
Consensus pattern (37 bp):
ATGTTCTTTAGCGGCGATTCTACGACAAACGCCGCTA
Found at i:17680038 original size:79 final size:77
Alignment explanation
Indices: 17679889--17680045 Score: 181
Period size: 79 Copynumber: 2.0 Consensus size: 77
17679879 GCTAAAGGTC
* ** ** * * *
17679889 ATGTTCTTTAGCGGCGCTTCAAAAAAACGCCGCTAAAGGTCATGTTCTTTAGCGGCGCTTTCTCA
1 ATGTTCTTTAGCGGCGATTCAAAAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCATACTCA
*
17679954 GAAACGCCGCTA
66 CAAACGCCGCTA
* *
17679966 ATGTTCTTTAGCGGCGATTCTACGACAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCATAC-
1 ATGTTCTTTAGCGGCGATTC-A-AAAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCATACT
17680030 CAACAAACGCCGCTA
64 C-ACAAACGCCGCTA
17680045 A
1 A
17680046 AGCTCATGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
77 19 0.29
78 2 0.03
79 45 0.68
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (77 bp):
ATGTTCTTTAGCGGCGATTCAAAAAAACGCCGCTAAAGAACATGACCTTTAGCAGCGCATACTCA
CAAACGCCGCTA
Found at i:17680105 original size:43 final size:45
Alignment explanation
Indices: 17680032--17680132 Score: 118
Period size: 44 Copynumber: 2.3 Consensus size: 45
17680022 GCGCATACCA
* *
17680032 ACAAACGCCGCTAAAGCTCATGTTCTTTTAGCGGTG-CCTTTTCC
1 ACAAACGCCGCTAAAGCTAATGTTCTTTTAGCGGCGTCCTTTTCC
* **
17680076 ACAAACGCCGCTGCAAG-TAATGTTC-TTTAGCGGCGTTTTTTTCC
1 ACAAACGCCGCT-AAAGCTAATGTTCTTTTAGCGGCGTCCTTTTCC
*
17680120 ACAAACGTCGCTA
1 ACAAACGCCGCTA
17680133 TGGTCATGCT
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
43 9 0.19
44 36 0.75
45 3 0.06
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.31
Consensus pattern (45 bp):
ACAAACGCCGCTAAAGCTAATGTTCTTTTAGCGGCGTCCTTTTCC
Found at i:17680572 original size:21 final size:21
Alignment explanation
Indices: 17680548--17680598 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
17680538 TTCTTCTGAA
*
17680548 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
* *
17680569 CCTCTACTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
17680590 CCTCGGCTT
1 CCTCTGCTT
17680599 TAAGTTGTAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.04, C:0.47, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:17686545 original size:29 final size:29
Alignment explanation
Indices: 17686503--17686558 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
17686493 AAAAGCCCTT
17686503 TTTTTTCAATATTTACCGAAATGGGCCGG
1 TTTTTTCAATATTTACCGAAATGGGCCGG
*
17686532 TTTTTT-AATTATTTACCGGAATGGGCC
1 TTTTTTCAA-TATTTACCGAAATGGGCC
17686559 ATTTTCCGCG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 2 0.08
29 23 0.92
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (29 bp):
TTTTTTCAATATTTACCGAAATGGGCCGG
Found at i:17686982 original size:29 final size:29
Alignment explanation
Indices: 17686948--17687003 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
17686938 CGCGGAAAAT
17686948 GGCCCATTCCGGTAAATAATT-AAAAAACC
1 GGCCCATTCCGGTAAAT-ATTGAAAAAACC
*
17686977 GGCCCATTTCGGTAAATATTGAAAAAA
1 GGCCCATTCCGGTAAATATTGAAAAAA
17687004 AGGGCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.23
Consensus pattern (29 bp):
GGCCCATTCCGGTAAATATTGAAAAAACC
Found at i:17689243 original size:25 final size:25
Alignment explanation
Indices: 17689215--17689710 Score: 165
Period size: 25 Copynumber: 19.6 Consensus size: 25
17689205 ATAATTAAGC
*
17689215 TATGTAAGCTATGTAAGTTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
*
17689240 TATGTAAGTTATGTATTAAGTTATTTAT
1 TATGTAAGTTATG---TAAGTTATGTAT
* * *
17689268 TATGAAAATTATATAAGTTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* * *
17689293 TATG-AATATTATGTAAGTTGTGAAT
1 TATGTAA-GTTATGTAAGTTATGTAT
*
17689318 TATGTAAGTGATGT-A-TTATGATCAAT
1 TATGTAAGTTATGTAAGTTATG-T--AT
*
17689344 TATGTAAGTTATGT-A-TTATGAAAAT
1 TATGTAAGTTATGTAAGTTATG--TAT
* * * *
17689369 TATGTAAGCTGTGT-ACTGTAT-AAGT
1 TATGTAAGTTATGTAAGT-TATGTA-T
* *
17689394 TATGTAAGTTATGAAAATTATGTAAGT
1 TATGTAAGTTATGTAAGTTATGT-A-T
* * *
17689421 TATGTAAGTT-TTTGA-TTATGAAAAT
1 TATGTAAGTTATGTAAGTTATG--TAT
* * * *
17689446 TAAGTAACTTATG-CA-TTATGAAAAT
1 TATGTAAGTTATGTAAGTTATG--TAT
*
17689471 TATGTAAGTTCA-AT-A-TTATGTAAGT
1 TATGTAAGTT-ATGTAAGTTATGT-A-T
* * *
17689496 TATGT-A-TTACGAAAATTATGTA-
1 TATGTAAGTTATGTAAGTTATGTAT
* *
17689518 -A-GTTCAATATTATTTAAGTTATGTAT
1 TATG-T-AA-GTTATGTAAGTTATGTAT
* * *
17689544 TATGAAAATTATGTAAGTTGTGTA-
1 TATGTAAGTTATGTAAGTTATGTAT
* * *
17689568 TAGTATAAGTTATGTAGGTTATGAAAAT
1 TA-TGTAAGTTATGTAAGTTATG--TAT
* *
17689596 TATGTAAGTTATGTAAGTTATTTTT
1 TATGTAAGTTATGTAAGTTATGTAT
* * *
17689621 TATGAAAATTAAGTAAGTTATGTAT
1 TATGTAAGTTATGTAAGTTATGTAT
* * *
17689646 TATGAAAATTATGTAAGTTCA-ATAT
1 TATGTAAGTTATGTAAGTT-ATGTAT
* *
17689671 TATGTAAGTTATGTACCA-TGAAG-AT
1 TATGTAAGTTATGTA--AGTTATGTAT
17689696 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
17689711 TATTGTGTAG
Statistics
Matches: 365, Mismatches: 65, Indels: 82
0.71 0.13 0.16
Matches are distributed among these distances:
20 1 0.00
21 2 0.01
22 1 0.00
23 7 0.02
24 11 0.03
25 247 0.68
26 35 0.10
27 37 0.10
28 24 0.07
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (25 bp):
TATGTAAGTTATGTAAGTTATGTAT
Found at i:17689245 original size:16 final size:16
Alignment explanation
Indices: 17689224--17689685 Score: 97
Period size: 16 Copynumber: 28.9 Consensus size: 16
17689214 CTATGTAAGC
17689224 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
17689240 TATGTAAGTTATG---
1 TATGTAAGTTATGTAT
*
17689253 TAT-TAAGTTATTTAT
1 TATGTAAGTTATGTAT
* * *
17689268 TATGAAAATTATATAAGT
1 TATGTAAGTTATGT-A-T
17689286 TATGT-A-TTATGAATAT
1 TATGTAAGTTATG--TAT
* *
17689302 TATGTAAGTTGTGAAT
1 TATGTAAGTTATGTAT
*
17689318 TATGTAAGTGATGTAT
1 TATGTAAGTTATGTAT
17689334 TATGATCAA-TTATGTAAGT
1 TATG-T-AAGTTATGT-A-T
*
17689353 TATGT-A-TTATGAAAAT
1 TATGTAAGTTATG--TAT
* * *
17689369 TATGTAAGCTGTGTAC
1 TATGTAAGTTATGTAT
* *
17689385 TGTATAAGTTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
17689403 TATGAAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
*
17689421 TATGTAAGTT-TTTGAT
1 TATGTAAGTTATGT-AT
* * *
17689437 TATGAAAATTAAGTAACT
1 TATGTAAGTTATGT-A-T
* *
17689455 TATG-CA-TTATGAAAAT
1 TATGTAAGTTATG--TAT
*
17689471 TATGTAAGTTCA-ATAT
1 TATGTAAGTT-ATGTAT
17689487 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
17689503 TACG-AA---A---AT
1 TATGTAAGTTATGTAT
*
17689512 TATGTAAGTTCA-ATAT
1 TATGTAAGTT-ATGTAT
*
17689528 TATTTAAGTTATGTAT
1 TATGTAAGTTATGTAT
17689544 TATG-AA---A---AT
1 TATGTAAGTTATGTAT
*
17689553 TATGTAAGTTGTGTA-
1 TATGTAAGTTATGTAT
*
17689568 TAGTATAAGTTATGTAGGT
1 TA-TGTAAGTTATGTA--T
* *
17689587 TATGAAAATTATGTAAGT
1 TATGTAAGTTATGT-A-T
* *
17689605 TATGTAAGTTATTTTT
1 TATGTAAGTTATGTAT
* * *
17689621 TATGAAAATTAAGTAAGT
1 TATGTAAGTTATGT-A-T
*
17689639 TATGT-A-TTATGAAAAT
1 TATGTAAGTTATG--TAT
*
17689655 TATGTAAGTTCA-ATAT
1 TATGTAAGTT-ATGTAT
17689671 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
17689686 CCATGAAGAT
Statistics
Matches: 322, Mismatches: 68, Indels: 112
0.64 0.14 0.22
Matches are distributed among these distances:
9 11 0.03
10 4 0.01
12 10 0.03
13 3 0.01
14 1 0.00
15 12 0.04
16 172 0.53
17 24 0.07
18 75 0.23
19 10 0.03
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.44
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Found at i:17689251 original size:9 final size:9
Alignment explanation
Indices: 17689210--17689810 Score: 195
Period size: 9 Copynumber: 70.4 Consensus size: 9
17689200 TAAGTATAAT
*
17689210 TAAGCTATG
1 TAAGTTATG
*
17689219 TAAGCTATG
1 TAAGTTATG
17689228 TAAGTTATG
1 TAAGTTATG
17689237 T-A-TTATG
1 TAAGTTATG
17689244 TAAGTTATG
1 TAAGTTATG
17689253 TATTAAGTTAT-
1 ---TAAGTTATG
*
17689264 TTA-TTATG
1 TAAGTTATG
* * *
17689272 AAAATTATA
1 TAAGTTATG
17689281 TAAGTTATG
1 TAAGTTATG
17689290 T-A-TTATG
1 TAAGTTATG
*
17689297 -AATATTATG
1 TAA-GTTATG
*
17689306 TAAGTTGTG
1 TAAGTTATG
17689315 -AA-TTATG
1 TAAGTTATG
*
17689322 TAAGTGATG
1 TAAGTTATG
17689331 T-A-TTATG
1 TAAGTTATG
17689338 ATCAA-TTATG
1 -T-AAGTTATG
17689348 TAAGTTATG
1 TAAGTTATG
17689357 T-A-TTATG
1 TAAGTTATG
* *
17689364 AAAATTATG
1 TAAGTTATG
* *
17689373 TAAGCTGTG
1 TAAGTTATG
*
17689382 T-ACTGTA--
1 TAAGT-TATG
17689389 TAAGTTATG
1 TAAGTTATG
17689398 TAAGTTATG
1 TAAGTTATG
* *
17689407 AAAATTATG
1 TAAGTTATG
17689416 TAAGTTATG
1 TAAGTTATG
*
17689425 TAAGTT-TT
1 TAAGTTATG
*
17689433 TGA-TTATG
1 TAAGTTATG
* * *
17689441 AAAATTAAG
1 TAAGTTATG
*
17689450 TAACTTATG
1 TAAGTTATG
*
17689459 -CA-TTATG
1 TAAGTTATG
* *
17689466 AAAATTATG
1 TAAGTTATG
*
17689475 TAAGTTCA-A
1 TAAGTT-ATG
17689484 T-A-TTATG
1 TAAGTTATG
17689491 TAAGTTATG
1 TAAGTTATG
*
17689500 T-A-TTACG
1 TAAGTTATG
* *
17689507 AAAATTATG
1 TAAGTTATG
*
17689516 TAAGTTCA-A
1 TAAGTT-ATG
*
17689525 T-A-TTATT
1 TAAGTTATG
17689532 TAAGTTATG
1 TAAGTTATG
17689541 T-A-TTATG
1 TAAGTTATG
* *
17689548 AAAATTATG
1 TAAGTTATG
*
17689557 TAAGTTGTG
1 TAAGTTATG
17689566 TATAG-TA--
1 TA-AGTTATG
17689573 TAAGTTATG
1 TAAGTTATG
*
17689582 TAGGTTATG
1 TAAGTTATG
* *
17689591 AAAATTATG
1 TAAGTTATG
17689600 TAAGTTATG
1 TAAGTTATG
17689609 TAAGTTAT-
1 TAAGTTATG
**
17689617 T-TTTTATG
1 TAAGTTATG
* * *
17689625 AAAATTAAG
1 TAAGTTATG
17689634 TAAGTTATG
1 TAAGTTATG
17689643 T-A-TTATG
1 TAAGTTATG
* *
17689650 AAAATTATG
1 TAAGTTATG
*
17689659 TAAGTTCA-A
1 TAAGTT-ATG
17689668 T-A-TTATG
1 TAAGTTATG
17689675 TAAGTTATG
1 TAAGTTATG
**
17689684 T-A-CCATG
1 TAAGTTATG
17689691 -AAGATTATG
1 TAAG-TTATG
17689700 TAAGTTATG
1 TAAGTTATG
*
17689709 TATA-TTGTG
1 TA-AGTTATG
*
17689718 TAGGTTATG
1 TAAGTTATG
*
17689727 TATGTGTATAATG
1 TA--AGT-T-ATG
*
17689740 AAAGTTATG
1 TAAGTTATG
*
17689749 TAAGTTGTG
1 TAAGTTATG
*
17689758 T-A-TAATG
1 TAAGTTATG
17689765 TAAGTTATG
1 TAAGTTATG
*
17689774 TAAGTTAAG
1 TAAGTTATG
*
17689783 T-A-TAAT-
1 TAAGTTATG
*
17689789 TAAGCTATG
1 TAAGTTATG
17689798 TAAGTTATG
1 TAAGTTATG
17689807 TAAG
1 TAAG
17689811 ATGTGATAGT
Statistics
Matches: 431, Mismatches: 95, Indels: 132
0.66 0.14 0.20
Matches are distributed among these distances:
6 6 0.01
7 81 0.19
8 45 0.10
9 264 0.61
10 18 0.04
11 4 0.01
12 9 0.02
13 4 0.01
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (9 bp):
TAAGTTATG
Found at i:17689499 original size:41 final size:41
Alignment explanation
Indices: 17689444--17689605 Score: 209
Period size: 41 Copynumber: 3.9 Consensus size: 41
17689434 GATTATGAAA
* * *
17689444 ATTAAGTAACTTATGCATTATGAAAATTATGTAAGTTCAAT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
*
17689485 ATTATGTAAGTTATGTATTACGAAAATTATGTAAGTTCAAT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
* ***
17689526 ATTATTTAAGTTATGTATTATGAAAATTATGTAAGTTGTGT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
*
17689567 A-TAGTATAAGTTATGTAGGTTATGAAAATTATGTAAGTT
1 ATTA-TGTAAGTTATGTA--TTATGAAAATTATGTAAGTT
17689606 ATGTAAGTTA
Statistics
Matches: 108, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 86 0.80
43 20 0.19
ACGTcount: A:0.38, C:0.03, G:0.16, T:0.43
Consensus pattern (41 bp):
ATTATGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
Found at i:17689553 original size:184 final size:184
Alignment explanation
Indices: 17689342--17689780 Score: 614
Period size: 184 Copynumber: 2.3 Consensus size: 184
17689332 ATTATGATCA
17689342 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGCTGTGTACT-GTATAAGTTATGTAAGTTAT
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGCTGTGTA-TAGTATAAGTTATGTAAGTTAT
17689406 GAAAATTATGTAAGTTATGTAAGTT-TTTGATTATGAAAATTAAGTAACTTATGCATTATGAAAA
65 GAAAATTATGTAAGTTATGTAAGTTATTT-ATTATGAAAATTAAGTAACTTATGCATTATGAAAA
**
17689470 TTATGTAAGTTCAATATTATGTAAGTTATGTATTACGAAAATTATGTAAGTTCAAT
129 TTATGTAAGTTCAATATTATGTAAGTTATGTACCACGAAAATTATGTAAGTTCAAT
* * *
17689526 ATTATTTAAGTTATGTATTATGAAAATTATGTAAGTTGTGTATAGTATAAGTTATGTAGGTTATG
1 ATTATGTAAGTTATGTATTATGAAAATTATGTAAGCTGTGTATAGTATAAGTTATGTAAGTTATG
* * *
17689591 AAAATTATGTAAGTTATGTAAGTTATTTTTTATGAAAATTAAGTAAGTTATGTATTATGAAAATT
66 AAAATTATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAACTTATGCATTATGAAAATT
* *
17689656 ATGTAAGTTCAATATTATGTAAGTTATGTACCATGAAGATTATGTAAGTT-ATGTAT
131 ATGTAAGTTCAATATTATGTAAGTTATGTACCACGAAAATTATGTAAGTTCA---AT
* * * * * *
17689712 ATTGTGTAGGTTATGTATGTGTATAATGAAAGTTATGTAAGTTGTGTATAATGTAAGTTATGTAA
1 ATTATGTAAGTTATGTA----T-T-ATGAAAATTATGTAAGCTGTGTATAGTATAAGTTATGTAA
17689777 GTTA
60 GTTA
17689781 AGTATAATTA
Statistics
Matches: 227, Mismatches: 17, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
183 2 0.01
184 164 0.72
185 3 0.01
186 16 0.07
190 1 0.00
191 1 0.00
192 40 0.18
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.43
Consensus pattern (184 bp):
ATTATGTAAGTTATGTATTATGAAAATTATGTAAGCTGTGTATAGTATAAGTTATGTAAGTTATG
AAAATTATGTAAGTTATGTAAGTTATTTATTATGAAAATTAAGTAACTTATGCATTATGAAAATT
ATGTAAGTTCAATATTATGTAAGTTATGTACCACGAAAATTATGTAAGTTCAAT
Found at i:17689624 original size:43 final size:41
Alignment explanation
Indices: 17689454--17689645 Score: 181
Period size: 41 Copynumber: 4.8 Consensus size: 41
17689444 ATTAAGTAAC
* * *
17689454 TTATGCATTATGAAAATTATGTAAGTTCA-ATATTA-TGTAAG
1 TTATGTATTATGAAAATTATGTAAGTT-ATGTA-TAGTATAAG
* * *
17689495 TTATGTATTACGAAAATTATGTAAGTTCA-ATATTA-TTTAAG
1 TTATGTATTATGAAAATTATGTAAGTT-ATGTA-TAGTATAAG
*
17689536 TTATGTATTATGAAAATTATGTAAGTTGTGTATAGTATAAG
1 TTATGTATTATGAAAATTATGTAAGTTATGTATAGTATAAG
17689577 TTATGTAGGTTATGAAAATTATGTAAGTTATGTA-AGT-T-A-
1 TTATGTA--TTATGAAAATTATGTAAGTTATGTATAGTATAAG
*
17689616 TT-T-T-TTATGAAAATTAAGTAAGTTATGTAT
1 TTATGTATTATGAAAATTATGTAAGTTATGTAT
17689646 TATGAAAATT
Statistics
Matches: 137, Mismatches: 9, Indels: 16
0.85 0.06 0.10
Matches are distributed among these distances:
34 24 0.18
37 1 0.01
38 1 0.01
39 2 0.01
40 3 0.02
41 79 0.58
42 3 0.02
43 24 0.18
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.44
Consensus pattern (41 bp):
TTATGTATTATGAAAATTATGTAAGTTATGTATAGTATAAG
Found at i:17689658 original size:34 final size:35
Alignment explanation
Indices: 17689526--17689658 Score: 98
Period size: 34 Copynumber: 3.9 Consensus size: 35
17689516 TAAGTTCAAT
* *
17689526 ATTATTTAAGTTATGTA-TTATGAAAATTATGTAA
1 ATTATGTAAGTTATGTAGTTATGAAAATTATGAAA
* * * * **
17689560 GTTGTGTATAG-TAT-AAGTTATGTAGGTTATGAAA
1 ATTATGTA-AGTTATGTAGTTATGAAAATTATGAAA
***
17689594 ATTATGTAAGTTATGTAAGTTAT--TTTTTATGAAA
1 ATTATGTAAGTTATGT-AGTTATGAAAATTATGAAA
*
17689628 ATTAAGTAAGTTATGTA-TTATGAAAATTATG
1 ATTATGTAAGTTATGTAGTTATGAAAATTATG
17689659 TAAGTTCAAT
Statistics
Matches: 74, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
32 4 0.05
33 4 0.05
34 58 0.78
35 2 0.03
36 6 0.08
ACGTcount: A:0.38, C:0.00, G:0.17, T:0.45
Consensus pattern (35 bp):
ATTATGTAAGTTATGTAGTTATGAAAATTATGAAA
Found at i:17689678 original size:41 final size:41
Alignment explanation
Indices: 17689628--17689705 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
17689618 TTTTATGAAA
**
17689628 ATTAAGTAAGTTATGTATTATGAAAATTATGTAAGTTCAAT
1 ATTAAGTAAGTTATGTACCATGAAAATTATGTAAGTTCAAT
* *
17689669 ATTATGTAAGTTATGTACCATGAAGATTATGTAAGTT
1 ATTAAGTAAGTTATGTACCATGAAAATTATGTAAGTT
17689706 ATGTATATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.41
Consensus pattern (41 bp):
ATTAAGTAAGTTATGTACCATGAAAATTATGTAAGTTCAAT
Found at i:17689749 original size:49 final size:48
Alignment explanation
Indices: 17689670--17689808 Score: 129
Period size: 49 Copynumber: 2.8 Consensus size: 48
17689660 AAGTTCAATA
** * * *
17689670 TTATGTAAGTTATGTACCATGAAGATTATGTAAGTTATGTATATTGTGTAGG
1 TTATGTAAGTTA-GTATAATAAAG-TTATGTAAGTTATGTATA--ATGTAAG
* *
17689722 TTATGTATG-T-GTATAATGAAAGTTATGTAAGTTGTGTATAATGTAAG
1 TTATGTAAGTTAGTATAAT-AAAGTTATGTAAGTTATGTATAATGTAAG
* *
17689769 TTATGTAAGTTAAGTATAATTAAGCTATGTAAGTTATGTA
1 TTATGTAAGTT-AGTATAATAAAGTTATGTAAGTTATGTA
17689809 AGATGTGATA
Statistics
Matches: 72, Mismatches: 11, Indels: 11
0.77 0.12 0.12
Matches are distributed among these distances:
47 13 0.18
48 1 0.01
49 39 0.54
50 10 0.14
51 1 0.01
52 8 0.11
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (48 bp):
TTATGTAAGTTAGTATAATAAAGTTATGTAAGTTATGTATAATGTAAG
Found at i:17689761 original size:25 final size:25
Alignment explanation
Indices: 17689670--17689808 Score: 135
Period size: 25 Copynumber: 5.6 Consensus size: 25
17689660 AAGTTCAATA
**
17689670 TTATGTAAGTTATGTACCATG-AAG
1 TTATGTAAGTTATGTATAATGTAAG
* *
17689694 ATTATGTAAGTTATGTATATTGTGTAGG
1 -TTATGTAAGTTATGTATA--ATGTAAG
* *
17689722 TTATGT-A--TGTGTATAATGAAAG
1 TTATGTAAGTTATGTATAATGTAAG
*
17689744 TTATGTAAGTTGTGTATAATGTAAG
1 TTATGTAAGTTATGTATAATGTAAG
*
17689769 TTATGTAAGTTAAGTATAAT-TAAG
1 TTATGTAAGTTATGTATAATGTAAG
*
17689793 CTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
17689809 AGATGTGATA
Statistics
Matches: 95, Mismatches: 13, Indels: 13
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.11
23 1 0.01
24 25 0.26
25 48 0.51
26 1 0.01
27 8 0.08
28 2 0.02
ACGTcount: A:0.34, C:0.02, G:0.22, T:0.42
Consensus pattern (25 bp):
TTATGTAAGTTATGTATAATGTAAG
Found at i:17690529 original size:21 final size:21
Alignment explanation
Indices: 17690505--17690577 Score: 62
Period size: 21 Copynumber: 3.3 Consensus size: 21
17690495 AGATGTTTAT
*
17690505 ATAAATACGCTGAAAATATAA
1 ATAAATACACTGAAAATATAA
17690526 ATAAATA-A-T-ATAATATCAATAA
1 ATAAATACACTGA-AA-AT--ATAA
17690548 TATTAAATACACTGAAAATATAA
1 -A-TAAATACACTGAAAATATAA
17690571 ATAAATA
1 ATAAATA
17690578 GTCCCAAAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 18
0.69 0.02 0.30
Matches are distributed among these distances:
18 1 0.02
19 3 0.07
20 2 0.05
21 13 0.31
22 5 0.12
23 5 0.12
24 6 0.14
25 3 0.07
26 3 0.07
27 1 0.02
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (21 bp):
ATAAATACACTGAAAATATAA
Found at i:17690975 original size:29 final size:29
Alignment explanation
Indices: 17690934--17691009 Score: 145
Period size: 29 Copynumber: 2.7 Consensus size: 29
17690924 AATCTAAACA
17690934 ACATA-GCTTAACATTCAAGTGCAGAATC
1 ACATATGCTTAACATTCAAGTGCAGAATC
17690962 ACATATGCTTAACATTCAAGTGCAGAATC
1 ACATATGCTTAACATTCAAGTGCAGAATC
17690991 ACATATGCTTAACATTCAA
1 ACATATGCTTAACATTCAA
17691010 AATGTTTAAC
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 5 0.11
29 42 0.89
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (29 bp):
ACATATGCTTAACATTCAAGTGCAGAATC
Found at i:17691020 original size:16 final size:16
Alignment explanation
Indices: 17690999--17691056 Score: 80
Period size: 16 Copynumber: 3.4 Consensus size: 16
17690989 TCACATATGC
17690999 TTAACATTCAAAATGT
1 TTAACATTCAAAATGT
*
17691015 TTAACATTCAAAACTATGC
1 TTAACATTC-AAA--ATGT
17691034 TTAACATTCAAAATGT
1 TTAACATTCAAAATGT
17691050 TTAACAT
1 TTAACAT
17691057 AGCTTAACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
16 19 0.51
17 3 0.08
18 3 0.08
19 12 0.32
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.36
Consensus pattern (16 bp):
TTAACATTCAAAATGT
Found at i:17691039 original size:19 final size:18
Alignment explanation
Indices: 17690993--17691047 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 18
17690983 GCAGAATCAC
17690993 ATATGCTTAACATTC-AA
1 ATATGCTTAACATTCAAA
*
17691010 A-ATGTTTAACATTCAAA
1 ATATGCTTAACATTCAAA
17691027 ACTATGCTTAACATTCAAA
1 A-TATGCTTAACATTCAAA
17691046 AT
1 AT
17691048 GTTTAACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
16 12 0.36
17 4 0.12
18 1 0.03
19 16 0.48
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (18 bp):
ATATGCTTAACATTCAAA
Found at i:17693051 original size:14 final size:14
Alignment explanation
Indices: 17693034--17693096 Score: 72
Period size: 14 Copynumber: 4.4 Consensus size: 14
17693024 TAAAGCGGCT
*
17693034 TAAACCCCAAACCT
1 TAAACCCCAAACCC
**
17693048 TAAACCTTAAACCC
1 TAAACCCCAAACCC
*
17693062 CAAACTCCCAAACCC
1 TAAAC-CCCAAACCC
*
17693077 TAAACCCCAAACAC
1 TAAACCCCAAACCC
17693091 TAAACC
1 TAAACC
17693097 TATATCATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
14 29 0.73
15 11 0.28
ACGTcount: A:0.44, C:0.43, G:0.00, T:0.13
Consensus pattern (14 bp):
TAAACCCCAAACCC
Found at i:17693056 original size:21 final size:21
Alignment explanation
Indices: 17693032--17693097 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
17693022 ACTAAAGCGG
17693032 CTTAAACCCCAAAC-CTTAAAC
1 CTTAAACCCCAAACAC-TAAAC
* *
17693053 CTTAAACCCCAAACTCCCAAAC
1 CTTAAACCCCAAAC-ACTAAAC
*
17693075 CCTAAACCCCAAACACTAAAC
1 CTTAAACCCCAAACACTAAAC
17693096 CT
1 CT
17693098 ATATCATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
21 20 0.53
22 17 0.45
23 1 0.03
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.15
Consensus pattern (21 bp):
CTTAAACCCCAAACACTAAAC
Found at i:17693080 original size:22 final size:21
Alignment explanation
Indices: 17693034--17693088 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 21
17693024 TAAAGCGGCT
** *
17693034 TAAACCCCAAACCTTAAACCT
1 TAAACCCCAAACCCCAAACCC
17693055 TAAACCCCAAACTCCCAAACCC
1 TAAACCCCAAAC-CCCAAACCC
17693077 TAAACCCCAAAC
1 TAAACCCCAAAC
17693089 ACTAAACCTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
21 12 0.40
22 18 0.60
ACGTcount: A:0.44, C:0.44, G:0.00, T:0.13
Consensus pattern (21 bp):
TAAACCCCAAACCCCAAACCC
Found at i:17693095 original size:7 final size:7
Alignment explanation
Indices: 17693034--17693115 Score: 58
Period size: 7 Copynumber: 11.7 Consensus size: 7
17693024 TAAAGCGGCT
17693034 TAAACCC
1 TAAACCC
* *
17693041 CAAACCT
1 TAAACCC
*
17693048 TAAACCT
1 TAAACCC
17693055 TAAACCC
1 TAAACCC
*
17693062 CAAACTCC
1 TAAAC-CC
*
17693070 CAAACCC
1 TAAACCC
17693077 TAAACCC
1 TAAACCC
* *
17693084 CAAACAC
1 TAAACCC
17693091 TAAA-CC
1 TAAACCC
* * *
17693097 TATATCA
1 TAAACCC
17693104 TAAACCC
1 TAAACCC
17693111 TAAAC
1 TAAAC
17693116 TCAAAACTCT
Statistics
Matches: 58, Mismatches: 15, Indels: 4
0.75 0.19 0.05
Matches are distributed among these distances:
6 4 0.07
7 47 0.81
8 7 0.12
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAACCC
Found at i:17693095 original size:29 final size:28
Alignment explanation
Indices: 17693034--17693096 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
17693024 TAAAGCGGCT
* ** *
17693034 TAAACCCCAAACCTTAAACCTTAAACCC
1 TAAACCCCAAACCCTAAACCCCAAACAC
*
17693062 CAAACTCCCAAACCCTAAACCCCAAACAC
1 TAAAC-CCCAAACCCTAAACCCCAAACAC
17693091 TAAACC
1 TAAACC
17693097 TATATCATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.44, C:0.43, G:0.00, T:0.13
Consensus pattern (28 bp):
TAAACCCCAAACCCTAAACCCCAAACAC
Found at i:17693122 original size:27 final size:26
Alignment explanation
Indices: 17693077--17693156 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 26
17693067 TCCCAAACCC
* * *
17693077 TAAACCCCAAACACTAAAC-CTATATCA
1 TAAACCCTAAACTCAAAACTCTA-AT-A
17693104 TAAACCCTAAACTCAAAACTCTAATA
1 TAAACCCTAAACTCAAAACTCTAATA
**
17693130 TTCACCCTAAACTCAAAACTCTAATA
1 TAAACCCTAAACTCAAAACTCTAATA
17693156 T
1 T
17693157 TCACAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
26 26 0.55
27 18 0.38
28 3 0.06
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (26 bp):
TAAACCCTAAACTCAAAACTCTAATA
Found at i:17693140 original size:26 final size:26
Alignment explanation
Indices: 17693107--17693160 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
17693097 TATATCATAA
17693107 ACCCTAAACTCAAAACTCTAATATTC
1 ACCCTAAACTCAAAACTCTAATATTC
17693133 ACCCTAAACTCAAAACTCTAATATTC
1 ACCCTAAACTCAAAACTCTAATATTC
17693159 AC
1 AC
17693161 AAAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.26
Consensus pattern (26 bp):
ACCCTAAACTCAAAACTCTAATATTC
Found at i:17693767 original size:114 final size:114
Alignment explanation
Indices: 17693615--17694007 Score: 606
Period size: 114 Copynumber: 3.4 Consensus size: 114
17693605 CTATTGGCTC
* * * * *
17693615 TATAACTCAAGACCAAACGCTGCATTTTGGTTAAGATATTTTGCGGCGCTTTTCACAAAGCACCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTACAATGCGCCG
* * * *
17693680 TTAATACTATGATTTAGCGGCGTTTTTTCATAAGCGCCACTAATTCTAA
66 CTAATACTGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAA
* * *
17693729 TATACCTCAAGACCAAACGCAGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTATAATGCGCCA
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTACAATGCGCCG
* *
17693794 CTAATACTGTGCTTTAGCGGCGTTTTTGCATAAGTGCCAATAATTCTAA
66 CTAATACTGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAA
**
17693843 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCATTTTTTACAATGCGCCG
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTACAATGCGCCG
* *
17693908 CTAATATTGTGCTTTAGCGGCGTTGTTGCATAAGCGCCACTAATTCTAA
66 CTAATACTGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAA
* *
17693957 TATACCTCAAGACCTAACACTGCGTTTTGGTTAAGATATTTTGCGGCGCTT
1 TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTT
17694008 GCAAATAAAC
Statistics
Matches: 252, Mismatches: 27, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 252 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (114 bp):
TATACCTCAAGACCAAACGCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTTTACAATGCGCCG
CTAATACTGTGCTTTAGCGGCGTTTTTGCATAAGCGCCACTAATTCTAA
Found at i:17697186 original size:166 final size:166
Alignment explanation
Indices: 17696901--17697389 Score: 834
Period size: 166 Copynumber: 2.9 Consensus size: 166
17696891 TCTAAAATAG
* * *
17696901 GCATACTGTTAGTTCATGCCATTGTTTTAGATGTTAATTTTCTGTACATTACAGATACTGTGGCC
1 GCATACTATTAGTTCATGCCATTGTTTTAGATGTCAATTTTCTATACATTACAGATACTGTGGCC
* * * *
17696966 AGGGAAACATTAGATCAAGTTATGGCTAATGCAATTTCAAAATTTGGCTCTAATCGATCTGCAGC
66 AGGGAAACATTAGATCAAGTTATGGCTGATGCACTTTCAAAATATGGTTCTAATCGATCTGCAGC
* * *
17697031 ATACATTTCATGTCTTATTTTTGCAATCGATTTGCA
131 ATACATTTCATGTCTTCTTTTTGCAATCGATCTACA
*
17697067 GCATACTATTAATTCATGCCATTGTTTTAGATGTCAATTTTCTATACATTACAGATACTGTGGCC
1 GCATACTATTAGTTCATGCCATTGTTTTAGATGTCAATTTTCTATACATTACAGATACTGTGGCC
*
17697132 AGGGAAACATTAGATCAAGTTATGGCTGATGCACTTTCAAAATCTGGTTCTAATCGATCTGCAGC
66 AGGGAAACATTAGATCAAGTTATGGCTGATGCACTTTCAAAATATGGTTCTAATCGATCTGCAGC
17697197 ATACATTTCATGTCTTCTTTTTGCAATCGATCTACA
131 ATACATTTCATGTCTTCTTTTTGCAATCGATCTACA
* **
17697233 TCATACTATTAGTTCATGCCATTGTTTTAGATGTCAATTTTCTATACATTACAGATGTTGTGGCC
1 GCATACTATTAGTTCATGCCATTGTTTTAGATGTCAATTTTCTATACATTACAGATACTGTGGCC
*
17697298 AGGGAAACATTAGATCAAGTTATGGCAGATGCACTTTCAAAATATGGTTCTAATCGATCTGCAGC
66 AGGGAAACATTAGATCAAGTTATGGCTGATGCACTTTCAAAATATGGTTCTAATCGATCTGCAGC
17697363 ATACATTTCATGTCTTCTTTTTGCAAT
131 ATACATTTCATGTCTTCTTTTTGCAAT
17697390 GGCATTTTAA
Statistics
Matches: 306, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 306 1.00
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.38
Consensus pattern (166 bp):
GCATACTATTAGTTCATGCCATTGTTTTAGATGTCAATTTTCTATACATTACAGATACTGTGGCC
AGGGAAACATTAGATCAAGTTATGGCTGATGCACTTTCAAAATATGGTTCTAATCGATCTGCAGC
ATACATTTCATGTCTTCTTTTTGCAATCGATCTACA
Found at i:17698492 original size:16 final size:16
Alignment explanation
Indices: 17698473--17698520 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
17698463 TGATTATAGT
17698473 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
*
17698489 TCTATTCCATTACAAC
1 TCTATTCCATTACAGC
17698505 TCTATTCCATTACAGC
1 TCTATTCCATTACAGC
17698521 GAACCAAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.27, C:0.31, G:0.04, T:0.38
Consensus pattern (16 bp):
TCTATTCCATTACAGC
Found at i:17704519 original size:17 final size:17
Alignment explanation
Indices: 17704454--17704524 Score: 58
Period size: 17 Copynumber: 4.3 Consensus size: 17
17704444 TCAATAATTT
17704454 ATTAAAATT-TT-AAAA
1 ATTAAAATTATTAAAAA
* *
17704469 ATTCAAATAATATAAAAA
1 ATTAAAATTAT-TAAAAA
** * *
17704487 A-TATTATTTTTTAAAA
1 ATTAAAATTATTAAAAA
17704503 ATTAAAATTATTAAAAA
1 ATTAAAATTATTAAAAA
17704520 ATTAA
1 ATTAA
17704525 TTAATTGTTA
Statistics
Matches: 40, Mismatches: 12, Indels: 6
0.69 0.21 0.10
Matches are distributed among these distances:
15 7 0.17
16 7 0.17
17 21 0.52
18 5 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
ATTAAAATTATTAAAAA
Found at i:17705109 original size:45 final size:45
Alignment explanation
Indices: 17705045--17705130 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
17705035 TCTTGACCAC
* * *
17705045 ATATAAATAATTAATAATAAATATTGTGTAATTTAATTAAAATTA
1 ATATAAATAATTAATAATAAATACTATATAATTTAATTAAAATTA
*
17705090 ATATAAATAATTTATAATAAATACTATATAATTTAATTAAA
1 ATATAAATAATTAATAATAAATACTATATAATTTAATTAAA
17705131 CATTTAGTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (45 bp):
ATATAAATAATTAATAATAAATACTATATAATTTAATTAAAATTA
Found at i:17706164 original size:26 final size:25
Alignment explanation
Indices: 17706113--17706165 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
17706103 CTAGTGGTGT
**
17706113 ATAAGACTGTACATTTTTTTGGTAA
1 ATAAGACTGTACATTTTTTTAATAA
*
17706138 ATAAGATTGTACATTTTTTTTAATAA
1 ATAAGACTGTACA-TTTTTTTAATAA
17706164 AT
1 AT
17706166 TATGTGATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 12 0.50
26 12 0.50
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (25 bp):
ATAAGACTGTACATTTTTTTAATAA
Found at i:17709861 original size:67 final size:67
Alignment explanation
Indices: 17709753--17709973 Score: 209
Period size: 67 Copynumber: 3.3 Consensus size: 67
17709743 CATTGATTGT
* *
17709753 CATAGTCGAGCCATGGTCTTACACCTTAATCCTTA-TT-TTTAAAGTCCT-GTAAAACTCTGTTG
1 CATAGTCGAGCTATGGTCTTACACCTTAATCC--ACTTGTTTAAAGTCCTGGT-AAACTCTATTG
17709815 GATGC
63 GATGC
* * * * **
17709820 CATAGCCGAGCTATGGTCTTACACCTGAATCCACTTGTTTAATGTCTTGGTGGACTCTATTGGAT
1 CATAGTCGAGCTATGGTCTTACACCTTAATCCACTTGTTTAAAGTCCTGGTAAACTCTATTGGAT
17709885 GC
66 GC
* * * ** *
17709887 CATAGTCGAGTTATGGTCTTACACCTTAATCC-CTATGTTTAATA-TCTTGATGGACTCAATTGG
1 CATAGTCGAGCTATGGTCTTACACCTTAATCCACT-TGTTTAA-AGTCCTGGTAAACTCTATTGG
*
17709950 TTGC
64 ATGC
* *
17709954 CATAATCGAACTATGGTCTT
1 CATAGTCGAGCTATGGTCTT
17709974 GCAAACCTCT
Statistics
Matches: 131, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
65 1 0.01
66 4 0.03
67 124 0.95
68 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (67 bp):
CATAGTCGAGCTATGGTCTTACACCTTAATCCACTTGTTTAAAGTCCTGGTAAACTCTATTGGAT
GC
Done.