Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64892201
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1760000 characters in sequence are not A, C, G, or T
File 57 of 221
Found at i:16423250 original size:28 final size:28
Alignment explanation
Indices: 16423203--16423393 Score: 163
Period size: 28 Copynumber: 6.8 Consensus size: 28
16423193 TATTGCCATG
* *
16423203 AGGCTTTCTTTTTTAGAGGTTGCCACAA
1 AGGCTTTCCTTTGTAGAGGTTGCCACAA
* * *
16423231 AGGCTTTCCTTTATAAAGGTTTCCTACAA
1 AGGCTTTCCTTTGTAGAGGTTGCC-ACAA
* *
16423260 AGGTTTTCCTTTGTAGAGGTTTGCCATAA
1 AGGCTTTCCTTTGTAGAGG-TTGCCACAA
*
16423289 AGGCTTTCC-TTGCAGAGGTTCGCCACAA
1 AGGCTTTCCTTTGTAGAGGTT-GCCACAA
* * *
16423317 AGGC-TTCCTCTGTAGAGGTTCGCCATAG
1 AGGCTTTCCTTTGTAGAGGTT-GCCACAA
** * * *
16423345 AGATTTTCCTTTGCAGAGTTTTTCCACAA
1 AGGCTTTCCTTTGTAGAG-GTTGCCACAA
*
16423374 AGGCTTTCCTTT-TGGAGGTT
1 AGGCTTTCCTTTGTAGAGGTT
16423394 TACTATCAAG
Statistics
Matches: 128, Mismatches: 29, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
27 8 0.06
28 58 0.45
29 56 0.44
30 6 0.05
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (28 bp):
AGGCTTTCCTTTGTAGAGGTTGCCACAA
Found at i:16423306 original size:85 final size:85
Alignment explanation
Indices: 16423217--16423384 Score: 205
Period size: 85 Copynumber: 2.0 Consensus size: 85
16423207 TTTCTTTTTT
* * * *
16423217 AGAGGTT-GCCACAAAGGCTTTCCTTTATAAAGGTTTC-CTACAAAGGTTTTCCTTTGTAGAGGT
1 AGAGGTTCGCCACAAAGGC-TTCCTCTATAAAGG-TTCGCCACAAAGATTTTCCTTTGCAGAGGT
*
16423280 TTGCCATAAAGGCTTTCCTTGC
64 TTGCCACAAAGGCTTTCCTTGC
* * * * *
16423302 AGAGGTTCGCCACAAAGGCTTCCTCTGTAGAGGTTCGCCATAGAGATTTTCCTTTGCAGAGTTTT
1 AGAGGTTCGCCACAAAGGCTTCCTCTATAAAGGTTCGCCACAAAGATTTTCCTTTGCAGAGGTTT
*
16423367 TCCACAAAGGCTTTCCTT
66 GCCACAAAGGCTTTCCTT
16423385 TTGGAGGTTT
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
84 3 0.04
85 56 0.80
86 11 0.16
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (85 bp):
AGAGGTTCGCCACAAAGGCTTCCTCTATAAAGGTTCGCCACAAAGATTTTCCTTTGCAGAGGTTT
GCCACAAAGGCTTTCCTTGC
Found at i:16423449 original size:28 final size:29
Alignment explanation
Indices: 16423406--16423470 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 29
16423396 CTATCAAGAG
16423406 TTTCCTTTGCAAAGTTTTGCCACAAAATA
1 TTTCCTTTGCAAAGTTTTGCCACAAAATA
* ** *
16423435 TTTCCTTT-CAGAGTTTTGTTACAAAATC
1 TTTCCTTTGCAAAGTTTTGCCACAAAATA
*
16423463 TTTTCTTT
1 TTTCCTTT
16423471 TTCTAGCGCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 23 0.74
29 8 0.26
ACGTcount: A:0.25, C:0.18, G:0.09, T:0.48
Consensus pattern (29 bp):
TTTCCTTTGCAAAGTTTTGCCACAAAATA
Found at i:16423678 original size:50 final size:50
Alignment explanation
Indices: 16423586--16423680 Score: 118
Period size: 50 Copynumber: 1.9 Consensus size: 50
16423576 TAGTTGTTTT
* * ** *
16423586 CATATGATGCCATAACCTACCAGTTATGGTCTTATACAATATGGTCTTTC
1 CATATGACGCCATAACCCACCAACTATGGTCTTACACAATATGGTCTTTC
* **
16423636 CATATGACGCCATAGCCCACCAACTATGGTCTTACATGATATGGT
1 CATATGACGCCATAACCCACCAACTATGGTCTTACACAATATGGT
16423681 GCCATGGAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 37 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (50 bp):
CATATGACGCCATAACCCACCAACTATGGTCTTACACAATATGGTCTTTC
Found at i:16436054 original size:6 final size:7
Alignment explanation
Indices: 16436037--16436103 Score: 95
Period size: 7 Copynumber: 9.7 Consensus size: 7
16436027 CTAAGTTAGA
16436037 AAAAATG
1 AAAAATG
16436044 AAAAATG
1 AAAAATG
16436051 AAAAAATG
1 -AAAAATG
16436059 -AAAATG
1 AAAAATG
16436065 -AAAATG
1 AAAAATG
16436071 -AAAATG
1 AAAAATG
16436077 AAAAATG
1 AAAAATG
16436084 AAAAATG
1 AAAAATG
16436091 AAAAAATG
1 -AAAAATG
16436099 AAAAA
1 AAAAA
16436104 GTAAAAATAG
Statistics
Matches: 57, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
6 18 0.32
7 25 0.44
8 14 0.25
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:16437496 original size:44 final size:44
Alignment explanation
Indices: 16437427--16437793 Score: 185
Period size: 44 Copynumber: 7.9 Consensus size: 44
16437417 TGTAAGGAAA
* * *
16437427 CAGATTTAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
** *
16437471 CAGATTGAAGCTATTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
** * * * *
16437515 C-GAATT-AAAATA-AAGGATCTTATCTCTCTGA-AGTTAGAGTAGAGTAGATCG
1 CAG-ATTGAAGCTAGAA--ATCCTATCTCCCTGAGA-TT--A-CAGCG--GA--G
*
16437566 CATCAGATTGAAGCCAGAAAT-CTCATCTCCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAGAAATCCT-ATCTCCCTGAGATTACAGCGGAG
* * *
16437613 TAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
** ** * *
16437657 CAGATT-AAAATA-AAGGATTTTATCTCTCTGA-AGTTACAGTAGAGAAGATCG
1 CAGATTGAAGCTAGAA--ATCCTATCTCCCTGAGA-TTAC---AGCG--GA--G
* *
16437708 CATCAGATTGAAGCCAGAAAT-CTCATCTCCCTGAGATTATAGCGGAG
1 ---CAGATTGAAGCTAGAAATCCT-ATCTCCCTGAGATTACAGCGGAG
*
16437755 CAGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAG
1 CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAG
16437794 TGAAGCGGAT
Statistics
Matches: 243, Mismatches: 42, Indels: 76
0.67 0.12 0.21
Matches are distributed among these distances:
42 2 0.01
43 11 0.05
44 148 0.61
45 4 0.02
46 1 0.00
47 8 0.03
49 8 0.03
51 8 0.03
52 1 0.00
53 2 0.01
54 37 0.15
55 9 0.04
56 4 0.02
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCTAGAAATCCTATCTCCCTGAGATTACAGCGGAG
Found at i:16437683 original size:142 final size:141
Alignment explanation
Indices: 16437427--16437855 Score: 732
Period size: 142 Copynumber: 3.0 Consensus size: 141
16437417 TGTAAGGAAA
* * *
16437427 CAGATTTAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTATTAATCCT
1 CAGATTGAAGCCAGAAATCTCATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
16437492 ATCTCCCTGAGATTACAGTGGAGCGAATTAAAATAAAGGATCTTATCTCTCTGAAGTTAGAGTAG
66 ATCTCCCTGAGATTACAGTGGAGCG-ATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
16437557 AGTAGATCGCAT
130 AGTAGATCGCAT
*
16437569 CAGATTGAAGCCAGAAATCTCATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTCATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
*
16437634 ATCTCCCTGAGATTACAGTGGAGCAGATTAAAATAAAGGATTTTATCTCTCTGAAGTTACAGTAG
66 ATCTCCCTGAGATTACAGTGGAGC-GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
16437699 AGAAGATCGCAT
130 AGTAGATCGCAT
*
16437711 CAGATTGAAGCCAGAAATCTCATCTCCCTGAGATTATAGCGGAGCAGATTGAAGCTAGTAATCCT
1 CAGATTGAAGCCAGAAATCTCATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
* *
16437776 ATCTCCCTGAGATTACAGTGAAGCGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAA
66 ATCTCCCTGAGATTACAGTGGAGC-GATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAG
*
16437841 AGTAGATCGTAT
130 AGTAGATCGCAT
16437853 CAG
1 CAG
16437856 GTCTTATCTC
Statistics
Matches: 271, Mismatches: 15, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
142 270 1.00
143 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (141 bp):
CAGATTGAAGCCAGAAATCTCATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCTAGTAATCCT
ATCTCCCTGAGATTACAGTGGAGCGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGA
GTAGATCGCAT
Found at i:16437975 original size:50 final size:50
Alignment explanation
Indices: 16437920--16438596 Score: 174
Period size: 50 Copynumber: 13.5 Consensus size: 50
16437910 TCCCAGGCAG
* * *
16437920 TGCAGTGGAATAGATTAAAGCCACAACGATGAATTTTGCCTCCCTGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACAT
* * * ** *
16437970 TGCAGTTAAAAAGATTAAAGCTAC-A-GTAGTGAATCTTACCTCCCTGGTAG
1 TGCAGTGAAAAAGATTAAAGCCACAACG-A-TGAATCTTGCCTCCCTGACAT
* * * * * *
16438020 TGCAGTGGAACAGATTAAAGTCACATCGGTGAATCTTGCGTCCCTGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACAT
* ** * * *
16438070 TGCAGTTAAAAAGATTAAAGCTGC-A-GTAGCGAATCTT-ACTCCCTAGGCGA-
1 TGCAGTGAAAAAGATTAAAGCCACAACG-A-TGAATCTTGCCTCCCT-GAC-AT
* * * * * * * *
16438120 TGCAGCGGAACAGATTAAAACCACAACGGTGAATCTTGCTTCCCCGATAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACAT
* * * * * *
16438170 TACAGTTAAAAAGATTAAAGCTACAAC-A-GCAAATCTT-ACTCCCCAGGCGA-
1 TGCAGTGAAAAAGATTAAAGCCACAACGATG--AATCTTGCCT-CCCTGAC-AT
* ** * * *
16438220 TGCAG-CAGAGCAGATTAAAGCCACAAATG-TGAATCTTG-CTACCCCGATAT
1 TGCAGTGA-AAAAGATTAAAGCCAC-AACGATGAATCTTGCCT-CCCTGACAT
* * * * ** * * *
16438270 TGCAGTTAAAAAGATTAAAGCTATAGC-A-GCAAATCTAACCTCCCAGGCAA
1 TGCAGTGAAAAAGATTAAAGCCACAACGATG--AATCTTGCCTCCCTGACAT
* ** * * * * *
16438320 TGCAGTGGAGTAGATTAAAACCACAATG--GCATATCTTGCTTCCCCGAAAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGATG-A-ATCTTGCCTCCCTGACAT
* * * * ** * * * * * *
16438370 TGTAGTTAAAAAGACTAAAGCCACAGCGGCGAGTGTTACTTCCCTGGCAA
1 TGCAGTGAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACAT
* ** * **
16438420 CGCAGTGAAGCAGATTAAAGCCACAACGGTGAATCTTG-CTTTCTCGACAT
1 TGCAGTGAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCT-GACAT
* * * * * *
16438470 TGCAGAT-AAAAGGATTAAAGTCACAACGACGAATC-T-CACTCGCTCAGCTAG
1 TGCAG-TGAAAAAGATTAAAGCCACAACGATGAATCTTGC-CTCCCTGA-C-AT
* ** * * *
16438521 TGTAGTAGAGCAA-ATTAAAGCCACAACGGTGAATCTTGCTTCCCCGACAT
1 TGCAGT-GAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACAT
* * *
16438571 TGCAGTTAAAAAGATTGAAGCTACAA
1 TGCAGTGAAAAAGATTAAAGCCACAA
16438597 AGCTACGAAT
Statistics
Matches: 424, Mismatches: 161, Indels: 84
0.63 0.24 0.13
Matches are distributed among these distances:
48 4 0.01
49 21 0.05
50 348 0.82
51 39 0.09
52 11 0.03
53 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (50 bp):
TGCAGTGAAAAAGATTAAAGCCACAACGATGAATCTTGCCTCCCTGACAT
Found at i:16438075 original size:100 final size:99
Alignment explanation
Indices: 16437902--16438595 Score: 682
Period size: 100 Copynumber: 6.9 Consensus size: 99
16437892 AGAATTACAG
* * * * *
16437902 ATCTTATCTCCCAGGCAGTGCAGTGGAATAGATTAAAGCCACAACGATGAATTTTGCCTCCCTGA
1 ATCTTA-CTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGA
* *
16437967 CATTGCAGTTAAAAAGATTAAAGCTACAGTAGTGA
65 CATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGA
* * * * * *
16438002 ATCTTACCTCCCTGGTAGTGCAGTGGAACAGATTAAAGTCACATCGGTGAATCTTGCGTCCCTGA
1 ATCTTA-CTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGA
* *
16438067 CATTGCAGTTAAAAAGATTAAAGCTGCAGTAGCGA
65 CATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGA
* *
16438102 ATCTTACTCCCTAGGC-GATGCAGCGGAACAGATTAAAACCACAACGGTGAATCTTGCTTCCCCG
1 ATCTTACTCCC-AGGCAG-TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCG
* * * *
16438166 ATATTACAGTTAAAAAGATTAAAGCTACAACAGCAA
64 ACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGA
** * ** *
16438202 ATCTTACTCCCCAGGC-GATGCAGCAGAGCAGATTAAAGCCACAAATGTGAATCTTGCTACCCCG
1 ATCTTACT-CCCAGGCAG-TGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCG
* * *
16438266 ATATTGCAGTTAAAAAGATTAAAGCTATAGCAGCAA
64 ACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGA
* * ** * * *
16438302 ATCTAACCTCCCAGGCAATGCAGTGGAGTAGATTAAAACCACAATGG-CATATCTTGCTTCCCCG
1 ATCTTA-CTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGA-ATCTTGCTTCCCCG
* * * * *
16438366 AAATTGTAGTTAAAAAGACTAAAGCCACAGCGGCGA
64 ACATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGA
* * * ** * *
16438402 GTGTTACTTCCCTGGCAACGCAGT-GAAGCAGATTAAAGCCACAACGGTGAATCTTGCTTTCTCG
1 ATCTTAC-TCCCAGGCAGTGCAGTGGAA-CAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCG
* * *
16438466 ACATTGCAGATAAAAGGATTAAAG-TCACAAC-GACGA
64 ACATTGCAGTTAAAAAGATTAAAGCT-ACAGCAG-CGA
* * * * *
16438502 ATCTCACTCGCTCA-GCTAGTGTAGTAGAGCAAATTAAAGCCACAACGGTGAATCTTGCTTCCCC
1 ATCTTACTC-C-CAGGC-AGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCC
*
16438566 GACATTGCAGTTAAAAAGATTGAAGCTACA
63 GACATTGCAGTTAAAAAGATTAAAGCTACA
16438596 AAGCTACGAA
Statistics
Matches: 494, Mismatches: 84, Indels: 31
0.81 0.14 0.05
Matches are distributed among these distances:
99 13 0.03
100 409 0.83
101 69 0.14
102 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (99 bp):
ATCTTACTCCCAGGCAGTGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTTGCTTCCCCGAC
ATTGCAGTTAAAAAGATTAAAGCTACAGCAGCGA
Found at i:16445429 original size:16 final size:16
Alignment explanation
Indices: 16445408--16445438 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16445398 TTCACTAATA
*
16445408 TGTCTTTTGTATTTTC
1 TGTCTTTTATATTTTC
16445424 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
16445439 ACATTCGTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTCTTTTATATTTTC
Found at i:16446608 original size:19 final size:19
Alignment explanation
Indices: 16446584--16446623 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16446574 ATTAATTTTG
16446584 ATCAAGTAAAATT-AAATTA
1 ATCAAGT-AAATTAAAATTA
*
16446603 ATCAAGTCAATTAAAATTA
1 ATCAAGTAAATTAAAATTA
16446622 AT
1 AT
16446624 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (19 bp):
ATCAAGTAAATTAAAATTA
Found at i:16447610 original size:16 final size:17
Alignment explanation
Indices: 16447568--16447614 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
16447558 AGGATCATTG
16447568 AGTTTATTTATT-TTTTT
1 AGTTTATTT-TTATTTTT
16447585 AGTTTATTTTTATTTTT
1 AGTTTATTTTTATTTTT
*
16447602 AG-TTGTTTTTATT
1 AGTTTATTTTTATT
16447615 GTTACTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (17 bp):
AGTTTATTTTTATTTTT
Found at i:16454801 original size:18 final size:18
Alignment explanation
Indices: 16454778--16454824 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
16454768 CTTTTAGGTT
16454778 TATTTTTCTTTTATCTTC
1 TATTTTTCTTTTATCTTC
16454796 TATTTTTCTTTTATCTTC
1 TATTTTTCTTTTATCTTC
16454814 TATTTTTCTTT
1 TATTTTTCTTT
16454825 GGTATTTTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (18 bp):
TATTTTTCTTTTATCTTC
Found at i:16455887 original size:12 final size:12
Alignment explanation
Indices: 16455870--16455908 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
16455860 AGACGACTTC
16455870 ATATTGTATTAA
1 ATATTGTATTAA
*
16455882 ATATTGTA-TCA
1 ATATTGTATTAA
16455893 ATATTGTATTAA
1 ATATTGTATTAA
16455905 ATAT
1 ATAT
16455909 AGCACAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATTGTATTAA
Found at i:16458431 original size:37 final size:37
Alignment explanation
Indices: 16458381--16458453 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
16458371 ACAACACTAA
*
16458381 GAGCTTTCAGTTTCCTAGAAATCCCCATATTTCAAGT
1 GAGCTTTCAGTTTCCTAGAAATCCACATATTTCAAGT
* * *
16458418 GAGC-TTCAAGTTTCCTGGACATCTACATATTTCAAG
1 GAGCTTTC-AGTTTCCTAGAAATCCACATATTTCAAG
16458454 GGAATACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
36 3 0.10
37 28 0.90
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (37 bp):
GAGCTTTCAGTTTCCTAGAAATCCACATATTTCAAGT
Found at i:16463977 original size:19 final size:20
Alignment explanation
Indices: 16463940--16463977 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16463930 AAATAAGCTC
*
16463940 TTAGGCTAGGCATTGACAAG
1 TTAGCCTAGGCATTGACAAG
16463960 TTAGCCTAGGCA-TGACAA
1 TTAGCCTAGGCATTGACAA
16463978 CCACATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
TTAGCCTAGGCATTGACAAG
Found at i:16472667 original size:22 final size:22
Alignment explanation
Indices: 16472642--16472686 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
16472632 ATTATGATGA
16472642 TTGATATGT-TGAGATTGATATT
1 TTGATATGTATGAGATT-ATATT
*
16472664 TTGATATGTATGCGATTATATT
1 TTGATATGTATGAGATTATATT
16472686 T
1 T
16472687 GTGTTGATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.51
Consensus pattern (22 bp):
TTGATATGTATGAGATTATATT
Found at i:16475190 original size:21 final size:23
Alignment explanation
Indices: 16475161--16475202 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
16475151 CAGTGGCATC
16475161 GCAACCAAAC-AT-ACTTAATAT
1 GCAACCAAACAATAACTTAATAT
*
16475182 GCAATCAAACAATAACTTAAT
1 GCAACCAAACAATAACTTAAT
16475203 GAGTCGCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 2 0.11
23 7 0.39
ACGTcount: A:0.50, C:0.21, G:0.05, T:0.24
Consensus pattern (23 bp):
GCAACCAAACAATAACTTAATAT
Found at i:16477345 original size:27 final size:28
Alignment explanation
Indices: 16477258--16477355 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
16477248 CATGAGATTG
* * *
16477258 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-AATTATATA
*
16477287 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
16477315 GCACTAAGTGTGCGAG-TTAATTATATA
1 GCACTAAGTGTGCGAGTTTAATTATATA
*
16477342 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
16477356 GACTTAATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 23 0.37
28 22 0.35
29 18 0.29
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTAATTATATA
Found at i:16477368 original size:27 final size:27
Alignment explanation
Indices: 16477258--16477369 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
16477248 CATGAGATTG
* * *
16477258 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GATTT-AATTATATA
*
16477287 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-TTTAATTATATA
*
16477315 GCACTAAGTGTGCGAGTTAATTATATA
1 GCACTAAGTGTGCGATTTAATTATATA
* *
16477342 GCACTGAGTGTGCGGACTTAATTTATAT
1 GCACTAAGTGTGC-GATTTAA-TTATAT
16477370 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 22 0.31
28 28 0.39
29 22 0.31
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.34
Consensus pattern (27 bp):
GCACTAAGTGTGCGATTTAATTATATA
Found at i:16491999 original size:27 final size:28
Alignment explanation
Indices: 16491915--16492012 Score: 135
Period size: 27 Copynumber: 3.5 Consensus size: 28
16491905 CATGAGATTG
* * * *
16491915 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGCGAGTTT-GATTATATA
16491944 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
16491972 GCACTAAGTGTGCGAG-TTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
16491999 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
16492013 GACTTAATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 24 0.38
28 22 0.34
29 18 0.28
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.32
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:16492023 original size:27 final size:27
Alignment explanation
Indices: 16491943--16492025 Score: 96
Period size: 27 Copynumber: 3.0 Consensus size: 27
16491933 TAAATTGTAC
* *
16491943 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
16491971 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
16491998 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
16492025 A
1 A
16492026 TTTTTGAATC
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
27 30 0.60
28 20 0.40
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:16492026 original size:29 final size:27
Alignment explanation
Indices: 16491915--16492026 Score: 98
Period size: 28 Copynumber: 4.0 Consensus size: 27
16491905 CATGAGATTG
** * *
16491915 GCACTAAGTGTGCGGGTTTAAATTGTACA
1 GCACTAAGTGTGC-GACTT-AATTATATA
* *
16491944 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGA-CTTAATTATATA
* *
16491972 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGACTTAATTATATA
*
16491999 GCACTGAGTGTGCGGACTTAATATATAT
1 GCACTAAGTGTGC-GACTTAAT-TATAT
16492027 TTTTGAATCA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
27 23 0.32
28 28 0.39
29 21 0.29
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
GCACTAAGTGTGCGACTTAATTATATA
Found at i:16509078 original size:22 final size:22
Alignment explanation
Indices: 16509050--16509094 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
16509040 TTTTTGGAAG
16509050 ATTGAATTGGAAAAACCACATA
1 ATTGAATTGGAAAAACCACATA
*
16509072 ATTGAATTGGTAAAACCACATA
1 ATTGAATTGGAAAAACCACATA
16509094 A
1 A
16509095 GCTGCGAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.24
Consensus pattern (22 bp):
ATTGAATTGGAAAAACCACATA
Found at i:16519623 original size:37 final size:37
Alignment explanation
Indices: 16519582--16519659 Score: 104
Period size: 37 Copynumber: 2.1 Consensus size: 37
16519572 ACAATTAGTG
* * *
16519582 TGTTATCGGGTGGATTGGCTCTTATGAGC-ATCTGGCA
1 TGTTATCGAGTGGATTAGCTCTTACGAGCGAT-TGGCA
*
16519619 TGTTATTGAGTGGATTAGCTCTTACGAGCGATTGGCA
1 TGTTATCGAGTGGATTAGCTCTTACGAGCGATTGGCA
16519656 TGTT
1 TGTT
16519660 TCATTTAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
37 34 0.94
38 2 0.06
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.37
Consensus pattern (37 bp):
TGTTATCGAGTGGATTAGCTCTTACGAGCGATTGGCA
Found at i:16539245 original size:20 final size:20
Alignment explanation
Indices: 16539220--16539257 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
16539210 CCCTAACCAA
16539220 AGGGTCCTTAAATATTACTT
1 AGGGTCCTTAAATATTACTT
16539240 AGGGTCCTTAAATATTAC
1 AGGGTCCTTAAATATTAC
16539258 ACTTTCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (20 bp):
AGGGTCCTTAAATATTACTT
Found at i:16541585 original size:59 final size:62
Alignment explanation
Indices: 16541514--16541630 Score: 159
Period size: 62 Copynumber: 1.9 Consensus size: 62
16541504 ATCACTTTAA
* * ** * *
16541514 TATTAAATTAATATAATATTT-A-T-CAAGATAAATTTTAGATTGAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTAACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
16541573 TATTAAAATAATAGAATATTTAACTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATTTAACTACAAGATAAACATTAAATTAAATTTAATATTAA
16541631 GATAATCACT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 19 0.39
60 1 0.02
61 1 0.02
62 28 0.57
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (62 bp):
TATTAAAATAATAGAATATTTAACTACAAGATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:16541656 original size:20 final size:18
Alignment explanation
Indices: 16541609--16541657 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
16541599 CAAGATAAAC
16541609 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
16541626 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
16541646 ATTAAATTAATA
1 ATTAAATTAATA
16541658 AAATACTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
17 8 0.30
18 1 0.04
19 3 0.11
20 15 0.56
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:16542571 original size:16 final size:16
Alignment explanation
Indices: 16542550--16542580 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16542540 CTATTTATAC
*
16542550 AAAATATAAAAGACAG
1 AAAATACAAAAGACAG
16542566 AAAATACAAAAGACA
1 AAAATACAAAAGACA
16542581 TTATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.10, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAATACAAAAGACAG
Found at i:16543463 original size:24 final size:24
Alignment explanation
Indices: 16543415--16543461 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
16543405 ACTGGTCATA
*
16543415 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
16543439 GAGAGATTTGAGGAGTGAATATT
1 GAGAGAATTGAGGAG-GAATATT
16543462 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:16544599 original size:28 final size:28
Alignment explanation
Indices: 16544559--16544661 Score: 170
Period size: 28 Copynumber: 3.7 Consensus size: 28
16544549 ACCGGAACTG
*
16544559 TATTGGGCTAAGGCCCACATTGCTACTA
1 TATTGGGCTAAGGCCCACATTGTTACTA
16544587 TATTGGGCTAAGGCCCACATTGTTACTA
1 TATTGGGCTAAGGCCCACATTGTTACTA
* *
16544615 TAGTGGGCTAAGGCCCACATTGTTACTG
1 TATTGGGCTAAGGCCCACATTGTTACTA
*
16544643 TATTGGACTAAGGCCCACA
1 TATTGGGCTAAGGCCCACA
16544662 CTGTATTGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 70 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (28 bp):
TATTGGGCTAAGGCCCACATTGTTACTA
Found at i:16557537 original size:11 final size:13
Alignment explanation
Indices: 16557509--16557540 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
16557499 TAGAACAATC
16557509 AAAAATAATTTGT
1 AAAAATAATTTGT
16557522 AAAAATAA-TT-T
1 AAAAATAATTTGT
16557533 AAAAATAA
1 AAAAATAA
16557541 GATTTTTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (13 bp):
AAAAATAATTTGT
Found at i:16559748 original size:20 final size:20
Alignment explanation
Indices: 16559725--16559796 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
16559715 CCGAATAGAG
*
16559725 CAGAACAGAATAAAATGGAA
1 CAGAACAGAACAAAATGGAA
* * *
16559745 CAGAGCAGAGCAATACT-GAA
1 CAGAACAGAACAA-AATGGAA
* *
16559765 CAGAACAGAACAGAATGGAG
1 CAGAACAGAACAAAATGGAA
*
16559785 CAGAGCAGAACA
1 CAGAACAGAACA
16559797 TAGCATATAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.05
20 36 0.90
21 2 0.05
ACGTcount: A:0.51, C:0.17, G:0.25, T:0.07
Consensus pattern (20 bp):
CAGAACAGAACAAAATGGAA
Found at i:16559749 original size:25 final size:25
Alignment explanation
Indices: 16559703--16559753 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
16559693 ACGCAATTCA
* *
16559703 AACAGAATAGAACCGAATAGAGCAG
1 AACAGAATAAAACCGAACAGAGCAG
**
16559728 AACAGAATAAAATGGAACAGAGCAG
1 AACAGAATAAAACCGAACAGAGCAG
16559753 A
1 A
16559754 GCAATACTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.55, C:0.14, G:0.24, T:0.08
Consensus pattern (25 bp):
AACAGAATAAAACCGAACAGAGCAG
Found at i:16560936 original size:42 final size:42
Alignment explanation
Indices: 16560776--16560937 Score: 146
Period size: 42 Copynumber: 3.9 Consensus size: 42
16560766 AGTGAGTTAA
* * * *
16560776 ACGGCCTGGACACACCCCCATGTCCTTGCCCGTGTGCCTCAC
1 ACGGCCTGGGCACACGCCTATGTCCTTGCCCGTGTGGCTCAC
* ** * * * * *
16560818 ATGATCTGGGAACACGCCTATGTCGTTGCCCATGTTGTTCAC
1 ACGGCCTGGGCACACGCCTATGTCCTTGCCCGTGTGGCTCAC
* * * *
16560860 ATGGCCTAGGCACACGCCTAT-ACCATTGCTCGTGTGGCTCAC
1 ACGGCCTGGGCACACGCCTATGTCC-TTGCCCGTGTGGCTCAC
* *
16560902 ACGGCCTGGGCACACGCCTATGTCCCTGGCCGTGTG
1 ACGGCCTGGGCACACGCCTATGTCCTTGCCCGTGTG
16560938 TTTCTAAAAC
Statistics
Matches: 90, Mismatches: 28, Indels: 4
0.74 0.23 0.03
Matches are distributed among these distances:
41 1 0.01
42 87 0.97
43 2 0.02
ACGTcount: A:0.16, C:0.35, G:0.25, T:0.23
Consensus pattern (42 bp):
ACGGCCTGGGCACACGCCTATGTCCTTGCCCGTGTGGCTCAC
Found at i:16561013 original size:42 final size:42
Alignment explanation
Indices: 16560966--16561048 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
16560956 CGAGTTACAC
*
16560966 AGCCTGGA-TACACACCCATGTCCCTACCCATGTGGCTCACAT
1 AGCCT-GACTACACACCCATGTCCCTACCCATATGGCTCACAT
* * **
16561008 AGCCTGACTACACGCCCGTGTCCCTGGCCATATGGCTCACA
1 AGCCTGACTACACACCCATGTCCCTACCCATATGGCTCACA
16561049 CGGTCTCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.06
42 33 0.94
ACGTcount: A:0.22, C:0.39, G:0.19, T:0.20
Consensus pattern (42 bp):
AGCCTGACTACACACCCATGTCCCTACCCATATGGCTCACAT
Found at i:16572665 original size:22 final size:22
Alignment explanation
Indices: 16572615--16572682 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
16572605 AATAGAATAT
* * *
16572615 TAGGCACCGAAGTCCAAATCAC
1 TAGGCACCGAAGTGCAAAACAG
*
16572637 TAAGCACCGAAGTGCAAAACAG
1 TAGGCACCGAAGTGCAAAACAG
*
16572659 TAGGCACCAAAGTGCAAAACAG
1 TAGGCACCGAAGTGCAAAACAG
16572681 TA
1 TA
16572683 AGTGCTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.43, C:0.25, G:0.21, T:0.12
Consensus pattern (22 bp):
TAGGCACCGAAGTGCAAAACAG
Found at i:16573217 original size:20 final size:20
Alignment explanation
Indices: 16573192--16573238 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
16573182 CAATATTCAT
16573192 ATATTCTTTTATCTT-TCAAC
1 ATATTCTTTTAT-TTATCAAC
16573212 ATATTC-TTTATTTATCAAC
1 ATATTCTTTTATTTATCAAC
*
16573231 ATTTTCTT
1 ATATTCTT
16573239 GTAAACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.08
19 15 0.62
20 7 0.29
ACGTcount: A:0.26, C:0.17, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATTCTTTTATTTATCAAC
Found at i:16575841 original size:50 final size:50
Alignment explanation
Indices: 16575728--16575969 Score: 277
Period size: 50 Copynumber: 4.7 Consensus size: 50
16575718 ACATGTCAAA
* ** * * *
16575728 GCCATGTCCTAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGGTGCCAAC
**
16575779 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * *
16575829 GCCATGTTCCAGACATGGTCTTACATGAGACCTCTCATCTTGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* *
16575879 ACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG-TGCCAAC
* * *
16575935 GTCATGTCCCAGATATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
16575970 TTACCCAAAT
Statistics
Matches: 163, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
50 93 0.57
51 27 0.17
53 4 0.02
55 2 0.01
56 37 0.23
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:16585952 original size:30 final size:30
Alignment explanation
Indices: 16585917--16585976 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
16585907 GAATTATTTG
* *
16585917 TAAAATTTTGTTG-CTCTTTTTGTAAATAT
1 TAAAAATTAGTTGTCTCTTTTTGTAAATAT
16585946 TAAAAATTAGTTGTCTCTTTTTGTAAATAT
1 TAAAAATTAGTTGTCTCTTTTTGTAAATAT
16585976 T
1 T
16585977 TTTAAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.30, C:0.07, G:0.10, T:0.53
Consensus pattern (30 bp):
TAAAAATTAGTTGTCTCTTTTTGTAAATAT
Found at i:16586063 original size:16 final size:15
Alignment explanation
Indices: 16586036--16586069 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
16586026 ATAACTAGTA
*
16586036 TATAATTATATTTAT
1 TATAATTATATTAAT
16586051 TATAATATATATTAAT
1 TATAAT-TATATTAAT
16586067 TAT
1 TAT
16586070 TATCAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:16600547 original size:21 final size:20
Alignment explanation
Indices: 16600520--16600573 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
16600510 TCTAAGAAAA
*
16600520 TAAAAATAAAACAACTATAAGC
1 TAAAAATAAAA-AAATA-AAGC
16600542 -AAAAATAGAAAAAATAAAGC
1 TAAAAATA-AAAAAATAAAGC
16600562 TAAAAATAAAAA
1 TAAAAATAAAAA
16600574 TAAAATCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
20 8 0.28
21 18 0.62
22 3 0.10
ACGTcount: A:0.72, C:0.07, G:0.06, T:0.15
Consensus pattern (20 bp):
TAAAAATAAAAAAATAAAGC
Found at i:16602215 original size:28 final size:28
Alignment explanation
Indices: 16602161--16602240 Score: 85
Period size: 28 Copynumber: 2.9 Consensus size: 28
16602151 AGAAAAACAA
* * *
16602161 ATAGAAAGAATAATAAGAA-AAA-AAGC
1 ATAGAAATAACAATAAAAATAAATAAGC
*
16602187 ATGATAAAT-ACAATAAAAATAAATAAGC
1 AT-AGAAATAACAATAAAAATAAATAAGC
*
16602215 ATAGAAATAAGAATAAAAATAAATAA
1 ATAGAAATAACAATAAAAATAAATAA
16602241 AAATAAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
26 10 0.23
27 12 0.27
28 22 0.50
ACGTcount: A:0.69, C:0.04, G:0.10, T:0.17
Consensus pattern (28 bp):
ATAGAAATAACAATAAAAATAAATAAGC
Found at i:16602224 original size:12 final size:12
Alignment explanation
Indices: 16602207--16602251 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
16602197 CAATAAAAAT
* *
16602207 AAATAAGCATAG
1 AAATAAGAATAA
16602219 AAATAAGAATAA
1 AAATAAGAATAA
16602231 AAAT-A-AATAA
1 AAATAAGAATAA
16602241 AAATAA-AATAA
1 AAATAAGAATAA
16602252 TGAGGAAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
10 9 0.30
11 7 0.23
12 14 0.47
ACGTcount: A:0.73, C:0.02, G:0.07, T:0.18
Consensus pattern (12 bp):
AAATAAGAATAA
Found at i:16605052 original size:20 final size:20
Alignment explanation
Indices: 16605024--16605065 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
16605014 TAGCAGTTAT
16605024 AAATCAAAACA-AAAAATCCA
1 AAATCAAAA-ATAAAAATCCA
* *
16605044 AAATTAAAAATATAAATCCA
1 AAATCAAAAATAAAAATCCA
16605064 AA
1 AA
16605066 GAGGCCATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.69, C:0.14, G:0.00, T:0.17
Consensus pattern (20 bp):
AAATCAAAAATAAAAATCCA
Found at i:16605997 original size:17 final size:18
Alignment explanation
Indices: 16605965--16606000 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
16605955 CCGTGTGGTT
16605965 CACCTGTGTGGGCCCACA
1 CACCTGTGTGGGCCCACA
16605983 CACCTGTGT-GGCCCACA
1 CACCTGTGTGGGCCCACA
16606000 C
1 C
16606001 GGCCTAATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.17, C:0.42, G:0.25, T:0.17
Consensus pattern (18 bp):
CACCTGTGTGGGCCCACA
Found at i:16620276 original size:11 final size:11
Alignment explanation
Indices: 16620259--16620301 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
16620249 AATCATTTAA
16620259 TAATAAAATAT
1 TAATAAAATAT
* *
16620270 TACTAAAAATCT
1 TAAT-AAAATAT
16620282 TAATAAAATAT
1 TAATAAAATAT
16620293 TAAATAAAA
1 T-AATAAAA
16620302 AACATTTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 10 0.38
12 16 0.62
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:16622852 original size:5 final size:5
Alignment explanation
Indices: 16622837--16622893 Score: 105
Period size: 5 Copynumber: 11.2 Consensus size: 5
16622827 AATTGAATAA
16622837 TATTAC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC
1 TATT-C TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC TATTC
16622888 TATTC T
1 TATTC T
16622894 TATATTTCTA
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 47 0.92
6 4 0.08
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTC
Found at i:16624359 original size:18 final size:18
Alignment explanation
Indices: 16624332--16624368 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
16624322 TCATTGCACT
* *
16624332 ATTTTCAAACCATTTCAA
1 ATTTTAAAACCAATTCAA
16624350 ATTTTAAAACCAATTCAA
1 ATTTTAAAACCAATTCAA
16624368 A
1 A
16624369 ACAGTACTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (18 bp):
ATTTTAAAACCAATTCAA
Found at i:16625177 original size:22 final size:22
Alignment explanation
Indices: 16625147--16625189 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16625137 TAATAGGACA
* *
16625147 GTAGGCACCGTAGTGCAAAATT
1 GTAGCCACCGAAGTGCAAAATT
16625169 GTAGCCACCGAAGTGCAAAAT
1 GTAGCCACCGAAGTGCAAAAT
16625190 GATAAGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.21, G:0.26, T:0.19
Consensus pattern (22 bp):
GTAGCCACCGAAGTGCAAAATT
Found at i:16627289 original size:30 final size:29
Alignment explanation
Indices: 16627255--16627321 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
16627245 CACCCTTAAA
** * *
16627255 ATATTTACACTATTGGCCCTTCAATTTTTT
1 ATATTTACACT-TTAACCCTTCAAATTTTG
*
16627285 ATATTTTCACTTTAACCCTTCAAATTTTG
1 ATATTTACACTTTAACCCTTCAAATTTTG
16627314 ATTATTTA
1 A-TATTTA
16627322 TTCTTGGGCC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (29 bp):
ATATTTACACTTTAACCCTTCAAATTTTG
Found at i:16627462 original size:20 final size:19
Alignment explanation
Indices: 16627437--16627475 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
16627427 AACTTCTCCA
16627437 CATTTTATCACTTTTATTTC
1 CATTTTATCAC-TTTATTTC
* *
16627457 CATTTTTTCTCTTTATTTC
1 CATTTTATCACTTTATTTC
16627476 ACTTTATCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (19 bp):
CATTTTATCACTTTATTTC
Found at i:16628220 original size:28 final size:27
Alignment explanation
Indices: 16628156--16628220 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 27
16628146 TATTCAGTAT
*
16628156 CAGTACAGTGTGGGCCTTAGCCCAATA
1 CAGTACAGTGTGGGCCTAAGCCCAATA
* **
16628183 TAAAAACAGTGTGGGCCTAAGCCCAATA
1 -CAGTACAGTGTGGGCCTAAGCCCAATA
16628211 CAGTATCAGT
1 CAGTA-CAGT
16628221 ATGGTGCAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (27 bp):
CAGTACAGTGTGGGCCTAAGCCCAATA
Found at i:16628610 original size:27 final size:27
Alignment explanation
Indices: 16628580--16628722 Score: 171
Period size: 27 Copynumber: 5.3 Consensus size: 27
16628570 GGTATTACAG
*
16628580 TAATTTTACCCATTGGGGGTATTTCGA
1 TAATTTTACCCATTGAGGGTATTTCGA
* * *
16628607 TAATTTAACCTATCGAGGGTATTTCGA
1 TAATTTTACCCATTGAGGGTATTTCGA
*
16628634 TAATTTTACCC-TTCGAGGGTATTTCAA
1 TAATTTTACCCATT-GAGGGTATTTCGA
* **
16628661 TAATTTTACTCATTGAGGGTATTTTTA
1 TAATTTTACCCATTGAGGGTATTTCGA
* **
16628688 TAATTTTTCCCATCAAGGGTATTTCGA
1 TAATTTTACCCATTGAGGGTATTTCGA
16628715 TAATTTTA
1 TAATTTTA
16628723 GGCCCATTAC
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
26 1 0.01
27 93 0.97
28 2 0.02
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (27 bp):
TAATTTTACCCATTGAGGGTATTTCGA
Found at i:16628667 original size:81 final size:82
Alignment explanation
Indices: 16628554--16628722 Score: 223
Period size: 81 Copynumber: 2.1 Consensus size: 82
16628544 CCTAGCATTC
* * * *
16628554 ATTTTACCCTAACGGGGGTATTACAGTAATTTTACCCATTGGGGGTATTTCGATAATTTAACCTA
1 ATTTTACCCTAACGAGGGTATTACAATAATTTTACCCATTGAGGGTATTTCGATAATTTAACCCA
*
16628619 TCGAGGGTATTTCGATA
66 TCAAGGGTATTTCGATA
* * * ** **
16628636 ATTTTACCCT-TCGAGGGTATTTCAATAATTTTACTCATTGAGGGTATTTTTATAATTTTTCCCA
1 ATTTTACCCTAACGAGGGTATTACAATAATTTTACCCATTGAGGGTATTTCGATAATTTAACCCA
16628700 TCAAGGGTATTTCGATA
66 TCAAGGGTATTTCGATA
16628717 ATTTTA
1 ATTTTA
16628723 GGCCCATTAC
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
81 65 0.87
82 10 0.13
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (82 bp):
ATTTTACCCTAACGAGGGTATTACAATAATTTTACCCATTGAGGGTATTTCGATAATTTAACCCA
TCAAGGGTATTTCGATA
Found at i:16628721 original size:54 final size:54
Alignment explanation
Indices: 16628554--16628722 Score: 171
Period size: 54 Copynumber: 3.1 Consensus size: 54
16628544 CCTAGCATTC
* * * ***
16628554 ATTTTACCCTAACGGGGGTATTAC-AGTAATTTTACCCATTGGGGGTATTTCGATA
1 ATTTTA-CCTATCGAGGGTATTTCGA-TAATTTTACCCATCAAGGGTATTTCGATA
* * * *
16628609 ATTTAACCTATCGAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTTCAATA
1 ATTTTACCTATCGAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCGATA
* ** *
16628663 ATTTTA-CTCATTGAGGGTATTTTTATAATTTTTCCCATCAAGGGTATTTCGATA
1 ATTTTACCT-ATCGAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCGATA
16628717 ATTTTA
1 ATTTTA
16628723 GGCCCATTAC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
53 2 0.02
54 88 0.92
55 6 0.06
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (54 bp):
ATTTTACCTATCGAGGGTATTTCGATAATTTTACCCATCAAGGGTATTTCGATA
Found at i:16636823 original size:27 final size:28
Alignment explanation
Indices: 16636785--16636844 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
16636775 AGCTGTCAGT
* * *
16636785 ACAGT-ATATGTGGTAAAGTCACTAGTA
1 ACAGTAATATGTGGCAAAGCCACTAGAA
*
16636812 ACAGTAAT-TGTGGCAGAGCCACTAGAA
1 ACAGTAATATGTGGCAAAGCCACTAGAA
16636839 ACAGTA
1 ACAGTA
16636845 CTTCCTCCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.23
Consensus pattern (28 bp):
ACAGTAATATGTGGCAAAGCCACTAGAA
Found at i:16637019 original size:27 final size:26
Alignment explanation
Indices: 16636980--16637240 Score: 288
Period size: 27 Copynumber: 9.7 Consensus size: 26
16636970 CCCTTACGGG
* *
16636980 GGTATTACAGTAATTTTACCCATCGGA
1 GGTATTTCGGTAATTTTACCCATC-GA
*
16637007 GGTATTTCGGTAATTTTACCCATCTA
1 GGTATTTCGGTAATTTTACCCATCGA
* * *
16637033 GGATATTTCGATAATTTTACCCTTCGGG
1 GG-TATTTCGGTAATTTTACCCATC-GA
***
16637061 GGTATTTTAATAATTTTACCCATCGA
1 GGTATTTCGGTAATTTTACCCATCGA
*
16637087 GGGTATTTCGGTAATTTTACCCATCAA
1 -GGTATTTCGGTAATTTTACCCATCGA
* *
16637114 GGGTATTTCGTTAATTTTACCCATCAA
1 -GGTATTTCGGTAATTTTACCCATCGA
* *
16637141 GGGTATTTTGGTAATTTTACCCATCAA
1 -GGTATTTCGGTAATTTTACCCATCGA
*
16637168 GTGTATTTCAGTAATTTTACCCATCGA
1 G-GTATTTCGGTAATTTTACCCATCGA
* *
16637195 GAGTATTTCGATAATTTTACCCATCAA
1 G-GTATTTCGGTAATTTTACCCATCGA
16637222 GGGTATTTCGGTAATTTTA
1 -GGTATTTCGGTAATTTTA
16637241 GGCCCATTAA
Statistics
Matches: 203, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.02
27 195 0.96
28 3 0.01
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (26 bp):
GGTATTTCGGTAATTTTACCCATCGA
Found at i:16637100 original size:81 final size:81
Alignment explanation
Indices: 16636964--16637240 Score: 342
Period size: 81 Copynumber: 3.4 Consensus size: 81
16636954 CCTAGCAGTC
**
16636964 ATTTTACCCTTACGGGGGTATTACAGTAATTTTACCCATCG-GAGGTATTTCGGTAATTTTACCC
1 ATTTTACCCTT-CGGGGGTATTTTAGTAATTTTACCCATCGAG-GGTATTTCGGTAATTTTACCC
*
16637028 ATCTAGGATATTTCGATA
64 ATCAAGGATATTTCGATA
*
16637046 ATTTTACCCTTCGGGGGTATTTTAATAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
1 ATTTTACCCTTCGGGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
* *
16637111 CAAGGGTATTTCGTTA
66 CAAGGATATTTCGATA
* ** * * * *
16637127 ATTTTACCCATCAAGGGTATTTTGGTAATTTTACCCATCAAGTGTATTTCAGTAATTTTACCCAT
1 ATTTTACCCTTCGGGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
*
16637192 CGA-GAGTATTTCGATA
66 CAAGGA-TATTTCGATA
* ** **
16637208 ATTTTACCCATCAAGGGTATTTCGGTAATTTTA
1 ATTTTACCCTTCGGGGGTATTTTAGTAATTTTA
16637241 GGCCCATTAA
Statistics
Matches: 175, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
80 1 0.01
81 162 0.93
82 12 0.07
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (81 bp):
ATTTTACCCTTCGGGGGTATTTTAGTAATTTTACCCATCGAGGGTATTTCGGTAATTTTACCCAT
CAAGGATATTTCGATA
Found at i:16642170 original size:6 final size:6
Alignment explanation
Indices: 16642161--16642186 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16642151 TCTTTTCTTT
16642161 TTTTAA TTTTAA TTTTAA TTTTAA TT
1 TTTTAA TTTTAA TTTTAA TTTTAA TT
16642187 AATTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:16651003 original size:26 final size:27
Alignment explanation
Indices: 16650962--16651013 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
16650952 CAAACAGATC
* *
16650962 CCAAATACCCACTTAACCTTGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
16650989 CCAAA-ACCCAATTAACCTAGCCCAA
1 CCAAATACCCAATTAACCTAGCCCAA
16651014 CTAACGTGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.40, C:0.40, G:0.04, T:0.15
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:16652409 original size:28 final size:28
Alignment explanation
Indices: 16652377--16652454 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
16652367 CTCTTTCCAA
16652377 TATTTTAACATTTTAATTTATCTC-AACT
1 TATTTTAACATTTTAATTTAT-TCAAACT
* * *
16652405 TATTTCAATATTGTTAATTTATTCAAATT
1 TATTTTAACATT-TTAATTTATTCAAACT
*
16652434 TATTTTAACCTTTTAATTTAT
1 TATTTTAACATTTTAATTTAT
16652455 ACATATTATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 21 0.50
29 21 0.50
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTTTAACATTTTAATTTATTCAAACT
Found at i:16654556 original size:9 final size:9
Alignment explanation
Indices: 16654544--16654588 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
16654534 ATATTAAAAA
16654544 TATAAATTT
1 TATAAATTT
16654553 TATAAATTT
1 TATAAATTT
16654562 TATAAATATT
1 TATAAAT-TT
16654572 T-TGAAA-TT
1 TAT-AAATTT
16654580 TA-AAATTT
1 TATAAATTT
16654588 T
1 T
16654589 TTTGTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
7 3 0.09
8 6 0.19
9 17 0.53
10 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (9 bp):
TATAAATTT
Found at i:16663292 original size:18 final size:18
Alignment explanation
Indices: 16663251--16663296 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
16663241 TTAAATGGTC
*
16663251 TAAAAAATTA-TTATATT
1 TAAAAAATAATTTATATT
*
16663268 TACAAAAATAATTTATGTT
1 TA-AAAAATAATTTATATT
16663287 T-AAAAATAAT
1 TAAAAAATAAT
16663297 CATCAAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 11 0.44
18 7 0.28
19 7 0.28
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TAAAAAATAATTTATATT
Found at i:16663753 original size:113 final size:106
Alignment explanation
Indices: 16663566--16663925 Score: 391
Period size: 96 Copynumber: 3.4 Consensus size: 106
16663556 AGTTTTGGTT
* * * * * * * *
16663566 TGTCAATGGCTGGTATCAGAATATGAGGAAAAGTAAAAAAAAAAATTTGGTGATGGTCTGCCAAT
1 TGTCAATAGCAGGTATCAGTATACGA-AAAAAGTAAAAAAAAAATTTTGGTGGTGGCCTGCCAAT
*
16663631 GGCCTGCACCACCTTTTTTTTGGAATTTTTTTTACTTTTTTCG
65 GGCCGGCACCACC-TTTTTTTGGAATTTTTTTTACTTTTTTCG
*
16663674 TGTCAATAGCAGGTATCAATATACGAAAAAAGTAAAAAAAAAATTCTTTTTTTGGTGGTGGCCTG
1 TGTCAATAGCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAA------TTTTGGTGGTGGCCTG
*
16663739 CCAATGGCCGGCACCACCTTTCTTGTGGGAATTTTTTTTTACTTTTTTCG
60 CCAATGGCCGGCACCACCTTT-TT-TTGGAA-TTTTTTTTACTTTTTTCG
* * **
16663789 TGTCAATAGCAAGTATTAGTATATAAAAAAAGTAGAAAAAAAAATTTTGGTGGTGGCCTGCCAAT
1 TGTCAATAGCAGGTATCAGTATACGAAAAAAGTA-AAAAAAAAATTTTGGTGGTGGCCTGCCAAT
16663854 GGCCGGCACCA-C------T----TTTTTTTTACTTTTTTCG
65 GGCCGGCACCACCTTTTTTTGGAATTTTTTTTACTTTTTTCG
*
16663885 TGTCAATACCAGGTATCAGTATACGAAAAAAGTAAAAAAAA
1 TGTCAATAGCAGGTATCAGTATACGAAAAAAGTAAAAAAAA
16663926 TTCTCACAAA
Statistics
Matches: 220, Mismatches: 22, Indels: 33
0.80 0.08 0.12
Matches are distributed among these distances:
95 7 0.03
96 47 0.21
107 16 0.07
108 21 0.10
109 1 0.00
110 32 0.15
112 3 0.01
113 32 0.15
114 5 0.02
115 47 0.21
116 9 0.04
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (106 bp):
TGTCAATAGCAGGTATCAGTATACGAAAAAAGTAAAAAAAAAATTTTGGTGGTGGCCTGCCAATG
GCCGGCACCACCTTTTTTTGGAATTTTTTTTACTTTTTTCG
Found at i:16664753 original size:18 final size:18
Alignment explanation
Indices: 16664715--16664756 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
16664705 GTTATACTTG
* *
16664715 TTAAAAATTAAAAAAGCT
1 TTAAAAATAAAAAAAGAT
*
16664733 TTAAAAATAAAAAAATAT
1 TTAAAAATAAAAAAAGAT
16664751 TTAAAA
1 TTAAAA
16664757 GTTTATTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (18 bp):
TTAAAAATAAAAAAAGAT
Found at i:16665534 original size:22 final size:21
Alignment explanation
Indices: 16665494--16665537 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
16665484 TATCGAAAAA
16665494 TAAACTTTTAAATAATTTTTT
1 TAAACTTTTAAATAATTTTTT
*
16665515 TAAACTTTTAAA-ATTTTTTT
1 TAAACTTTTAAATAATTTTTT
16665535 TAA
1 TAA
16665538 TATTTAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.57
Consensus pattern (21 bp):
TAAACTTTTAAATAATTTTTT
Found at i:16665544 original size:19 final size:19
Alignment explanation
Indices: 16665494--16665534 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
16665484 TATCGAAAAA
16665494 TAAACTTTTAAATAATTTTTT
1 TAAACTTTT-AA-AATTTTTT
16665515 TAAACTTTTAAAATTTTTT
1 TAAACTTTTAAAATTTTTT
16665534 T
1 T
16665535 TAATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 9 0.45
20 2 0.10
21 9 0.45
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TAAACTTTTAAAATTTTTT
Found at i:16670355 original size:42 final size:42
Alignment explanation
Indices: 16670296--16670432 Score: 157
Period size: 42 Copynumber: 3.5 Consensus size: 42
16670286 ATTCATTGGT
* *
16670296 GGTTGCTAAGTGCTGATTCCACAGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGC
* *
16670338 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGC
*
16670371 GGTTGCTAAGTGCTAATTCCACCGTATCTTAAATGTGAAGGC
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGC
*
16670413 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
16670433 CCCGAGGGGT
Statistics
Matches: 78, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
33 21 0.27
34 3 0.04
35 1 0.01
36 2 0.03
37 3 0.04
38 3 0.04
39 2 0.03
40 1 0.01
41 2 0.03
42 40 0.51
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (42 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGC
Found at i:16670381 original size:75 final size:75
Alignment explanation
Indices: 16670258--16670434 Score: 309
Period size: 75 Copynumber: 2.4 Consensus size: 75
16670248 ATTGAATATA
* *
16670258 AAGGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACAGTAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTAATTCCACAGTAT
16670323 CTTAAATGTG
66 CTTAAATGTG
*
16670333 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTAT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTAATTCCACAGTAT
16670398 CTTAAATGTG
66 CTTAAATGTG
* *
16670408 AAGGCGGTTGCTAAGTGTTGATTCCCC
1 AAGGGGGTTGCTAAGTGCTGATTCCCC
16670435 CGAGGGGTTG
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 97 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (75 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTAATTCCACAGTAT
CTTAAATGTG
Found at i:16670460 original size:102 final size:102
Alignment explanation
Indices: 16670336--16670533 Score: 308
Period size: 102 Copynumber: 1.9 Consensus size: 102
16670326 AAATGTGAAG
* * * * * *
16670336 GGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTAATTCCACCGTATCTT
1 GGGGTTGCTAAGCGCCGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTAATCCCACCGTATCTT
*
16670401 AAATGTG-AAGGCGGTTGCTAAGTGTTGATTCCCCCGA
66 AAATGTGAAAGG-GGTTGCTAAGTGCTGATTCCCCCGA
*
16670438 GGGGTTGCTAAGCGCCGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTGATCCCACCGTATCTT
1 GGGGTTGCTAAGCGCCGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTAATCCCACCGTATCTT
16670503 AAATGTGAAAGGGGTTGCTAAGTGCTGATTC
66 AAATGTGAAAGGGGTTGCTAAGTGCTGATTC
16670534 ACCGACTCAT
Statistics
Matches: 87, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 83 0.95
103 4 0.05
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (102 bp):
GGGGTTGCTAAGCGCCGATTCCCCAAATCATCGGTGGTTGCTAAGTGCTAATCCCACCGTATCTT
AAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCGA
Found at i:16674032 original size:23 final size:22
Alignment explanation
Indices: 16673992--16674040 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
16673982 CTTTATTTGA
16673992 TAAAATGTTTTGATATAACAAAT
1 TAAAATGTTTTGATATAA-AAAT
*
16674015 TAAAATGTTTTTGA-ATAAAAGT
1 TAAAATG-TTTTGATATAAAAAT
16674037 TAAA
1 TAAA
16674041 GTTGAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 11 0.46
24 6 0.25
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (22 bp):
TAAAATGTTTTGATATAAAAAT
Found at i:16674303 original size:20 final size:21
Alignment explanation
Indices: 16674253--16674294 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
16674243 CAATAAATTA
*
16674253 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACATTTT
16674274 CAAAAAGTATCGATACATTTT
1 CAAAAAGTATCGATACATTTT
16674295 ACCAAGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
CAAAAAGTATCGATACATTTT
Found at i:16674560 original size:16 final size:17
Alignment explanation
Indices: 16674539--16674571 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
16674529 ACAATAAGAG
16674539 AGATC-ATCAAGACAAA
1 AGATCAATCAAGACAAA
*
16674555 AGATCAATCAATACAAA
1 AGATCAATCAAGACAAA
16674572 TTTAGTGCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.58, C:0.18, G:0.09, T:0.15
Consensus pattern (17 bp):
AGATCAATCAAGACAAA
Found at i:16688269 original size:46 final size:44
Alignment explanation
Indices: 16688165--16688272 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
16688155 TGTCTTTGAC
** * * *
16688165 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
16688209 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
16688255 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
16688273 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:16688648 original size:30 final size:30
Alignment explanation
Indices: 16688612--16688669 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16688602 CCTCGACTCT
*
16688612 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
16688642 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
16688670 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:16689441 original size:40 final size:40
Alignment explanation
Indices: 16689379--16689473 Score: 145
Period size: 40 Copynumber: 2.3 Consensus size: 40
16689369 CTTTTCTTTC
* *
16689379 TTTCTTTCCTTCCTTCCTTCTCTGTTTCGTTTTGCTCTCTG
1 TTTCTTT-CTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
*
16689420 TTTCTTTCTTTCTCCCTTCTCTGTTTTGTTTTGCTCTCTG
1 TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
16689460 TTTCTTTTCTTTCT
1 TTTC-TTTCTTTCT
16689474 TTCTTTGTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
40 34 0.68
41 16 0.32
ACGTcount: A:0.00, C:0.28, G:0.08, T:0.63
Consensus pattern (40 bp):
TTTCTTTCTTTCTCCCTTCTCTGTTTCGTTTTGCTCTCTG
Found at i:16689499 original size:3 final size:3
Alignment explanation
Indices: 16689491--16689544 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
16689481 TCATATATAT
*
16689491 ATA ATA ATA AT- ATA ATA AT- ATA AT- ATA AT- ATA AT- ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16689534 ATA AT- ATA ATA
1 ATA ATA ATA ATA
16689545 TAAAAACATA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 12 0.28
3 31 0.72
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
ATA
Found at i:16689507 original size:5 final size:5
Alignment explanation
Indices: 16689483--16689547 Score: 75
Period size: 5 Copynumber: 13.2 Consensus size: 5
16689473 TTTCTTTGTC
16689483 ATATA TATATA ATAATA ATAT- A-ATA ATATA ATATA ATATA ATAT- AT-TA
1 ATATA -ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
16689531 ATAATA ATATA ATATA A
1 AT-ATA ATATA ATATA A
16689548 AAACATAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.06
4 6 0.11
5 30 0.57
6 14 0.26
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:16689507 original size:8 final size:8
Alignment explanation
Indices: 16689494--16689547 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
16689484 TATATATATA
16689494 ATAATAAT
1 ATAATAAT
16689502 ATAATAAT
1 ATAATAAT
16689510 ATAATATAAT
1 AT-A-ATAAT
16689520 ATAAT-AT
1 ATAATAAT
16689527 ATTAATAAT
1 A-TAATAAT
16689536 A-ATATAAT
1 ATA-ATAAT
16689544 ATAA
1 ATAA
16689548 AAACATAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
7 4 0.10
8 23 0.57
9 6 0.15
10 7 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATAATAAT
Found at i:16689534 original size:29 final size:28
Alignment explanation
Indices: 16689483--16689547 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
16689473 TTTCTTTGTC
16689483 ATATATATATAATAATAATATAATAATATA
1 ATATA-ATATAAT-ATAATATAATAATATA
*
16689513 ATATAATATAATATATTAATAATAATATA
1 ATATAATATAATATAAT-ATAATAATATA
16689542 ATATAA
1 ATATAA
16689548 AAACATAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAATATAATATAATATAATAATATA
Found at i:16689555 original size:13 final size:13
Alignment explanation
Indices: 16689497--16689556 Score: 57
Period size: 13 Copynumber: 4.4 Consensus size: 13
16689487 ATATATAATA
*
16689497 ATAATATAATAAT
1 ATAATATAAAAAT
16689510 ATAATATAATATAAT
1 ATAATATAA-A-AAT
* *
16689525 ATATTAATAATAAT
1 ATAAT-ATAAAAAT
*
16689539 ATAATATAAAAAC
1 ATAATATAAAAAT
16689552 ATAAT
1 ATAAT
16689557 TATTACTTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 20 0.53
14 7 0.18
15 7 0.18
16 4 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAATATAAAAAT
Found at i:16689556 original size:24 final size:23
Alignment explanation
Indices: 16689489--16689547 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
16689479 TGTCATATAT
*
16689489 ATATAATAATAATATAATAATATA
1 ATATAAT-ATAATATAATAAAATA
*
16689513 ATATAATATAATATATTAATAATA
1 ATATAATATAATATAATAA-AATA
16689537 ATATAATATAA
1 ATATAATATAA
16689548 AAACATAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 11 0.34
24 21 0.66
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATATAATATAATATAATAAAATA
Found at i:16690306 original size:89 final size:89
Alignment explanation
Indices: 16690155--16690384 Score: 262
Period size: 89 Copynumber: 2.6 Consensus size: 89
16690145 AGAGATTCTA
* * * *
16690155 GCGTGTTATCGATTGGAAAGCTCTTATGAGCAAAATGGCGTGTTATCGGGGGAGAATATTTAGAC
1 GCGTGTTATCGATTGCAAAGCTCTTATGAGCAAAATGACATGTTATCAGGGGAGAATATTTAGAC
16690220 TACGGGCTTTGCACTGTGTATCTG
66 TACGGGCTTTGCACTGTGTATCTG
* * ** *
16690244 GCGTGTTATCGATTGCAAAGGTCTTATGAGTAATTTGACATGTTATCAGGGGAGAATATTTAGCC
1 GCGTGTTATCGATTGCAAAGCTCTTATGAGCAAAATGACATGTTATCAGGGGAGAATATTTAGAC
* * * *
16690309 TACGGGCTTTGTATTATATGCATCTG
66 TACGGGCTTTGCA--CTGTGTATCTG
* * * * * *
16690335 GTGTATTATCGGTTGGAATAGCTCTTATGAGCAAATTGGCATGTTATCAG
1 GCGTGTTATCGATTGCAA-AGCTCTTATGAGCAAAATGACATGTTATCAG
16690385 ATGGTTACTC
Statistics
Matches: 117, Mismatches: 21, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
89 68 0.58
91 22 0.19
92 27 0.23
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.34
Consensus pattern (89 bp):
GCGTGTTATCGATTGCAAAGCTCTTATGAGCAAAATGACATGTTATCAGGGGAGAATATTTAGAC
TACGGGCTTTGCACTGTGTATCTG
Found at i:16692070 original size:16 final size:17
Alignment explanation
Indices: 16692043--16692080 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
16692033 GAAATTAAGA
16692043 TTTACATCCCCCACTAT
1 TTTACATCCCCCACTAT
16692060 TTTACATCCCCCACTAT
1 TTTACATCCCCCACTAT
16692077 TTTA
1 TTTA
16692081 GCAACCATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.24, C:0.37, G:0.00, T:0.39
Consensus pattern (17 bp):
TTTACATCCCCCACTAT
Found at i:16696434 original size:16 final size:15
Alignment explanation
Indices: 16696415--16696453 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
16696405 AGGTTTTCAT
16696415 TTTTTTTTC-TTTTC
1 TTTTTTTTCTTTTTC
16696429 TCTTTTTTTCTTTTTC
1 T-TTTTTTTCTTTTTC
16696445 TTTTGTTTT
1 TTTT-TTTT
16696454 TGTTTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.05
15 11 0.50
16 10 0.45
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:16696436 original size:15 final size:14
Alignment explanation
Indices: 16696416--16696448 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
16696406 GGTTTTCATT
16696416 TTTTTTTCTTTTCTC
1 TTTTTTTCTTTT-TC
16696431 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
16696445 TTTT
1 TTTT
16696449 GTTTTTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:16696459 original size:16 final size:15
Alignment explanation
Indices: 16696407--16696459 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 15
16696397 CTTAGCTTAG
16696407 GTTTTCATTTTTTTTT
1 GTTTTC-TTTTTTTTT
*
16696423 CTTTTCTCTTTTTTTCT
1 GTTTTCT-TTTTTTT-T
16696440 -TTTTCTTTTGTTTTT
1 GTTTTCTTTT-TTTTT
16696455 GTTTT
1 GTTTT
16696460 TATTCTAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
15 5 0.16
16 26 0.81
17 1 0.03
ACGTcount: A:0.02, C:0.11, G:0.06, T:0.81
Consensus pattern (15 bp):
GTTTTCTTTTTTTTT
Found at i:16697566 original size:21 final size:21
Alignment explanation
Indices: 16697541--16697589 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
16697531 ACAAAATAAT
16697541 AAGATTTAAAAGAAGTTAAATG
1 AAGATTTAAAAGAAGTTAAA-G
* *
16697563 -AGATTTAAGAGATGTTAAAG
1 AAGATTTAAAAGAAGTTAAAG
16697583 AAGATTT
1 AAGATTT
16697590 TTTTTTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 23 0.96
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (21 bp):
AAGATTTAAAAGAAGTTAAAG
Found at i:16706521 original size:125 final size:121
Alignment explanation
Indices: 16706321--16706666 Score: 516
Period size: 125 Copynumber: 2.8 Consensus size: 121
16706311 TTATTTCGAG
16706321 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
* *
16706385 GAAATCATGCCCTCGTGGATGCGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTTTT
65 GAAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAG--A-AAA--TTTTT
* * * * *
16706447 TTGACATTTCTGAGCAAATAGTAT-AAATTGGCTCTACTAGGATGTTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
16706511 AAATCGTGCCCTCGTGGACGCGGTTTTGCTACAGTAGGTCATGTAAGAAAATTTTT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAATTTTT
* * *
16706567 TTAACGTTTTTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGGGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
*
16706632 AAATCGCGCCCTCGTGGACGCGATTTTGCTACAGT
66 AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGT
16706667 CGCAAGTTTG
Statistics
Matches: 200, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
120 26 0.13
121 68 0.34
122 3 0.01
123 1 0.00
125 80 0.40
126 21 0.10
127 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (121 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGTGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAAATTTTT
Found at i:16706972 original size:18 final size:18
Alignment explanation
Indices: 16706946--16706989 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
16706936 GATTCGGAAA
* * *
16706946 AGGATACATGTAAGGGTT
1 AGGAAACATATAAGGGCT
16706964 AGGAAACATATAAGGGCT
1 AGGAAACATATAAGGGCT
16706982 AGGAAACA
1 AGGAAACA
16706990 CACCTGGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.18
Consensus pattern (18 bp):
AGGAAACATATAAGGGCT
Found at i:16707634 original size:7 final size:7
Alignment explanation
Indices: 16707624--16707648 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16707614 TTATATACAT
16707624 AATACTA
1 AATACTA
16707631 AATACTA
1 AATACTA
16707638 AATACTA
1 AATACTA
16707645 AATA
1 AATA
16707649 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:16708766 original size:31 final size:31
Alignment explanation
Indices: 16708731--16708795 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
16708721 GCCATTGATG
16708731 AAAATATAAAAAAAATTAAAATTATATTAAA
1 AAAATATAAAAAAAATTAAAATTATATTAAA
* ** * *
16708762 AAAATTTAAAATTATTTAAAATTATTTTAAA
1 AAAATATAAAAAAAATTAAAATTATATTAAA
16708793 AAA
1 AAA
16708796 TGAAATTGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AAAATATAAAAAAAATTAAAATTATATTAAA
Found at i:16708778 original size:10 final size:10
Alignment explanation
Indices: 16708746--16708793 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
16708736 ATAAAAAAAA
16708746 TTAAAATTAT
1 TTAAAATTAT
**
16708756 ATTAAAAAAAT
1 -TTAAAATTAT
16708767 TTAAAATTAT
1 TTAAAATTAT
16708777 TTAAAATTATT
1 TTAAAATTA-T
16708788 TTAAAA
1 TTAAAA
16708794 AATGAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 17 0.53
11 15 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTAAAATTAT
Found at i:16708793 original size:21 final size:21
Alignment explanation
Indices: 16708737--16708782 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
16708727 GATGAAAATA
*
16708737 TAAAAAAAATTAAAATTATAT
1 TAAAAAAATTTAAAATTATAT
16708758 TAAAAAAATTTAAAATTAT-T
1 TAAAAAAATTTAAAATTATAT
16708778 TAAAA
1 TAAAA
16708783 TTATTTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAAAATTTAAAATTATAT
Found at i:16708851 original size:40 final size:40
Alignment explanation
Indices: 16708807--16708895 Score: 169
Period size: 40 Copynumber: 2.2 Consensus size: 40
16708797 GAAATTGAGG
16708807 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
*
16708847 GGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
16708887 GGAAATTGA
1 GGAAATTGA
16708896 GAGGATTAGA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (40 bp):
GGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAA
Found at i:16709450 original size:28 final size:30
Alignment explanation
Indices: 16709418--16709479 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
16709408 GCGATTACAC
*
16709418 ATATTAAAAATGAAT-A-TTAACAATTTTA
1 ATATTAAAAATAAATAATTTAACAATTTTA
*
16709446 ATATTAAAACTAAATAATTTAACAATTTTA
1 ATATTAAAAATAAATAATTTAACAATTTTA
16709476 ATAT
1 ATAT
16709480 GAAATAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 13 0.43
29 1 0.03
30 16 0.53
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (30 bp):
ATATTAAAAATAAATAATTTAACAATTTTA
Found at i:16720067 original size:12 final size:12
Alignment explanation
Indices: 16720050--16720101 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
16720040 ATATCAATCG
16720050 AACTTTATTTAT
1 AACTTTATTTAT
16720062 AACTTTATATATAT
1 AACTTTAT-T-TAT
**
16720076 GATTTTTATTTAT
1 -AACTTTATTTAT
*
16720089 AACTTTATATAT
1 AACTTTATTTAT
16720101 A
1 A
16720102 TGATTTCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 18 0.56
13 4 0.12
14 4 0.12
15 6 0.19
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.56
Consensus pattern (12 bp):
AACTTTATTTAT
Found at i:16720083 original size:27 final size:27
Alignment explanation
Indices: 16720053--16720107 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
16720043 TCAATCGAAC
16720053 TTTATTTATAACTTTATATATATGATT
1 TTTATTTATAACTTTATATATATGATT
16720080 TTTATTTATAACTTTATATATATGATT
1 TTTATTTATAACTTTATATATATGATT
16720107 T
1 T
16720108 CCGAATATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTATTTATAACTTTATATATATGATT
Found at i:16720116 original size:27 final size:27
Alignment explanation
Indices: 16720059--16720116 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
16720049 GAACTTTATT
** *
16720059 TATAACTTTATATATATGATTTTTATT
1 TATAACTTTATATATATGATTTCGATA
16720086 TATAACTTTATATATATGATTTCCGA-A
1 TATAACTTTATATATATGATTT-CGATA
16720113 TATA
1 TATA
16720117 GATAGGACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (27 bp):
TATAACTTTATATATATGATTTCGATA
Found at i:16721643 original size:36 final size:36
Alignment explanation
Indices: 16721593--16721664 Score: 87
Period size: 36 Copynumber: 2.0 Consensus size: 36
16721583 TTTTTACTGT
16721593 TATTTATTTAAAAATGTAAA-AT-AAAAATTAACATAA
1 TATTTATTTAAAAA--TAAATATGAAAAATTAACATAA
*
16721629 TATTT-TTTATAAAATAAATTTGAAAAATTAACATAA
1 TATTTATTTA-AAAATAAATATGAAAAATTAACATAA
16721665 AAATATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
34 4 0.12
35 5 0.16
36 23 0.72
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.39
Consensus pattern (36 bp):
TATTTATTTAAAAATAAATATGAAAAATTAACATAA
Found at i:16725096 original size:22 final size:22
Alignment explanation
Indices: 16725070--16725123 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 22
16725060 ATATTCAAAC
*
16725070 AATAATAACAAAATAGTAGCAA
1 AATAATAACAAAATAGTAACAA
* * **
16725092 TATAAAAACGGAATAGTAACAA
1 AATAATAACAAAATAGTAACAA
*
16725114 AACAATAACA
1 AATAATAACA
16725124 TAACAACAAC
Statistics
Matches: 23, Mismatches: 9, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.63, C:0.11, G:0.09, T:0.17
Consensus pattern (22 bp):
AATAATAACAAAATAGTAACAA
Found at i:16728204 original size:12 final size:13
Alignment explanation
Indices: 16728182--16728210 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
16728172 TGATTAAATG
16728182 AATTAAAAAGCCA
1 AATTAAAAAGCCA
16728195 AATT-AAAAGCCA
1 AATTAAAAAGCCA
16728207 AATT
1 AATT
16728211 TTGCTCATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.59, C:0.14, G:0.07, T:0.21
Consensus pattern (13 bp):
AATTAAAAAGCCA
Found at i:16736258 original size:25 final size:25
Alignment explanation
Indices: 16736204--16736308 Score: 119
Period size: 25 Copynumber: 4.3 Consensus size: 25
16736194 AACGGATGAA
*
16736204 CAGAGAGCACAAATGTGCTAAT--T
1 CAGAGAGCACAAACGTGCTAATAAT
* *
16736227 --GATGAGCACTAACATGCTAATAAT
1 CAGA-GAGCACAAACGTGCTAATAAT
16736251 CAGAGAGCACAAACGTGCTAATAAT
1 CAGAGAGCACAAACGTGCTAATAAT
* * *
16736276 CAGAGAGCACCAATGTGCTAACAAT
1 CAGAGAGCACAAACGTGCTAATAAT
16736301 CAGAGAGC
1 CAGAGAGC
16736309 GCGCTAAGGT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
21 2 0.03
22 15 0.22
24 1 0.01
25 49 0.71
26 2 0.03
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.18
Consensus pattern (25 bp):
CAGAGAGCACAAACGTGCTAATAAT
Found at i:16737750 original size:13 final size:13
Alignment explanation
Indices: 16737732--16737769 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
16737722 AGTTCTTCAT
*
16737732 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
16737745 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
16737758 TACTTTTGAGAA
1 TGCTTTTGAGAA
16737770 ATTTGAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:16742375 original size:20 final size:21
Alignment explanation
Indices: 16742352--16742403 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
16742342 ATCTATCATT
16742352 TATTTATTTATTGTT-TTGAA
1 TATTTATTTATTGTTCTTGAA
16742372 TATTTATTCT-TTGTTCTTGAA
1 TATTTATT-TATTGTTCTTGAA
16742393 T-TTTATATTAT
1 TATTTAT-TTAT
16742404 AGTTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (21 bp):
TATTTATTTATTGTTCTTGAA
Found at i:16743296 original size:16 final size:16
Alignment explanation
Indices: 16743253--16743297 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
16743243 CACTGGAATT
*
16743253 GAATAGGATTGTAATG
1 GAATAGAATTGTAATG
* *
16743269 GAAAAGAGTTGTAATG
1 GAATAGAATTGTAATG
*
16743285 GTATAGAATTGTA
1 GAATAGAATTGTA
16743298 GTTAGTAATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.29, T:0.31
Consensus pattern (16 bp):
GAATAGAATTGTAATG
Found at i:16743576 original size:10 final size:10
Alignment explanation
Indices: 16743516--16743587 Score: 63
Period size: 10 Copynumber: 6.6 Consensus size: 10
16743506 ATAATAAATT
16743516 ATTTAATCATA
1 ATTTAAT-ATA
*
16743527 TTTTAATATA
1 ATTTAATATA
16743537 ATTATTAAATATA
1 A-T-TT-AATATA
*
16743550 ATTTAATAACA
1 ATTTAAT-ATA
16743561 ATTTTAATATA
1 A-TTTAATATA
16743572 ATTTAATATA
1 ATTTAATATA
*
16743582 AATTAA
1 ATTTAA
16743588 ATTATATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
10 20 0.39
11 15 0.29
12 9 0.18
13 7 0.14
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (10 bp):
ATTTAATATA
Found at i:16743585 original size:11 final size:11
Alignment explanation
Indices: 16743528--16743585 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
16743518 TTAATCATAT
*
16743528 TTTAATATAAT
1 TTTAATATAAA
16743539 TATTAA-ATATAA
1 T-TTAATATA-AA
16743551 TTTAATA-ACAA
1 TTTAATATA-AA
16743562 TTTTAATAT-AA
1 -TTTAATATAAA
16743573 TTTAATATAAA
1 TTTAATATAAA
16743584 TT
1 TT
16743586 AAATTATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
10 8 0.21
11 17 0.44
12 14 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (11 bp):
TTTAATATAAA
Found at i:16743585 original size:22 final size:22
Alignment explanation
Indices: 16743517--16743585 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 22
16743507 TAATAAATTA
*
16743517 TTTAATCATATTTTAATAT-AAT
1 TTTAAT-ATAATTTAATATAAAT
16743539 TATTAAATATAATTTAATA-ACAAT
1 T-TT-AATATAATTTAATATA-AAT
16743563 TTTAATATAATTTAATATAAAT
1 TTTAATATAATTTAATATAAAT
16743585 T
1 T
16743586 AAATTATATT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
22 19 0.46
23 15 0.37
24 7 0.17
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATATAATTTAATATAAAT
Found at i:16746056 original size:18 final size:18
Alignment explanation
Indices: 16746035--16746094 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
16746025 AAATCAAATA
16746035 ATTATTTTAAATATCATT
1 ATTATTTTAAATATCATT
* *
16746053 ATTATTTT-TATAT-ATAA
1 ATTATTTTAAATATCAT-T
* *
16746070 AATATTTCAAATATCATT
1 ATTATTTTAAATATCATT
16746088 ATT-TTTT
1 ATTATTTT
16746095 TCATCTACAC
Statistics
Matches: 31, Mismatches: 8, Indels: 7
0.67 0.17 0.15
Matches are distributed among these distances:
16 2 0.06
17 13 0.42
18 14 0.45
19 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
ATTATTTTAAATATCATT
Found at i:16748411 original size:28 final size:29
Alignment explanation
Indices: 16748347--16748417 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
16748337 CTTTAGAGTG
*
16748347 CACCACAAAGGCATTCATTTTTCATAGAT
1 CACCACAAAGGCTTTCATTTTTCATAGAT
*
16748376 CACTACAAAGGCTTTCA-TTTTCATAGAT
1 CACCACAAAGGCTTTCATTTTTCATAGAT
**
16748404 TGCCACAAAGGCTT
1 CACCACAAAGGCTT
16748418 CCAATTCTCT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 22 0.59
29 15 0.41
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (29 bp):
CACCACAAAGGCTTTCATTTTTCATAGAT
Found at i:16751473 original size:30 final size:29
Alignment explanation
Indices: 16751412--16751473 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
16751402 ATTCTCAGAT
* * **
16751412 TTTTTTACGGCTTAACTAAAACCCTTTAA
1 TTTTTTAAGACTTAACTAAAACCCTCCAA
*
16751441 TTTTTTAAGACTTAACTATAACCCTCCCAA
1 TTTTTTAAGACTTAACTAAAACCCT-CCAA
16751471 TTT
1 TTT
16751474 ACAATTAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.42
Consensus pattern (29 bp):
TTTTTTAAGACTTAACTAAAACCCTCCAA
Found at i:16753881 original size:27 final size:27
Alignment explanation
Indices: 16753841--16753916 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
16753831 AAATGTGGTT
* *
16753841 CTTA-AGAGTGTGCCACAAAGGCGTTC
1 CTTATAGAGTTTGCCACAAAGGCATTC
16753867 CTTATAGAGTTTGCCACAAAGGCATTC
1 CTTATAGAGTTTGCCACAAAGGCATTC
16753894 CTT-T-GATGTTTAGCCACAAAGGC
1 CTTATAGA-GTTT-GCCACAAAGGC
16753917 TTTTATTGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
25 2 0.04
26 9 0.20
27 34 0.76
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (27 bp):
CTTATAGAGTTTGCCACAAAGGCATTC
Found at i:16758938 original size:127 final size:125
Alignment explanation
Indices: 16758780--16759026 Score: 345
Period size: 127 Copynumber: 2.0 Consensus size: 125
16758770 AAAATTTTGT
* * *
16758780 ATTTTAAAATTTTAAAAGGATATTTTTCTATTTAGGTTTAACGAGAAAA-TCGAGACCCCGTAAG
1 ATTTTAAAATTTTAAAAGGATATTTTGCTATTTACGTTTAACGAGAAAACT-GA-AACCCGTAAG
** * *
16758844 TTAGGGTAC-AGTTTCTTGAATTCCCAAAAATGTGAAGTATTGCCTTATATCGAGATTTCTTTC
64 TTAGGGTACGA-TTTCTCAAATT-CCAAAAATGCGAAATATTGCCTTATATCGAGATTTCTTTC
*
16758907 ATTTTAAAATTTTAAAAGGATATTTTGCTATTTACGTTTAACGAGAAAACTGAAACCTGTAAGTT
1 ATTTTAAAATTTTAAAAGGATATTTTGCTATTTACGTTTAACGAGAAAACTGAAACCCGTAAGTT
* * *
16758972 AGGGTACGATTTCTCAAATTTCTAAAATGCGAAATATTGCCTTATTTCGAGATTT
66 AGGGTACGATTTCTCAAATTCCAAAAATGCGAAATATTGCCTTATATCGAGATTT
16759027 TTATTAAATT
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
125 30 0.28
126 26 0.24
127 50 0.47
128 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (125 bp):
ATTTTAAAATTTTAAAAGGATATTTTGCTATTTACGTTTAACGAGAAAACTGAAACCCGTAAGTT
AGGGTACGATTTCTCAAATTCCAAAAATGCGAAATATTGCCTTATATCGAGATTTCTTTC
Found at i:16766041 original size:6 final size:6
Alignment explanation
Indices: 16766030--16766055 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16766020 ATTATTCTGC
16766030 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
16766056 TAAAACAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:16770112 original size:13 final size:14
Alignment explanation
Indices: 16770074--16770115 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
16770064 TATGTGAAGA
16770074 ATATTATTTAAAATT
1 ATATTA-TTAAAATT
*
16770089 ATCATTTTTAAAATT
1 AT-ATTATTAAAATT
16770104 -TATTATTAAAAT
1 ATATTATTAAAAT
16770116 AAAATTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 10 0.42
16 3 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTATTAAAATT
Found at i:16770135 original size:18 final size:18
Alignment explanation
Indices: 16770097--16770132 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16770087 TTATCATTTT
*
16770097 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
16770115 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
16770133 TAATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:16770165 original size:9 final size:9
Alignment explanation
Indices: 16770151--16770183 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
16770141 TAAAATGATA
16770151 AATTATATT
1 AATTATATT
16770160 AATTATATT
1 AATTATATT
16770169 AATTAT-TT
1 AATTATATT
16770177 -ATTATAT
1 AATTATAT
16770184 GACTAAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.22
8 3 0.13
9 15 0.65
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATTATATT
Found at i:16770201 original size:38 final size:39
Alignment explanation
Indices: 16770125--16770202 Score: 90
Period size: 38 Copynumber: 2.0 Consensus size: 39
16770115 TAAAATTTAA
*
16770125 ATATTAAATAATTTATTAAAATGATAAATTATATTAATT
1 ATATTAAATAATTTATTAAAATGATAAATTATAATAATT
* *
16770164 ATATT-AATTATTTATT-ATATGACTAAA-TATAAATAATT
1 ATATTAAATAATTTATTAAAATGA-TAAATTAT-AATAATT
16770202 A
1 A
16770203 AATATGCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
37 8 0.24
38 21 0.62
39 5 0.15
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (39 bp):
ATATTAAATAATTTATTAAAATGATAAATTATAATAATT
Done.