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 10 of 221
Found at i:3268789 original size:16 final size:18
Alignment explanation
Indices: 3268770--3268804 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3268760 GTAAATATAC
3268770 AAAAT-AAAGAATA-AAA
1 AAAATGAAAGAATAGAAA
3268786 AAAATGAAAGAATAGAAA
1 AAAATGAAAGAATAGAAA
3268804 A
1 A
3268805 TGGGTGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 8 0.47
18 4 0.24
ACGTcount: A:0.77, C:0.00, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAATGAAAGAATAGAAA
Found at i:3280528 original size:156 final size:156
Alignment explanation
Indices: 3279839--3280620 Score: 1026
Period size: 156 Copynumber: 5.0 Consensus size: 156
3279829 CAAAAGAAAA
* * *
3279839 GTTCATAGTTCATTATCCTTGATTTGACTTTTATATCCCTATCTCCATCCTCAAACACACGACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
* * * *
3279904 AAACTATAAATACGA-GCACAAGAAAATACCATTTTTTCCTT-TGGGAGTAATTTCTCAGATGGC
66 AAAATATAAATA-AATGCACAAGAACATACCATTTTCTCCTTGT-GGAGTAATTTCTCAGATGGC
* * *
3279967 TTCCTTGATATAGTTTCCTGAAAAGGAT
129 TTCCTCGATACAGTTTCCTGAAAAGGGT
* *
3279995 GCTCGTAGTTTATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
* * *
3280060 AAAATATAAATATATGCACAAGAACATACCATTTTCTCCTTGGGGAGTAATTTCTCATATGGCTT
66 AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGG---
3280125 CTTCCTCGATACAGTTTCCTG-AAAGGGTT
128 CTTCCTCGATACAGTTTCCTGAAAAGGG-T
* * * * * * * *
3280154 TTTC-TAGTTCATCACCCTTGATTTGAC-CTTATGTTCATATCTCAATCCTAAAACACACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
*
3280217 AAAATATAAATACAA-GCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCCCAGATGGCT
66 AAAATATAAATA-AATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGG--
3280281 TCTTCCTCGATACAGTTTCCTGAAAAGGGT
128 -CTTCCTCGATACAGTTTCCTGAAAAGGGT
* * * *
3280311 GTTCCTAGTTCATTATCCTTGATTTGACTTTTATGTTCCTATCTCCATCCTCTAACGCACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
*
3280376 AAAGTATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGGCTT
66 AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGGCTT
* * *
3280441 CCTCGATTCAATTTCCTGAAAAAGGT
131 CCTCGATACAGTTTCCTGAAAAGGGT
* * *
3280467 GTTCGTAGTTCGTTATCCTTGATTTGACATTTATATTCCTATCTCTATCCTCAAACACACAACTC
1 GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
* ** * *
3280532 AAGATATAAATATGTACACAAGAACATACCATTTTCTCCTTG-GAGAGTAATTCCTCAGATGGC-
66 AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTG-GAGTAATTTCTCAGATGGCT
*
3280595 T--TCGATACAATTTCCTGAAAAGGGT
130 TCCTCGATACAGTTTCCTGAAAAGGGT
3280620 G
1 G
3280621 CATGTAGTTA
Statistics
Matches: 557, Mismatches: 57, Indels: 27
0.87 0.09 0.04
Matches are distributed among these distances:
153 23 0.04
155 3 0.01
156 252 0.45
157 115 0.21
158 55 0.10
159 109 0.20
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.35
Consensus pattern (156 bp):
GTTCGTAGTTCATTATCCTTGATTTGACTTTTATATTCCTATCTCCATCCTCAAACACACAACTC
AAAATATAAATAAATGCACAAGAACATACCATTTTCTCCTTGTGGAGTAATTTCTCAGATGGCTT
CCTCGATACAGTTTCCTGAAAAGGGT
Found at i:3280658 original size:130 final size:132
Alignment explanation
Indices: 3280497--3280748 Score: 384
Period size: 130 Copynumber: 1.9 Consensus size: 132
3280487 GATTTGACAT
* * **
3280497 TTATATTCCTATCTCTATCCTCAAACACACAACTCAAGATATAAATATGTACACAAGAACATACC
1 TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACCTACACAAGAACATACC
*
3280562 ATTTTCTCCTTGGAGAGTAA-TTCCTCAGATGGC-TTCGATACAATTTCCTGAAAAGGGTGCATG
66 ATTTTCTCCTTGGAGAGTAACTT-CTCAGATGGCTTTCAATACAATTTCCTGAAAAGGGTGCATG
3280625 TAG
130 TAG
* *
3280628 TTATA-TCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATGCCTGCACAAGAACATACC
1 TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACCTACACAAGAACATACC
*
3280692 GTTTTCTCCTTGGAGAGTAACTTCTCAGATGGCTTGTTCAATACAATTTCCTGAAAA
66 ATTTTCTCCTTGGAGAGTAACTTCTCAGATGGC-T-TTCAATACAATTTCCTGAAAA
3280749 AGATGCAGAG
Statistics
Matches: 109, Mismatches: 8, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
130 82 0.75
131 7 0.06
133 20 0.18
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (132 bp):
TTATATTCCTATCTCCATCCTCAAACACACAACTCAAAATATAAATACCTACACAAGAACATACC
ATTTTCTCCTTGGAGAGTAACTTCTCAGATGGCTTTCAATACAATTTCCTGAAAAGGGTGCATGT
AG
Found at i:3281911 original size:22 final size:22
Alignment explanation
Indices: 3281859--3281911 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
3281849 AAAACAAAAC
* *
3281859 AAATACAGTAATTAAACATTTA
1 AAATACCGTAATTAAACATGTA
* *
3281881 AACAT-CCGTAATTCAATATGTA
1 AA-ATACCGTAATTAAACATGTA
3281903 AAATACCGT
1 AAATACCGT
3281912 TTGAGCTTCC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (22 bp):
AAATACCGTAATTAAACATGTA
Found at i:3282709 original size:65 final size:65
Alignment explanation
Indices: 3282633--3282772 Score: 165
Period size: 65 Copynumber: 2.2 Consensus size: 65
3282623 CTAGTGTATA
*** * * * * *
3282633 TATATATGATATTTGTTAATATAAGAGTGTTATTAGATCTATTAAAAATCGTTCTAGAAGGATCT
1 TATATATGATATTTACCAATATAAGAGTATTATCAGATATATTAAAAACCATTCTAGAAGGATCT
* * * *
3282698 TATATATGATATTTACCAATGTAAGAGTATTGTCAGATATATTAGAAACCATTCTAGAAGGGTCT
1 TATATATGATATTTACCAATATAAGAGTATTATCAGATATATTAAAAACCATTCTAGAAGGATCT
3282763 TAT-TATGATA
1 TATATATGATA
3282773 GATCATAGTG
Statistics
Matches: 63, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 7 0.11
65 56 0.89
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.39
Consensus pattern (65 bp):
TATATATGATATTTACCAATATAAGAGTATTATCAGATATATTAAAAACCATTCTAGAAGGATCT
Found at i:3286035 original size:39 final size:39
Alignment explanation
Indices: 3285992--3286091 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 39
3285982 ATCGGTGGAT
**
3285992 TCTGGTATGGTGTTTTATGATCTTTTATGCT-ACTTTCAG
1 TCTGGTATGGTGTTTTATGATCTGCTATGCTGA-TTTCAG
* * *
3286031 TCTGGTATGAG-GTTTGATCATCTGCTCTGCTGATTTCAG
1 TCTGGTATG-GTGTTTTATGATCTGCTATGCTGATTTCAG
3286070 TCTGGTATGGTGTTTTACTGAT
1 TCTGGTATGGTGTTTTA-TGAT
3286092 GGTTTCATGG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
38 1 0.02
39 44 0.88
40 5 0.10
ACGTcount: A:0.15, C:0.14, G:0.24, T:0.47
Consensus pattern (39 bp):
TCTGGTATGGTGTTTTATGATCTGCTATGCTGATTTCAG
Found at i:3288085 original size:74 final size:74
Alignment explanation
Indices: 3287986--3288133 Score: 235
Period size: 74 Copynumber: 2.0 Consensus size: 74
3287976 ATTCACTCGG
* * * *
3287986 TTGTTGTAGTTTAACTCAAATTATTGTTGGAATATTTTCAAATATTTATAGTATTCAAATAATTA
1 TTGTAGTAGTTTAACTCAAACTATTGTTGGAACATTTTCAAATATTTACAGTATTCAAATAATTA
3288051 TAAATGAAA
66 TAAATGAAA
*
3288060 TTGTAGTAGTTTAAC-CTAAACTATTGTTGGAACATTTTCAAATATTTACAGTGTTCAAATAATT
1 TTGTAGTAGTTTAACTC-AAACTATTGTTGGAACATTTTCAAATATTTACAGTATTCAAATAATT
3288124 ATAAATGAAA
65 ATAAATGAAA
3288134 GGATGTAATA
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
73 1 0.01
74 67 0.99
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.42
Consensus pattern (74 bp):
TTGTAGTAGTTTAACTCAAACTATTGTTGGAACATTTTCAAATATTTACAGTATTCAAATAATTA
TAAATGAAA
Found at i:3290925 original size:18 final size:20
Alignment explanation
Indices: 3290902--3290939 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3290892 AAATTATATA
3290902 TATAAAC-TT-GAATTTTTT
1 TATAAACTTTAGAATTTTTT
3290920 TATAAACTTTAGAATTTTTT
1 TATAAACTTTAGAATTTTTT
3290940 AAATAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (20 bp):
TATAAACTTTAGAATTTTTT
Found at i:3301146 original size:21 final size:19
Alignment explanation
Indices: 3301109--3301147 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
3301099 AATTAAGATA
*
3301109 AATATTAAAATTTTACACT
1 AATATTAAAATTGTACACT
3301128 AATATTATAAATTGGTACAC
1 AATATTA-AAATT-GTACAC
3301148 ATCGGAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 5 0.29
21 5 0.29
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (19 bp):
AATATTAAAATTGTACACT
Found at i:3303842 original size:12 final size:13
Alignment explanation
Indices: 3303821--3303850 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
3303811 CATTAAATAA
3303821 AAAAATTTAAAAC
1 AAAAATTTAAAAC
3303834 AAAAA-TTAAAAC
1 AAAAATTTAAAAC
3303846 AAAAA
1 AAAAA
3303851 ACAAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATTTAAAAC
Found at i:3303851 original size:13 final size:14
Alignment explanation
Indices: 3303820--3303851 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3303810 TCATTAAATA
3303820 AAAAAATTTAAAAC
1 AAAAAATTTAAAAC
3303834 -AAAAA-TTAAAAC
1 AAAAAATTTAAAAC
3303846 AAAAAA
1 AAAAAA
3303852 CAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.16
Consensus pattern (14 bp):
AAAAAATTTAAAAC
Found at i:3304404 original size:11 final size:11
Alignment explanation
Indices: 3304366--3304411 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
3304356 ACAACAACAA
3304366 CAAAATAGTAG
1 CAAAATAGTAG
* *
3304377 CAATATAATAG
1 CAAAATAGTAG
*
3304388 CGAAATAGTAG
1 CAAAATAGTAG
*
3304399 CAAAATAGCAG
1 CAAAATAGTAG
3304410 CA
1 CA
3304412 TAACAACAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.52, C:0.13, G:0.17, T:0.17
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:3304978 original size:109 final size:109
Alignment explanation
Indices: 3304778--3304985 Score: 337
Period size: 109 Copynumber: 1.9 Consensus size: 109
3304768 TGAGTTTAAA
* *
3304778 TTCAATAGGATATTTGACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
1 TTCAAAAGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
* *
3304843 CTCGAATTTCCAAACGTAAAGCATTGCCTTATTTTTGAAAAGTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTT
* *
3304887 TTCAAAAGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTT
1 TTCAAAAGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTT
*
3304951 CCTCGAATTTCCAAACGCAAAATATTGCCTTATTT
65 CCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
3304986 GGAAACATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 1 0.01
109 90 0.99
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
TTCAAAAGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTT
Found at i:3306577 original size:20 final size:20
Alignment explanation
Indices: 3306541--3306580 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3306531 TCCTATTGTT
3306541 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
3306561 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
3306581 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:3307338 original size:44 final size:44
Alignment explanation
Indices: 3307276--3307691 Score: 182
Period size: 44 Copynumber: 9.6 Consensus size: 44
3307266 GATCTACTCT
* * * * * *
3307276 ACTGTAACCTTAGAGAGATAAGATCATTTATTTTAATCCGTTCT
1 ACTGTAATCTCAGGGAGATAAGATCATTTACTTTAATCCGCTCC
* * * * **
3307320 ACTGTAATCTCAGGGAGATAGGATTA-CTAGCTTCAATCTACTCC
1 ACTGTAATCTCAGGGAGATAAGATCATTTA-CTTTAATCCGCTCC
* * ** *
3307364 GCTGTAATCTCAGGGAGATAAGATCTGAAATT-CTTTGGTCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATC---ATTTACTTTAATCCGCTCC
* *
3307410 ACTGTAATCTCAGGGAGATAAGATC-TCTTATTTTAATCCGCCCC
1 ACTGTAATCTCAGGGAGATAAGATCAT-TTACTTTAATCCGCTCC
* * ** *
3307454 ACTGTAA-CTTCAGGGAGATAGGAT-AGTGT-CTTCGATCTGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCA-TTTACTTTAATCCGCTCC
* * * ** * *
3307497 GCTGTAATCTCAGGGAGATAAGATCTGAAATT-GTTTGGTCTGTTCC
1 ACTGTAATCTCAGGGAGATAAGATC---ATTTACTTTAATCCGCTCC
* * * * ** *
3307543 ACTGTAATCTCAGGGAGATAAGA-C-CTGA-TGTGATCTTCTCT
1 ACTGTAATCTCAGGGAGATAAGATCATTTACTTTAATCCGCTCC
*
3307584 ACTGTAA-CTTCAGAGAGATAAGATC-----CTTTAATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCATTTACTTTAATCCGCTCC
* * * * * * *
3307623 ATTGTAATCTCAAGGAGATAGGATTA-CTATCTTTGATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCATTTA-CTTTAATCCGCTCC
*
3307667 GCTGTAATCTCAGGGAGATAAGATC
1 ACTGTAATCTCAGGGAGATAAGATC
3307692 TCTGGCTTCA
Statistics
Matches: 279, Mismatches: 68, Indels: 50
0.70 0.17 0.13
Matches are distributed among these distances:
39 26 0.09
40 2 0.01
41 29 0.10
42 1 0.00
43 34 0.12
44 115 0.41
45 2 0.01
46 67 0.24
47 2 0.01
48 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCATTTACTTTAATCCGCTCC
Found at i:3307432 original size:46 final size:46
Alignment explanation
Indices: 3307355--3307692 Score: 227
Period size: 46 Copynumber: 7.8 Consensus size: 46
3307345 ACTAGCTTCA
* *
3307355 ATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTG
* *** *
3307401 GTCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA-T-TTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTG
* * * * *
3307445 ATCCGCCCCACTGTAA-CTTCAGGGAGATAGGA--T--AGTGTCTTCG
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAAT-TCTTTG
* *
3307488 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTGTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTG
* * * *
3307534 GTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG--A---TGTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTG
* * * *
3307575 ATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATC-------CTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAATTCTTTG
* * * * *
3307614 ATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T--ACTATCTTTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTTG
*
3307658 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
3307693 CTGGCTTCAA
Statistics
Matches: 225, Mismatches: 48, Indels: 39
0.72 0.15 0.12
Matches are distributed among these distances:
39 26 0.12
40 2 0.01
41 29 0.13
42 2 0.01
43 29 0.13
44 63 0.28
45 3 0.01
46 69 0.31
47 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (46 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTG
Found at i:3307519 original size:87 final size:85
Alignment explanation
Indices: 3307320--3307694 Score: 284
Period size: 87 Copynumber: 4.3 Consensus size: 85
3307310 AATCCGTTCT
* * * ** *
3307320 ACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATA
1 ACTGTAATCTCAGGGAGATAAGATCT-CTA-TTTTAATCCGCTCCACTGTAATCTCAGGGAGATA
* *
3307384 AGAT-CTGAAATTCTTTGGTCTGCTCC
64 GGATACTG----TC-TTGATCTGCTCC
*
3307410 ACTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCCCCACTGTAA-CTTCAGGGAGATA
1 ACTGTAATCTCAGGGAGATAAGATCTC-TATTTTAATCCGCTCCACTGTAATC-TCAGGGAGATA
*
3307474 GGATAGTGTCTTCGATCTGCTCC
64 GGATACTGTCTT-GATCTGCTCC
* ** ** * *
3307497 GCTGTAATCTCAGGGAGATAAGATCTGAAATTGTTTGGTCTGTTCCACTGTAATCTCAGGGAGAT
1 ACTGTAATCTCAGGGAGATAAGATCT-CTA-T-TTTAATCCGCTCCACTGTAATCTCAGGGAGAT
* * * * *
3307562 AAGA-CCTGAT-GTGATCTTCTCT
63 AGGATACTG-TCTTGATCTGCTCC
* * *
3307584 ACTGTAA-CTTCAGAGAGATAAGATC-C---TTTAATCCGCTCCATTGTAATCTCAAGGAGATAG
1 ACTGTAATC-TCAGGGAGATAAGATCTCTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAG
*
3307644 GATTACTATCTTTGATCTGCTCC
65 GA-TACTGTC-TTGATCTGCTCC
*
3307667 GCTGTAATCTCAGGGAGATAAGATCTCT
1 ACTGTAATCTCAGGGAGATAAGATCTCT
3307695 GGCTTCAATT
Statistics
Matches: 226, Mismatches: 41, Indels: 41
0.73 0.13 0.13
Matches are distributed among these distances:
80 29 0.13
81 1 0.00
82 2 0.01
83 30 0.13
84 2 0.01
86 3 0.01
87 66 0.29
88 4 0.02
89 30 0.13
90 54 0.24
91 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (85 bp):
ACTGTAATCTCAGGGAGATAAGATCTCTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGG
ATACTGTCTTGATCTGCTCC
Found at i:3307547 original size:133 final size:134
Alignment explanation
Indices: 3307276--3307565 Score: 426
Period size: 133 Copynumber: 2.2 Consensus size: 134
3307266 GATCTACTCT
* * * ** *
3307276 ACTGTAACCTTAGAGAGATAAGATCATTTATTTTAATCCGTTCTACTGTAATCTCAGGGAGATAG
1 ACTGTAATCTCAGGGAGATAAGATCATTTATTTTAATCCGCCCCACTGTAATCTCAGGGAGATAG
3307341 GATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
66 GATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
3307406 CTCC
131 CTCC
3307410 ACTGTAATCTCAGGGAGATAAGATC-TCTTATTTTAATCCGCCCCACTGTAA-CTTCAGGGAGAT
1 ACTGTAATCTCAGGGAGATAAGATCAT-TTATTTTAATCCGCCCCACTGTAATC-TCAGGGAGAT
* * * *
3307473 AGGA-TAGT-GTCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTGTTTGGT
64 AGGATTACTAG-CTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGT
*
3307536 CTGTTCC
128 CTGCTCC
3307543 ACTGTAATCTCAGGGAGATAAGA
1 ACTGTAATCTCAGGGAGATAAGA
3307566 CCTGATGTGA
Statistics
Matches: 142, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
132 1 0.01
133 84 0.59
134 57 0.40
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (134 bp):
ACTGTAATCTCAGGGAGATAAGATCATTTATTTTAATCCGCCCCACTGTAATCTCAGGGAGATAG
GATTACTAGCTTCAATCTACTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTG
CTCC
Found at i:3307709 original size:44 final size:44
Alignment explanation
Indices: 3307320--3307711 Score: 195
Period size: 44 Copynumber: 9.0 Consensus size: 44
3307310 AATCCGTTCT
* * *
3307320 ACTGTAATCTCAGGGAGATAGGAT-TACTAGCTTCAATCTACTCC
1 ACTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCC
* * * ***
3307364 GCTGTAATCTCAGGGAGATAAGATCTGAAAT-TCTTTGGTCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCT---CTGGCTTCAATCTGCTCC
*** * * *
3307410 ACTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCCCC
1 ACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCC
* ** * *
3307454 ACTGTAA-CTTCAGGGAGATAGGAT-AGTGTCTTCGATCTGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCC
* * * *** *
3307497 GCTGTAATCTCAGGGAGATAAGATCTGAAATTG-TTTGGTCTGTTCC
1 ACTGTAATCTCAGGGAGATAAGATCT---CTGGCTTCAATCTGCTCC
* * * *
3307543 ACTGTAATCTCAGGGAGATAAGA-C-CT-GATGT-GATCTTCTCT
1 ACTGTAATCTCAGGGAGATAAGATCTCTGGCT-TCAATCTGCTCC
* *
3307584 ACTGTAA-CTTCAGAGAGATAAGATC-CT---TT-AATCCGCTCC
1 ACTGTAATC-TCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCC
* * * ** **
3307623 ATTGTAATCTCAAGGAGATAGGAT-TACTATCTTTGATCTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCT-CTGGCTTCAATCTGCTCC
* *
3307667 GCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATTTGCTCC
1 ACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCC
3307711 A
1 A
3307712 ATGCAACCGA
Statistics
Matches: 264, Mismatches: 62, Indels: 44
0.71 0.17 0.12
Matches are distributed among these distances:
39 25 0.09
40 6 0.02
41 28 0.11
42 4 0.02
43 34 0.13
44 94 0.36
45 3 0.01
46 67 0.25
47 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (44 bp):
ACTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCC
Found at i:3307851 original size:88 final size:88
Alignment explanation
Indices: 3307727--3308176 Score: 799
Period size: 88 Copynumber: 5.2 Consensus size: 88
3307717 ACCGATGGAT
*
3307727 GCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
3307790 CCAGCTCTATCACAACCGAAAGAG
65 CCAGCTCTATCACAACCGAAAGAG
3307814 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
3307879 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
3307902 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
3307967 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
3307990 GCAAGGTTTGTGTCTTCGATCTGCTT--C-G-C--TGTAGGAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
3308049 CAGCTCTATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
*
3308072 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
*
3308137 CAGCTCCATCACAACCGAAAGAG
66 CAGCTCTATCACAACCGAAAGAG
*
3308160 GCAAGGTTTGTGACTTC
1 GCAAGGTTTGTGTCTTC
3308177 ATTGATCTGT
Statistics
Matches: 351, Mismatches: 4, Indels: 15
0.95 0.01 0.04
Matches are distributed among these distances:
82 79 0.23
84 2 0.01
85 2 0.01
86 7 0.02
87 7 0.02
88 254 0.72
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (88 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
CAGCTCTATCACAACCGAAAGAG
Found at i:3308109 original size:170 final size:174
Alignment explanation
Indices: 3307727--3308176 Score: 795
Period size: 170 Copynumber: 2.6 Consensus size: 174
3307717 ACCGATGGAT
*
3307727 GCAAGGCTTTGT-T-TTCGATCTGCTTCGCTGTTAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
1 GCAAGG-TTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAA
3307790 CCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGG
65 CCAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTC-CTGTC-ATGTAGG
3307855 AAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAG
128 AAGGCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAG
3307902 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
3307967 CAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTT-C-G-C-TGTAGGAAG
66 CAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCCTGTCATGTAGGAAG
3308028 GCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAG
131 GCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAG
*
3308072 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTTAAC
1 GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
* *
3308137 CAGCTCCATCACAACCGAAAGAGGCAAGGTTTGTGACTTC
66 CAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTC
3308177 ATTGATCTGT
Statistics
Matches: 269, Mismatches: 4, Indels: 9
0.95 0.01 0.03
Matches are distributed among these distances:
170 155 0.58
172 1 0.00
173 1 0.00
174 6 0.02
175 7 0.03
176 99 0.37
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (174 bp):
GCAAGGTTTGTGTCTTCGATCTGCTTCGCTGTCAATGTAGGAAGGCAAGATCTTTTGTCTTCAAC
CAGCTCTATCACAACCGAAAGAGGCAAGGTTTGTGTCTTCGATCTGCTTCCTGTCATGTAGGAAG
GCAAGATCTTTTGTCTTCAACCAGCTCTATCACAACCGAAAGAG
Found at i:3312533 original size:19 final size:20
Alignment explanation
Indices: 3312504--3312555 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
3312494 CACTTCGTGA
*
3312504 AAATCTAATGCCTATG-ATG
1 AAATGTAATGCCTATGCATG
* **
3312523 CAATGTAATGCAAATGCATG
1 AAATGTAATGCCTATGCATG
3312543 AAATG-AATGCCTA
1 AAATGTAATGCCTA
3312556 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCCTATGCATG
Found at i:3314120 original size:109 final size:109
Alignment explanation
Indices: 3313920--3314127 Score: 346
Period size: 109 Copynumber: 1.9 Consensus size: 109
3313910 TGAGTTTAAA
* *
3313920 TTCAATAGGATATTTGACAATTTGGTTAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
1 TTCAAAAGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
*
3313985 CTCGAATTTCCAAACGTAAAACATTGCCTTATTTTTGAAAAGTT
66 CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTT
* *
3314029 TTCAAAAGGATATTT-AGCTATTTGGTCGAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTT
1 TTCAAAAGGATATTTGA-CAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTT
*
3314093 CCTCGAATTTCCAAACGCAAAATATTGCCTTATTT
65 CCTCGAATTTCCAAACGCAAAACATTGCCTTATTT
3314128 GGAAACATTT
Statistics
Matches: 92, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 1 0.01
109 91 0.99
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (109 bp):
TTCAAAAGGATATTTGACAATTTGGTCAAACGAGAAATCGAAACCCAGTACCTTAGGGCACGTTC
CTCGAATTTCCAAACGCAAAACATTGCCTTATTTTTGAAAAGTT
Found at i:3314672 original size:9 final size:10
Alignment explanation
Indices: 3314631--3314677 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
3314621 CTATCATAAA
3314631 ATATAAAAAGT
1 ATATAAAAA-T
*
3314642 ATGTATATAAAT
1 A--TATAAAAAT
3314654 ATATAAAAAT
1 ATATAAAAAT
3314664 ATA-AAAAAT
1 ATATAAAAAT
3314673 ATATA
1 ATATA
3314678 CTCCTATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
9 9 0.29
10 12 0.39
11 1 0.03
12 2 0.06
13 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:3315719 original size:20 final size:20
Alignment explanation
Indices: 3315683--3315722 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3315673 TCCTATTGTT
3315683 GTTTTGTTACTGTTTGCTGC
1 GTTTTGTTACTGTTTGCTGC
*
3315703 GTTTCTGTTTCTG-TTGCTGC
1 GTTT-TGTTACTGTTTGCTGC
3315723 TTCCGTCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.03, C:0.17, G:0.25, T:0.55
Consensus pattern (20 bp):
GTTTTGTTACTGTTTGCTGC
Found at i:3323867 original size:18 final size:18
Alignment explanation
Indices: 3323844--3323935 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
3323834 CCCAACTACT
*
3323844 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
3323862 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
3323880 GTATATGT-AATAGTACC
1 GTATACGTGAATAGTACC
*
3323897 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
3323915 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
3323933 GTA
1 GTA
3323936 AACGATCGTA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
17 15 0.23
18 51 0.77
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:3323895 original size:35 final size:36
Alignment explanation
Indices: 3323844--3323935 Score: 159
Period size: 35 Copynumber: 2.6 Consensus size: 36
3323834 CCCAACTACT
*
3323844 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
3323880 GTATATGT-AATAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
3323915 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
3323936 AACGATCGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
35 33 0.63
36 19 0.37
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:3327487 original size:11 final size:11
Alignment explanation
Indices: 3327473--3327507 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3327463 ATATTCAAAC
3327473 AATAATAACAA
1 AATAATAACAA
*
3327484 AATATTAACAA
1 AATAATAACAA
*
3327495 TATAATAACAA
1 AATAATAACAA
3327506 AA
1 AA
3327508 CGACAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAATAACAA
Found at i:3328156 original size:21 final size:21
Alignment explanation
Indices: 3328132--3328171 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3328122 TTAGAAATAA
*
3328132 TTTTGTCCCAAGAGTATTTTT
1 TTTTGTCCCAAAAGTATTTTT
*
3328153 TTTTGTCTCAAAAGTATTT
1 TTTTGTCCCAAAAGTATTT
3328172 GAAAAGCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (21 bp):
TTTTGTCCCAAAAGTATTTTT
Found at i:3332142 original size:26 final size:28
Alignment explanation
Indices: 3332084--3332141 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
3332074 AATATTATAT
3332084 AAAAA-TAAAAAAATAATTAACTTTTAA
1 AAAAATTAAAAAAATAATTAACTTTTAA
* * *
3332111 AAAAATTAAAAAAA-ACTTAATTTTTCA
1 AAAAATTAAAAAAATAATTAACTTTTAA
3332138 AAAA
1 AAAA
3332142 TATATATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 19 0.70
28 8 0.30
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (28 bp):
AAAAATTAAAAAAATAATTAACTTTTAA
Found at i:3332225 original size:30 final size:31
Alignment explanation
Indices: 3332190--3332252 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
3332180 AACTCTAAAC
* *
3332190 TCTAAATATTCAAAACAATA-TATCTAAATT
1 TCTAAAAATTCAAAACAATATTACCTAAATT
3332220 TCTAAAAATTCAAAACAATATTACCTAAATT
1 TCTAAAAATTCAAAACAATATTACCTAAATT
3332251 TC
1 TC
3332253 CAAGATAGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 19 0.63
31 11 0.37
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (31 bp):
TCTAAAAATTCAAAACAATATTACCTAAATT
Found at i:3334065 original size:18 final size:20
Alignment explanation
Indices: 3334021--3334078 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 20
3334011 TTACACTTTA
*
3334021 ATATTTTTATTATTTTCTAT
1 ATATTTTTATTATTTTATAT
* *
3334041 AT-TTTTTTTTGTTTTAT-T
1 ATATTTTTATTATTTTATAT
*
3334059 ATATTTTTAATGATTTTATA
1 ATATTTTT-ATTATTTTATA
3334079 AATAATACAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 3 0.10
19 17 0.59
20 9 0.31
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (20 bp):
ATATTTTTATTATTTTATAT
Found at i:3338030 original size:3 final size:3
Alignment explanation
Indices: 3338022--3338079 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
3338012 TAGATAAAAG
3338022 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
3338070 AGA AGA AGA A
1 AGA AGA AGA A
3338080 TAGAATAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:3338537 original size:16 final size:17
Alignment explanation
Indices: 3338515--3338554 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
3338505 GAATTCTTTA
3338515 AAAATTA-TAAAA-AAT
1 AAAATTATTAAAATAAT
3338530 ATAAATTATTAAAATAAT
1 A-AAATTATTAAAATAAT
3338548 AAAATTA
1 AAAATTA
3338555 CATTTTAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 6 0.27
17 11 0.50
18 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTATTAAAATAAT
Found at i:3339185 original size:10 final size:9
Alignment explanation
Indices: 3339122--3339223 Score: 57
Period size: 10 Copynumber: 10.8 Consensus size: 9
3339112 ACTTTATAAA
3339122 ATTTTATAATT
1 ATTTTAT-A-T
*
3339133 ATTTTCTAT
1 ATTTTATAT
3339142 ATTTCTATAT
1 ATTT-TATAT
3339152 ATTTTATGAT
1 ATTTTAT-AT
*
3339162 -TTTTGTAT
1 ATTTTATAT
3339170 -TTTTATATT
1 ATTTTATA-T
*
3339179 ATTTTATTAA
1 ATTTTA-TAT
*
3339189 AATTTA-AT
1 ATTTTATAT
3339197 ATTTTCATATT
1 ATTTT-ATA-T
*
3339208 ATTTTTTAT
1 ATTTTATAT
*
3339217 CTTTTAT
1 ATTTTAT
3339224 CATTTTTTGC
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
8 13 0.18
9 21 0.29
10 24 0.33
11 14 0.19
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (9 bp):
ATTTTATAT
Found at i:3343322 original size:302 final size:306
Alignment explanation
Indices: 3342771--3343388 Score: 1073
Period size: 302 Copynumber: 2.0 Consensus size: 306
3342761 ATTATATAAT
* *
3342771 AAAATTAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCGGG
1 AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGG
*
3342836 CCCAACCCGGCCCATGGACTCCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
66 CCCAACCCGGCCCATGGACACCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
* *
3342901 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTGGTA
131 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTAGCA
*
3342966 TTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
196 CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
* * *
3343031 TAAGGATTAGGAA-GG-A-C-AATGGGTAGTTCTAAGTATTGTATC
261 TAAGGATTAAGAAGGGAAGCTAATAGGCAGTTCTAAGTATTGTATC
3343073 AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGG
1 AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGG
* *
3343138 CCCAACTCGGCCCATGGACACCTCTAGTTCCAAGACACGGCTATGTGATGTTTCATTCGGGCATA
66 CCCAACCCGGCCCATGGACACCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
*
3343203 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGGTGATTAAGTCTTAGCTCGATTAGCA
131 AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTAGCA
3343268 CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
196 CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
3343333 TAAGGATTAAGAAGGGTAATGGCTAATAGGCAGTTCTAAGTATTGTATC
261 TAAGGATTAAGAAGGG-AA--GCTAATAGGCAGTTCTAAGTATTGTATC
3343382 AAAAATA
1 AAAAATA
3343389 GCAGATATAA
Statistics
Matches: 297, Mismatches: 12, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
302 263 0.89
303 2 0.01
305 1 0.00
308 1 0.00
309 30 0.10
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (306 bp):
AAAAATAATACAGACGAGCTAAGCCAGACTCGGGATTAGCAAACAGGCCTAAAATTTTAGTCAGG
CCCAACCCGGCCCATGGACACCTCTAGTTCCAAGACACGACTATGTGATGTTTCATTCGGGCATA
AAATATTAAAATTGAATCTATAAGTGTTAAATATAGTGGATGATTAAGTCTTAGCTCGATTAGCA
CTGGTATTGTTGTCAATAAAAGAGGACGTGGGTTCGAGTGCGCTGAAGCGCATTATCCTCCTATT
TAAGGATTAAGAAGGGAAGCTAATAGGCAGTTCTAAGTATTGTATC
Found at i:3347023 original size:19 final size:19
Alignment explanation
Indices: 3346999--3347082 Score: 52
Period size: 19 Copynumber: 4.6 Consensus size: 19
3346989 ATATATACTA
3346999 AATAAATTAATAATAAAAT
1 AATAAATTAATAATAAAAT
* *
3347018 AATAAAAT-ATCATTTAAAA-
1 AATAAATTAAT-A-ATAAAAT
*
3347037 AATAAATTAA-AAT--ATT
1 AATAAATTAATAATAAAAT
* * *
3347053 AATAAACTAATAATTAATT
1 AATAAATTAATAATAAAAT
*
3347072 AATTAATTAAT
1 AATAAATTAAT
3347083 CTAAAATATC
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
15 1 0.02
16 9 0.18
17 4 0.08
18 3 0.06
19 27 0.54
20 6 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
AATAAATTAATAATAAAAT
Found at i:3349824 original size:27 final size:27
Alignment explanation
Indices: 3349789--3349843 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
3349779 AGAACCCACG
3349789 AACCATGAACCTCAAATCCAAACCTTA
1 AACCATGAACCTCAAATCCAAACCTTA
* * *
3349816 AACCTTGAACTTCGAATCCAAACCTTA
1 AACCATGAACCTCAAATCCAAACCTTA
3349843 A
1 A
3349844 CCCCAAACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.42, C:0.31, G:0.05, T:0.22
Consensus pattern (27 bp):
AACCATGAACCTCAAATCCAAACCTTA
Found at i:3361563 original size:4 final size:4
Alignment explanation
Indices: 3361554--3361667 Score: 183
Period size: 4 Copynumber: 28.5 Consensus size: 4
3361544 AAATTTAGAG
* *
3361554 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAGA CAGA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
3361602 CAGA CAGA CAGA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
3361650 CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CA
3361668 GGTAAGCAAC
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 108 1.00
ACGTcount: A:0.50, C:0.25, G:0.04, T:0.20
Consensus pattern (4 bp):
CATA
Found at i:3373331 original size:83 final size:83
Alignment explanation
Indices: 3373192--3373358 Score: 280
Period size: 83 Copynumber: 2.0 Consensus size: 83
3373182 CCGCCGTCGT
*
3373192 AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACTGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTT
*
3373257 AATTGCAATATCAGGGAA
66 AATTACAATATCAGGGAA
* * * *
3373275 AGCTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTT
1 AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTT
3373340 AATTACAATATCAGGGAA
66 AATTACAATATCAGGGAA
3373358 A
1 A
3373359 CCAGATCCGC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
83 78 1.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.32
Consensus pattern (83 bp):
AGCTTCAATCTGTTCCACTACACCGCTAAGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTT
AATTACAATATCAGGGAA
Found at i:3373449 original size:100 final size:101
Alignment explanation
Indices: 3373277--3374407 Score: 1514
Period size: 100 Copynumber: 11.3 Consensus size: 101
3373267 TCAGGGAAAG
* *
3373277 CTTCAATCTGTTCTACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* ** * * *
3373342 TTACAATATCAGGGAAACCAGATCCGCCGTCGTAG-
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* *
3373377 CTTCAATCTGTTTCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
** * * *
3373442 TTGCAATATCAGGGAAACCAGATCCACC-TTCGTAG-
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTT-GTAGA
* *
3373477 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
3373542 TTGTGCTGTCGGGGAAACCAGATCCGCCGTTGT-GA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* * * *
3373577 TTTCAATCTGCTCCACTGCACCGCCAAGGAAGTAAGATCCGCCGTTGTGGCTTTAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
3373642 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGT-GA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* * * *
3373677 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCCACCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* *
3373742 TTGCGCTGTCGGGGAAACCAAATCCGCCATTGTAG-
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* *
3373777 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTCTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* ** * * ** *
3373842 TTACAATATCAGGGAAACCAGATCTACCGTCGTAG-
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* * * *
3373877 CTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATTCACCGTTGTGGCTTTAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
* *
3373942 TTGCGCTGTCGGGGAAACCAAATCCGCCGTTAT-GA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* * * * *
3373977 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTCA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
** * * * *
3374042 TTGCAATATCAGGGAAACCAGATCTGCCGTCGTAG-
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* * *
3374077 CTTCAATTTGTTCCACTGCACTGCTAAGGAAGTAAGATCCGCCATTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
3374142 TTGCGCTGTCGGGGAAACCAGATCCGTCGTTGT-GA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
* * * *
3374177 CTTCAATCTGCTCCACTGCACCGCCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
3374242 TTGCGCTGTCGGGGAAACCAGATCCGCCATTGT-GA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
** * * *
3374277 CTTCAATCTGCTCCACTATACCGCCAGGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
1 CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
*
3374342 TTGCGCTGTCAGGGAAACCAGATCCGCCGTTGT-GA
66 TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
*
3374377 CTTCAATCTGCTCCACTACAAC-GCTAAGGAA
1 CTTCAATCTGCTCCACTGC-ACTGCTAAGGAA
3374408 ATAAAAATAT
Statistics
Matches: 918, Mismatches: 105, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
99 4 0.00
100 908 0.99
101 6 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (101 bp):
CTTCAATCTGCTCCACTGCACTGCTAAGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAA
TTGCGCTGTCGGGGAAACCAGATCCGCCGTTGTAGA
Found at i:3374408 original size:50 final size:50
Alignment explanation
Indices: 3374153--3374408 Score: 151
Period size: 50 Copynumber: 5.1 Consensus size: 50
3374143 TGCGCTGTCG
* * * *
3374153 GGGAAACCAGATCCGTCGTTGTGACTTCAATCTGCTCCACTGCACCGCCA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
*** * * ** ** * * * *
3374203 GGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGC-GCTG-TCG
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAAC-GCT-A
* * * *
3374253 GGGAAACCAGATCCGCCATTGTGACTTCAATCTGCTCCACTATACCGCCA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
*** * ** ** * * *
3374303 GGGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAATTGC-GCTG-TCA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAAC-GCT-A
3374353 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
1 GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
*
3374403 AGGAAA
1 GGGAAA
3374409 TAAAAATATA
Statistics
Matches: 142, Mismatches: 56, Indels: 16
0.66 0.26 0.07
Matches are distributed among these distances:
49 2 0.01
50 137 0.96
51 3 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
GGGAAACCAGATCCGCCGTTGTGACTTCAATCTGCTCCACTACAACGCTA
Found at i:3375726 original size:6 final size:7
Alignment explanation
Indices: 3375709--3375741 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
3375699 GCCTCTCTAT
3375709 TTTTTCA
1 TTTTTCA
3375716 TTTTTCA
1 TTTTTCA
3375723 -TTTTCA
1 TTTTTCA
3375729 TCTTTTCA
1 T-TTTTCA
3375737 TTTTT
1 TTTTT
3375742 ACACATCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:3376271 original size:5 final size:5
Alignment explanation
Indices: 3376261--3376332 Score: 64
Period size: 5 Copynumber: 14.8 Consensus size: 5
3376251 TGTTAAAAAA
* *
3376261 ATATT ATATT ATAGTA ATGATT ATGTT -T-TT ATATT ATATT ATTATT
1 ATATT ATATT ATA-TT AT-ATT ATATT ATATT ATATT ATATT A-TATT
3376307 A-A-T ATATT ATATT ATATT ATA-T ATAT
1 ATATT ATATT ATATT ATATT ATATT ATAT
3376333 ACATAAAACA
Statistics
Matches: 56, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
3 4 0.07
4 8 0.14
5 32 0.57
6 11 0.20
7 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:3376314 original size:19 final size:19
Alignment explanation
Indices: 3376290--3376332 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3376280 ATTATGTTTT
3376290 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
3376309 TATATTATATTATATTATA
1 TATATTATATTATATTATA
3376328 TATAT
1 TATAT
3376333 ACATAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:3376365 original size:18 final size:19
Alignment explanation
Indices: 3376337--3376376 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
3376327 ATATATACAT
*
3376337 AAAACAAAAGAAAGAATAG
1 AAAACAAAAGAAAGAAAAG
3376356 AAAA-AAAAGAAAGAAAAG
1 AAAACAAAAGAAAGAAAAG
3376374 AAA
1 AAA
3376377 CAGAATAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.03
Consensus pattern (19 bp):
AAAACAAAAGAAAGAAAAG
Found at i:3377353 original size:44 final size:45
Alignment explanation
Indices: 3377247--3377380 Score: 144
Period size: 44 Copynumber: 3.0 Consensus size: 45
3377237 ACAGGACAGA
* * *
3377247 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* * * *
3377293 ATAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
** * *
3377337 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATAAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3377381 CAGGATATTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 36 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATAAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:3381458 original size:13 final size:13
Alignment explanation
Indices: 3381440--3381465 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3381430 TGTTCAATTT
3381440 TTTACTAGAAAAC
1 TTTACTAGAAAAC
3381453 TTTACTAGAAAAC
1 TTTACTAGAAAAC
3381466 AAATCTCTTT
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:3387160 original size:28 final size:29
Alignment explanation
Indices: 3387118--3387198 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
3387108 AATTTTAATA
*
3387118 AAAAAATACATAAAATTTATTAAAAAT-CAG
1 AAAAAAT-TATAAAATTTA-TAAAAATGCAG
* * * *
3387148 -AAAAATTGTAAAATATATAGAAATGTAG
1 AAAAAATTATAAAATTTATAAAAATGCAG
3387176 AAAAAATTATAAAATTTTATAAA
1 AAAAAATTATAAAA-TTTATAAA
3387199 GTCGTAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 6 0.15
28 10 0.25
29 18 0.45
30 6 0.15
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAAAATTATAAAATTTATAAAAATGCAG
Found at i:3387516 original size:24 final size:25
Alignment explanation
Indices: 3387483--3387531 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
3387473 ATTTTCATAT
*
3387483 TTTTTCTTATATTTAATAAATTTTA
1 TTTTTCTTATATTTAATAAAATTTA
* *
3387508 TTTTT-TTATTTTTATTAAAATTTA
1 TTTTTCTTATATTTAATAAAATTTA
3387532 ATAATTTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
TTTTTCTTATATTTAATAAAATTTA
Found at i:3387518 original size:34 final size:33
Alignment explanation
Indices: 3387480--3387565 Score: 84
Period size: 34 Copynumber: 2.5 Consensus size: 33
3387470 ACAATTTTCA
*
3387480 TATTTTTTCTTATATTTAATAAATTTTATT-TTTT
1 TATTTTTT-TTA-ATTTAATAAATTTTATTAATTT
* *
3387514 TATTTTTATTAAAATTTAATAATTTTTATTGAATTT
1 TATTTTT-TT-TAATTTAATAAATTTTATT-AATTT
3387550 TATTTTTTGTTAATTT
1 TATTTTTT-TTAATTT
3387566 TTTTCCATGT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
34 24 0.56
35 8 0.19
36 11 0.26
ACGTcount: A:0.29, C:0.01, G:0.02, T:0.67
Consensus pattern (33 bp):
TATTTTTTTTAATTTAATAAATTTTATTAATTT
Found at i:3391381 original size:37 final size:37
Alignment explanation
Indices: 3391331--3391405 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
3391321 TATATTAGTA
3391331 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
1 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
3391368 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
1 AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
3391405 A
1 A
3391406 TTGATAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.37
Consensus pattern (37 bp):
AGTGTTATTTTTGGAAGATGTCATATGAACAATTAAG
Found at i:3392637 original size:38 final size:37
Alignment explanation
Indices: 3392572--3392663 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 37
3392562 ACCAGATTGG
* *
3392572 CACCTAGTGCCTCATCAGATAGTTCGAAGCAAAGTTGA
1 CACCTAGTGTCTCATCGGATAGTTCGAAGCAAAG-TGA
* *
3392610 CACCTAGTGTCTCATCGGCCTAG-TCGAAGTAAAGTGA
1 CACCTAGTGTCTCATCGG-ATAGTTCGAAGCAAAGTGA
* * *
3392647 TACCCAGTATCTCATCG
1 CACCTAGTGTCTCATCG
3392664 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 17 0.37
38 26 0.57
39 3 0.07
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (37 bp):
CACCTAGTGTCTCATCGGATAGTTCGAAGCAAAGTGA
Found at i:3392843 original size:18 final size:17
Alignment explanation
Indices: 3392797--3392850 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
3392787 TTTCCAATTC
3392797 TCAATTCAAATTCACTT
1 TCAATTCAAATTCACTT
*
3392814 TCATTTCAAAATGT-ACTT
1 TCAATTC-AAAT-TCACTT
3392832 TCAATATCAAATTCACTT
1 TCAAT-TCAAATTCACTT
3392850 T
1 T
3392851 TTTCTCACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
17 7 0.23
18 21 0.68
19 3 0.10
ACGTcount: A:0.35, C:0.20, G:0.02, T:0.43
Consensus pattern (17 bp):
TCAATTCAAATTCACTT
Found at i:3394116 original size:29 final size:29
Alignment explanation
Indices: 3394074--3394130 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
3394064 ATCTTTTCTT
* *
3394074 AATTTATTTTATAATATAATAATATAATC
1 AATTTAATTTATAATATAATAAAATAATC
3394103 AATTTAATTTATAATATAATAAAATAAT
1 AATTTAATTTATAATATAATAAAATAAT
3394131 AACAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (29 bp):
AATTTAATTTATAATATAATAAAATAATC
Found at i:3410849 original size:18 final size:18
Alignment explanation
Indices: 3410826--3410863 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3410816 TGTCACCTAA
* *
3410826 TTATTAGTAAGTTTACAC
1 TTATTAATAAATTTACAC
3410844 TTATTAATAAATTTACAC
1 TTATTAATAAATTTACAC
3410862 TT
1 TT
3410864 TGGTCACTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (18 bp):
TTATTAATAAATTTACAC
Found at i:3414772 original size:12 final size:12
Alignment explanation
Indices: 3414755--3414779 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3414745 AGTCGATAAG
3414755 AAAAAACAAAAC
1 AAAAAACAAAAC
3414767 AAAAAACAAAAC
1 AAAAAACAAAAC
3414779 A
1 A
3414780 GTAAGACCGA
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:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACAAAAC
Found at i:3418854 original size:14 final size:14
Alignment explanation
Indices: 3418832--3418873 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
3418822 TCTTTATAAA
3418832 TTTAAAATTTAGTC
1 TTTAAAATTTAGTC
* *
3418846 TTTATAATTTTA-TT
1 TTTA-AAATTTAGTC
3418860 TTTAAAATTTAGTC
1 TTTAAAATTTAGTC
3418874 CCTTTACTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 6 0.27
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (14 bp):
TTTAAAATTTAGTC
Found at i:3418884 original size:28 final size:30
Alignment explanation
Indices: 3418828--3418898 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 30
3418818 TGATTCTTTA
*
3418828 TAAA-TTTAAAATTTAGTCTTTATAA-TTT
1 TAAATTTTAAAATTTAGTCCTTATAATTTT
* *
3418856 T-ATTTTTAAAATTTAGTCCCTT-TACTTTT
1 TAAATTTTAAAATTTAGT-CCTTATAATTTT
3418885 TAAATTTTAAAATT
1 TAAATTTTAAAATT
3418899 CAAATCCATC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 1 0.03
28 16 0.46
29 7 0.20
30 11 0.31
ACGTcount: A:0.35, C:0.07, G:0.03, T:0.55
Consensus pattern (30 bp):
TAAATTTTAAAATTTAGTCCTTATAATTTT
Found at i:3420492 original size:96 final size:94
Alignment explanation
Indices: 3420358--3420573 Score: 272
Period size: 96 Copynumber: 2.3 Consensus size: 94
3420348 TAAAAATTAC
* * *
3420358 ATTTATTAGATTTTTT-CTTAAAAACCTTAAACACTAAACCCTAATCTATTTTTTTTAAATTTAT
1 ATTTATTTGATTTTTTCCTT-AAAA-CTTAAACACTAAACCCTAATCTAATTTTTTAAAATTTAT
* *
3420422 AATTAATTTACTCAAGTAACCCTAAACCCTA
64 AATTAATTTAATCAAGAAACCCTAAACCCTA
**
3420453 ATTTATTTGATTTTTTCCTTGAAAACTATAAATGCTAAACCCTAATCTAATTTTTTAAAATTTAT
1 ATTTATTTGATTTTTTCCTT-AAAACT-TAAACACTAAACCCTAATCTAATTTTTTAAAATTTAT
* * * *
3420518 AGTTAATTTAATTAAGAAATCCTAAACCCTT
64 AATTAATTTAATCAAGAAACCCTAAACCCTA
* *
3420549 ATTTATTTAATTTTTCCCTTAAAAC
1 ATTTATTTGATTTTTTCCTTAAAAC
3420574 CCTAAAATCT
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
95 22 0.21
96 83 0.79
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (94 bp):
ATTTATTTGATTTTTTCCTTAAAACTTAAACACTAAACCCTAATCTAATTTTTTAAAATTTATAA
TTAATTTAATCAAGAAACCCTAAACCCTA
Found at i:3421066 original size:9 final size:9
Alignment explanation
Indices: 3421052--3421078 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3421042 CTTGAACACA
3421052 AAAAAGCAC
1 AAAAAGCAC
3421061 AAAAAGCAC
1 AAAAAGCAC
3421070 AAAAAGCAC
1 AAAAAGCAC
3421079 GGCCACCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.67, C:0.22, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAGCAC
Found at i:3438900 original size:16 final size:16
Alignment explanation
Indices: 3438879--3438910 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
3438869 TCACCATTAT
3438879 GGATCAAATCATCCCA
1 GGATCAAATCATCCCA
3438895 GGATCAAATCATCCCA
1 GGATCAAATCATCCCA
3438911 CCTAAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.31, G:0.12, T:0.19
Consensus pattern (16 bp):
GGATCAAATCATCCCA
Found at i:3441530 original size:20 final size:20
Alignment explanation
Indices: 3441474--3441521 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3441464 ATTACAAAAG
* *
3441474 AAAAGTTCAAAATAATTTTT
1 AAAATTTCAAAACAATTTTT
3441494 AAAATTTCAAAACAATTTTT
1 AAAATTTCAAAACAATTTTT
3441514 AAATATTT
1 AAA-ATTT
3441522 ATAAAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (20 bp):
AAAATTTCAAAACAATTTTT
Found at i:3442274 original size:19 final size:17
Alignment explanation
Indices: 3442252--3442285 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
3442242 TTTTCTCATA
3442252 AAAAATATTAAAAATATT
1 AAAAA-ATTAAAAATATT
3442270 AAAAAATTAAAAATAT
1 AAAAAATTAAAAATAT
3442286 ATTGAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAATTAAAAATATT
Found at i:3442282 original size:8 final size:9
Alignment explanation
Indices: 3442252--3442285 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
3442242 TTTTCTCATA
3442252 AAAAATATT
1 AAAAATATT
3442261 AAAAATATT
1 AAAAATATT
3442270 AAAAA-ATT
1 AAAAATATT
3442278 AAAAATAT
1 AAAAATAT
3442286 ATTGAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
AAAAATATT
Found at i:3442297 original size:19 final size:18
Alignment explanation
Indices: 3442253--3442297 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
3442243 TTTCTCATAA
3442253 AAAATATT-AAAAATATT
1 AAAATATTAAAAAATATT
*
3442270 AAAAAATTAAAAATATATT
1 AAAATATTAAAAA-ATATT
*
3442289 GAAATATTA
1 AAAATATTA
3442298 TAAGAAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 7 0.30
18 4 0.17
19 12 0.52
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAAATATTAAAAAATATT
Found at i:3442341 original size:29 final size:31
Alignment explanation
Indices: 3442309--3442373 Score: 80
Period size: 29 Copynumber: 2.1 Consensus size: 31
3442299 AAGAAAACAT
*
3442309 AAAAAGGTATAAAATTTA-T-AAAACTAATA
1 AAAAAGATATAAAATTTATTAAAAACTAATA
* *
3442338 AAAAATATTTAAAATTTATTAAAAAACTAATA
1 AAAAAGATATAAAATTTATT-AAAAACTAATA
3442370 AAAA
1 AAAA
3442374 TTCATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 15 0.50
30 1 0.03
32 14 0.47
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (31 bp):
AAAAAGATATAAAATTTATTAAAAACTAATA
Found at i:3442384 original size:20 final size:18
Alignment explanation
Indices: 3442355--3442416 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 18
3442345 TTTAAAATTT
3442355 ATTA-AAAAACTAATAAAA
1 ATTATAAAAACT-ATAAAA
**
3442373 ATTCATAAAAACTTATAAGT
1 ATT-ATAAAAAC-TATAAAA
*
3442393 ATTATAAAAAATATAAAA
1 ATTATAAAAACTATAAAA
3442411 A-TATAA
1 ATTATAA
3442417 TAAGTTCTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 8 0.22
20 13 0.36
21 1 0.03
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.29
Consensus pattern (18 bp):
ATTATAAAAACTATAAAA
Found at i:3442419 original size:20 final size:20
Alignment explanation
Indices: 3442333--3442419 Score: 61
Period size: 21 Copynumber: 4.3 Consensus size: 20
3442323 TTTATAAAAC
* *
3442333 TAATAAAAAATATTTAAAATT
1 TAATAAAAAATA-TAAAAATA
*
3442354 TATTAAAAAACTAATAAAAAT-
1 TAATAAAAAA-T-ATAAAAATA
* * * *
3442375 TCATAAAAACT-TATAAGTA
1 TAATAAAAAATATAAAAATA
*
3442394 TTATAAAAAATATAAAAATA
1 TAATAAAAAATATAAAAATA
3442414 TAATAA
1 TAATAA
3442420 GTTCTAATAA
Statistics
Matches: 50, Mismatches: 12, Indels: 9
0.70 0.17 0.13
Matches are distributed among these distances:
18 5 0.10
19 9 0.18
20 12 0.24
21 16 0.32
22 7 0.14
23 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.32
Consensus pattern (20 bp):
TAATAAAAAATATAAAAATA
Found at i:3442951 original size:19 final size:19
Alignment explanation
Indices: 3442912--3442975 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
3442902 CAATGACTTT
* *
3442912 TTTTTATATT-TTTAGAA-
1 TTTTTATATTCTTCATAAG
3442929 TTTTTATATTCTTCATAAG
1 TTTTTATATTCTTCATAAG
*
3442948 TTTTTAT-TAACTTCTATAAG
1 TTTTTATAT-TCTTC-ATAAG
3442968 TTTTTATA
1 TTTTTATA
3442976 AAATTTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
17 10 0.26
18 6 0.15
19 11 0.28
20 12 0.31
ACGTcount: A:0.28, C:0.06, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTATATTCTTCATAAG
Found at i:3446241 original size:29 final size:29
Alignment explanation
Indices: 3446207--3446276 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
3446197 ATTAATAATC
*
3446207 ATAAAATTATAGTTTAAT-TTCT-AAAAAT
1 ATAAAATTATAATTTAATCTT-TAAAAAAT
*
3446235 ACTAAAATTTTAATTTAATCTTTAAAAAAT
1 A-TAAAATTATAATTTAATCTTTAAAAAAT
*
3446265 ATAAAAATATAA
1 ATAAAATTATAA
3446277 ACTATTAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.71
30 9 0.26
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (29 bp):
ATAAAATTATAATTTAATCTTTAAAAAAT
Found at i:3446711 original size:12 final size:14
Alignment explanation
Indices: 3446694--3446725 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
3446684 TCTGCACGAG
3446694 AAAAATT-AATA-A
1 AAAAATTAAATATA
3446706 AAAAATTAAATATA
1 AAAAATTAAATATA
3446720 AAAAAT
1 AAAAAT
3446726 CCTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAAATTAAATATA
Found at i:3452444 original size:20 final size:22
Alignment explanation
Indices: 3452405--3452444 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3452395 ATCATTTTCT
3452405 TACCAATTGCATTATTTATCGG
1 TACCAATTGCATTATTTATCGG
3452427 TACCAATT-CATT-TTTATC
1 TACCAATTGCATTATTTATC
3452445 AAATTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.28, C:0.20, G:0.07, T:0.45
Consensus pattern (22 bp):
TACCAATTGCATTATTTATCGG
Found at i:3469026 original size:65 final size:64
Alignment explanation
Indices: 3468929--3469051 Score: 167
Period size: 65 Copynumber: 1.9 Consensus size: 64
3468919 TAGAGGAGCC
* *
3468929 TAATTAAATTTGCTAAAAACTTCAAAGAAGAAATGAAAATTTTCAAAAACTTTGGGGGTCTAAT
1 TAATTAAATTTGCTAAAAACTTCAAAGAAGAAATCAAAAGTTTCAAAAACTTTGGGGGTCTAAT
* * * *
3468993 TAATTAAAATTTTCTAAAAATTTC-AAGAGAGAAATCAAAAGTTTCCAAAATTTTGGGGG
1 TAATT-AAATTTGCTAAAAACTTCAAAGA-AGAAATCAAAAGTTTCAAAAACTTTGGGGG
3469052 GCATTTGTCA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
64 9 0.18
65 42 0.82
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.32
Consensus pattern (64 bp):
TAATTAAATTTGCTAAAAACTTCAAAGAAGAAATCAAAAGTTTCAAAAACTTTGGGGGTCTAAT
Found at i:3470541 original size:15 final size:15
Alignment explanation
Indices: 3470517--3470572 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 15
3470507 ACAATTGTAA
3470517 TAAAAGAAAAAAATG
1 TAAAAGAAAAAAATG
* *
3470532 TAAAATAAAAAAA-A
1 TAAAAGAAAAAAATG
3470546 TAAAAGGAAAAAAATTG
1 TAAAA-GAAAAAAA-TG
3470563 TAAAAAGAAA
1 T-AAAAGAAA
3470573 GACAAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 5 0.15
15 19 0.58
17 5 0.15
18 4 0.12
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (15 bp):
TAAAAGAAAAAAATG
Found at i:3470549 original size:14 final size:14
Alignment explanation
Indices: 3470515--3470560 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
3470505 AGACAATTGT
3470515 AATAAAAGAAAAAA
1 AATAAAAGAAAAAA
* *
3470529 ATGTAAAATAAAAAA
1 A-ATAAAAGAAAAAA
*
3470544 AATAAAAGGAAAAA
1 AATAAAAGAAAAAA
3470558 AAT
1 AAT
3470561 TGTAAAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (14 bp):
AATAAAAGAAAAAA
Found at i:3470556 original size:20 final size:20
Alignment explanation
Indices: 3470515--3470556 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
3470505 AGACAATTGT
* *
3470515 AATAAAAGAAAAAAATGTAA
1 AATAAAAGAAAAAAAAGGAA
3470535 AATAAAA-AAAATAAAAGGAA
1 AATAAAAGAAAA-AAAAGGAA
3470555 AA
1 AA
3470557 AAATTGTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (20 bp):
AATAAAAGAAAAAAAAGGAA
Found at i:3471554 original size:17 final size:19
Alignment explanation
Indices: 3471524--3471561 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
3471514 AATACAAATT
*
3471524 AACCCTCAGGCC-AAACTA
1 AACCCTCAGCCCAAAACTA
3471542 AACCCT-AGCCCAAAACTA
1 AACCCTCAGCCCAAAACTA
3471560 AA
1 AA
3471562 AAATTTTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.45, C:0.37, G:0.08, T:0.11
Consensus pattern (19 bp):
AACCCTCAGCCCAAAACTA
Found at i:3472814 original size:26 final size:29
Alignment explanation
Indices: 3472774--3472834 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 29
3472764 CTATTTGATA
*
3472774 TTATCTATTTTAAATTG-TTTC-A-TATT
1 TTATCTATTTCAAATTGCTTTCTATTATT
*
3472800 TTATTTATTTCAAATTGCTTTCTATTATT
1 TTATCTATTTCAAATTGCTTTCTATTATT
3472829 TTATCT
1 TTATCT
3472835 TAAACTGTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 15 0.52
27 4 0.14
28 1 0.03
29 9 0.31
ACGTcount: A:0.25, C:0.10, G:0.03, T:0.62
Consensus pattern (29 bp):
TTATCTATTTCAAATTGCTTTCTATTATT
Found at i:3474512 original size:34 final size:34
Alignment explanation
Indices: 3474469--3474534 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
3474459 CAGTAAAATG
*
3474469 TTTTCGTAAAATGATTT-CTGAAAAATATTTTAC
1 TTTTCGTAAAATGATTTACTGAAAAACATTTTAC
*
3474502 TTTTCTGTAAAATGATTTACTGGAAAACATTTT
1 TTTTC-GTAAAATGATTTACTGAAAAACATTTT
3474535 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.41
35 12 0.41
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGAAAAACATTTTAC
Found at i:3480865 original size:3 final size:3
Alignment explanation
Indices: 3480859--3480917 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
3480849 AAGATATTGG
* * *
3480859 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGAA TTA -GA GGA TAA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG-A TGA TGA TGA TGA TGA
*
3480904 TGA TGA CGA TGA TG
1 TGA TGA TGA TGA TG
3480918 GAGAAGATGA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.94
4 2 0.04
ACGTcount: A:0.36, C:0.02, G:0.32, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:3480938 original size:15 final size:15
Alignment explanation
Indices: 3480914--3480947 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3480904 TGATGACGAT
*
3480914 GATGGAGAAGATGAA
1 GATGGAGAAGAAGAA
*
3480929 GATGGTGAAGAAGAA
1 GATGGAGAAGAAGAA
3480944 GATG
1 GATG
3480948 AGGAGGAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.41, T:0.15
Consensus pattern (15 bp):
GATGGAGAAGAAGAA
Found at i:3501658 original size:25 final size:26
Alignment explanation
Indices: 3501624--3501681 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
3501614 TATATTTCTC
* *
3501624 AAAATTTTACTA-GGGAAAAAAGGTT
1 AAAATTTTACCAGGGGAAAAAACGTT
* *
3501649 AAAATTTTACCAGGGGTAAAATCGTT
1 AAAATTTTACCAGGGGAAAAAACGTT
3501675 AAAATTT
1 AAAATTT
3501682 GTTGAAGGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.45, C:0.07, G:0.17, T:0.31
Consensus pattern (26 bp):
AAAATTTTACCAGGGGAAAAAACGTT
Found at i:3504428 original size:24 final size:24
Alignment explanation
Indices: 3504396--3504443 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
3504386 ACATGTTTAG
3504396 GAGAATGTATGTGAATGAATGCAA
1 GAGAATGTATGTGAATGAATGCAA
3504420 GAGAATGTATGTGAATGAATGCAA
1 GAGAATGTATGTGAATGAATGCAA
3504444 TATTATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.04, G:0.29, T:0.25
Consensus pattern (24 bp):
GAGAATGTATGTGAATGAATGCAA
Found at i:3507280 original size:20 final size:21
Alignment explanation
Indices: 3507243--3507281 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3507233 GATAAAATAA
3507243 TTTTTCCTATAAAGATCCAAG
1 TTTTTCCTATAAAGATCCAAG
*
3507264 TTTTTCTTATAAA-ATCCA
1 TTTTTCCTATAAAGATCCA
3507282 GTTAATTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTTTCCTATAAAGATCCAAG
Found at i:3507808 original size:18 final size:18
Alignment explanation
Indices: 3507777--3507824 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
3507767 TGTTTTTCGT
**
3507777 TTTCAAAATATTATTC-A
1 TTTCAAAACGTTATTCAA
*
3507794 TTTACAAATCGTTATTCAA
1 TTT-CAAAACGTTATTCAA
3507813 TTTCAAAACGTT
1 TTTCAAAACGTT
3507825 TTTATTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.38, C:0.15, G:0.04, T:0.44
Consensus pattern (18 bp):
TTTCAAAACGTTATTCAA
Found at i:3509393 original size:19 final size:19
Alignment explanation
Indices: 3509371--3509407 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3509361 CATCCTCTAA
3509371 TTTGA-TTTTCACAATTTAT
1 TTTGATTTTTCA-AATTTAT
3509390 TTTGATTTTTCAAATTTA
1 TTTGATTTTTCAAATTTA
3509408 GCCTACTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.27, C:0.08, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTGATTTTTCAAATTTAT
Found at i:3516588 original size:55 final size:59
Alignment explanation
Indices: 3516477--3516589 Score: 153
Period size: 55 Copynumber: 2.0 Consensus size: 59
3516467 AGAAATAGTG
* * * * *
3516477 AAAATGGAGAAATAGGAAACATTTGGAAATGAGATTTGGTTTTCTCCAAAATGAAAATT
1 AAAATGAAGAAATAGGAAACATTTAGAAATGAAATGTGGTTTTCTCCAAAACGAAAATT
3516536 AAAATGAAGAAATA-GAAACATTTAGAAAT-AAATGT-G-TTTCTCCAAAACGAAAAT
1 AAAATGAAGAAATAGGAAACATTTAGAAATGAAATGTGGTTTTCTCCAAAACGAAAAT
3516590 GAATAAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 17 0.35
56 1 0.02
57 4 0.08
58 14 0.29
59 13 0.27
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.27
Consensus pattern (59 bp):
AAAATGAAGAAATAGGAAACATTTAGAAATGAAATGTGGTTTTCTCCAAAACGAAAATT
Found at i:3519369 original size:50 final size:50
Alignment explanation
Indices: 3519254--3519446 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
3519244 GATAATAACA
* ** * *
3519254 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
3519305 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3519355 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
3519405 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3519447 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 96 0.74
51 33 0.26
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:3519819 original size:30 final size:30
Alignment explanation
Indices: 3519784--3519841 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3519774 CCTCGACTCT
*
3519784 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
3519814 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
3519842 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:3526311 original size:50 final size:50
Alignment explanation
Indices: 3526196--3526388 Score: 296
Period size: 50 Copynumber: 3.8 Consensus size: 50
3526186 GATAATAACA
* ** * *
3526196 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * *
3526247 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
3526297 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
3526347 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
3526389 TTACCCAAAT
Statistics
Matches: 129, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
50 96 0.74
51 33 0.26
ACGTcount: A:0.20, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:3526504 original size:13 final size:13
Alignment explanation
Indices: 3526483--3526513 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3526473 GCTTAGATCA
*
3526483 TCATCAAATAAAT
1 TCATAAAATAAAT
3526496 TCATAAAATAAAT
1 TCATAAAATAAAT
3526509 TCATA
1 TCATA
3526514 GTTGCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:3526761 original size:30 final size:30
Alignment explanation
Indices: 3526726--3526783 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
3526716 CCTCGACTCT
*
3526726 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* * *
3526756 AACTTTTACATAATTACATTTTTTCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
3526784 AAGGCTCAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.02, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:3529141 original size:18 final size:18
Alignment explanation
Indices: 3529118--3529154 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3529108 TTACACACAC
*
3529118 TTAAATTTAAGAGAAAGT
1 TTAAATTTAAAAGAAAGT
3529136 TTAAATTTAAAAGAAAGT
1 TTAAATTTAAAAGAAAGT
3529154 T
1 T
3529155 GTAGAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (18 bp):
TTAAATTTAAAAGAAAGT
Found at i:3544729 original size:39 final size:36
Alignment explanation
Indices: 3544672--3544743 Score: 92
Period size: 39 Copynumber: 1.9 Consensus size: 36
3544662 AAATTATAAA
*
3544672 TAATAATAAATAATAAATTTTAGAAAATTTATTAAATTT
1 TAATAAGAAATAATAAATTTT---AAATTTATTAAATTT
3544711 TAATAAGAATATAA-AAATTTTAAATTTATTAAA
1 TAATAAGAA-ATAATAAATTTTAAATTTATTAAA
3544744 ATTAGAATTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
36 12 0.39
39 15 0.48
40 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (36 bp):
TAATAAGAAATAATAAATTTTAAATTTATTAAATTT
Found at i:3545052 original size:47 final size:48
Alignment explanation
Indices: 3544976--3545074 Score: 130
Period size: 47 Copynumber: 2.1 Consensus size: 48
3544966 TTTTACGGAA
*
3544976 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGA-CTTTATAAAAT
1 TTTATATTTCTTTACATTTTCTATAATTTT-TTACGATCTTTATAAAAT
* * * *
3545024 TTTATATTTTTTTATA-TTTCTATTATTTTTTACGATTTTTATAAAAT
1 TTTATATTTCTTTACATTTTCTATAATTTTTTACGATCTTTATAAAAT
3545071 TTTA
1 TTTA
3545075 CAATATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
46 6 0.13
47 25 0.56
48 14 0.31
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (48 bp):
TTTATATTTCTTTACATTTTCTATAATTTTTTACGATCTTTATAAAAT
Found at i:3545098 original size:47 final size:46
Alignment explanation
Indices: 3544991--3545101 Score: 116
Period size: 47 Copynumber: 2.3 Consensus size: 46
3544981 ATTTCTTTAC
* * * * *
3544991 ATTTTGTATAATTTTCTTACGACTTTATAAAATTTTATATTTTTTTAT
1 ATTTTCTAT-ATTTT-TTACGACTTTATAAAATTTTACAATATATTAT
*
3545039 A-TTTCTATTATTTTTTACGATTTTTATAAAATTTTACAATATATTAT
1 ATTTTCTA-TATTTTTTACGA-CTTTATAAAATTTTACAATATATTAT
*
3545086 ATTTTTTATATTTTTT
1 ATTTTCTATATTTTTT
3545102 TCTAATTTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
46 6 0.11
47 40 0.75
48 7 0.13
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (46 bp):
ATTTTCTATATTTTTTACGACTTTATAAAATTTTACAATATATTAT
Found at i:3545408 original size:88 final size:84
Alignment explanation
Indices: 3545196--3545416 Score: 282
Period size: 86 Copynumber: 2.5 Consensus size: 84
3545186 AATTTTTAAT
* **
3545196 AAAATAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTATGTATTTTGAAAGTT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAA-TTTGAGGG-CTTTTTTATACATTTTGAAAGTT
*
3545261 CAAATACCCAATTGAATGCAA
64 CAAATACCCAAATGAATGCAA
*
3545282 AAAAAAGGGGCCTAATTGCTTTTTTTGAAAAGATTTGAGGGCTTTTTTGATACATTTTGAAAGTT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAA-ATTTGAGGGCTTTTTT-ATACATTTTGAAAGTT
* * *
3545347 CAAGTATCCAAATGAGTGCAA
64 CAAATACCCAAATGAATGCAA
*
3545368 AAAAAGCAGGGGCTTAATTG-TATTTTTTCTAAAAATTTGAGGGCTTTTT
1 AAAAA--AGGGGCTTAATTGCT-TTTTTT-GAAAAATTTGAGGGCTTTTT
3545417 GCACCCTTAA
Statistics
Matches: 119, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
85 7 0.06
86 73 0.61
87 2 0.02
88 33 0.28
89 4 0.03
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.38
Consensus pattern (84 bp):
AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAATTTGAGGGCTTTTTTATACATTTTGAAAGTTCA
AATACCCAAATGAATGCAA
Found at i:3550903 original size:28 final size:29
Alignment explanation
Indices: 3550850--3550905 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
3550840 CTCAAAAAAA
**
3550850 ATTACAAAAAATTTAAAATATTTATAAAG
1 ATTACAAAAAATTTAAAATAAATATAAAG
3550879 ATTA-AAAAAATTCTAAAA-AAATATAAA
1 ATTACAAAAAATT-TAAAATAAATATAAA
3550906 AAGGTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (29 bp):
ATTACAAAAAATTTAAAATAAATATAAAG
Found at i:3552814 original size:3 final size:3
Alignment explanation
Indices: 3552803--3552866 Score: 85
Period size: 3 Copynumber: 21.3 Consensus size: 3
3552793 CAATAATACC
* * *
3552803 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
3552848 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
3552867 GCAAAAGTAC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 1 0.02
3 52 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3554695 original size:41 final size:41
Alignment explanation
Indices: 3554638--3554964 Score: 136
Period size: 44 Copynumber: 7.8 Consensus size: 41
3554628 TAGTGTTTTC
* *
3554638 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGACCTGATGT
* *
3554679 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCCT--T-T
1 GATCTTCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATGT
* ** * * * * *
3554718 AATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACT-ATCTTT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TGT
* * * * *
3554762 GACCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGACCTG--A---TGT
* *
3554808 GGTCTGT-TCCACTATAATCTCAGGGAGATAAGACCTGATGT
1 GATCT-TCTCCACTGTAATCTCAGGGAGATAAGACCTGATGT
* *
3554849 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCCT--T-T
1 GATCTTCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATGT
* ** * * * * *
3554888 AATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACT-ATCATT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGA--CCTGAT--GT
* *
3554932 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGA
3554965 TCTGCTTCTT
Statistics
Matches: 217, Mismatches: 47, Indels: 41
0.71 0.15 0.13
Matches are distributed among these distances:
39 48 0.22
40 13 0.06
41 55 0.25
42 8 0.04
43 1 0.00
44 56 0.26
45 1 0.00
46 35 0.16
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
GATCTTCTCCACTGTAATCTCAGGGAGATAAGACCTGATGT
Found at i:3554745 original size:80 final size:80
Alignment explanation
Indices: 3554650--3554917 Score: 270
Period size: 80 Copynumber: 3.2 Consensus size: 80
3554640 TCTGCTCCGC
*
3554650 TGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
1 TGTAATCTCAAGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
3554715 TTTAATCCGCTCCAT
66 TTTAATCCGCTCCAT
* * * * * ** *
3554730 TGTAATCTCAAGGAGATAGGATTACT-ATCTTTGACCTGCTCCGCTGTAA-TCTCAGGGAGATAA
1 TGTAATCTCAAGGAGATAAGA--CCTGA--TGTGATCTTCTCTACTGTAACT-TCAGAGAGATAA
** * * *
3554793 GATCTGAAATTCTTTGGTCTGTTCCAC
61 GATC-------CTTTAATCCGCTCCAT
* *
3554820 TATAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
1 TGTAATCTCAAGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
3554885 TTTAATCCGCTCCAT
66 TTTAATCCGCTCCAT
3554900 TGTAATCTCAAGGAGATA
1 TGTAATCTCAAGGAGATA
3554918 GGATTACTAT
Statistics
Matches: 143, Mismatches: 31, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
80 46 0.32
81 1 0.01
82 3 0.02
83 30 0.21
87 30 0.21
88 3 0.02
89 1 0.01
90 29 0.20
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (80 bp):
TGTAATCTCAAGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
TTTAATCCGCTCCAT
Found at i:3554789 original size:44 final size:44
Alignment explanation
Indices: 3554723--3554992 Score: 161
Period size: 44 Copynumber: 6.3 Consensus size: 44
3554713 CCTTTAATCC
* * *
3554723 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * **
3554767 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGACCT
* * * * *
3554813 GTTCCACTATAATCTCAGGGAGATAAGA--CCTGA--TGTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGACCT
* * * *
3554854 TCTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTTAATCC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGA-CCT
* * * * *
3554893 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * * *
3554937 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCT-TCTTTAACCA
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTTGACCT
3554981 GCTCCACTGTAA
1 GCTCCACTGTAA
3554993 CCAATGAAGG
Statistics
Matches: 168, Mismatches: 41, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
39 23 0.14
40 4 0.02
41 29 0.17
43 1 0.01
44 72 0.43
45 5 0.03
46 34 0.20
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
Found at i:3554941 original size:170 final size:170
Alignment explanation
Indices: 3554652--3554968 Score: 616
Period size: 170 Copynumber: 1.9 Consensus size: 170
3554642 TGCTCCGCTG
3554652 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
*
3554717 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGACCTGCTCCGCTGTAATCT
3554782 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
131 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
3554822 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
*
3554887 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGATCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGACCTGCTCCGCTGTAATCT
3554952 CAGGGAGATAAGATCTG
131 CAGGGAGATAAGATCTG
3554969 CTTCTTTAAC
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 145 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (170 bp):
TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGACCTGCTCCGCTGTAATCT
CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
Found at i:3554962 original size:83 final size:82
Alignment explanation
Indices: 3554690--3554966 Score: 267
Period size: 83 Copynumber: 3.3 Consensus size: 82
3554680 ATCTTCTCTA
3554690 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
1 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
*
3554755 TATCTTTGACCTGCTCCG
66 TATC-TTGATCTGCTCCG
* ** * * * * *
3554773 CTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGAT
1 CTGTAACT-TCAGAGAGATAAGATC-------CTTTAATCCGCTCCATTGTAATCTCAAGGAGAT
* * * * **
3554837 AAGA--CCTGAT-GTGATCTTCTCTA
58 AGGATTACT-ATCTTGATCTGCTCCG
3554860 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
1 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
3554925 TATCATTGATCTGCTCCG
66 TATC-TTGATCTGCTCCG
*
3554943 CTGTAA-TCTCAGGGAGATAAGATC
1 CTGTAACT-TCAGAGAGATAAGATC
3554967 TGCTTCTTTA
Statistics
Matches: 149, Mismatches: 30, Indels: 30
0.71 0.14 0.14
Matches are distributed among these distances:
80 29 0.19
81 2 0.01
82 4 0.03
83 51 0.34
87 29 0.19
88 3 0.02
89 2 0.01
90 29 0.19
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (82 bp):
CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
TATCTTGATCTGCTCCG
Found at i:3571834 original size:42 final size:41
Alignment explanation
Indices: 3571783--3571864 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 41
3571773 ATTTGGTTCA
* *
3571783 ATTTTTTAGG-CTTAATTTTTTTATATATGAGTTCA-ATATTGT
1 ATTTATTAGGTCTT-ATTTATTTAT-T-TGAGTTCAGATATTGT
3571825 ATTTATTAGGTTCTTATTTATTTATTTGAGTTCAGATATT
1 ATTTATTAGG-TCTTATTTATTTATTTGAGTTCAGATATT
3571865 TTTTAAGTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
41 8 0.23
42 15 0.43
43 9 0.26
44 3 0.09
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (41 bp):
ATTTATTAGGTCTTATTTATTTATTTGAGTTCAGATATTGT
Found at i:3576780 original size:46 final size:48
Alignment explanation
Indices: 3576684--3576781 Score: 121
Period size: 46 Copynumber: 2.1 Consensus size: 48
3576674 TTTTACGGAA
*
3576684 TTTATATTTCTTTACATTTTGTATAATTTTCTTACGACTTTATAAAAT
1 TTTATATTTCTTTACATTTTCTATAATTTTCTTACGACTTTATAAAAT
* * * *
3576732 TTTATATTTTTTTATA-TTTCTATTATTTT-TTACGA-TTTTTATAAAT
1 TTTATATTTCTTTACATTTTCTATAATTTTCTTACGACTTTATA-AAAT
3576778 TTTA
1 TTTA
3576782 CCAATATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
45 5 0.11
46 14 0.32
47 11 0.25
48 14 0.32
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (48 bp):
TTTATATTTCTTTACATTTTCTATAATTTTCTTACGACTTTATAAAAT
Found at i:3576991 original size:86 final size:86
Alignment explanation
Indices: 3576896--3577117 Score: 272
Period size: 85 Copynumber: 2.6 Consensus size: 86
3576886 TAATTTTTAT
* * **
3576896 AAAATAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTATGTATTTTGAAAGTT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGG-CTTTTTGATACATTTTGAAAGTT
*
3576961 CAAATACCCAATTGAATGC-AA
65 CAAATACCCAAATGAATGCAAA
*
3576982 AAAAAAGGGGCCTAATTGCTTTTTTTG-AAAAGATTTGAGGGCTTTTTGATACATTTTGAAAGTT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAAG-TTTGAGGGCTTTTTGATACATTTTGAAAGTT
* * *
3577046 CAAGTATCCAAATGAGTGCAAA
65 CAAATACCCAAATGAATGCAAA
*
3577068 AAAAAGCAGGGGCTTAATTG-TATTTTTTCTAAAAA-TTTGAGGGCTTTTTG
1 AAAAA--AGGGGCTTAATTGCT-TTTTTT-GAAAAAGTTTGAGGGCTTTTTG
3577118 CACCCTTAAG
Statistics
Matches: 118, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
85 40 0.34
86 40 0.34
87 1 0.01
88 33 0.28
90 4 0.03
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (86 bp):
AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGCTTTTTGATACATTTTGAAAGTTC
AAATACCCAAATGAATGCAAA
Found at i:3577066 original size:85 final size:85
Alignment explanation
Indices: 3576896--3577117 Score: 277
Period size: 86 Copynumber: 2.6 Consensus size: 85
3576886 TAATTTTTAT
* * **
3576896 AAAATAGGGGCTTAATTGCTTTTTTTGAAAAAGTTTGAGGGTCTTTTTTATGTATTTTGAAAGTT
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAA-TTTGAGGG-CTTTTTGATACATTTTGAAAGTT
*
3576961 CAAATACCCAATTGAATGC-AA
64 CAAATACCCAAATGAATGCAAA
*
3576982 AAAAAAGGGGCCTAATTGCTTTTTTTGAAAAGATTTGAGGGCTTTTTGATACATTTTGAAAGTTC
1 AAAAAAGGGGCTTAATTGCTTTTTTTGAAAA-ATTTGAGGGCTTTTTGATACATTTTGAAAGTTC
* * *
3577047 AAGTATCCAAATGAGTGCAAA
65 AAATACCCAAATGAATGCAAA
*
3577068 AAAAAGCAGGGGCTTAATTG-TATTTTTTCTAAAAATTTGAGGGCTTTTTG
1 AAAAA--AGGGGCTTAATTGCT-TTTTTT-GAAAAATTTGAGGGCTTTTTG
3577118 CACCCTTAAG
Statistics
Matches: 119, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
85 35 0.29
86 44 0.37
87 2 0.02
88 34 0.29
89 4 0.03
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (85 bp):
AAAAAAGGGGCTTAATTGCTTTTTTTGAAAAATTTGAGGGCTTTTTGATACATTTTGAAAGTTCA
AATACCCAAATGAATGCAAA
Found at i:3582523 original size:9 final size:9
Alignment explanation
Indices: 3582511--3582573 Score: 54
Period size: 9 Copynumber: 6.8 Consensus size: 9
3582501 AAAAATTACA
3582511 AAAAAATTT
1 AAAAAATTT
*
3582520 AAAATATTT
1 AAAAAATTT
* *
3582529 ATAAAGATTA
1 A-AAAAATTT
3582539 AAAAAATTCT
1 AAAAAATT-T
*
3582549 AAAAAATAT
1 AAAAAATTT
**
3582558 AAAAAAGGT
1 AAAAAATTT
3582567 AAAAAAT
1 AAAAAAT
3582574 AAAAATTTTT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
9 29 0.67
10 14 0.33
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3584471 original size:3 final size:3
Alignment explanation
Indices: 3584460--3584520 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
3584450 CAATAATACC
* * *
3584460 AAT ACT AAT AAT AGT AA- AGAT GAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
3584505 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
3584521 GCAAAAGTAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 49 0.98
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3586370 original size:41 final size:41
Alignment explanation
Indices: 3586313--3586639 Score: 136
Period size: 44 Copynumber: 7.8 Consensus size: 41
3586303 TAGTGTTTTC
* *
3586313 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGACCTGATGT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGACCTGATGT
* *
3586354 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCCT--T-T
1 GATCTTCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATGT
* ** * * * * *
3586393 AATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACT-ATCTTT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGA--CCTGA--TGT
* * * * *
3586437 GACCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGACCTG--A---TGT
* *
3586483 GGTCTGT-TCCACTATAATCTCAGGGAGATAAGACCTGATGT
1 GATCT-TCTCCACTGTAATCTCAGGGAGATAAGACCTGATGT
* *
3586524 GATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATCCT--T-T
1 GATCTTCTCCACTGTAATC-TCAGGGAGATAAGA-CCTGATGT
* ** * * * * *
3586563 AATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACT-ATCATT
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGA--CCTGAT--GT
* *
3586607 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
1 GATCTTCTCCACTGTAATCTCAGGGAGATAAGA
3586640 TCTGCTTCTT
Statistics
Matches: 217, Mismatches: 47, Indels: 41
0.71 0.15 0.13
Matches are distributed among these distances:
39 48 0.22
40 13 0.06
41 55 0.25
42 8 0.04
43 1 0.00
44 56 0.26
45 1 0.00
46 35 0.16
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (41 bp):
GATCTTCTCCACTGTAATCTCAGGGAGATAAGACCTGATGT
Found at i:3586420 original size:80 final size:80
Alignment explanation
Indices: 3586325--3586592 Score: 270
Period size: 80 Copynumber: 3.2 Consensus size: 80
3586315 TCTGCTCCGC
*
3586325 TGTAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
1 TGTAATCTCAAGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
3586390 TTTAATCCGCTCCAT
66 TTTAATCCGCTCCAT
* * * * * ** *
3586405 TGTAATCTCAAGGAGATAGGATTACT-ATCTTTGACCTGCTCCGCTGTAA-TCTCAGGGAGATAA
1 TGTAATCTCAAGGAGATAAGA--CCTGA--TGTGATCTTCTCTACTGTAACT-TCAGAGAGATAA
** * * *
3586468 GATCTGAAATTCTTTGGTCTGTTCCAC
61 GATC-------CTTTAATCCGCTCCAT
* *
3586495 TATAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
1 TGTAATCTCAAGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
3586560 TTTAATCCGCTCCAT
66 TTTAATCCGCTCCAT
3586575 TGTAATCTCAAGGAGATA
1 TGTAATCTCAAGGAGATA
3586593 GGATTACTAT
Statistics
Matches: 143, Mismatches: 31, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
80 46 0.32
81 1 0.01
82 3 0.02
83 30 0.21
87 30 0.21
88 3 0.02
89 1 0.01
90 29 0.20
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (80 bp):
TGTAATCTCAAGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCC
TTTAATCCGCTCCAT
Found at i:3586464 original size:44 final size:44
Alignment explanation
Indices: 3586398--3586667 Score: 161
Period size: 44 Copynumber: 6.3 Consensus size: 44
3586388 CCTTTAATCC
* * *
3586398 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * **
3586442 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGA-AATTCTTTGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T-ACTA-TCTTTGACCT
* * * * *
3586488 GTTCCACTATAATCTCAGGGAGATAAGA--CCTGA--TGTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-ATCTTTGACCT
* * * *
3586529 TCTCTACTGTAA-CTTCAGAGAGATAAGA-T-C---CTTTAATCC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTATCTTTGA-CCT
* * * * *
3586568 GCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
* * * *
3586612 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCT-TCTTTAACCA
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-TACTATCTTTGACCT
3586656 GCTCCACTGTAA
1 GCTCCACTGTAA
3586668 CCAATGAAGG
Statistics
Matches: 168, Mismatches: 41, Indels: 34
0.69 0.17 0.14
Matches are distributed among these distances:
39 23 0.14
40 4 0.02
41 29 0.17
43 1 0.01
44 72 0.43
45 5 0.03
46 34 0.20
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGACCT
Found at i:3586616 original size:170 final size:170
Alignment explanation
Indices: 3586327--3586643 Score: 616
Period size: 170 Copynumber: 1.9 Consensus size: 170
3586317 TGCTCCGCTG
3586327 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
*
3586392 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCTTTGACCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGACCTGCTCCGCTGTAATCT
3586457 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
131 CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
3586497 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
1 TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
*
3586562 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGATCTGCTCCGCTGTAATCT
66 TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGACCTGCTCCGCTGTAATCT
3586627 CAGGGAGATAAGATCTG
131 CAGGGAGATAAGATCTG
3586644 CTTCTTTAAC
Statistics
Matches: 145, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
170 145 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (170 bp):
TAATCTCAGGGAGATAAGACCTGATGTGATCTTCTCTACTGTAACTTCAGAGAGATAAGATCCTT
TAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTACTATCATTGACCTGCTCCGCTGTAATCT
CAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTA
Found at i:3586637 original size:83 final size:82
Alignment explanation
Indices: 3586365--3586641 Score: 267
Period size: 83 Copynumber: 3.3 Consensus size: 82
3586355 ATCTTCTCTA
3586365 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
1 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
*
3586430 TATCTTTGACCTGCTCCG
66 TATC-TTGATCTGCTCCG
* ** * * * * *
3586448 CTGTAA-TCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTGTTCCACTATAATCTCAGGGAGAT
1 CTGTAACT-TCAGAGAGATAAGATC-------CTTTAATCCGCTCCATTGTAATCTCAAGGAGAT
* * * * **
3586512 AAGA--CCTGAT-GTGATCTTCTCTA
58 AGGATTACT-ATCTTGATCTGCTCCG
3586535 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
1 CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
3586600 TATCATTGATCTGCTCCG
66 TATC-TTGATCTGCTCCG
*
3586618 CTGTAA-TCTCAGGGAGATAAGATC
1 CTGTAACT-TCAGAGAGATAAGATC
3586642 TGCTTCTTTA
Statistics
Matches: 149, Mismatches: 30, Indels: 30
0.71 0.14 0.14
Matches are distributed among these distances:
80 29 0.19
81 2 0.01
82 4 0.03
83 51 0.34
87 29 0.19
88 3 0.02
89 2 0.01
90 29 0.19
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (82 bp):
CTGTAACTTCAGAGAGATAAGATCCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGATTAC
TATCTTGATCTGCTCCG
Found at i:3587812 original size:21 final size:21
Alignment explanation
Indices: 3587786--3587832 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3587776 GGTATAGCAG
*
3587786 GATCACCACATGCCCCAATCT
1 GATCACCACATACCCCAATCT
** *
3587807 GATCACTTCATACCCCATTCT
1 GATCACCACATACCCCAATCT
3587828 GATCA
1 GATCA
3587833 ATATTTGAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.26
Consensus pattern (21 bp):
GATCACCACATACCCCAATCT
Found at i:3588843 original size:9 final size:9
Alignment explanation
Indices: 3588831--3588859 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
3588821 CATATTTTTA
3588831 TTTTGATTT
1 TTTTGATTT
3588840 TTTTGA-TT
1 TTTTGATTT
3588848 TTTTGATTT
1 TTTTGATTT
3588857 TTT
1 TTT
3588860 GAATTCATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.10, T:0.79
Consensus pattern (9 bp):
TTTTGATTT
Found at i:3588849 original size:7 final size:8
Alignment explanation
Indices: 3588831--3588861 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
3588821 CATATTTTTA
3588831 TTTTGATTT
1 TTTTGA-TT
3588840 TTTTGATT
1 TTTTGATT
3588848 TTTTGATT
1 TTTTGATT
3588856 TTTTGA
1 TTTTGA
3588862 ATTCATGAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.74
Consensus pattern (8 bp):
TTTTGATT
Found at i:3591469 original size:19 final size:20
Alignment explanation
Indices: 3591440--3591488 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
3591430 CACTTCGTGA
* *
3591440 AAATCTAATGCATATG-ATG
1 AAATGTAATGCAGATGCATG
*
3591459 CAATGTAATGCAGATGCATG
1 AAATGTAATGCAGATGCATG
3591479 AAATG-AATGC
1 AAATGTAATGC
3591489 CTAAAGAGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (20 bp):
AAATGTAATGCAGATGCATG
Done.