Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 14 of 335
Found at i:4902255 original size:31 final size:31
Alignment explanation
Indices: 4902220--4902279 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
4902210 ATGATTGAAT
*
4902220 TATTCAAAAAATTTTATTCAAGTCCCTAAAC
1 TATTCAAAAAATTTTATTCAAGTCACTAAAC
* *
4902251 TATTCAAAAATTTTTATTTAAGTCACTAA
1 TATTCAAAAAATTTTATTCAAGTCACTAA
4902280 GTGGTTAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (31 bp):
TATTCAAAAAATTTTATTCAAGTCACTAAAC
Found at i:4905186 original size:15 final size:15
Alignment explanation
Indices: 4905168--4905210 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
4905158 ATTCAATGTT
*
4905168 TAATAATTTAAAAAG
1 TAATAATTTAAAAAA
*
4905183 TAATTATTTGAAAAAA
1 TAATAATTT-AAAAAA
*
4905199 TATTAATTTAAA
1 TAATAATTTAAA
4905211 TTGAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (15 bp):
TAATAATTTAAAAAA
Found at i:4923302 original size:26 final size:26
Alignment explanation
Indices: 4923270--4923333 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
4923260 ACACTTGAAT
4923270 TTTTCCAAAGCACTTCTCAAAAATAC
1 TTTTCCAAAGCACTTCTCAAAAATAC
* * *
4923296 TTTTCCACAA-CACTTTTCAAAAGTAT
1 TTTTCCA-AAGCACTTCTCAAAAATAC
*
4923322 TTTTCAAAAGCA
1 TTTTCCAAAGCA
4923334 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 2 0.06
26 28 0.88
27 2 0.06
ACGTcount: A:0.38, C:0.23, G:0.05, T:0.34
Consensus pattern (26 bp):
TTTTCCAAAGCACTTCTCAAAAATAC
Found at i:4923622 original size:7 final size:7
Alignment explanation
Indices: 4923581--4923620 Score: 71
Period size: 7 Copynumber: 5.7 Consensus size: 7
4923571 AACCACCAAT
4923581 TCACCTA
1 TCACCTA
4923588 TCACCTA
1 TCACCTA
4923595 TCACCTA
1 TCACCTA
4923602 TCACCTA
1 TCACCTA
*
4923609 TCACCAA
1 TCACCTA
4923616 TCACC
1 TCACC
4923621 AAAACCCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.30, C:0.45, G:0.00, T:0.25
Consensus pattern (7 bp):
TCACCTA
Found at i:4926235 original size:14 final size:14
Alignment explanation
Indices: 4926218--4926273 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 14
4926208 TGATTCATTA
*
4926218 AATTTTATAATATT
1 AATTTTATAATAAT
4926232 AATTATTA-AA-AAT
1 AATT-TTATAATAAT
4926245 AATTTTATAAT--T
1 AATTTTATAATAAT
*
4926257 AAATTTA-AATAAT
1 AATTTTATAATAAT
4926270 AATT
1 AATT
4926274 CGATTTGTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 11
0.71 0.06 0.23
Matches are distributed among these distances:
11 3 0.09
12 10 0.29
13 12 0.35
14 6 0.18
15 3 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AATTTTATAATAAT
Found at i:4926270 original size:25 final size:27
Alignment explanation
Indices: 4926218--4926273 Score: 73
Period size: 25 Copynumber: 2.1 Consensus size: 27
4926208 TGATTCATTA
*
4926218 AATTTTATAATATTAATTATTAAAAAT
1 AATTTTATAATATTAAATATTAAAAAT
4926245 AATTTTAT-A-ATTAAAT-TTAAATAAT
1 AATTTTATAATATTAAATATTAAA-AAT
4926270 AATT
1 AATT
4926274 CGATTTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 5 0.19
25 13 0.48
26 1 0.04
27 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
AATTTTATAATATTAAATATTAAAAAT
Found at i:4927532 original size:21 final size:21
Alignment explanation
Indices: 4927503--4927545 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4927493 ATGATTTAAA
*
4927503 TCTCAAATATTGTTATAAGTG
1 TCTCAAATATTGGTATAAGTG
* *
4927524 TCTCGAATATTGGTATAGGTG
1 TCTCAAATATTGGTATAAGTG
4927545 T
1 T
4927546 ATAATAGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (21 bp):
TCTCAAATATTGGTATAAGTG
Found at i:4928039 original size:23 final size:23
Alignment explanation
Indices: 4928011--4928054 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
4928001 TTTATACTAT
4928011 TCTCTGTCTTTTAACACGCTTTC
1 TCTCTGTCTTTTAACACGCTTTC
*
4928034 TCTCTGTCTTTTGACACGCTT
1 TCTCTGTCTTTTAACACGCTT
4928055 CTTTCTTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.30, G:0.11, T:0.48
Consensus pattern (23 bp):
TCTCTGTCTTTTAACACGCTTTC
Found at i:4928699 original size:23 final size:23
Alignment explanation
Indices: 4928671--4928715 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4928661 AAGAGAAAGG
4928671 AGAAGATTGCGTTGAAAAATGGA
1 AGAAGATTGCGTTGAAAAATGGA
*
4928694 AGAAGATTGTGTTGAAAAATGG
1 AGAAGATTGCGTTGAAAAATGG
4928716 CAAATCTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.02, G:0.31, T:0.24
Consensus pattern (23 bp):
AGAAGATTGCGTTGAAAAATGGA
Found at i:4934236 original size:24 final size:24
Alignment explanation
Indices: 4934204--4934250 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4934194 GTAATTCTTA
4934204 AAAAAAATTAAGATTAAATATTTT
1 AAAAAAATTAAGATTAAATATTTT
4934228 AAAAAAATTAAGATTAAATATTT
1 AAAAAAATTAAGATTAAATATTT
4934251 CTTTTTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AAAAAAATTAAGATTAAATATTTT
Found at i:4934994 original size:23 final size:24
Alignment explanation
Indices: 4934949--4934996 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
4934939 AAATAAAAAA
4934949 ATTTAAAATATAATAAATCAAATAT
1 ATTTAAAATATAATAAA-CAAATAT
4934974 ATTTAAAAATATAA-AAA-AAATAT
1 ATTT-AAAATATAATAAACAAATAT
4934997 TAAAACAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 6 0.27
25 7 0.32
26 9 0.41
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (24 bp):
ATTTAAAATATAATAAACAAATAT
Found at i:4944612 original size:22 final size:22
Alignment explanation
Indices: 4944587--4944630 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
4944577 TTTATTTTAA
*
4944587 ATATTT-TTTTTTAATATTATAT
1 ATATTTATTTTGTAAT-TTATAT
4944609 ATATTTATTTTGTAATTTATAT
1 ATATTTATTTTGTAATTTATAT
4944631 TCAGAGTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
ATATTTATTTTGTAATTTATAT
Found at i:4950914 original size:15 final size:15
Alignment explanation
Indices: 4950877--4950914 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
4950867 AAATTATCAC
4950877 ATATTTT-TTCTTTA
1 ATATTTTATTCTTTA
*
4950891 ATA-TTTATTTTTTA
1 ATATTTTATTCTTTA
4950905 ATATTTTATT
1 ATATTTTATT
4950915 ATATCATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 3 0.14
14 12 0.57
15 6 0.29
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (15 bp):
ATATTTTATTCTTTA
Found at i:4964877 original size:21 final size:20
Alignment explanation
Indices: 4964853--4964894 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
4964843 TGCTGTTTTA
4964853 TTTTGCTGTTAAA-ATCACTTT
1 TTTTG-TGTTAAACATCA-TTT
*
4964874 TTTTGTTTTAAACATCATTT
1 TTTTGTGTTAAACATCATTT
4964894 T
1 T
4964895 CACCTTTGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.24, C:0.12, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTGTGTTAAACATCATTT
Found at i:4976280 original size:18 final size:18
Alignment explanation
Indices: 4976246--4976294 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
4976236 ACACATAAAG
4976246 TTAGATAAAAAAACACT-T
1 TTAGAT-AAAAAACACTAT
* *
4976264 TTGAGGTAAAAAGCACTAT
1 TT-AGATAAAAAACACTAT
4976283 TTAGATAAAAAA
1 TTAGATAAAAAA
4976295 AATATTGTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 19 0.76
19 6 0.24
ACGTcount: A:0.53, C:0.08, G:0.12, T:0.27
Consensus pattern (18 bp):
TTAGATAAAAAACACTAT
Found at i:4984313 original size:27 final size:27
Alignment explanation
Indices: 4984283--4984334 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
4984273 TTAAAATTTA
*
4984283 ATTTTAAATGTTAAATTGATTAATGGT
1 ATTTTAAATGTTAAATTGATGAATGGT
4984310 ATTTTAAATGTTAAATTGATGAATG
1 ATTTTAAATGTTAAATTGATGAATG
4984335 TAATATGTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (27 bp):
ATTTTAAATGTTAAATTGATGAATGGT
Found at i:4984586 original size:21 final size:21
Alignment explanation
Indices: 4984562--4984627 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
4984552 ACTCATATGA
*
4984562 GTTTCAGTTTAACCCTTCTGG
1 GTTTCAATTTAACCCTTCTGG
* * *
4984583 GTTTCAATTTAGCTCTTCTGA
1 GTTTCAATTTAACCCTTCTGG
* * *
4984604 GCTTCAAATTAA-CCTTATGG
1 GTTTCAATTTAACCCTTCTGG
4984624 GTTT
1 GTTT
4984628 TTGTTCAGCT
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 8 0.24
21 26 0.76
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.44
Consensus pattern (21 bp):
GTTTCAATTTAACCCTTCTGG
Found at i:4984657 original size:41 final size:42
Alignment explanation
Indices: 4984557--4984670 Score: 122
Period size: 41 Copynumber: 2.7 Consensus size: 42
4984547 AGTTAACTCA
* * *
4984557 TATGAGTTTCAGTTTAACCCTTCTGGGTTTCAATTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCAATTCAGCTCT
* ** ***
4984599 TCTGAGCTTCAAATTAA-CCTTATGGGTTTTTGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTCAATTCAGCTCT
* *
4984640 TATGAGCTTCCGTTTAACCCTTACGGGTTTC
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTC
4984671 TATTTAACAC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
41 32 0.57
42 24 0.43
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCAATTCAGCTCT
Found at i:4988726 original size:49 final size:50
Alignment explanation
Indices: 4988671--4988790 Score: 163
Period size: 49 Copynumber: 2.4 Consensus size: 50
4988661 ATCTAGTACG
* **
4988671 CATAGTAGCCTGCACTTAGTACTACACATGCGACC-AATTATCCAG-TACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCAT-CAGATACA
* * *
4988720 CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACA
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCAGATACA
4988770 CATAGTAGCCTGCACTTAGTA
1 CATAGTAGCCTGCACTTAGTA
4988791 GTAGTCTGCA
Statistics
Matches: 62, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
49 34 0.55
50 28 0.45
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (50 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCTAACCATCAGATACA
Found at i:4988794 original size:17 final size:17
Alignment explanation
Indices: 4988772--4988807 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4988762 CTGATACACA
4988772 TAGTAGCCTGCACTTAG
1 TAGTAGCCTGCACTTAG
*
4988789 TAGTAGTCTGCACTTAG
1 TAGTAGCCTGCACTTAG
4988806 TA
1 TA
4988808 CTACACACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (17 bp):
TAGTAGCCTGCACTTAG
Found at i:4992532 original size:46 final size:44
Alignment explanation
Indices: 4992480--4992565 Score: 136
Period size: 46 Copynumber: 1.9 Consensus size: 44
4992470 CAGAACGAAA
*
4992480 TGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAAGAT
1 TGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAGACAAGAT
*
4992526 TGAGCCATGTAAGTCCATATTATATATGGCATTGGAGACA
1 TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACA
4992566 GGAATAATTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 17 0.45
46 21 0.55
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (44 bp):
TGAGCCATGTAAGTCCATATTAAATATGGCATTGGAGACAAGAT
Found at i:4992579 original size:44 final size:45
Alignment explanation
Indices: 4992482--4992606 Score: 135
Period size: 44 Copynumber: 2.8 Consensus size: 45
4992472 GAACGAAATG
* * *
4992482 AGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAAGATTG
1 AGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAAGAATA
* *
4992528 AGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATA
1 AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
** * * *
4992572 ATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
4992607 CAGGATATTG
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 35 0.53
45 1 0.02
46 30 0.45
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.28
Consensus pattern (45 bp):
AGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAAGAATA
Found at i:4995306 original size:47 final size:46
Alignment explanation
Indices: 4995154--4995330 Score: 182
Period size: 47 Copynumber: 3.8 Consensus size: 46
4995144 TGTAACCCGC
* * * *
4995154 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
* * *
4995200 CCATAAGTAAACTCGGATTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC-G--GAC-A-TTCACAT
* * *
4995250 -C-TCA-CGAACTCAGACTCAACTCAACGAGTTCGGACATTCCACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATT-CACAT
4995294 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
4995331 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 15, Indels: 19
0.76 0.11 0.14
Matches are distributed among these distances:
42 2 0.02
43 1 0.01
44 6 0.06
45 1 0.01
46 34 0.32
47 52 0.49
48 2 0.02
49 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACAT
Found at i:4995322 original size:94 final size:93
Alignment explanation
Indices: 4995162--4995333 Score: 263
Period size: 94 Copynumber: 1.8 Consensus size: 93
4995152 GCCCATAAGT
* * * * *
4995162 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTAAACTCGGATTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTAAACTCGGACTCAACTCAA
4995227 CGAGTTCAGATGCCTAGTTACATCTCAC
66 CGAGTTCAGATGCCTAGTTACATCTCAC
* *
4995255 GAACTCAGACTCAACTCAACGAGTTCGGACATTCCACATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATT-CACATCCATAAGTAAACTCGGACTCAACTCA
*
4995320 ACGAGTTCGGATGC
65 ACGAGTTCAGATGC
4995334 TCAACCATTC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 29 0.41
94 41 0.59
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTAAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:4995786 original size:30 final size:30
Alignment explanation
Indices: 4995752--4995811 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
4995742 CCTTAATACG
4995752 AACTTTGGCAAAATTAC-CATTTTGCCCCTA
1 AACTTTGGCAAAATTACAC-TTTTGCCCCTA
* *
4995782 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGCAAAATTACACTTTTGCCCCTA
4995812 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 26 0.96
31 1 0.04
ACGTcount: A:0.28, C:0.27, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCCTA
Found at i:4997983 original size:13 final size:13
Alignment explanation
Indices: 4997962--4997991 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
4997952 ATATAACCGA
4997962 TTCATATAGCCAT
1 TTCATATAGCCAT
*
4997975 TTCATATAGTCAT
1 TTCATATAGCCAT
4997988 TTCA
1 TTCA
4997992 AAGTGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:5005803 original size:201 final size:198
Alignment explanation
Indices: 5005404--5005804 Score: 730
Period size: 198 Copynumber: 2.0 Consensus size: 198
5005394 CATAAGCAAA
*
5005404 AAGTTAGTTAATATTGGAGAACAAGGGTAGAGAAGATACAGACACAGATATCTAGCAGATATCTT
1 AAGTTAGTTAATATTGGAGAACAAGGGTAGAGAAGATACAGACACAGAGATCTAGCAGATATCTT
5005469 AAAGCTAAGATATCAAAAAGGGTAGAGATGATACCCATAAGTATGGTTGAAGAATCAACATCTAA
66 AAAGCTAAGATATCAAAAAGGGTAGAGATGATACCCATAAGTATGGTTGAAGAATCAACATCTAA
5005534 AAGGATGCTTTTACAATTATAATGCATGTACCAGAAAACTAGCAACTGAAGCTTACAAGTGGTGG
131 AAGGATGCTTTTACAATTATAATGCATGTACCAGAAAACTAGCAACTGAAGCTTACAAGTGGTGG
5005599 TCG
196 TCG
* *
5005602 AAGTTGGTTAATATTGGAGAACAAGGGTAGAGAAGATACAGACACGGAGATCTAGCAGATATCTT
1 AAGTTAGTTAATATTGGAGAACAAGGGTAGAGAAGATACAGACACAGAGATCTAGCAGATATCTT
5005667 AAAGCTAAGATATCAAAAAGGGTAGAGATGATACCCATAATAAGTATGGTTGAAGAATCAACATC
66 AAAGCTAAGATATCAAAAAGGGTAGAGATGATACCC---ATAAGTATGGTTGAAGAATCAACATC
* *
5005732 TAAAAGGATGCTTTTACAATTATAATGCATGTACTATAAAACTAGCAACTGAAGCTTACAAGTGG
128 TAAAAGGATGCTTTTACAATTATAATGCATGTACCAGAAAACTAGCAACTGAAGCTTACAAGTGG
5005797 TGGTCG
193 TGGTCG
5005803 AA
1 AA
5005805 TTCGAGCAGT
Statistics
Matches: 195, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
198 98 0.50
201 97 0.50
ACGTcount: A:0.41, C:0.13, G:0.22, T:0.24
Consensus pattern (198 bp):
AAGTTAGTTAATATTGGAGAACAAGGGTAGAGAAGATACAGACACAGAGATCTAGCAGATATCTT
AAAGCTAAGATATCAAAAAGGGTAGAGATGATACCCATAAGTATGGTTGAAGAATCAACATCTAA
AAGGATGCTTTTACAATTATAATGCATGTACCAGAAAACTAGCAACTGAAGCTTACAAGTGGTGG
TCG
Found at i:5012435 original size:46 final size:46
Alignment explanation
Indices: 5012368--5012496 Score: 231
Period size: 46 Copynumber: 2.8 Consensus size: 46
5012358 TGTAACCCGC
* * *
5012368 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5012414 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
5012460 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
5012497 TGCTCAACCA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 80 1.00
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:5012515 original size:46 final size:45
Alignment explanation
Indices: 5012373--5012515 Score: 146
Period size: 46 Copynumber: 3.1 Consensus size: 45
5012363 CCCGCCCATA
* ** * *
5012373 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
*** *
5012418 AAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCC-T
5012464 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-ACCATCCT
5012511 AGTGA
1 AGTGA
5012516 CATGTCACTT
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
46 82 0.93
47 1 0.01
48 5 0.06
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.21
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCACCATCCT
Found at i:5022551 original size:22 final size:22
Alignment explanation
Indices: 5022523--5022567 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5022513 TGGGCTGGTG
5022523 TAAGTCACATTTCATTGCTCAT
1 TAAGTCACATTTCATTGCTCAT
5022545 TAAGTCACATTTCATTGCTCAT
1 TAAGTCACATTTCATTGCTCAT
5022567 T
1 T
5022568 CGTGTTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (22 bp):
TAAGTCACATTTCATTGCTCAT
Found at i:5032804 original size:53 final size:53
Alignment explanation
Indices: 5032740--5032845 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
5032730 TATACGGAAT
*
5032740 TACGGAATCACATTATCACATTATACCGATGCCATAGCCCAGCTATGGTCTTA
1 TACGGAATCACATTATCACATTACACCGATGCCATAGCCCAGCTATGGTCTTA
*
5032793 TACGGAGTCACATTATCACATTACACCGATGCCATAGCCCAGCTATGGTCTTA
1 TACGGAATCACATTATCACATTACACCGATGCCATAGCCCAGCTATGGTCTTA
5032846 ATCGGGCGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.29, C:0.27, G:0.16, T:0.27
Consensus pattern (53 bp):
TACGGAATCACATTATCACATTACACCGATGCCATAGCCCAGCTATGGTCTTA
Found at i:5039814 original size:53 final size:53
Alignment explanation
Indices: 5039737--5039871 Score: 191
Period size: 53 Copynumber: 2.5 Consensus size: 53
5039727 CGCATATCAT
* * *
5039737 ACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATTAT
1 ACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATTAC
* * * *
5039790 ATCGATGCCATAGCTCAGCTATGGTCTTATACGGAGTCACATTATCACATTGC
1 ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC
5039843 ACCGATGCCATAGCCCAGCTATGGTCTTA
1 ACCGATGCCATAGCCCAGCTATGGTCTTA
5039872 ATCGGGCGCA
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 1 0.01
53 71 0.99
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (53 bp):
ACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATTAC
Found at i:5042668 original size:2 final size:2
Alignment explanation
Indices: 5042656--5042695 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
5042646 GGTTTGAGAC
*
5042656 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5042696 GGAAATGAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5045683 original size:21 final size:21
Alignment explanation
Indices: 5045657--5045697 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5045647 AGACAAGCGA
* *
5045657 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
5045678 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
5045698 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:5050933 original size:7 final size:7
Alignment explanation
Indices: 5050914--5050948 Score: 61
Period size: 7 Copynumber: 4.9 Consensus size: 7
5050904 TTGTCAAATT
5050914 TTTTATCA
1 TTTTAT-A
5050922 TTTTATA
1 TTTTATA
5050929 TTTTATA
1 TTTTATA
5050936 TTTTATA
1 TTTTATA
5050943 TTTTAT
1 TTTTAT
5050949 GTGACGAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.78
8 6 0.22
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:5051115 original size:25 final size:25
Alignment explanation
Indices: 5051069--5051141 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 25
5051059 ACTTTGAAAT
**
5051069 TTTTTAAACACAAATAACTAAATATAA
1 TTTTTAAA-A-AAATATTTAAATATAA
*
5051096 TTTTTAAAAAAATATTTAAATGTAA
1 TTTTTAAAAAAATATTTAAATATAA
** *
5051121 AATATAAAAAAA-ATTTAAATA
1 TTTTTAAAAAAATATTTAAATA
5051142 AATAATTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
24 8 0.21
25 22 0.56
26 1 0.03
27 8 0.21
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (25 bp):
TTTTTAAAAAAATATTTAAATATAA
Found at i:5059242 original size:2 final size:2
Alignment explanation
Indices: 5059235--5059268 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5059225 AAGGCCGCTA
5059235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5059269 TAACAATCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5062235 original size:46 final size:46
Alignment explanation
Indices: 5062183--5062358 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
5062173 TGGTTGAGCA
*
5062183 TCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
5062229 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
5062274 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
5062322 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5062359 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.58
47 27 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:5062339 original size:93 final size:93
Alignment explanation
Indices: 5062180--5062350 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
5062170 GGATGGTTGA
* **
5062180 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5062245 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * *
5062273 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
5062338 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
5062351 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTCGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:5065225 original size:2 final size:2
Alignment explanation
Indices: 5065218--5065245 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5065208 AGGCATAAAT
5065218 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5065246 GATTTAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5065308 original size:19 final size:18
Alignment explanation
Indices: 5065284--5065326 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
5065274 TAGATTTAAA
5065284 ATAAAATGCATAAAATA-AT
1 ATAAAAT-CA-AAAATATAT
*
5065303 ATAAAATCAACAATATAT
1 ATAAAATCAAAAATATAT
5065321 ATAAAA
1 ATAAAA
5065327 AATAATAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 5 0.23
18 10 0.45
19 7 0.32
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (18 bp):
ATAAAATCAAAAATATAT
Found at i:5065512 original size:23 final size:21
Alignment explanation
Indices: 5065482--5065524 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5065472 ATAGCTTAAT
5065482 ATAAATAATATATATAAAAATA
1 ATAAATAATATATA-AAAAATA
*
5065504 ATAATATAATATTTAAAAAAT
1 ATAA-ATAATATATAAAAAAT
5065525 GTTCATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
ATAAATAATATATAAAAAATA
Found at i:5066600 original size:28 final size:29
Alignment explanation
Indices: 5066568--5066651 Score: 127
Period size: 28 Copynumber: 3.0 Consensus size: 29
5066558 AACACACCAG
* *
5066568 TATAATCC-TCCAAAACACACCAGTATCA
1 TATAATCCATCCAAAACACACCAGAATAA
*
5066596 TATAATCCTTCC-AAACACACCAGAATAA
1 TATAATCCATCCAAAACACACCAGAATAA
5066624 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCCATCCAAAACACACCAGAATA
5066652 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.30, G:0.04, T:0.20
Consensus pattern (29 bp):
TATAATCCATCCAAAACACACCAGAATAA
Found at i:5066623 original size:23 final size:23
Alignment explanation
Indices: 5066554--5066651 Score: 72
Period size: 28 Copynumber: 3.8 Consensus size: 23
5066544 AAATGTCCAA
*
5066554 CCAAAACACACCAGTATAATCCT
1 CCAAAACACACCAGAATAATCCT
5066577 CCAAAACACACCAGTATCATATAATCCTT
1 CCAAAACACACCAG----A-ATAATCC-T
5066606 CC-AAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----A-ATAATCC-T
5066634 CCAAAACACACCAGAATA
1 CCAAAACACACCAGAATA
5066652 GCACAAAGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
23 14 0.22
24 3 0.05
25 1 0.02
28 32 0.50
29 14 0.22
ACGTcount: A:0.47, C:0.32, G:0.04, T:0.17
Consensus pattern (23 bp):
CCAAAACACACCAGAATAATCCT
Found at i:5075092 original size:17 final size:17
Alignment explanation
Indices: 5075070--5075113 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
5075060 GAGAAAATTA
5075070 AATATTTTTATTAAAAT
1 AATATTTTTATTAAAAT
* *
5075087 AATATTTTAATTAAGAT
1 AATATTTTTATTAAAAT
5075104 --TATTTTTATT
1 AATATTTTTATT
5075114 TAATAGACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.38
17 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
AATATTTTTATTAAAAT
Found at i:5075939 original size:6 final size:6
Alignment explanation
Indices: 5075928--5075961 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5075918 TGAATTATTC
5075928 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTT
5075962 TGTGTTTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:5076862 original size:19 final size:19
Alignment explanation
Indices: 5076826--5076864 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
5076816 GAAATATTTA
*
5076826 TTTTGATGTTTTTAATATT
1 TTTTGATGTTTATAATATT
5076845 TTTTGATGTATTATATATAT
1 TTTTGATGT-TTATA-ATAT
5076865 AAATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 4 0.24
21 4 0.24
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (19 bp):
TTTTGATGTTTATAATATT
Found at i:5079553 original size:24 final size:24
Alignment explanation
Indices: 5079509--5079555 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5079499 GATAAATTAA
5079509 TAATAATTCAAAAAAATTTAAAAG
1 TAATAATTCAAAAAAATTTAAAAG
* *
5079533 TAATACTT-AAAAATATATTAAAA
1 TAATAATTCAAAAAAAT-TTAAAA
5079556 ATTCTATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
TAATAATTCAAAAAAATTTAAAAG
Found at i:5085600 original size:2 final size:2
Alignment explanation
Indices: 5085593--5085635 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
5085583 CCTTTTCCTT
* * * *
5085593 TC TC TC TC TC TC TC TC TC CC TC TC CC TC TC CC TC TC CC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5085635 T
1 T
5085636 TTTGTTCTAA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.58, G:0.00, T:0.42
Consensus pattern (2 bp):
TC
Found at i:5085602 original size:6 final size:6
Alignment explanation
Indices: 5085594--5085634 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
5085584 CTTTTCCTTT
* *
5085594 CTCTCT CTCTCT CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
1 CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTCC CTCTC
5085635 TTTTGTTCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (6 bp):
CTCTCC
Found at i:5101284 original size:47 final size:47
Alignment explanation
Indices: 5101231--5101324 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
5101221 ATTTTGACAG
5101231 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
1 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
5101278 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
1 TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
5101325 CTCATTCAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (47 bp):
TTAACAATTTCTGAATGTGTTGCAACTAATCATTGAATATTCATGTA
Found at i:5104702 original size:67 final size:67
Alignment explanation
Indices: 5104594--5104729 Score: 272
Period size: 67 Copynumber: 2.0 Consensus size: 67
5104584 GCTTTGACTG
5104594 GTTTTGAAGGTTTTAAATCTCTGATAATGCTTGGTTTAATATTTTAACAGGGATGAGGAGTATGA
1 GTTTTGAAGGTTTTAAATCTCTGATAATGCTTGGTTTAATATTTTAACAGGGATGAGGAGTATGA
5104659 CC
66 CC
5104661 GTTTTGAAGGTTTTAAATCTCTGATAATGCTTGGTTTAATATTTTAACAGGGATGAGGAGTATGA
1 GTTTTGAAGGTTTTAAATCTCTGATAATGCTTGGTTTAATATTTTAACAGGGATGAGGAGTATGA
5104726 CC
66 CC
5104728 GT
1 GT
5104730 GGTAAGAGGA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 69 1.00
ACGTcount: A:0.28, C:0.09, G:0.24, T:0.39
Consensus pattern (67 bp):
GTTTTGAAGGTTTTAAATCTCTGATAATGCTTGGTTTAATATTTTAACAGGGATGAGGAGTATGA
CC
Found at i:5119209 original size:22 final size:22
Alignment explanation
Indices: 5119181--5119223 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
5119171 CATTTTCTAA
5119181 TAGATTTAATGAATAAATTCAC
1 TAGATTTAATGAATAAATTCAC
5119203 TAGATTTAATGAATAAATTCA
1 TAGATTTAATGAATAAATTCA
5119224 ATATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (22 bp):
TAGATTTAATGAATAAATTCAC
Found at i:5124696 original size:15 final size:14
Alignment explanation
Indices: 5124668--5124712 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
5124658 ATGATTTTAC
5124668 ATTTAATATTTATTA
1 ATTT-ATATTTATTA
*
5124683 ATGTTATTTTTATTAA
1 AT-TTATATTTATT-A
5124699 ATTTATATTTATTA
1 ATTTATATTTATTA
5124713 TGAAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 1 0.04
15 20 0.77
16 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
ATTTATATTTATTA
Found at i:5126626 original size:18 final size:18
Alignment explanation
Indices: 5126605--5126795 Score: 165
Period size: 18 Copynumber: 10.6 Consensus size: 18
5126595 TAACTGATTA
*
5126605 TTACTGAATAATTTACTG
1 TTACTGAATAATTGACTG
* *
5126623 TTACCGGATAATTGACTG
1 TTACTGAATAATTGACTG
* * *
5126641 TTACTGGAT-ATTAAACTA
1 TTACTGAATAATT-GACTG
* *
5126659 TTACTGAATAATTGAATA
1 TTACTGAATAATTGACTG
*
5126677 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
5126695 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
5126713 TCACTGAATGAATT-ACTG
1 TTACTGAAT-AATTGACTG
* *
5126731 TTACTGAATAACTTAATTG
1 TTACTGAATAA-TTGACTG
* *
5126750 TTACTGAATATTTGA-TT
1 TTACTGAATAATTGACTG
5126767 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
5126785 TTACTGGATAA
1 TTACTGAATAA
5126796 CCGATCAATT
Statistics
Matches: 143, Mismatches: 22, Indels: 16
0.79 0.12 0.09
Matches are distributed among these distances:
17 21 0.15
18 102 0.71
19 20 0.14
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.40
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:5126842 original size:36 final size:36
Alignment explanation
Indices: 5126802--5126875 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
5126792 ATAACCGATC
* **
5126802 AATTGATCGATACTGAATAACTGGTTATTATTGAAT
1 AATTGATCGATACCGAATAACTGACTATTATTGAAT
* * *
5126838 AATTGATTGTTACCGAATAATTGACTATTATTGAAT
1 AATTGATCGATACCGAATAACTGACTATTATTGAAT
5126874 AA
1 AA
5126876 ATAATTGTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (36 bp):
AATTGATCGATACCGAATAACTGACTATTATTGAAT
Found at i:5126873 original size:18 final size:18
Alignment explanation
Indices: 5126827--5126875 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5126817 AATAACTGGT
*
5126827 TATTATTGAATAATTGAT
1 TATTATTGAATAATTGAC
* **
5126845 TGTTACCGAATAATTGAC
1 TATTATTGAATAATTGAC
5126863 TATTATTGAATAA
1 TATTATTGAATAA
5126876 ATAATTGTTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (18 bp):
TATTATTGAATAATTGAC
Found at i:5128435 original size:16 final size:15
Alignment explanation
Indices: 5128414--5128447 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5128404 AGATGATTCC
*
5128414 AAATAAACATGTACGA
1 AAATAAACAGGTAC-A
5128430 AAATAAACAGGTACA
1 AAATAAACAGGTACA
5128445 AAA
1 AAA
5128448 GCTATAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.62, C:0.12, G:0.12, T:0.15
Consensus pattern (15 bp):
AAATAAACAGGTACA
Found at i:5128729 original size:8 final size:8
Alignment explanation
Indices: 5128716--5128742 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5128706 TATATAATTT
5128716 CAAGATCA
1 CAAGATCA
5128724 CAAGATCA
1 CAAGATCA
5128732 CAAGATCA
1 CAAGATCA
5128740 CAA
1 CAA
5128743 CGAGTCTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.52, C:0.26, G:0.11, T:0.11
Consensus pattern (8 bp):
CAAGATCA
Found at i:5138030 original size:24 final size:23
Alignment explanation
Indices: 5137992--5138038 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
5137982 TATTTTATTT
*
5137992 AATTATATTCTAAATTTAATTTTA
1 AATTATATTCTAAA-TAAATTTTA
5138016 AATTATATATC-AAATAAATTTTA
1 AATTATAT-TCTAAATAAATTTTA
5138039 TAACTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 11 0.52
25 2 0.10
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATATTCTAAATAAATTTTA
Found at i:5150894 original size:61 final size:61
Alignment explanation
Indices: 5150829--5150953 Score: 180
Period size: 61 Copynumber: 2.0 Consensus size: 61
5150819 ATACTAAACT
* * * *
5150829 AAACACAACAATTTATAATATAAT-CTTAAATTATTAATAAATTAATTTTAGAATAATTACA
1 AAACAAAACAATTTATAACATAATAC-TAAATTATTAACAAATTAATTTTAAAATAATTACA
* *
5150890 AAACAAAACAATTTATAACATAATACTAAATTATTGACAAATTAATTTTAAAATAATTATA
1 AAACAAAACAATTTATAACATAATACTAAATTATTAACAAATTAATTTTAAAATAATTACA
5150951 AAA
1 AAA
5150954 ATAAAAAAAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 56 0.98
62 1 0.02
ACGTcount: A:0.55, C:0.08, G:0.02, T:0.35
Consensus pattern (61 bp):
AAACAAAACAATTTATAACATAATACTAAATTATTAACAAATTAATTTTAAAATAATTACA
Found at i:5155852 original size:77 final size:77
Alignment explanation
Indices: 5155725--5155886 Score: 297
Period size: 77 Copynumber: 2.1 Consensus size: 77
5155715 AAGAACGCAG
5155725 GTGTCTTTGCTGAAACTGCATGGGCTGGACCTGCATACTATTTGCTATTATATATGCTTTGCAGT
1 GTGTCTTTGCTGAAACTGCATGGGCTGGACCTGCATACTATTTGCTATTATATATGCTTTGCAGT
*
5155790 CATGTAAGCTTT
66 CATATAAGCTTT
* *
5155802 GTGTCTTTGCTGAAACTGCATGGGCTGGAGCTGCATGCTATTTGCTATTATATATGCTTTGCAGT
1 GTGTCTTTGCTGAAACTGCATGGGCTGGACCTGCATACTATTTGCTATTATATATGCTTTGCAGT
5155867 CATATAAGCTTT
66 CATATAAGCTTT
5155879 GTGTCTTT
1 GTGTCTTT
5155887 ATTTCACTAG
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 82 1.00
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.40
Consensus pattern (77 bp):
GTGTCTTTGCTGAAACTGCATGGGCTGGACCTGCATACTATTTGCTATTATATATGCTTTGCAGT
CATATAAGCTTT
Found at i:5156840 original size:31 final size:31
Alignment explanation
Indices: 5156805--5156863 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5156795 CCGAGTCTGG
*
5156805 CTTCTCTGCTGAAGTTGCAGATAGATACTGA
1 CTTCTCTGCTGAAGATGCAGATAGATACTGA
*
5156836 CTTCTCTGCTGAAGATGCAGATTGATAC
1 CTTCTCTGCTGAAGATGCAGATAGATAC
5156864 GTTACCGCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.32
Consensus pattern (31 bp):
CTTCTCTGCTGAAGATGCAGATAGATACTGA
Found at i:5159771 original size:18 final size:18
Alignment explanation
Indices: 5159742--5159818 Score: 82
Period size: 18 Copynumber: 4.3 Consensus size: 18
5159732 TACGACCGTT
*
5159742 TACAGTACTATTCACGTA
1 TACAGCACTATTCACGTA
*
5159760 TATAGCACTATTCACGTA
1 TACAGCACTATTCACGTA
* * *
5159778 TACGGCACTATTTACGAA
1 TACAGCACTATTCACGTA
* * *
5159796 TACGGTACTGTTCACGTA
1 TACAGCACTATTCACGTA
5159814 TACAG
1 TACAG
5159819 TAGTTGGGAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (18 bp):
TACAGCACTATTCACGTA
Found at i:5168541 original size:81 final size:81
Alignment explanation
Indices: 5168405--5168566 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
5168395 GTTTAACACT
*
5168405 GCATTGTACATTCATGAAATTGGTTCGGTAAGAAATGTACAAAATAAAACTAGTGGTAAGAGAGG
1 GCATTGTACATTCATGAAATTGGTTCGGTAAGAAATGTACAAAATAAAACCAGTGGTAAGAGAGG
5168470 GTAACAGATATGCCTC
66 GTAACAGATATGCCTC
*
5168486 GCATTGTACATTCATGAAATTGGTTCGGTAAGAAATGTACAAAATAAAACCAGTGGTAATAGAGG
1 GCATTGTACATTCATGAAATTGGTTCGGTAAGAAATGTACAAAATAAAACCAGTGGTAAGAGAGG
5168551 GTAACAGATATGCCTC
66 GTAACAGATATGCCTC
5168567 TATCATAGAG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (81 bp):
GCATTGTACATTCATGAAATTGGTTCGGTAAGAAATGTACAAAATAAAACCAGTGGTAAGAGAGG
GTAACAGATATGCCTC
Found at i:5190841 original size:19 final size:17
Alignment explanation
Indices: 5190790--5190891 Score: 56
Period size: 18 Copynumber: 5.9 Consensus size: 17
5190780 ATATGTAATG
5190790 ATAATATTTA-TACAATT
1 ATAATATTTATTA-AATT
5190807 ATAATATTTTATTTAAATT
1 ATAATA-TTTA-TTAAATT
5190826 AGTAGATATTTATT-AATT
1 A-TA-ATATTTATTAAATT
5190844 AT--TA-TTATTATAATT
1 ATAATATTTATTA-AATT
*
5190859 AAGAAATATTTATT-AATT
1 -A-TAATATTTATTAAATT
* *
5190877 A-AATAATTATAAAAT
1 ATAATATTTATTAAAT
5190892 AAGATTTTTA
Statistics
Matches: 69, Mismatches: 3, Indels: 27
0.70 0.03 0.27
Matches are distributed among these distances:
13 5 0.07
14 2 0.03
15 12 0.17
16 4 0.06
17 8 0.12
18 13 0.19
19 9 0.13
20 13 0.19
21 3 0.04
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (17 bp):
ATAATATTTATTAAATT
Found at i:5190895 original size:33 final size:33
Alignment explanation
Indices: 5190831--5190895 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
5190821 AAATTAGTAG
* * *
5190831 ATATTTATTAATTATTATTATTATAATTAAGAA
1 ATATTTATTAATTATAATAATTATAAATAAGAA
5190864 ATATTTATTAATTA-AATAATTATAAAATAAGA
1 ATATTTATTAATTATAATAATTAT-AAATAAGA
5190896 TTTTTATGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 7 0.25
33 21 0.75
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (33 bp):
ATATTTATTAATTATAATAATTATAAATAAGAA
Found at i:5192147 original size:12 final size:12
Alignment explanation
Indices: 5192130--5192154 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5192120 GCTGACTACT
5192130 GTTACTGTTACC
1 GTTACTGTTACC
5192142 GTTACTGTTACC
1 GTTACTGTTACC
5192154 G
1 G
5192155 ATTCGACACT
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:0.16, C:0.24, G:0.20, T:0.40
Consensus pattern (12 bp):
GTTACTGTTACC
Found at i:5192182 original size:45 final size:45
Alignment explanation
Indices: 5192132--5192238 Score: 153
Period size: 45 Copynumber: 2.4 Consensus size: 45
5192122 TGACTACTGT
*
5192132 TACTGTTACCGTTACTGTTACCGATTC-GACACTTTGTGTGTCGAA
1 TACTGTTACCGTTACTGTTACAGATTCAG-CACTTTGTGTGTCGAA
* * *
5192177 TACTGTTACCGCTACTATTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
*
5192222 TACTGTTACTGTTACTG
1 TACTGTTACCGTTACTG
5192239 CTACTGCTAC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 53 0.98
46 1 0.02
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (45 bp):
TACTGTTACCGTTACTGTTACAGATTCAGCACTTTGTGTGTCGAA
Found at i:5192253 original size:18 final size:18
Alignment explanation
Indices: 5192222--5192256 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5192212 GTGTGTTGAA
* *
5192222 TACTGTTACTGTTACTGC
1 TACTGCTACCGTTACTGC
5192240 TACTGCTACCGTTACTG
1 TACTGCTACCGTTACTG
5192257 ATTACTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (18 bp):
TACTGCTACCGTTACTGC
Found at i:5194028 original size:16 final size:16
Alignment explanation
Indices: 5194007--5194040 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
5193997 TGACATAGAA
5194007 TTAGAGCTTTAAATTG
1 TTAGAGCTTTAAATTG
5194023 TTAGAGCTTTAAATTG
1 TTAGAGCTTTAAATTG
5194039 TT
1 TT
5194041 TATATGCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (16 bp):
TTAGAGCTTTAAATTG
Found at i:5195978 original size:3 final size:3
Alignment explanation
Indices: 5195966--5196001 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
5195956 ATCGAAATTT
5195966 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5196002 AATTGGAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:5200806 original size:22 final size:22
Alignment explanation
Indices: 5200767--5200825 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 22
5200757 GTTTTAAGAA
*
5200767 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
5200788 TTGTTTTAATATTTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
5200810 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
5200826 GATTTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.21
21 16 0.47
22 11 0.32
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:5200842 original size:26 final size:24
Alignment explanation
Indices: 5200796--5200844 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
5200786 ATTTGTTTTA
*
5200796 ATATTTATTTTTATGTTTTTAAAT
1 ATATTTATTTTTATATTTTTAAAT
5200820 ATATTTGATTTATTATATTTTTAAA
1 ATATTT-ATTT-TTATATTTTTAAA
5200845 ATTTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 4 0.18
26 12 0.55
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (24 bp):
ATATTTATTTTTATATTTTTAAAT
Found at i:5200855 original size:25 final size:26
Alignment explanation
Indices: 5200799--5200856 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
5200789 TGTTTTAATA
*
5200799 TTTATTT-TTATGTTTTTAAATATAT
1 TTTATTTATTATATTTTTAAATATAT
* *
5200824 TTGATTTATTATATTTTTAAA-ATTT
1 TTTATTTATTATATTTTTAAATATAT
5200849 TTTATTTA
1 TTTATTTA
5200857 ATAAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.67
Consensus pattern (26 bp):
TTTATTTATTATATTTTTAAATATAT
Found at i:5201167 original size:24 final size:23
Alignment explanation
Indices: 5201140--5201184 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
5201130 AATAATTTGT
5201140 ATATT-TTATAAATTTATAAAAAAA
1 ATATTATT-TAAATTT-TAAAAAAA
5201164 ATATTATTTAAATTTTAAAAA
1 ATATTATTTAAATTTTAAAAA
5201185 TATTCTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.30
24 12 0.60
25 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATATTATTTAAATTTTAAAAAAA
Found at i:5201223 original size:15 final size:15
Alignment explanation
Indices: 5201205--5201258 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 15
5201195 TTATCATCAA
5201205 AAAAATTTATATTAT
1 AAAAATTTATATTAT
5201220 AAAAATTT-TA-TA-
1 AAAAATTTATATTAT
* *
5201232 ATATATTTAT-TTAT
1 AAAAATTTATATTAT
*
5201246 AAAAAATTATATT
1 AAAAATTTATATT
5201259 GAATGACATA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
12 6 0.20
13 5 0.17
14 9 0.30
15 10 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAATTTATATTAT
Found at i:5203268 original size:34 final size:33
Alignment explanation
Indices: 5203230--5203311 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 33
5203220 AAATTCACAT
5203230 TTCAAA-TCACTTTCAATGCCAATT-TCACTTTCAA
1 TTCAAATTCACTTTCAAT-CCAATTCTCA--TTCAA
* *
5203264 TTCAAATTCACAATTCAATTCAATTCTCATTCAA
1 TTCAAATTCAC-TTTCAATCCAATTCTCATTCAA
5203298 TTCAAATTCACTTT
1 TTCAAATTCACTTT
5203312 TCCACTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 2 0.05
34 22 0.52
35 9 0.21
36 9 0.21
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.40
Consensus pattern (33 bp):
TTCAAATTCACTTTCAATCCAATTCTCATTCAA
Found at i:5203271 original size:18 final size:17
Alignment explanation
Indices: 5203230--5203311 Score: 87
Period size: 17 Copynumber: 4.8 Consensus size: 17
5203220 AAATTCACAT
5203230 TTCAAA-TCACTTTCAA
1 TTCAAATTCACTTTCAA
* *
5203246 TGCCAATTTCACTTTCAA
1 T-TCAAATTCACTTTCAA
*
5203264 TTCAAATTCACAATTCAA
1 TTCAAATTCAC-TTTCAA
* *
5203282 TTC-AATTCTCATTCAA
1 TTCAAATTCACTTTCAA
5203298 TTCAAATTCACTTT
1 TTCAAATTCACTTT
5203312 TCCACTTTTT
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
16 10 0.19
17 25 0.46
18 19 0.35
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.40
Consensus pattern (17 bp):
TTCAAATTCACTTTCAA
Found at i:5204478 original size:2 final size:2
Alignment explanation
Indices: 5204471--5204496 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5204461 ACTTTATTTC
5204471 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5204497 GTTACTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5204520 original size:3 final size:3
Alignment explanation
Indices: 5204506--5204567 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
5204496 TGTTACTTAC
* *
5204506 TAA TAT TAA TAA TAA TAA TACA TTA TAA TAA T-A TAA T-A TAA T-A
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
5204549 TAA T-A TAA TAA TATA TAA T
1 TAA TAA TAA TAA TA-A TAA T
5204568 TCATAAATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
2 8 0.16
3 36 0.73
4 5 0.10
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5204535 original size:10 final size:8
Alignment explanation
Indices: 5204506--5204567 Score: 58
Period size: 8 Copynumber: 7.5 Consensus size: 8
5204496 TGTTACTTAC
5204506 TAATATTAA
1 TAATA-TAA
5204515 TAATAATAA
1 TAAT-ATAA
5204524 TACATTATAA
1 TA-A-TATAA
5204534 TAATATAA
1 TAATATAA
5204542 T-ATA-ATA
1 TAATATA-A
5204549 TAATATAA
1 TAATATAA
5204557 TAATAT-A
1 TAATATAA
5204564 TAAT
1 TAAT
5204568 TCATAAATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
6 1 0.02
7 10 0.21
8 16 0.34
9 11 0.23
10 8 0.17
11 1 0.02
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATATAA
Found at i:5204535 original size:13 final size:11
Alignment explanation
Indices: 5204506--5204567 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 11
5204496 TGTTACTTAC
*
5204506 TAATATTAATAA
1 TAATAATAAT-A
5204518 TAATAATACATTA
1 TAATAATA-A-TA
5204531 TAATAATATAATA
1 TAAT-A-ATAATA
5204544 TAAT-ATAATA
1 TAATAATAATA
5204554 TAATAAT-ATA
1 TAATAATAATA
5204564 TAAT
1 TAAT
5204568 TCATAAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
10 17 0.39
11 2 0.05
12 7 0.16
13 12 0.27
14 3 0.07
15 3 0.07
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (11 bp):
TAATAATAATA
Found at i:5204543 original size:5 final size:5
Alignment explanation
Indices: 5204533--5204567 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
5204523 ATACATTATA
5204533 ATAAT ATAAT ATAAT ATAAT ATAAT A-ATAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT
5204568 TCATAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.04
5 26 0.93
6 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:5204692 original size:12 final size:12
Alignment explanation
Indices: 5204661--5204699 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
5204651 AATCATAATT
5204661 TAATAATT-TAA
1 TAATAATTATAA
*
5204672 TATAAAATTATAA
1 TA-ATAATTATAA
5204685 TAATAATTATAA
1 TAATAATTATAA
5204697 TAA
1 TAA
5204700 ATATCTATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 2 0.08
12 17 0.71
13 5 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:5204712 original size:24 final size:23
Alignment explanation
Indices: 5204658--5204714 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
5204648 AACAATCATA
5204658 ATTTAATAATTTAATATAAAATT
1 ATTTAATAATTTAATATAAAATT
* *
5204681 ATAATAATAATTATAATA-AATATCT
1 AT-TTAATAATT-TAATATAAAAT-T
5204706 ATTTAATAA
1 ATTTAATAA
5204715 CAAATACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 2 0.07
24 18 0.64
25 8 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTTAATAATTTAATATAAAATT
Found at i:5205015 original size:12 final size:12
Alignment explanation
Indices: 5204960--5205021 Score: 58
Period size: 12 Copynumber: 5.3 Consensus size: 12
5204950 ATTTTATTTC
5204960 ATAA-TATAATA
1 ATAATTATAATA
5204971 AT-ATTAATAATA
1 ATAATT-ATAATA
*
5204983 ATATTTA-AATA
1 ATAATTATAATA
* **
5204994 AAAACCATAATA
1 ATAATTATAATA
5205006 ATAATTATAATA
1 ATAATTATAATA
5205018 ATAA
1 ATAA
5205022 ATTGATAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
10 1 0.03
11 10 0.26
12 26 0.67
13 2 0.05
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATTATAATA
Found at i:5206361 original size:22 final size:23
Alignment explanation
Indices: 5206335--5206380 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
5206325 CAACCAAATC
5206335 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
5206357 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
5206380 A
1 A
5206381 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:5206386 original size:23 final size:23
Alignment explanation
Indices: 5206342--5206386 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5206332 ATCAATTCAA
*
5206342 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
5206365 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
5206387 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:5214388 original size:53 final size:53
Alignment explanation
Indices: 5214321--5214454 Score: 207
Period size: 53 Copynumber: 2.5 Consensus size: 53
5214311 ACAAGTGTGC
* *
5214321 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
* *
5214374 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
*
5214427 CCGTATAAGACCAT-GTCTGGGATATGGC
1 CCGTATAAGACCATAG-CTGGGCTATGGC
5214455 TTCAGTATGA
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
52 1 0.01
53 74 0.99
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTACAATGTGATAATGTGACT
Found at i:5221975 original size:53 final size:53
Alignment explanation
Indices: 5221834--5221984 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
5221824 ACAAGTGTGC
* **
5221834 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
5221887 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
5221940 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
5221985 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:5227318 original size:5 final size:5
Alignment explanation
Indices: 5227297--5227349 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
5227287 TGTTAAAATA
* *
5227297 TATAT TAAAT TATTAT TATAT TATAG TATAT TATATT ATATAT TATAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATA-T -TATAT TATAT
5227345 TATAT
1 TATAT
5227350 AAATAAGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.76
6 6 0.15
7 4 0.10
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:5227328 original size:10 final size:9
Alignment explanation
Indices: 5227294--5227350 Score: 59
Period size: 8 Copynumber: 6.6 Consensus size: 9
5227284 ATGTGTTAAA
5227294 ATATATATT
1 ATATATATT
*
5227303 AAAT-TATT
1 ATATATATT
5227311 AT-TATATT
1 ATATATATT
5227319 ATAGTATATT
1 ATA-TATATT
5227329 ATAT-TA-T
1 ATATATATT
5227336 ATATTATATT
1 ATA-TATATT
5227346 ATATA
1 ATATA
5227351 AATAAGTAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 5 0.12
8 14 0.35
9 8 0.20
10 13 0.32
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:5227340 original size:12 final size:12
Alignment explanation
Indices: 5227295--5227350 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
5227285 TGTGTTAAAA
*
5227295 TATATATTAAAT
1 TATATATTATAT
5227307 TAT-TATTATATT
1 TATATATTATA-T
5227319 ATAGTATATTATAT
1 -TA-TATATTATAT
5227333 TATATATTATAT
1 TATATATTATAT
5227345 TATATA
1 TATATA
5227351 AATAAGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 6 0.15
12 20 0.51
13 4 0.10
14 2 0.05
15 7 0.18
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (12 bp):
TATATATTATAT
Found at i:5228687 original size:18 final size:19
Alignment explanation
Indices: 5228666--5228704 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5228656 ATATATAGAT
5228666 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
5228684 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
5228703 AT
1 AT
5228705 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:5229054 original size:39 final size:39
Alignment explanation
Indices: 5228944--5229078 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
5228934 GACCTCGAGT
* * * *
5228944 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTACTTCGGCTAG-TC
** ** * *
5228985 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
* *
5229023 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTACTTCG-GCTAGTC
*
5229062 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
5229079 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTACTTCGGCTAGTC
Found at i:5230712 original size:51 final size:51
Alignment explanation
Indices: 5230641--5230754 Score: 183
Period size: 51 Copynumber: 2.2 Consensus size: 51
5230631 CTGATCACAT
* *
5230641 TTATCACTTGTTACTGATCAGATAAGTGTAGCTAAAACTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAACTACCACTTATCAC
*
5230692 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAGCTACCACTTATCAC
1 TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAACTACCACTTATCAC
* *
5230743 TTGTCGCTTGTC
1 TTATCACTTGTC
5230755 GCTTGTCACT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 58 1.00
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (51 bp):
TTATCACTTGTCACTGATCAGATAAATGTAGCTAAAACTACCACTTATCAC
Found at i:5233349 original size:77 final size:76
Alignment explanation
Indices: 5233246--5233389 Score: 218
Period size: 77 Copynumber: 1.9 Consensus size: 76
5233236 ATTACCTAGT
*
5233246 TTTCGAATTTTTCTTTACCAACTTTACTATTTGTCATGATTACAAATCCATGCTTATCTACTATC
1 TTTCGAATTTTTCTTTACCAACTTTACTATTTGTCATGATTACAAATCCATGCTTATCCACTATC
5233311 ACTTGACCTAA
66 ACTTGACCTAA
* * * *
5233322 TTTCTGAA-TTTTCTTTTAGCAGCTTTACTATTTGTCATGATTATAAATTCATGCTTATCCACTA
1 TTTC-GAATTTTTC-TTTACCAACTTTACTATTTGTCATGATTACAAATCCATGCTTATCCACTA
5233386 TCAC
64 TCAC
5233390 CTTTAATGGT
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
76 9 0.15
77 52 0.85
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (76 bp):
TTTCGAATTTTTCTTTACCAACTTTACTATTTGTCATGATTACAAATCCATGCTTATCCACTATC
ACTTGACCTAA
Found at i:5237928 original size:121 final size:121
Alignment explanation
Indices: 5237714--5237949 Score: 445
Period size: 121 Copynumber: 2.0 Consensus size: 121
5237704 TTTACGTCAC
5237714 ATATTTGGACTGATTTCAGGGTAAATCTAATTTGTCACAGTACTATGTCATGCCAAACCTAGCTA
1 ATATTTGGACTGATTTCAGGGTAAATCTAATTTGTCACAGTACTATGTCATGCCAAACCTAGCTA
5237779 ACATGTAGGAATCAGTACGCAAGAGGGCGATTTCAAGGTAATCCAATTCTCATGGT
66 ACATGTAGGAATCAGTACGCAAGAGGGCGATTTCAAGGTAATCCAATTCTCATGGT
* *
5237835 ATATTTGGACTGATTTCAGGGTAAATCTAATTTGTCTCAGTACTATGTCATGCCAAACCTAGCTG
1 ATATTTGGACTGATTTCAGGGTAAATCTAATTTGTCACAGTACTATGTCATGCCAAACCTAGCTA
*
5237900 ACATGTAGGAATCAGTACGCAAGGGGGCGATTTCAAGGTAATCCAATTCT
66 ACATGTAGGAATCAGTACGCAAGAGGGCGATTTCAAGGTAATCCAATTCT
5237950 TATGAACGTC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
121 112 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (121 bp):
ATATTTGGACTGATTTCAGGGTAAATCTAATTTGTCACAGTACTATGTCATGCCAAACCTAGCTA
ACATGTAGGAATCAGTACGCAAGAGGGCGATTTCAAGGTAATCCAATTCTCATGGT
Found at i:5245870 original size:3 final size:3
Alignment explanation
Indices: 5245864--5245910 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
5245854 TTTTTCTTAA
5245864 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5245911 AGTGTGATCT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5256524 original size:12 final size:12
Alignment explanation
Indices: 5256507--5256534 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5256497 TTTTTACCAT
5256507 ATTTGGAGTTGG
1 ATTTGGAGTTGG
5256519 ATTTGGAGTTGG
1 ATTTGGAGTTGG
5256531 ATTT
1 ATTT
5256535 TCAAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.46
Consensus pattern (12 bp):
ATTTGGAGTTGG
Found at i:5258327 original size:20 final size:20
Alignment explanation
Indices: 5258302--5258343 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
5258292 TGCATTTTCA
5258302 AAGATACCATGGTTTGAATT
1 AAGATACCATGGTTTGAATT
5258322 AAGATACCATGGTTTGAATT
1 AAGATACCATGGTTTGAATT
5258342 AA
1 AA
5258344 CTTTTTAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (20 bp):
AAGATACCATGGTTTGAATT
Found at i:5271008 original size:15 final size:16
Alignment explanation
Indices: 5270988--5271017 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
5270978 TTGCTTTTTT
5270988 TTAATAT-ATAAAAAA
1 TTAATATGATAAAAAA
5271003 TTAATATGATAAAAA
1 TTAATATGATAAAAA
5271018 CAGTGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (16 bp):
TTAATATGATAAAAAA
Found at i:5295278 original size:15 final size:15
Alignment explanation
Indices: 5295258--5295309 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
5295248 ACTACAAAAC
5295258 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
5295273 ATTTATAATTGAAATAAAT
1 ATTTATTATT--AAT--AT
*
5295292 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
5295307 ATT
1 ATT
5295310 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 14 0.47
17 5 0.17
19 11 0.37
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:5295295 original size:19 final size:19
Alignment explanation
Indices: 5295271--5295307 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5295261 TATTATTAAT
*
5295271 ATATTTATAATTGAAATAA
1 ATATTTATAATTAAAATAA
*
5295290 ATATTTATTATTAAAATA
1 ATATTTATAATTAAAATA
5295308 TTAATATTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:5295368 original size:15 final size:16
Alignment explanation
Indices: 5295348--5295377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5295338 AGAATATTAA
5295348 TTAAAA-TTATTATTT
1 TTAAAATTTATTATTT
5295363 TTAAAATTTATTATT
1 TTAAAATTTATTATT
5295378 AAAATAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAAATTTATTATTT
Found at i:5295603 original size:19 final size:19
Alignment explanation
Indices: 5295571--5295607 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5295561 TTTATAAATA
*
5295571 ATTTTCTATTAAACAAACT
1 ATTTTCTATAAAACAAACT
*
5295590 ATTTTTTATAAAACAAAC
1 ATTTTCTATAAAACAAAC
5295608 ACAATAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.14, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTTCTATAAAACAAACT
Found at i:5300316 original size:4 final size:4
Alignment explanation
Indices: 5300307--5300346 Score: 62
Period size: 4 Copynumber: 9.8 Consensus size: 4
5300297 TACTCAAATT
*
5300307 ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATGAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-AC ATA
5300347 TCTTGACATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 29 0.88
5 4 0.12
ACGTcount: A:0.50, C:0.20, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:5304991 original size:13 final size:13
Alignment explanation
Indices: 5304973--5304998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5304963 AATGAAGTCT
5304973 AACTATAAACGAG
1 AACTATAAACGAG
5304986 AACTATAAACGAG
1 AACTATAAACGAG
5304999 GAAAAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (13 bp):
AACTATAAACGAG
Found at i:5306572 original size:17 final size:15
Alignment explanation
Indices: 5306546--5306579 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 15
5306536 AAATTATACT
5306546 TTTATTTTTTAACATA
1 TTTATTTTTTAA-ATA
5306562 TTTATTTTTTTAAATA
1 TTTA-TTTTTTAAATA
5306578 TT
1 TT
5306580 AAATTATCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTATTTTTTAAATA
Found at i:5306976 original size:7 final size:7
Alignment explanation
Indices: 5306964--5306992 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5306954 TTCAAGTATA
5306964 AATAGAG
1 AATAGAG
5306971 AATAGAG
1 AATAGAG
5306978 AATAGAG
1 AATAGAG
5306985 AATAGAG
1 AATAGAG
5306992 A
1 A
5306993 GCATTTACTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.14
Consensus pattern (7 bp):
AATAGAG
Found at i:5321912 original size:9 final size:9
Alignment explanation
Indices: 5321898--5321936 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5321888 ATAGTTTAAT
5321898 AATAAAAGA
1 AATAAAAGA
5321907 AATAAAAGA
1 AATAAAAGA
*
5321916 AATAAAACA
1 AATAAAAGA
*
5321925 ATAGAAAAGA
1 A-ATAAAAGA
5321935 AA
1 AA
5321937 CAGAGAAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 19 0.73
10 7 0.27
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (9 bp):
AATAAAAGA
Found at i:5321966 original size:17 final size:14
Alignment explanation
Indices: 5321958--5321984 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5321948 AAGAAATAGG
5321958 AAAGAAAAAGAAAT
1 AAAGAAAAAGAAAT
5321972 AAAGAAAAAGAAA
1 AAAGAAAAAGAAA
5321985 GGGAGAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAGAAAT
Found at i:5322679 original size:16 final size:17
Alignment explanation
Indices: 5322646--5322694 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
5322636 ATATATGTGA
*
5322646 ATATTGATTTGTAATAG
1 ATATTGATTTGAAATAG
5322663 ATATTGA-TTGAAATAG
1 ATATTGATTTGAAATAG
*
5322679 AAAATGTGATTTGAAA
1 -ATAT-TGATTTGAAA
5322695 ACCCTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.30
17 10 0.37
18 3 0.11
19 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (17 bp):
ATATTGATTTGAAATAG
Found at i:5324665 original size:3 final size:3
Alignment explanation
Indices: 5324648--5324696 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
5324638 GAATGGTAAG
* *
5324648 TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5324696 T
1 T
5324697 TTGAATTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5327247 original size:25 final size:26
Alignment explanation
Indices: 5327200--5327249 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
5327190 ATGTGAAGTT
*
5327200 TTTTTAATTTTACAAATAGTGTTAAA
1 TTTTTAATTTTACAAATAATGTTAAA
**
5327226 TTTTTAATTTTTTAAA-AATGTTAA
1 TTTTTAATTTTACAAATAATGTTAA
5327250 TTAGGGACAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (26 bp):
TTTTTAATTTTACAAATAATGTTAAA
Found at i:5332437 original size:16 final size:16
Alignment explanation
Indices: 5332416--5332449 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
5332406 TTGTTGGATA
*
5332416 TGAATGTGTTTAGTAC
1 TGAATGTGCTTAGTAC
5332432 TGAATGTGCTTAGTAC
1 TGAATGTGCTTAGTAC
5332448 TG
1 TG
5332450 TTATCAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (16 bp):
TGAATGTGCTTAGTAC
Found at i:5340861 original size:46 final size:45
Alignment explanation
Indices: 5340809--5341012 Score: 188
Period size: 46 Copynumber: 4.5 Consensus size: 45
5340799 GTCGATGCCG
* * *
5340809 TGTCCCAGACAGGTCTTACACTGA-CACATGTAACCGT-GCTGACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCT---CGTAGCCGACGCA
*
5340855 TGTCCCATACATGTCTTACACT-AGCACATCTCGTAGCCGACGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATCTCGTAGCCGACGCA
* *
5340899 TGTCCCAGACATGTCTGACACTG-GCTATCATCTCG-AGGCCGATGCA
1 TGTCCCAGACATGTCTTACACTGAGC-A-CATCTCGTA-GCCGACGCA
* * * *
5340945 TGTCCCAGACATGTCTTACACTG-GCTC-TCATACTGTGGCTGATGCA
1 TGTCCCAGACATGTCTTACACTGAGCACATC-T-C-GTAGCCGACGCA
5340991 TGTCCCAGACATGTCTTACACT
1 TGTCCCAGACATGTCTTACACT
5341013 AGCCCTCGTC
Statistics
Matches: 137, Mismatches: 11, Indels: 20
0.82 0.07 0.12
Matches are distributed among these distances:
43 5 0.04
44 32 0.23
45 4 0.03
46 96 0.70
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (45 bp):
TGTCCCAGACATGTCTTACACTGAGCACATCTCGTAGCCGACGCA
Found at i:5341012 original size:92 final size:91
Alignment explanation
Indices: 5340852--5341068 Score: 249
Period size: 92 Copynumber: 2.4 Consensus size: 91
5340842 CCGTGCTGAC
*
5340852 GCATGTCCCATACATGTCTTACACTAG-CACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
1 GCATGTCCCATACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
* * *
5340916 ACACTGGCTATCATCTCGAGGCCGAT
66 ACACTAGCCATCATCTCAAGGCCGAT
* * * * *
5340942 GCATGTCCCAGACATGTCTTACACTGGCTCTCATACT-GTGGCTGATGCATGTCCCAGACATGTC
1 GCATGTCCCATACATGTCTTACACTGGC-CACAT-CTCGTAGCCGACGCATGTCCCAGACATGTC
* * * *
5341006 TTACACTAGCCCTCGTCTCAATGCCGAT
64 TGACACTAGCCATCATCTCAAGGCCGAT
*
5341034 GCCATGTCTCATACATGGTCTTACACTGGCACACA
1 G-CATGTCCCATACAT-GTCTTACACTGGC-CACA
5341069 AATCTCATGT
Statistics
Matches: 105, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
90 25 0.24
92 50 0.48
93 14 0.13
94 16 0.15
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (91 bp):
GCATGTCCCATACATGTCTTACACTGGCCACATCTCGTAGCCGACGCATGTCCCAGACATGTCTG
ACACTAGCCATCATCTCAAGGCCGAT
Found at i:5341035 original size:46 final size:44
Alignment explanation
Indices: 5340852--5341060 Score: 181
Period size: 46 Copynumber: 4.6 Consensus size: 44
5340842 CCGTGCTGAC
* *
5340852 GCATGTCCCATACATGTCTTACACTAGCACATC-TCGTA-GCCGAC
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCATC-TATGCCGAT
* * * *
5340896 GCATGTCCCAGACATGTCTGACACTGGCTATCATCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* * *
5340942 GCATGTCCCAGACATGTCTTACACTGGCTC-TCATACTGTGGCTGAT
1 GCATGTCCCAGACATGTCTTACACTAGC-CATCAT-CTAT-GCCGAT
* *
5340988 GCATGTCCCAGACATGTCTTACACTAGCCCTCGTCTCAATGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCCATCATCT--ATGCCGAT
* *
5341034 GCCATGTCTCATACATGGTCTTACACT
1 G-CATGTCCCAGACAT-GTCTTACACT
5341061 GGCACACAAA
Statistics
Matches: 137, Mismatches: 16, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
43 4 0.03
44 27 0.20
45 4 0.03
46 77 0.56
47 15 0.11
48 10 0.07
ACGTcount: A:0.22, C:0.32, G:0.19, T:0.27
Consensus pattern (44 bp):
GCATGTCCCAGACATGTCTTACACTAGCCATCATCTATGCCGAT
Done.