Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 16 of 378
Found at i:4367004 original size:16 final size:16
Alignment explanation
Indices: 4366973--4367005 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4366963 AAAATAATTA
4366973 AATATGTATGTTTAAT
1 AATATGTATGTTTAAT
4366989 AATAT-TATGTTATAAT
1 AATATGTATGTT-TAAT
4367005 A
1 A
4367006 TTCATTATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.48
Consensus pattern (16 bp):
AATATGTATGTTTAAT
Found at i:4371346 original size:4 final size:4
Alignment explanation
Indices: 4371337--4371361 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4371327 ATACAATTTA
4371337 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
4371362 GTTAAAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:4376374 original size:27 final size:27
Alignment explanation
Indices: 4376336--4376392 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
4376326 ATAATAAAAT
*
4376336 ACTGGTCTTGCCTCTGTCAGAGGCGGC
1 ACTGGTCTTGCCTCTGCCAGAGGCGGC
*
4376363 ACTGGTCTTGCCTTTGCCAGAGGCGGC
1 ACTGGTCTTGCCTCTGCCAGAGGCGGC
4376390 ACT
1 ACT
4376393 AGTTGGTATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.12, C:0.30, G:0.32, T:0.26
Consensus pattern (27 bp):
ACTGGTCTTGCCTCTGCCAGAGGCGGC
Found at i:4376688 original size:81 final size:81
Alignment explanation
Indices: 4376534--4376699 Score: 289
Period size: 81 Copynumber: 2.0 Consensus size: 81
4376524 AAAAACAAAA
*
4376534 ATTTAAATACTATACCTAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACAT
1 ATTTAAATACTATACATAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACAT
*
4376599 ATTTTTTTATAATTTT
66 ATTGTTTTATAATTTT
*
4376615 ATTTAAATATTTATACATAATAAAACATGTATCTCATTACAATAATAGTT-TTTTCCAAATAACA
1 ATTTAAATA-CTATACATAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACA
4376679 TATTGTTTTATAATTTT
65 TATTGTTTTATAATTTT
4376696 ATTT
1 ATTT
4376700 CTTATTAACT
Statistics
Matches: 81, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
81 43 0.53
82 38 0.47
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (81 bp):
ATTTAAATACTATACATAATAAAACATGTATCTCATTACAATAATAGTTATTTTCCAAATAACAT
ATTGTTTTATAATTTT
Found at i:4377140 original size:27 final size:27
Alignment explanation
Indices: 4377102--4377155 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
4377092 ATACCAAATG
* *
4377102 GTGCCGCCTCTGGCAGAGGCAAGACCA
1 GTGCCGCCTCTGACAGAGACAAGACCA
4377129 GTGCCGCCTCTGACAGAGACAAGACCA
1 GTGCCGCCTCTGACAGAGACAAGACCA
4377156 ATATTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.26, C:0.33, G:0.30, T:0.11
Consensus pattern (27 bp):
GTGCCGCCTCTGACAGAGACAAGACCA
Found at i:4381141 original size:30 final size:30
Alignment explanation
Indices: 4381107--4381169 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4381097 CCTTATTTTA
4381107 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
*
4381137 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAGACAT
4381167 TTG
1 TTG
4381170 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGACAT
Found at i:4382413 original size:20 final size:20
Alignment explanation
Indices: 4382388--4382427 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
4382378 ACAGCATGTA
4382388 AGTTCAATTCTTGATTATTT
1 AGTTCAATTCTTGATTATTT
4382408 AGTTCAATTCTTGATTATTT
1 AGTTCAATTCTTGATTATTT
4382428 CTTGTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.10, G:0.10, T:0.55
Consensus pattern (20 bp):
AGTTCAATTCTTGATTATTT
Found at i:4383217 original size:52 final size:50
Alignment explanation
Indices: 4383156--4383366 Score: 243
Period size: 52 Copynumber: 4.2 Consensus size: 50
4383146 ATGGAAAAGG
* *
4383156 TGTGATATGTGCGCCCGTATAAGACCATAGTTGGGCTATGGCATCGGTGCAA
1 TGTGATATGTGCTCCCGTATAAGACCATAATTGGGCTATGGCATCGGTG--A
* *
4383208 TGTGATATGTGCTCCTGTATAAGACTATAATTGGGCTATGGCATCGGTGTGA
1 TGTGATATGTGCTCCCGTATAAGACCATAATTGGGCTATGGCATC-G-GTGA
* * *
4383260 TGTGATAATGTGCTTCCGTATAAGACCATATTTGGGATATGGCATCGGT-A
1 TGTGAT-ATGTGCTCCCGTATAAGACCATAATTGGGCTATGGCATCGGTGA
* * * *
4383310 --TGATATGTG-ACCCGTGTAAGACCATAACTGGGCTATGGCTTCGGTG-
1 TGTGATATGTGCTCCCGTATAAGACCATAATTGGGCTATGGCATCGGTGA
4383356 TGTGATATGTG
1 TGTGATATGTG
4383367 ACTATGTGCA
Statistics
Matches: 137, Mismatches: 16, Indels: 16
0.81 0.09 0.09
Matches are distributed among these distances:
46 29 0.21
47 5 0.04
48 13 0.09
50 1 0.01
51 2 0.01
52 49 0.36
53 35 0.26
54 3 0.02
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (50 bp):
TGTGATATGTGCTCCCGTATAAGACCATAATTGGGCTATGGCATCGGTGA
Found at i:4383284 original size:105 final size:98
Alignment explanation
Indices: 4383156--4383357 Score: 253
Period size: 105 Copynumber: 2.0 Consensus size: 98
4383146 ATGGAAAAGG
*
4383156 TGTGATATGTGCGCCCGTATAAGACCATAGTTGGGCTATGGCATCGGTGCAATGTGATATGTG-C
1 TGTGATATGTGCGCCCGTATAAGACCATAGTTGGGATATGGCATCGGT---A--TGATATGTGAC
* *
4383220 TCCTGTATAAGACTATAATTGGGCTATGGCATCGGTGTGA
61 -CC-GTATAAGACCATAACTGGGCTATGGCATCGGTGTGA
** *
4383260 TGTGATAATGTGCTTCCGTATAAGACCATATTTGGGATATGGCATCGGTATGATATGTGACCCGT
1 TGTGAT-ATGTGCGCCCGTATAAGACCATAGTTGGGATATGGCATCGGTATGATATGTGACCCGT
* *
4383325 GTAAGACCATAACTGGGCTATGGCTTCGGTGTG
65 ATAAGACCATAACTGGGCTATGGCATCGGTGTG
4383358 TGATATGTGA
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
99 31 0.35
100 11 0.12
101 1 0.01
102 1 0.01
104 6 0.07
105 38 0.43
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.31
Consensus pattern (98 bp):
TGTGATATGTGCGCCCGTATAAGACCATAGTTGGGATATGGCATCGGTATGATATGTGACCCGTA
TAAGACCATAACTGGGCTATGGCATCGGTGTGA
Found at i:4384340 original size:20 final size:20
Alignment explanation
Indices: 4384312--4384350 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4384302 CACCACACAG
*
4384312 CCTACCCACACGGGCGTGTC
1 CCTACCCACAAGGGCGTGTC
*
4384332 CCTATCCACAAGGGCGTGT
1 CCTACCCACAAGGGCGTGT
4384351 GGCCCTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.38, G:0.26, T:0.18
Consensus pattern (20 bp):
CCTACCCACAAGGGCGTGTC
Found at i:4384754 original size:18 final size:18
Alignment explanation
Indices: 4384731--4384768 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
4384721 TGCTTGGAAA
4384731 GAAATAATGCAACTTAGT
1 GAAATAATGCAACTTAGT
4384749 GAAATAATGCAACTTAGT
1 GAAATAATGCAACTTAGT
4384767 GA
1 GA
4384769 TAGCTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (18 bp):
GAAATAATGCAACTTAGT
Found at i:4385148 original size:30 final size:30
Alignment explanation
Indices: 4385112--4385286 Score: 287
Period size: 30 Copynumber: 5.8 Consensus size: 30
4385102 ACTTTTCTCA
*
4385112 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
4385142 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4385172 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
4385202 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4385232 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4385262 ACTAGCTACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
4385287 TTTGTACCCA
Statistics
Matches: 134, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 134 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.23
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4385177 original size:60 final size:60
Alignment explanation
Indices: 4385112--4385286 Score: 323
Period size: 60 Copynumber: 2.9 Consensus size: 60
4385102 ACTTTTCTCA
*
4385112 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
4385172 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
* *
4385232 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCTACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
4385287 TTTGTACCCA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 112 1.00
ACGTcount: A:0.25, C:0.49, G:0.03, T:0.23
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4385854 original size:25 final size:25
Alignment explanation
Indices: 4385826--4385909 Score: 82
Period size: 25 Copynumber: 3.3 Consensus size: 25
4385816 ATATATTAGG
4385826 TATAT-TTTAAATTCTATATTATGTATA
1 TATATATTT-AATTCTATATTAT-T-TA
* * *
4385853 TATATATTTTATACTATTTTATTTA
1 TATATATTTAATTCTATATTATTTA
*
4385878 TATATCTTTAATAT-TATATTATTTA
1 TATATATTTAAT-TCTATATTATTTA
4385903 TATATAT
1 TATATAT
4385910 CAATTTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
25 28 0.60
26 1 0.02
27 15 0.32
28 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.60
Consensus pattern (25 bp):
TATATATTTAATTCTATATTATTTA
Found at i:4385960 original size:22 final size:24
Alignment explanation
Indices: 4385932--4385990 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
4385922 ACATGTTATC
4385932 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
4385954 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
4385979 TTATGTACATAT
1 TTATGTATATAT
4385991 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:4385980 original size:25 final size:25
Alignment explanation
Indices: 4385948--4385996 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4385938 ATATATCTTA
**
4385948 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
4385973 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
4385997 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:4386179 original size:16 final size:15
Alignment explanation
Indices: 4386155--4386202 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
4386145 TAATTATTAT
*
4386155 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
4386171 TATTTTAATATTTTA
1 TATTTTAATATTTTA
4386186 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
4386202 T
1 T
4386203 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:4386190 original size:7 final size:8
Alignment explanation
Indices: 4386155--4386206 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
4386145 TAATTATTAT
*
4386155 TATTCTAA
1 TATTTTAA
*
4386163 TATTTTGA
1 TATTTTAA
4386171 TATTTTAA
1 TATTTTAA
4386179 TATTTT-A
1 TATTTTAA
4386186 TATTTTATA
1 TATTTTA-A
*
4386195 TATTTTAT
1 TATTTTAA
4386203 TATT
1 TATT
4386207 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:4392281 original size:17 final size:17
Alignment explanation
Indices: 4392261--4392293 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
4392251 AGGGCATCTT
4392261 AAAA-AAAAAGAGAAAAG
1 AAAAGAAAAA-AGAAAAG
4392278 AAAAGAAAAAAGAAAA
1 AAAAGAAAAAAGAAAA
4392294 AGAGAGAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:4393241 original size:14 final size:14
Alignment explanation
Indices: 4393222--4393256 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
4393212 CGCTGAGGTA
* *
4393222 TTTTCAATTTTTGT
1 TTTTCAATTTATGC
4393236 TTTTCAATTTATGC
1 TTTTCAATTTATGC
4393250 TTTTCAA
1 TTTTCAA
4393257 AAAATCAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (14 bp):
TTTTCAATTTATGC
Found at i:4393357 original size:73 final size:73
Alignment explanation
Indices: 4393237--4393403 Score: 244
Period size: 73 Copynumber: 2.3 Consensus size: 73
4393227 AATTTTTGTT
*
4393237 TTTCAATTTATGCTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
1 TTTCAATTTATGCTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGACACG
* *
4393302 CTGAGGTAA
65 CCGAGATAA
* *
4393311 TTTCAATTTATGCTTTTCAAAAATTAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGGCACGC
1 TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGACACGC
*
4393376 CGAGATAT
66 CGAGATAA
* * *
4393384 TTTTAATTTCTGTTTTTCAA
1 TTTCAATTTATGCTTTTCAA
4393404 TTTCTGCTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 66 0.79
74 18 0.21
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (73 bp):
TTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCAGGACACGC
CGAGATAA
Found at i:4393427 original size:13 final size:13
Alignment explanation
Indices: 4393383--4393427 Score: 72
Period size: 13 Copynumber: 3.4 Consensus size: 13
4393373 CGCCGAGATA
4393383 TTTTTAATTTCTG
1 TTTTTAATTTCTG
4393396 TTTTTCAATTTCTG
1 TTTTT-AATTTCTG
*
4393410 CTTTTAATTTCTG
1 TTTTTAATTTCTG
4393423 TTTTT
1 TTTTT
4393428 CAAAAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (13 bp):
TTTTTAATTTCTG
Found at i:4393716 original size:73 final size:73
Alignment explanation
Indices: 4393615--4394789 Score: 1489
Period size: 73 Copynumber: 15.9 Consensus size: 73
4393605 ATGTTTCTAA
* * * *
4393615 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
4393680 TGTTTGTC
66 TGTTTGTC
* * *
4393688 AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
*
4393753 TGTTTTTC
66 TGTTTGTC
* * *
4393761 AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 -AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTT
*
4393826 TTGTTTGTC
65 CTGTTTGTC
*
4393835 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
4393900 TGTCTT-TC
66 TGT-TTGTC
* * *
4393908 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*
4393973 TTTGTTTGTC
64 TCTGTTTGTC
*
4393983 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
*
4394048 TATCTT-TC
66 TGT-TTGTC
* * * * *
4394056 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACTTCAA-A-ACGCTGAGATAATTTT-TAT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCAAT
4394118 TTCTG-TT-TC
63 TTCTGTTTGTC
* * * * *
4394127 AAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
4394192 TGTCTT-TC
66 TGT-TTGTC
* *
4394200 AAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGCTCACGTGCTGAGGTATTTTCA
1 -AAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC--GCTGAGGTATTTTCA
4394264 ATTTCTGTCTCTATTTGTC
61 ATTTCTG------TTTGTC
* *
4394283 -AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
4394347 TGTTTGTC
66 TGTTTGTC
* * * *
4394355 AAAAAACAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
*
4394420 TGTTTTTC
66 TGTTTGTC
* * *
4394428 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAACCTCAAG--ACGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*
4394491 TTTGTTTGTC
64 TCTGTTTGTC
* * *
4394501 AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
*
4394566 TGTTTTTC
66 TGTTTGTC
* * * *
4394574 AAAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACATGCTGAGGTAATTTCAATT
1 --AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATT
*
4394639 TTTGTTTGTC
64 TCTGTTTGTC
*
4394649 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATG-TGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
* *
4394713 TGTCTTTTAA
66 TGT-TTGT-C
* * * *
4394723 AAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTGTTTTCCATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
4394786 TGTT
66 TGTT
4394790 CTTCAATTTC
Statistics
Matches: 968, Mismatches: 97, Indels: 75
0.85 0.09 0.07
Matches are distributed among these distances:
69 33 0.03
70 6 0.01
71 56 0.06
72 28 0.03
73 400 0.41
74 122 0.13
75 236 0.24
77 21 0.02
78 22 0.02
80 34 0.04
81 5 0.01
82 2 0.00
83 3 0.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (73 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTC
TGTTTGTC
Found at i:4393985 original size:148 final size:147
Alignment explanation
Indices: 4393595--4394916 Score: 1602
Period size: 148 Copynumber: 8.9 Consensus size: 147
4393585 AATTTTCGTT
* * * *
4393595 TTTTTAATTTATG-TTTCTAAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * *
4393659 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCC
65 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
4393724 TCAAGACACGTTGAGGTA
130 TCAAGACACGCTGAGGTA
* *
4393742 TTTTCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGATAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTG-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
4393806 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
4393871 TCAAGACACGTTGAGGTA
130 TCAAGACACGCTGAGGTA
* *
4393889 TTTTCAATTTCTGTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACA
1 TTTTCAATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
*
4393954 CGCTGAGGTAATTTCAATTTTTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
65 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
4394019 TCAAGACACGTTGAGGTA
130 TCAAGACACGCTGAGGTA
* * * *
4394037 TTTTCAATTTCTATCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACTTCAA-A-A
1 TTTTCAATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* ** * * * *
4394100 CGCTGAGATAATTTTTATTTCTG-TT-TCAAAATTCAACTCATACTGCAAGAAGTGAGTTGAGCC
65 CGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
*
4394163 TCAAGACACGTTGAGGTA
130 TCAAGACACGCTGAGGTA
* * *
4394181 TTTTCAATTTCTGTCTTTCAAAAAATTCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGCTC
1 TTTTCAATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-AC
* *
4394245 ACGTGCTGAGGTATTTTCAATTTCTGTCTCTATTTGTC-AAAATCAACTCATATTGTGAGAGGTG
64 AC--GCTGAGGTAATTTCAATTTCTG------TTTGTCAAAAATCAACTCATATTGCGAGAGGTG
*
4394309 AGTTGAGCCTCAGGACACGCTGAGGTA
121 AGTTGAGCCTCAAGACACGCTGAGGTA
* * *
4394336 TTTTCAATTTCTGTTTGTC-AAAAAA-CAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTCTGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * *
4394399 CGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAA
65 CGCTGAGGTAATTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
4394464 CCTCAAG--ACGCTGAGGTA
128 CCTCAAGACACGCTGAGGTA
* * * *
4394482 ATTTCAATTTTTGTTTGTC--AAAACTCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * *
4394545 CGTTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGATAGGTGAGTTGAG
65 CGCTGAGGTAATTTCAATTTCTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
* *
4394610 CCTCAGGACATGCTGAGGTA
128 CCTCAAGACACGCTGAGGTA
* *
4394630 ATTTCAATTTTTGTTTGTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
1 TTTTCAATTTCTGTTT-TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACA
* * * * * *
4394693 TG-TGAGGTATTTTCAATTTCTGTCTTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAA
65 CGCTGAGGTAATTTCAATTTCTGT-TTGT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
4394757 CCTCAAG--ACGCTGAGGTGTTTTCCA
128 CCTCAAGACACGCTGA-G-G---T--A
*
4394782 TTTCTGTTCTTCAATTTCTGTGTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCT
1 ------TT-TTCAATTTCTGT-TTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
** *
4394847 CGGGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAG
58 CAAGACACGCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAG
4394912 TTGAG
123 TTGAG
4394917 TCTCGGCTCA
Statistics
Matches: 1050, Mismatches: 80, Indels: 77
0.87 0.07 0.06
Matches are distributed among these distances:
143 1 0.00
144 105 0.10
145 17 0.02
146 155 0.15
147 212 0.20
148 313 0.30
149 4 0.00
150 1 0.00
151 22 0.02
152 1 0.00
153 33 0.03
154 8 0.01
155 64 0.06
156 2 0.00
158 1 0.00
159 13 0.01
160 33 0.03
161 45 0.04
162 20 0.02
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.33
Consensus pattern (147 bp):
TTTTCAATTTCTGTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACAC
GCTGAGGTAATTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
CAAGACACGCTGAGGTA
Found at i:4394936 original size:75 final size:72
Alignment explanation
Indices: 4394791--4394959 Score: 203
Period size: 75 Copynumber: 2.2 Consensus size: 72
4394781 ATTTCTGTTC
*
4394791 TTCAATTTCTGTGTTTCAAAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGACACG
1 TTCAATTTCTGT-TTTC--AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGCACACG
4394856 CTGAGGTAAT
63 CTGAGGTAAT
* * * *
4394866 TTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATG
1 TTCAATTTCTGTTT-TCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGG--CACACG
**
4394931 CTGAGGTCTT
63 CTGAGGTAAT
*
4394941 TTTAATTTCTGCTTTTCAA
1 TTCAATTTCTG-TTTTCAA
4394960 TTTCTGTTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
73 37 0.45
74 2 0.02
75 40 0.49
76 3 0.04
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.36
Consensus pattern (72 bp):
TTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGCACACGCTG
AGGTAAT
Found at i:4394970 original size:14 final size:14
Alignment explanation
Indices: 4394939--4394989 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
4394929 TGCTGAGGTC
4394939 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
4394952 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
4394966 TTTTTTTCAATTTATA
1 --TTTTTCAATTTCTG
4394982 TTTTTCAA
1 TTTTTCAA
4394990 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
16 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.65
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:4394985 original size:16 final size:16
Alignment explanation
Indices: 4394953--4394986 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4394943 TAATTTCTGC
* *
4394953 TTTTCAATTTCTGTTT
1 TTTTCAATTTATATTT
4394969 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
4394985 TT
1 TT
4394987 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:4395080 original size:178 final size:165
Alignment explanation
Indices: 4394649--4395267 Score: 725
Period size: 178 Copynumber: 3.7 Consensus size: 165
4394639 TTTGTTTGTC
** * *
4394649 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACATG-TGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
* * * * * * *
4394713 TGTCTTTTAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG---AC--GCTGAGG
66 TGT-TTGT-CAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGCTCACATGATGAGG
* * **
4394773 TGTTTTCCATTTCTGTTCTTCAATTTCTG-T-GTTTCAA
128 TCTTTTCAATTTCTGTTCTTCAATTTCTGTTCG-TAAAA
*
4394810 AAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
* *
4394875 TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCT
66 TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGATGAGGTCT
* **
4394940 TTTTAATTTCTGCTT-TTCAATTTCTGTTTTTTTCAATTTATA
131 TTTCAATTTCTG-TTCTTCAATTTCTG--TTCGT-AA---A-A
4394982 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
1 ------AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTC
* *
4395047 AATTTTTGTTTGTCAGAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGATG
60 AATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGATG
4395112 AGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAA
125 AGGTCTTTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAA
* * *
4395153 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTA-ATTTCAATTT
* * * *
4395218 CTGTTTTTCAAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGG
65 CTGTTTGTC-AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
4395268 GACACGCTGA
Statistics
Matches: 398, Mismatches: 35, Indels: 44
0.83 0.07 0.09
Matches are distributed among these distances:
159 1 0.00
160 34 0.09
161 45 0.11
162 22 0.06
164 30 0.08
165 55 0.14
166 15 0.04
167 38 0.10
171 2 0.01
172 2 0.01
175 2 0.01
176 3 0.01
177 2 0.01
178 147 0.37
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.35
Consensus pattern (165 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTC
TGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGATGAGGTCT
TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAA
Found at i:4395087 original size:73 final size:73
Alignment explanation
Indices: 4394970--4395340 Score: 262
Period size: 73 Copynumber: 4.8 Consensus size: 73
4394960 TTTCTGTTTT
* * *
4394970 TTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
4395035 TGAGGTAA
66 TGAGGTAA
* * * * *
4395043 TTTCAATTTTTGTTTGTCAGAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACAT
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG--GACAC
* **
4395108 GATGAGGTCT
64 GCTGAGGTAA
* ** * * * * *
4395118 TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAAAAAAATCA-ACT-C-ATATTGCGAGAGGTG
1 TTTCAATTTCTG---------TT-TG-TC-AAAAATCAACTCATATTGCGAGA--G-GTGAGTTG
* *
4395180 AGTTGAGCCTCAGGACACGCTGAGGTATT
51 AG-----CCTCGGGACACGCTGAGGTA-A
* * * *
4395209 TTTAAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGGACACG
1 TTTCAATTTCTGTTTGTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACG
4395274 CTGAGGTAA
65 CTGAGGTAA
* *
4395283 TTTCAATTTCTGTTTGTCAAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGG
1 TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
4395341 CTCACATGCT
Statistics
Matches: 227, Mismatches: 45, Indels: 52
0.70 0.14 0.16
Matches are distributed among these distances:
73 89 0.39
74 16 0.07
75 40 0.18
80 18 0.08
81 4 0.02
82 3 0.01
83 2 0.01
84 4 0.02
85 3 0.01
86 5 0.02
87 16 0.07
90 10 0.04
91 12 0.05
92 5 0.02
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (73 bp):
TTTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGC
TGAGGTAA
Found at i:4395138 original size:14 final size:14
Alignment explanation
Indices: 4395119--4395146 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4395109 ATGAGGTCTT
4395119 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
4395133 TTCAATTTCTGTTC
1 TTCAATTTCTGTTC
4395147 GTAAAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (14 bp):
TTCAATTTCTGTTC
Found at i:4395261 original size:75 final size:73
Alignment explanation
Indices: 4395152--4395377 Score: 301
Period size: 75 Copynumber: 3.0 Consensus size: 73
4395142 TGTTCGTAAA
4395152 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTT-AATT
4395217 TCTGTTTTTC
64 TCTGTTTTTC
* * * *
4395227 AAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACACGCTGAGGTATTTTTAATTT
*
4395292 CTGTTTGTC
65 CTGTTTTTC
* * * *
4395301 -AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGCTCACATGCTGAGGTCTTTTTAAT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG---ACACGCTGAGGTATTTTTAAT
*
4395365 TTCTGCTTTTC
63 TTCTGTTTTTC
4395376 AA
1 AA
4395378 TTTCTGTTTT
Statistics
Matches: 131, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
72 2 0.02
73 34 0.26
74 13 0.10
75 81 0.62
76 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACGCTGAGGTATTTTTAATTTC
TGTTTTTC
Found at i:4395289 original size:165 final size:164
Alignment explanation
Indices: 4394988--4395296 Score: 458
Period size: 165 Copynumber: 1.9 Consensus size: 164
4394978 TATATTTTTC
* * *
4394988 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACACGCTGAGGTAATTTCAATTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTAAATTTC
* * * * * **
4395053 TGTTTGTCAGAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCTCACATGATGAGGTCT
66 TGTTTGTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGC-CACACGATGAGGTAA
4395118 TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAA
130 TTTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAA
*
4395153 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTTAAATTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA-ATTTAAATTT
* * *
4395218 CTGTTTTTCAAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGG-GACACGCTGAGGTA
65 CTGTTTGTC-AAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGCCACACGATGAGGTA
4395282 ATTTCAATTTCTGTT
129 ATTTCAATTTCTGTT
4395297 TGTCAAAAAT
Statistics
Matches: 128, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
165 77 0.60
166 15 0.12
167 36 0.28
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (164 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTAAATTTC
TGTTTGTCAAAAATCAACTCATATTGCGAAAGATGAGTTGAGCCTCGGCCACACGATGAGGTAAT
TTCAATTTCTGTTCTTCAATTTCTGTTCGTAAAA
Found at i:4395379 original size:14 final size:15
Alignment explanation
Indices: 4395354--4395395 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
4395344 ACATGCTGAG
*
4395354 GTCTTTTTAATTTCT
1 GTCTTTTCAATTTCT
4395369 G-CTTTTCAATTTCT
1 GTCTTTTCAATTTCT
*
4395383 GTTTTTTCAATTT
1 GTCTTTTCAATTT
4395396 ATATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.14, C:0.14, G:0.07, T:0.64
Consensus pattern (15 bp):
GTCTTTTCAATTTCT
Found at i:4395391 original size:15 final size:14
Alignment explanation
Indices: 4395357--4395406 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
4395347 TGCTGAGGTC
4395357 TTTTT-AATTTCTG
1 TTTTTCAATTTCTG
*
4395370 CTTTTCAATTTCTG
1 TTTTTCAATTTCTG
* *
4395384 TTTTTTCAATTTATA
1 -TTTTTCAATTTCTG
4395399 TTTTTCAA
1 TTTTTCAA
4395407 AAATCAATTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 16 0.52
15 11 0.35
ACGTcount: A:0.20, C:0.12, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTTTCAATTTCTG
Found at i:4396189 original size:30 final size:30
Alignment explanation
Indices: 4396153--4396326 Score: 269
Period size: 30 Copynumber: 5.8 Consensus size: 30
4396143 ACTTTTCTCA
*
4396153 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
4396183 ACTAGCCACACATTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
* *
4396213 ACTAGCCACTCTTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
4396243 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
** *
4396273 ACTAGCCAC-TTTTTTTCACCACCAACTCC
1 ACTAGCCACACCTTTTCCACCACCAACTCC
*
4396302 ACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACACCTTTTCCACCACCA
4396327 CTTGTACCTA
Statistics
Matches: 130, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
29 26 0.20
30 104 0.80
ACGTcount: A:0.26, C:0.48, G:0.03, T:0.23
Consensus pattern (30 bp):
ACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4396218 original size:60 final size:60
Alignment explanation
Indices: 4396153--4396326 Score: 305
Period size: 60 Copynumber: 2.9 Consensus size: 60
4396143 ACTTTTCTCA
* *
4396153 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACATTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
4396213 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
* *
4396273 ACTAGCCACT-TTTTTTCACCACCAACTCCACTAGCCACACCTTCTCCACCACCA
1 ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCA
4396327 CTTGTACCTA
Statistics
Matches: 110, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 42 0.38
60 68 0.62
ACGTcount: A:0.26, C:0.48, G:0.03, T:0.23
Consensus pattern (60 bp):
ACTAGCCACTCTTTTTCCACCACCAACTCCACTAGCCACACCTTTTCCACCACCAACTCC
Found at i:4396277 original size:90 final size:89
Alignment explanation
Indices: 4396153--4396326 Score: 276
Period size: 89 Copynumber: 1.9 Consensus size: 89
4396143 ACTTTTCTCA
*
4396153 ACTAGCCACTCCTTTTCCACCACCAACTCCACTAGCCACACATTTTCCACCACCAACTCCACTAG
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCAC-CATTTTCCACCACCAACTCCACTAG
* * *
4396218 CCACTCTTTTTCCACCACCAACTCC
65 CCACACCTTCTCCACCACCAACTCC
** *
4396243 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACTTTTTTTCACCACCAACTCCACTAGC
1 ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACCATTTTCCACCACCAACTCCACTAGC
4396308 CACACCTTCTCCACCACCA
66 CACACCTTCTCCACCACCA
4396327 CTTGTACCTA
Statistics
Matches: 77, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 39 0.51
90 38 0.49
ACGTcount: A:0.26, C:0.48, G:0.03, T:0.23
Consensus pattern (89 bp):
ACTAGCCACACCTTTTCCACCACCAACTCCACTAGCCACCATTTTCCACCACCAACTCCACTAGC
CACACCTTCTCCACCACCAACTCC
Found at i:4396995 original size:22 final size:24
Alignment explanation
Indices: 4396967--4397025 Score: 68
Period size: 25 Copynumber: 2.5 Consensus size: 24
4396957 ACATGTTATC
4396967 TTATGTATATATCTT-A-ACTATA
1 TTATGTATATATCTTAACACTATA
* *
4396989 TTATGTATGTATTTTTAACACTATA
1 TTATGTATATA-TCTTAACACTATA
*
4397014 TTATGTACATAT
1 TTATGTATATAT
4397026 TTTTAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.33
23 3 0.10
24 2 0.07
25 15 0.50
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (24 bp):
TTATGTATATATCTTAACACTATA
Found at i:4397015 original size:25 final size:25
Alignment explanation
Indices: 4396983--4397031 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4396973 ATATATCTTA
**
4396983 ACTATATTATGTATGTATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
4397008 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
4397032 TATTATCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:4397208 original size:16 final size:15
Alignment explanation
Indices: 4397184--4397231 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
4397174 TAATTATTAT
*
4397184 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
4397200 TATTTTAATATTTTA
1 TATTTTAATATTTTA
4397215 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
4397231 T
1 T
4397232 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:4397219 original size:7 final size:8
Alignment explanation
Indices: 4397184--4397235 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
4397174 TAATTATTAT
*
4397184 TATTCTAA
1 TATTTTAA
*
4397192 TATTTTGA
1 TATTTTAA
4397200 TATTTTAA
1 TATTTTAA
4397208 TATTTT-A
1 TATTTTAA
4397215 TATTTTATA
1 TATTTTA-A
*
4397224 TATTTTAT
1 TATTTTAA
4397232 TATT
1 TATT
4397236 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:4399553 original size:16 final size:16
Alignment explanation
Indices: 4399535--4399564 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4399525 ATTAATTTCT
4399535 TTTTTATA-ATAAATG
1 TTTTTATAGATAAATG
4399550 TTTTTATAGATAAAT
1 TTTTTATAGATAAAT
4399565 TGGATTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
TTTTTATAGATAAATG
Found at i:4407763 original size:3 final size:3
Alignment explanation
Indices: 4407755--4407779 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4407745 CAGCTTCACT
4407755 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
4407780 AACATTGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4408549 original size:16 final size:15
Alignment explanation
Indices: 4408523--4408552 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
4408513 TATTAAAATT
4408523 TAAAATTATTATTAC
1 TAAAATTATTATTAC
4408538 TAAAATTAATTATTA
1 TAAAATT-ATTATTA
4408553 AAATAAAAAA
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATTATTATTAC
Found at i:4421981 original size:5 final size:4
Alignment explanation
Indices: 4421928--4421980 Score: 52
Period size: 4 Copynumber: 13.0 Consensus size: 4
4421918 CAAAAAAGAG
* * * * *
4421928 TAAA GAAA TAAA TGAA TGAA TGAA TACA TAAA TAAA TAAA TAAA TAAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA T-AAA
4421977 TAAA
1 TAAA
4421981 ACAATACACA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
4 38 0.90
5 4 0.10
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:4426563 original size:2 final size:2
Alignment explanation
Indices: 4426556--4426597 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
4426546 ATCAAGTTTA
4426556 AT AT AT AT 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 AT AT AT AT
4426598 CACTTAATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4427918 original size:3 final size:3
Alignment explanation
Indices: 4427910--4427947 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4427900 TAAAAGATCC
4427910 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4427948 ATATAAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4430793 original size:21 final size:23
Alignment explanation
Indices: 4430758--4430800 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
4430748 ATAAATAAAT
*
4430758 ATTGATAAATTTAATTAAATTTA
1 ATTGATAAATTTAATAAAATTTA
4430781 ATTGA-AAA-TTAATAAAATTT
1 ATTGATAAATTTAATAAAATTT
4430801 TTTTGGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (23 bp):
ATTGATAAATTTAATAAAATTTA
Found at i:4437778 original size:93 final size:93
Alignment explanation
Indices: 4437650--4437818 Score: 293
Period size: 93 Copynumber: 1.8 Consensus size: 93
4437640 GCCCATAAGG
* * *
4437650 GAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAAATCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
4437715 CGAGCTCGGATGCCTAGTTACATCTCAC
66 CGAGCTCGGATGCCTAGTTACATCTCAC
*
4437743 GAACTCGGACTCAAATCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAAATCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
4437808 CGAGTTCGGAT
66 CGAGCTCGGAT
4437819 ACCCAACTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAAATCAACGAGCTCGGACGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCAC
Found at i:4437817 original size:46 final size:46
Alignment explanation
Indices: 4437642--4437817 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
4437632 TGTAACCCGC
* * *
4437642 CCATAAGGGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
4437688 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C--GTTCGCAT
* * * *
4437738 -C-TCA-CGAACTCGGACTCAAATCAACGAGTTCGGACGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
*
4437781 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
4437818 TACCCAACTA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 3 0.03
43 3 0.03
44 2 0.02
45 2 0.02
46 62 0.57
47 27 0.25
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:4447396 original size:12 final size:12
Alignment explanation
Indices: 4447379--4447405 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4447369 CATTTAATCT
4447379 TCATGCAATTTG
1 TCATGCAATTTG
4447391 TCATGCAATTTG
1 TCATGCAATTTG
4447403 TCA
1 TCA
4447406 ACAATCTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (12 bp):
TCATGCAATTTG
Found at i:4449384 original size:21 final size:21
Alignment explanation
Indices: 4449358--4449398 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4449348 ACCTGCTCAA
*
4449358 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGTTGTGGAGTAC
4449379 ACTCCACCTGTTGTGGAGTA
1 ACTCCACCTGTTGTGGAGTA
4449399 TCGTTTGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (21 bp):
ACTCCACCTGTTGTGGAGTAC
Found at i:4453323 original size:24 final size:24
Alignment explanation
Indices: 4453150--4453309 Score: 257
Period size: 24 Copynumber: 6.7 Consensus size: 24
4453140 GATTCAACTC
* * *
4453150 CGCACACATAGTGCCAAATAATTA
1 CGCACACATAGTGCCATACAAATA
*
4453174 CGCACACATAGTGCCATACATATA
1 CGCACACATAGTGCCATACAAATA
4453198 CGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
* *
4453222 TGCACACATAGTGCCATACAAATG
1 CGCACACATAGTGCCATACAAATA
4453246 CGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
4453270 CGCACACATAGTGCCATACAAATA
1 CGCACACATAGTGCCATACAAATA
*
4453294 CGCATACATAGTGCCA
1 CGCACACATAGTGCCA
4453310 CTCAAATCCG
Statistics
Matches: 126, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 126 1.00
ACGTcount: A:0.39, C:0.28, G:0.14, T:0.19
Consensus pattern (24 bp):
CGCACACATAGTGCCATACAAATA
Found at i:4455123 original size:12 final size:12
Alignment explanation
Indices: 4455106--4455132 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4455096 CATTTAATCT
4455106 TCATGCAATTTG
1 TCATGCAATTTG
4455118 TCATGCAATTTG
1 TCATGCAATTTG
4455130 TCA
1 TCA
4455133 ACAATCTCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (12 bp):
TCATGCAATTTG
Found at i:4462335 original size:12 final size:12
Alignment explanation
Indices: 4462317--4462366 Score: 64
Period size: 12 Copynumber: 4.1 Consensus size: 12
4462307 TGGATTTTTT
4462317 AAAATGGAAATG
1 AAAATGGAAATG
*
4462329 GAAATGGAAATG
1 AAAATGGAAATG
* *
4462341 AAAATGAAAATA
1 AAAATGGAAATG
4462353 AAAATGAGAAATG
1 AAAATG-GAAATG
4462366 A
1 A
4462367 TTCATTTGCA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
12 26 0.84
13 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:4462355 original size:5 final size:6
Alignment explanation
Indices: 4462317--4462366 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
4462307 TGGATTTTTT
* * * *
4462317 AAAATG GAAATG GAAATG GAAATG AAAATG AAAATA AAAATG AGAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG A-AAATG
4462366 A
1 A
4462367 TTCATTTGCA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.62, C:0.00, G:0.22, T:0.16
Consensus pattern (6 bp):
AAAATG
Found at i:4466900 original size:21 final size:21
Alignment explanation
Indices: 4466876--4466930 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
4466866 TCTAATGCCA
4466876 TCGCTGCTGCCTCTACCTCCC
1 TCGCTGCTGCCTCTACCTCCC
* * *
4466897 TCGCTGCTACCGCTGCCTCCC
1 TCGCTGCTGCCTCTACCTCCC
**
4466918 TTTCTGCTGCCTC
1 TCGCTGCTGCCTC
4466931 CGCTCTAAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.04, C:0.49, G:0.16, T:0.31
Consensus pattern (21 bp):
TCGCTGCTGCCTCTACCTCCC
Found at i:4473589 original size:24 final size:25
Alignment explanation
Indices: 4473553--4473600 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
4473543 TCAAACATGC
4473553 ATTTAGGTCAATTTAACCCTAGGGT
1 ATTTAGGTCAATTTAACCCTAGGGT
* * *
4473578 ATTTCGGT-AATTTATCTCTAGGG
1 ATTTAGGTCAATTTAACCCTAGGG
4473601 GTAAAACTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (25 bp):
ATTTAGGTCAATTTAACCCTAGGGT
Found at i:4475150 original size:26 final size:26
Alignment explanation
Indices: 4475081--4475215 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
4475071 ACATGAATTC
*
4475081 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
4475107 TTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
4475132 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
*
4475158 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
4475184 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
4475210 TTATCA
1 TTATCA
4475216 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 24 0.24
26 78 0.76
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:4479411 original size:24 final size:26
Alignment explanation
Indices: 4479375--4479423 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
4479365 TCAAACATGC
4479375 ATTTAGGTCAATTTAAC-CCTAGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGT
* *
4479400 ATTTCGGT-AATTTATCTCCTAGGG
1 ATTTAGGTCAATTTAACTCCTAGGG
4479424 GTAAAACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.24, C:0.16, G:0.20, T:0.39
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACTCCTAGGGT
Found at i:4480975 original size:26 final size:26
Alignment explanation
Indices: 4480906--4481040 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
4480896 GACATGATTC
*
4480906 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
4480932 TTATCAT-GAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
4480957 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
*
4480983 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
4481009 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
4481035 TTATCA
1 TTATCA
4481041 ATTTGTATCA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
25 24 0.24
26 78 0.76
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.33
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:4481399 original size:9 final size:9
Alignment explanation
Indices: 4481385--4481656 Score: 92
Period size: 9 Copynumber: 29.6 Consensus size: 9
4481375 TTTTTATGTA
4481385 TTATGTAAG
1 TTATGTAAG
*
4481394 TTATGTAAA
1 TTATGTAAG
4481403 TTATGTAAG
1 TTATGTAAG
** *
4481412 TTAAATAGG
1 TTATGTAAG
*
4481421 TTTATGTAAA
1 -TTATGTAAG
4481431 TTATGTAAG
1 TTATGTAAG
*
4481440 ATATGATATA-
1 TTATG-TA-AG
* *
4481450 TATATATATAT
1 T-TATGTA-AG
4481461 TTATGT-A-
1 TTATGTAAG
4481468 TTATGTAAG
1 TTATGTAAG
*
4481477 TTATGTAAA
1 TTATGTAAG
*
4481486 TTATATAAG
1 TTATGTAAG
* * **
4481495 TTGTTTATC
1 TTATGTAAG
*
4481504 TTATGTAAA
1 TTATGTAAG
4481513 TTATGTAAG
1 TTATGTAAG
* *
4481522 ATATGATATATAT
1 -T-T-ATGTA-AG
4481535 TTATGTAA-
1 TTATGTAAG
*
4481543 TT-GGTAAG
1 TTATGTAAG
*
4481551 TTATGTAAA
1 TTATGTAAG
4481560 TTATGTAAG
1 TTATGTAAG
* * **
4481569 TTGTTTATC
1 TTATGTAAG
*
4481578 TTATGTAAA
1 TTATGTAAG
4481587 TTATG-AACG
1 TTATGTAA-G
* *
4481596 ATATGATCTATAT
1 -T-T-ATGTA-AG
4481609 TTATGT-A-
1 TTATGTAAG
*
4481616 TTACGTAAG
1 TTATGTAAG
*
4481625 TTATGTAAA
1 TTATGTAAG
*
4481634 TTATGTAAA
1 TTATGTAAG
4481643 TTATGTAAG
1 TTATGTAAG
*
4481652 ATATG
1 TTATG
4481657 ATATATATAT
Statistics
Matches: 192, Mismatches: 50, Indels: 42
0.68 0.18 0.15
Matches are distributed among these distances:
7 15 0.08
8 10 0.05
9 123 0.64
10 24 0.12
11 9 0.05
12 8 0.04
13 2 0.01
14 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:4481464 original size:83 final size:82
Alignment explanation
Indices: 4481370--4481651 Score: 334
Period size: 83 Copynumber: 3.5 Consensus size: 82
4481360 GGGGCGTTAC
* ***
4481370 ATATATTTTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTAAATAGGT-TTATGTAAATTA
1 ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTGTTTA--TCTTATGTAAATTA
4481434 TGTAAGATATGATATATAT
64 TGTAAGATATGATATATAT
*
4481453 ATATATATTTATGTATTATGTAAGTTATGTAAATTATATAAGTTGTTTATCTTATGTAAATTATG
1 ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTGTTTATCTTATGTAAATTATG
4481518 TAAGATATG--ATATAT
66 TAAGATATGATATATAT
* *
4481533 AT-T-TATGTA---ATT-GGTAAGTTATGTAAATTATGTAAGTTGTTTATCTTATGTAAATTATG
1 ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTGTTTATCTTATGTAAATTATG
*
4481592 -AACGATATGATCTATAT
66 TAA-GATATGATATATAT
* * * *
4481609 TTATGTA-TTACGTAAGTTATGTAAATTATGTAAATTATGTAAG
1 ATATATATTTATGT-A-TTATGTAAGTTATGTAAATTATGTAAG
4481652 ATATGATATA
Statistics
Matches: 174, Mismatches: 13, Indels: 24
0.82 0.06 0.11
Matches are distributed among these distances:
73 2 0.01
74 51 0.29
75 3 0.02
76 6 0.03
77 3 0.02
78 7 0.04
79 1 0.01
80 8 0.05
81 2 0.01
82 25 0.14
83 66 0.38
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.47
Consensus pattern (82 bp):
ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTGTTTATCTTATGTAAATTATG
TAAGATATGATATATAT
Found at i:4481475 original size:74 final size:76
Alignment explanation
Indices: 4481370--4481646 Score: 316
Period size: 74 Copynumber: 3.6 Consensus size: 76
4481360 GGGGCGTTAC
* *
4481370 ATATATTTTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTAAATAGGT-TTATGTAAATTA
1 ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATATAGGTCTTATGTAAATTA
4481434 TGTAAGATATG
66 TGTAAGATATG
* * *
4481445 ATATATATATATATATTTATGTATTATGTAAGTTATGTAAATTATATAAGTTGTTTA--TCTTAT
1 --------ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATATAGGTCTTAT
4481508 GTAAATTATGTAAGATATG
58 GTAAATTATGTAAGATATG
* * *
4481527 ATATATATTTATGTAATT-GGTAAGTTATGTAAATTATGTAAGTTGTTTA--TCTTATGTAAATT
1 ATATATATTTATGT-ATTATGTAAGTTATGTAAATTATGTAAGTTATATAGGTCTTATGTAAATT
4481589 ATG-AACGATATG
65 ATGTAA-GATATG
* * *
4481601 ATCTATATTTATGTATTACGTAAGTTATGTAAATTATGTAAATTAT
1 ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTAT
4481647 GTAAGATATG
Statistics
Matches: 179, Mismatches: 11, Indels: 17
0.86 0.05 0.08
Matches are distributed among these distances:
73 5 0.03
74 103 0.58
75 3 0.02
81 1 0.01
82 23 0.13
83 44 0.25
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.47
Consensus pattern (76 bp):
ATATATATTTATGTATTATGTAAGTTATGTAAATTATGTAAGTTATATAGGTCTTATGTAAATTA
TGTAAGATATG
Found at i:4482148 original size:102 final size:102
Alignment explanation
Indices: 4481919--4482296 Score: 550
Period size: 102 Copynumber: 3.7 Consensus size: 102
4481909 AATTTGTTGA
* * * * *
4481919 ACAA-TTAATTTAATTAGGTTATTTAACAAA-AAAATAAAAGTAAATAAAATATTTTTCGTAATT
1 ACAATTTAATTTAATTAGGTAATTTAA-AAATAAAATAAAAGTAGACAAAATATTTTTTGTGATT
*
4481982 AAAATAAAAT--AAAAAATATTTAAAAAAACTTTAAAT
65 AAAATAAAATGCATAAAATATTTAAAAAAACTTTAAAT
* * * * * *
4482018 ATAATGTAATTTAACTAGGTAATTTAAAAATAAAATAAGAGTAGACATAATATTTTTTGTTATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
4482083 AAATAAAATGCACTAAAATATTT-AAAAAACTTTAAAT
66 AAATAAAATGCA-TAAAATATTTAAAAAAACTTTAAAT
* * *
4482120 ACAATTTAACTTAATTAGGTAATTTAAAAATAAAATAAGAGTAGACATAATATTTTTTGTGATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
4482185 AAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
66 AAATAAAATGC-ATAAAATATTTAAAAAAACTTTAAAT
*
4482223 ACAATTTAATTTAATTAGGTAATTTAAAAAAAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
4482288 AAATAAAAT
66 AAATAAAAT
4482297 AAAATAAAAT
Statistics
Matches: 252, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
99 6 0.02
100 56 0.22
102 96 0.38
103 94 0.37
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (102 bp):
ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
AAATAAAATGCATAAAATATTTAAAAAAACTTTAAAT
Found at i:4482249 original size:103 final size:103
Alignment explanation
Indices: 4481919--4482307 Score: 565
Period size: 103 Copynumber: 3.8 Consensus size: 103
4481909 AATTTGTTGA
* * * * *
4481919 ACAA-TTAATTTAATTAGGTTATTTAACAAA-AAAATAAAAGTAAATAAAATATTTTTCGTAATT
1 ACAATTTAATTTAATTAGGTAATTTAA-AAATAAAATAAAAGTAGACAAAATATTTTTTGTGATT
4481982 AAAATAAAAT--AA-AAAATATTTAAAAAAACTTTAAAT
65 AAAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
* * * * * *
4482018 ATAATGTAATTTAACTAGGTAATTTAAAAATAAAATAAGAGTAGACATAATATTTTTTGTTATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
*
4482083 AAATAAAATGCACTAAAATATTT-AAAAAACTTTAAAT
66 AAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
* * *
4482120 ACAATTTAACTTAATTAGGTAATTTAAAAATAAAATAAGAGTAGACATAATATTTTTTGTGATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
4482185 AAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
66 AAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
*
4482223 ACAATTTAATTTAATTAGGTAATTTAAAAAAAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
1 ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
**
4482288 AAATAAAATAAAATAAAATA
66 AAATAAAATGCAATAAAATA
4482308 ACATATTCAA
Statistics
Matches: 261, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
99 6 0.02
100 56 0.21
102 97 0.37
103 102 0.39
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (103 bp):
ACAATTTAATTTAATTAGGTAATTTAAAAATAAAATAAAAGTAGACAAAATATTTTTTGTGATTA
AAATAAAATGCAATAAAATATTTAAAAAAACTTTAAAT
Found at i:4482269 original size:205 final size:201
Alignment explanation
Indices: 4481919--4482296 Score: 569
Period size: 205 Copynumber: 1.9 Consensus size: 201
4481909 AATTTGTTGA
* * *
4481919 ACAATTAATTTAATTAGGTTATTTAACAAAAAAATAAAAGTAAATAAAATATTTTTCGTAATTAA
1 ACAATTAACTTAATTAGGTAATTTAACAAAAAAATAAAAGTAAACAAAATATTTTTCGTAATTAA
* *
4481984 AATAAAATAAAAAATATTTAAAAAAACTTTAAATATAATGTAATTTAACTAGGTAATTTAAAAAT
66 AATAAAATAAAAAATATTTAAAAAAACTTTAAATACAATGTAATTTAACTAGGTAATTTAAAAAA
* * *
4482049 AAAATAAGAGTAGACATAATATTTTTTGTTATTAAAATAAAATGCACTAAAATATTTAAAAAACT
131 AAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATGCACTAAAATATTTAAAAAACT
4482114 TTAAAT
196 TTAAAT
* * * * *
4482120 ACAATTTAACTTAATTAGGTAATTTAA-AAATAAAATAAGAGTAGACATAATATTTTTTGTGATT
1 ACAA-TTAACTTAATTAGGTAATTTAACAAA-AAAATAAAAGTAAACAAAATATTTTTCGTAATT
* *
4482184 AAAATAAAATGCAATAAAATATTTAAAAAAACTTTAAATACAATTTAATTTAATTAGGTAATTTA
64 AAAATAAAAT--AA-AAAATATTTAAAAAAACTTTAAATACAATGTAATTTAACTAGGTAATTTA
4482249 AAAAAAAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAAT
126 AAAAAAAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAAT
4482297 AAAATAAAAT
Statistics
Matches: 157, Mismatches: 15, Indels: 6
0.88 0.08 0.03
Matches are distributed among these distances:
201 7 0.04
202 57 0.36
204 2 0.01
205 91 0.58
ACGTcount: A:0.54, C:0.04, G:0.07, T:0.35
Consensus pattern (201 bp):
ACAATTAACTTAATTAGGTAATTTAACAAAAAAATAAAAGTAAACAAAATATTTTTCGTAATTAA
AATAAAATAAAAAATATTTAAAAAAACTTTAAATACAATGTAATTTAACTAGGTAATTTAAAAAA
AAAATAAAAGTAGACAAAATATTTTTTGTGATTAAAATAAAATGCACTAAAATATTTAAAAAACT
TTAAAT
Found at i:4485682 original size:21 final size:22
Alignment explanation
Indices: 4485658--4485698 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
4485648 TCTGTAAGTA
*
4485658 TTCATATTCAAATA-TATTTGT
1 TTCATATTAAAATACTATTTGT
*
4485679 TTCATTTTAAAATACTATTT
1 TTCATATTAAAATACTATTT
4485699 TCTTTATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (22 bp):
TTCATATTAAAATACTATTTGT
Found at i:4488292 original size:26 final size:26
Alignment explanation
Indices: 4488263--4488370 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
4488253 TGATACAAAT
4488263 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
4488289 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4488315 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
4488341 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
4488367 TGAT
1 TGAT
4488371 GGGAATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:4489866 original size:26 final size:26
Alignment explanation
Indices: 4489837--4489889 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
4489827 TTTACAGTTT
*
4489837 TACCCTTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
4489863 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
4489889 T
1 T
4489890 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:4492666 original size:20 final size:21
Alignment explanation
Indices: 4492599--4492680 Score: 77
Period size: 20 Copynumber: 4.0 Consensus size: 21
4492589 TAAATTAATT
4492599 TTATTAAACTTTTAAATAAAA
1 TTATTAAACTTTTAAATAAAA
* *
4492620 TAAAATT-AA-TTTGT--ATAAAT
1 T--TATTAAACTTT-TAAATAAAA
4492640 TTA-TAAACTTTT-AATAAAA
1 TTATTAAACTTTTAAATAAAA
4492659 TTATTAAACTTTTAAATAAAA
1 TTATTAAACTTTTAAATAAAA
4492680 T
1 T
4492681 AAAATTAATT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
17 1 0.02
18 4 0.08
19 11 0.22
20 15 0.31
21 12 0.24
22 3 0.06
23 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (21 bp):
TTATTAAACTTTTAAATAAAA
Found at i:4492669 original size:60 final size:60
Alignment explanation
Indices: 4492599--4492713 Score: 214
Period size: 60 Copynumber: 1.9 Consensus size: 60
4492589 TAAATTAATT
4492599 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAAATT-TATAAACTTTTAATAAAA
1 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTAT-AATTATATAAACTTTTAATAAAA
4492659 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAATTATATAAACTTTTAA
1 TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAATTATATAAACTTTTAA
4492714 ATTATTTTAT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
59 4 0.07
60 50 0.93
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.44
Consensus pattern (60 bp):
TTATTAAACTTTTAAATAAAATAAAATTAATTTGTATAATTATATAAACTTTTAATAAAA
Found at i:4492769 original size:35 final size:34
Alignment explanation
Indices: 4492712--4492779 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
4492702 ATAAACTTTT
* **
4492712 AAATTATTTTATTTTATTTAAAAGT-AAATTAATG
1 AAATTAATTTATTTTAAATAAAA-TAAAATTAATG
4492746 AAATTAATTTACTTTTAAATAAAATAAAATTAAT
1 AAATTAATTTA-TTTTAAATAAAATAAAATTAAT
4492780 TTGTATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (34 bp):
AAATTAATTTATTTTAAATAAAATAAAATTAATG
Found at i:4492802 original size:150 final size:147
Alignment explanation
Indices: 4492556--4493001 Score: 752
Period size: 150 Copynumber: 3.0 Consensus size: 147
4492546 TAATTTGTAT
* *
4492556 TAAAATTTTAAATAATTTTATTTTATTTAAAAGTAAATTAATTTTATTAA-ACTTTTAAATAAAA
1 TAAACTTTTAAATTATTTTATTTTATTTAAAAGTAAATTAATTTTATTAATACTTTTAAATAAAA
*
4492620 TAAAATTAATTTGTATAAATTTATAAACTTTTAATAAAATTATTAAACTTTTAAATAAAATAAAA
66 TAAAATTAATTTGTATAATTTTATAAACTTTTAATAAAATTATTAAACTTTTAAATAAAATAAAA
4492685 TTAATTTGTATAATTATA
131 TTAATTTGTA-AATTATA
***
4492703 TAAACTTTTAAATTATTTTATTTTATTTAAAAGTAAATTAATGAAATTAATTTACTTTTAAATAA
1 TAAACTTTTAAATTATTTTATTTTATTTAAAAGTAAATTAATTTTATTAA--TACTTTTAAATAA
*
4492768 AATAAAATTAATTTGTATAATTTTATAAAATTTTAATAAAATTATTAAACTTTTAAATAAAATAA
64 AATAAAATTAATTTGTATAATTTTATAAACTTTTAATAAAATTATTAAACTTTTAAATAAAATAA
4492833 AATTAATTTGTACAATTATA
129 AATTAATTTGTA-AATTATA
4492853 TAAACTTTTAAATTATTTTATTTTATTTAAAAGTAAATTAATTTTATTAAT-CTTTTAAATAAAA
1 TAAACTTTTAAATTATTTTATTTTATTTAAAAGTAAATTAATTTTATTAATACTTTTAAATAAAA
**
4492917 TAAAATTGTTTTGTATAATTTTATAAACTTTTAATAAAATTATTAAACTTTTAAATAAAATAAAA
66 TAAAATTAATTTGTATAATTTTATAAACTTTTAATAAAATTATTAAACTTTTAAATAAAATAAAA
*
4492982 TTAATTTGTAAATTTTA
131 TTAATTTGTAAATTATA
4492999 TAA
1 TAA
4493002 TTGTGGACGA
Statistics
Matches: 281, Mismatches: 15, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
146 9 0.03
147 130 0.46
148 1 0.00
150 141 0.50
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.47
Consensus pattern (147 bp):
TAAACTTTTAAATTATTTTATTTTATTTAAAAGTAAATTAATTTTATTAATACTTTTAAATAAAA
TAAAATTAATTTGTATAATTTTATAAACTTTTAATAAAATTATTAAACTTTTAAATAAAATAAAA
TTAATTTGTAAATTATA
Found at i:4492884 original size:55 final size:59
Alignment explanation
Indices: 4492746--4492896 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 59
4492736 TAAATTAATG
* * * *
4492746 AAATTAATTTACTTTTAAATAAAATAAAATTAATTTGTATAATTTTATAAAATTTTAATA
1 AAATTATTTTACTTTTAAATAAAATAAAATTAATTTGTACAATTATATAAAACTTT-ATA
**
4492806 AAATTATTAAACTTTTAAATAAAATAAAATTAATTTGTACAATTATAT-AAACTTT-T-
1 AAATTATTTTACTTTTAAATAAAATAAAATTAATTTGTACAATTATATAAAACTTTATA
**
4492862 AAATTATTTTA-TTTTATTTAAAAGT-AAATTAATTT
1 AAATTATTTTACTTTTAAATAAAA-TAAAATTAATTT
4492897 TATTAATCTT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
55 20 0.25
56 10 0.12
57 1 0.01
59 6 0.08
60 43 0.54
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (59 bp):
AAATTATTTTACTTTTAAATAAAATAAAATTAATTTGTACAATTATATAAAACTTTATA
Found at i:4493367 original size:21 final size:21
Alignment explanation
Indices: 4493343--4493396 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
4493333 TATATACCCT
4493343 AAACCTTAAACCCAAAATAAC
1 AAACCTTAAACCCAAAATAAC
** *
4493364 AAACCCCAAGCCCAAAATAAC
1 AAACCTTAAACCCAAAATAAC
4493385 AAACCTTAAACC
1 AAACCTTAAACC
4493397 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.54, C:0.33, G:0.02, T:0.11
Consensus pattern (21 bp):
AAACCTTAAACCCAAAATAAC
Found at i:4493408 original size:28 final size:28
Alignment explanation
Indices: 4493377--4493431 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
4493367 CCCCAAGCCC
*
4493377 AAAATAAC-AAACCTTAAAC-CATAAATTT
1 AAAAT-ACTAAACATTAAACGC-TAAATTT
4493405 AAAATACTAAACATTAAACGCTAAATT
1 AAAATACTAAACATTAAACGCTAAATT
4493432 GTAAGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 2 0.08
28 21 0.88
29 1 0.04
ACGTcount: A:0.56, C:0.16, G:0.02, T:0.25
Consensus pattern (28 bp):
AAAATACTAAACATTAAACGCTAAATTT
Found at i:4494132 original size:18 final size:17
Alignment explanation
Indices: 4494109--4494143 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
4494099 AAAGTCAGTT
*
4494109 TCAAATATCAAAATAAAA
1 TCAAAT-TCAAAACAAAA
4494127 TCAAATTCAAAACAAAA
1 TCAAATTCAAAACAAAA
4494144 ATAAGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.66, C:0.14, G:0.00, T:0.20
Consensus pattern (17 bp):
TCAAATTCAAAACAAAA
Found at i:4494328 original size:2 final size:2
Alignment explanation
Indices: 4494321--4494348 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4494311 GAAATGTACA
4494321 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
4494349 TAAAATAATT
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):
AT
Found at i:4496936 original size:41 final size:41
Alignment explanation
Indices: 4496534--4496928 Score: 551
Period size: 41 Copynumber: 9.7 Consensus size: 41
4496524 GTTTTAACCA
* * *
4496534 GAAACGCCGCTATTGCTCGATTTTTAGTGGTGTTTGAACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
*
4496575 GAAACGCCGCTATTGCTCGATTTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
** * *
4496616 GAAACGCTACTGTTGCTCAGTTTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* * *
4496657 GAAATGCCGCTATTGCTCGGTTTTTAGTGGCATTTGGACAT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* * *
4496698 GAAACGCCTCTATTGCTCGGTTTTTAGTGGCATTTGGACAT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* * *
4496739 GAAACGCCTCTATTGCTCGGTTTTTAGTGGCGTTTGAACAT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* *
4496780 GAAACGCCGCTATTGTTCAG-TTTTAGTGGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
* *
4496820 GAAACGCCGCTATTGCTCTGTTTTTAGTTGCGTTTGGACCT
1 GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
*
4496861 -AAAGCGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACTT
1 GAAA-CGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
**
4496902 GAAACGCCGCTATTGCTTTGTTTTTAG
1 GAAACGCCGCTATTGCTCGGTTTTTAG
4496929 CAGCGTTTTA
Statistics
Matches: 320, Mismatches: 31, Indels: 6
0.90 0.09 0.02
Matches are distributed among these distances:
40 39 0.12
41 278 0.87
42 3 0.01
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.37
Consensus pattern (41 bp):
GAAACGCCGCTATTGCTCGGTTTTTAGTGGCGTTTGGACCT
Found at i:4499643 original size:21 final size:20
Alignment explanation
Indices: 4499611--4499658 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
4499601 AATACATCTA
*
4499611 AAAACATAAAAACA-AATATT
1 AAAACA-AAAAAAATAATATT
*
4499631 AAAACAAATAAAAATGATATT
1 AAAACAAA-AAAAATAATATT
4499652 AAAACAA
1 AAAACAA
4499659 TTCTTAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 10 0.42
21 12 0.50
ACGTcount: A:0.71, C:0.08, G:0.02, T:0.19
Consensus pattern (20 bp):
AAAACAAAAAAAATAATATT
Found at i:4506782 original size:16 final size:16
Alignment explanation
Indices: 4506711--4506782 Score: 101
Period size: 16 Copynumber: 4.6 Consensus size: 16
4506701 ACAACTGAAT
*
4506711 TATT-CATTACAGGTC
1 TATTCCATTACAGCTC
*
4506726 TATTCTATTACAGCTC
1 TATTCCATTACAGCTC
*
4506742 TATTCCATTACAACTC
1 TATTCCATTACAGCTC
*
4506758 TATTACATTACAGCTC
1 TATTCCATTACAGCTC
4506774 TATTCCATT
1 TATTCCATT
4506783 CCTCCCAACC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
15 4 0.08
16 45 0.92
ACGTcount: A:0.28, C:0.25, G:0.06, T:0.42
Consensus pattern (16 bp):
TATTCCATTACAGCTC
Found at i:4513006 original size:37 final size:37
Alignment explanation
Indices: 4512950--4513162 Score: 135
Period size: 37 Copynumber: 5.9 Consensus size: 37
4512940 TTGTCATGAA
* *
4512950 CCAACCATGGTCTTGCACTTTATCACAATGCCATAGC
1 CCAACTATGGTCTTACACTTTATCACAATGCCATAGC
* * *
4512987 CCAGCTATGGTCTTACACTTTATTACGATGCCATAGC
1 CCAACTATGGTCTTACACTTTATCACAATGCCATAGC
* * *
4513024 CC-ACTTATGGTCTTACACGTATATACATATAATGCCATAGT
1 CCAAC-TATGGTCTTACAC-TTTAT-C--ACAATGCCATAGC
* * ** *
4513065 TCAACCATGGTCTTACA---T-TCATGATGCCATAAC
1 CCAACTATGGTCTTACACTTTATCACAATGCCATAGC
* *
4513098 CCAATTATGGTCTTTTCAC--TA--A-AATGCCATAGC
1 CCAACTATGGTC-TTACACTTTATCACAATGCCATAGC
* *
4513131 CCAGCTATGGTCTTACA-TTCA-CACAATGCCAT
1 CCAACTATGGTCTTACACTTTATCACAATGCCAT
4513163 GGTTCAACCA
Statistics
Matches: 137, Mismatches: 26, Indels: 28
0.72 0.14 0.15
Matches are distributed among these distances:
32 4 0.03
33 39 0.28
34 6 0.04
35 10 0.07
36 2 0.01
37 48 0.35
38 4 0.03
41 22 0.16
42 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (37 bp):
CCAACTATGGTCTTACACTTTATCACAATGCCATAGC
Found at i:4513108 original size:33 final size:33
Alignment explanation
Indices: 4513066--4513162 Score: 88
Period size: 33 Copynumber: 2.9 Consensus size: 33
4513056 TGCCATAGTT
* **
4513066 CAACCATGGTCTTACATTCATGATGCCATAACC
1 CAACTATGGTCTTACATTCAAAATGCCATAACC
* * * *
4513099 CAATTATGGTCTTTTCACT-AAAATGCCATAGCC
1 CAACTATGGTC-TTACATTCAAAATGCCATAACC
*
4513132 CAGCTATGGTCTTACATTCACACAATGCCAT
1 CAACTATGGTCTTACATTCA-A-AATGCCAT
4513163 GGTTCAACCA
Statistics
Matches: 49, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
32 5 0.10
33 30 0.61
34 6 0.12
35 8 0.16
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (33 bp):
CAACTATGGTCTTACATTCAAAATGCCATAACC
Found at i:4518292 original size:22 final size:22
Alignment explanation
Indices: 4518265--4518314 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
4518255 AACACTTTTT
4518265 AATAATGAAAAAGG-AAAAGAAA
1 AATAAT-AAAAAGGTAAAAGAAA
* * *
4518287 AATAATTAAATGGTATAAGAAA
1 AATAATAAAAAGGTAAAAGAAA
4518309 AATAAT
1 AATAAT
4518315 TTTTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (22 bp):
AATAATAAAAAGGTAAAAGAAA
Found at i:4526463 original size:33 final size:33
Alignment explanation
Indices: 4526421--4526486 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4526411 GGGAGAAAAC
4526421 TTTGAAACATTTGAAAGAGAGACTTTTCTCAAT
1 TTTGAAACATTTGAAAGAGAGACTTTTCTCAAT
4526454 TTTGAAACATTTGAAAGAGAGACTTTTCTCAAT
1 TTTGAAACATTTGAAAGAGAGACTTTTCTCAAT
4526487 GGTGGCAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (33 bp):
TTTGAAACATTTGAAAGAGAGACTTTTCTCAAT
Found at i:4532969 original size:118 final size:118
Alignment explanation
Indices: 4532761--4532991 Score: 372
Period size: 118 Copynumber: 2.0 Consensus size: 118
4532751 TGTTTTCCAT
* * *
4532761 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGGTAAGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCAGGGTAAGGTGCTTGGGTTGTCATT
4532826 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
* *
4532879 GGTTATGAGTATAGCTCAAATCGTGACTGACTGAGTAACCAGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCAGGGTAAGGTGCTTGGGTTGTCATT
* ****
4532944 CTATTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
66 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
4532992 ACCGGAAATA
Statistics
Matches: 103, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 103 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.29
Consensus pattern (118 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCAGGGTAAGGTGCTTGGGTTGTCATT
CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:4533146 original size:9 final size:10
Alignment explanation
Indices: 4533118--4533145 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
4533108 ATAAAATTTA
4533118 AAAAAAAAAG
1 AAAAAAAAAG
4533128 AAAAAAAAAG
1 AAAAAAAAAG
4533138 AAAAAAAA
1 AAAAAAAA
4533146 GTACTAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:4536454 original size:20 final size:22
Alignment explanation
Indices: 4536417--4536461 Score: 58
Period size: 20 Copynumber: 2.1 Consensus size: 22
4536407 TATATTTATC
*
4536417 TATACTATATGTTATAAAAATA
1 TATACTATATGTTATAAAAAAA
*
4536439 TATACT-TAT-TTTTAAAAAAA
1 TATACTATATGTTATAAAAAAA
4536459 TAT
1 TAT
4536462 TATAATTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 3 0.14
22 6 0.29
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (22 bp):
TATACTATATGTTATAAAAAAA
Found at i:4536469 original size:20 final size:22
Alignment explanation
Indices: 4536432--4536471 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4536422 TATATGTTAT
*
4536432 AAAAATATATACTTATTTTTAA
1 AAAAATATATACTAATTTTTAA
4536454 AAAAATAT-TA-TAATTTTT
1 AAAAATATATACTAATTTTT
4536472 GTCATATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAATATATACTAATTTTTAA
Found at i:4541243 original size:3 final size:3
Alignment explanation
Indices: 4541229--4541489 Score: 107
Period size: 3 Copynumber: 86.0 Consensus size: 3
4541219 TTAACGTGTC
* * * **
4541229 ATT ATT ACT ATT ATT TTT ATT TTT ATT ACC ATT ATT ATT ATT A-T ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* ** *
4541276 -TGT ATT -TAT ATTT ATT -TT ATT -TT AAT ACC ATT ATT ATT ACT ACTT
1 AT-T ATT AT-T A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
* *
4541321 CCATT ATT -TT -TT ATT -TCT AACT ATT ATT ATT TTT ATGT ATAT ATT
1 --ATT ATT ATT ATT ATT AT-T -ATT ATT ATT ATT ATT AT-T AT-T ATT
* * * *
4541366 ATT ATT -TAT ATT ATT GTT ATT ATT ACT ATT ATT AAAT ATT CTT ATT
1 ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT
* * * *
4541412 ATT ACT ATT ATT TTT ATT CCTT -TT ATT ATT GTTT ATT -TT CATT A-T
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT -ATT ATT ATT -ATT ATT
*
4541457 ATT ATT ATT ATT ACTT -CT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT
4541490 TTTTTTGTAC
Statistics
Matches: 192, Mismatches: 39, Indels: 54
0.67 0.14 0.19
Matches are distributed among these distances:
2 21 0.11
3 145 0.76
4 22 0.11
5 3 0.02
6 1 0.01
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:4542089 original size:11 final size:11
Alignment explanation
Indices: 4542073--4542098 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4542063 TCATTTATCA
4542073 TCATATTTATT
1 TCATATTTATT
4542084 TCATATTTATT
1 TCATATTTATT
4542095 TCAT
1 TCAT
4542099 TTTGTTCTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.12, G:0.00, T:0.62
Consensus pattern (11 bp):
TCATATTTATT
Found at i:4543187 original size:24 final size:26
Alignment explanation
Indices: 4543149--4543198 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
4543139 AATAACGAGA
4543149 ATAAATAAAAGTAAT-ATGTAAAAAAT
1 ATAAATAAAAGTAATGA-GTAAAAAAT
4543175 ATAAAT-AAA-TAATGAGTAAAAAAT
1 ATAAATAAAAGTAATGAGTAAAAAAT
4543199 GTACAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 13 0.57
25 4 0.17
26 6 0.26
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (26 bp):
ATAAATAAAAGTAATGAGTAAAAAAT
Found at i:4543206 original size:22 final size:21
Alignment explanation
Indices: 4543181--4543228 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4543171 AAATATAAAT
4543181 AAATAATGAGTAAAAAATGTAC
1 AAATAATGAGT-AAAAATGTAC
* * *
4543203 AAATAATGGGTGAAAATGTAT
1 AAATAATGAGTAAAAATGTAC
4543224 AAATA
1 AAATA
4543229 TGAATAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.25
Consensus pattern (21 bp):
AAATAATGAGTAAAAATGTAC
Found at i:4543263 original size:4 final size:4
Alignment explanation
Indices: 4543249--4543282 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
4543239 AAATACAAGG
*
4543249 TAAA GAAA TAAA TAAA T-AA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
4543283 TAGTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
TAAA
Found at i:4543294 original size:15 final size:15
Alignment explanation
Indices: 4543254--4543284 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4543244 CAAGGTAAAG
4543254 AAATAAATAAATAAT
1 AAATAAATAAATAAT
4543269 AAATAAATAAATAAT
1 AAATAAATAAATAAT
4543284 A
1 A
4543285 GTAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATAAATAAATAAT
Found at i:4543445 original size:13 final size:14
Alignment explanation
Indices: 4543429--4543466 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
4543419 GGGTAAATCA
4543429 AAATAAAATAAAT-
1 AAATAAAATAAATG
*
4543442 AAATTAAAT-AATG
1 AAATAAAATAAATG
4543455 AAATAAAATAAA
1 AAATAAAATAAA
4543467 GGACCAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
12 3 0.14
13 16 0.76
14 2 0.10
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAAAATAAATG
Found at i:4544527 original size:3 final size:3
Alignment explanation
Indices: 4544519--4544556 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
4544509 GGACTGTTTA
4544519 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
4544557 CATCTTGGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:4544893 original size:19 final size:19
Alignment explanation
Indices: 4544869--4544906 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4544859 ATACCTAACT
4544869 GAATCGATGTCTAAATGAC
1 GAATCGATGTCTAAATGAC
4544888 GAATCGATGTCTAAATGAC
1 GAATCGATGTCTAAATGAC
4544907 TTGTGATATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (19 bp):
GAATCGATGTCTAAATGAC
Found at i:4546143 original size:13 final size:13
Alignment explanation
Indices: 4546125--4546201 Score: 93
Period size: 13 Copynumber: 5.9 Consensus size: 13
4546115 ATATCTTCAT
4546125 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
4546138 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
4546151 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
*
4546164 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
4546177 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
*
4546190 TGCTTTGGAAAA
1 TGCTTTTGAAAA
4546202 ATTTAAGTGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
12 2 0.04
13 51 0.93
14 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:4546183 original size:39 final size:39
Alignment explanation
Indices: 4546125--4546201 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
4546115 ATATCTTCAT
*
4546125 TGCTTTTGAAAAGTGCTTTTGAAAAGTG-TTGTGGAAAAG
1 TGCTTTTGAAAAGTACTTTTGAAAAGTGCTT-TGGAAAAG
* *
4546164 TGCTTTTGAGAAGTACTTTTGAGAAGTGCTTTGGAAAA
1 TGCTTTTGAAAAGTACTTTTGAAAAGTGCTTTGGAAAA
4546202 ATTTAAGTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 32 0.94
40 2 0.06
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (39 bp):
TGCTTTTGAAAAGTACTTTTGAAAAGTGCTTTGGAAAAG
Found at i:4548058 original size:17 final size:17
Alignment explanation
Indices: 4548032--4548064 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4548022 AATATTTAAT
4548032 TTTAAATTTAGAAAATA
1 TTTAAATTTAGAAAATA
*
4548049 TTTAATTTTAGAAAAT
1 TTTAAATTTAGAAAAT
4548065 TAGGTGGCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAGAAAATA
Found at i:4551154 original size:20 final size:19
Alignment explanation
Indices: 4551129--4551170 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
4551119 AAATCGGGGG
*
4551129 TAAGTAAATAAACATATGAA
1 TAAGTAAACAAACATAT-AA
*
4551149 TAAGTAAACAAACTTATAA
1 TAAGTAAACAAACATATAA
4551168 TAA
1 TAA
4551171 AAAATGATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (19 bp):
TAAGTAAACAAACATATAA
Found at i:4551473 original size:3 final size:3
Alignment explanation
Indices: 4551465--4551525 Score: 79
Period size: 3 Copynumber: 20.3 Consensus size: 3
4551455 GACAATAAAG
*
4551465 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAA- AAT AAG
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
* *
4551510 AGT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT A
4551526 CATTAAAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.92
4 2 0.04
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4551813 original size:3 final size:3
Alignment explanation
Indices: 4551800--4551949 Score: 107
Period size: 3 Copynumber: 50.0 Consensus size: 3
4551790 ATGTGTATAT
*
4551800 ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
4551848 ATAA ATGG A-A ATA GTA ATG A-A ATGGC ATT AGA ATA A-A ATA A-A TATA
1 AT-A AT-A ATA ATA ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA -ATA
* *
4551894 AGT- ATA A-A TATA ATG ATG ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
4551939 ATA ATA A-A ATA
1 ATA ATA ATA ATA
4551950 GAGCGACAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
2 9 0.08
3 100 0.85
4 7 0.06
5 2 0.02
ACGTcount: A:0.62, C:0.01, G:0.07, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:4552131 original size:19 final size:19
Alignment explanation
Indices: 4552094--4552132 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4552084 AAATAATCAT
*
4552094 AGTAATAATAATAAGTTAA
1 AGTAATAATAATAAATTAA
4552113 AGTAATAATAA-AATATTAA
1 AGTAATAATAATAA-ATTAA
4552132 A
1 A
4552133 TATGTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 2 0.11
19 16 0.89
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (19 bp):
AGTAATAATAATAAATTAA
Found at i:4552754 original size:11 final size:11
Alignment explanation
Indices: 4552738--4552763 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4552728 AAGGTAAAAA
4552738 TTTATTATTTT
1 TTTATTATTTT
4552749 TTTATTATTTT
1 TTTATTATTTT
4552760 TTTA
1 TTTA
4552764 GATCTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTATTTT
Found at i:4553851 original size:44 final size:44
Alignment explanation
Indices: 4553781--4553938 Score: 167
Period size: 44 Copynumber: 3.6 Consensus size: 44
4553771 ATTTCTAGCT
* *
4553781 TGTTACCCTACTGCATAGGGGTTTAAGGCCCATCGCCTTCGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATC
* ***** ***
4553825 TGTTTCCCTACTGCTTAGGGGGTTAAGATTTGT-AAATTC-AGTC
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGA-TC
* *
4553868 TGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTTGATC
1 TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATC
*
4553912 TGTTTCCCTACTGCTTAGGGGGTTAAG
1 TGTTACCCTACTGCTTAGGGGGTTAAG
4553939 ATTTGTAAAT
Statistics
Matches: 87, Mismatches: 24, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
42 1 0.01
43 31 0.36
44 54 0.62
45 1 0.01
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.35
Consensus pattern (44 bp):
TGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCGATC
Found at i:4553887 original size:87 final size:87
Alignment explanation
Indices: 4553756--4554156 Score: 500
Period size: 87 Copynumber: 4.6 Consensus size: 87
4553746 CCATTTCAGA
* * * * *
4553756 GAGAAAAGATTTGTAATTTCTAGCTTGTTACCCTACTGCATAGGGGTTTAAGGCCCATCGCCTTC
1 GAGACAAGATTTGTAAATTC-AGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTC
*
4553821 GATCTGTTTCC-CTACTGCTTAGG
65 GATCTG-CTCCACTACTGCTTAGG
* ** * * *
4553844 GGGTTAAGATTTGTAAATTCAGTCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATCGCCTTTG
1 GAGACAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
*
4553909 ATCTGTTTCC-CTACTGCTTAGG
66 ATCTG-CTCCACTACTGCTTAGG
* ** * * ** *
4553931 GGGTTAAGATTTGTAAATTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTTTG
1 GAGACAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
*
4553996 ATTTGCTCCACTACTGCTTAGG
66 ATCTGCTCCACTACTGCTTAGG
* * * *
4554018 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTATTGCTTAGGGGGTTAAGGCCCTTCGTCTTCG
1 GAGACAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
* *
4554083 ATTTGCTCCACTACTACTTAGG
66 ATCTGCTCCACTACTGCTTAGG
*
4554105 GAGACAAGATCTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
1 GAGACAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGG
4554157 TCTGTGAATT
Statistics
Matches: 286, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
86 3 0.01
87 267 0.93
88 16 0.06
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (87 bp):
GAGACAAGATTTGTAAATTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCATCGCCTTCG
ATCTGCTCCACTACTGCTTAGG
Found at i:4554161 original size:43 final size:43
Alignment explanation
Indices: 4553823--4554168 Score: 190
Period size: 43 Copynumber: 8.0 Consensus size: 43
4553813 TCGCCTTCGA
* *
4553823 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTCAG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAG
* *** *
4553866 TCTGTTACCCTACTGCTTAGGGGTTTAAGGCCCATC-G-CCTTTGA-
1 TCTGTTACCCTACTGCTTAGGGGGTTAA-G---ATCTGTAAATTCAG
* * *
4553910 TCTGTTTCCCTACTGCTTAGGGGGTTAAGATTTGTAAATTTAG
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAG
* ** * **
4553953 CCTGTTACCCTACTGCTTAGGGGGTTAAGGCCCT-T-CATCTTTG
1 TCTGTTACCCTACTGCTTAGGGGGTTAA-GATCTGTAAAT-TCAG
* * * **
4553996 ATTTGCT-CCACTACTGCTTAGGGAGACAAGATCTGTAAATTCAG
1 -TCTGTTACC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAG
* * ** *
4554040 CCTGTTACCCTATTGCTTAGGGGGTTAAGGCCCTTCGT--CTTC-G
1 TCTGTTACCCTACTGCTTAGGGGGTTAA-GATC-T-GTAAATTCAG
* * * * **
4554083 ATTTGCT-CCACTACTACTTAGGGAGACAAGATCTGTAAATTCAG
1 -TCTGTTACC-CTACTGCTTAGGGGGTTAAGATCTGTAAATTCAG
* * *
4554127 CCTGTTACCCTACTGCTTAGGGGGTTAAGGTCTGTGAATTCA
1 TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCA
4554169 CCGATCTAGG
Statistics
Matches: 218, Mismatches: 62, Indels: 46
0.67 0.19 0.14
Matches are distributed among these distances:
40 2 0.01
41 3 0.01
42 6 0.03
43 118 0.54
44 78 0.36
45 6 0.03
46 3 0.01
47 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.35
Consensus pattern (43 bp):
TCTGTTACCCTACTGCTTAGGGGGTTAAGATCTGTAAATTCAG
Found at i:4560876 original size:7 final size:7
Alignment explanation
Indices: 4560858--4560906 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
4560848 ACCTTTGTTC
*
4560858 ATTTTTC
1 ATTTTTT
4560865 ATTTTTGT
1 ATTTTT-T
*
4560873 TTTTTTT
1 ATTTTTT
*
4560880 A-ATTTT
1 ATTTTTT
4560886 ATTTTTT
1 ATTTTTT
4560893 ATTTTTT
1 ATTTTTT
4560900 ATTTTTT
1 ATTTTTT
4560907 TTATAAATCT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
6 5 0.14
7 25 0.71
8 5 0.14
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.82
Consensus pattern (7 bp):
ATTTTTT
Found at i:4561806 original size:2 final size:2
Alignment explanation
Indices: 4561799--4561832 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
4561789 TACTTTTGTT
4561799 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4561833 TATTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4561822 original size:15 final size:15
Alignment explanation
Indices: 4561802--4561831 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4561792 TTTTGTTTAT
4561802 ATATATATATATATA
1 ATATATATATATATA
4561817 ATATATATATATATA
1 ATATATATATATATA
4561832 TTATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:4561822 original size:17 final size:17
Alignment explanation
Indices: 4561800--4561832 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
4561790 ACTTTTGTTT
4561800 ATATATATATATATATA
1 ATATATATATATATATA
4561817 ATATATATATATATAT
1 ATATATATATATATAT
4561833 TATTTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATATATA
Found at i:4564346 original size:14 final size:15
Alignment explanation
Indices: 4564324--4564356 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4564314 ATTTTAATTT
*
4564324 AAAATTTAATAA-GA
1 AAAAATTAATAATGA
4564338 AAAAATTAATAATGA
1 AAAAATTAATAATGA
4564353 AAAA
1 AAAA
4564357 GGAAATGACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
AAAAATTAATAATGA
Found at i:4567820 original size:15 final size:15
Alignment explanation
Indices: 4567802--4567830 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4567792 AAATTCAATG
4567802 CTTAAATTTTTAATA
1 CTTAAATTTTTAATA
4567817 CTTAAATTTTTAAT
1 CTTAAATTTTTAAT
4567831 TTATCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
CTTAAATTTTTAATA
Found at i:4567848 original size:28 final size:28
Alignment explanation
Indices: 4567817--4567877 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
4567807 ATTTTTAATA
*
4567817 CTTAAATTTTTAATTTATCAAACACGCG
1 CTTAAAATTTTAATTTATCAAACACGCG
4567845 CTTAAAATTTTAATTTATCAAACACGCG
1 CTTAAAATTTTAATTTATCAAACACGCG
*
4567873 TTTAA
1 CTTAA
4567878 CTAGATAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.07, T:0.39
Consensus pattern (28 bp):
CTTAAAATTTTAATTTATCAAACACGCG
Found at i:4569059 original size:9 final size:9
Alignment explanation
Indices: 4569022--4569059 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
4569012 TTATATTTAC
4569022 TTTTTAAAA
1 TTTTTAAAA
4569031 -TTTTAAATA
1 TTTTTAAA-A
*
4569040 TTTTTACAA
1 TTTTTAAAA
4569049 TTTTTAAAA
1 TTTTTAAAA
4569058 TT
1 TT
4569060 CAAACTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:4569553 original size:25 final size:25
Alignment explanation
Indices: 4569501--4569553 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4569491 ATTTTTAAAT
* * **
4569501 TTTTTTTGTAATAATAAGAAAATTA
1 TTTTTTTATAAAAATAAGAAAAAAA
4569526 TTTTTTTATAAAAATAAGAAAAAAA
1 TTTTTTTATAAAAATAAGAAAAAAA
4569551 TTT
1 TTT
4569554 AATAATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTTTTATAAAAATAAGAAAAAAA
Found at i:4576462 original size:18 final size:20
Alignment explanation
Indices: 4576418--4576462 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 20
4576408 TTTCCAAAAA
4576418 TTAATT-AACTTCAACAATT
1 TTAATTAAACTTCAACAATT
* *
4576437 TCATTTAAACTT-AA-AATT
1 TTAATTAAACTTCAACAATT
4576455 TTAATTAA
1 TTAATTAA
4576463 TTTTATTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 10 0.48
19 6 0.29
20 5 0.24
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAATTAAACTTCAACAATT
Done.