Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 125 of 325
Found at i:40168541 original size:25 final size:25
Alignment explanation
Indices: 40168512--40168563 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
40168502 AGGAATAATT
**
40168512 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
40168537 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
40168562 TG
1 TG
40168564 TCAAGCCAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:40169219 original size:10 final size:10
Alignment explanation
Indices: 40169204--40169231 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
40169194 ATATTACATG
40169204 TTTACTTTGT
1 TTTACTTTGT
40169214 TTTACTTTGT
1 TTTACTTTGT
40169224 TTTACTTT
1 TTTACTTT
40169232 TTCTCCTAAT
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:0.11, C:0.11, G:0.07, T:0.71
Consensus pattern (10 bp):
TTTACTTTGT
Found at i:40170293 original size:21 final size:21
Alignment explanation
Indices: 40170240--40170327 Score: 106
Period size: 21 Copynumber: 4.1 Consensus size: 21
40170230 ATATCGACTT
* **
40170240 TGTCG-ATCAGGCACTTTATG
1 TGTCGTATCAGGCACCTCGTG
*
40170260 TGTCGTATTTCAGGAACCTCGTG
1 TGTCGTA--TCAGGCACCTCGTG
40170283 TGTCGTATCAGGCACCTCGTG
1 TGTCGTATCAGGCACCTCGTG
*
40170304 TGTCGTTTCAGGCACCTCGTG
1 TGTCGTATCAGGCACCTCGTG
40170325 TGT
1 TGT
40170328 TGTTTCAAGC
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
20 5 0.08
21 37 0.63
23 17 0.29
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (21 bp):
TGTCGTATCAGGCACCTCGTG
Found at i:40170332 original size:21 final size:21
Alignment explanation
Indices: 40170258--40170339 Score: 110
Period size: 21 Copynumber: 3.8 Consensus size: 21
40170248 AGGCACTTTA
*
40170258 TGTGTCGTATTTCAGGAACCTCG
1 TGTGTCG--TTTCAGGCACCTCG
*
40170281 TGTGTCGTATCAGGCACCTCG
1 TGTGTCGTTTCAGGCACCTCG
40170302 TGTGTCGTTTCAGGCACCTCG
1 TGTGTCGTTTCAGGCACCTCG
* *
40170323 TGTGTTGTTTCAAGCAC
1 TGTGTCGTTTCAGGCAC
40170340 TTATGTGTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 47 0.87
23 7 0.13
ACGTcount: A:0.15, C:0.24, G:0.27, T:0.34
Consensus pattern (21 bp):
TGTGTCGTTTCAGGCACCTCG
Found at i:40173223 original size:11 final size:11
Alignment explanation
Indices: 40173207--40173231 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
40173197 ATATCTAGAA
40173207 TTCTCTTCATT
1 TTCTCTTCATT
40173218 TTCTCTTCATT
1 TTCTCTTCATT
40173229 TTC
1 TTC
40173232 ATTAACTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:40174511 original size:25 final size:25
Alignment explanation
Indices: 40174482--40174533 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
40174472 AAGAATAATT
**
40174482 TGAATATTTGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
40174507 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
40174532 TG
1 TG
40174534 TTAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:40175563 original size:16 final size:16
Alignment explanation
Indices: 40175542--40175609 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
40175532 TTTGGTTCGC
40175542 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40175558 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
40175574 TGTAATGGATTAGAGG
1 TGTATTGGATTAGAGG
40175590 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
40175606 TGTA
1 TGTA
40175610 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.37, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:40175863 original size:16 final size:16
Alignment explanation
Indices: 40175826--40175867 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
40175816 TTAATCATAT
*
40175826 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
40175842 TT-AAATATATTATAA
1 TTAAAATATATTATAA
40175857 TTAAAATATAT
1 TTAAAATATAT
40175868 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:40175874 original size:14 final size:15
Alignment explanation
Indices: 40175835--40175876 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
40175825 TTTAAACATA
*
40175835 ATTATTATTAAATAT
1 ATTATAATTAAATAT
40175850 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
40175864 A-TATAATTTAATA
1 ATTATAATTAAATA
40175877 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:40175994 original size:14 final size:15
Alignment explanation
Indices: 40175945--40175996 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40175935 ATAAAATATA
40175945 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40175960 TATTAAATATATTAT
1 AATTAAATATATTAT
40175975 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40175988 AATTTAATA
1 AATTAAATA
40175997 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40176064 original size:119 final size:120
Alignment explanation
Indices: 40175829--40176149 Score: 619
Period size: 119 Copynumber: 2.7 Consensus size: 120
40175819 ATCATATTTA
40175829 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40175894 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
40175949 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-AATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40176013 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
*
40176068 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTATTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
40176133 TATTCTTATAT-AATTTA
66 TATTCTTATATGAATTTA
40176150 ATAAAACAAT
Statistics
Matches: 199, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
119 124 0.62
120 75 0.38
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:40176106 original size:18 final size:18
Alignment explanation
Indices: 40176085--40176132 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
40176075 TTATTATTAA
40176085 ATATATTATAATTAAAAT
1 ATATATTATAATTAAAAT
40176103 ATATAATT-TAA-TAAAAT
1 ATAT-ATTATAATTAAAAT
*
40176120 -TAT-TAATAATTAA
1 ATATATTATAATTAA
40176133 TATTCTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.04
15 3 0.12
16 6 0.23
17 6 0.23
18 7 0.27
19 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATATATTATAATTAAAAT
Found at i:40176113 original size:14 final size:15
Alignment explanation
Indices: 40176064--40176115 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40176054 ATAAAATATA
40176064 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
40176079 TATTAAATATATTAT
1 AATTAAATATATTAT
40176094 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
40176107 AATTTAATA
1 AATTAAATA
40176116 AAATTATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:40176122 original size:44 final size:43
Alignment explanation
Indices: 40176041--40176124 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
40176031 CTCAAATCAT
* *
40176041 AATATATGATACTATAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATATAAAATATAAATTAACAAAATTATTATTA
* *
40176084 AATATATTATAAT-TAAAATATATAATTTAATAAAATTATTA
1 AATATATGATAATATAAAATATA-AA-TTAACAAAATTATTA
40176125 ATAATTAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 9 0.26
43 13 0.37
44 13 0.37
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (43 bp):
AATATATGATAATATAAAATATAAATTAACAAAATTATTATTA
Found at i:40178454 original size:12 final size:13
Alignment explanation
Indices: 40178426--40178459 Score: 61
Period size: 12 Copynumber: 2.7 Consensus size: 13
40178416 TGGAGAAAGC
40178426 AAAGCAAAGGAAG
1 AAAGCAAAGGAAG
40178439 AAAGCAAAGG-AG
1 AAAGCAAAGGAAG
40178451 AAAGCAAAG
1 AAAGCAAAG
40178460 CAAAGAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.62, C:0.09, G:0.29, T:0.00
Consensus pattern (13 bp):
AAAGCAAAGGAAG
Found at i:40178531 original size:19 final size:19
Alignment explanation
Indices: 40178504--40178540 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
40178494 AATCGGGCAA
40178504 AACAAAAGAGGCAAAGGGG
1 AACAAAAGAGGCAAAGGGG
* *
40178523 AACAGAAGAGGCAGAGGG
1 AACAAAAGAGGCAAAGGG
40178541 TAAAACAGGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.41, T:0.00
Consensus pattern (19 bp):
AACAAAAGAGGCAAAGGGG
Found at i:40179426 original size:24 final size:24
Alignment explanation
Indices: 40179399--40179445 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40179389 ATTGAAATGG
40179399 ATTG-ATTTATTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
40179423 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
40179446 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:40179648 original size:41 final size:39
Alignment explanation
Indices: 40179603--40179738 Score: 152
Period size: 40 Copynumber: 3.5 Consensus size: 39
40179593 CGACTTCGAG
*
40179603 TCGATGAGGCACTGGGTGTCAATTTACTACTTCGGATTAAT
1 TCGATGAGGCACTGGGTGTCAA-TTACTACTTCGAATT-AT
* *
40179644 TCGATGAGGCACTGGGTGCCAATT--TACTTC-AATTTAG
1 TCGATGAGGCACTGGGTGTCAATTACTACTTCGAA-TTAT
* **
40179681 TCGATGAGACACAAGGTGTCAAATTACTACTTCGAATTAT
1 TCGATGAGGCACTGGGTGTC-AATTACTACTTCGAATTAT
*
40179721 CCGATGAGGCACTGGGTG
1 TCGATGAGGCACTGGGTG
40179739 CCAAACTGGT
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
37 18 0.23
38 12 0.15
40 25 0.32
41 23 0.29
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (39 bp):
TCGATGAGGCACTGGGTGTCAATTACTACTTCGAATTAT
Found at i:40185665 original size:48 final size:48
Alignment explanation
Indices: 40185609--40185707 Score: 180
Period size: 48 Copynumber: 2.1 Consensus size: 48
40185599 TCTAGTCGTT
*
40185609 ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTTAGA
1 ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
*
40185657 ATTCTCACACAAATTGGTAACAACCTATGAATTCTATAAAATGTCAGA
1 ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
40185705 ATT
1 ATT
40185708 TTCCATAATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.09, T:0.31
Consensus pattern (48 bp):
ATTCTCACACAAATTGATAACAACCTATGAATTCTATAAAATGTCAGA
Found at i:40189702 original size:18 final size:19
Alignment explanation
Indices: 40189658--40189706 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
40189648 AGGCATTTTC
40189658 CAACCTTAACATACAAAAT
1 CAACCTTAACATACAAAAT
* *
40189677 AAATCTTAACATAC-AAAT
1 CAACCTTAACATACAAAAT
40189695 CAACCTTAACAT
1 CAACCTTAACAT
40189707 TCATCACATG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
18 14 0.54
19 12 0.46
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (19 bp):
CAACCTTAACATACAAAAT
Found at i:40195836 original size:24 final size:24
Alignment explanation
Indices: 40195809--40195854 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
40195799 AAAGTTACTT
40195809 GTAAAACTAAAATTACATGCATAA
1 GTAAAACTAAAATTACATGCATAA
*
40195833 GTAAGACTAAAATTACATGCAT
1 GTAAAACTAAAATTACATGCAT
40195855 GTAGTTAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (24 bp):
GTAAAACTAAAATTACATGCATAA
Found at i:40197091 original size:27 final size:27
Alignment explanation
Indices: 40197059--40197111 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
40197049 TACAATCTAT
40197059 AGTTTGCTTGTTTCCTTAGAAACAATG
1 AGTTTGCTTGTTTCCTTAGAAACAATG
40197086 AGTTTGCTTGTTTCCTTAGAAACAAT
1 AGTTTGCTTGTTTCCTTAGAAACAAT
40197112 CATTGGACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (27 bp):
AGTTTGCTTGTTTCCTTAGAAACAATG
Found at i:40208979 original size:61 final size:61
Alignment explanation
Indices: 40208884--40209053 Score: 174
Period size: 61 Copynumber: 2.9 Consensus size: 61
40208874 TTATTATTAA
** * * * *
40208884 ATTTTAATAGGATTATAATTAAATGTAATTTAATAAAAATAAAAATAAATAATTTAATCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAAC
**
40208945 ATTTTAATATAATTATTATTAAATATAATTTAAT---AAT---AATGTATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAAC
* *
40209000 ATTCTTAATGTAATTATTATTAAAATATGAA-TTAATAAAAATAAAAATACATAA
1 ATT-TTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAAAAATAAATAA
40209054 GATTAGAAAA
Statistics
Matches: 89, Mismatches: 11, Indels: 16
0.77 0.09 0.14
Matches are distributed among these distances:
55 17 0.19
56 16 0.18
57 11 0.12
58 5 0.06
60 3 0.03
61 30 0.34
63 7 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (61 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAAATAATTTAATAAC
Found at i:40208980 original size:55 final size:57
Alignment explanation
Indices: 40208921--40209044 Score: 164
Period size: 55 Copynumber: 2.2 Consensus size: 57
40208911 ATTTAATAAA
* *
40208921 AATAAAAATAAATAATTTAATCATATT-TTAATATAATTATTATT-AAATAT-AATTT
1 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAA-TT
* ** *
40208976 AATAATAATGTATAATTTAATAACATTCTTAATGTAATTATTATTAAAATATGAATT
1 AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAATT
40209033 AATAAAAATAAA
1 AATAAAAATAAA
40209045 AATACATAAG
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
55 22 0.39
56 16 0.28
57 17 0.30
58 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (57 bp):
AATAAAAATAAATAATTTAATAACATTCTTAATATAATTATTATTAAAATATGAATT
Found at i:40212241 original size:14 final size:14
Alignment explanation
Indices: 40212222--40212248 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40212212 TATACTTCAC
40212222 GGTGTAAGTGAAAT
1 GGTGTAAGTGAAAT
40212236 GGTGTAAGTGAAA
1 GGTGTAAGTGAAA
40212249 GAAAGAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.26
Consensus pattern (14 bp):
GGTGTAAGTGAAAT
Found at i:40218124 original size:40 final size:40
Alignment explanation
Indices: 40218065--40218316 Score: 330
Period size: 40 Copynumber: 6.3 Consensus size: 40
40218055 CATTTGAATG
*
40218065 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
40218105 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
40218145 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
40218185 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
40218225 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
40218265 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
40218305 ATATCC-GGCTAA
1 ATATCCGGGCTAA
40218317 ATTCCGAAGA
Statistics
Matches: 193, Mismatches: 16, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
39 7 0.04
40 183 0.95
41 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:40226546 original size:40 final size:40
Alignment explanation
Indices: 40226487--40226737 Score: 321
Period size: 40 Copynumber: 6.3 Consensus size: 40
40226477 CATTTGAATG
*
40226487 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
40226527 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
40226567 TTATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
40226607 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
40226647 ATATCC-GGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
40226686 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
40226726 ATATCC-GGCTAA
1 ATATCCGGGCTAA
40226738 ATTCCGAAGA
Statistics
Matches: 191, Mismatches: 16, Indels: 9
0.88 0.07 0.04
Matches are distributed among these distances:
39 44 0.23
40 144 0.75
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:40229049 original size:20 final size:20
Alignment explanation
Indices: 40228991--40229049 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
40228981 TATTCTATGA
40228991 TATTATA-TAAATTAACGAA-
1 TATTATATTAAATTAAC-AAT
* * **
40229010 -AATATATTTAATTATTAAT
1 TATTATATTAAATTAACAAT
40229029 TATTATATTAAATTAACAAT
1 TATTATATTAAATTAACAAT
40229049 T
1 T
40229050 GCGTATCTTT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
18 7 0.24
19 6 0.21
20 16 0.55
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (20 bp):
TATTATATTAAATTAACAAT
Found at i:40232888 original size:39 final size:39
Alignment explanation
Indices: 40232833--40232933 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
40232823 ATCGCGATCT
**
40232833 GAAGCCCGAAATCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
40232872 GAAGCCCGAAGGCTAACTGAAGTACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
40232911 AAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
40232934 TCATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:40232946 original size:39 final size:39
Alignment explanation
Indices: 40232834--40232978 Score: 159
Period size: 39 Copynumber: 3.7 Consensus size: 39
40232824 TCGCGATCTG
** * *
40232834 AAGCCCGAAATCTAACTGAAGCACATAAGTGCTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCTCATAAGTGCTAAACGA
40232873 AAGCCCGAAGGCTAACTGAAG-TACATAAGTGCTAAACGA
1 AAGCCCGAAGGCTAACTGAAGCT-CATAAGTGCTAAACGA
* *
40232912 AAGCCCGAAGGCTAACTGAAGCTCATCAGAGCT-AACTGA
1 AAGCCCGAAGGCTAACTGAAGCTCATAAGTGCTAAAC-GA
* * * *
40232951 AACCCCAAAAGGGTAACTGAAACTCATA
1 AAGCCC-GAAGGCTAACTGAAGCTCATA
40232979 TGAGTTAACG
Statistics
Matches: 91, Mismatches: 11, Indels: 7
0.83 0.10 0.06
Matches are distributed among these distances:
38 3 0.03
39 70 0.77
40 18 0.20
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (39 bp):
AAGCCCGAAGGCTAACTGAAGCTCATAAGTGCTAAACGA
Found at i:40236284 original size:31 final size:31
Alignment explanation
Indices: 40236249--40236398 Score: 167
Period size: 31 Copynumber: 4.8 Consensus size: 31
40236239 CTTGTCACTT
* *
40236249 GTAGCCGAAGCTACCACTATTCACTGATTAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* * * *
40236280 GTAGCCGGAGTTACCATTTTTTTATCT-ATCAG
1 GTAGCCGAAGCTACCA-CTTTTCA-CTGATCAG
* * *
40236312 GTAGCCGGAGCTACCACTTTTCACTAACCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
40236343 GTAGCAGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
40236374 GTAGTCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
40236399 TGTCATTTGT
Statistics
Matches: 99, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.02
31 72 0.73
32 23 0.23
33 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:40236358 original size:63 final size:62
Alignment explanation
Indices: 40236249--40236398 Score: 167
Period size: 63 Copynumber: 2.4 Consensus size: 62
40236239 CTTGTCACTT
* * ** * * * * * *
40236249 GTAGCCGAAGCTACCACTATTCACTGATTAGGTAGCCGGAGTTACCATTTTTTTATCT-ATCAG
1 GTAGCCGAAGCTACCACTTTTCACTAACCAGGTAGCAGAAGCTACCA-CTTTTCA-CTGATCAA
*
40236312 GTAGCCGGAGCTACCACTTTTCACTAACCAGGTAGCAGAAGCTACCACTTTTCACTGATCAA
1 GTAGCCGAAGCTACCACTTTTCACTAACCAGGTAGCAGAAGCTACCACTTTTCACTGATCAA
*
40236374 GTAGTCGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
40236399 TGTCATTTGT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
61 2 0.03
62 32 0.44
63 39 0.53
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (62 bp):
GTAGCCGAAGCTACCACTTTTCACTAACCAGGTAGCAGAAGCTACCACTTTTCACTGATCAA
Found at i:40236475 original size:50 final size:51
Alignment explanation
Indices: 40236374--40236502 Score: 170
Period size: 50 Copynumber: 2.5 Consensus size: 51
40236364 CACTGATCAA
* * * *
40236374 GTAGTCGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTGATCAGATAAGT
* * * *
40236425 GTAGCCGAAGTTATCACTTATCACTT-TCACTTGTCCTTGATTAGTTAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTGATCAGATAAGT
*
40236475 GTAGCCGAAGCTATTACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
40236503 TGCCATGGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
50 44 0.66
51 23 0.34
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCACTTGTCATTGATCAGATAAGT
Found at i:40237816 original size:39 final size:39
Alignment explanation
Indices: 40237754--40237854 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
40237744 ATCGTGATCT
** * *
40237754 GAAGCCCGAAATCTAGCTAAAGCACATAAGTGCTAAACA
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
**
40237793 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAATG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
40237832 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
40237855 TCATCAGAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.40, C:0.23, G:0.24, T:0.14
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACA
Found at i:40244629 original size:46 final size:45
Alignment explanation
Indices: 40244557--40244730 Score: 179
Period size: 46 Copynumber: 3.8 Consensus size: 45
40244547 GTAACCCGCT
* *
40244557 CATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATC
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCATC
* * * *
40244603 CATAAGTGAACTCGGACTCAAATCAACGAGCTCGGATGCCTAG-TTA
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTAGCATC
*** * * *
40244649 CATCTCTCGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATC
1 CATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTAGCATC
*
40244696 CATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
40244731 ATGCCCAAAC
Statistics
Matches: 102, Mismatches: 21, Indels: 10
0.77 0.16 0.08
Matches are distributed among these distances:
45 1 0.01
46 66 0.65
47 33 0.32
48 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (45 bp):
CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTAGCATC
Found at i:40244675 original size:93 final size:93
Alignment explanation
Indices: 40244563--40244735 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
40244553 CGCTCATAAG
* * *
40244563 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAAATCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAAATCA
40244628 ACGAGCTCGGATGCCTAGTTACATCTCT
66 ACGAGCTCGGATGCCTAGTTACATCTCT
* *
40244656 CGAACTCGGACTCAACTCAACGAGCTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAAATCA
*
40244721 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
40244736 CAAACATCCT
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAAATCA
ACGAGCTCGGATGCCTAGTTACATCTCT
Found at i:40252101 original size:28 final size:28
Alignment explanation
Indices: 40252069--40252281 Score: 121
Period size: 28 Copynumber: 7.5 Consensus size: 28
40252059 CCTTTAACAG
*
40252069 GTTTT-CCACAAAGGTTTACTTTCTAGA
1 GTTTTGCCACAAAGGTTTACTTTCAAGA
* * * * *
40252096 GTTTTTCCATAAAGGCTGTCCTTT-AACA
1 GTTTTGCCACAAAGG-TTTACTTTCAAGA
* * * * *
40252124 GGTTCGCTACAAAGGCTTACCTTTCTAGA
1 GTTTTGCCACAAAGGTTTA-CTTTCAAGA
* * *
40252153 GTTTTGCCACAAAGGCTCTCCTTT-AACA
1 GTTTTGCCACAAAGG-TTTACTTTCAAGA
* * *
40252181 GGTTTGCCACAAAGGCTTACATTTCTAGA
1 GTTTTGCCACAAAGGTTTAC-TTTCAAGA
* * * *
40252210 GTTTTGCCCCAAAGGCTATCCTTT-AATA
1 GTTTTGCCACAAAGG-TTTACTTTCAAGA
*
40252238 -TGTTTGCCACAAAGGTTTACCTTTCCAGA
1 GT-TTTGCCACAAAGGTTTA-CTTTCAAGA
*
40252267 GTTTTTCCACAAAGG
1 GTTTTGCCACAAAGG
40252282 CTATCATTTA
Statistics
Matches: 132, Mismatches: 42, Indels: 22
0.67 0.21 0.11
Matches are distributed among these distances:
27 11 0.08
28 61 0.46
29 56 0.42
30 4 0.03
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (28 bp):
GTTTTGCCACAAAGGTTTACTTTCAAGA
Found at i:40252168 original size:57 final size:57
Alignment explanation
Indices: 40252059--40252569 Score: 533
Period size: 57 Copynumber: 9.0 Consensus size: 57
40252049 CAAAAGATGC
** * * * *
40252059 CCTTTAACAGGTTTTCCACAAAGGTTTA-CTTTCTAGAGTTTTTCCATAAAGGCTGT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* *
40252115 CCTTTAACAGGTTCGCTACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTCT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * *
40252172 CCTTTAACAGGTTTGCCACAAAGGCTTACATTTCTAGAGTTTTGCCCCAAAGGCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * * *
40252229 CCTTTAATATGTTTGCCACAAAGGTTTACCTTTCCAGAGTTTTTCCACAAAGGCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * ** * * * ** *
40252286 CATTTAACAAGTTCGCCTTATAGGCTTACCTTTTTAGAGTTTTTCCATGAAGTCTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * *
40252343 CCTTTAATAGGTGT-GCCATAAAGGCTTACCTTTCCAGTGTTTTGCCATAAAGGCTAT
1 CCTTTAACAGGT-TCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * * * *
40252400 CCTTTAATAGGTTCACCACATAGGCTTAACTTTCTAGAGTTTTGCGATAAAGACTAT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
* * * * * * *
40252457 CCTTTAACAGGTTCACCACAAAGGCTTACATTTCCAGAGTTTTTCCAAAAAAGGTTGT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCC-ACAAAGGCTAT
* * *
40252515 CCTTTAATAGGTTTGCCACATAGGCTTACCTTTCTAGAGTTTTGCCGA-AAAGGCT
1 CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCC-ACAAAGGCT
40252570 TTTCTTCTCC
Statistics
Matches: 380, Mismatches: 71, Indels: 7
0.83 0.16 0.02
Matches are distributed among these distances:
56 25 0.07
57 307 0.81
58 48 0.13
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (57 bp):
CCTTTAACAGGTTCGCCACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTAT
Found at i:40252348 original size:171 final size:170
Alignment explanation
Indices: 40252059--40252569 Score: 603
Period size: 171 Copynumber: 3.0 Consensus size: 170
40252049 CAAAAGATGC
* * *
40252059 CCTTTAACAGGTTTTCCACAAAGGTTTACTTTCTAGAGTTTTTCCATAAAGGCTGTCCTTTAACA
1 CCTTTAATAGGTTTACCACAAAGGTTTACTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAACA
* * * * *
40252124 GGTTCG-CTACAAAGGCTTACCTTTCTAGAGTTTTGCCACAAAGGCTCTCCTTTAACAGGTTTGC
66 GGTTCGCCT-CAAAGGCTTACCTTTCTAGAGTTTTTCCAAAAAGTCTATCCTTTAATAGGTTTGC
* **
40252188 CACAAAGGCTTACATTTCTAGAGTTTTGCCCCAAAGGCTAT
130 CACAAAGGCTTACCTTTCTAGAGTTTTGCCAAAAAGGCTAT
* * * * *
40252229 CCTTTAATATGTTTGCCACAAAGGTTTACCTTTCCAGAGTTTTTCCACAAAGGCTATCATTTAAC
1 CCTTTAATAGGTTTACCACAAAGGTTTA-CTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAAC
* * * * ** *
40252294 AAGTTCGCCTTATAGGCTTACCTTTTTAGAGTTTTTCCATGAAGTCTATCCTTTAATAGGTGTGC
65 AGGTTCGCCTCAAAGGCTTACCTTTCTAGAGTTTTTCCAAAAAGTCTATCCTTTAATAGGTTTGC
* * * *
40252359 CATAAAGGCTTACCTTTCCAGTGTTTTGCCATAAAGGCTAT
130 CACAAAGGCTTACCTTTCTAGAGTTTTGCCAAAAAGGCTAT
* * * * * *
40252400 CCTTTAATAGGTTCACCACATAGGCTTAACTTTCTAGAGTTTTGCGATAAAGACTATCCTTTAAC
1 CCTTTAATAGGTTTACCACAAAGG-TTTACTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAAC
* * * * *
40252465 AGGTTCACCACAAAGGCTTACATTTCCAGAGTTTTTCCAAAAAAGGT-TGTCCTTTAATAGGTTT
65 AGGTTCGCCTCAAAGGCTTACCTTTCTAGAGTTTTTCC-AAAAA-GTCTATCCTTTAATAGGTTT
* *
40252529 GCCACATAGGCTTACCTTTCTAGAGTTTTGCCGAAAAGGCT
128 GCCACAAAGGCTTACCTTTCTAGAGTTTTGCCAAAAAGGCT
40252570 TTTCTTCTCC
Statistics
Matches: 283, Mismatches: 53, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
170 25 0.09
171 198 0.70
172 58 0.20
173 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.35
Consensus pattern (170 bp):
CCTTTAATAGGTTTACCACAAAGGTTTACTTTCTAGAGTTTTTCCATAAAGGCTATCCTTTAACA
GGTTCGCCTCAAAGGCTTACCTTTCTAGAGTTTTTCCAAAAAGTCTATCCTTTAATAGGTTTGCC
ACAAAGGCTTACCTTTCTAGAGTTTTGCCAAAAAGGCTAT
Found at i:40252374 original size:28 final size:28
Alignment explanation
Indices: 40252330--40252411 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
40252320 TAGAGTTTTT
* *
40252330 CCATGAAGTCTATCCTTTAATAGGTGTG
1 CCATAAAGGCTATCCTTTAATAGGTGTG
* * *
40252358 CCATAAAGGCT-TACCTTTCCAGT-GTTTTG
1 CCATAAAGGCTAT-CCTTT--AATAGGTGTG
40252387 CCATAAAGGCTATCCTTTAATAGGT
1 CCATAAAGGCTATCCTTTAATAGGT
40252412 TCACCACATA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
27 3 0.07
28 16 0.38
29 20 0.48
30 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (28 bp):
CCATAAAGGCTATCCTTTAATAGGTGTG
Found at i:40252771 original size:53 final size:53
Alignment explanation
Indices: 40252689--40252791 Score: 172
Period size: 53 Copynumber: 1.9 Consensus size: 53
40252679 TCCTTAAAAT
40252689 TTTCCATATGATGCCATAACCCACCAGTTA-GGATCTTACACGATATGGTCTTC
1 TTTCCATATGATGCCATAACCCACCAGTTATGG-TCTTACACGATATGGTCTTC
* *
40252742 TTTCCATATGATGTCATAACCCACTAGTTATGGTCTTACACGATATGGTC
1 TTTCCATATGATGCCATAACCCACCAGTTATGGTCTTACACGATATGGTC
40252792 GTTTAGTGTC
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 45 0.96
54 2 0.04
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (53 bp):
TTTCCATATGATGCCATAACCCACCAGTTATGGTCTTACACGATATGGTCTTC
Found at i:40254395 original size:17 final size:18
Alignment explanation
Indices: 40254335--40254395 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
40254325 ACCCTCCTAC
40254335 TATATTATAT-GATGTTATA
1 TATATTATATAG-T-TTATA
* *
40254354 TCATACTATATAGTATATAA
1 T-ATATTATATAGTTTAT-A
40254374 TATATTA-ATAGTTTATA
1 TATATTATATAGTTTATA
40254391 TATAT
1 TATAT
40254396 GCTGCAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
17 6 0.17
18 8 0.23
19 9 0.26
20 11 0.31
21 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (18 bp):
TATATTATATAGTTTATA
Found at i:40254571 original size:5 final size:5
Alignment explanation
Indices: 40254565--40254598 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
40254555 TCTACTATAC
* *
40254565 AATAC AATAC AATAT AATAT AATAT AATAT AATA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA
40254599 ATAGTTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (5 bp):
AATAT
Found at i:40269613 original size:17 final size:17
Alignment explanation
Indices: 40269591--40269624 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40269581 TTGCTTGTAC
*
40269591 ATGAATAAATGAATAAA
1 ATGAATAAATAAATAAA
*
40269608 ATGAATACATAAATAAA
1 ATGAATAAATAAATAAA
40269625 GGCTCAAGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.03, G:0.09, T:0.24
Consensus pattern (17 bp):
ATGAATAAATAAATAAA
Found at i:40272004 original size:86 final size:86
Alignment explanation
Indices: 40271818--40272018 Score: 235
Period size: 86 Copynumber: 2.3 Consensus size: 86
40271808 ATTTTCGAGA
* * * *
40271818 TATGATTACATGTAAGACGATGTCTGGGAAATTGGCATTGTATTGTGATTACGTGTAAGACGATG
1 TATGATTACATGTAAGACGATGTCTAGGAAATTGGCATCGTATTATGATTACGTGTAAGACCATG
**
40271883 TCTAGGACATTGGCATTGTAT
66 TCTAGGACATTGGCATAATAT
* * * **
40271904 TATGATTACGTGTAAGATGATGTCTAGGACATTGGCATCGT-TATATGATTTTGTGTAAGACCAT
1 TATGATTACATGTAAGACGATGTCTAGGAAATTGGCATCGTAT-TATGATTACGTGTAAGACCAT
40271968 GTCTAGGACATTGGCATAA-AT
65 GTCTAGGACATTGGCATAATAT
* * * *
40271989 ATGTGATAACATGTAAGACCATATCTAGGA
1 -TATGATTACATGTAAGACGATGTCTAGGA
40272019 TATGACATTG
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
85 3 0.03
86 93 0.97
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.34
Consensus pattern (86 bp):
TATGATTACATGTAAGACGATGTCTAGGAAATTGGCATCGTATTATGATTACGTGTAAGACCATG
TCTAGGACATTGGCATAATAT
Found at i:40272010 original size:43 final size:43
Alignment explanation
Indices: 40271818--40271984 Score: 237
Period size: 43 Copynumber: 3.9 Consensus size: 43
40271808 ATTTTCGAGA
* * *
40271818 TATGATTACATGTAAGACGATGTCTGGGAAATTGGCATTGTAT
1 TATGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT
*
40271861 TGTGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT
1 TATGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT
* *
40271904 TATGATTACGTGTAAGATGATGTCTAGGACATTGGCATCGT-T
1 TATGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT
** *
40271946 ATATGATTTTGTGTAAGACCATGTCTAGGACATTGGCAT
1 -TATGATTACGTGTAAGACGATGTCTAGGACATTGGCAT
40271985 AAATATGTGA
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
42 1 0.01
43 111 0.99
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (43 bp):
TATGATTACGTGTAAGACGATGTCTAGGACATTGGCATTGTAT
Found at i:40274972 original size:35 final size:35
Alignment explanation
Indices: 40274881--40275047 Score: 165
Period size: 35 Copynumber: 4.6 Consensus size: 35
40274871 CATGGCAAAG
* *
40274881 TGTGAAATGTAGGTATGGTATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
40274916 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
* *
40274951 TGTGAAATATAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-T-T---ATCCATACTGAGC
*** * * *
40274991 TAACAAATGTAGGTATGGCATT-TCCCATACCGAGT
1 TGTGAAATGTAGGTATGGTATTAT-CCATACTGAGC
**
40275026 TGAAAAATGTAGGTATGGTATT
1 TGTGAAATGTAGGTATGGTATT
40275048 TCAATGAGGA
Statistics
Matches: 113, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
34 1 0.01
35 81 0.72
36 1 0.01
37 1 0.01
38 1 0.01
39 1 0.01
40 27 0.24
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.34
Consensus pattern (35 bp):
TGTGAAATGTAGGTATGGTATTATCCATACTGAGC
Found at i:40275000 original size:75 final size:75
Alignment explanation
Indices: 40274881--40275051 Score: 203
Period size: 75 Copynumber: 2.4 Consensus size: 75
40274871 CATGGCAAAG
*** *
40274881 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATT-TC
*
40274940 CCATACTGAGC
65 CCATACCGAGC
*
40274951 TGTGAAATATAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
*
40275016 CATACCGAGT
66 CATACCGAGC
**
40275026 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
40275052 TGAGGAAAAC
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
70 17 0.20
73 4 0.05
74 5 0.06
75 59 0.69
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGGCATTTCC
CATACCGAGC
Found at i:40282471 original size:40 final size:37
Alignment explanation
Indices: 40282370--40282535 Score: 173
Period size: 35 Copynumber: 4.6 Consensus size: 37
40282360 CATGGCAAAG
40282370 TGTGAAATGTAGGTATGG--TATCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
*
40282405 TGTGAAATGTAGGTATGGTAT-T-ATCCATACTGAGC
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
40282440 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTA-TATC--ATCCATACTGAGT
*** ** * *
40282480 TAACAAATGTAGGTATGACATTTC--CCATACCGAGT
1 TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
**
40282515 TGAAAAATGTAGGTATGGTAT
1 TGTGAAATGTAGGTATGGTAT
40282536 TTCAATGAGG
Statistics
Matches: 111, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
35 77 0.69
36 2 0.02
37 2 0.02
39 3 0.03
40 27 0.24
ACGTcount: A:0.32, C:0.11, G:0.23, T:0.33
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATATCATCCATACTGAGT
Found at i:40282490 original size:75 final size:75
Alignment explanation
Indices: 40282370--40282540 Score: 203
Period size: 75 Copynumber: 2.4 Consensus size: 75
40282360 CATGGCAAAG
*** **
40282370 TGTGAAATGTAGGTATGG---TATC--ATCCATACTGAGTTGTGAAATGTAGGTATGGTATTAT-
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGACATT-TC
*
40282429 CCATACTGAGC
65 CCATACCGAGC
40282440 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGACATTTCC
1 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGACATTTCC
*
40282505 CATACCGAGT
66 CATACCGAGC
**
40282515 TGAAAAATGTAGGTATGGTATT-TCAA
1 TGTGAAATGTAGGTATGGTATTATCAA
40282541 TGAGGAAAAC
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
70 18 0.21
73 4 0.05
74 5 0.06
75 59 0.69
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (75 bp):
TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGTTAACAAATGTAGGTATGACATTTCC
CATACCGAGC
Found at i:40287448 original size:12 final size:12
Alignment explanation
Indices: 40287431--40287460 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
40287421 ACAAAATCCG
40287431 AATTTAATTTCC
1 AATTTAATTTCC
*
40287443 AATTTAATTTCT
1 AATTTAATTTCC
40287455 AATTTA
1 AATTTA
40287461 TTTAATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTAATTTCC
Found at i:40289888 original size:18 final size:18
Alignment explanation
Indices: 40289865--40289902 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
40289855 TACTAACCTT
40289865 TATCCCTTTTCATTAATA
1 TATCCCTTTTCATTAATA
40289883 TATCCCTTTTCATTAATA
1 TATCCCTTTTCATTAATA
40289901 TA
1 TA
40289903 AAGTCCGCTT
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:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
TATCCCTTTTCATTAATA
Found at i:40291467 original size:19 final size:20
Alignment explanation
Indices: 40291443--40291482 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
40291433 AGGGGGAAAG
* *
40291443 TGGGAGAGAGTAAAAA-TTT
1 TGGGAGAAAATAAAAAGTTT
40291462 TGGGAGAAAATAAAAAGTTT
1 TGGGAGAAAATAAAAAGTTT
40291482 T
1 T
40291483 ACAGGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.45, C:0.00, G:0.28, T:0.28
Consensus pattern (20 bp):
TGGGAGAAAATAAAAAGTTT
Found at i:40294376 original size:10 final size:10
Alignment explanation
Indices: 40294363--40294392 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
40294353 TTAGTTTAGG
40294363 TTTAGTTTTC
1 TTTAGTTTTC
40294373 TTTAGGTTTTC
1 TTTA-GTTTTC
40294384 TTTAGTTTT
1 TTTAGTTTT
40294393 TCTCCGCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.10, C:0.07, G:0.13, T:0.70
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:40296544 original size:38 final size:38
Alignment explanation
Indices: 40296493--40296567 Score: 114
Period size: 38 Copynumber: 2.0 Consensus size: 38
40296483 TTGATTCATT
40296493 ACGTGGTGCTAAGTAGATATACCACGATTAAACATGTA
1 ACGTGGTGCTAAGTAGATATACCACGATTAAACATGTA
* * * *
40296531 ACGTGGTGCTAAGTGGATATGCCACGGTTATACATGT
1 ACGTGGTGCTAAGTAGATATACCACGATTAAACATGT
40296568 TAATTTGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (38 bp):
ACGTGGTGCTAAGTAGATATACCACGATTAAACATGTA
Found at i:40303411 original size:55 final size:54
Alignment explanation
Indices: 40303352--40303467 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 54
40303342 TAAGTCACAC
40303352 GCCCATGAGCAAGGCCGTGTGTCACACATGGCTAAGACACACGACCAG-GTCTCAT
1 GCCCATGAGCAAGGCCGTGTGTCACACATGGCTAAGACACACG-CCAGTGTCTC-T
* * * * *
40303407 GCCCATGTGCTAGGCTGTGTGTCACACATGGCTGAGACACATGCCAGTGTCTCT
1 GCCCATGAGCAAGGCCGTGTGTCACACATGGCTAAGACACACGCCAGTGTCTCT
40303461 GCCCATG
1 GCCCATG
40303468 TGAACGAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
54 12 0.22
55 43 0.78
ACGTcount: A:0.22, C:0.30, G:0.27, T:0.21
Consensus pattern (54 bp):
GCCCATGAGCAAGGCCGTGTGTCACACATGGCTAAGACACACGCCAGTGTCTCT
Found at i:40305234 original size:17 final size:17
Alignment explanation
Indices: 40305212--40305256 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
40305202 TTTTTATCAT
40305212 TTATCATTTATCGAGCA
1 TTATCATTTATCGAGCA
*
40305229 TTATCATTTATCGGGCA
1 TTATCATTTATCGAGCA
40305246 TTATCATTTAT
1 TTATCATTTAT
40305257 TTCAAGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.47
Consensus pattern (17 bp):
TTATCATTTATCGAGCA
Found at i:40306647 original size:22 final size:22
Alignment explanation
Indices: 40306602--40306657 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
40306592 TTGTCCGAGA
40306602 TATCGCGATATCCTCTTCTAGG
1 TATCGCGATATCCTCTTCTAGG
*
40306624 TATCGCAATATCCTCTT-TAGGG
1 TATCGCGATATCCTCTTCTA-GG
*
40306646 TATTGCGATATC
1 TATCGCGATATC
40306658 ACCTAAGTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 28 0.93
ACGTcount: A:0.21, C:0.23, G:0.18, T:0.38
Consensus pattern (22 bp):
TATCGCGATATCCTCTTCTAGG
Found at i:40307377 original size:42 final size:43
Alignment explanation
Indices: 40307255--40307402 Score: 235
Period size: 43 Copynumber: 3.5 Consensus size: 43
40307245 TTATTTGAAA
* *
40307255 AAACGCCGCTAAAGGTCATGGCCTTTAGCAGCGCTTTTCCAAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
***
40307298 AAACATGGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
*
40307341 AAACGCCGCTATAGGTCAT-GCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
40307383 AAACGCCGCTAAAGGTCATG
1 AAACGCCGCTAAAGGTCATG
40307403 AAATTTAAAA
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 41 0.44
43 53 0.56
ACGTcount: A:0.24, C:0.30, G:0.22, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
Found at i:40307585 original size:19 final size:19
Alignment explanation
Indices: 40307540--40307586 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
40307530 ATCAAATTAA
* *
40307540 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAC
*
40307559 AATCAAAACT-AAAATAAAC
1 AAT-AAAAATAAAAATAAAC
40307578 AATAAAAAT
1 AATAAAAAT
40307587 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.06, G:0.02, T:0.19
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAC
Found at i:40311111 original size:3 final size:3
Alignment explanation
Indices: 40311103--40311127 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40311093 GTTGGAGCTC
40311103 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
40311128 TGCAGTTGCT
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:40313775 original size:4 final size:4
Alignment explanation
Indices: 40313768--40313792 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40313758 TAAAGATATA
40313768 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
40313793 GTAAAATGAC
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:40314118 original size:3 final size:3
Alignment explanation
Indices: 40314100--40314164 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
40314090 ATATAATACC
* * * *
40314100 AAT AGT AAT AAT -AT AAT AAT GAC AA- AAGT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
40314144 AAT AAT AAT -AT CAAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT
40314165 GATGACGATA
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
2 6 0.12
3 40 0.80
4 4 0.08
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:40315938 original size:89 final size:90
Alignment explanation
Indices: 40315838--40316085 Score: 276
Period size: 89 Copynumber: 2.8 Consensus size: 90
40315828 TGCCCTACTA
* *
40315838 CAACTTCAGGGAGGTAAGGTTTGTTTTGATCTGCTCCACTGTAACTTC-GAGAGATAAGATCTGT
1 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGT
* *
40315902 GATTTAACTTCAATCTATTCCACTG
66 GATTTAACTTCAACCTACTCCACTG
* * * ** *
40315927 TAACTTTAGGGAAATAATATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-
1 CAACTTCAGGGAGATAAGGTTTG-T-T-TTGA-TCTGCTCCACTGCAACTTCAGAGAGATAAGAT
* *
40315991 CT-CG---TAATTTCAACCTACTCCACTG
62 CTGTGATTTAACTTCAACCTACTCCACTG
* *
40316016 CAACTTCAGGGAGATAAGG-TTGTTTTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGT
1 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGT
*
40316080 AATTTA
66 GATTTA
40316086 GCTTTAAACT
Statistics
Matches: 127, Mismatches: 22, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
84 29 0.23
85 5 0.04
86 1 0.01
87 1 0.01
88 3 0.02
89 51 0.40
90 1 0.01
91 1 0.01
92 4 0.03
93 20 0.16
94 11 0.09
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (90 bp):
CAACTTCAGGGAGATAAGGTTTGTTTTGATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGT
GATTTAACTTCAACCTACTCCACTG
Found at i:40316016 original size:44 final size:42
Alignment explanation
Indices: 40315964--40316085 Score: 149
Period size: 40 Copynumber: 2.9 Consensus size: 42
40315954 CTTCAGTCTG
40315964 CTCCACTGCAACTTCAGAGAGATAAGACTCGTAATTTCAACCTA
1 CTCCACTGCAACTTCAGAGAGATAAGA-TCGTAATTT-AACCTA
* * * * *
40316008 CTCCACTGCAACTTCAGGGAGATAAGGTTGT--TTTGATCTA
1 CTCCACTGCAACTTCAGAGAGATAAGATCGTAATTTAACCTA
*
40316048 CTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTA
1 CTCCACTGCAACTTCAGAGAGATAAGATC-GTAATTTA
40316086 GCTTTAAACT
Statistics
Matches: 65, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
40 29 0.45
41 5 0.08
43 6 0.09
44 25 0.38
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (42 bp):
CTCCACTGCAACTTCAGAGAGATAAGATCGTAATTTAACCTA
Found at i:40316129 original size:178 final size:178
Alignment explanation
Indices: 40315838--40316170 Score: 488
Period size: 178 Copynumber: 1.9 Consensus size: 178
40315828 TGCCCTACTA
* * * *
40315838 CAACTTCAGGGAGGTAAGGTTTGTTTTGATCTGCTCCACTGTAACTTCGAGAGATAAGATCTGTG
1 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTTCGAGAGATAAGATCTGTA
* * *
40315903 ATTTAACTTCAATCTATTCCACTGTAACTTTAGGGAAATAATATTTGCTATCTTCAGTCTGCTCC
66 ATTTAACTTCAAACTATTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCC
*
40315968 ACTGCAACTTCAGAGAGATAAGACTCGTAATTTCAACCTACTCCACTG
131 ACTGCAACTCCAGAGAGATAAGACTCGTAATTTCAACCTACTCCACTG
*
40316016 CAACTTCAGGGAGATAAGG-TTGTTTTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGT
1 CAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTTC-GAGAGATAAGATCTGT
* * * * * * *
40316080 AATTTAGCTTTAAACTGTTTCACTGCAATTTTAGGTAAATAAGATTTGCTATCTTTAGTCTGCTC
65 AATTTAACTTCAAACTATTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGCTC
* *
40316145 CACTGCAACTCCAGGGAGATGAGACT
130 CACTGCAACTCCAGAGAGATAAGACT
40316171 TGTGTTGATC
Statistics
Matches: 136, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
177 25 0.18
178 111 0.82
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (178 bp):
CAACTTCAGGGAGATAAGGTTTGTTTTGATCTACTCCACTGCAACTTCGAGAGATAAGATCTGTA
ATTTAACTTCAAACTATTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCC
ACTGCAACTCCAGAGAGATAAGACTCGTAATTTCAACCTACTCCACTG
Found at i:40316207 original size:135 final size:135
Alignment explanation
Indices: 40316008--40316350 Score: 508
Period size: 135 Copynumber: 2.5 Consensus size: 135
40315998 TTTCAACCTA
* * *
40316008 CTCCACTGCAACTTCAGGGAGATAAG-GTTGTTTTGATCTACTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTCTTGATCTGCTCTACTGCAACTTCAGAGAGATA
* * * * *
40316072 AGATCTGTAATTTAGCTTTAAACTGTTTCACTGCAATTTTAGGTAAATAAGATTTGCTATCTTTA
66 AGATCTGTAATTTAGCTTCAAACTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCA
40316137 GTCTG
131 GTCTG
* * * * *
40316142 CTCCACTGCAACTCCAGGGAGATGAGACTTGTGTTGATCTGCTCTGCTGCAACTTCAAAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTTGTCTTGATCTGCTCTACTGCAACTTCAGAGAGATA
*
40316207 AGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCA
66 AGATCTGTAATTTAGCTTCAAACTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCA
40316272 GTCTG
131 GTCTG
* *
40316277 CTCCACTGCAACTTCAGAGAGATAAGACTTGTATCTTCGACCTGCTCTACTGCAACTTCAGAGAG
1 CTCCACTGCAACTTCAGGGAGATAAGACTTG--TCTT-GATCTGCTCTACTGCAACTTCAGAGAG
40316342 ATAAGATCT
63 ATAAGATCT
40316351 ATTTTGATCT
Statistics
Matches: 185, Mismatches: 20, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
134 24 0.13
135 125 0.68
137 3 0.02
138 33 0.18
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (135 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTTGTCTTGATCTGCTCTACTGCAACTTCAGAGAGATA
AGATCTGTAATTTAGCTTCAAACTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCTTCA
GTCTG
Found at i:40316300 original size:94 final size:94
Alignment explanation
Indices: 40316179--40316483 Score: 351
Period size: 94 Copynumber: 3.3 Consensus size: 94
40316169 CTTGTGTTGA
**
40316179 TCTGCTCTGCTGCAACTTCAAAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
1 TCTGCTCCACTGCAACTTCAAAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
*
40316244 TTTAGGGAAATAAGATTTGCTATCTTCAG
66 TTCAGGGAAATAAGATTTGCTATCTTCAG
* * * * *
40316273 TCTGCTCCACTGCAACTTCAGAGAGATAAGA-CTTGT-A--T--CTTCGACCTGCTCTACTGCAA
1 TCTGCTCCACTGCAACTTCAAAGAGATAAGATC-TGTAATTTAGCTTCAATCTGTTCCACTGCAA
* * * *
40316332 CTTCAGAGAGATAAGA--T-CTATTTTGA-
65 CTTCAGGGAAATAAGATTTGCTATCTTCAG
* * * * *
40316358 TCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGTAATTTAGCTTTAATCCGTTCCAGTGTAAC
1 TCTGCTCCACTGCAACTTCAAAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
40316423 TTCAGGGAAATAAGATTTGCTATCTTCAG
66 TTCAGGGAAATAAGATTTGCTATCTTCAG
* **
40316452 TCTGCTCCGCTGCAACTTCAGGGAGATAAGAT
1 TCTGCTCCACTGCAACTTCAAAGAGATAAGAT
40316484 TTTTGACTTC
Statistics
Matches: 170, Mismatches: 30, Indels: 22
0.77 0.14 0.10
Matches are distributed among these distances:
85 32 0.19
86 9 0.05
87 1 0.01
88 1 0.01
89 30 0.18
90 27 0.16
91 1 0.01
92 1 0.01
93 9 0.05
94 59 0.35
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (94 bp):
TCTGCTCCACTGCAACTTCAAAGAGATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAAC
TTCAGGGAAATAAGATTTGCTATCTTCAG
Found at i:40316363 original size:179 final size:179
Alignment explanation
Indices: 40316139--40316482 Score: 548
Period size: 179 Copynumber: 1.9 Consensus size: 179
40316129 TATCTTTAGT
* * *
40316139 CTGCTCCACTGCAACTCCAGGGAGATGAGACTTGTGTTGATCTGCTCTGCTGCAACTTCAAAGAG
1 CTGCTCCACTGCAACTCCAGAGAGATAAGACTTGTGTTGATCTGCTCTACTGCAACTTCAAAGAG
* *
40316204 ATAAGATCTGTAATTTAGCTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTATCT
66 ATAAGATCTGTAATTTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCT
40316269 TCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTATCTTCGAC
131 TCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTATCTTCGAC
* *
40316318 CTGCTCTACTGCAACTTCAGAGAGATAAGATCTAT-T-TTGATCTGCTCTACTGCAACTTCAAAG
1 CTGCTCCACTGCAACTCCAGAGAGATAAGA-CT-TGTGTTGATCTGCTCTACTGCAACTTCAAAG
* * *
40316381 AGATAAGATCTGTAATTTAGCTTTAATCCGTTCCAGTGTAACTTCAGGGAAATAAGATTTGCTAT
64 AGATAAGATCTGTAATTTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTAT
* *
40316446 CTTCAGTCTGCTCCGCTGCAACTTCAGGGAGATAAGA
129 CTTCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGA
40316483 TTTTTGACTT
Statistics
Matches: 151, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
179 147 0.97
180 3 0.02
181 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (179 bp):
CTGCTCCACTGCAACTCCAGAGAGATAAGACTTGTGTTGATCTGCTCTACTGCAACTTCAAAGAG
ATAAGATCTGTAATTTAGCTTCAATCCGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATCT
TCAGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTATCTTCGAC
Found at i:40316375 original size:41 final size:42
Alignment explanation
Indices: 40316222--40316391 Score: 173
Period size: 44 Copynumber: 4.0 Consensus size: 42
40316212 TGTAATTTAG
* * * * * *
40316222 CTTCAATCTGTTCCACTGCAACTTTAGGGAAATAAGATTTGCTAT
1 CTTCGATCTGCTCTACTGCAACTTCAGAGAGATAAGA--T-CTAT
* *
40316267 CTTC-AGTCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGTAT
1 CTTCGA-TCTGCTCTACTGCAACTTCAGAGAGATAAGA--TCTAT
*
40316311 CTTCGACCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAT
1 CTTCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAT
* *
40316353 -TTTGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCT
1 CTTCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT
40316392 GTAATTTAGC
Statistics
Matches: 111, Mismatches: 12, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
41 36 0.32
42 4 0.04
44 37 0.33
45 34 0.31
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (42 bp):
CTTCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAT
Found at i:40316513 original size:44 final size:45
Alignment explanation
Indices: 40316420--40316522 Score: 129
Period size: 44 Copynumber: 2.3 Consensus size: 45
40316410 GTTCCAGTGT
* * * *
40316420 AACTTCAGGGAAATAAGATTTGCTATCTTCAGTCTGCTCCGCTGC
1 AACTTCAGGGAGATAAGATTTGCTATCTTCAATCTACTCCGCTGA
*
40316465 AACTTCAGGGAGATAAGATTT-TTGA-CTTCAATCTACTCCGCTGA
1 AACTTCAGGGAGATAAGATTTGCT-ATCTTCAATCTACTCCGCTGA
*
40316509 AACTTCAAGGAGAT
1 AACTTCAGGGAGAT
40316523 CTACTATGGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 30 0.59
45 21 0.41
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.30
Consensus pattern (45 bp):
AACTTCAGGGAGATAAGATTTGCTATCTTCAATCTACTCCGCTGA
Found at i:40316614 original size:68 final size:68
Alignment explanation
Indices: 40316505--40317442 Score: 1344
Period size: 68 Copynumber: 13.8 Consensus size: 68
40316495 ATCTACTCCG
* * ** * *
40316505 CTGAAACTTCAAGGAGATCTACTATGGCTTCGAGCCGCTCCAATGCCATTTTAGGGAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
40316570 CCA
66 CCA
* * * * * *
40316573 CTGAAACTTCAAGGAGATCTGTTATGGCTTCTAGCCACTCCAATGCCATTTCAGGAAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
40316638 CCA
66 CCA
* * *
40316641 CTGAAACTTCAAGGAGATCTACTATGGCTTTTAGCCGCTCCAACGCCATTTCAGGAAGAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
40316706 CCA
66 CCA
* * * * *
40316709 CTGAAACTTCAAGGAGATCTGATTTGACTTTTAGCCGCTCCAACGCTATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
*
40316774 CCG
66 CCA
* * *
40316777 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGTCGCTCCAACGCCATTTCAGGAAGAAGAAAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
*
40316842 CCG
66 CCA
* * *
40316845 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAATGTCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
*
40316910 CCG
66 CCA
* * * * *
40316913 CTAAAACCTCAAGGAGATCTACTGTGGCTTTTAGCCGCCCCAACGCCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
40316978 CCA
66 CCA
* *
40316981 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCACTCCAACTCCATTTCAGGG-GAGAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGA-AGAGA
*
40317045 TCCT
65 TCCA
* * *
40317049 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCACTTCAACGCCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
40317114 CCA
66 CCA
*
40317117 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACTCCATTTCAGGG-GAGAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGA-AGAGA
*
40317181 TCCT
65 TCCA
* * * *
40317185 CTGAAACTTCAAGAAGATCTGCTGTGGCTTTTAGCCACTCCAATGCCATTTCAGGGAAAAGAGAT
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
40317250 CCA
66 CCA
* **
40317253 CTGAAACTTCAAGAAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTTTGGG-GAAAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAG-AAGAGA
40317317 TCCA
65 TCCA
* *
40317321 CTGAAACTTCAAGTAGATCTGCTGTGGTTTTTAGCCGCTCCAACGCCATTTCAGGG-GAAAGAGA
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAG-AAGAGA
*
40317385 TCCT
65 TCCA
40317389 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAG
1 CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAG
40317443 AGAGGGGATT
Statistics
Matches: 790, Mismatches: 75, Indels: 10
0.90 0.09 0.01
Matches are distributed among these distances:
67 2 0.00
68 786 0.99
69 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.25
Consensus pattern (68 bp):
CTGAAACTTCAAGGAGATCTGCTGTGGCTTTTAGCCGCTCCAACGCCATTTCAGGGAGAAGAGAT
CCA
Found at i:40324833 original size:4 final size:4
Alignment explanation
Indices: 40324826--40324850 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
40324816 TAAAGATATA
40324826 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
40324851 GTAAAATGAC
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:40325034 original size:63 final size:64
Alignment explanation
Indices: 40324952--40325082 Score: 237
Period size: 63 Copynumber: 2.1 Consensus size: 64
40324942 TCTGTAGTTT
40324952 AAAAGAAAACTATGTAAAGGATATAAATAAATAAAATGATAACAACAAGAATAAAATACGTAAA
1 AAAAGAAAACTATGTAAAGGATATAAATAAATAAAATGATAACAACAAGAATAAAATACGTAAA
* *
40325016 AAAATAAAA-TATGTAAAGGATATAAATAAATAAAATGATAATAACAAGAATAAAATACGTAAA
1 AAAAGAAAACTATGTAAAGGATATAAATAAATAAAATGATAACAACAAGAATAAAATACGTAAA
40325079 AAAA
1 AAAA
40325083 AATAAAAGTA
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
63 57 0.88
64 8 0.12
ACGTcount: A:0.66, C:0.05, G:0.10, T:0.20
Consensus pattern (64 bp):
AAAAGAAAACTATGTAAAGGATATAAATAAATAAAATGATAACAACAAGAATAAAATACGTAAA
Found at i:40325242 original size:3 final size:3
Alignment explanation
Indices: 40325224--40325300 Score: 79
Period size: 3 Copynumber: 26.0 Consensus size: 3
40325214 ATATAATACC
* * * *
40325224 AAT AGT AAT AAT -AT AAT AAT GAC AA- AAGT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
40325268 AAT AAT AAT AAT AAT AAT AAT -AT CAAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT
40325301 TATGATGATG
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
2 6 0.10
3 52 0.84
4 4 0.06
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40328338 original size:15 final size:14
Alignment explanation
Indices: 40328319--40328358 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
40328309 CCATGGCCAT
40328319 TAAACCTTAAACCA
1 TAAACCTTAAACCA
*
40328333 TAAAACCCTAAACCA
1 T-AAACCTTAAACCA
*
40328348 TAGACCTTAAA
1 TAAACCTTAAA
40328359 TATTAAACCC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.20
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:40328547 original size:37 final size:39
Alignment explanation
Indices: 40328489--40328579 Score: 132
Period size: 37 Copynumber: 2.4 Consensus size: 39
40328479 TTTTTTGGGG
*
40328489 TTTAAGGTTTTAGGGGTTATAGTTTAGTGTTTATG-GTT
1 TTTAAGGTTTTAGGGGTTATAGATTAGTGTTTATGAGTT
* *
40328527 TTTAAGG-TTTCGGGGTTATAGATTAGTGTTTATGATTT
1 TTTAAGGTTTTAGGGGTTATAGATTAGTGTTTATGAGTT
*
40328565 TTTAAGGGTTTAGGG
1 TTTAAGGTTTTAGGG
40328580 TTTTAGGGGT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
37 25 0.53
38 16 0.34
39 6 0.13
ACGTcount: A:0.20, C:0.01, G:0.30, T:0.49
Consensus pattern (39 bp):
TTTAAGGTTTTAGGGGTTATAGATTAGTGTTTATGAGTT
Found at i:40328693 original size:40 final size:40
Alignment explanation
Indices: 40328619--40328788 Score: 268
Period size: 41 Copynumber: 4.2 Consensus size: 40
40328609 TTTTGACCAT
*
40328619 AAACGCTGCTATTGCTCTAGTTTTTAGCGGCGTTTTTGGTA
1 AAACGCCGCTATTGCTCTA-TTTTTAGCGGCGTTTTTGGTA
* *
40328660 AAACGCTGCTATTGCTCTGTTTTTAGCGGCGTTTTTGGTAA
1 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGT-A
* *
40328701 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTGTTTGCTA
1 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGTA
40328741 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGATA
1 AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGG-TA
40328782 AAACGCC
1 AAACGCC
40328789 ACTAAAAACG
Statistics
Matches: 120, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
40 57 0.47
41 63 0.52
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (40 bp):
AAACGCCGCTATTGCTCTATTTTTAGCGGCGTTTTTGGTA
Found at i:40328764 original size:81 final size:82
Alignment explanation
Indices: 40328598--40328788 Score: 273
Period size: 81 Copynumber: 2.3 Consensus size: 82
40328588 GTTATATGAC
* * * *
40328598 TTTTAGCGGCG-TTTT-GACCATAAACGCTGCTATTGCTCTAGTTTTTAGCGGCGTTTTTGGTAA
1 TTTTAGCGGCGTTTTTGGA-TA-AAACGCCGCTATTGCTCTAGTTTTTAGCGGCGTGTTTGCTAA
* *
40328661 AACGCTGCTATTGCTCTGT
64 AACGCCGCTATTGCTCTAT
40328680 TTTTAGCGGCGTTTTTGG-TAAAAACGCCGCTATTGCTCTA-TTTTTAGCGGCGTGTTTGCTAAA
1 TTTTAGCGGCGTTTTTGGAT-AAAACGCCGCTATTGCTCTAGTTTTTAGCGGCGTGTTTGCTAAA
40328743 ACGCCGCTATTGCTCTAT
65 ACGCCGCTATTGCTCTAT
40328761 TTTTAGCGGCGTTTTTGGATAAAACGCC
1 TTTTAGCGGCGTTTTTGGATAAAACGCC
40328789 ACTAAAAACG
Statistics
Matches: 99, Mismatches: 6, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
81 63 0.64
82 30 0.30
83 5 0.05
84 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (82 bp):
TTTTAGCGGCGTTTTTGGATAAAACGCCGCTATTGCTCTAGTTTTTAGCGGCGTGTTTGCTAAAA
CGCCGCTATTGCTCTAT
Found at i:40334987 original size:84 final size:84
Alignment explanation
Indices: 40334836--40335071 Score: 240
Period size: 84 Copynumber: 2.8 Consensus size: 84
40334826 TTTACAAATA
* * * * * * *
40334836 TCGCAACAAAGGCTTCCTTTAACAGAGAACGCCACGAATGCTTCCTTTAATAGAGATCGCCGA-A
1 TCGCTACAAAGGCTTCCTTTAACAGAGATCACCACAAAAGCTTCCTTTAACAGAGATCACC-ACA
*
40334900 AAGGAATCCTTTAACAAAGC
65 AAGGAATCCATTAACAAAGC
* * * * *
40334920 TCGCTACAAAGGCTTCTTTTAACAGCGATCATCACAAAGGCTTTCTTTAACAGAGATCACCACAA
1 TCGCTACAAAGGCTTCCTTTAACAGAGATCACCACAAAAGCTTCCTTTAACAGAGATCACCACAA
** *** *
40334985 AGGCTTCCATTAATGGAGG
66 AGGAATCCATTAACAAAGC
* * * * *
40335004 TCGCTACAAAAGATTCCTTTAACAGAGATCACCACAAAAGATTCCTTTAACAGATATTACCACAA
1 TCGCTACAAAGGCTTCCTTTAACAGAGATCACCACAAAAGCTTCCTTTAACAGAGATCACCACAA
40335069 AGG
66 AGG
40335072 CTTCCCTTCT
Statistics
Matches: 123, Mismatches: 28, Indels: 2
0.80 0.18 0.01
Matches are distributed among these distances:
83 1 0.01
84 122 0.99
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (84 bp):
TCGCTACAAAGGCTTCCTTTAACAGAGATCACCACAAAAGCTTCCTTTAACAGAGATCACCACAA
AGGAATCCATTAACAAAGC
Found at i:40335076 original size:28 final size:28
Alignment explanation
Indices: 40334802--40335076 Score: 212
Period size: 28 Copynumber: 9.8 Consensus size: 28
40334792 CATTCCCTTT
* *
40334802 CAGAGAT-AGCCACAAAGGCTTCATTTTA
1 CAGAGATCA-CCACAAAGGCTTCCTTTAA
* * * *
40334830 CAAATATCGCAACAAAGGCTTCCTTTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
* * * *
40334858 CAGAGAACGCCACGAATGCTTCCTTTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
* * **
40334886 TAGAGATCGCCGA-AAAGGAATCCTTTAA
1 CAGAGATCACC-ACAAAGGCTTCCTTTAA
* * * * *
40334914 CAAAGCTCGCTACAAAGGCTTCTTTTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
* * *
40334942 CAGCGATCATCACAAAGGCTTTCTTTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
*
40334970 CAGAGATCACCACAAAGGCTTCCATTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
** * * * * *
40334998 TGGAGGTCGCTACAAAAGATTCCTTTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
* *
40335026 CAGAGATCACCACAAAAGATTCCTTTAA
1 CAGAGATCACCACAAAGGCTTCCTTTAA
* *
40335054 CAGATATTACCACAAAGGCTTCC
1 CAGAGATCACCACAAAGGCTTCC
40335077 CTTCTCTTGG
Statistics
Matches: 190, Mismatches: 54, Indels: 6
0.76 0.22 0.02
Matches are distributed among these distances:
27 1 0.01
28 188 0.99
29 1 0.01
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.24
Consensus pattern (28 bp):
CAGAGATCACCACAAAGGCTTCCTTTAA
Found at i:40335285 original size:53 final size:53
Alignment explanation
Indices: 40335198--40335345 Score: 143
Period size: 53 Copynumber: 2.8 Consensus size: 53
40335188 AAATATTTCC
** * *
40335198 ATATGATGTCATAACCCACCAGTTACAGTCTTACACGATATGGTCTTCTTTTT
1 ATATGATACCATAACCCACCAGTTACAATCTTACACGATATGATCTTCTTTTT
* * * * ***
40335251 ATATGATACCATACCCCACCAGTTATAATTTTACATGATATGATCTTCTTCCC
1 ATATGATACCATAACCCACCAGTTACAATCTTACACGATATGATCTTCTTTTT
** * * * *
40335304 ATATGATGTCACAACCCACCAATTACGATCTTACACAATATG
1 ATATGATACCATAACCCACCAGTTACAATCTTACACGATATG
40335346 GTCCATTAGT
Statistics
Matches: 74, Mismatches: 21, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
53 74 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (53 bp):
ATATGATACCATAACCCACCAGTTACAATCTTACACGATATGATCTTCTTTTT
Found at i:40338035 original size:25 final size:24
Alignment explanation
Indices: 40338000--40338051 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 24
40337990 ACAAACACAA
40338000 CTCTTTATGAGCGTCCTGATATAGG
1 CTCTTTATGAGCGTCCTGATAT-GG
* *
40338025 CTCTTTTTGAGCTTCCTGATATGG
1 CTCTTTATGAGCGTCCTGATATGG
40338049 CTC
1 CTC
40338052 GCTTGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.40
Consensus pattern (24 bp):
CTCTTTATGAGCGTCCTGATATGG
Found at i:40339226 original size:59 final size:59
Alignment explanation
Indices: 40339151--40339270 Score: 231
Period size: 59 Copynumber: 2.0 Consensus size: 59
40339141 AGACACGAAA
*
40339151 GTATGTCTCAGTCGTGTGTGACACACGGCTTTGCACACAAGTGTGTGGTTTGGTCGTGT
1 GTATGTCTCAGCCGTGTGTGACACACGGCTTTGCACACAAGTGTGTGGTTTGGTCGTGT
40339210 GTATGTCTCAGCCGTGTGTGACACACGGCTTTGCACACAAGTGTGTGGTTTGGTCGTGT
1 GTATGTCTCAGCCGTGTGTGACACACGGCTTTGCACACAAGTGTGTGGTTTGGTCGTGT
40339269 GT
1 GT
40339271 TCCCTGCATT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.33
Consensus pattern (59 bp):
GTATGTCTCAGCCGTGTGTGACACACGGCTTTGCACACAAGTGTGTGGTTTGGTCGTGT
Found at i:40342016 original size:54 final size:54
Alignment explanation
Indices: 40341896--40342024 Score: 147
Period size: 54 Copynumber: 2.4 Consensus size: 54
40341886 AGTTTGTATA
* *
40341896 AGATATTATAA-TTATTTAATTTTATTTTTACCTAATTAATATTCAGTTATACTT
1 AGATATT-TAATTTATTAAATTTTATTTTTACCTAATTAATATTCAGTTATAATT
* * * *
40341950 AGATATTAAATTTATTAAATTTTATTTTTA-TTAAATTAATATTTAGATTCTAATT
1 AGATATTTAATTTATTAAATTTTATTTTTACCT-AATTAATATTCAG-TTATAATT
*
40342005 TG-TATTTAATTTATTAAATT
1 AGATATTTAATTTATTAAATT
40342025 AAACTAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
53 3 0.05
54 54 0.84
55 7 0.11
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (54 bp):
AGATATTTAATTTATTAAATTTTATTTTTACCTAATTAATATTCAGTTATAATT
Found at i:40342398 original size:19 final size:19
Alignment explanation
Indices: 40342374--40342414 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
40342364 ATCTTTATGA
*
40342374 GAAACACACTTCAGTTGGT
1 GAAACACACTTCAGTTGAT
40342393 GAAACACACTTCAGTTGAT
1 GAAACACACTTCAGTTGAT
40342412 GAA
1 GAA
40342415 CTTTTCTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (19 bp):
GAAACACACTTCAGTTGAT
Found at i:40350067 original size:23 final size:23
Alignment explanation
Indices: 40350012--40350058 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
40350002 TTGGCTAATG
40350012 TGGCCTATATGTCTTATGTTGTT
1 TGGCCTATATGTCTTATGTTGTT
40350035 TGGCCTATATGTCTTATGTTGTT
1 TGGCCTATATGTCTTATGTTGTT
40350058 T
1 T
40350059 TGGTTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.13, C:0.13, G:0.21, T:0.53
Consensus pattern (23 bp):
TGGCCTATATGTCTTATGTTGTT
Found at i:40351038 original size:43 final size:43
Alignment explanation
Indices: 40350981--40351125 Score: 177
Period size: 43 Copynumber: 3.3 Consensus size: 43
40350971 CGTTTATTTA
* * * *
40350981 AAAAATGCCGCTAAAGATCACGACATTTAGCGACGTTTTTTCC
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGTCTTTTCC
* * *
40351024 ACAAACGCTGCTAAAGATCACAACCTTTAGCGGC-TCCTTTTCC
1 AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGT-CTTTTCC
*
40351067 TATAAACGCCGCTAAAGATCACGACCTTTAGCGGCG-CTTTTCTC
1 -AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGTCTTTTC-C
40351111 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
40351126 AGTCATAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.01
43 54 0.62
44 32 0.37
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGATCACGACCTTTAGCGGCGTCTTTTCC
Found at i:40355849 original size:6 final size:6
Alignment explanation
Indices: 40355831--40355875 Score: 54
Period size: 6 Copynumber: 7.0 Consensus size: 6
40355821 CTAACCTCTA
*
40355831 TTTTAT ATTTTAT TTTTAT TTTTGT ATTTTAT TTTTAT TTATTAT
1 TTTTAT -TTTTAT TTTTAT TTTTAT -TTTTAT TTTTAT TT-TTAT
40355876 CAATGTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 19 0.56
7 15 0.44
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTTAT
Found at i:40355849 original size:13 final size:13
Alignment explanation
Indices: 40355829--40355868 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
40355819 CACTAACCTC
40355829 TATTTTATATTTTA
1 TATTTTAT-TTTTA
*
40355843 T-TTTTATTTTTG
1 TATTTTATTTTTA
40355855 TATTTTATTTTTA
1 TATTTTATTTTTA
40355868 T
1 T
40355869 TTATTATCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.22
13 17 0.74
14 1 0.04
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.78
Consensus pattern (13 bp):
TATTTTATTTTTA
Found at i:40355858 original size:19 final size:19
Alignment explanation
Indices: 40355831--40355875 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
40355821 CTAACCTCTA
40355831 TTTTATATTTTATTTTTAT
1 TTTTATATTTTATTTTTAT
*
40355850 TTTTGTATTTTATTTTTAT
1 TTTTATATTTTATTTTTAT
40355869 TTATTAT
1 TT-TTAT
40355876 CAATGTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 20 0.87
20 3 0.13
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTATATTTTATTTTTAT
Found at i:40355875 original size:13 final size:12
Alignment explanation
Indices: 40355831--40355875 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 12
40355821 CTAACCTCTA
40355831 TTTTATATTTTAT
1 TTTTAT-TTTTAT
*
40355844 TTTTATTTTTGT
1 TTTTATTTTTAT
40355856 ATTTTATTTTTAT
1 -TTTTATTTTTAT
40355869 TTATTAT
1 TT-TTAT
40355876 CAATGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
12 7 0.25
13 21 0.75
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:40356181 original size:7 final size:7
Alignment explanation
Indices: 40356169--40356194 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40356159 CCATTAATCC
40356169 CTAAACT
1 CTAAACT
40356176 CTAAACT
1 CTAAACT
40356183 CTAAACT
1 CTAAACT
40356190 CTAAA
1 CTAAA
40356195 ATCCTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (7 bp):
CTAAACT
Found at i:40356471 original size:22 final size:22
Alignment explanation
Indices: 40356422--40356476 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
40356412 CATTAATTAA
* *
40356422 CTAAA-CCCTAAACTCTTAATC
1 CTAAATCCCTAAACCCTAAATC
* *
40356443 TTTAATCCCTAAACCCTAAATC
1 CTAAATCCCTAAACCCTAAATC
40356465 CTAAAT-CCTAAA
1 CTAAATCCCTAAA
40356477 ATATAAACTC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 9 0.33
22 18 0.67
ACGTcount: A:0.40, C:0.31, G:0.00, T:0.29
Consensus pattern (22 bp):
CTAAATCCCTAAACCCTAAATC
Found at i:40356535 original size:15 final size:14
Alignment explanation
Indices: 40356506--40356541 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
40356496 GACCCCTAAC
40356506 CCCTAAACCATAAT
1 CCCTAAACCATAAT
40356520 CCCTAAACCTATAAT
1 CCCTAAACC-ATAAT
*
40356535 CCATAAA
1 CCCTAAA
40356542 ACTTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.22
Consensus pattern (14 bp):
CCCTAAACCATAAT
Found at i:40356730 original size:15 final size:14
Alignment explanation
Indices: 40356710--40356750 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40356700 ATGTGATGTT
40356710 TTTTAGGGTTTAGTA
1 TTTTAGGGTTTA-TA
*
40356725 TTTTAGGGGTTATA
1 TTTTAGGGTTTATA
*
40356739 GTTTAGGGTTTA
1 TTTTAGGGTTTA
40356751 AGATTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (14 bp):
TTTTAGGGTTTATA
Found at i:40356776 original size:54 final size:53
Alignment explanation
Indices: 40356711--40356813 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 53
40356701 TGTGATGTTT
* *
40356711 TTTAGGGTTTAGTATTTT-AGGGGTTATAGTTTAGGGTTTAAGATTTTTTAATG
1 TTTAGGGTTTAGTATTTTAAGGAG-TATAGATTAGGGTTTAAGATTTTTTAATG
* * *
40356764 TTTAGGAGTTTAGTGTTTTAAGGAGTATAGATTAGTGTTTATGATTTTTT
1 TTTAGG-GTTTAGTATTTTAAGGAGTATAGATTAGGGTTTAAGATTTTTT
40356814 GGGGGTTTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 6 0.14
54 33 0.77
55 4 0.09
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.51
Consensus pattern (53 bp):
TTTAGGGTTTAGTATTTTAAGGAGTATAGATTAGGGTTTAAGATTTTTTAATG
Found at i:40356940 original size:40 final size:40
Alignment explanation
Indices: 40356843--40356946 Score: 147
Period size: 41 Copynumber: 2.6 Consensus size: 40
40356833 GGTTATATGA
*
40356843 CTTTTAACGGCGTTTTACCAAAAACGCCGCTAATGCTCTG
1 CTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTG
* *
40356883 CTTTTTAGAGGCGTTTTACCAAAAGCGCCGCTAATGCTCTAG
1 C-TTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCT-G
*
40356925 -TTTTAGCGGCGTTTTAACAAAA
1 CTTTTAGCGGCGTTTTACCAAAA
40356947 CACCTCTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
40 21 0.37
41 35 0.61
42 1 0.02
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (40 bp):
CTTTTAGCGGCGTTTTACCAAAAACGCCGCTAATGCTCTG
Found at i:40358609 original size:29 final size:29
Alignment explanation
Indices: 40358550--40358609 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
40358540 AGTGATTTGT
* *
40358550 TAAAATTGAATCAAATCAAAATTTCATTA
1 TAAAATTGAATCAAATCAAAAGTTAATTA
*
40358579 TAAAATTGAATGAAATC-AAAGTTAATGTA
1 TAAAATTGAATCAAATCAAAAGTTAAT-TA
40358608 TA
1 TA
40358610 GTTTTAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (29 bp):
TAAAATTGAATCAAATCAAAAGTTAATTA
Found at i:40368141 original size:9 final size:9
Alignment explanation
Indices: 40368117--40368151 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
40368107 AAAATTTATT
40368117 AAAATAAAA
1 AAAATAAAA
**
40368126 ATTATAAAA
1 AAAATAAAA
40368135 AAAATAAAA
1 AAAATAAAA
40368144 AAAATAAA
1 AAAATAAA
40368152 TTATTCAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (9 bp):
AAAATAAAA
Found at i:40369060 original size:26 final size:26
Alignment explanation
Indices: 40369023--40369076 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
40369013 AAAGCATAAA
* *
40369023 CATAAACTGAAAAACAATCACGTGTC
1 CATAAACCGAAAAACAATCACGCGTC
40369049 CATAAACCGAAAAACAATCACGCGTC
1 CATAAACCGAAAAACAATCACGCGTC
40369075 CA
1 CA
40369077 AAGCCCCTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.28, G:0.11, T:0.15
Consensus pattern (26 bp):
CATAAACCGAAAAACAATCACGCGTC
Found at i:40379659 original size:51 final size:49
Alignment explanation
Indices: 40379547--40379662 Score: 130
Period size: 51 Copynumber: 2.3 Consensus size: 49
40379537 TTTATAACAA
* *
40379547 CCATGCAAATGTATTTGGATAGGAAAATGTCTCATTTCATTGAAACTGT
1 CCATGCTAATGTATTTGGATAGGAAAATGTCTCATTGCATTGAAACTGT
*
40379596 CCATGCTAATGTATTTGGTTGAGGAAAAATGTCTTCA-TGCATTTGAAA-TCGT
1 CCATGCTAATGTATTTGGAT-AGG-AAAATGTC-TCATTGCA-TTGAAACT-GT
*
40379648 CCATG-TCATGTATTT
1 CCATGCTAATGTATTT
40379663 AAATGAGATA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
49 18 0.31
50 3 0.05
51 21 0.36
52 16 0.28
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (49 bp):
CCATGCTAATGTATTTGGATAGGAAAATGTCTCATTGCATTGAAACTGT
Found at i:40379701 original size:50 final size:50
Alignment explanation
Indices: 40379647--40379742 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
40379637 TTTGAAATCG
*
40379647 TCCATG-TCATGTATTTAAATGAGATAAACGTCTCTATGCATTGAAAACCA
1 TCCATGATCATGTATTTAAATGACA-AAACGTCTCTATGCATTGAAAACCA
* * * *
40379697 TCCATGATCATGTATTTGAATTACAAAACGTCTTTGTGCATTGAAA
1 TCCATGATCATGTATTTAAATGACAAAACGTCTCTATGCATTGAAA
40379743 TTGTCCATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 25 0.62
51 15 0.38
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (50 bp):
TCCATGATCATGTATTTAAATGACAAAACGTCTCTATGCATTGAAAACCA
Found at i:40379794 original size:19 final size:20
Alignment explanation
Indices: 40379737--40379804 Score: 84
Period size: 19 Copynumber: 3.3 Consensus size: 20
40379727 TCTTTGTGCA
40379737 TTGAAATTGTCCATGTCCCATGC
1 TTGAAATTGTCCA--T-CCATGC
40379760 TTGAAATTGTCCATCCATGC
1 TTGAAATTGTCCATCCATGC
* *
40379780 TTGAAA-TGTCTATCCTTGC
1 TTGAAATTGTCCATCCATGC
40379799 TTGAAA
1 TTGAAA
40379805 CATTCATCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.40
20 12 0.28
21 1 0.02
23 13 0.30
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (20 bp):
TTGAAATTGTCCATCCATGC
Found at i:40381106 original size:88 final size:88
Alignment explanation
Indices: 40381001--40381180 Score: 333
Period size: 88 Copynumber: 2.0 Consensus size: 88
40380991 AATTATAAGC
* *
40381001 AATTATACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATGGATTTATAAACAAA
1 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATAGATTTATAAACAAA
40381066 TTCCTTATAACTGCACCATTAAT
66 TTCCTTATAACTGCACCATTAAT
*
40381089 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTACCTTAATAGATTTATAAACAAA
1 AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATAGATTTATAAACAAA
40381154 TTCCTTATAACTGCACCATTAAT
66 TTCCTTATAACTGCACCATTAAT
40381177 AATT
1 AATT
40381181 CTTAAGTAAA
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (88 bp):
AATTACACCCAAATCGAATTATTAGGTGGCTTTCAAAACACTAACTTAATAGATTTATAAACAAA
TTCCTTATAACTGCACCATTAAT
Found at i:40383266 original size:14 final size:14
Alignment explanation
Indices: 40383247--40383277 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
40383237 ATCCAAACAA
40383247 TAACAATAAAATAG
1 TAACAATAAAATAG
*
40383261 TAACAATATAATAG
1 TAACAATAAAATAG
40383275 TAA
1 TAA
40383278 AACTGTAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.26
Consensus pattern (14 bp):
TAACAATAAAATAG
Found at i:40383529 original size:19 final size:19
Alignment explanation
Indices: 40383505--40383560 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
40383495 ATATACACAT
40383505 TTGTCATTTACTAATCAAG
1 TTGTCATTTACTAATCAAG
*
40383524 TTGTC----ACCAAT-AA-
1 TTGTCATTTACTAATCAAG
40383537 -TGTCATTTACTAATCAAG
1 TTGTCATTTACTAATCAAG
40383555 TTGTCA
1 TTGTCA
40383561 CCGATAATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 4 0.14
14 2 0.07
15 5 0.18
16 5 0.18
17 2 0.07
19 10 0.36
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
TTGTCATTTACTAATCAAG
Found at i:40383541 original size:31 final size:31
Alignment explanation
Indices: 40383506--40383570 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
40383496 TATACACATT
40383506 TGTCATTTACTAATCAAGTTGTCACCAATAA
1 TGTCATTTACTAATCAAGTTGTCACCAATAA
*
40383537 TGTCATTTACTAATCAAGTTGTCACCGATAA
1 TGTCATTTACTAATCAAGTTGTCACCAATAA
40383568 TGT
1 TGT
40383571 AACTTTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.37
Consensus pattern (31 bp):
TGTCATTTACTAATCAAGTTGTCACCAATAA
Found at i:40387843 original size:9 final size:9
Alignment explanation
Indices: 40387825--40387861 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
40387815 TATTTTTTGA
*
40387825 TATTCAAAT
1 TATTCGAAT
40387834 TATTCGAAT
1 TATTCGAAT
*
40387843 TATTCGAGT
1 TATTCGAAT
40387852 TATTCGAAT
1 TATTCGAAT
40387861 T
1 T
40387862 CAAAAACTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:40388065 original size:14 final size:15
Alignment explanation
Indices: 40388047--40388081 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
40388037 AAAACAACAG
*
40388047 TAAAAATAATAGCAA
1 TAAAAAAAATAGCAA
40388062 -AAAAAAAATAGCAA
1 TAAAAAAAATAGCAA
40388076 TAAAAA
1 TAAAAA
40388082 CAACACCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.74, C:0.06, G:0.06, T:0.14
Consensus pattern (15 bp):
TAAAAAAAATAGCAA
Found at i:40389423 original size:23 final size:23
Alignment explanation
Indices: 40389370--40389426 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
40389360 ATAGGGTCTG
*
40389370 TTTATGCATGTTATATTCAATGC
1 TTTATGCGTGTTATATTCAATGC
* * * *
40389393 TTTGTGCGTGTTATATTTAGTGT
1 TTTATGCGTGTTATATTCAATGC
40389416 TTTATGCGTGT
1 TTTATGCGTGT
40389427 GATACTTGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.18, C:0.09, G:0.21, T:0.53
Consensus pattern (23 bp):
TTTATGCGTGTTATATTCAATGC
Found at i:40393971 original size:46 final size:47
Alignment explanation
Indices: 40393819--40393996 Score: 193
Period size: 46 Copynumber: 3.8 Consensus size: 47
40393809 CACATTATGA
*
40393819 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATCGAGATGA-
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGAC-TCGAGAT-AT
* * * * **
40393867 GTGCTAGTGTAAGA-CATGTCTAGGATAT-GCATCAGCCTCGAGACGT
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATC-GACTCGAGATAT
* * * *
40393913 AAGCAAGGGTAAGA-CATGTCTAGGACATGGCATCGACTTGAGATAT
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTCGAGATAT
*
40393959 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGAC
40393997 ACCTTACCCC
Statistics
Matches: 107, Mismatches: 19, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
46 53 0.50
47 42 0.39
48 12 0.11
ACGTcount: A:0.29, C:0.20, G:0.30, T:0.21
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGACTCGAGATAT
Found at i:40396784 original size:13 final size:13
Alignment explanation
Indices: 40396766--40396790 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40396756 TGCCTAAGCA
40396766 TCACTTGGTAGCG
1 TCACTTGGTAGCG
40396779 TCACTTGGTAGC
1 TCACTTGGTAGC
40396791 CAGGTAGTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.32
Consensus pattern (13 bp):
TCACTTGGTAGCG
Found at i:40402449 original size:30 final size:30
Alignment explanation
Indices: 40402413--40402474 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
40402403 CTTAACAAGA
*
40402413 AAATGCCTTTAGAATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
40402443 AAATGCCTTTAAAATAATAACAAAATTAAC
1 AAATGCCTTTAAAATAATAACAAAATTAAC
40402473 AA
1 AA
40402475 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.13, G:0.05, T:0.26
Consensus pattern (30 bp):
AAATGCCTTTAAAATAATAACAAAATTAAC
Found at i:40405518 original size:17 final size:19
Alignment explanation
Indices: 40405485--40405522 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
40405475 ATTATTTGGA
40405485 TATTGTATAACTCTTGTTT
1 TATTGTATAACTCTTGTTT
40405504 TATTGT-TAA-TCTTGTTT
1 TATTGTATAACTCTTGTTT
40405521 TA
1 TA
40405523 GAGGTATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 3 0.16
19 6 0.32
ACGTcount: A:0.21, C:0.08, G:0.11, T:0.61
Consensus pattern (19 bp):
TATTGTATAACTCTTGTTT
Found at i:40411316 original size:49 final size:50
Alignment explanation
Indices: 40411247--40411487 Score: 238
Period size: 49 Copynumber: 4.8 Consensus size: 50
40411237 ATCTATTGTG
* * * * *
40411247 AGGTCACGTGAGTAGTACTAAGTGCAAGCTACTATGTGTACCGGATTATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAATT
*
40411297 -GGT-AGCATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCCAATAACTT
1 AGGTCA-CATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAA-TT
* * * ** * * **
40411347 CGATCACGTGTGTAGTACTAAGTGCAGGCTACTACATCTATC-AGATGGTT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGA-ATAATT
* * * *
40411397 AGGTCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACTGAATAATT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAATT
* *
40411447 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACC
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACC
40411488 AGATAGCTTT
Statistics
Matches: 156, Mismatches: 29, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 74 0.47
50 44 0.28
51 36 0.23
52 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCGAATAATT
Found at i:40418925 original size:50 final size:49
Alignment explanation
Indices: 40418758--40419002 Score: 276
Period size: 49 Copynumber: 4.9 Consensus size: 49
40418748 TCTATTGTGA
* * * *
40418758 GGTCACGTGTGTAGTACTAAGTACAGGCTACTACATGTACCGGATTATT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * * * *
40418807 GGTCGCATTTGTAGTACAAAGTGCAGGCTACTATGCGTACCCA-ATAACTT
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAA-TT
* * * **
40418857 CGATCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTATCAGATGGTT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
40418907 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
1 -GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
* * * *
40418957 GGTCGCGTGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATA
1 GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
40419003 GCTTTGGCTA
Statistics
Matches: 161, Mismatches: 31, Indels: 8
0.81 0.16 0.04
Matches are distributed among these distances:
49 76 0.47
50 52 0.32
51 33 0.20
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (49 bp):
GGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATT
Found at i:40420391 original size:12 final size:12
Alignment explanation
Indices: 40420360--40420401 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
40420350 TCGGCGAGTT
40420360 ACACGGG-TGAGG
1 ACACGGGCTGA-G
*
40420372 ACATGGGCTGAG
1 ACACGGGCTGAG
*
40420384 ACACGGGCTAAG
1 ACACGGGCTGAG
40420396 ACACGG
1 ACACGG
40420402 TCGTGTGTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
12 23 0.88
13 3 0.12
ACGTcount: A:0.29, C:0.21, G:0.40, T:0.10
Consensus pattern (12 bp):
ACACGGGCTGAG
Found at i:40421456 original size:23 final size:26
Alignment explanation
Indices: 40421428--40421481 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
40421418 CACACGTTTA
40421428 TAATTTTGAAAAAA-A-A-AGATTTT
1 TAATTTTGAAAAAATAGATAGATTTT
*
40421451 TAATTTTTTAAAAAATAGATAGATTTT
1 TAA-TTTTGAAAAAATAGATAGATTTT
40421478 TAAT
1 TAAT
40421482 ATTAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 3 0.12
24 10 0.38
25 1 0.04
26 2 0.08
27 10 0.38
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (26 bp):
TAATTTTGAAAAAATAGATAGATTTT
Found at i:40426303 original size:16 final size:16
Alignment explanation
Indices: 40426282--40426327 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
40426272 AATTGGGTTG
40426282 AGAAAATTATTTAATT
1 AGAAAATTATTTAATT
*
40426298 AGAAAATTAATTAATT
1 AGAAAATTATTTAATT
40426314 --AAAATTAATTTAAT
1 AGAAAATT-ATTTAAT
40426328 AAATAATGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 6 0.22
15 6 0.22
16 15 0.56
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
AGAAAATTATTTAATT
Done.