Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D04
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: 52479919
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 336953 characters in sequence are not A, C, G, or T
File 162 of 173
Found at i:48491134 original size:8 final size:8
Alignment explanation
Indices: 48491108--48491150 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
48491098 GCATGGTAAT
48491108 TGGGTTTG
1 TGGGTTTG
*
48491116 TGGGTAT-
1 TGGGTTTG
48491123 TGGGTTTG
1 TGGGTTTG
*
48491131 TGGGTAT-
1 TGGGTTTG
48491138 TGGGTTTG
1 TGGGTTTG
48491146 TGGGT
1 TGGGT
48491151 ATTGGGTCCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.05, C:0.00, G:0.49, T:0.47
Consensus pattern (8 bp):
TGGGTTTG
Found at i:48501818 original size:32 final size:32
Alignment explanation
Indices: 48501777--48501853 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
48501767 GACACGACCG
* * *
48501777 TGTGGGCCACACGGGCTAGGTCAAGT-TGGGCA
1 TGTGGGCCACACAGGCAAGGCCAA-TCTGGGCA
* *
48501809 TGTGCGCCACACAGGCAAGGCCAATCTGGGCG
1 TGTGGGCCACACAGGCAAGGCCAATCTGGGCA
48501841 TGTGGGCCACACA
1 TGTGGGCCACACA
48501854 TGCGTATGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 1 0.03
32 37 0.97
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.16
Consensus pattern (32 bp):
TGTGGGCCACACAGGCAAGGCCAATCTGGGCA
Found at i:48504162 original size:18 final size:18
Alignment explanation
Indices: 48504139--48504176 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
48504129 ATCCCAATGA
48504139 TCGCCAGCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
48504157 TCGCCAGCACCTTCTTCT
1 TCGCCAGCACCTTCTTCT
48504175 TC
1 TC
48504177 ACCACCAACC
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:0.11, C:0.45, G:0.11, T:0.34
Consensus pattern (18 bp):
TCGCCAGCACCTTCTTCT
Found at i:48504970 original size:3 final size:3
Alignment explanation
Indices: 48504962--48504990 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
48504952 TCTTAATACT
48504962 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
48504991 TAATAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:48505081 original size:19 final size:21
Alignment explanation
Indices: 48505057--48505095 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
48505047 AGTAAAACAA
*
48505057 AAAAT-ATTACAA-AATATAC
1 AAAATAATAACAACAATATAC
48505076 AAAATAATAACAACAATATA
1 AAAATAATAACAACAATATA
48505096 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (21 bp):
AAAATAATAACAACAATATAC
Found at i:48505275 original size:27 final size:27
Alignment explanation
Indices: 48505228--48505293 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
48505218 AATACGAGTA
48505228 GTGCCGCCAATCAATACGGCACCATTG
1 GTGCCGCCAATCAATACGGCACCATTG
* *
48505255 GTGCCGCCAAT-GATATTGGCACCATTG
1 GTGCCGCCAATCAATA-CGGCACCATTG
*
48505282 GTGCCACCAATC
1 GTGCCGCCAATC
48505294 CCATTGGCGT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 3 0.09
27 31 0.91
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (27 bp):
GTGCCGCCAATCAATACGGCACCATTG
Found at i:48505299 original size:27 final size:27
Alignment explanation
Indices: 48505228--48505301 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
48505218 AATACGAGTA
* *
48505228 GTGCCGCCAATCA-ATACGGCACCATTG
1 GTGCCACCAATCACAT-TGGCACCATTG
* * *
48505255 GTGCCGCCAATGATATTGGCACCATTG
1 GTGCCACCAATCACATTGGCACCATTG
*
48505282 GTGCCACCAATCCCATTGGC
1 GTGCCACCAATCACATTGGC
48505302 GTGACCAAGG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 38 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (27 bp):
GTGCCACCAATCACATTGGCACCATTG
Found at i:48505381 original size:24 final size:24
Alignment explanation
Indices: 48505354--48505399 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
48505344 AGGTTTTTTT
48505354 TATATATTTTGGTAAATAAAAATA
1 TATATATTTTGGTAAATAAAAATA
48505378 TATATATTTTGGTAAATAAAAA
1 TATATATTTTGGTAAATAAAAA
48505400 AAAAGTTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (24 bp):
TATATATTTTGGTAAATAAAAATA
Found at i:48505950 original size:5 final size:5
Alignment explanation
Indices: 48505942--48505978 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
48505932 GAATTTTGTT
48505942 TTATA TTATA TTATA TTATA TTATA TTATA TT-TA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA
48505979 CTGATTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.13
5 27 0.87
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TTATA
Found at i:48506510 original size:17 final size:17
Alignment explanation
Indices: 48506476--48506510 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
48506466 AATTTTAAAA
*
48506476 TATTTTTAAAATACTTT
1 TATTTTTAAAATAATTT
*
48506493 TATTTTTAAATTAATTT
1 TATTTTTAAAATAATTT
48506510 T
1 T
48506511 TTGGTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTTTTAAAATAATTT
Found at i:48511793 original size:2 final size:2
Alignment explanation
Indices: 48511786--48511815 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
48511776 TCTATCTATC
48511786 TA TA TA TA TA TA TA TA TA TA TA TA TGA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
48511816 TTATGCTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48512973 original size:23 final size:22
Alignment explanation
Indices: 48512903--48513010 Score: 107
Period size: 23 Copynumber: 5.0 Consensus size: 22
48512893 CCTGATCAGT
*
48512903 ATACGACACA-TAAGTGCCTGA
1 ATACGACACACGAAGTGCCTGA
*
48512924 A-ACGAC-CACGAGGTGCCTG-
1 ATACGACACACGAAGTGCCTGA
*
48512943 ATACGACACACGAGGTGCCTGA
1 ATACGACACACGAAGTGCCTGA
**
48512965 TATACGACACATAAAGTGCCTGA
1 -ATACGACACACGAAGTGCCTGA
**
48512988 GATACGACACATAAAGTGCCTGA
1 -ATACGACACACGAAGTGCCTGA
48513011 TCGGCAAGGC
Statistics
Matches: 76, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
19 3 0.04
20 18 0.24
21 14 0.18
23 41 0.54
ACGTcount: A:0.35, C:0.25, G:0.23, T:0.17
Consensus pattern (22 bp):
ATACGACACACGAAGTGCCTGA
Found at i:48513961 original size:22 final size:22
Alignment explanation
Indices: 48513936--48513983 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
48513926 TCTTCCCCTG
*
48513936 TTTTC-GTCTCTTTCTCTGTTTC
1 TTTTCTGT-TCTTCCTCTGTTTC
*
48513958 TTTTCTGTTCTTCCTTTGTTTC
1 TTTTCTGTTCTTCCTCTGTTTC
48513980 TTTT
1 TTTT
48513984 TTCTTTTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (22 bp):
TTTTCTGTTCTTCCTCTGTTTC
Found at i:48514037 original size:3 final size:3
Alignment explanation
Indices: 48514029--48514087 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
48514019 ATGCATTAGT
*
48514029 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATA TTA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
*
48514075 TCA T-A TAA TAA TA
1 TAA TAA TAA TAA TA
48514088 TTTTATTCAC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.92
4 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:48514259 original size:30 final size:27
Alignment explanation
Indices: 48514218--48514282 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 27
48514208 TTTCCTATAA
*
48514218 TATATTATTTTAATTTTAATTAATATAATT
1 TATAATATTTTAA-TTTAA-TAATAT-ATT
*
48514248 TATAATATTTTAATTTAATAATATTTT
1 TATAATATTTTAATTTAATAATATATT
48514275 TATAATAT
1 TATAATAT
48514283 AAATCAAGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
27 10 0.30
28 6 0.18
29 5 0.15
30 12 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TATAATATTTTAATTTAATAATATATT
Found at i:48514265 original size:25 final size:26
Alignment explanation
Indices: 48514230--48514282 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
48514220 TATTATTTTA
48514230 ATTTTAATTAAT-ATA-ATTTATAAT
1 ATTTTAATTAATAATATATTTATAAT
*
48514254 ATTTTAATTTAATAATATTTTTATAAT
1 ATTTTAA-TTAATAATATATTTATAAT
48514281 AT
1 AT
48514283 AAATCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 7 0.28
25 5 0.20
26 3 0.12
27 10 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTAATTAATAATATATTTATAAT
Found at i:48514268 original size:16 final size:16
Alignment explanation
Indices: 48514223--48514274 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
48514213 TATAATATAT
48514223 TATTTTAATTTTAATTAA
1 TATTTTAA-TTTAA-TAA
48514241 TA---TAATTT-ATAA
1 TATTTTAATTTAATAA
48514253 TATTTTAATTTAATAA
1 TATTTTAATTTAATAA
48514269 TATTTT
1 TATTTT
48514275 TATAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
12 5 0.17
13 1 0.03
14 3 0.10
15 9 0.30
16 10 0.33
18 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTAATTTAATAA
Found at i:48518560 original size:90 final size:93
Alignment explanation
Indices: 48518339--48518562 Score: 269
Period size: 96 Copynumber: 2.4 Consensus size: 93
48518329 CTTTCTGATT
* * * *
48518339 AATTTTAG-TTTTATACATTATGAATTGGTTCAATTTAATTCCTTTAATTTGAAGTTTTAAAATT
1 AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAATTCCTTTAATTGGAAGTTTTAAAATT
* * *
48518403 GTAATCTTGGTATTTGTATTTTAATTTGGTT
66 GTAATCTT-GTA--TATATTTTAATTTAGTC
* * *
48518434 AATTTTAATTCTTATACTTTTCGAATTGGTTAAATTTAATT-CTTGTAATTGGAAGTTTTAAAAT
1 AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAATTCCTT-TAATTGGAAGTTTTAAAAT
*
48518498 TGTAGTC-T-TA-ATATTTTAATTTAGTC
65 TGTAATCTTGTATATATTTTAATTTAGTC
*
48518524 AATTTTAGTTTTTATACTTTTTGAATTAGTTAAATTTAA
1 AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAA
48518563 ACCTAAACAA
Statistics
Matches: 112, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
90 48 0.43
93 2 0.02
95 11 0.10
96 51 0.46
ACGTcount: A:0.30, C:0.05, G:0.11, T:0.53
Consensus pattern (93 bp):
AATTTTAGTTTTTATACTTTTTGAATTGGTTAAATTTAATTCCTTTAATTGGAAGTTTTAAAATT
GTAATCTTGTATATATTTTAATTTAGTC
Found at i:48520891 original size:27 final size:30
Alignment explanation
Indices: 48520847--48520903 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
48520837 ATAATCATAA
*
48520847 TTTAATTCACTTTTATTCAAT-TC-ATATT
1 TTTAATTCACTTTAATTCAATATCGATATT
48520875 TTTAATTCA-TTTAATTCAATATCGATATT
1 TTTAATTCACTTTAATTCAATATCGATATT
48520904 CACCTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 10 0.38
28 11 0.42
29 5 0.19
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (30 bp):
TTTAATTCACTTTAATTCAATATCGATATT
Found at i:48521653 original size:13 final size:13
Alignment explanation
Indices: 48521635--48521675 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
48521625 CTCAATTTTC
48521635 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
48521648 TCTTTTCTTTCTT
1 TCTTTTCTTTCTT
* *
48521661 TC-CTTCTTTCCT
1 TCTTTTCTTTCTT
48521673 TCT
1 TCT
48521676 CTGTTTCGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TCTTTTCTTTCTT
Found at i:48521889 original size:8 final size:8
Alignment explanation
Indices: 48521876--48521938 Score: 74
Period size: 8 Copynumber: 7.8 Consensus size: 8
48521866 GTTTATTTAA
48521876 AATATAAT
1 AATATAAT
48521884 AATATAAT
1 AATATAAT
48521892 AATATAAT
1 AATATAAT
48521900 AATATAAT
1 AATATAAT
* *
48521908 -ATAATTTAC
1 AAT-A-TAAT
48521917 AATATAAT
1 AATATAAT
*
48521925 AAAATAAT
1 AATATAAT
48521933 AATATA
1 AATATA
48521939 CTTCAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
7 2 0.04
8 39 0.85
9 3 0.07
10 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATAAT
Found at i:48524380 original size:18 final size:19
Alignment explanation
Indices: 48524359--48524400 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
48524349 ATATATAGAT
48524359 ATATATAATAAGAT-ATAA
1 ATATATAATAAGATGATAA
*
48524377 ATATATAATAAGATGATAT
1 ATATATAATAAGATGATAA
48524396 ATATA
1 ATATA
48524401 ACTAGTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 14 0.64
19 8 0.36
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
ATATATAATAAGATGATAA
Found at i:48524411 original size:35 final size:33
Alignment explanation
Indices: 48524356--48524420 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 33
48524346 GAGATATATA
48524356 GATATATATAATAAGATATAAATATATAATAAGAT
1 GATATATATAATAAGATAT-AATA-ATAATAAGAT
*
48524391 GATATATATAACT-AGTTATAATAATAATAA
1 GATATATATAA-TAAGATATAATAATAATAA
48524421 TAATAATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 7 0.25
34 4 0.14
35 16 0.57
36 1 0.04
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.35
Consensus pattern (33 bp):
GATATATATAATAAGATATAATAATAATAAGAT
Found at i:48524416 original size:3 final size:3
Alignment explanation
Indices: 48524408--48524434 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
48524398 ATAACTAGTT
48524408 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
48524435 GGACAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:48525197 original size:8 final size:8
Alignment explanation
Indices: 48525184--48525216 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
48525174 ATTCAAAAGG
48525184 TATTTTTT
1 TATTTTTT
48525192 TATTTTTT
1 TATTTTTT
48525200 T-TATTTTT
1 TAT-TTTTT
48525208 TATTTTTT
1 TATTTTTT
48525216 T
1 T
48525217 TTGCAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 1 0.04
8 21 0.91
9 1 0.04
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TATTTTTT
Found at i:48525200 original size:9 final size:9
Alignment explanation
Indices: 48525186--48525217 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
48525176 TCAAAAGGTA
48525186 TTTTTTTAT
1 TTTTTTTAT
48525195 TTTTTTTA-
1 TTTTTTTAT
48525203 -TTTTTTAT
1 TTTTTTTAT
48525211 TTTTTTT
1 TTTTTTT
48525218 TGCAAATAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.09, C:0.00, G:0.00, T:0.91
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:48525208 original size:16 final size:16
Alignment explanation
Indices: 48525187--48525217 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
48525177 CAAAAGGTAT
48525187 TTTTTTATTTTTTTTA
1 TTTTTTATTTTTTTTA
48525203 TTTTTTATTTTTTTT
1 TTTTTTATTTTTTTT
48525218 TGCAAATAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTTTATTTTTTTTA
Found at i:48525870 original size:12 final size:12
Alignment explanation
Indices: 48525849--48525885 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
48525839 ATTCCAAAGA
*
48525849 TGAAAGCTTGAT
1 TGAAAACTTGAT
48525861 TGAAAACTTGAT
1 TGAAAACTTGAT
*
48525873 TAAAAACTTGAT
1 TGAAAACTTGAT
48525885 T
1 T
48525886 ATTAAATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (12 bp):
TGAAAACTTGAT
Found at i:48528540 original size:21 final size:21
Alignment explanation
Indices: 48528515--48528565 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
48528505 TTATATATTT
48528515 TTTAAAAGTAATATTGATAA-AA
1 TTTAAAA--AATATTGATAATAA
*
48528537 -TTAAAACATATTGATAATAA
1 TTTAAAAAATATTGATAATAA
48528557 TTTAAAAAA
1 TTTAAAAAA
48528566 ATAATGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 10 0.40
20 2 0.08
21 13 0.52
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.35
Consensus pattern (21 bp):
TTTAAAAAATATTGATAATAA
Found at i:48528549 original size:19 final size:21
Alignment explanation
Indices: 48528525--48528563 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
48528515 TTTAAAAGTA
48528525 ATATTGATAA-AA-TTAAAAC
1 ATATTGATAATAATTTAAAAC
48528544 ATATTGATAATAATTTAAAA
1 ATATTGATAATAATTTAAAA
48528564 AAATAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 2 0.11
21 6 0.33
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (21 bp):
ATATTGATAATAATTTAAAAC
Found at i:48530930 original size:31 final size:29
Alignment explanation
Indices: 48530892--48530968 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
48530882 CTAACGGCTC
* *
48530892 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTAAC-ACGTCA-AACATA
* **
48530923 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACACGTCAAACATA
48530952 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
48530969 CTGAGCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 22 0.55
30 3 0.08
31 15 0.38
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.25
Consensus pattern (29 bp):
AGTGACTAAAATGTAACACGTCAAACATA
Found at i:48538049 original size:23 final size:23
Alignment explanation
Indices: 48538006--48538054 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
48537996 TTTCTAAATT
48538006 TAGATAGAATACTCTAAAAAAACTG
1 TAGATAGAATACTCT--AAAAACTG
48538031 TAGATAGAACT-CTCT-AAAACTG
1 TAGATAGAA-TACTCTAAAAACTG
48538053 TA
1 TA
48538055 CTAAGTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
22 9 0.39
25 13 0.57
26 1 0.04
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (23 bp):
TAGATAGAATACTCTAAAAACTG
Found at i:48546912 original size:40 final size:40
Alignment explanation
Indices: 48546857--48546937 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
48546847 ATTTTTTCAA
* *
48546857 GTATATTTTAATTTTGGCAACTTTGACAACCGTACACTCC
1 GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
48546897 GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
1 GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
48546937 G
1 G
48546938 CAATGAAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.37
Consensus pattern (40 bp):
GTATATTTTAATTTTGGAAACTTTGACAACAGTACACTCC
Found at i:48548850 original size:108 final size:110
Alignment explanation
Indices: 48548583--48548892 Score: 444
Period size: 108 Copynumber: 2.8 Consensus size: 110
48548573 GAAATTCAAG
** * *
48548583 AGGATATTTTTCTATTTGGTTAAATGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* **
48548648 GAATTTCCCAAATGCAAAACATTGCCTTATTTCGAATTTTTTTAAA
66 GAATTT-CCAAACGCAAAACATTGCCTTATTTCGAATAATTTTAAA
* * * *
48548694 AGGATATTTAGCCATTTGGTTGAACGAGAAAAATCGACACCCAACACCTTAGGGCATGTTTCCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* * *
48548759 GAATTTTCAAACGCAAAACATTGCCTTATTT-TAA-AATTTTGAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTCGAATAATTTTAAA
*
48548802 AGGATATTTAGCTATTTTGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
* *
48548867 GAATTTCCAAACGCTAAATATTGCCT
66 GAATTTCCAAACGCAAAACATTGCCT
48548893 CAATTAGAAA
Statistics
Matches: 177, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
108 89 0.50
109 2 0.01
110 23 0.13
111 63 0.36
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (110 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACCTTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTCGAATAATTTTAAA
Found at i:48549530 original size:3 final size:3
Alignment explanation
Indices: 48549514--48549577 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
48549504 AAAATAAAAT
* * * * *
48549514 TAA TAA TAGT TAA TAA TAG TAA TAA TAA TGA TAA TAA CAC TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
48549560 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
48549578 ACTAAATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
3 48 0.96
4 2 0.04
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:48553532 original size:41 final size:41
Alignment explanation
Indices: 48553475--48553557 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
48553465 CTACATAGAG
*
48553475 AGCCATGCTTGTTGACACGGGATACATGGTATAAAATCGCC
1 AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
48553516 AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
1 AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
48553557 A
1 A
48553558 TGGGAGTGGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (41 bp):
AGCCATGCTTGTTGACACGGGATACAAGGTATAAAATCGCC
Found at i:48556136 original size:11 final size:12
Alignment explanation
Indices: 48556109--48556134 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48556099 TTTTTCTAAC
48556109 TTTCCTTTTTTT
1 TTTCCTTTTTTT
48556121 TTTCCTTTTTTT
1 TTTCCTTTTTTT
48556133 TT
1 TT
48556135 CCATTCTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTCCTTTTTTT
Found at i:48562467 original size:17 final size:17
Alignment explanation
Indices: 48562445--48562478 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
48562435 CAATTTTGAC
48562445 TATATAAAATCTAAAAT
1 TATATAAAATCTAAAAT
*
48562462 TATATAACATCTAAAAT
1 TATATAAAATCTAAAAT
48562479 ATACATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (17 bp):
TATATAAAATCTAAAAT
Found at i:48571848 original size:25 final size:25
Alignment explanation
Indices: 48571819--48571903 Score: 73
Period size: 25 Copynumber: 3.3 Consensus size: 25
48571809 GCCAATATTT
*
48571819 GGAAGCTCCGGATAGCCATTAATCG
1 GGAAGCTCCGGAAAGCCATTAATCG
* ** **
48571844 GGAAGTTCATGAAAGAGAATTTAATCG
1 GGAAGCTCCGGAAAG-CCA-TTAATCG
*
48571871 GGAAGCTTC-GAAGAGCCATTAATCG
1 GGAAGCTCCGGAA-AGCCATTAATCG
48571896 GGAAGCTC
1 GGAAGCTC
48571904 ATGAAAGAGC
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
25 25 0.56
26 5 0.11
27 15 0.33
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (25 bp):
GGAAGCTCCGGAAAGCCATTAATCG
Found at i:48571868 original size:27 final size:27
Alignment explanation
Indices: 48571837--48571922 Score: 108
Period size: 27 Copynumber: 3.3 Consensus size: 27
48571827 CGGATAGCCA
*
48571837 TTAATCGGGAAGTTCATGAAAGAGAAT
1 TTAATCGGGAAGTTCATGAAAGAGCAT
48571864 TTAATCGGGAAGCTTC--G-AAGAGCCA-
1 TTAATCGGGAAG-TTCATGAAAGAG-CAT
*
48571889 TTAATCGGGAAGCTCATGAAAGAGCAT
1 TTAATCGGGAAGTTCATGAAAGAGCAT
48571916 TTAATCG
1 TTAATCG
48571923 AAAAGCCTTG
Statistics
Matches: 51, Mismatches: 2, Indels: 12
0.78 0.03 0.18
Matches are distributed among these distances:
24 2 0.04
25 17 0.33
26 5 0.10
27 24 0.47
28 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (27 bp):
TTAATCGGGAAGTTCATGAAAGAGCAT
Found at i:48571890 original size:52 final size:52
Alignment explanation
Indices: 48571832--48571993 Score: 211
Period size: 52 Copynumber: 3.1 Consensus size: 52
48571822 AGCTCCGGAT
* * *
48571832 AGCCATTAATCGGGAAGTTCATGAAAGAGAATTTAATCGGGAAGCTTCGAAG
1 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAGCTTCGAAG
* *
48571884 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGAAAAGCCTT-GGAG
1 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAG-CTTCGAAG
* * * *
48571936 AGCCATTAATCGAGAAGCTCA-CAAAGAGCCTTTAATCGGAAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAGCT-TCGAAG
48571988 AGCCAT
1 AGCCAT
48571994 ATATCAGGAT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
50 2 0.02
51 19 0.20
52 72 0.75
53 3 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (52 bp):
AGCCATTAATCGGGAAGCTCATGAAAGAGCATTTAATCGGAAAGCTTCGAAG
Found at i:48571963 original size:26 final size:26
Alignment explanation
Indices: 48571832--48571993 Score: 116
Period size: 26 Copynumber: 6.2 Consensus size: 26
48571822 AGCTCCGGAT
* *
48571832 AGCCATTAATCGGGAAGTTCATGAAAG
1 AGCCATTAATCGGGAAGCTCA-CAAAG
* * *
48571859 AG-AATTTAATCGGGAAGCT-TCGAAG
1 AGCCA-TTAATCGGGAAGCTCACAAAG
*
48571884 AGCCATTAATCGGGAAGCTCATGAAAG
1 AGCCATTAATCGGGAAGCTCA-CAAAG
** ****
48571911 AG-CATTTAATCGAAAAGC-CTTGGAG
1 AGCCA-TTAATCGGGAAGCTCACAAAG
*
48571936 AGCCATTAATCGAGAAGCTCACAAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
* * *
48571962 AGCCTTTAATCGGAAAGCTCACGAAG
1 AGCCATTAATCGGGAAGCTCACAAAG
48571988 AGCCAT
1 AGCCAT
48571994 ATATCAGGAT
Statistics
Matches: 103, Mismatches: 25, Indels: 15
0.72 0.17 0.10
Matches are distributed among these distances:
25 35 0.34
26 37 0.36
27 31 0.30
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.20
Consensus pattern (26 bp):
AGCCATTAATCGGGAAGCTCACAAAG
Found at i:48574102 original size:12 final size:12
Alignment explanation
Indices: 48574085--48574110 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
48574075 ATATATATAC
48574085 TAATTTAATTCA
1 TAATTTAATTCA
48574097 TAATTTAATTCA
1 TAATTTAATTCA
48574109 TA
1 TA
48574111 CATTCTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTTAATTCA
Found at i:48574597 original size:24 final size:23
Alignment explanation
Indices: 48574566--48574612 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
48574556 TATTCACACA
48574566 TATTCTTA-CTTAATTTCAAATGT
1 TATTCTTACCTTAATTT-AAATGT
*
48574589 TATTACTTACCTTACTTTAAATGT
1 TATT-CTTACCTTAATTTAAATGT
48574613 CTCATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.30, C:0.15, G:0.04, T:0.51
Consensus pattern (23 bp):
TATTCTTACCTTAATTTAAATGT
Found at i:48575319 original size:29 final size:29
Alignment explanation
Indices: 48575262--48575318 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
48575252 TTTTCTTCCC
48575262 CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
1 CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
*
48575291 CTGTTCTTC-TTTTGTT-TCTTTTTCTTTT
1 CTGTT-TTCGTTTTGTTCTCTGTTTCTTTT
48575319 TATTTACTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.42
29 12 0.46
30 3 0.12
ACGTcount: A:0.00, C:0.18, G:0.11, T:0.72
Consensus pattern (29 bp):
CTGTTTTCGTTTTGTTCTCTGTTTCTTTT
Found at i:48578340 original size:29 final size:29
Alignment explanation
Indices: 48578301--48578383 Score: 127
Period size: 26 Copynumber: 3.0 Consensus size: 29
48578291 ATAATTCGTA
*
48578301 AAAAAGATATAAAAATGTAATTTTATAGT
1 AAAAAGTTATAAAAATGTAATTTTATAGT
*
48578330 AAAAAGTTATAAAAATGT-AGTTT-TA-T
1 AAAAAGTTATAAAAATGTAATTTTATAGT
48578356 AAAAAGTTATAAAAATGTAATTTTATAG
1 AAAAAGTTATAAAAATGTAATTTTATAG
48578384 ATATGCATAA
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
26 19 0.40
27 6 0.12
28 6 0.12
29 17 0.35
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (29 bp):
AAAAAGTTATAAAAATGTAATTTTATAGT
Found at i:48580806 original size:30 final size:29
Alignment explanation
Indices: 48580770--48580829 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
48580760 ATAATTTGTG
*
48580770 AAAATTGAATC-AAATCAAATTTTCATGTAT
1 AAAATTGAA-CAAAATCAAAGTTT-ATGTAT
*
48580800 AAAATTGCACAAAATCAAAGTTTATGTAT
1 AAAATTGAACAAAATCAAAGTTTATGTAT
48580829 A
1 A
48580830 GTTTTGAGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 8 0.30
30 19 0.70
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.33
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAGTTTATGTAT
Found at i:48581220 original size:3 final size:3
Alignment explanation
Indices: 48581214--48581292 Score: 56
Period size: 3 Copynumber: 25.3 Consensus size: 3
48581204 ATTATTTCAC
* * *
48581214 TAT TAT TAT CAT TAT TAT ATAG TAT TAT TAAT TGAAT TGT TAT TATT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT T-AT T--AT TAT TAT TA-T
48581261 TAT TAT TA- TATT TAT TAT T-T TAT TA- TAT TAT T
1 TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT T
48581293 GTCATTTTAT
Statistics
Matches: 62, Mismatches: 6, Indels: 16
0.74 0.07 0.19
Matches are distributed among these distances:
2 6 0.10
3 42 0.68
4 10 0.16
5 4 0.06
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:48581277 original size:19 final size:17
Alignment explanation
Indices: 48581253--48581289 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
48581243 AATTGAATTG
48581253 TTATTATTTATTATTATAT
1 TTATTA-TT-TTATTATAT
48581272 TTATTATTTTATTATAT
1 TTATTATTTTATTATAT
48581289 T
1 T
48581290 ATTGTCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.56
18 2 0.11
19 6 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTATTTTATTATAT
Found at i:48581278 original size:22 final size:22
Alignment explanation
Indices: 48581253--48581319 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 22
48581243 AATTGAATTG
48581253 TTATTATTTATTATTATATTTA
1 TTATTATTTATTATTATATTTA
48581275 TTA-T-TTTATTA-TATTATTGTCA
1 TTATTATTTATTATTA-TATT-T-A
48581297 TT-TTATTTCATTATT-TATGTTA
1 TTATTATTT-ATTATTATAT-TTA
48581319 T
1 T
48581320 CATTTTGTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
19 2 0.05
20 11 0.30
21 2 0.05
22 9 0.24
23 7 0.19
24 5 0.14
25 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (22 bp):
TTATTATTTATTATTATATTTA
Found at i:48585279 original size:3 final size:3
Alignment explanation
Indices: 48585271--48585367 Score: 131
Period size: 3 Copynumber: 32.3 Consensus size: 3
48585261 CGTTTTCGAG
* * *
48585271 GGA GGA GGA GGA GAA GGA GGA GGA GGA AGA GCA GGA GGA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
* * * *
48585319 GGA GGA AGA GCA GGA GGA GGA GGA GGA GGA GGA AGA GCA GGA GGA GGA
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA GGA
48585367 G
1 G
48585368 AGGCATTCGA
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.37, C:0.03, G:0.60, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:48585307 original size:27 final size:27
Alignment explanation
Indices: 48585276--48585367 Score: 175
Period size: 27 Copynumber: 3.4 Consensus size: 27
48585266 TCGAGGGAGG
*
48585276 AGGAGGAGAAGGAGGAGGAGGAAGAGC
1 AGGAGGAGGAGGAGGAGGAGGAAGAGC
48585303 AGGAGGAGGAGGAGGAGGAGGAAGAGC
1 AGGAGGAGGAGGAGGAGGAGGAAGAGC
48585330 AGGAGGAGGAGGAGGAGGAGGAAGAGC
1 AGGAGGAGGAGGAGGAGGAGGAAGAGC
48585357 AGGAGGAGGAG
1 AGGAGGAGGAG
48585368 AGGCATTCGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 64 1.00
ACGTcount: A:0.38, C:0.03, G:0.59, T:0.00
Consensus pattern (27 bp):
AGGAGGAGGAGGAGGAGGAGGAAGAGC
Found at i:48585949 original size:30 final size:29
Alignment explanation
Indices: 48585893--48585959 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
48585883 ATCTTTATGA
* *
48585893 TTTTTAAAAGATTAAATTAAATTTTTATAT
1 TTTTTAAAAAATTAAAGTAAATTTTTAT-T
48585923 TTTTTAAAAAATTAAAGTATAA-TTTTATT
1 TTTTTAAAAAATTAAAGTA-AATTTTTATT
48585952 TTTATTAA
1 TTT-TTAA
48585960 TTTAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 4 0.12
30 27 0.82
31 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (29 bp):
TTTTTAAAAAATTAAAGTAAATTTTTATT
Found at i:48587099 original size:52 final size:52
Alignment explanation
Indices: 48587025--48587126 Score: 204
Period size: 52 Copynumber: 2.0 Consensus size: 52
48587015 TGCCACAACT
48587025 AGTTATCCTTAATTCAGGTGTTACTCAAAAATTGCTTCAATAATCTCTCCAC
1 AGTTATCCTTAATTCAGGTGTTACTCAAAAATTGCTTCAATAATCTCTCCAC
48587077 AGTTATCCTTAATTCAGGTGTTACTCAAAAATTGCTTCAATAATCTCTCC
1 AGTTATCCTTAATTCAGGTGTTACTCAAAAATTGCTTCAATAATCTCTCC
48587127 CTTTGACAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (52 bp):
AGTTATCCTTAATTCAGGTGTTACTCAAAAATTGCTTCAATAATCTCTCCAC
Found at i:48587942 original size:39 final size:39
Alignment explanation
Indices: 48587883--48588012 Score: 117
Period size: 39 Copynumber: 3.2 Consensus size: 39
48587873 TAGATGTTAC
* *
48587883 TTAGTATTATTGTTA-AAAAACTAA-TATTATTATTATGG
1 TTAGTATTATT-TTAGTAAAACTAATTATTATTGTTATGG
48587921 TTAGTTATTATTTTAGTAAAACCCTAATTATTATTGTTA--G
1 TTAG-TATTATTTTAGTAAAA--CTAATTATTATTGTTATGG
*
48587961 TTAGTATTATTTCAGTATAAAAC-AATTATTATTGTTATTGTG
1 TTAGTATTATTTTAG--TAAAACTAATTATTATTGTTA-TG-G
48588003 TTAGTTATTA
1 TTAG-TATTA
48588013 GGATTAGTGG
Statistics
Matches: 77, Mismatches: 3, Indels: 19
0.78 0.03 0.19
Matches are distributed among these distances:
38 21 0.27
39 22 0.29
40 5 0.06
41 9 0.12
42 15 0.19
43 5 0.06
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (39 bp):
TTAGTATTATTTTAGTAAAACTAATTATTATTGTTATGG
Found at i:48587995 original size:38 final size:40
Alignment explanation
Indices: 48587896--48587997 Score: 113
Period size: 38 Copynumber: 2.6 Consensus size: 40
48587886 GTATTATTGT
* * *
48587896 TAAAAAACTAA-TATTATTATTATGGTTAGTTATTATTTTAG
1 TAAAACACTAATTATTATTGTTA--GTTAGTTATTATTTCAG
*
48587937 TAAAACCCTAATTATTATTGTTAGTTAG-TATTATTTCAG
1 TAAAACACTAATTATTATTGTTAGTTAGTTATTATTTCAG
48587976 TATAAA-AC-AATTATTATTGTTA
1 TA-AAACACTAATTATTATTGTTA
48587998 TTGTGTTAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
38 14 0.26
39 13 0.24
40 8 0.15
41 9 0.17
42 10 0.19
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (40 bp):
TAAAACACTAATTATTATTGTTAGTTAGTTATTATTTCAG
Found at i:48589867 original size:48 final size:48
Alignment explanation
Indices: 48589815--48589968 Score: 254
Period size: 48 Copynumber: 3.2 Consensus size: 48
48589805 GAAGGTATGC
* *
48589815 GGGCCATCAGCACCGACATGAGGAGGAGCGCGATAAACCAACGTAGTA
1 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
48589863 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
1 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
* * * *
48589911 GGGCCATCAGCACCGACAGGAAGAGGAGCACGAGAAACCACCGTATTA
1 GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
48589959 GGGCCATCAG
1 GGGCCATCAG
48589969 GGGGGACAGA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 100 1.00
ACGTcount: A:0.33, C:0.27, G:0.31, T:0.10
Consensus pattern (48 bp):
GGGCCATCAGCACCGACATGAGGAGGAGCACGATAAACCACCGTAGTA
Found at i:48596770 original size:21 final size:21
Alignment explanation
Indices: 48596744--48596784 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
48596734 AATATAATAG
48596744 CAAAAT-GATAGTAAACAACAA
1 CAAAATAGA-AGTAAACAACAA
48596765 CAAAATAGAAGTAAACAACA
1 CAAAATAGAAGTAAACAACA
48596785 CTGAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.63, C:0.15, G:0.10, T:0.12
Consensus pattern (21 bp):
CAAAATAGAAGTAAACAACAA
Found at i:48599261 original size:15 final size:15
Alignment explanation
Indices: 48599241--48599271 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
48599231 TCGCCATTGT
48599241 TATATATTTTTAATA
1 TATATATTTTTAATA
*
48599256 TATATATTTTTTATA
1 TATATATTTTTAATA
48599271 T
1 T
48599272 GTCAACACGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TATATATTTTTAATA
Found at i:48601668 original size:42 final size:42
Alignment explanation
Indices: 48601609--48601690 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
48601599 CATAGCGAGC
48601609 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTAGA
1 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTAGA
48601651 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTA
1 TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTA
48601691 TCTGTCTTTG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (42 bp):
TGTTCTTGATCCCGAATTTGAAGCCTCTGCAATTCTTGTAGA
Found at i:48603351 original size:27 final size:27
Alignment explanation
Indices: 48603287--48603358 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
48603277 GGTGGAGGGC
* *
48603287 CTGCCACAGGCGACACCAAAGGTGTCT
1 CTGCCACAGGCGACACCAAAGGTGCCA
* * *
48603314 GTGGCAAAGGCGACACCAAAGGTGCCA
1 CTGCCACAGGCGACACCAAAGGTGCCA
*
48603341 CTGCCACAGGCGGCACCA
1 CTGCCACAGGCGACACCA
48603359 TTTCAATTAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.28, C:0.33, G:0.29, T:0.10
Consensus pattern (27 bp):
CTGCCACAGGCGACACCAAAGGTGCCA
Found at i:48603406 original size:9 final size:9
Alignment explanation
Indices: 48603392--48603421 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
48603382 CAGTTCAGCT
48603392 GAAGGAGAA
1 GAAGGAGAA
48603401 GAAGGAGAA
1 GAAGGAGAA
*
48603410 GAAGAAGAA
1 GAAGGAGAA
48603419 GAA
1 GAA
48603422 AAAGGTGGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (9 bp):
GAAGGAGAA
Found at i:48603458 original size:15 final size:15
Alignment explanation
Indices: 48603438--48603490 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
48603428 GGTGCCGGAA
48603438 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
* * *
48603453 AGAGAAAGGAGAAAG
1 AAAGAAAAGAAAAAG
*
48603468 AAAGAGAAGAAAAA-
1 AAAGAAAAGAAAAAG
48603482 AATAGAAAA
1 AA-AGAAAA
48603491 AATAATGTAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 2 0.07
15 27 0.93
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:48603868 original size:76 final size:77
Alignment explanation
Indices: 48603709--48603887 Score: 195
Period size: 76 Copynumber: 2.3 Consensus size: 77
48603699 AAACTAATAT
* *
48603709 TATTATTATGGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTATTTTAGTTAGTATGATTGT
1 TATTATTATTGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTATATTAGTTAGTATGATTGT
*** *
48603774 TAGTTTTTAAAT
66 TAGTTAAAAAAC
*** * *
48603786 TA-TATTATTGTTAGTTATTATTTTTAGT-AAAACCCTAATTATTACTATTAGTTAGTATTATT-
1 TATTATTATTGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTA-TATTAGTTAGTATGATTG
48603848 TTGAG-TAAAAAAC
65 TT-AGTTAAAAAAC
48603861 TATTATTATTGTGTTAGTTATTAGGAT
1 TATTATTA-T-TGTTAGTTATTAGGAT
48603888 TAGTGGTTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 9
0.78 0.13 0.08
Matches are distributed among these distances:
75 24 0.29
76 43 0.52
77 3 0.04
78 13 0.16
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (77 bp):
TATTATTATTGTTAGTTATTAGGATGAGTAAAAACCCTAATTATTATATTAGTTAGTATGATTGT
TAGTTAAAAAAC
Found at i:48607333 original size:153 final size:154
Alignment explanation
Indices: 48607054--48607559 Score: 766
Period size: 153 Copynumber: 3.3 Consensus size: 154
48607044 ACTTCAAAAC
* * *
48607054 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGCTCATATTTTTTTCCCGGATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCAGGATTTTATTACTTT
* *
48607119 CAAAAAATATACTATTTTCTAATTTTCTAATTTTATATTATTTTAGTACATTATGTTTGAAATGT
66 CAAAAAATATACTATTTTCTGATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGT
* * *
48607184 ATTAATTAATTGTGTTTTTTAAAT
131 ATTAATTTAGTGTGTGTTTTAAAT
* **
48607208 AAATTTAGTAAAAAACCTTTATTTCGGCCATTTGTTCGTA-TTTTTTCCAAAATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCAGGATTTTATTACTTT
*
48607272 CAAAAAATATACTATTTTCTGATTTTCTGATTTTACATTATTTTAGTACATTATGTTTGAAATGT
66 CAAAAAATATACTATTTTCTGATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGT
48607337 ATTAATTTAGTGTGTGTTTTAAAT
131 ATTAATTTAGTGTGTGTTTTAAAT
*
48607361 AAATTTAGTAAAAAACCCTTATTTCGGCC-TTTGTTCGTATTTTTTTCCTGGATTTTATTACTTT
1 AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCAGGATTTTATTACTTT
* * *
48607425 CAAAAAATATATTATTTTC-GTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATG
66 CAAAAAATATACTATTTTCTG-ATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATG
* *
48607489 TATTAATTTAGTGTATGTTTTATAT
130 TATTAATTTAGTGTGTGTTTTAAAT
* * * * *
48607514 AAATTTACTACAAAAACCTTTATTTTGGCCCTTTATTCGTATTTTT
1 AAATTTAGTA-AAAAACCCTTATTTCGGCCATTTGTTCGTATTTTT
48607560 CTTATTTTCA
Statistics
Matches: 323, Mismatches: 25, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
152 11 0.03
153 244 0.76
154 54 0.17
155 14 0.04
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (154 bp):
AAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCAGGATTTTATTACTTT
CAAAAAATATACTATTTTCTGATTTTCTAATTTTACATTATTTTAGTACATTATGTTTGAAATGT
ATTAATTTAGTGTGTGTTTTAAAT
Found at i:48607834 original size:11 final size:11
Alignment explanation
Indices: 48607812--48607906 Score: 53
Period size: 10 Copynumber: 9.0 Consensus size: 11
48607802 AAAAAATACC
48607812 TTTCCTTAT-TT
1 TTTCCTT-TCTT
48607823 TTT-CTTTCTT
1 TTTCCTTTCTT
48607833 TTTCCTTTC--
1 TTTCCTTTCTT
* *
48607842 CTCCCTCTTCTT
1 TTTCCT-TTCTT
*
48607854 TTTCTCATTTC-C
1 TTTC-C-TTTCTT
48607866 TTTCCTTTC-T
1 TTTCCTTTCTT
* *
48607876 TCTCCTTTCCT
1 TTTCCTTTCTT
48607887 TTT-CTTTCTT
1 TTTCCTTTCTT
48607897 TTT-CTTTCTT
1 TTTCCTTTCTT
48607907 CTCCTTCTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
9 5 0.07
10 39 0.58
11 12 0.18
12 6 0.09
13 4 0.06
14 1 0.01
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCCTTTCTT
Found at i:48607903 original size:20 final size:20
Alignment explanation
Indices: 48607826--48607921 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 20
48607816 CTTATTTTTT
*
48607826 CTTTCTTTTTCCTTTCC-TCC
1 CTTTCTTTTT-CTTTCCTTTC
48607846 CTCTTCTTTTTCTCATTTCCTTTC
1 CT-TTC-TTTT-TC-TTTCCTTTC
* * *
48607870 CTTTCTTCTCCTTTCCTTTT
1 CTTTCTTTTTCTTTCCTTTC
48607890 CTTTCTTTTTCTTT-CTTCTC
1 CTTTCTTTTTCTTTCCTT-TC
48607910 C-TTCTTTCTTCT
1 CTTTCTTT-TTCT
48607922 CCTTCAGCCG
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
19 9 0.15
20 28 0.45
21 4 0.06
22 8 0.13
23 9 0.15
24 4 0.06
ACGTcount: A:0.01, C:0.34, G:0.00, T:0.65
Consensus pattern (20 bp):
CTTTCTTTTTCTTTCCTTTC
Found at i:48607922 original size:13 final size:13
Alignment explanation
Indices: 48607870--48607926 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
48607860 ATTTCCTTTC
48607870 CTTTCTTCTCCTTT
1 CTTTCTTCTCC-TT
**
48607884 CCTTTTCTTTCTTTTT
1 -C-TTTC-TTCTCCTT
48607900 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
48607913 CTTTCTTCTCCTT
1 CTTTCTTCTCCTT
48607926 C
1 C
48607927 AGCCGAATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 20 0.56
14 4 0.11
15 2 0.06
16 6 0.17
17 4 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (13 bp):
CTTTCTTCTCCTT
Found at i:48608005 original size:27 final size:27
Alignment explanation
Indices: 48607956--48608021 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
48607946 ATATAAGAGG
** *
48607956 CTGGTGCCGCCTATGGTAGTGGCACAT
1 CTGGTGCCGCCTATGCCACTGGCACAT
* * *
48607983 TTGGTGCCGCCTCTGCCACTGGCACCT
1 CTGGTGCCGCCTATGCCACTGGCACAT
48608010 CTGGTGCCGCCT
1 CTGGTGCCGCCT
48608022 GTGGCAGGCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.09, C:0.35, G:0.30, T:0.26
Consensus pattern (27 bp):
CTGGTGCCGCCTATGCCACTGGCACAT
Found at i:48610532 original size:24 final size:25
Alignment explanation
Indices: 48610483--48610538 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
48610473 TCTTTTTAGC
* *
48610483 TTAGTTTTTATTCTCTTCTCTATTT
1 TTAGGTTTTATTCTCTTATCTATTT
48610508 TTAGGTTTTAGTTCT-TTATCT-TTT
1 TTAGGTTTTA-TTCTCTTATCTATTT
*
48610532 TCAGGTT
1 TTAGGTT
48610539 AGTGGTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 9 0.33
25 14 0.52
26 4 0.15
ACGTcount: A:0.12, C:0.12, G:0.11, T:0.64
Consensus pattern (25 bp):
TTAGGTTTTATTCTCTTATCTATTT
Found at i:48612712 original size:16 final size:16
Alignment explanation
Indices: 48612693--48612723 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
48612683 TTAAAAAAGT
48612693 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
48612709 TTTCAAATTTATATG
1 TTTCAAATATATATG
48612724 CTCTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:48613120 original size:18 final size:20
Alignment explanation
Indices: 48613093--48613141 Score: 61
Period size: 18 Copynumber: 2.6 Consensus size: 20
48613083 ATTAGGTTAA
*
48613093 TATTTCTTTTTATAA-AT-T
1 TATTTATTTTTATAACATCT
48613111 TATTTATTTTTA-AACATCT
1 TATTTATTTTTATAACATCT
48613130 T-TTTATTTTTAT
1 TATTTATTTTTAT
48613142 TTTCTTTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.07
18 23 0.85
19 2 0.07
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTTATTTTTATAACATCT
Found at i:48614386 original size:20 final size:20
Alignment explanation
Indices: 48614280--48614389 Score: 57
Period size: 20 Copynumber: 5.5 Consensus size: 20
48614270 ATATAATTTT
* **
48614280 TCATAAAAATGATTGAAAAA
1 TCATAAAAATTATAAAAAAA
*
48614300 TCATAAAAGATTGTAAAAAAA
1 TCATAAAA-ATTATAAAAAAA
* *
48614321 -AATTAAATATTA-AAAAATATA
1 TCA-TAAAAATTATAAAAA-A-A
* * *
48614342 T-ATGAAAATTGAT-ATAAAC
1 TCATAAAAATT-ATAAAAAAA
*
48614361 TTATAAAAATTATAAAAAAA
1 TCATAAAAATTATAAAAAAA
48614381 TCATAAAAA
1 TCATAAAAA
48614390 CTTAATCTGG
Statistics
Matches: 66, Mismatches: 15, Indels: 18
0.67 0.15 0.18
Matches are distributed among these distances:
19 8 0.12
20 40 0.61
21 18 0.27
ACGTcount: A:0.63, C:0.04, G:0.05, T:0.28
Consensus pattern (20 bp):
TCATAAAAATTATAAAAAAA
Found at i:48614525 original size:2 final size:2
Alignment explanation
Indices: 48614518--48614543 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48614508 TATATTTTTA
48614518 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
48614544 TATCTTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48614839 original size:8 final size:9
Alignment explanation
Indices: 48614818--48614880 Score: 56
Period size: 9 Copynumber: 6.8 Consensus size: 9
48614808 TATTATGATT
48614818 TTTTTATAA
1 TTTTTATAA
48614827 TTTTTATAA
1 TTTTTATAA
**
48614836 TTTTATATGG
1 TTTT-TATAA
48614846 TTTTTA-ATA
1 TTTTTATA-A
* *
48614855 TTTTAATATT
1 TTTTTATA-A
48614865 TTTTTATAA
1 TTTTTATAA
48614874 TTTTTAT
1 TTTTTAT
48614881 TCTTTTTAAA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
9 27 0.63
10 16 0.37
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (9 bp):
TTTTTATAA
Found at i:48614849 original size:19 final size:19
Alignment explanation
Indices: 48614827--48614877 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
48614817 TTTTTTATAA
48614827 TTTTTATAATTTT-ATATGG
1 TTTTTATAATTTTAATAT-G
*
48614846 TTTTTA-ATATTTTAATATT
1 TTTTTATA-ATTTTAATATG
48614865 TTTTTATAATTTT
1 TTTTTATAATTTT
48614878 TATTCTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 1 0.04
19 22 0.79
20 5 0.18
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTTTATAATTTTAATATG
Found at i:48614886 original size:19 final size:18
Alignment explanation
Indices: 48614827--48614888 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
48614817 TTTTTTATAA
**
48614827 TTTTTATAATTTTATATGG
1 TTTTTATAATTTT-TATTT
*
48614846 TTTTTA-ATATTTTAATATT
1 TTTTTATA-ATTTTTAT-TT
*
48614865 TTTTTATAATTTTTATTC
1 TTTTTATAATTTTTATTT
48614883 TTTTTA
1 TTTTTA
48614889 AAGAATTCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 10 0.29
19 24 0.69
20 1 0.03
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTATAATTTTTATTT
Found at i:48614987 original size:10 final size:10
Alignment explanation
Indices: 48614955--48615024 Score: 56
Period size: 10 Copynumber: 7.1 Consensus size: 10
48614945 TTTTTTTATA
48614955 TTTATAATTT
1 TTTATAATTT
48614965 TTAATATAATTT
1 TT--TATAATTT
*
48614977 TTTAT-AGTT
1 TTTATAATTT
* *
48614986 TTAATAAGTT
1 TTTATAATTT
*
48614996 TATAT-A-TT
1 TTTATAATTT
48615004 TTTATAATTT
1 TTTATAATTT
*
48615014 TTTTTAATTT
1 TTTATAATTT
48615024 T
1 T
48615025 ATGGGAAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
8 6 0.12
9 9 0.18
10 24 0.49
12 10 0.20
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTATAATTT
Found at i:48614992 original size:19 final size:18
Alignment explanation
Indices: 48614970--48615016 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
48614960 AATTTTTAAT
48614970 ATAATTTTTTATAGTTTTA
1 ATAATTTTTTATA-TTTTA
* * *
48614989 ATAAGTTTATATATTTTT
1 ATAATTTTTTATATTTTA
48615007 ATAATTTTTT
1 ATAATTTTTT
48615017 TTAATTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (18 bp):
ATAATTTTTTATATTTTA
Found at i:48615023 original size:19 final size:19
Alignment explanation
Indices: 48614955--48615024 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
48614945 TTTTTTTATA
48614955 TTTATAATTTTTAATATAATTT
1 TTTATAA-TTTT--TATAATTT
* * *
48614977 TTTATAGTTTTAATAAGTT
1 TTTATAATTTTTATAATTT
*
48614996 TATAT-ATTTTTATAATTT
1 TTTATAATTTTTATAATTT
*
48615014 TTTTTAATTTT
1 TTTATAATTTT
48615025 ATGGGAAAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
18 13 0.34
19 15 0.39
21 4 0.11
22 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (19 bp):
TTTATAATTTTTATAATTT
Found at i:48619667 original size:43 final size:43
Alignment explanation
Indices: 48619619--48619704 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
48619609 TGAAATTAGG
48619619 GTTAAAAAAGTAAGATGAATTGGTTGAGAAAGATCCCCTCCTC
1 GTTAAAAAAGTAAGATGAATTGGTTGAGAAAGATCCCCTCCTC
48619662 GTTAAAAAAGTAAGATGAATTGGTTGAGAAAGATCCCCTCCTC
1 GTTAAAAAAGTAAGATGAATTGGTTGAGAAAGATCCCCTCCTC
48619705 TCATGGGTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.21, T:0.26
Consensus pattern (43 bp):
GTTAAAAAAGTAAGATGAATTGGTTGAGAAAGATCCCCTCCTC
Found at i:48621388 original size:15 final size:15
Alignment explanation
Indices: 48621370--48621411 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
48621360 TTTTGGGTAT
*
48621370 TTTTTTTCATTTATG
1 TTTTTTTCATTTATA
*
48621385 TTTTTTTAATTT-TA
1 TTTTTTTCATTTATA
48621399 TTTTTTTC-TTTAT
1 TTTTTTTCATTTAT
48621412 TTTCCATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 3 0.13
14 9 0.39
15 11 0.48
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTTTTTCATTTATA
Found at i:48626233 original size:43 final size:43
Alignment explanation
Indices: 48626186--48626356 Score: 245
Period size: 43 Copynumber: 4.0 Consensus size: 43
48626176 TATGTGCTAG
* *
48626186 TATAATTGCTTTGGCTTGTCCGATGATGCACTGTGTGTGCCAA
1 TATAATTGCTTCGGCTTGTCCGATGATGCACTATGTGTGCCAA
* *
48626229 TATAATTGCTTCGGCTTGTCCGATGATGCACTGTGTGCGCCAA
1 TATAATTGCTTCGGCTTGTCCGATGATGCACTATGTGTGCCAA
*
48626272 TATAATTGCTTCGGCTTGTCCGATGATGCACTATATGTGCCAA
1 TATAATTGCTTCGGCTTGTCCGATGATGCACTATGTGTGCCAA
* * * * *
48626315 TATATTTCCTTCAGTTTATCCGATGATGCACTATG-GTGCCAA
1 TATAATTGCTTCGGCTTGTCCGATGATGCACTATGTGTGCCAA
48626357 ATTGGGATAT
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
42 7 0.06
43 110 0.94
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (43 bp):
TATAATTGCTTCGGCTTGTCCGATGATGCACTATGTGTGCCAA
Found at i:48627356 original size:19 final size:19
Alignment explanation
Indices: 48627332--48627442 Score: 177
Period size: 19 Copynumber: 5.8 Consensus size: 19
48627322 AATCTTCAGG
48627332 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48627351 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* **
48627370 AATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48627389 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
48627408 GATATATAATCTTAGATAT
1 GATATGCAATCTTAGATAT
48627427 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
48627443 AGATATGATT
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 82 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:48627382 original size:38 final size:38
Alignment explanation
Indices: 48627339--48627442 Score: 199
Period size: 38 Copynumber: 2.7 Consensus size: 38
48627329 AGGGATATGC
48627339 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
*
48627377 AATCTTAGATATGATATGCAATCTTAGATATGATATAT
1 AATCTTAGATATGATATGCAATCTTAGATATAATATAT
48627415 AATCTTAGATATGATATGCAATCTTAGA
1 AATCTTAGATATGATATGCAATCTTAGA
48627443 AGATATGATT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 65 1.00
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.38
Consensus pattern (38 bp):
AATCTTAGATATGATATGCAATCTTAGATATAATATAT
Found at i:48627468 original size:22 final size:22
Alignment explanation
Indices: 48627421--48627465 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
48627411 ATATAATCTT
*
48627421 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATCATAGA
* *
48627443 AGATATGATTTTGTAATCATAGA
1 AGATATGA-TATGCAATCATAGA
48627466 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.07, G:0.18, T:0.36
Consensus pattern (22 bp):
AGATATGATATGCAATCATAGA
Found at i:48628119 original size:22 final size:21
Alignment explanation
Indices: 48628094--48628147 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
48628084 TATAAATATT
*
48628094 TTATTTATTTATTTATATGTAA
1 TTATTTATTTATCTATATGT-A
*
48628116 TTATTTTTTTATCTATATGTA
1 TTATTTATTTATCTATATGTA
48628137 TATATTTATTT
1 T-TATTTATTT
48628148 TAGTATACAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (21 bp):
TTATTTATTTATCTATATGTA
Found at i:48628145 original size:26 final size:26
Alignment explanation
Indices: 48628062--48628148 Score: 67
Period size: 22 Copynumber: 3.4 Consensus size: 26
48628052 TCATATACGC
* * *
48628062 ATATTTATTTTTTGTA-GTATAATATAA
1 ATATTTATTTTTT-TATCTAT-ATGTAT
* *
48628089 ATATTTTATTTATTTATTTATATG--T
1 ATA-TTTATTTTTTTATCTATATGTAT
48628114 A-A-TTATTTTTTTATCTATATGTAT
1 ATATTTATTTTTTTATCTATATGTAT
48628138 ATATTTATTTT
1 ATATTTATTTT
48628149 AGTATACATA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
22 17 0.35
24 3 0.06
25 2 0.04
26 7 0.15
27 7 0.15
28 12 0.25
ACGTcount: A:0.31, C:0.01, G:0.05, T:0.63
Consensus pattern (26 bp):
ATATTTATTTTTTTATCTATATGTAT
Found at i:48635414 original size:27 final size:29
Alignment explanation
Indices: 48635370--48635431 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
48635360 AATTTAATTA
*
48635370 CTAA-TTAATTACTAAATATTTTTA-TTT
1 CTAATTTAATTACTAAATATTTCTATTTT
*
48635397 CTAATTTAATTCCT-AATATTTCTATTTT
1 CTAATTTAATTACTAAATATTTCTATTTT
48635425 CTAATTT
1 CTAATTT
48635432 CACACTTACT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.56
Consensus pattern (29 bp):
CTAATTTAATTACTAAATATTTCTATTTT
Found at i:48642143 original size:21 final size:20
Alignment explanation
Indices: 48642108--48642163 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 20
48642098 ATTTTTTTAC
*
48642108 CTTGAACCCGAAACCCTAGAT
1 CTTGAACCCG-AACCATAGAT
* *
48642129 CTTGGACCTCGAACCATGGAT
1 CTTGAACC-CGAACCATAGAT
48642150 CTTGAACCCGAACC
1 CTTGAACCCGAACC
48642164 TCAAACAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 6 0.20
21 22 0.73
22 2 0.07
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.20
Consensus pattern (20 bp):
CTTGAACCCGAACCATAGAT
Found at i:48650564 original size:22 final size:22
Alignment explanation
Indices: 48650536--48650582 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
48650526 TATGCACTAT
48650536 TAAACGGAGAGCACTAATGTGC
1 TAAACGGAGAGCACTAATGTGC
48650558 TAAACGGAGAGCACTAATGTGC
1 TAAACGGAGAGCACTAATGTGC
48650580 TAA
1 TAA
48650583 TAATCAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (22 bp):
TAAACGGAGAGCACTAATGTGC
Found at i:48654236 original size:20 final size:20
Alignment explanation
Indices: 48654200--48654237 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48654190 TCACGTAAGC
*
48654200 AATTAATTAATTTTAAAAAA
1 AATTAATTAATTATAAAAAA
48654220 AATTAA-TAATTCATAAAA
1 AATTAATTAATT-ATAAAA
48654238 TTTTTAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTAATTAATTATAAAAAA
Found at i:48654831 original size:22 final size:22
Alignment explanation
Indices: 48654803--48654850 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
48654793 AATGAGCCAT
48654803 TTGAATCATGATTTATACCCAA
1 TTGAATCATGATTTATACCCAA
48654825 TTGAATCATGATTTATACCCAA
1 TTGAATCATGATTTATACCCAA
48654847 TTGA
1 TTGA
48654851 GTCCCTTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (22 bp):
TTGAATCATGATTTATACCCAA
Found at i:48694557 original size:16 final size:18
Alignment explanation
Indices: 48694518--48694559 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
48694508 TCAGTTTATA
48694518 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
48694535 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
48694552 A-ATTTATA
1 ATATTTATA
48694560 ATACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:48695514 original size:22 final size:21
Alignment explanation
Indices: 48695468--48695530 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
48695458 GCTTTTTCAA
48695468 ATTTTTAAAATTTAAATAATT
1 ATTTTTAAAATTTAAATAATT
48695489 -TTTTTAAAAATTTTAAAT-ATT
1 ATTTTT-AAAA-TTTAAATAATT
* *
48695510 A-TTTTGACATTTAAA-AATT
1 ATTTTTAAAATTTAAATAATT
48695529 AT
1 AT
48695531 ATTATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
19 10 0.29
20 7 0.20
21 11 0.31
22 7 0.20
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTTAAAATTTAAATAATT
Found at i:48700240 original size:22 final size:22
Alignment explanation
Indices: 48700212--48700256 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
48700202 ATAGGTAGTG
48700212 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
48700234 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
48700256 T
1 T
48700257 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:48703945 original size:22 final size:22
Alignment explanation
Indices: 48703917--48703958 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
48703907 GGGAGTGTAA
48703917 GAATATTCTGTAAATATTTTAG
1 GAATATTCTGTAAATATTTTAG
* *
48703939 GAATATTTTGTAGATATTTT
1 GAATATTCTGTAAATATTTT
48703959 TTTTATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.50
Consensus pattern (22 bp):
GAATATTCTGTAAATATTTTAG
Found at i:48705627 original size:14 final size:15
Alignment explanation
Indices: 48705596--48705624 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48705586 TCAAACAAAA
48705596 AATAAATTATATTTT
1 AATAAATTATATTTT
48705611 AATAAATTATATTT
1 AATAAATTATATTT
48705625 AATTGTACTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATAAATTATATTTT
Found at i:48723434 original size:27 final size:27
Alignment explanation
Indices: 48723397--48723457 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
48723387 TATTAAGTTT
48723397 AATGT-AACCCTCCTCAATACGCAACC
1 AATGTGAACCCTCCTCAATACGCAACC
*
48723423 AATGTGAACCCTCCTCAATACGCGACC
1 AATGTGAACCCTCCTCAATACGCAACC
48723450 AATGTGAA
1 AATGTGAA
48723458 GCTATTGCCC
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 5 0.15
27 28 0.85
ACGTcount: A:0.34, C:0.33, G:0.13, T:0.20
Consensus pattern (27 bp):
AATGTGAACCCTCCTCAATACGCAACC
Found at i:48727146 original size:23 final size:21
Alignment explanation
Indices: 48727113--48727164 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 21
48727103 TTAAATTTTA
*
48727113 TTATATATATACATGCATACATTT
1 TTATA-ATATACATACAT--ATTT
*
48727137 TTATAATATACGTACATATTT
1 TTATAATATACATACATATTT
48727158 TTATAAT
1 TTATAAT
48727165 TTATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
23 10 0.38
24 5 0.19
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (21 bp):
TTATAATATACATACATATTT
Found at i:48727225 original size:35 final size:36
Alignment explanation
Indices: 48727155--48727225 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
48727145 TACGTACATA
*
48727155 TTTTTATAATTTATATATATACATACTTATATATAT
1 TTTTTATAATTTATATATATACATACATATATATAT
* * * *
48727191 TTTTTATATTTTATA-ATTTATATACATATCTATAT
1 TTTTTATAATTTATATATATACATACATATATATAT
48727226 ATATCTATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 16 0.53
36 14 0.47
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.58
Consensus pattern (36 bp):
TTTTTATAATTTATATATATACATACATATATATAT
Found at i:48727267 original size:42 final size:42
Alignment explanation
Indices: 48727149--48727285 Score: 109
Period size: 42 Copynumber: 3.2 Consensus size: 42
48727139 ATAATATACG
* * * *
48727149 TACATATTTTTATAATTTATATATATACATACTTATATATA-TTT
1 TACATA-TTTTATAATTTATATAAATATATA--TATACATACTTA
** * * *
48727193 TTTATATTTTATAATTTATATACATATCTATATATAT-CTATA
1 TACATATTTTATAATTTATATAAATATATATATACATACT-TA
*
48727235 TACATATTTTTTAATTT-TCATAAATATATATATACATACTTA
1 TACATATTTTATAATTTAT-ATAAATATATATATACATACTTA
*
48727277 TATATATTT
1 TACATATTT
48727286 CTTATTATAT
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
41 9 0.12
42 40 0.53
43 23 0.30
44 4 0.05
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (42 bp):
TACATATTTTATAATTTATATAAATATATATATACATACTTA
Found at i:48731191 original size:11 final size:13
Alignment explanation
Indices: 48731175--48731208 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
48731165 AATTTTACGA
48731175 AAAAATTTCG-T-
1 AAAAATTTCGTTC
48731186 AAAAATTTCGTTC
1 AAAAATTTCGTTC
48731199 AAAAATTTCG
1 AAAAATTTCG
48731209 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:48732386 original size:27 final size:26
Alignment explanation
Indices: 48732350--48732400 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
48732340 AAATATAAAG
48732350 GGGGTTGCTAACTGCTGATTTCCCCAA
1 GGGGTTGCTAACTGCTGA-TTCCCCAA
* *
48732377 GGGGTTGCTAAGTGTTGATTCCCC
1 GGGGTTGCTAACTGCTGATTCCCC
48732401 GATTCATTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (26 bp):
GGGGTTGCTAACTGCTGATTCCCCAA
Found at i:48732454 original size:103 final size:103
Alignment explanation
Indices: 48732272--48732505 Score: 396
Period size: 103 Copynumber: 2.3 Consensus size: 103
48732262 ATGGAATATG
* *
48732272 AAGGGGTTGCTAAGTGCTGATTCCTCGACTCAATGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGACTCAATGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
48732337 TTTAAATATAAAGGGGGTTGCTAACTGCTGATTTCCCC
66 TTTAAATATAAAGGGGGTTGCTAACTGCTGATTCCCCC
* *
48732375 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGTTGATTCCCCGACTCAATGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* * *
48732440 TTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTTAAATATAAAGGGGGTTGCTAACTGCTGATTCCCCC
48732478 AAGGGGTTGCTAAGTGTTGATTCCCCGA
1 AAGGGGTTGCTAAGTGTTGATTCCCCGA
48732506 ATGATTAATT
Statistics
Matches: 123, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 123 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (103 bp):
AAGGGGTTGCTAAGTGTTGATTCCCCGACTCAATGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTTAAATATAAAGGGGGTTGCTAACTGCTGATTCCCCC
Found at i:48737261 original size:33 final size:33
Alignment explanation
Indices: 48737219--48737531 Score: 145
Period size: 33 Copynumber: 8.7 Consensus size: 33
48737209 AATATGAAGG
*
48737219 GGTTGCTAAGTGCTGATTCCTCGACTCAATGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCAATGGT
* *
48737252 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--T-CA-AT---GGT
* * *
48737295 GGTTGCTAAGTGCTGATTCCCCAATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCAATGGT
* *
48737328 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A-C--TCAA--T---GGT
48737371 GGTTGCTAAGTGCTGATT-CCC--C-CAA-GG-
1 GGTTGCTAAGTGCTGATTCCCCGACTCAATGGT
* *
48737398 GGTTGCTAAGTGCTGATTCCCCGGA-TGATTGGT
1 GGTTGCTAAGTGCTGATTCCCC-GACTCAATGGT
* * *
48737431 GGTTGCTAAGTGCTGATTCCACCATATCTTTGAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CC-GA-C--TCAA--TG---GT
* *
48737474 GGTTGCTAAGTGCTGATTCCCCGAATCACTGGT
1 GGTTGCTAAGTGCTGATTCCCCGACTCAATGGT
*
48737507 GGTTGCTAAGTGCTGAATCCACCGA
1 GGTTGCTAAGTGCTGATTCC-CCGA
48737532 TAACGGTTAA
Statistics
Matches: 216, Mismatches: 26, Indels: 75
0.68 0.08 0.24
Matches are distributed among these distances:
27 18 0.08
28 5 0.02
31 1 0.00
32 2 0.01
33 82 0.38
34 13 0.06
35 2 0.01
36 4 0.02
37 2 0.01
38 9 0.04
39 1 0.00
40 5 0.02
41 4 0.02
42 5 0.02
43 63 0.29
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGACTCAATGGT
Found at i:48737303 original size:76 final size:74
Alignment explanation
Indices: 48737209--48737417 Score: 311
Period size: 76 Copynumber: 2.8 Consensus size: 74
48737199 GAGTACATGG
48737209 AATATGAA-GGGGTTGCTAAGTGCTGATTCCTCGACTCAATGGTGGTTGCTAAGTGCTGATTCCA
1 AATATGAAGGGGGTTGCTAAGTGCTGATTCC-C-ACTCAATGGTGGTTGCTAAGTGCTGATTCCA
48737273 CCGTATCTTTA
64 CCGTATCTTTA
* * *
48737284 AATATAAAGGGGGTTGCTAAGTGCTGATTCCCCAATTCATTGGTGGTTGCTAAGTGCTGATTCCA
1 AATATGAAGGGGGTTGCTAAGTGCTGATT-CCC-ACTCAATGGTGGTTGCTAAGTGCTGATTCCA
48737349 CCGTATCTTTA
64 CCGTATCTTTA
*
48737360 AATGTGAAGGGGGTTGCTAAGTGCTGATTCCC-C-CAA-GG-GGTTGCTAAGTGCTGATTCC
1 AATATGAAGGGGGTTGCTAAGTGCTGATTCCCACTCAATGGTGGTTGCTAAGTGCTGATTCC
48737418 CCGGATGATT
Statistics
Matches: 124, Mismatches: 8, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
70 20 0.16
71 2 0.02
72 2 0.02
75 10 0.08
76 88 0.71
77 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (74 bp):
AATATGAAGGGGGTTGCTAAGTGCTGATTCCCACTCAATGGTGGTTGCTAAGTGCTGATTCCACC
GTATCTTTA
Found at i:48737313 original size:43 final size:41
Alignment explanation
Indices: 48737252--48737390 Score: 159
Period size: 43 Copynumber: 3.5 Consensus size: 41
48737242 ACTCAATGGT
48737252 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATATAAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAAT-T-AAGGG
* * *
48737295 GGTTGCTAAGTGCTGATTCC-CC--A--ATT-CATT--GGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATTAAGGG
48737328 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAAT-T-AAGGG
48737371 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
48737391 CCCAAGGGGT
Statistics
Matches: 80, Mismatches: 6, Indels: 20
0.75 0.06 0.19
Matches are distributed among these distances:
33 22 0.28
34 2 0.03
36 2 0.03
37 2 0.03
38 4 0.05
39 2 0.03
40 2 0.03
42 2 0.03
43 42 0.52
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTTAAATTAAGGG
Found at i:48737415 original size:103 final size:103
Alignment explanation
Indices: 48737293--48737495 Score: 345
Period size: 103 Copynumber: 2.0 Consensus size: 103
48737283 AAATATAAAG
*
48737293 GGGGTTGCTAAGTGCTGATTCCCC-AATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 GGGGTTGCTAAGTGCTGATTCCCCGAA-TCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCT
*
48737357 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCAA
65 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
* *
48737396 GGGGTTGCTAAGTGCTGATTCCCCGGATGATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTT
1 GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTT
*
48737461 TGAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
48737496 GAATCACTGG
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
103 93 0.99
104 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.29, T:0.32
Consensus pattern (103 bp):
GGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCTT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCAA
Found at i:48741235 original size:24 final size:27
Alignment explanation
Indices: 48741199--48741247 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
48741189 TTGGTATATT
*
48741199 TATATTAACTTATTTTA-ATTTTATCA
1 TATATTAACTTATGTTATATTTTATCA
48741225 TATA-TAA-TTATGTTATATTTTAT
1 TATATTAACTTATGTTATATTTTAT
48741248 TTTATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 10 0.48
26 4 0.19
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (27 bp):
TATATTAACTTATGTTATATTTTATCA
Found at i:48741603 original size:31 final size:30
Alignment explanation
Indices: 48741565--48741629 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
48741555 ATAAAATATT
*
48741565 ATTAAATTATTTGAGAA-TTTTTATTTAAGTC
1 ATTAAATTA-TTCA-AATTTTTTATTTAAGTC
48741596 ATTAAATTATTCAAATTTTTTTATTTAAGTC
1 ATTAAATTATTCAAA-TTTTTTATTTAAGTC
48741627 ATT
1 ATT
48741630 GGACTGTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 2 0.06
30 3 0.10
31 26 0.84
ACGTcount: A:0.35, C:0.05, G:0.06, T:0.54
Consensus pattern (30 bp):
ATTAAATTATTCAAATTTTTTATTTAAGTC
Found at i:48750773 original size:19 final size:19
Alignment explanation
Indices: 48750730--48750773 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
48750720 TAAAAAAATT
48750730 ATTTTTAAACTTTTTTTAC
1 ATTTTTAAACTTTTTTTAC
* **
48750749 AATTTTAATTTTTTTTTAC
1 ATTTTTAAACTTTTTTTAC
48750768 ATTTTT
1 ATTTTT
48750774 TGTAATAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.07, G:0.00, T:0.68
Consensus pattern (19 bp):
ATTTTTAAACTTTTTTTAC
Found at i:48750914 original size:21 final size:21
Alignment explanation
Indices: 48750844--48750921 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
48750834 TATTTTTATA
*
48750844 ATTTATTTATTTATTTATTTCC
1 ATTT-TTTATATATTTATTTCC
* **
48750866 TAGATTTTATATATATTT-TTCTGA
1 ---ATTTTTTATATATTTATT-TCC
48750890 ATTTTTTATATATTTATTTCC
1 ATTTTTTATATATTTATTTCC
*
48750911 ATTTTTCATAT
1 ATTTTTTATAT
48750922 TTTTTAATGT
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
21 25 0.58
22 2 0.05
23 2 0.05
24 10 0.23
25 4 0.09
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.64
Consensus pattern (21 bp):
ATTTTTTATATATTTATTTCC
Found at i:48757313 original size:15 final size:15
Alignment explanation
Indices: 48757269--48757327 Score: 73
Period size: 15 Copynumber: 3.9 Consensus size: 15
48757259 ATCCACCGCC
*
48757269 AGGATATCCTCCTCA
1 AGGATACCCTCCTCA
* *
48757284 AGGTTATCCTCCTCA
1 AGGATACCCTCCTCA
*
48757299 AGGATACCCTGCTCA
1 AGGATACCCTCCTCA
*
48757314 GGGATACCCTCCTC
1 AGGATACCCTCCTC
48757328 CTTATGCTCC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (15 bp):
AGGATACCCTCCTCA
Found at i:48760797 original size:21 final size:21
Alignment explanation
Indices: 48760771--48760811 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48760761 ATCTGCTCAA
* *
48760771 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
48760792 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
48760812 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:48763891 original size:14 final size:14
Alignment explanation
Indices: 48763868--48763901 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
48763858 TATCATTCCT
*
48763868 TTATTATGTTGCTA
1 TTATTTTGTTGCTA
*
48763882 TTATTTTGTTGTTA
1 TTATTTTGTTGCTA
48763896 TTATTT
1 TTATTT
48763902 AGATATTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.12, T:0.68
Consensus pattern (14 bp):
TTATTTTGTTGCTA
Found at i:48775560 original size:98 final size:96
Alignment explanation
Indices: 48775393--48775583 Score: 215
Period size: 98 Copynumber: 2.0 Consensus size: 96
48775383 TAGATGCATG
* * * * *
48775393 TAGAGGTGATTCTAGTGAAGCAGACTTGAAGAGACAAAATGAGATGCTTGTATGCAAATTTGGCA
1 TAGAGATGAATCTAGTGAAGCAGACTTAAAGAGACAAAATGAGATGCTTGTAGGCAAACTTGGCA
**
48775458 AAGCGAGCCTAAAGAGGTAAAATAAGACATT
66 AAGCGAGCCTAAAGAGACAAAATAAGACATT
* * *
48775489 TAGAGATGAATCTGGTGAAGCAGACTTATAAAGAGGCAAAATGAGATGCCTTAG-AGGCGAACTT
1 TAGAGATGAATCTAGTGAAGCAGAC-T-TAAAGAGACAAAATGAGATG-CTT-GTAGGCAAACTT
* * *
48775553 -GCGAAGCGAGCTTGAAGAGACAAAATAAGAC
62 GGCAAAGCGAGCCTAAAGAGACAAAATAAGAC
48775584 GCCTAAGAGG
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
96 22 0.28
97 1 0.01
98 44 0.56
99 10 0.13
100 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (96 bp):
TAGAGATGAATCTAGTGAAGCAGACTTAAAGAGACAAAATGAGATGCTTGTAGGCAAACTTGGCA
AAGCGAGCCTAAAGAGACAAAATAAGACATT
Found at i:48776685 original size:46 final size:46
Alignment explanation
Indices: 48776614--48776715 Score: 143
Period size: 46 Copynumber: 2.2 Consensus size: 46
48776604 CAAGGCGACC
* * * * * *
48776614 CCTTTTT-GTGGCACGAGGGTGACCCCTTAATAGGAGGGGGAGGGT
1 CCTTTTTAGCGGCACGAGAGTAACCCCTTAATAAGAAGGGGAGGCT
48776659 CCTTTTTAGCGGCACGAGAGTAACCCCTTAATAAGAAGGGGAGGCT
1 CCTTTTTAGCGGCACGAGAGTAACCCCTTAATAAGAAGGGGAGGCT
48776705 CCTTTTTAGCG
1 CCTTTTTAGCG
48776716 AACTTTTTCT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 7 0.14
46 43 0.86
ACGTcount: A:0.22, C:0.21, G:0.32, T:0.25
Consensus pattern (46 bp):
CCTTTTTAGCGGCACGAGAGTAACCCCTTAATAAGAAGGGGAGGCT
Found at i:48778963 original size:77 final size:79
Alignment explanation
Indices: 48778832--48778990 Score: 268
Period size: 77 Copynumber: 2.0 Consensus size: 79
48778822 AGCCACTAGC
48778832 AATGTTTATGAAGATCAGGTGAGTTGAGATTTGGGTAGGATACTGATATAAG-A-AGTCTTTTAA
1 AATGTTTATGAAGATCAGGTGAGTTGAGATTTGGGTAGGATACTGATATAAGAAGAGTCTTTTAA
*
48778895 GCCATTTTTGTAAT
66 GCCATTTTAGTAAT
** *
48778909 AATGTTTATGAAGATTGGGTGAGTTGAGATTTGGGTAGGATACTGATATCAGAAGAGTCTTTTAA
1 AATGTTTATGAAGATCAGGTGAGTTGAGATTTGGGTAGGATACTGATATAAGAAGAGTCTTTTAA
48778974 GCCATTTTAGTAAT
66 GCCATTTTAGTAAT
48778988 AAT
1 AAT
48778991 TAAGATGGGA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
77 49 0.64
78 1 0.01
79 26 0.34
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.37
Consensus pattern (79 bp):
AATGTTTATGAAGATCAGGTGAGTTGAGATTTGGGTAGGATACTGATATAAGAAGAGTCTTTTAA
GCCATTTTAGTAAT
Found at i:48783840 original size:29 final size:29
Alignment explanation
Indices: 48783808--48783865 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
48783798 ATAAAATCAC
* *
48783808 AATCAAATTTTCATATAT-AAATTGCACAT
1 AATCAAAGTTT-ATATATCAAATTACACAT
*
48783837 AATCAAAGTTTATGTATCAAATTACACAT
1 AATCAAAGTTTATATATCAAATTACACAT
48783866 TAAATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (29 bp):
AATCAAAGTTTATATATCAAATTACACAT
Done.