Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 95 of 410
Found at i:27829298 original size:23 final size:25
Alignment explanation
Indices: 27829260--27829310 Score: 72
Period size: 23 Copynumber: 2.1 Consensus size: 25
27829250 TATATATTTT
27829260 TATATTTTTATAAATAT-TATATGTA
1 TATATTTTTATAAATATAT-TATGTA
27829285 TATATTTTT-T-AATATATTATGTA
1 TATATTTTTATAAATATATTATGTA
27829308 TAT
1 TAT
27829311 TGTGTACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 14 0.56
24 2 0.08
25 9 0.36
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (25 bp):
TATATTTTTATAAATATATTATGTA
Found at i:27831108 original size:40 final size:41
Alignment explanation
Indices: 27831050--27831137 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 41
27831040 ATTTTATTTG
* *
27831050 AATTTTTGTAAATATTTTGTAGTGTTAATAATAAGTTTTAT
1 AATTTTTGTAAATATTTTGTAGTATTAATAATAAGTCTTAT
* * * * *
27831091 -ATTTTTGTGAATCTTTTGTATTATTAATTATAGGTCTTAT
1 AATTTTTGTAAATATTTTGTAGTATTAATAATAAGTCTTAT
27831131 AATTTTT
1 AATTTTT
27831138 TCCATTTTTT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 33 0.85
41 6 0.15
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (41 bp):
AATTTTTGTAAATATTTTGTAGTATTAATAATAAGTCTTAT
Found at i:27831232 original size:35 final size:34
Alignment explanation
Indices: 27831184--27831284 Score: 157
Period size: 35 Copynumber: 2.9 Consensus size: 34
27831174 TTGTTGTTAG
*
27831184 AGTTTTAAATCTTATTATTTTTGTTTCATTTTTGT
1 AGTTTTAAGTCTTATTATTTTTGTTTCATTTTT-T
27831219 AGTTTTAAGTCTTATTATTTTTGTTTCATTTTTT
1 AGTTTTAAGTCTTATTATTTTTGTTTCATTTTTT
* * *
27831253 AATTTTAAGCCTTATCATTTTTGTTTCATTTT
1 AGTTTTAAGTCTTATTATTTTTGTTTCATTTT
27831285 GGTGAATATT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
34 30 0.48
35 32 0.52
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (34 bp):
AGTTTTAAGTCTTATTATTTTTGTTTCATTTTTT
Found at i:27831267 original size:34 final size:35
Alignment explanation
Indices: 27831194--27831284 Score: 148
Period size: 34 Copynumber: 2.6 Consensus size: 35
27831184 AGTTTTAAAT
* *
27831194 CTTATTATTTTTGTTTCATTTTTGTAGTTTTAAGT
1 CTTATTATTTTTGTTTCATTTTTGTAATTTTAAGC
27831229 CTTATTATTTTTGTTTCATTTTT-TAATTTTAAGC
1 CTTATTATTTTTGTTTCATTTTTGTAATTTTAAGC
*
27831263 CTTATCATTTTTGTTTCATTTT
1 CTTATTATTTTTGTTTCATTTT
27831285 GGTGAATATT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 30 0.57
35 23 0.43
ACGTcount: A:0.18, C:0.09, G:0.08, T:0.66
Consensus pattern (35 bp):
CTTATTATTTTTGTTTCATTTTTGTAATTTTAAGC
Found at i:27834777 original size:20 final size:21
Alignment explanation
Indices: 27834752--27834791 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
27834742 TTTTCAATGA
27834752 ATTTTTATTTATA-AAATTAT
1 ATTTTTATTTATATAAATTAT
*
27834772 ATTTTTATTTTTATAAATTA
1 ATTTTTATTTATATAAATTA
27834792 AATAAAACAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTATTTATATAAATTAT
Found at i:27840326 original size:3 final size:3
Alignment explanation
Indices: 27840318--27840380 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
27840308 ATAACAAACC
*
27840318 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAA AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
27840366 AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG
27840381 TGGAGATACT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:27847551 original size:3 final size:3
Alignment explanation
Indices: 27847543--27847609 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
27847533 TTTTAATTGA
* * *
27847543 ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT CTT AGTT CGTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT -ATT
* *
27847590 ATT ACT ATT -TT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT
27847610 TTGCATTATT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.88
4 4 0.08
ACGTcount: A:0.27, C:0.06, G:0.03, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:27853729 original size:3 final size:3
Alignment explanation
Indices: 27853721--27853795 Score: 150
Period size: 3 Copynumber: 25.0 Consensus size: 3
27853711 TCATCAGTAG
27853721 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27853769 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
27853796 CGTTTTAGTT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 72 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:27866259 original size:46 final size:46
Alignment explanation
Indices: 27866192--27866407 Score: 315
Period size: 46 Copynumber: 4.7 Consensus size: 46
27866182 GGCAACCTGA
27866192 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
27866238 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
27866284 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
27866330 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
27866376 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
27866408 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 156 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:27866387 original size:138 final size:130
Alignment explanation
Indices: 27866142--27866407 Score: 379
Period size: 138 Copynumber: 2.0 Consensus size: 130
27866132 AGTGTGCTCT
*
27866142 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
27866207 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
27866272 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
*
27866337 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
27866402 ATGGCA
123 ATGGCA
27866408 TCATGTCAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
130 48 0.40
132 1 0.01
133 1 0.01
136 2 0.02
138 67 0.56
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:27871553 original size:46 final size:46
Alignment explanation
Indices: 27871486--27871701 Score: 315
Period size: 46 Copynumber: 4.7 Consensus size: 46
27871476 GGCAACCTGA
27871486 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*
27871532 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* *
27871578 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
*** * * *
27871624 GAACAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
* * * *
27871670 GAGTAAGACCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACCATGGCA
27871702 TCATGTCAAA
Statistics
Matches: 156, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 156 1.00
ACGTcount: A:0.40, C:0.15, G:0.24, T:0.21
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATAAAAT
Found at i:27871681 original size:138 final size:130
Alignment explanation
Indices: 27871436--27871701 Score: 379
Period size: 138 Copynumber: 2.0 Consensus size: 130
27871426 AGTGTGCTCT
*
27871436 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
* * * * * *
27871501 TGAAAGATACCATGGCAACCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
27871566 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGATATGAAATGAACAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG--A-G---TG--CAAG
*
27871631 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACT
58 ACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACC
27871696 ATGGCA
123 ATGGCA
27871702 TCATGTCAAA
Statistics
Matches: 119, Mismatches: 9, Indels: 8
0.88 0.07 0.06
Matches are distributed among these distances:
130 48 0.40
132 1 0.01
133 1 0.01
136 2 0.02
138 67 0.56
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGAGTGCAAGACCATGGT
TGAAAGATACCATGGCAACATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:27877243 original size:45 final size:44
Alignment explanation
Indices: 27877180--27877296 Score: 137
Period size: 45 Copynumber: 2.6 Consensus size: 44
27877170 ACAACCATCA
* **
27877180 TGGTGGTTTATCCACAACCTACATGGTAGCTTG-CTTGTGAATAT
1 TGGTGGTTTGTCCACAACCTACATGGTAGCTTGTC-TGCAAATAT
* *
27877224 TGGTGGCTTTGTCCACAACCTACATTGCAGCTTGTCTGCAAATAT
1 TGGTGG-TTTGTCCACAACCTACATGGTAGCTTGTCTGCAAATAT
* *
27877269 TGTTAGTTTTGTCCACAACCTACATGGT
1 TGGT-GGTTTGTCCACAACCTACATGGT
27877297 GGTTTATCCA
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
44 6 0.10
45 53 0.87
46 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (44 bp):
TGGTGGTTTGTCCACAACCTACATGGTAGCTTGTCTGCAAATAT
Found at i:27877311 original size:113 final size:113
Alignment explanation
Indices: 27877113--27877325 Score: 320
Period size: 113 Copynumber: 1.9 Consensus size: 113
27877103 GGAAGAATTT
*
27877113 GTGGCTTCGTCCACAACCTACATAGCAGCTTATCTACAAATATTGGTGGCTTCGTCCACAACCAT
1 GTGGCTTCGTCCACAACCTACATAGCAGCTTATCTACAAATATTGGTAGCTTCGTCCACAACCAT
*
27877178 CATGGTGGTTTATCCACAACCTACATGGTAGCTTGCTTGTGAATATTG
66 CATGGTGGTTTATCCACAACCTACATGGCAGCTTGCTTGTGAATATTG
* * * * * * *
27877226 GTGGCTTTGTCCACAACCTACATTGCAGCTTGTCTGCAAATATTGTTAGTTTTGTCCACAACC-T
1 GTGGCTTCGTCCACAACCTACATAGCAGCTTATCTACAAATATTGGTAGCTTCGTCCACAACCAT
*
27877290 ACATGGTGGTTTATCCACAACCTATATGGCAGCTTG
66 -CATGGTGGTTTATCCACAACCTACATGGCAGCTTG
27877326 TCTGTGTTGG
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 1 0.01
113 88 0.99
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (113 bp):
GTGGCTTCGTCCACAACCTACATAGCAGCTTATCTACAAATATTGGTAGCTTCGTCCACAACCAT
CATGGTGGTTTATCCACAACCTACATGGCAGCTTGCTTGTGAATATTG
Found at i:27883089 original size:20 final size:20
Alignment explanation
Indices: 27883066--27883166 Score: 89
Period size: 20 Copynumber: 5.0 Consensus size: 20
27883056 GTGCTACGGA
27883066 TTGCACTTCGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
* * *
27883086 TTGCACTTTGGTGTCTCTAT
1 TTGCACTTCGGTGCCTCTGT
** *
27883106 TCACACTTCAGTGCCTCT-T
1 TTGCACTTCGGTGCCTCTGT
*
27883125 ATTGCACATT-TGTGCCTCTGT
1 -TTGCAC-TTCGGTGCCTCTGT
* *
27883146 CTGCACTTTGGTGCCTCTGT
1 TTGCACTTCGGTGCCTCTGT
27883166 T
1 T
27883167 ACGCATCTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
19 3 0.05
20 57 0.90
21 3 0.05
ACGTcount: A:0.10, C:0.28, G:0.20, T:0.43
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGT
Found at i:27883153 original size:40 final size:39
Alignment explanation
Indices: 27883065--27883166 Score: 109
Period size: 40 Copynumber: 2.6 Consensus size: 39
27883055 TGTGCTACGG
*
27883065 ATTGCACTTCGGTGCCTCTGTTTGCACTTTGGTGTCTCT
1 ATTGCACTTCGGTGCCTCTGTTTGCACTTTGGTGCCTCT
* *
27883104 ATTCACACTTCAGTGCCTCT-TATTGCACATTT-GTGCCTCT
1 ATT-GCACTTCGGTGCCTCTGT-TTGCAC-TTTGGTGCCTCT
* *
27883144 GTCTGCACTTTGGTGCCTCTGTT
1 AT-TGCACTTCGGTGCCTCTGTT
27883167 ACGCATCTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
39 4 0.08
40 42 0.82
41 5 0.10
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (39 bp):
ATTGCACTTCGGTGCCTCTGTTTGCACTTTGGTGCCTCT
Found at i:27885609 original size:44 final size:45
Alignment explanation
Indices: 27885514--27885647 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
27885504 ACAGGACAAA
* *
27885514 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
27885560 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
27885604 ACAGGAATAATTCATGTAAGTCCATATCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
27885648 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:27893877 original size:42 final size:42
Alignment explanation
Indices: 27893818--27893974 Score: 172
Period size: 42 Copynumber: 3.7 Consensus size: 42
27893808 TTAGCATTAG
*
27893818 TATGAG-TTATCATGTAAGACCATATCTGGGATATGGCGTTGA
1 TATGAGATT-TCATGTAAGACCATATCTGGGATATGGCGTCGA
* * *
27893860 TATGATATTTCATGTAAGACCATATTTGGGACATGGCGTCGA
1 TATGAGATTTCATGTAAGACCATATCTGGGATATGGCGTCGA
* * * * * *
27893902 AATGAGAATTCGTATAAGACCATATTTGGGATATGGCATCGA
1 TATGAGATTTCATGTAAGACCATATCTGGGATATGGCGTCGA
* ** *
27893944 TGTGAGATCCCATGTAAGACCATGTCTGGGA
1 TATGAGATTTCATGTAAGACCATATCTGGGA
27893975 CATAACATTG
Statistics
Matches: 94, Mismatches: 20, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
42 92 0.98
43 2 0.02
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (42 bp):
TATGAGATTTCATGTAAGACCATATCTGGGATATGGCGTCGA
Found at i:27899264 original size:39 final size:40
Alignment explanation
Indices: 27899164--27899346 Score: 167
Period size: 40 Copynumber: 4.6 Consensus size: 40
27899154 TCGAATGATG
* * *
27899164 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
27899204 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
*
27899244 TCCGGGCTAAG-CCCGAAGGCATTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * * *
27899283 CCCGGGTTAAGTCCCAAAGGCATTCGTGCGAGTCACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
* **
27899324 -CCAGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
27899347 TGAGCGAGTC
Statistics
Matches: 115, Mismatches: 23, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
39 33 0.29
40 73 0.63
41 9 0.08
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:27899307 original size:79 final size:80
Alignment explanation
Indices: 27899164--27899315 Score: 202
Period size: 79 Copynumber: 1.9 Consensus size: 80
27899154 TCGAATGATG
* * * *
27899164 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCAAAGGCATTC
27899229 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
27899244 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCAAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCAAAGGCAT
27899306 TCGTGCGAGT
64 TCGTGCGAGT
27899316 CACTATAACC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
78 1 0.02
79 44 0.70
80 18 0.29
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCAAAGGCATTC
GTGCGAGTTAATAAA
Found at i:27905071 original size:42 final size:42
Alignment explanation
Indices: 27905005--27905139 Score: 137
Period size: 42 Copynumber: 3.2 Consensus size: 42
27904995 GGCTGCACGG
* * * *
27905005 AAGCACATAAGTGCTAAACTGAAACCCATAAGGGTTGAACAA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACAA
* * * * *
27905047 AAGTTTATAAGAGCTAAACAGAAACCCGTGAGGGTTAAACTA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACAA
* * * *
27905089 TAGCTCAAAAGAGCTAAACAGAAACTCATTAGGGTTAAACGAA
1 AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAAC-AA
27905132 AA-CTCATA
1 AAGCTCATA
27905140 TGAGTTAACT
Statistics
Matches: 73, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 71 0.97
43 2 0.03
ACGTcount: A:0.45, C:0.17, G:0.19, T:0.19
Consensus pattern (42 bp):
AAGCTCATAAGAGCTAAACAGAAACCCATAAGGGTTAAACAA
Found at i:27909266 original size:23 final size:23
Alignment explanation
Indices: 27909236--27909283 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
27909226 ATAAGAATAA
27909236 ACAAGCATTATTGACTAAATGGT
1 ACAAGCATTATTGACTAAATGGT
27909259 ACAAGCATTATTGACTAAATGGT
1 ACAAGCATTATTGACTAAATGGT
27909282 AC
1 AC
27909284 TTAAAGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (23 bp):
ACAAGCATTATTGACTAAATGGT
Found at i:27922613 original size:20 final size:20
Alignment explanation
Indices: 27922584--27922628 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
27922574 AGCACATGTA
* *
27922584 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
27922604 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
27922624 TTCAT
1 TTCAT
27922629 TTTAGTACCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:27924915 original size:37 final size:37
Alignment explanation
Indices: 27924874--27924988 Score: 160
Period size: 37 Copynumber: 3.1 Consensus size: 37
27924864 ACTATCTTGT
27924874 TTTGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCA
1 TTTGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCA
* * *
27924911 TTTGGCATGTTATCGGTTGGATTAAG-TCTTATAAGAA
1 TTTGGCGTGTTATCGGTTGGATT-AGCTCTTATGAGCA
* * *
27924948 TTTGGTGTGTTATCGGCTGGATTAGCTCTTATGAGCG
1 TTTGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCA
27924985 TTTG
1 TTTG
27924989 ACATGTTTTG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
36 2 0.03
37 63 0.94
38 2 0.03
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (37 bp):
TTTGGCGTGTTATCGGTTGGATTAGCTCTTATGAGCA
Found at i:27930664 original size:49 final size:49
Alignment explanation
Indices: 27930555--27930732 Score: 186
Period size: 49 Copynumber: 3.7 Consensus size: 49
27930545 AATAATGCCA
* * *
27930555 ATGCCATGTCCCAGACTTGGTCTTACACTGGCTCATC--CATC-AAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCAAAATCGAAGCCG
* *
27930602 ATGCCATGTCCCAGACAGGGTCTTACACTGACTATCAAAATCGAGGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAAGCCG
* * * *
27930651 ACGCCATGTCCCAGACATGGTCTTACACT-AGCTCTCACATATCCG-TGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGA-CTATCA-AAAT-CGAAGCCG
**
27930701 ATGTAATGTCCCAGACATGGTCTTACACTGAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGAC
27930733 ACCTCTGTAA
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
46 3 0.03
47 30 0.27
48 4 0.04
49 37 0.33
50 34 0.31
51 3 0.03
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (49 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGACTATCAAAATCGAAGCCG
Found at i:27930725 original size:99 final size:96
Alignment explanation
Indices: 27930557--27930732 Score: 246
Period size: 99 Copynumber: 1.8 Consensus size: 96
27930547 TAATGCCAAT
* * *
27930557 GCCATGTCCCAGACTTGGTCTTACACTGGCTCATCCATCAAGCCGATGCCATGTCCCAGACAGGG
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGCCGATGCAATGTCCCAGACAGGG
27930622 TCTTACACTGACTATCAAAATCGAGGCCGAC
66 TCTTACACTGACTATCAAAATCGAGGCCGAC
** *
27930653 GCCATGTCCCAGACATGGTCTTACACTAGCTC-TCACATATCCGTGCCGATGTAATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTACACTAGCTCATC-C--AT-CAAGCCGATGCAATGTCCCAGAC
*
27930717 ATGGTCTTACACTGAC
62 AGGGTCTTACACTGAC
27930733 ACCTCTGTAA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
95 2 0.03
96 31 0.45
98 2 0.03
99 34 0.49
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (96 bp):
GCCATGTCCCAGACATGGTCTTACACTAGCTCATCCATCAAGCCGATGCAATGTCCCAGACAGGG
TCTTACACTGACTATCAAAATCGAGGCCGAC
Found at i:27932650 original size:47 final size:47
Alignment explanation
Indices: 27932580--27932874 Score: 473
Period size: 47 Copynumber: 6.3 Consensus size: 47
27932570 CCCTTCGGGA
* * * *
27932580 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
27932627 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27932674 CGTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27932721 CTTATCACATATATACACATTCACATTCGTCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* * *
27932768 CTTATCACATATATACATATTCACATTCGTCACATTGGCCATTCGAC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
27932815 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27932862 TTTACCACATATA
1 CTTATCACATATA
27932875 CATATCTTAT
Statistics
Matches: 232, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 232 1.00
ACGTcount: A:0.29, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
Found at i:27932728 original size:22 final size:22
Alignment explanation
Indices: 27932608--27932730 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
27932598 TTTCACATCC
*
27932608 ATCACATTGGCCATTTGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * *
27932630 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27932654 CATCACATTGGCCATTCGGCCGT
1 -ATCACATTGGCCATTCGGCCTT
** * *
27932677 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27932701 CGTCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
27932724 ATCACAT
1 ATCACAT
27932731 ATATACACAT
Statistics
Matches: 70, Mismatches: 21, Indels: 20
0.63 0.19 0.18
Matches are distributed among these distances:
22 30 0.43
23 9 0.13
24 9 0.13
25 22 0.31
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:27932822 original size:22 final size:23
Alignment explanation
Indices: 27932786--27932859 Score: 64
Period size: 22 Copynumber: 3.2 Consensus size: 23
27932776 ATATATACAT
*
27932786 ATTC-ACATTCGTCACATTGGCC
1 ATTCGACATTCATCACATTGGCC
* **
27932808 ATTCGACCTT-ATCACATATATACAC
1 ATTCGACATTCATCACAT-T-GGC-C
27932833 ATTC-ACATTCATCACATTGGCC
1 ATTCGACATTCATCACATTGGCC
27932855 ATTCG
1 ATTCG
27932860 GCTTTACCAC
Statistics
Matches: 39, Mismatches: 7, Indels: 11
0.68 0.12 0.19
Matches are distributed among these distances:
22 15 0.38
23 6 0.15
24 6 0.15
25 12 0.31
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.32
Consensus pattern (23 bp):
ATTCGACATTCATCACATTGGCC
Found at i:27936563 original size:40 final size:40
Alignment explanation
Indices: 27936519--27936846 Score: 501
Period size: 40 Copynumber: 8.4 Consensus size: 40
27936509 TCTTCGGGGT
* * *
27936519 TTAGCACGGATATATCACTAGCACGAATACTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* **
27936559 TTAGCCCGGATACATCACTAGCACGAATGCCCTTCGGGGC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
27936599 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* **
27936639 TTAGCCCGGATACATCACTAGCACGAATGCCCTTCGGGGC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27936679 TTAGCCCGGATACATCACTAGCACGAATGC-CTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
27936718 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG-GC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27936757 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27936797 TTAGCCCGGATACATCACTAGCACGAA---TCTTCGG--C
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27936832 TTAGCCCGGAT-CATC
1 TTAGCCCGGATACATC
27936847 GTCGAGACCT
Statistics
Matches: 268, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
34 4 0.01
35 12 0.04
37 7 0.03
39 75 0.28
40 170 0.63
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:27936603 original size:80 final size:80
Alignment explanation
Indices: 27936510--27936846 Score: 564
Period size: 80 Copynumber: 4.3 Consensus size: 80
27936500 CATGATTGCT
* * * *
27936510 CTTCGGGGTTTAGCACGGATATATCACTAGCACGAATACTCTTCGGAACTTAGCCCGGATACATC
1 CTTCGGGGCTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
27936575 ACTAGCACGAATGCC
66 ACTAGCACGAATGCC
*
27936590 CTTCGGGGCTTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
1 CTTCGGGGCTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
27936655 ACTAGCACGAATGCC
66 ACTAGCACGAATGCC
27936670 CTTCGGGGCTTAGCCCGGATACATCACTAGCACGAATGC-CTTCGGAACTTAGCCCGGATACATC
1 CTTCGGGGCTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
*
27936734 ACTAGCACGAATGCT
66 ACTAGCACGAATGCC
27936749 CTTC-GGGCTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
1 CTTCGGGGCTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
27936813 ACTAGCACGAAT---
66 ACTAGCACGAATGCC
27936825 CTTC--GGCTTAGCCCGGAT-CATC
1 CTTCGGGGCTTAGCCCGGATACATC
27936847 GTCGAGACCT
Statistics
Matches: 251, Mismatches: 5, Indels: 8
0.95 0.02 0.03
Matches are distributed among these distances:
74 4 0.02
75 14 0.06
76 4 0.02
78 34 0.14
79 80 0.32
80 115 0.46
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (80 bp):
CTTCGGGGCTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAACTTAGCCCGGATACATC
ACTAGCACGAATGCC
Found at i:27936968 original size:38 final size:38
Alignment explanation
Indices: 27936899--27936973 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
27936889 GAATTTTAAT
*
27936899 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
27936937 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
27936974 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:27939461 original size:47 final size:47
Alignment explanation
Indices: 27939391--27939684 Score: 491
Period size: 47 Copynumber: 6.3 Consensus size: 47
27939381 CCCTTCGGGA
* * * *
27939391 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
27939438 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27939485 CGTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
*
27939532 CTTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27939579 CTTATCACATATATACATATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
27939626 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
*
27939673 TTTA-CACATATA
1 CTTATCACATATA
27939685 CATATCTTAT
Statistics
Matches: 236, Mismatches: 11, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
46 8 0.03
47 228 0.97
ACGTcount: A:0.29, C:0.29, G:0.10, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
Found at i:27939539 original size:22 final size:22
Alignment explanation
Indices: 27939419--27939588 Score: 67
Period size: 22 Copynumber: 7.3 Consensus size: 22
27939409 TTTCACATCC
*
27939419 ATCACATTGGCCATTTGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * *
27939441 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27939465 CATCACATTGGCCATTCGGCCGT
1 -ATCACATTGGCCATTCGGCCTT
** * *
27939488 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27939512 CGTCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
** * *
27939535 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27939559 CGTCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
27939582 ATCACAT
1 ATCACAT
27939589 ATATACATAT
Statistics
Matches: 102, Mismatches: 31, Indels: 30
0.63 0.19 0.18
Matches are distributed among these distances:
22 41 0.40
23 14 0.14
24 14 0.14
25 33 0.32
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:27943375 original size:40 final size:40
Alignment explanation
Indices: 27943331--27943664 Score: 562
Period size: 40 Copynumber: 8.4 Consensus size: 40
27943321 TCTTCGGGGT
* * *
27943331 TTAGCACGGATATATCACTAGCACGAATACTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* **
27943371 TTAGCCCGGATACATCACTAGCACGAATGCCCTTCGGGGC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
27943411 TTAGCCCGGATATATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
* **
27943451 TTAGCCCGGATACATCACTAGCACGAATGCCCTTCGGGGC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27943491 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
*
27943531 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGG-GC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27943570 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27943610 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
1 TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
27943650 TTAGCCCGGATACAT
1 TTAGCCCGGATACAT
27943665 AGCACGAATC
Statistics
Matches: 274, Mismatches: 19, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 38 0.14
40 236 0.86
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAAC
Found at i:27943819 original size:38 final size:38
Alignment explanation
Indices: 27943750--27943824 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
27943740 GAATTTTAAT
*
27943750 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
27943788 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
27943825 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:27946315 original size:47 final size:47
Alignment explanation
Indices: 27946245--27946539 Score: 482
Period size: 47 Copynumber: 6.3 Consensus size: 47
27946235 CCCTTCGGGA
* * * *
27946245 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
27946292 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27946339 CGTATCACATATATACACATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27946386 CTTATCACATATATACACATTCACATTCGTCACATTGGCCATTTGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27946433 CTTATCACATATATACATATTCACATTCGTCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
27946480 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
* *
27946527 TTTACCACATATA
1 CTTATCACATATA
27946540 CATATCTTAT
Statistics
Matches: 234, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 234 1.00
ACGTcount: A:0.28, C:0.29, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACATTCACATTCATCACATTGGCCATTCGGC
Found at i:27946393 original size:22 final size:22
Alignment explanation
Indices: 27946273--27946395 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
27946263 TTTCACATCC
*
27946273 ATCACATTGGCCATTTGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * *
27946295 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27946319 CATCACATTGGCCATTCGGCCGT
1 -ATCACATTGGCCATTCGGCCTT
** * *
27946342 ATCACATATATACACATTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
27946366 CGTCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
27946389 ATCACAT
1 ATCACAT
27946396 ATATACACAT
Statistics
Matches: 70, Mismatches: 21, Indels: 20
0.63 0.19 0.18
Matches are distributed among these distances:
22 30 0.43
23 9 0.13
24 9 0.13
25 22 0.31
ACGTcount: A:0.28, C:0.29, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:27956034 original size:29 final size:29
Alignment explanation
Indices: 27955995--27956074 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 29
27955985 CTTAATAATC
*
27955995 AACCACGCACACTTAGTGCCATGTACTTT-A
1 AACC-CGCACACTTAGTGCCATGCA-TTTCA
*
27956025 AACTCGCACACTTAGTGCCATGCATTTCA
1 AACCCGCACACTTAGTGCCATGCATTTCA
*
27956054 AGCCCGCACACTTAGTGCCAT
1 AACCCGCACACTTAGTGCCAT
27956075 TCTCTCAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
28 3 0.07
29 39 0.87
30 3 0.07
ACGTcount: A:0.28, C:0.33, G:0.15, T:0.25
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCATGCATTTCA
Found at i:27962616 original size:58 final size:58
Alignment explanation
Indices: 27962524--27962675 Score: 142
Period size: 58 Copynumber: 2.6 Consensus size: 58
27962514 AATTTAAGCC
* *** * * * *
27962524 CGCACACACAGTGCCATACCCTTCGAGCTCGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACCCAGTGCCGTATATTTCCAGCA
* * * * * ** *
27962582 TGCACACATAGTGTCGTATTTTTCCAGCATGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACATAGTGCCATATATTTCCAGCACGCACACCCAGTGCCGTATATTTCCAGCA
* *
27962640 CGCACACTTATTGCCATATATTTCCAGCACGCACAC
1 CGCACACATAGTGCCATATATTTCCAGCACGCACAC
27962676 TTAGTGCCAA
Statistics
Matches: 72, Mismatches: 22, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
58 72 1.00
ACGTcount: A:0.24, C:0.34, G:0.15, T:0.28
Consensus pattern (58 bp):
CGCACACATAGTGCCATATATTTCCAGCACGCACACCCAGTGCCGTATATTTCCAGCA
Found at i:27962684 original size:29 final size:29
Alignment explanation
Indices: 27962553--27962684 Score: 147
Period size: 29 Copynumber: 4.6 Consensus size: 29
27962543 CCTTCGAGCT
** * * *
27962553 CGCACACCCAGTGCCGTATTTTTCCAGCT
1 CGCACACTTAGTGCCATATATTTCCAGCA
* * * * *
27962582 TGCACACATAGTGTCGTATTTTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
* *
27962611 TGCACACTTAGTGCCTTATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
*
27962640 CGCACACTTATTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATATATTTCCAGCA
27962669 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
27962685 ATCTCGTCAC
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 90 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.30
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATATTTCCAGCA
Found at i:27963518 original size:143 final size:141
Alignment explanation
Indices: 27963328--27963622 Score: 554
Period size: 143 Copynumber: 2.1 Consensus size: 141
27963318 AAATTCTATA
*
27963328 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACACAATTTCCTTTT
1 GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
27963393 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
66 TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
*
27963458 GAAGACAACAT
131 GAAAACAACAT
27963469 GCATGGCCGAATACTCATGCACACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
1 GCATGGCCGAATACTCATG--CACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTT
27963534 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
64 TTTGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCA
27963599 AGGAAAACAACAT
129 AGGAAAACAACAT
27963612 GCATGGCCGAA
1 GCATGGCCGAA
27963623 ATTTAACTCA
Statistics
Matches: 150, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
141 19 0.13
143 131 0.87
ACGTcount: A:0.39, C:0.29, G:0.11, T:0.21
Consensus pattern (141 bp):
GCATGGCCGAATACTCATGCACACACACATAACAACAAGAACTCAATGGCACAAAATTTCCTTTT
TGTTAAACATTCGAACTCACTCATCTCCATGCTTTCATCACAACAACATCAAAACACTCACCAAG
GAAAACAACAT
Found at i:27964784 original size:14 final size:14
Alignment explanation
Indices: 27964767--27964795 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
27964757 TTTCGTTAGT
27964767 TAAAAGGGGTTAAA
1 TAAAAGGGGTTAAA
27964781 TAAAAGGGGTTAAA
1 TAAAAGGGGTTAAA
27964795 T
1 T
27964796 GGTCATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (14 bp):
TAAAAGGGGTTAAA
Found at i:27965643 original size:20 final size:20
Alignment explanation
Indices: 27965615--27965676 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
27965605 GAATTGCACA
*
27965615 TACGTGCCCCTGTTTGTACT
1 TACGTGCCCTTGTTTGTACT
* * * *
27965635 TAGGTGCCCTTGAATTGCACA
1 TACGTGCCCTTG-TTTGTACT
27965656 TACGTGCCCTTGTTTGTACT
1 TACGTGCCCTTGTTTGTACT
27965676 T
1 T
27965677 CAATACCCAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.39
Consensus pattern (20 bp):
TACGTGCCCTTGTTTGTACT
Found at i:27965648 original size:41 final size:41
Alignment explanation
Indices: 27965604--27965735 Score: 169
Period size: 41 Copynumber: 3.2 Consensus size: 41
27965594 AGATTATTGT
* *
27965604 TGAATTGCACATACGTGCCCCTGTTTGTACTTAGGTGCCCT
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTAGGTACCCA
* *
27965645 TGAATTGCACATACGTGCCCTTGTTTGTACTTCA-ATACCCA
1 TGAATTGCACATACGTGCCCCTGTTTGTACTT-AGGTACCCA
* * * *
27965686 TGAATTACACACACGTGCCCCTATTTGTACTTCGGTACCCA
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTAGGTACCCA
27965727 TGAA-TGCAC
1 TGAATTGCAC
27965736 TTTTGTGCCC
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
40 4 0.05
41 73 0.94
42 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.17, T:0.32
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTAGGTACCCA
Found at i:27965663 original size:21 final size:21
Alignment explanation
Indices: 27965603--27965667 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
27965593 AAGATTATTG
27965603 TTGAATTGCACATACGTGCCC
1 TTGAATTGCACATACGTGCCC
* * * * *
27965624 CTG-TTTGTACTTAGGTGCCC
1 TTGAATTGCACATACGTGCCC
27965644 TTGAATTGCACATACGTGCCC
1 TTGAATTGCACATACGTGCCC
27965665 TTG
1 TTG
27965668 TTTGTACTTC
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
20 15 0.45
21 18 0.55
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (21 bp):
TTGAATTGCACATACGTGCCC
Found at i:27973312 original size:25 final size:27
Alignment explanation
Indices: 27973275--27973327 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
27973265 TCAAACATGC
27973275 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
27973301 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
27973327 A
1 A
27973328 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:27974842 original size:32 final size:32
Alignment explanation
Indices: 27974805--27974869 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
27974795 AATGCTTACC
27974805 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
27974837 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
27974869 A
1 A
27974870 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:27979651 original size:12 final size:12
Alignment explanation
Indices: 27979634--27979664 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
27979624 AGTACTACCT
27979634 CGGCCTCGACCA
1 CGGCCTCGACCA
27979646 CGGCCTCGACCA
1 CGGCCTCGACCA
27979658 CGGCCTC
1 CGGCCTC
27979665 TTCCCCGAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.13, C:0.52, G:0.26, T:0.10
Consensus pattern (12 bp):
CGGCCTCGACCA
Found at i:27981287 original size:25 final size:27
Alignment explanation
Indices: 27981250--27981302 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
27981240 TCAAACATGC
27981250 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
27981276 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
27981302 A
1 A
27981303 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:27982819 original size:32 final size:32
Alignment explanation
Indices: 27982782--27982846 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
27982772 AATGCTTACC
27982782 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
27982814 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
27982846 A
1 A
27982847 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:27985377 original size:21 final size:22
Alignment explanation
Indices: 27985341--27985384 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
27985331 AAGAAGAAAT
*
27985341 AAACAAATTTAGAAATTAAAGA
1 AAACAAATTAAGAAATTAAAGA
*
27985363 AAACAAA-TAAGAAATTTAAGA
1 AAACAAATTAAGAAATTAAAGA
27985384 A
1 A
27985385 CTAAGAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (22 bp):
AAACAAATTAAGAAATTAAAGA
Found at i:27989661 original size:15 final size:15
Alignment explanation
Indices: 27989613--27989692 Score: 60
Period size: 15 Copynumber: 5.4 Consensus size: 15
27989603 ATATCTTGGG
27989613 TTTCTTT-TTCCTGGA
1 TTTCTTTATTCC-GGA
* *
27989628 TATCTTTATTCTGGA
1 TTTCTTTATTCCGGA
27989643 TTTCTTTATTCC-GA
1 TTTCTTTATTCCGGA
* *
27989657 GTTTCTCTA-TCTTGGA
1 -TTTCTTTATTC-CGGA
*
27989673 TTTCTTTATT-CGGT
1 TTTCTTTATTCCGGA
27989687 TTTCTT
1 TTTCTT
27989693 GTTATCTTTG
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
14 12 0.24
15 33 0.65
16 6 0.12
ACGTcount: A:0.11, C:0.17, G:0.12, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCCGGA
Found at i:27994600 original size:2 final size:2
Alignment explanation
Indices: 27994593--27994626 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27994583 TCAAAAGAAA
27994593 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27994627 TAAGAACAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27998786 original size:46 final size:48
Alignment explanation
Indices: 27998637--27998811 Score: 175
Period size: 47 Copynumber: 3.7 Consensus size: 48
27998627 GGGTTATTGT
* * * * *
27998637 GAGCTAGTGTAA-AACATGTTTGGGACATGCATCAGCCAC-ATTACG-A
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGA-GATGTA
* * *
27998683 GAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GACATTGAGAT-TA
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATCAG-CCTCGAGATGTA
* *
27998731 GAGCTAGTGTAAGA-CATGTTTGGGACATGCCTCAGCCTCGAGATGTA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGAGATGTA
27998778 -AGCTAGTGTAAGACCATGTCTGGGACATGGCATC
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATC
27998812 GGCATCCTAC
Statistics
Matches: 105, Mismatches: 15, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
46 35 0.33
47 44 0.42
48 25 0.24
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (48 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGCATCAGCCTCGAGATGTA
Found at i:27998798 original size:94 final size:94
Alignment explanation
Indices: 27998637--27998812 Score: 266
Period size: 94 Copynumber: 1.9 Consensus size: 94
27998627 GGGTTATTGT
*
27998637 GAGCTAGTGTAAAACATGTTTGGGACATGCATCAGCCACATTACGAGAGCCAGTGTAAGACCATG
1 GAGCTAGTGTAAAACATGTTTGGGACATGCATCAGCCACATGACGAGAGCCAGTGTAAGACCATG
27998702 TCTGGGACATGGCATCGACATTGAGATTA
66 TCTGGGACATGGCATCGACATTGAGATTA
* * * * *
27998731 GAGCTAGTGTAAGACATGTTTGGGACATGCCTCAGCCTCGA-GATGTA-AGCTAGTGTAAGACCA
1 GAGCTAGTGTAAAACATGTTTGGGACATGCATCAGCCAC-ATGACG-AGAGCCAGTGTAAGACCA
27998794 TGTCTGGGACATGGCATCG
64 TGTCTGGGACATGGCATCG
27998813 GCATCCTACC
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
94 72 0.97
95 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (94 bp):
GAGCTAGTGTAAAACATGTTTGGGACATGCATCAGCCACATGACGAGAGCCAGTGTAAGACCATG
TCTGGGACATGGCATCGACATTGAGATTA
Found at i:28006351 original size:46 final size:47
Alignment explanation
Indices: 28006203--28006377 Score: 187
Period size: 47 Copynumber: 3.7 Consensus size: 47
28006193 GGGTTATTGT
** *
28006203 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCC-ACACTATGA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCCTTGA-GATGA
* * * * *
28006249 GAGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCATTGAGACGA
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTTGAGATGA
* *
28006297 GAGCTAGTGTAAGA-CATGTCTGGGACATGCCTCAGCCTTGAGATGTA
1 GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCCTTGAGATG-A
*
28006344 -AGCTAGTGTAAGACCATGTCCGGGACATGGCATC
1 GAGCTAGTGTAAGACCATGTCTGGGACAT-GCATC
28006378 AGTATCCTAC
Statistics
Matches: 106, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
46 38 0.36
47 40 0.38
48 27 0.25
49 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (47 bp):
GAGCTAGTGTAAGACCATGTCTGGGACATGCATCGGCCTTGAGATGA
Found at i:28006370 original size:94 final size:94
Alignment explanation
Indices: 28006203--28006377 Score: 237
Period size: 94 Copynumber: 1.9 Consensus size: 94
28006193 GGGTTATTGT
* *
28006203 GAGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACACTATGAGAGCCAATGTAAGACCATG
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACACGATGAGAGCCAATGTAAGACCATG
*
28006268 TCTAGGACATGGCATCGGCATTGAGACGA
66 TCCAGGACATGGCATCGGCATTGAGACGA
* ** * *
28006297 GAGCTAGTGTAAGACATGTCTGGGACATGCCTCAGCCTTGA-GATGTA-AGCTAGTGTAAGACCA
1 GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCC-ACACGATG-AGAGCCAATGTAAGACCA
*
28006360 TGTCCGGGACATGGCATC
64 TGTCCAGGACATGGCATC
28006378 AGTATCCTAC
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 68 0.97
95 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (94 bp):
GAGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACACGATGAGAGCCAATGTAAGACCATG
TCCAGGACATGGCATCGGCATTGAGACGA
Found at i:28008654 original size:18 final size:18
Alignment explanation
Indices: 28008621--28008660 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
28008611 AGTGACAAGT
28008621 AAAAAGAAAAGCAGAAGCAA
1 AAAAAGAAAA-CAGAAG-AA
28008641 AAAAAGAAAA-AGAAGAA
1 AAAAAGAAAACAGAAGAA
28008658 AAA
1 AAA
28008661 TAGTAACCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 5 0.25
20 10 0.50
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAACAGAAGAA
Found at i:28015659 original size:20 final size:20
Alignment explanation
Indices: 28015620--28015660 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
28015610 TAGATCGGGG
**
28015620 AAAGGAAAAATTATTGGATT
1 AAAGGAAAAATTATCAGATT
28015640 AAAGGAAAAATTATCAGATT
1 AAAGGAAAAATTATCAGATT
28015660 A
1 A
28015661 GTTGATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.02, G:0.17, T:0.27
Consensus pattern (20 bp):
AAAGGAAAAATTATCAGATT
Found at i:28025738 original size:31 final size:31
Alignment explanation
Indices: 28025700--28025761 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
28025690 TTACTATATG
28025700 AAAACACATTGTTAAATGTCAAAAGTCATCA
1 AAAACACATTGTTAAATGTCAAAAGTCATCA
*
28025731 AAAACACATTGTTAAATGTCAGAAGTCATCA
1 AAAACACATTGTTAAATGTCAAAAGTCATCA
28025762 CACTATCGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (31 bp):
AAAACACATTGTTAAATGTCAAAAGTCATCA
Found at i:28030226 original size:47 final size:47
Alignment explanation
Indices: 28030172--28030264 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
28030162 TCGCAACCTT
28030172 TTCGAACTAGTTTTTTAGATACAAGGGTGAAGATCACATTAGAGAGG
1 TTCGAACTAGTTTTTTAGATACAAGGGTGAAGATCACATTAGAGAGG
*
28030219 TTCGAACTAGTTTTTTAGATACAAGGGTGAATATCACATTAGAGAG
1 TTCGAACTAGTTTTTTAGATACAAGGGTGAAGATCACATTAGAGAG
28030265 ATAATTTTGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.31
Consensus pattern (47 bp):
TTCGAACTAGTTTTTTAGATACAAGGGTGAAGATCACATTAGAGAGG
Found at i:28033625 original size:28 final size:28
Alignment explanation
Indices: 28033556--28033656 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28033546 GACAAGATTG
* * * *
28033556 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
28033586 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28033614 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
28033643 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28033657 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28041585 original size:28 final size:28
Alignment explanation
Indices: 28041516--28041616 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28041506 GACAAGATTG
* * * *
28041516 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
28041546 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
28041574 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
28041603 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
28041617 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:28042843 original size:23 final size:23
Alignment explanation
Indices: 28042816--28042860 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
28042806 TATATGAGTC
28042816 TAAATTCAGGGAAAATTTACGAT
1 TAAATTCAGGGAAAATTTACGAT
28042839 TAAATTCAGGGAAAATTTACGA
1 TAAATTCAGGGAAAATTTACGA
28042861 AACCAGTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (23 bp):
TAAATTCAGGGAAAATTTACGAT
Found at i:28044714 original size:28 final size:28
Alignment explanation
Indices: 28044671--28044728 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
28044661 AGTTTCGATG
*
28044671 TAGAAACGATATAAGTGATCTCAAAACC
1 TAGAAACGATAGAAGTGATCTCAAAACC
* *
28044699 TAGAAGCGATAGAAGTGATCTCAAATCC
1 TAGAAACGATAGAAGTGATCTCAAAACC
28044727 TA
1 TA
28044729 AATCAACAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.22
Consensus pattern (28 bp):
TAGAAACGATAGAAGTGATCTCAAAACC
Found at i:28048317 original size:16 final size:18
Alignment explanation
Indices: 28048290--28048325 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
28048280 CCAATAGCAC
28048290 TTTTTCTGTTCT-TTTTT
1 TTTTTCTGTTCTCTTTTT
28048307 TTTTTCT-TTCTCTTTTT
1 TTTTTCTGTTCTCTTTTT
28048324 TT
1 TT
28048326 GTATATGTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTCTGTTCTCTTTTT
Found at i:28056251 original size:30 final size:29
Alignment explanation
Indices: 28056204--28056289 Score: 113
Period size: 30 Copynumber: 3.0 Consensus size: 29
28056194 GCATGGCTAT
28056204 GAATGTGATTTGGGCCTAATGGGCCATAC
1 GAATGTGATTTGGGCCTAATGGGCCATAC
*
28056233 GAATGTGATTTAGGGCCTAATGGGCCATAT
1 GAATGTGATTT-GGGCCTAATGGGCCATAC
**
28056263 GAA--TGATATTGGGCCTTGTGGGCCATA
1 GAATGTGAT-TTGGGCCTAATGGGCCATA
28056290 TGCATGTATG
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
28 19 0.37
29 13 0.25
30 20 0.38
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.29
Consensus pattern (29 bp):
GAATGTGATTTGGGCCTAATGGGCCATAC
Found at i:28062617 original size:2 final size:2
Alignment explanation
Indices: 28062612--28062651 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
28062602 TCATCCACAC
*
28062612 AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28062652 CGTTCTTTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28062907 original size:39 final size:39
Alignment explanation
Indices: 28062847--28062983 Score: 202
Period size: 39 Copynumber: 3.5 Consensus size: 39
28062837 TAAGCCTTCG
* ** *
28062847 GGACTTTAAGCCCGGATATATTTCTAGCATGTAGCCTGC
1 GGACTTTAAGTCCGGATATATTTCCCGCATATAGCCTGC
* * *
28062886 GGACCTGAAGTCCGGATATATTTCCCGCATATAGTCTGC
1 GGACTTTAAGTCCGGATATATTTCCCGCATATAGCCTGC
28062925 GGACTTTAAGTCCGGATATATTTCCCGCATATAGCCTGC
1 GGACTTTAAGTCCGGATATATTTCCCGCATATAGCCTGC
*
28062964 GGACTTTAAGTCTGGATATA
1 GGACTTTAAGTCCGGATATA
28062984 ATTTTCAAAT
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 87 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (39 bp):
GGACTTTAAGTCCGGATATATTTCCCGCATATAGCCTGC
Found at i:28066756 original size:18 final size:17
Alignment explanation
Indices: 28066729--28066776 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
28066719 CTACAGAATA
28066729 TTTTTT-TATTTTTTAT
1 TTTTTTGTATTTTTTAT
28066745 TTTTTTCGTA--TTTTAT
1 TTTTTT-GTATTTTTTAT
28066761 TTTTTTGTACTTTTTT
1 TTTTTTGTA-TTTTTT
28066777 TATCACGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.11
16 18 0.67
18 6 0.22
ACGTcount: A:0.10, C:0.04, G:0.04, T:0.81
Consensus pattern (17 bp):
TTTTTTGTATTTTTTAT
Found at i:28072498 original size:21 final size:21
Alignment explanation
Indices: 28072462--28072511 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 21
28072452 AAATCCTTTT
28072462 AAAATTTTTAATTTTTTAAAA
1 AAAATTTTTAATTTTTTAAAA
28072483 AATAATTTTTAATTTTTTAAAA
1 AA-AATTTTTAATTTTTTAAAA
28072505 AAAATTT
1 AAAATTT
28072512 ATGCAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AAAATTTTTAATTTTTTAAAA
Found at i:28072600 original size:2 final size:2
Alignment explanation
Indices: 28072590--28072635 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
28072580 CTCTCTTTAA
28072590 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28072631 AT AT A
1 AT AT A
28072636 AGCATGAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28081362 original size:16 final size:16
Alignment explanation
Indices: 28081341--28081375 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
28081331 ATGTGAAAGT
28081341 TAAATTCTAGTAGCTA
1 TAAATTCTAGTAGCTA
28081357 TAAATTCTAGTAGCTA
1 TAAATTCTAGTAGCTA
28081373 TAA
1 TAA
28081376 GGATCAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (16 bp):
TAAATTCTAGTAGCTA
Found at i:28082579 original size:57 final size:58
Alignment explanation
Indices: 28082433--28082583 Score: 146
Period size: 57 Copynumber: 2.6 Consensus size: 58
28082423 CATTGACCCT
* * * * * *
28082433 ATTATAGAAAGGATTTAGCCCGGATGGGTAATCCTGATATAATACCTCTCGAGTATAC
1 ATTATATAAAGGATTTAGCCTGGATTGGTAATCCTAATAGAATACCTCTCGAGCATAC
* * * * * *
28082491 ATTATGAT-TAGGGTTTAGCCTGGACTAGTAATCCTAATCGAGCT-CCTCT-GAGCATAC
1 ATTAT-ATAAAGGATTTAGCCTGGATTGGTAATCCTAATAGA-ATACCTCTCGAGCATAC
*
28082548 GTTATATAAAGGATTTAGCCTGGATTGGTAATCCTA
1 ATTATATAAAGGATTTAGCCTGGATTGGTAATCCTA
28082584 TTATATGATA
Statistics
Matches: 73, Mismatches: 17, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
56 2 0.03
57 35 0.48
58 34 0.47
59 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (58 bp):
ATTATATAAAGGATTTAGCCTGGATTGGTAATCCTAATAGAATACCTCTCGAGCATAC
Found at i:28085148 original size:84 final size:88
Alignment explanation
Indices: 28085019--28085178 Score: 220
Period size: 84 Copynumber: 1.9 Consensus size: 88
28085009 ATAGTATATG
* * *
28085019 AAAAAATGAAAATAATAATAATATTTTATTGGTGCCACTGATGTGTTAGGTGGCACCCAAATATT
1 AAAAAATGAAAATAATAATAATATTTTATTGGTGCCACCGATGTGTCAGGTGACACCCAAATATT
28085084 TTAAAAGTTTTAGCTAAAATGAT
66 TTAAAAGTTTTAGCTAAAATGAT
* ** *
28085107 AAAAAAT-AAAA-AATAAT-TTA-TTTATTGGTGCGGCCGATGTGTCAGGTGACACTCAAATATT
1 AAAAAATGAAAATAATAATAATATTTTATTGGTGCCACCGATGTGTCAGGTGACACCCAAATATT
*
28085168 TTAAAATTTTT
66 TTAAAAGTTTT
28085179 TTAAATCTGA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
84 45 0.70
85 2 0.03
86 6 0.09
87 4 0.06
88 7 0.11
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (88 bp):
AAAAAATGAAAATAATAATAATATTTTATTGGTGCCACCGATGTGTCAGGTGACACCCAAATATT
TTAAAAGTTTTAGCTAAAATGAT
Found at i:28087691 original size:25 final size:25
Alignment explanation
Indices: 28087657--28087706 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
28087647 CTTAGAAAAG
* *
28087657 TAAATCAAATAAATTTGGGGTTTGT
1 TAAATCAAATAAATGTGGGATTTGT
*
28087682 TAAATCAAATGAATGTGGGATTTGT
1 TAAATCAAATAAATGTGGGATTTGT
28087707 GTATGTCGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.36, C:0.04, G:0.22, T:0.38
Consensus pattern (25 bp):
TAAATCAAATAAATGTGGGATTTGT
Found at i:28088374 original size:67 final size:66
Alignment explanation
Indices: 28088266--28088435 Score: 288
Period size: 67 Copynumber: 2.6 Consensus size: 66
28088256 GTGATTTATG
* *
28088266 TATTGAATTTTCATTCTTGAATCAACTTAAATTATTTACATATATTTGCATTATGTTTCTATTTC
1 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTACATATATTTGCATTATATTTCTATTT-
28088331 TT
65 TT
28088333 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTACATATATTTGCATTATATTTCTATTTT
1 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTACATATATTTGCATTATATTTCTATTTT
28088398 T
66 T
* *
28088399 TATTGAATTTTCTTTCTT-TATCAACTTCAATTATTTA
1 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTA
28088436 AATGAACATG
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
65 18 0.18
66 19 0.19
67 62 0.63
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (66 bp):
TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTACATATATTTGCATTATATTTCTATTTT
T
Found at i:28088454 original size:65 final size:67
Alignment explanation
Indices: 28088266--28088455 Score: 215
Period size: 67 Copynumber: 2.9 Consensus size: 67
28088256 GTGATTTATG
* * ** ** *
28088266 TATTGAATTTTCATTCTTGAATCAACTTAAATTATTTACATATATTTGCATTATGTTTCTATTTC
1 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTAAATATACATGCAAAATATTTCTATTTC
28088331 TT
66 TT
* ** **
28088333 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTACATATATTTGCATTATATTTCTATTT-
1 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTAAATATACATGCAAAATATTTCTATTTC
28088397 TT
66 TT
* * *
28088399 TATTGAATTTTCTTTCTT-TATCAACTTCAATTATTTAAATGA-ACATGTAAAATATTT
1 TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTAAAT-ATACATGCAAAATATTT
28088456 GAATGAACTT
Statistics
Matches: 112, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
65 30 0.27
66 20 0.18
67 62 0.55
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.53
Consensus pattern (67 bp):
TATTGAATTTTCATTCTTGTATCAACTTAAATTATTTAAATATACATGCAAAATATTTCTATTTC
TT
Found at i:28090549 original size:24 final size:24
Alignment explanation
Indices: 28090499--28090552 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 24
28090489 AATCGAATTT
*
28090499 GCACACATAGTGCTCGTCACACTC
1 GCACACATAGTGCTAGTCACACTC
28090523 GCACACATAGTGCCATAG-CACAC-C
1 GCACACATAGTG-C-TAGTCACACTC
28090547 GCACAC
1 GCACAC
28090553 TCAGTGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
24 19 0.70
25 6 0.22
26 2 0.07
ACGTcount: A:0.30, C:0.39, G:0.17, T:0.15
Consensus pattern (24 bp):
GCACACATAGTGCTAGTCACACTC
Found at i:28093990 original size:18 final size:19
Alignment explanation
Indices: 28093969--28094013 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
28093959 ACTTCTTAAT
*
28093969 AAAATATAATCTACT-TTA
1 AAAATATAAACTACTATTA
*
28093987 AAAATATTAAACTAGTATTA
1 AAAATA-TAAACTACTATTA
28094007 AAAATAT
1 AAAATAT
28094014 TAATTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 6 0.26
19 8 0.35
20 9 0.39
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATATAAACTACTATTA
Found at i:28099635 original size:29 final size:28
Alignment explanation
Indices: 28099592--28099646 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
28099582 GAGATAAATC
*
28099592 GATTTGGATTTGGGCCATGCATATCAGCT
1 GATTTGGATTCGGGCCATG-ATATCAGCT
*
28099621 GATTTGGCTTCGGGCCATGATATCAG
1 GATTTGGATTCGGGCCATGATATCAG
28099647 TACTTTGGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (28 bp):
GATTTGGATTCGGGCCATGATATCAGCT
Found at i:28100482 original size:19 final size:19
Alignment explanation
Indices: 28100458--28100496 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
28100448 TTATCTAGCC
28100458 TAAGAATAATGGGGTTTTG
1 TAAGAATAATGGGGTTTTG
28100477 TAAGAATAATGGGGTTTTG
1 TAAGAATAATGGGGTTTTG
28100496 T
1 T
28100497 TTTAATTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.38
Consensus pattern (19 bp):
TAAGAATAATGGGGTTTTG
Found at i:28101153 original size:48 final size:46
Alignment explanation
Indices: 28101003--28101153 Score: 162
Period size: 48 Copynumber: 3.2 Consensus size: 46
28100993 TATGAGAGCC
** *
28101003 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATTTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGA-ATA-CAAAGCT
* * * *
28101051 AGTGTAAGACATGT-TGGGACATACATCGGCATTG-AGACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAATAC-AAAGCT
* *
28101096 AGTGTAAGACATGTCTGGGACATGCATAGGCCTCGCAATACACAAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTG-AATACA-AAGCT
28101144 AGTGTAAGAC
1 AGTGTAAGAC
28101154 CTCTCTAGGA
Statistics
Matches: 85, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
45 19 0.22
46 16 0.19
47 19 0.22
48 31 0.36
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAATACAAAGCT
Found at i:28101258 original size:49 final size:50
Alignment explanation
Indices: 28101186--28101318 Score: 171
Period size: 49 Copynumber: 2.7 Consensus size: 50
28101176 TGTAGTGTGT
* * *
28101186 CAGTGTAAGACCTATTTGGGACATGGCATCGGCAC-CGATGGATGAAAGC
1 CAGTGTAAGACCTGTTTGGGACATGGCATTGGCACTCGATAGATGAAAGC
* * * * *
28101235 CAGTGTAAGACCTGTCTGGGACATGGCATTGGC-CTTGTTATATGGAAGC
1 CAGTGTAAGACCTGTTTGGGACATGGCATTGGCACTCGATAGATGAAAGC
28101284 CAGTGTAAGACCATGTTTGGGACATGGCATTGGCA
1 CAGTGTAAGACC-TGTTTGGGACATGGCATTGGCA
28101319 TCTTAACCCA
Statistics
Matches: 72, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
48 1 0.01
49 51 0.71
50 20 0.28
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.25
Consensus pattern (50 bp):
CAGTGTAAGACCTGTTTGGGACATGGCATTGGCACTCGATAGATGAAAGC
Found at i:28106857 original size:49 final size:49
Alignment explanation
Indices: 28106783--28106912 Score: 154
Period size: 49 Copynumber: 2.6 Consensus size: 49
28106773 TGTAGTGTGT
* *
28106783 CAGTGTAAGACCTGTTTGGGACATGGCATCGACAC-CGATGGATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGC
* * * * * *
28106832 CAGTGTAAGACCTGTCTGGGGCATGGAATTGGCCTCGTTATATGAAAGC
1 CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGC
*
28106881 CAGTGTAAGACCATGTCTGGGACATGACATCG
1 CAGTGTAAGACC-TGTCTGGGACATGGCATCG
28106913 GCATCTTAAC
Statistics
Matches: 67, Mismatches: 12, Indels: 3
0.82 0.15 0.04
Matches are distributed among these distances:
48 1 0.01
49 51 0.76
50 15 0.22
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (49 bp):
CAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAGATGAAAGC
Found at i:28113989 original size:6 final size:6
Alignment explanation
Indices: 28113940--28113974 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
28113930 CCGAAAGAAA
* *
28113940 ATTTTC ATTTTC ATTTTC ATTTCC ATTTTA ATTTT
1 ATTTTC ATTTTC ATTTTC ATTTTC ATTTTC ATTTT
28113975 TAATTTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTTC
Found at i:28115437 original size:27 final size:26
Alignment explanation
Indices: 28115392--28115477 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 26
28115382 CCCTGTTTAG
* *
28115392 AATACTTTAGTTTACTAAAATTACCGA
1 AATACTTTAGTTT-GTAAAATTACTGA
*
28115419 AATACGTTTAGTTTGTAAAAATACTGA
1 AATAC-TTTAGTTTGTAAAATTACTGA
** *
28115446 AATACCCTCGATTTGTAAAATTACTGA
1 AATACTTTAG-TTTGTAAAATTACTGA
28115473 AATAC
1 AATAC
28115478 CTTCGACTTG
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 40 0.80
28 8 0.16
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (26 bp):
AATACTTTAGTTTGTAAAATTACTGA
Found at i:28115478 original size:27 final size:27
Alignment explanation
Indices: 28115430--28115489 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
28115420 ATACGTTTAG
28115430 TTTGTAAAAATACTGAAATACCCTCGA
1 TTTGTAAAAATACTGAAATACCCTCGA
* *
28115457 TTTGTAAAATTACTGAAATACCTTCGA
1 TTTGTAAAAATACTGAAATACCCTCGA
*
28115484 CTTGTA
1 TTTGTA
28115490 GCATTACCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.35
Consensus pattern (27 bp):
TTTGTAAAAATACTGAAATACCCTCGA
Found at i:28115522 original size:27 final size:27
Alignment explanation
Indices: 28115492--28115552 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
28115482 GACTTGTAGC
28115492 ATTACCAAAGTACCCCCGATTTACAGA
1 ATTACCAAAGTACCCCCGATTTACAGA
*** *
28115519 ATTACCATTTTACCCCCGATTTACATA
1 ATTACCAAAGTACCCCCGATTTACAGA
28115546 ATTACCA
1 ATTACCA
28115553 TTTTACTCCC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.30, G:0.07, T:0.30
Consensus pattern (27 bp):
ATTACCAAAGTACCCCCGATTTACAGA
Found at i:28115553 original size:27 final size:27
Alignment explanation
Indices: 28115502--28115696 Score: 111
Period size: 27 Copynumber: 6.8 Consensus size: 27
28115492 ATTACCAAAG
28115502 TACCCCCGATTTACAGAATTACCATTT
1 TACCCCCGATTTACAGAATTACCATTT
*
28115529 TACCCCCGATTTACATAATTACCATTT
1 TACCCCCGATTTACAGAATTACCATTT
* * *
28115556 TACTCCCGTTTTACCCTCGACTTACAGAATTACCATTT
1 TACCCCCG-ATT----T--AC--AG--AATTACCATTT
* * ****
28115594 TACCCTCGATTTATAGAATTTTTGTTT
1 TACCCCCGATTTACAGAATTACCATTT
** * **
28115621 TACCGTCGATTTATAGAATTACTGTTT
1 TACCCCCGATTTACAGAATTACCATTT
** *
28115648 TACCCTTGATTTACAGAATTACTATTT
1 TACCCCCGATTTACAGAATTACCATTT
* *
28115675 TACCCTCGATTTACAAAATTAC
1 TACCCCCGATTTACAGAATTAC
28115697 TAAAATACCC
Statistics
Matches: 135, Mismatches: 22, Indels: 22
0.75 0.12 0.12
Matches are distributed among these distances:
27 107 0.79
28 2 0.01
29 1 0.01
31 1 0.01
32 1 0.01
33 1 0.01
34 2 0.01
36 1 0.01
37 2 0.01
38 17 0.13
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCCCGATTTACAGAATTACCATTT
Found at i:28115697 original size:27 final size:27
Alignment explanation
Indices: 28115564--28115698 Score: 171
Period size: 27 Copynumber: 5.0 Consensus size: 27
28115554 TTTACTCCCG
* *
28115564 TTTTACCCTCGACTTACAGAATTACCA
1 TTTTACCCTCGATTTACAGAATTACTA
* ** *
28115591 TTTTACCCTCGATTTATAGAATTTTTG
1 TTTTACCCTCGATTTACAGAATTACTA
* * *
28115618 TTTTACCGTCGATTTATAGAATTACTG
1 TTTTACCCTCGATTTACAGAATTACTA
*
28115645 TTTTACCCTTGATTTACAGAATTACTA
1 TTTTACCCTCGATTTACAGAATTACTA
*
28115672 TTTTACCCTCGATTTACAAAATTACTA
1 TTTTACCCTCGATTTACAGAATTACTA
28115699 AAATACCCTT
Statistics
Matches: 93, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.28, C:0.20, G:0.09, T:0.43
Consensus pattern (27 bp):
TTTTACCCTCGATTTACAGAATTACTA
Found at i:28115705 original size:27 final size:27
Alignment explanation
Indices: 28115648--28115896 Score: 139
Period size: 27 Copynumber: 9.1 Consensus size: 27
28115638 ATTACTGTTT
* ***
28115648 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTTGATTTACAAAATTACTAAAA
*
28115675 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* ** *
28115702 TACCCTTGGTTTGTAAAATTACCAAAA
1 TACCCTTGATTTACAAAATTACTAAAA
* ** *
28115729 TACCCCT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACTAAAA
* *** **
28115756 TACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
** *
28115783 TACCCTT-AGTTTGTAAAATTACCAAAA
1 TACCCTTGA-TTTACAAAATTACTAAAA
* * **
28115810 TACCCCTAATTTACAAAGCTA-TAAAAA
1 TACCCTTGATTTACAAAATTACT-AAAA
28115837 TACCCTTGACTTT-CTAAAAATTA-TAGAAA
1 TACCCTTGA-TTTAC--AAAATTACTA-AAA
* * *
28115866 TACCATTGGTTTACAAAATTACTGAAA
1 TACCCTTGATTTACAAAATTACTAAAA
28115893 TACC
1 TACC
28115897 TTTGGTTTGT
Statistics
Matches: 179, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
27 153 0.85
28 9 0.05
29 17 0.09
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (27 bp):
TACCCTTGATTTACAAAATTACTAAAA
Found at i:28115722 original size:54 final size:54
Alignment explanation
Indices: 28115675--28115814 Score: 174
Period size: 54 Copynumber: 2.6 Consensus size: 54
28115665 ATTACTATTT
*
28115675 TACCCTCGA-TTTACAAAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAA
1 TACCC-CGAGTTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
* ** * *
28115729 TACCCCTAGTTTGTAAAATTACCAAAATACCCTTGGTTTGTGAAATTACCGAAA
1 TACCCCGAGTTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
** **
28115783 TACCCTTAGTTTGTAAAATTACCAAAATACCC
1 TACCCCGAGTTTACAAAATTACCAAAATACCC
28115815 CTAATTTACA
Statistics
Matches: 78, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
53 2 0.03
54 76 0.97
ACGTcount: A:0.38, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
TACCCCGAGTTTACAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAAAA
Found at i:28115722 original size:81 final size:81
Alignment explanation
Indices: 28115563--28115723 Score: 178
Period size: 81 Copynumber: 2.0 Consensus size: 81
28115553 TTTTACTCCC
* * ** **** *
28115563 GTTTTACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTATAGAATTTTTGTTTTACCGTC
1 GTTTTACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCTC
*
28115628 GATTTATAGAATTACT
66 GATTTATAAAATTACT
* * * *
28115644 GTTTTACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTT
1 GTTTTACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCTC
* *
28115709 GGTTTGTAAAATTAC
66 GATTTATAAAATTAC
28115724 CAAAATACCC
Statistics
Matches: 64, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (81 bp):
GTTTTACCCTCGACTTACAGAATTACCATTTTACCCTCGATTTACAAAATTACTAAAATACCCTC
GATTTATAAAATTACT
Found at i:28115733 original size:81 final size:80
Alignment explanation
Indices: 28115648--28115826 Score: 180
Period size: 81 Copynumber: 2.2 Consensus size: 80
28115638 ATTACTGTTT
* *** * *
28115648 TACCCTTGATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACTAAAATACCCTTGGTT
1 TACCCTTGATTTACA-AATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTTAGTT
28115713 TGTAAAATTACCAAAA
65 TGTAAAATTACCAAAA
* * * * *** *
28115729 TACCCCTAGTTTGTA-AAATTACCAAAATACCCTTGGTTTGTGAAATTACCGAAATACCCTTAGT
1 TA-CCCTTGATT-TACAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTTAGT
28115793 TTGTAAAATTACCAAAA
64 TTGTAAAATTACCAAAA
* *
28115810 TACCCCTAATTTACAAA
1 TACCCTTGATTTACAAA
28115827 GCTATAAAAA
Statistics
Matches: 77, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
79 2 0.03
80 8 0.10
81 57 0.74
82 8 0.10
83 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.08, T:0.34
Consensus pattern (80 bp):
TACCCTTGATTTACAAATTACCAAAATACCCTCGATTTACAAAATTACCAAAATACCCTTAGTTT
GTAAAATTACCAAAA
Found at i:28115837 original size:81 final size:81
Alignment explanation
Indices: 28115690--28115844 Score: 220
Period size: 81 Copynumber: 1.9 Consensus size: 81
28115680 TCGATTTACA
* * * ** * *
28115690 AAATTACTAAAATACCCTTGGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCAAA
1 AAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAACTACAAAA
28115755 ATACCCTTGGTTTGTG
66 ATACCCTTGGTTTGTG
* * *
28115771 AAATTACCGAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAGCTATAAAA
1 AAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAACTACAAAA
28115836 ATACCCTTG
66 ATACCCTTG
28115845 ACTTTCTAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 64 1.00
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (81 bp):
AAATTACCAAAATACCCTTAGTTTGTAAAATTACCAAAATACCCCTAATTTACAAAACTACAAAA
ATACCCTTGGTTTGTG
Found at i:28115901 original size:27 final size:27
Alignment explanation
Indices: 28115853--28115904 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
28115843 TGACTTTCTA
28115853 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
28115880 AAAATTACT-GAAATACCTTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
28115905 GTTGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.37
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:28116022 original size:27 final size:27
Alignment explanation
Indices: 28115945--28116022 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
28115935 AAATGATTAA
* *
28115945 AATACCCCT-AATAGGTAAAAAGACCGT
1 AATACCCCTGTAT-GGTAAAATGACCGT
* *
28115972 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTATGGTAAAATGACCGT
28115999 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTGTATGGTAAAATGAC
28116023 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 39 0.93
28 2 0.05
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (27 bp):
AATACCCCTGTATGGTAAAATGACCGT
Found at i:28117213 original size:25 final size:25
Alignment explanation
Indices: 28117181--28117228 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28117171 TTATAACATG
* * *
28117181 AAAATGACCGTTTTGCCCTTAGGTA
1 AAAATGACCATTATACCCTTAGGTA
28117206 AAAATGACCATTATACCCTTAGG
1 AAAATGACCATTATACCCTTAGG
28117229 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTATACCCTTAGGTA
Found at i:28117288 original size:20 final size:20
Alignment explanation
Indices: 28117272--28117350 Score: 149
Period size: 20 Copynumber: 4.0 Consensus size: 20
28117262 TAAACATGGT
28117272 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
28117292 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
28117312 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
28117332 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
28117351 TGTAATCATA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:28117332 original size:11 final size:11
Alignment explanation
Indices: 28117276--28117351 Score: 65
Period size: 11 Copynumber: 7.5 Consensus size: 11
28117266 CATGGTATGT
28117276 ATGATATGCAC
1 ATGATATGCAC
* *
28117287 ATGACATG--T
1 ATGATATGCAC
28117296 ATGATATGCAC
1 ATGATATGCAC
* *
28117307 ATGACATG--T
1 ATGATATGCAC
28117316 ATGATATGCAC
1 ATGATATGCAC
*
28117327 ATGATATG--T
1 ATGATATGCAC
28117336 ATGATATGCAC
1 ATGATATGCAC
28117347 ATGAT
1 ATGAT
28117352 GTAATCATAA
Statistics
Matches: 49, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 22 0.45
11 27 0.55
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:28117457 original size:24 final size:23
Alignment explanation
Indices: 28117401--28117567 Score: 192
Period size: 24 Copynumber: 7.0 Consensus size: 23
28117391 GAGGAAGTGA
*
28117401 AAAAGGGCTTATGCTCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
*
28117424 TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTAT
28117447 CAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
*
28117471 CAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTAT
* * *
28117495 TAAAGGGCTTATGCCCTAATTAT
1 AAAAGGGCTTATGCCCCAGTTAT
* *
28117518 AAAAAGGGCTTTTGCCTCAGTTATT
1 -AAAAGGGCTTATGCCCCAGTTA-T
*
28117543 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
28117567 A
1 A
28117568 TGATAAAGCA
Statistics
Matches: 123, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
23 40 0.33
24 73 0.59
25 10 0.08
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (23 bp):
AAAAGGGCTTATGCCCCAGTTAT
Found at i:28117470 original size:47 final size:47
Alignment explanation
Indices: 28117401--28117567 Score: 194
Period size: 47 Copynumber: 3.5 Consensus size: 47
28117391 GAGGAAGTGA
* *
28117401 AAAAGGGCTTATGCTCCAGTTAT-TAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* *
28117447 CAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTACGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
* * * * *
28117495 TAAAGGGCTTATGCCCTAATTATAAAAAGGGCTTTTGCCTCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTA-T
*
28117543 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
28117568 TGATAAAGCA
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
47 61 0.60
48 31 0.30
49 10 0.10
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAAGGGCTTATGCCCCAGTTAT
Found at i:28117523 original size:71 final size:71
Alignment explanation
Indices: 28117401--28117566 Score: 226
Period size: 71 Copynumber: 2.3 Consensus size: 71
28117391 GAGGAAGTGA
* * * *
28117401 AAAAGGGCTTATGCTCCAGTTATTAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATAAAAAGGGCTTATGCCCCA
28117466 GTTATC
66 GTTATC
* * *
28117472 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCTAATTATAAAAAGGGCTTTTGCCTCA
1 AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATAAAAAGGGCTTATGCCCCA
*
28117537 GTTATT
66 GTTATC
*
28117543 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTACGCC-CCAGTTAT
28117567 ATGATAAAGC
Statistics
Matches: 84, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
71 73 0.87
72 11 0.13
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (71 bp):
AAAAGGGCTTACGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATAAAAAGGGCTTATGCCCCA
GTTATC
Found at i:28117795 original size:31 final size:31
Alignment explanation
Indices: 28117760--28117823 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28117750 CGTTTACAGT
*
28117760 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
**
28117791 AAAGGCTTCGGCCCAGTGTTATGAAAAATGA
1 AAAGGCTTCGGCCCAGTAATATGAAAAATGA
28117822 AA
1 AA
28117824 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.39, C:0.16, G:0.23, T:0.22
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAAAATGA
Found at i:28121622 original size:44 final size:42
Alignment explanation
Indices: 28121559--28121717 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 42
28121549 TATGTGTTAT
28121559 CGTGTAAGACCACATCTGGGATGTTGGCATCGATTTGTGATTTA
1 CGTGTAAGACCACATCTGGGATGTTGGCATCGATTT-TGA-TTA
** ** *
28121603 CGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGAATT-
1 CGTGTAAGACCACATCTGGGATGTTGGCATCGAT-TTTG-ATTA
* * * *
28121645 CGTGTAAGACC-CTGTCTGGGACAG-TGGTATCAATATTTGATTA
1 CGTGTAAGACCAC-ATCTGGGA-TGTTGGCATCGAT-TTTGATTA
*
28121688 CATGTAAGACCACATCTGGGATGTTGGCAT
1 CGTGTAAGACCACATCTGGGATGTTGGCAT
28121718 TGTATGAGCG
Statistics
Matches: 92, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
42 29 0.32
43 32 0.35
44 31 0.34
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.31
Consensus pattern (42 bp):
CGTGTAAGACCACATCTGGGATGTTGGCATCGATTTTGATTA
Found at i:28121661 original size:42 final size:43
Alignment explanation
Indices: 28121558--28121698 Score: 126
Period size: 42 Copynumber: 3.3 Consensus size: 43
28121548 ATATGTGTTA
* ** * * *
28121558 TCGTGTAAGACCAC-ATCTGGGATGTTGGCATCGATTTGTGATT
1 TCGTGTAAGACC-CTGTCTGGGACATTGGCATCGATATATGAAT
*
28121601 TACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGAAT
1 T-CGTGTAAGACCCTGTCTGGGACATTGGCATCGATATATGAAT
* * * *
28121644 TCGTGTAAGACCCTGTCTGGGACAGTGGTATCAATATTTG-AT
1 TCGTGTAAGACCCTGTCTGGGACATTGGCATCGATATATGAAT
*
28121686 TACATGTAAGACC
1 T-CGTGTAAGACC
28121699 ACATCTGGGA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
42 31 0.38
43 23 0.28
44 27 0.33
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
TCGTGTAAGACCCTGTCTGGGACATTGGCATCGATATATGAAT
Found at i:28125434 original size:46 final size:46
Alignment explanation
Indices: 28125304--28125474 Score: 157
Period size: 46 Copynumber: 3.7 Consensus size: 46
28125294 ATTGTGGGCT
* * ** *
28125304 AGTGTAAGACATGTCTGGGACAAGCATCGGCCAT--ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CATCGA-GACAAAAGCC
* * * ** *
28125350 CGTGTAAGACCATGTCTGGGACATGGCATCGACATCGAGACGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACAAAAGCC
* * *
28125398 AGTGTAAGACATGTCTGAGATATGCATCGGCCTCGAGACAAAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACAAAAGCC
*
28125444 AGTGTAAGACATGTCTGGGACATGTATCGGC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC
28125475 TACAAGATGA
Statistics
Matches: 102, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
46 53 0.52
47 28 0.27
48 20 0.20
49 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACAAAAGCC
Found at i:28130847 original size:62 final size:62
Alignment explanation
Indices: 28130771--28130894 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
28130761 AACCATCTAA
28130771 GCTTAGGGATTACCTGCACAGTTAGAAACAAAGTGAGTTTACGAAAACTCAATGTGTAATCC
1 GCTTAGGGATTACCTGCACAGTTAGAAACAAAGTGAGTTTACGAAAACTCAATGTGTAATCC
28130833 GCTTAGGGATTACCTGCACAGTTAGAAACAAAGTGAGTTTACGAAAACTCAATGTGTAATCC
1 GCTTAGGGATTACCTGCACAGTTAGAAACAAAGTGAGTTTACGAAAACTCAATGTGTAATCC
28130895 CAATAACAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (62 bp):
GCTTAGGGATTACCTGCACAGTTAGAAACAAAGTGAGTTTACGAAAACTCAATGTGTAATCC
Found at i:28138598 original size:46 final size:45
Alignment explanation
Indices: 28138546--28138720 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
28138536 TGGTTGAGCA
28138546 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * * *
28138592 TTCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAA-T--G
**
28138637 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA-GGATGCGAATG
* * *
28138685 CCCGAGCTCGTTGAGTTGAGTTCGAGTTCACTTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGG
28138721 GGCGGGTTAC
Statistics
Matches: 107, Mismatches: 13, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 59 0.55
47 28 0.26
48 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAGGATGCGAATG
Found at i:28138702 original size:93 final size:93
Alignment explanation
Indices: 28138543--28138713 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
28138533 GGATGGTTGA
****
28138543 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAATGTTCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACACCCGAACTCGTTGAGT
28138608 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
28138636 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACACCCGAACTCGTTGAGT
*
28138701 TGAGTTCGAGTTC
66 TGAGTCCGAGTTC
28138714 ACTTAGGGGC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTACGGATGCGAACACCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28143627 original size:43 final size:43
Alignment explanation
Indices: 28143565--28143736 Score: 161
Period size: 43 Copynumber: 4.0 Consensus size: 43
28143555 ATCAAAATAT
* *
28143565 GATATTCGGG-CTTCGAGCCTAGCAGTCTATAATACCGGTGAAAC
1 GATA-TCGGGCCTT-GAGCCTAGCAGGCTATAATGCCGGTGAAAC
* * *
28143609 GATATCGGGCCTTGAGCCTAGTAGGCTATTATGCAGGTGAGATAC
1 GATATCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGA-A-AC
* * *
28143654 TAT-TCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGACAT
1 GATATCGGGCC-TTGAGCCTAGCAGGCTATAATGCCGGTGAAAC
* * * * *
28143697 GATATCGAGCCTCGAGCCTAGCGGGCGA-AATGCCGTTGAA
1 GATATCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAA
28143737 TGAATAAAAG
Statistics
Matches: 105, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
42 10 0.10
43 44 0.42
44 21 0.20
45 30 0.29
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (43 bp):
GATATCGGGCCTTGAGCCTAGCAGGCTATAATGCCGGTGAAAC
Found at i:28148527 original size:33 final size:33
Alignment explanation
Indices: 28148485--28148548 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
28148475 AACACAATAT
*
28148485 CAGTACAGTCTGGGCCAAAGCCCTATTCAGTCA
1 CAGTACAGTCTGGGCCAAAGCCCTATACAGTCA
**
28148518 CAGTACAGTCTGGGCCTTAGCCCTATACAGT
1 CAGTACAGTCTGGGCCAAAGCCCTATACAGT
28148549 AGCATTGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (33 bp):
CAGTACAGTCTGGGCCAAAGCCCTATACAGTCA
Found at i:28148548 original size:27 final size:28
Alignment explanation
Indices: 28148517--28148582 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
28148507 CTATTCAGTC
* * *
28148517 ACAGTA-CAGTCTGGGCCTTAGCCCTAT
1 ACAGTAGCAGTCTGGGCATAAGCCCAAT
* *
28148544 ACAGTAGCATTGTGGGCATAAGCCCAAT
1 ACAGTAGCAGTCTGGGCATAAGCCCAAT
*
28148572 ACAGTATCAGT
1 ACAGTAGCAGT
28148583 ATAAATGCGT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (28 bp):
ACAGTAGCAGTCTGGGCATAAGCCCAAT
Found at i:28151089 original size:55 final size:54
Alignment explanation
Indices: 28151003--28151256 Score: 244
Period size: 55 Copynumber: 4.8 Consensus size: 54
28150993 ATTAGGGTTT
* * *
28151003 AAGGATACCGTGTAA-ACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAA-GTTTCTAAGGC
* * * *
28151057 AAGGAAATCATGTAAGACCATGTCAAGACATGGC-ATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTT--TCTAAGGC
* * *
28151112 AAAGG-TCCCATGTAAGACCATG-CTAAGGCATGGC-ATTGGTGAG-TTCATAAGGC
1 -AAGGATACCATGTAAGACCATGTC-AAGACATGGCAATTGGTAAGTTTC-TAAGGC
* *
28151165 ATGGCTACCATGTAAGACCATGTCAAGACATGGCAA-TGGTAAGTTTC-AA---
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTCTAAGGC
* *
28151214 AAGGATACCATGTAAGACCATGACAAGTCATGGCAA-TGGTAAG
1 AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAG
28151257 GTACCCGTGT
Statistics
Matches: 168, Mismatches: 22, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
49 39 0.23
52 6 0.04
53 40 0.24
54 26 0.15
55 53 0.32
56 4 0.02
ACGTcount: A:0.35, C:0.17, G:0.25, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGTCAAGACATGGCAATTGGTAAGTTTCTAAGGC
Found at i:28151209 original size:108 final size:109
Alignment explanation
Indices: 28151013--28151209 Score: 283
Period size: 108 Copynumber: 1.8 Consensus size: 109
28151003 AAGGATACCG
*
28151013 TGTAAACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAATCATGTAAGACCAT
1 TGTAAACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
*
28151078 GTCAAGACATGGCATTGATAAGTTACTATAAGGCAAAGGTCCCA
66 GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
* * * **
28151122 TGTAAGACCATGCTAAGGCATGGC-ATTGGTGA-G-TTCATAAGGCATGGCTACCATGTAAGACC
1 TGTAA-ACCATGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGCAAGGAAACCATGTAAGACC
*
28151184 ATGTCAAGACATGGCAATGGTAAGTT
64 ATGTCAAGACATGGCAATGATAAGTT
28151210 TCAAAAGGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
107 3 0.04
108 46 0.59
109 12 0.15
110 17 0.22
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (109 bp):
TGTAAACCATGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGCAAGGAAACCATGTAAGACCAT
GTCAAGACATGGCAATGATAAGTTACTATAAGGCAAAGGTCCCA
Found at i:28159708 original size:42 final size:42
Alignment explanation
Indices: 28159609--28159766 Score: 234
Period size: 42 Copynumber: 3.8 Consensus size: 42
28159599 ACCAGCATAG
* *
28159609 AGCCTGCTAGGTAATAAACCTGAT-TCAATACACTGGCAT-AA
1 AGCCTGCTAGGCAATAAGCCTGATATC-ATACACTGGCATCAA
*
28159650 AGCCTGCTAGGCAATAAGCCTGATATCATACACTAGCATCAA
1 AGCCTGCTAGGCAATAAGCCTGATATCATACACTGGCATCAA
* *
28159692 AGCCTGCTAGGTAATAAGCCTGATATCATACACCGGCATCAA
1 AGCCTGCTAGGCAATAAGCCTGATATCATACACTGGCATCAA
28159734 AGCCTGCTAGGCAATAAGCCTGATAT-AT-CACTG
1 AGCCTGCTAGGCAATAAGCCTGATATCATACACTG
28159767 TTACAAAGTT
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
40 4 0.04
41 35 0.33
42 68 0.64
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (42 bp):
AGCCTGCTAGGCAATAAGCCTGATATCATACACTGGCATCAA
Found at i:28162182 original size:46 final size:46
Alignment explanation
Indices: 28162038--28162257 Score: 160
Period size: 46 Copynumber: 4.7 Consensus size: 46
28162028 ATTATGGGCT
* * * *
28162038 AGTGTAAGACATGTTTGGGACATGCATCGACCAT--ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCG-GCATCGA-GACGAGAGCC
* * * * *
28162084 TGTATAAGACCATGTCTGGGACATAGCATCGGCATCGAGATGAGTGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCGAGACGAGAGCC
* * *
28162132 AGTGTAAGACATGTCCGGGACATGCATCGTCCTCGAGACGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACG-AGAGCC
* * * * * * *
28162178 AGTGTAAGACTTGTCTGGGACATGTATTGAC-TACGAGATGATAGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCAT-CGAGACGAGAGCC
*
28162224 AGTGTAAGACCATGTCTGGGATATGGCATCGGCA
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCA
28162258 CCCTACCCCA
Statistics
Matches: 137, Mismatches: 27, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
45 2 0.01
46 67 0.49
47 42 0.31
48 25 0.18
49 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCATCGAGACGAGAGCC
Found at i:28164988 original size:54 final size:54
Alignment explanation
Indices: 28164904--28165037 Score: 241
Period size: 54 Copynumber: 2.5 Consensus size: 54
28164894 GTCGTTATAA
* *
28164904 GGGATTTAGCCTGGATTGGTAATCCTGACATCACCTTATGAGTTCATAAAATGG
1 GGGATTTAGCCTGGACTGGTAATCCCGACATCACCTTATGAGTTCATAAAATGG
28164958 GGGATTTAGCCTGGACTGGTAATCCCGACATCACCTTATGAGTTCATAAAATGG
1 GGGATTTAGCCTGGACTGGTAATCCCGACATCACCTTATGAGTTCATAAAATGG
*
28165012 GAGATTTAGCCTGGACTGGTAATCCC
1 GGGATTTAGCCTGGACTGGTAATCCC
28165038 ACCATGAGAT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 77 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (54 bp):
GGGATTTAGCCTGGACTGGTAATCCCGACATCACCTTATGAGTTCATAAAATGG
Done.