Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold357
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: 802879
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 6
Found at i:134920 original size:15 final size:15
Alignment explanation
Indices: 134900--134931 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
134890 AGGATTTTTC
134900 TTGGTCTATTACATT
1 TTGGTCTATTACATT
134915 TTGGTCTATTACATT
1 TTGGTCTATTACATT
134930 TT
1 TT
134932 CCTTTTGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.56
Consensus pattern (15 bp):
TTGGTCTATTACATT
Found at i:135044 original size:7 final size:7
Alignment explanation
Indices: 135032--135058 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
135022 TTGAATATCA
135032 AAATTTC
1 AAATTTC
135039 AAATTTC
1 AAATTTC
135046 AAATTTC
1 AAATTTC
135053 AAATTT
1 AAATTT
135059 ATGATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
AAATTTC
Found at i:137468 original size:2 final size:2
Alignment explanation
Indices: 137461--137495 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
137451 ATGACTTGGA
137461 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
137496 AGAATTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:138701 original size:16 final size:16
Alignment explanation
Indices: 138644--138706 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
138634 ATAGATTGAA
* *
138644 TATTTATAATTTTTAAA
1 TATTTA-AATTTTTTAT
138661 TATTTAAATTTATTTAT
1 TATTTAAATTT-TTTAT
138678 TA-TT---TTTTTTAT
1 TATTTAAATTTTTTAT
*
138690 TATTTAAATTTTATAT
1 TATTTAAATTTTTTAT
138706 T
1 T
138707 CGGTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
12 7 0.18
13 5 0.13
16 15 0.39
17 11 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTTAAATTTTTTAT
Found at i:140939 original size:3 final size:3
Alignment explanation
Indices: 140931--140981 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
140921 TGAACATGTT
140931 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
140979 TTA
1 TTA
140982 GAGAATTAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:143554 original size:21 final size:21
Alignment explanation
Indices: 143528--143571 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
143518 ATGTCAAGTC
143528 TATTATTAAAATATTTTATAT
1 TATTATTAAAATATTTTATAT
**
143549 TATTATTTTAATATTTTATAT
1 TATTATTAAAATATTTTATAT
143570 TA
1 TA
143572 AAATTATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TATTATTAAAATATTTTATAT
Found at i:145166 original size:30 final size:29
Alignment explanation
Indices: 145122--145207 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 29
145112 AAATAAGCTT
* *
145122 AATTTTAACGTTTAATTTATATATATATA
1 AATTTTAACATTTAATTTATATATAAATA
*
145151 AATTCTTAACCTTTAATTTATA-ATCAAATA
1 AATT-TTAACATTTAATTTATATAT-AAATA
* *
145181 ATTTTTTAATATTTAATTTATATATAA
1 A-ATTTTAACATTTAATTTATATATAA
145208 TTAAGCCCTT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
29 6 0.12
30 38 0.79
31 4 0.08
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (29 bp):
AATTTTAACATTTAATTTATATATAAATA
Found at i:145302 original size:30 final size:30
Alignment explanation
Indices: 145244--145305 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
145234 TCAAATAGAG
*
145244 ATTTATTTTGATACAAATCAAAAAATAAAA
1 ATTTATTTGGATACAAATCAAAAAATAAAA
145274 ATTTATTTGGATAC-AAT-AAAATATATAAAA
1 ATTTATTTGGATACAAATCAAAA-A-ATAAAA
145304 AT
1 AT
145306 CTACCTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 4 0.14
29 4 0.14
30 21 0.72
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (30 bp):
ATTTATTTGGATACAAATCAAAAAATAAAA
Found at i:145702 original size:32 final size:32
Alignment explanation
Indices: 145666--145726 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
145656 ACAAACGAGG
145666 AGAAAAGAT-TCAACTATACTAGTGTAAAAGTA
1 AGAAAAGATCT-AACTATACTAGTGTAAAAGTA
* *
145698 AGAAAGGATCTAATTATACTAGTGTAAAA
1 AGAAAAGATCTAACTATACTAGTGTAAAA
145727 TTAAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.49, C:0.08, G:0.16, T:0.26
Consensus pattern (32 bp):
AGAAAAGATCTAACTATACTAGTGTAAAAGTA
Found at i:146045 original size:2 final size:2
Alignment explanation
Indices: 146038--146093 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
146028 AACTAACTTA
146038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
146080 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
146094 GGTAGAGAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146645 original size:23 final size:21
Alignment explanation
Indices: 146623--146679 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
146613 AAAAATTTTA
146623 AAATATTTTTATATTAATATTT
1 AAATATTTTTATATTAA-ATTT
* *
146645 ATATA-TTTTATAATTTAATTT
1 AAATATTTTTAT-ATTAAATTT
146666 AAATATTTTT-TATT
1 AAATATTTTTATATT
146680 TATTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.10
21 15 0.50
22 12 0.40
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
AAATATTTTTATATTAAATTT
Found at i:148504 original size:3 final size:3
Alignment explanation
Indices: 148496--148521 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
148486 CATTATCTCT
148496 CAG CAG CAG CAG CAG CAG CAG CAG CA
1 CAG CAG CAG CAG CAG CAG CAG CAG CA
148522 ACCAGCTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.35, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:149268 original size:17 final size:16
Alignment explanation
Indices: 149246--149301 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
149236 CTAGTAATAT
149246 TTTTAATTAAATATAAA
1 TTTTAATT-AATATAAA
149263 TTTTAA-T-ATATTAATA
1 TTTTAATTAATA-TAA-A
149279 TTTTATATT-ATATAAA
1 TTTTA-ATTAATATAAA
149295 TTTTAAT
1 TTTTAAT
149302 ATTTTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 3 0.09
15 5 0.14
16 13 0.37
17 10 0.29
18 4 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAATTAATATAAA
Found at i:150209 original size:2 final size:2
Alignment explanation
Indices: 150202--150228 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
150192 GTAACAACAT
150202 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
150229 GTAATATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:150846 original size:21 final size:21
Alignment explanation
Indices: 150822--150865 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
150812 TAATAATTTA
150822 AACTTAAAATGATCTAAATCT
1 AACTTAAAATGATCTAAATCT
* *
150843 AACTTGAAATTATCTAAATCT
1 AACTTAAAATGATCTAAATCT
150864 AA
1 AA
150866 TTATACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (21 bp):
AACTTAAAATGATCTAAATCT
Found at i:151350 original size:19 final size:19
Alignment explanation
Indices: 151326--151430 Score: 63
Period size: 19 Copynumber: 5.2 Consensus size: 19
151316 TTAAATACGA
151326 TAATAAAATATAATATATT
1 TAATAAAATATAATATATT
* *
151345 TAAT-AAATATTAAAATAATA
1 TAATAAAATA-TAATAT-ATT
151365 TAATAAATATAATAAAATATATT
1 TAATAAA-AT-AT--AATATATT
*
151388 TAAATATAAT-TAATATA-T
1 T-AATAAAATATAATATATT
* *
151406 TAATATAATATGATTATATAT
1 TAATAAAATAT-AATATAT-T
151427 TAAT
1 TAAT
151431 TTTTATAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
17 8 0.12
18 8 0.12
19 20 0.29
20 6 0.09
21 8 0.12
22 3 0.04
23 6 0.09
24 9 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (19 bp):
TAATAAAATATAATATATT
Found at i:151365 original size:29 final size:30
Alignment explanation
Indices: 151327--151416 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 30
151317 TAAATACGAT
*
151327 AATAAAATATAATATATTTAATAAATATTA
1 AATATAATATAATATATTTAATAAATATTA
* *
151357 AA-ATAATATAATAAATATAATAAAATATATTTA
1 AATATAATATAATATATTTAAT--AA-ATA-TTA
151390 AATATAAT-TAATATA-TTAATATAATAT
1 AATATAATATAATATATTTAATA-AATAT
151417 GATTATATAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
29 17 0.35
30 6 0.12
31 3 0.06
32 7 0.14
33 11 0.22
34 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
AATATAATATAATATATTTAATAAATATTA
Found at i:151400 original size:43 final size:46
Alignment explanation
Indices: 151327--151415 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 46
151317 TAAATACGAT
*
151327 AATAAAATATAATATATTTAATAAATATTAA-A-A-TAATATAATA
1 AATAAAATAAAATATATTTAATAAATATTAATATATTAATATAATA
* *
151370 AATATAATAAAATATATTTAA-ATATAATTAATATATTAATATAATA
1 AATAAAATAAAATATATTTAATAAAT-ATTAATATATTAATATAATA
151416 TGATTATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
42 3 0.08
43 24 0.62
44 1 0.03
45 1 0.03
46 10 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (46 bp):
AATAAAATAAAATATATTTAATAAATATTAATATATTAATATAATA
Found at i:151436 original size:14 final size:14
Alignment explanation
Indices: 151419--151473 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
151409 TATAATATGA
151419 TTATATATTAATTT
1 TTATATATTAATTT
* *
151433 TTATAAATAAAATTT
1 TTATATAT-TAATTT
* *
151448 TTATATATTTATAT
1 TTATATATTAATTT
151462 TTATATAATTAA
1 TTATAT-ATTAA
151474 CGTAAAAATA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATATATTAATTT
Found at i:151442 original size:29 final size:29
Alignment explanation
Indices: 151391--151466 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
151381 ATATATTTAA
* *
151391 ATATAATTAATATATTA-ATATAATATGATT
1 ATAT-ATTAATAT-TTATAAATAAAATGATT
* **
151421 ATATATTAATTTTTATAAATAAAATTTTT
1 ATATATTAATATTTATAAATAAAATGATT
*
151450 ATATATTTATATTTATA
1 ATATATTAATATTTATA
151467 TAATTAACGT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 3 0.08
29 31 0.82
30 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
ATATATTAATATTTATAAATAAAATGATT
Found at i:152129 original size:28 final size:28
Alignment explanation
Indices: 152064--152129 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
152054 ATTTAATTAA
* *
152064 TTAATTAAA-ATATATTAAAATATTATT
1 TTAATTAAATATAAATAAAAATATTATT
152091 TTATATT-AATATTAAATAAAAATATT-TT
1 TTA-ATTAAATA-TAAATAAAAATATTATT
152119 TTAATTAAATA
1 TTAATTAAATA
152130 ATAATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 8 0.24
28 13 0.39
29 12 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTAATTAAATATAAATAAAAATATTATT
Found at i:152353 original size:24 final size:24
Alignment explanation
Indices: 152326--152373 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
152316 AAATTTGATA
*
152326 ATTTATATA-ATTTTATATTATATT
1 ATTTATATATATTATA-ATTATATT
*
152350 ATTTTTATATATTATAATTATATT
1 ATTTATATATATTATAATTATATT
152374 TAAAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTATATATATTATAATTATATT
Found at i:152362 original size:18 final size:19
Alignment explanation
Indices: 152335--152375 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
152325 AATTTATATA
152335 ATTT-TATATTAT-ATTAT
1 ATTTATATATTATAATTAT
*
152352 TTTTATATATTATAATTAT
1 ATTTATATATTATAATTAT
152371 ATTTA
1 ATTTA
152376 AAATATAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 8 0.40
19 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTATATATTATAATTAT
Found at i:152393 original size:16 final size:16
Alignment explanation
Indices: 152362--152404 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
152352 TTTTATATAT
*
152362 TATAATTATATTTAAAA
1 TATAA-TATATATAAAA
*
152379 TATAATATATATAAAT
1 TATAATATATATAAAA
*
152395 TTTAATATAT
1 TATAATATAT
152405 TAATAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 18 0.78
17 5 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
TATAATATATATAAAA
Found at i:152444 original size:17 final size:18
Alignment explanation
Indices: 152413--152447 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
152403 ATTAATAAGT
152413 TAAATTATATAAATTTAA
1 TAAATTATATAAATTTAA
152431 TAAATTAT-TAAATTTAA
1 TAAATTATATAAATTTAA
152448 ACTTTCATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TAAATTATATAAATTTAA
Found at i:152898 original size:24 final size:21
Alignment explanation
Indices: 152850--152891 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
152840 TATTCATAAA
*
152850 TAATAATAAATATTTTTATAT
1 TAATAATAAATATTTATATAT
*
152871 TAATAATTATATATTTATATA
1 TAATAA-TAAATATTTATATA
152892 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAATAATAAATATTTATATAT
Found at i:153332 original size:28 final size:27
Alignment explanation
Indices: 153277--153347 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
153267 GCCACTCATT
153277 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
*
153304 TGTTTGTTAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
153332 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
153348 AGGCTTGTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.23, C:0.06, G:0.24, T:0.48
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:155952 original size:21 final size:22
Alignment explanation
Indices: 155923--155968 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
155913 TGTTCAGATA
** *
155923 AGTAGTACTCCGCAGCAAGTGG
1 AGTAGTACTCCAAAACAAGTGG
155945 AGTA-TACTCCAAAACAAGTGG
1 AGTAGTACTCCAAAACAAGTGG
155966 AGT
1 AGT
155969 TTCAACAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AGTAGTACTCCAAAACAAGTGG
Found at i:157655 original size:28 final size:27
Alignment explanation
Indices: 157600--157665 Score: 98
Period size: 27 Copynumber: 2.4 Consensus size: 27
157590 GCCACCCATT
157600 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
157627 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
*
157655 TATTTGTCAAA
1 TGTTTGTCAAA
157666 TATGAAGGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.58
28 14 0.39
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.47
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:158041 original size:19 final size:18
Alignment explanation
Indices: 158017--158055 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
158007 TGTATTAATA
* *
158017 AATAATCTTTATATATTTT
1 AATAATATTTA-AAATTTT
158036 AATAATATTTAAAATTTT
1 AATAATATTTAAAATTTT
158054 AA
1 AA
158056 CATATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
AATAATATTTAAAATTTT
Found at i:160006 original size:10 final size:11
Alignment explanation
Indices: 159973--160012 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
159963 ATAAATATTT
* *
159973 AAATTAATTCA
1 AAATTAAATAA
159984 AAATTAAATAA
1 AAATTAAATAA
159995 AAATTAAA-AA
1 AAATTAAATAA
160005 AAATTAAA
1 AAATTAAA
160013 CCGTAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 10 0.37
11 17 0.63
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATTAAATAA
Found at i:161984 original size:22 final size:22
Alignment explanation
Indices: 161958--162000 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
161948 ATATTTTAAT
161958 TAAAT-TCAATTATAAAAATATA
1 TAAATATCAA-TATAAAAATATA
*
161980 TAAATATTAATATAAAAATAT
1 TAAATATCAATATAAAAATAT
162001 TTTTTAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
TAAATATCAATATAAAAATATA
Found at i:162699 original size:3 final size:3
Alignment explanation
Indices: 162691--162717 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
162681 ATATAATTTA
162691 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
162718 TAGTGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:169642 original size:20 final size:20
Alignment explanation
Indices: 169619--169665 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
169609 TATTAAAATT
*
169619 TATATAATACGAATTATTAA
1 TATATAATACGAAATATTAA
169639 TATATAATACGAAATATTAA
1 TATATAATACGAAATATTAA
169659 TATATAA
1 TATATAA
169666 AAGTGAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
TATATAATACGAAATATTAA
Found at i:171222 original size:42 final size:42
Alignment explanation
Indices: 171163--171247 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
171153 CTTATGAAAG
* * *
171163 CAATGATGAAGACAATTATTAATTCTTACAATTAGCCATGCT
1 CAATGATGAAAACAATTATTAAGTCTTACAATTAGCCAAGCT
171205 CAATGATGAAAACAATTATTAAGTCTTACAATTAGCCAAGCT
1 CAATGATGAAAACAATTATTAAGTCTTACAATTAGCCAAGCT
171247 C
1 C
171248 CCTTAAGCAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (42 bp):
CAATGATGAAAACAATTATTAAGTCTTACAATTAGCCAAGCT
Found at i:177372 original size:18 final size:19
Alignment explanation
Indices: 177351--177391 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
177341 TAATTTTAAA
*
177351 TTTAATAT-TATAT-AATT
1 TTTAATATAAATATAAATT
*
177368 TTTTATATAAATATAAATT
1 TTTAATATAAATATAAATT
177387 TTTAA
1 TTTAA
177392 AAAAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
17 7 0.37
18 4 0.21
19 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTAATATAAATATAAATT
Found at i:177397 original size:18 final size:18
Alignment explanation
Indices: 177360--177442 Score: 53
Period size: 18 Copynumber: 4.7 Consensus size: 18
177350 ATTTAATATT
* * *
177360 ATATAATTTTTTATATAA
1 ATATAAATTTTTAAAAAA
177378 ATATAAATTTTTAAAAAA
1 ATATAAATTTTTAAAAAA
* *
177396 AT-TTAA-TTTTAATAAAT
1 ATATAAATTTTTAA-AAAA
* * ** *
177413 ATTTTAATAATTAAAAAT
1 ATATAAATTTTTAAAAAA
177431 ATATAAATTTTT
1 ATATAAATTTTT
177443 TTGATAAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
16 6 0.12
17 8 0.16
18 33 0.65
19 4 0.08
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATATAAATTTTTAAAAAA
Found at i:177416 original size:17 final size:18
Alignment explanation
Indices: 177367--177416 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
177357 ATTATATAAT
*
177367 TTTTTATATAAATA-TAAA
1 TTTTTA-ATAAATATTTAA
*
177385 TTTTTAA-AAAAATTTAA
1 TTTTTAATAAATATTTAA
177402 -TTTTAATAAATATTT
1 TTTTTAATAAATATTT
177417 TAATAATTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 10 0.37
17 11 0.41
18 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTTTAATAAATATTTAA
Found at i:177771 original size:16 final size:16
Alignment explanation
Indices: 177750--177784 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
177740 TTTAACATGT
*
177750 TATTTTTAATTTTTTA
1 TATTTTTAATTATTTA
177766 TATTTTTAATTATTTA
1 TATTTTTAATTATTTA
177782 TAT
1 TAT
177785 ATATATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTTTTAATTATTTA
Found at i:177866 original size:15 final size:16
Alignment explanation
Indices: 177846--177901 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 16
177836 TAAATACAAA
177846 TATAAATTTTTAAT-T
1 TATAAATTTTTAATAT
*
177861 TATAAATATTTAATAT
1 TATAAATTTTTAATAT
177877 T-TAAAATTTTTAAATAT
1 TAT-AAATTTTT-AATAT
177894 TAATAAAT
1 T-ATAAAT
177902 ATAAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
15 14 0.41
16 9 0.26
17 6 0.18
18 4 0.12
19 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TATAAATTTTTAATAT
Found at i:177878 original size:17 final size:17
Alignment explanation
Indices: 177846--177903 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
177836 TAAATACAAA
*
177846 TATAAAT-TTTTA-ATT
1 TATAAATATTTAATATT
177861 TATAAATATTTAATATT
1 TATAAATATTTAATATT
*
177878 TA-AAATTTTTAAATATT
1 TATAAATATTT-AATATT
*
177895 AATAAATAT
1 TATAAATAT
177904 AAAAATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.20
16 11 0.31
17 12 0.34
18 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAAATATTTAATATT
Found at i:177902 original size:10 final size:9
Alignment explanation
Indices: 177887--177927 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
177877 TTAAAATTTT
177887 TAAATATTAA
1 TAAATA-TAA
177897 TAAATATAA
1 TAAATATAA
*
177906 -AAATATAT
1 TAAATATAA
177914 TAAATATAA
1 TAAATATAA
177923 TAAAT
1 TAAAT
177928 GATTATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 7 0.25
9 15 0.54
10 6 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAAATATAA
Found at i:177934 original size:20 final size:19
Alignment explanation
Indices: 177887--177936 Score: 68
Period size: 17 Copynumber: 2.7 Consensus size: 19
177877 TTAAAATTTT
*
177887 TAAATATTAATAAATATAA
1 TAAATATTATTAAATATAA
177906 -AAATA-TATTAAATATAA
1 TAAATATTATTAAATATAA
177923 TAAATGATTATTAA
1 TAAAT-ATTATTAA
177937 TCATATTCAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 11 0.41
18 9 0.33
19 1 0.04
20 6 0.22
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
TAAATATTATTAAATATAA
Found at i:179244 original size:13 final size:13
Alignment explanation
Indices: 179214--179260 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
179204 ACTTATATTC
*
179214 ATATTAAA-ATAT
1 ATATTAAACATAA
*
179226 ATATTAGACATAA
1 ATATTAAACATAA
179239 ATATTAAACATAA
1 ATATTAAACATAA
179252 ATACTTAAA
1 ATA-TTAAA
179261 AATATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 7 0.23
13 18 0.60
14 5 0.17
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (13 bp):
ATATTAAACATAA
Found at i:179874 original size:2 final size:2
Alignment explanation
Indices: 179862--179897 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
179852 GTACATCTTT
*
179862 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
179898 ATTTGTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:188665 original size:15 final size:15
Alignment explanation
Indices: 188642--188671 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
188632 ATGGAGAGAA
188642 ATAAATATATTTAAT
1 ATAAATATATTTAAT
*
188657 ATAAGTATATTTAAT
1 ATAAATATATTTAAT
188672 TTATATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATAAATATATTTAAT
Found at i:189663 original size:21 final size:19
Alignment explanation
Indices: 189611--189673 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 19
189601 TTTGTGGGTA
*
189611 AAAAAAATAA-ATAAATTG
1 AAAAAAATAATAAAAATTG
**
189629 AAAAAGTTAATAAAAATTG
1 AAAAAAATAATAAAAATTG
189648 AGAAAAAATAAGTAAAAA--G
1 A-AAAAAATAA-TAAAAATTG
189667 AAAAAAA
1 AAAAAAA
189674 GAAAATTAGT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
18 14 0.38
19 10 0.27
20 7 0.19
21 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (19 bp):
AAAAAAATAATAAAAATTG
Found at i:190400 original size:16 final size:16
Alignment explanation
Indices: 190373--190425 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
190363 AAATAATTAA
*
190373 AATTAATAAATGTATT
1 AATTTATAAATGTATT
*
190389 AATTTATGAATGT-TT
1 AATTTATAAATGTATT
* *
190404 AAATTTATAAATTTACT
1 -AATTTATAAATGTATT
190421 AATTT
1 AATTT
190426 TAATTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (16 bp):
AATTTATAAATGTATT
Found at i:191026 original size:21 final size:21
Alignment explanation
Indices: 190988--191027 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
190978 TATTAAAAAT
*
190988 TATTTTATATTGATATTTATA
1 TATTTTATATTGAAATTTATA
191009 TATTTTATAATT-AAATTTA
1 TATTTTAT-ATTGAAATTTA
191028 AATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TATTTTATATTGAAATTTATA
Found at i:192758 original size:23 final size:23
Alignment explanation
Indices: 192716--192774 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
192706 TTATGAAAGT
* *
192716 TAATA-TTATTTTTATTAAATTA
1 TAATATTTAATTTTATCAAATTA
192738 TAATATTTAATTTTATCAAATTA
1 TAATATTTAATTTTATCAAATTA
* *
192761 TATTATTAAATTTT
1 TAATATTTAATTTT
192775 TATTATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 5 0.16
23 27 0.84
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (23 bp):
TAATATTTAATTTTATCAAATTA
Found at i:193956 original size:21 final size:21
Alignment explanation
Indices: 193932--194000 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
193922 AAAACCCATA
193932 TTATTGTTAAAAAATTATCTT
1 TTATTGTTAAAAAATTATCTT
** *
193953 TTATAT-TATATAAATAA-TAAATA
1 TTAT-TGT-TA-AAA-AATTATCTT
193976 TTATTGTTAAAAAATTATCTT
1 TTATTGTTAAAAAATTATCTT
193997 TTAT
1 TTAT
194001 ATTATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 6 0.17
23 11 0.31
24 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
TTATTGTTAAAAAATTATCTT
Found at i:193978 original size:44 final size:44
Alignment explanation
Indices: 193929--194016 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
193919 TTAAAAACCC
193929 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
1 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
193973 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
1 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
194017 TTCAAAACCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (44 bp):
ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
Found at i:194011 original size:21 final size:21
Alignment explanation
Indices: 193943--194011 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
193933 TATTGTTAAA
193943 AAATTATCTTTTATATTATAT
1 AAATTATCTTTTATATTATAT
** * * *
193964 AAATAATAAATATTATTGTTA-AA
1 AAAT--TATCTTTTA-TATTATAT
193987 AAATTATCTTTTATATTATAT
1 AAATTATCTTTTATATTATAT
194008 AAAT
1 AAAT
194012 AATAATTCAA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
23 11 0.32
24 4 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
AAATTATCTTTTATATTATAT
Found at i:194032 original size:44 final size:44
Alignment explanation
Indices: 193940--194038 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
193930 TATTATTGTT
** ** *
193940 AAAAAATTATCTTTTATATTATATAAATAATAAATATTATTGTT
1 AAAAAATTATCTTTTATATTATATAAATAATAAATAAAACCGTA
*
193984 AAAAAATTATCTTTTATATTATATAAATAATAATTCAAAACCG-A
1 AAAAAATTATCTTTTATATTATATAAATAATAAAT-AAAACCGTA
194028 AAAAAATTATC
1 AAAAAATTATC
194039 AAATACCATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 45 0.94
45 3 0.06
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (44 bp):
AAAAAATTATCTTTTATATTATATAAATAATAAATAAAACCGTA
Found at i:210640 original size:48 final size:49
Alignment explanation
Indices: 210588--210683 Score: 151
Period size: 48 Copynumber: 2.0 Consensus size: 49
210578 AGTTTCGATG
* *
210588 ATTCAAGTTTGAATTAAATCAAGTTTG-GA-GTTGTTTATAGTAATTTAT
1 ATTCAAGTTCGAATTAAATCAAGTTTGAAACG-TGTTTATAGTAATTTAT
210636 ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTA
1 ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTA
210684 GATCAATGGA
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
48 26 0.59
49 17 0.39
50 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.43
Consensus pattern (49 bp):
ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTAT
Found at i:229116 original size:15 final size:15
Alignment explanation
Indices: 229093--229122 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
229083 ATGGAGAGAA
229093 ATAAATATATTTAAT
1 ATAAATATATTTAAT
*
229108 ATAAGTATATTTAAT
1 ATAAATATATTTAAT
229123 TTATATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
ATAAATATATTTAAT
Found at i:230108 original size:21 final size:19
Alignment explanation
Indices: 230056--230110 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
230046 TTTGTGGGTA
*
230056 AAAAAAATAA-ATAAATTG
1 AAAAAAATAATAAAAATTG
**
230074 AAAAAGTTAATAAAAATTG
1 AAAAAAATAATAAAAATTG
230093 AGAAAAAATAAGTAAAAA
1 A-AAAAAATAA-TAAAAA
230111 GAAAAAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 8 0.28
19 8 0.28
20 7 0.24
21 6 0.21
ACGTcount: A:0.71, C:0.00, G:0.09, T:0.20
Consensus pattern (19 bp):
AAAAAAATAATAAAAATTG
Found at i:230834 original size:16 final size:16
Alignment explanation
Indices: 230807--230859 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
230797 AAATAATTAA
*
230807 AATTAATAAATGTATT
1 AATTTATAAATGTATT
*
230823 AATTTATGAATGT-TT
1 AATTTATAAATGTATT
* *
230838 AAATTTATAAATTTACT
1 -AATTTATAAATGTATT
230855 AATTT
1 AATTT
230860 TAATTTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
15 2 0.07
16 27 0.90
17 1 0.03
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (16 bp):
AATTTATAAATGTATT
Found at i:231459 original size:21 final size:21
Alignment explanation
Indices: 231421--231460 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
231411 TATTAAAAAT
*
231421 TATTTTATATTGATATTTATA
1 TATTTTATATTGAAATTTATA
231442 TATTTTATAATT-AAATTTA
1 TATTTTAT-ATTGAAATTTA
231461 AATAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
TATTTTATATTGAAATTTATA
Found at i:231878 original size:23 final size:21
Alignment explanation
Indices: 231850--231910 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 21
231840 GCATTTATTT
*
231850 TTATATAATAAAAATTATATAA
1 TTATATAATAAAAATAATAT-A
231872 TGTATATAGATACAAAGATAATATA
1 T-TATATA-ATA-AAA-ATAATATA
*
231897 TTACATAATAAAAA
1 TTATATAATAAAAA
231911 ATAGATCGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
21 1 0.03
22 4 0.12
23 9 0.27
24 8 0.24
25 5 0.15
26 6 0.18
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (21 bp):
TTATATAATAAAAATAATATA
Found at i:233182 original size:23 final size:23
Alignment explanation
Indices: 233140--233200 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
233130 TTATGAAAGT
* *
233140 TAATA-TTATTTTTATTAAATTA
1 TAATATTTAATTTTATCAAATTA
233162 TAATATTTAATTTTATCAAATTA
1 TAATATTTAATTTTATCAAATTA
* *
233185 TATTATTAAATTTTAT
1 TAATATTTAATTTTAT
233201 TATTAATCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
22 5 0.15
23 29 0.85
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
TAATATTTAATTTTATCAAATTA
Found at i:233204 original size:13 final size:13
Alignment explanation
Indices: 233151--233206 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
233141 AATATTATTT
233151 TTATTAAATTATA
1 TTATTAAATTATA
* *
233164 ATATTTAA-T-T-
1 TTATTAAATTATA
*
233174 TTATCAAATTATA
1 TTATTAAATTATA
*
233187 TTATTAAATTTTA
1 TTATTAAATTATA
233200 TTATTAA
1 TTATTAA
233207 TCAATAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
10 5 0.15
11 2 0.06
12 2 0.06
13 24 0.73
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTAAATTATA
Found at i:234375 original size:21 final size:21
Alignment explanation
Indices: 234351--234419 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
234341 AAAACCCATA
234351 TTATTGTTAAAAAATTATCTT
1 TTATTGTTAAAAAATTATCTT
** *
234372 TTATAT-TATATAAATAA-TAAATA
1 TTAT-TGT-TA-AAA-AATTATCTT
234395 TTATTGTTAAAAAATTATCTT
1 TTATTGTTAAAAAATTATCTT
234416 TTAT
1 TTAT
234420 ATTATATAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 6 0.17
23 11 0.31
24 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (21 bp):
TTATTGTTAAAAAATTATCTT
Found at i:234397 original size:44 final size:44
Alignment explanation
Indices: 234348--234435 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
234338 TTAAAAACCC
234348 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
1 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
234392 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
1 ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
234436 TTCAAAACCG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (44 bp):
ATATTATTGTTAAAAAATTATCTTTTATATTATATAAATAATAA
Found at i:234430 original size:21 final size:21
Alignment explanation
Indices: 234362--234430 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
234352 TATTGTTAAA
234362 AAATTATCTTTTATATTATAT
1 AAATTATCTTTTATATTATAT
** * * *
234383 AAATAATAAATATTATTGTTA-AA
1 AAAT--TATCTTTTA-TATTATAT
234406 AAATTATCTTTTATATTATAT
1 AAATTATCTTTTATATTATAT
234427 AAAT
1 AAAT
234431 AATAATTCAA
Statistics
Matches: 34, Mismatches: 10, Indels: 8
0.65 0.19 0.15
Matches are distributed among these distances:
20 4 0.12
21 15 0.44
23 11 0.32
24 4 0.12
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.49
Consensus pattern (21 bp):
AAATTATCTTTTATATTATAT
Found at i:234451 original size:44 final size:44
Alignment explanation
Indices: 234359--234457 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
234349 TATTATTGTT
** ** *
234359 AAAAAATTATCTTTTATATTATATAAATAATAAATATTATTGTT
1 AAAAAATTATCTTTTATATTATATAAATAATAAATAAAACCGTA
*
234403 AAAAAATTATCTTTTATATTATATAAATAATAATTCAAAACCG-A
1 AAAAAATTATCTTTTATATTATATAAATAATAAAT-AAAACCGTA
234447 AAAAAATTATC
1 AAAAAATTATC
234458 AAATACCATA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
44 45 0.94
45 3 0.06
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (44 bp):
AAAAAATTATCTTTTATATTATATAAATAATAAATAAAACCGTA
Found at i:251082 original size:49 final size:49
Alignment explanation
Indices: 251010--251106 Score: 158
Period size: 49 Copynumber: 2.0 Consensus size: 49
251000 CAGTTCGATG
* * **
251010 ATTCAAGTTTGAATTAAATCAAGTTTGGAGTGTGTTTATAGTAATTTAT
1 ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTAT
251059 ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTA
1 ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTA
251107 GATCAATGGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (49 bp):
ATTCAAGTTCGAATTAAATCAAGTTTGAAACGTGTTTATAGTAATTTAT
Found at i:253199 original size:5 final size:5
Alignment explanation
Indices: 253189--253219 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
253179 AGAGGAACAA
*
253189 ATTTT ATTTT ATTTT ACTTT ATTTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
253220 ATAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:253362 original size:36 final size:36
Alignment explanation
Indices: 253284--253363 Score: 85
Period size: 34 Copynumber: 2.2 Consensus size: 36
253274 TTTTTAATTT
*
253284 TTTAAAATATATATATTTTATACATATTTAAATAAA
1 TTTAAAATATATATATTATATACATATTTAAATAAA
* *
253320 TATAAAA-ATATA-ATTATATATATATATTAAA-AATA
1 TTTAAAATATATATATTATATACATAT-TTAAATAA-A
253355 CTTTAAAAT
1 -TTTAAAAT
253364 TTTAAATATT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
34 13 0.36
35 11 0.31
36 12 0.33
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (36 bp):
TTTAAAATATATATATTATATACATATTTAAATAAA
Found at i:255714 original size:18 final size:19
Alignment explanation
Indices: 255678--255720 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
255668 AATTTTTGTT
255678 TAAATTTTTTAAATATTAAA
1 TAAA-TTTTTAAATATTAAA
255698 TAAATTTTTAAAT-TTAAA
1 TAAATTTTTAAATATTAAA
255716 TAAAT
1 TAAAT
255721 AATTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 10 0.43
19 9 0.39
20 4 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAAATTTTTAAATATTAAA
Found at i:255867 original size:21 final size:20
Alignment explanation
Indices: 255842--255881 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
255832 GATCTTAAAA
*
255842 ATATTAAATATTTTAAATTTT
1 ATATTAAATA-ATTAAATTTT
*
255863 ATATTATATAATTAAATTT
1 ATATTAAATAATTAAATTT
255882 AAATAAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATTAAATAATTAAATTTT
Found at i:263527 original size:6 final size:7
Alignment explanation
Indices: 263509--263535 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
263499 ATCAAATCCC
263509 ATTTTTA
1 ATTTTTA
263516 ATTTTTA
1 ATTTTTA
263523 ATTTTTA
1 ATTTTTA
263530 ATTTTT
1 ATTTTT
263536 CTCATTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
ATTTTTA
Found at i:263984 original size:36 final size:35
Alignment explanation
Indices: 263943--264043 Score: 106
Period size: 29 Copynumber: 2.9 Consensus size: 35
263933 AAGAATCACG
263943 TAAATATAATATTTATAAAATATTTAAAATATAATA
1 TAAATATAATATTT-TAAAATATTTAAAATATAATA
263979 TAAATAT-ATATTTT-AAA-ATTT---ATATAATA
1 TAAATATAATATTTTAAAATATTTAAAATATAATA
* *
264008 TAAATTATTAATATATTAAAATATATATAAATATAA
1 TAAA-TA-TAATATTTTAAAATATTTA-AAATATAA
264044 AAAATTATAA
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
29 12 0.22
30 2 0.04
31 1 0.02
32 10 0.19
33 6 0.11
34 4 0.07
35 6 0.11
36 7 0.13
38 6 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (35 bp):
TAAATATAATATTTTAAAATATTTAAAATATAATA
Found at i:264008 original size:34 final size:33
Alignment explanation
Indices: 263943--264052 Score: 102
Period size: 32 Copynumber: 3.3 Consensus size: 33
263933 AAGAATCACG
*
263943 TAAATATAATATTTATAAAATATT-TAAAATATAATA
1 TAAATAT-ATATTT-TAAAAT-TTATATAATATAA-A
263979 TAAATATATATTTTAAAATTTATATAATATAAA
1 TAAATATATATTTTAAAATTTATATAATATAAA
* * * *
264012 TTATTA-ATATATTAAAATATATATAAATATAAA
1 TAAATATATATTTTAAAATTTATAT-AATATAAA
264045 -AAAT-TATA
1 TAAATATATA
264053 AATATGATTA
Statistics
Matches: 64, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
32 21 0.33
33 15 0.23
34 15 0.23
35 6 0.09
36 7 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (33 bp):
TAAATATATATTTTAAAATTTATATAATATAAA
Found at i:264021 original size:18 final size:17
Alignment explanation
Indices: 264000--264057 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 17
263990 TTTAAAATTT
264000 ATATAATATAAATTATTA
1 ATATAATA-AAATTATTA
*
264018 ATATATTAAAATATATATAA
1 ATATAATAAAAT-TAT-T-A
*
264038 ATATAA-AAAATTATAA
1 ATATAATAAAATTATTA
264054 ATAT
1 ATAT
264058 GATTATGATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 5 0.15
17 4 0.12
18 13 0.38
19 6 0.18
20 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATAAAATTATTA
Found at i:264030 original size:23 final size:23
Alignment explanation
Indices: 263970--264032 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
263960 AAATATTTAA
* *
263970 AATATAATATAAATATATATTTT
1 AATATATTATAAATATAAATTTT
*
263993 AAAAT-TTATATAATATAAATTATT
1 AATATATTATA-AATATAAATT-TT
264017 AATATATTA-AAATATA
1 AATATATTATAAATATA
264033 TATAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 4 0.12
23 19 0.58
24 7 0.21
25 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATATATTATAAATATAAATTTT
Found at i:264040 original size:20 final size:19
Alignment explanation
Indices: 264020--264096 Score: 65
Period size: 18 Copynumber: 4.2 Consensus size: 19
264010 AATTATTAAT
*
264020 ATATTAAAATAT-ATATAA
1 ATATAAAAATATGATATAA
264038 ATATAAAAA-AT--TATAA
1 ATATAAAAATATGATATAA
**
264054 ATATGATTATGATATGATA-AA
1 ATAT-A--AAAATATGATATAA
264075 ATATAAAAATATGATATAA
1 ATATAAAAATATGATATAA
264094 ATA
1 ATA
264097 CATGAATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
16 9 0.19
17 3 0.06
18 17 0.36
19 7 0.15
20 3 0.06
21 6 0.13
22 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
ATATAAAAATATGATATAA
Found at i:264049 original size:36 final size:35
Alignment explanation
Indices: 263949--264083 Score: 102
Period size: 37 Copynumber: 3.9 Consensus size: 35
263939 CACGTAAATA
* *
263949 TAATATTTATAAAATATTTAAAATATAATATAAA-TA-
1 TAATATAT-TAAAATATATAAAATATAA-A-AAATTAT
* * *
263985 T-ATATTTTAAAATTTATATAATAT---AAATTAT
1 TAATATATTAAAATATATAAAATATAAAAAATTAT
264016 TAATATATTAAAATATATATAAATATAAAAAATTAT
1 TAATATATTAAAATATATA-AAATATAAAAAATTAT
* **
264052 AAATATGATTATGATATGATAAAATATAAAAA
1 TAATAT-ATTAAAATAT-ATAAAATATAAAAA
264084 TATGATATAA
Statistics
Matches: 81, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
29 3 0.04
30 2 0.02
31 1 0.01
32 15 0.19
33 5 0.06
34 14 0.17
35 6 0.07
36 13 0.16
37 19 0.23
38 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (35 bp):
TAATATATTAAAATATATAAAATATAAAAAATTAT
Found at i:264054 original size:16 final size:16
Alignment explanation
Indices: 264009--264057 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 16
263999 TATATAATAT
264009 AAATTATTAATATATTAAA
1 AAATTA-TAA-ATA-TAAA
*
264028 ATATATATAAATATAAA
1 AAAT-TATAAATATAAA
264045 AAATTATAAATAT
1 AAATTATAAATAT
264058 GATTATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 9 0.33
17 7 0.26
18 3 0.11
19 6 0.22
20 2 0.07
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATTATAAATATAAA
Found at i:264732 original size:8 final size:8
Alignment explanation
Indices: 264716--264835 Score: 56
Period size: 8 Copynumber: 14.8 Consensus size: 8
264706 AAAAAATTTA
264716 AAATAATAT
1 AAAT-ATAT
264725 AAATATAT
1 AAATATAT
264733 AAATATAT
1 AAATATAT
264741 CAAA-AT-T
1 -AAATATAT
*
264748 AATATAAGAT
1 AA-AT-ATAT
264758 AAAT-TAT
1 AAATATAT
*
264765 TAATATATT
1 AAATATA-T
*
264774 AAA-ATTT
1 AAATATAT
264781 AAATATATAT
1 -AA-ATATAT
264791 ATAATATAT
1 A-AATATAT
*
264800 TAA-ATAT
1 AAATATAT
264807 -AAT-TAT
1 AAATATAT
*
264813 AATATATAA
1 AA-ATATAT
*
264822 AAATAGAT
1 AAATATAT
264830 AAATAT
1 AAATAT
264836 CATGCAAGTA
Statistics
Matches: 85, Mismatches: 11, Indels: 31
0.67 0.09 0.24
Matches are distributed among these distances:
6 7 0.08
7 13 0.15
8 33 0.39
9 25 0.29
10 7 0.08
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (8 bp):
AAATATAT
Found at i:264745 original size:27 final size:28
Alignment explanation
Indices: 264713--264826 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 28
264703 AATAAAAAAT
264713 TTAAAATAATATAA-ATATATAAATATA
1 TTAAAATAATATAAGATATATAAATATA
* *
264740 TCAAAATTAATATAAGATAAATTATTAATATA
1 TTAAAA-TAATATAAGAT--A-TATAAATATA
* *
264772 TTAAAAT-TTA-AATATATATATAATATA
1 TTAAAATAATATAAGATATATA-AATATA
* *
264799 TTAAATATAATTATAATATATAAAAATA
1 TTAAA-ATAA-TATAAGATATATAAATA
264827 GATAAATATC
Statistics
Matches: 69, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
26 3 0.04
27 17 0.25
28 10 0.14
29 6 0.09
30 8 0.12
31 11 0.16
32 14 0.20
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.39
Consensus pattern (28 bp):
TTAAAATAATATAAGATATATAAATATA
Found at i:264746 original size:18 final size:18
Alignment explanation
Indices: 264725--264835 Score: 66
Period size: 20 Copynumber: 5.8 Consensus size: 18
264715 AAAATAATAT
*
264725 AAATATATAAATATATCA
1 AAATATATAAATATATTA
*
264743 AAATTAATATAAGATAAATTA
1 AAA-T-ATATAA-ATATATTA
*
264764 TTAATATATTAAA-AT-TTA
1 -AAATATA-TAAATATATTA
264782 AATATATATATAATATATT-
1 AA-ATATATA-AATATATTA
*
264801 AAATATAATTATAATATATAA
1 AAATAT-A-TA-AATATATTA
*
264822 AAATAGATAAATAT
1 AAATATATAAATAT
264836 CATGCAAGTA
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
17 3 0.04
18 22 0.30
19 9 0.12
20 23 0.31
21 15 0.20
22 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.39
Consensus pattern (18 bp):
AAATATATAAATATATTA
Found at i:264813 original size:20 final size:20
Alignment explanation
Indices: 264767--264819 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
264757 TAAATTATTA
*
264767 ATATAT-TAAAAT-TTAAAT
1 ATATATATAATATATTAAAT
264785 ATATATATAATATATTAAAT
1 ATATATATAATATATTAAAT
264805 ATA-ATTATAATATAT
1 ATATA-TATAATATAT
264820 AAAAATAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 6 0.19
19 6 0.19
20 19 0.61
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATATATAATATATTAAAT
Found at i:266095 original size:19 final size:19
Alignment explanation
Indices: 266055--266096 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
266045 AAATTAAAAA
* * *
266055 AAATTATTTTTCGTTAATT
1 AAATTATTTTTCATGAAAT
266074 AAATTATTTTTCATGAAAT
1 AAATTATTTTTCATGAAAT
266093 AAAT
1 AAAT
266097 AAAAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (19 bp):
AAATTATTTTTCATGAAAT
Found at i:267979 original size:26 final size:27
Alignment explanation
Indices: 267950--268015 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
267940 AATTTTTTTT
*
267950 AAAATATAATTT-TTT-AATCTTTACAA
1 AAAATATAATTTATTTGAAT-TTTAAAA
267976 AAAATAATTAATTTATTTGAATTTTAAAA
1 AAAAT-A-TAATTTATTTGAATTTTAAAA
268005 ATAAATA-AATT
1 A-AAATATAATT
268016 ACATAAAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
26 5 0.15
27 5 0.15
28 6 0.18
29 11 0.32
30 7 0.21
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (27 bp):
AAAATATAATTTATTTGAATTTTAAAA
Found at i:268860 original size:24 final size:24
Alignment explanation
Indices: 268833--268878 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
268823 TATTTAGATA
268833 TAAGTATAAGAT-TAAAAATTTATT
1 TAAGTATAA-ATATAAAAATTTATT
*
268857 TAAGTATAAATATAAGAATTTA
1 TAAGTATAAATATAAAAATTTA
268879 ACAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (24 bp):
TAAGTATAAATATAAAAATTTATT
Found at i:268886 original size:129 final size:126
Alignment explanation
Indices: 268638--268886 Score: 322
Period size: 129 Copynumber: 1.9 Consensus size: 126
268628 TATTTCAAAT
* * *
268638 AAAAAATCAGTTCTAAAAAGTAAAAAAATAATTTAGATAGAATTTAAAACTAAGTTTATCTAGAT
1 AAAAAATCAGTTCTAAAAAATAAAAAAACAATTTAGATAGAAATTAAAACTAAGTTTATCTAGAT
* * *
268703 ATAAGTTTAAGATTAAAGATTTATTTAAATACAAATTAAAAATTAATAATAAAAACATGATA
66 ATAAGTATAAGATTAAAAATTTATTTAAATACAAATTAAAAATT-ATAAAAAAAACATGATA
* * *
268765 AAAAAATCAGTTTTAAAAAAT-GAAAAACAATTTAGATAGAAATTAAAACATAAGAGTTTATTTA
1 AAAAAATCAGTTCTAAAAAATAAAAAAACAATTTAGATAGAAATTAAAAC-T-A-AGTTTATCTA
* * *
268829 GATATAAGTATAAGATTAAAAATTTATTTAAGTATAAATATAAGAATT-TAACAAAAAA
63 GATATAAGTATAAGATTAAAAATTTATTTAAATACAAAT-TAAAAATTATAA-AAAAAA
268887 TAAAAATTTA
Statistics
Matches: 105, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
126 25 0.24
127 20 0.19
128 4 0.04
129 49 0.47
130 7 0.07
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (126 bp):
AAAAAATCAGTTCTAAAAAATAAAAAAACAATTTAGATAGAAATTAAAACTAAGTTTATCTAGAT
ATAAGTATAAGATTAAAAATTTATTTAAATACAAATTAAAAATTATAAAAAAAACATGATA
Found at i:269463 original size:20 final size:21
Alignment explanation
Indices: 269428--269468 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
269418 AATATAATCT
*
269428 ATATATATTTAATTTTTAAATA
1 ATATATATTT-ATTTTAAAATA
269450 ATATATATTT-TTTTAAAAT
1 ATATATATTTATTTTAAAAT
269469 TCATAATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATATATATTTATTTTAAAATA
Found at i:269905 original size:15 final size:16
Alignment explanation
Indices: 269887--269924 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
269877 ATAAATTTTA
269887 AATTTAA-TTTTTAAT
1 AATTTAATTTTTTAAT
269902 AATTTAATTTTTTAAT
1 AATTTAATTTTTTAAT
*
269918 ATTTTAA
1 AATTTAA
269925 AATATAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
AATTTAATTTTTTAAT
Found at i:269996 original size:21 final size:21
Alignment explanation
Indices: 269950--269997 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
269940 TTAAAAAATT
*
269950 ATATAATTTATTATTCATATG
1 ATATAATTTATTATTCATAAG
269971 ATATAATTATATTATAT-ATAAG
1 ATATAATT-TATTAT-TCATAAG
269993 -TATAA
1 ATATAA
269998 AGTAATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.54
22 10 0.42
23 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (21 bp):
ATATAATTTATTATTCATAAG
Found at i:273933 original size:152 final size:152
Alignment explanation
Indices: 273657--273960 Score: 581
Period size: 152 Copynumber: 2.0 Consensus size: 152
273647 TCGTGTGCTT
*
273657 AATCTAAGCAGTTGATATTTTATGAGGCTTTATTGAGTTAATGGTCTTTCCATCTTAAACTCTAC
1 AATCTAAGCAGTTGATATTCTATGAGGCTTTATTGAGTTAATGGTCTTTCCATCTTAAACTCTAC
273722 ATTGAGCGCATTAAATTGCTCCCCATATCCGACCTTTTAAATCTTCATTAAGACTGAATTGTATC
66 ATTGAGCGCATTAAATTGCTCCCCATATCCGACCTTTTAAATCTTCATTAAGACTGAATTGTATC
273787 TGTTTGCTTGAGCATATGTATG
131 TGTTTGCTTGAGCATATGTATG
*
273809 AATCTAAGCAGTTGATATTCTATGAGGCTTTATTGAGTTAATGGTCTTTCCATCTTAAACTTTAC
1 AATCTAAGCAGTTGATATTCTATGAGGCTTTATTGAGTTAATGGTCTTTCCATCTTAAACTCTAC
*
273874 ATTGGGCGCATTAAATTGCTCCCCATATCCGACCTTTTAAATCTTCATTAAGACTGAATTGTATC
66 ATTGAGCGCATTAAATTGCTCCCCATATCCGACCTTTTAAATCTTCATTAAGACTGAATTGTATC
273939 TGTTTGCTTGAGCATATGTATG
131 TGTTTGCTTGAGCATATGTATG
273961 CATACTTCCA
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
152 149 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (152 bp):
AATCTAAGCAGTTGATATTCTATGAGGCTTTATTGAGTTAATGGTCTTTCCATCTTAAACTCTAC
ATTGAGCGCATTAAATTGCTCCCCATATCCGACCTTTTAAATCTTCATTAAGACTGAATTGTATC
TGTTTGCTTGAGCATATGTATG
Found at i:288765 original size:2 final size:2
Alignment explanation
Indices: 288758--288827 Score: 104
Period size: 2 Copynumber: 35.0 Consensus size: 2
288748 GTGTGGATGA
* * *
288758 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT GT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
288800 AT AT AT AT AT AT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288828 TCTCATTCAC
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:289000 original size:2 final size:2
Alignment explanation
Indices: 288958--288992 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
288948 GACTATAAAA
288958 AT AT -T 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
288993 GTTATATAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:292920 original size:2 final size:2
Alignment explanation
Indices: 292915--292959 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
292905 TATGTGTATG
292915 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
292957 TA T
1 TA T
292960 TGTTTCAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:294860 original size:18 final size:18
Alignment explanation
Indices: 294834--294883 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
294824 ATATTTATAT
*
294834 ATAAATTTTAATATATTA
1 ATAATTTTTAATATATTA
*
294852 ATAATTTTTATTATA-TA
1 ATAATTTTTAATATATTA
*
294869 AT--TTTTTAAAATATT
1 ATAATTTTTAATATATT
294884 TATATAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 9 0.33
16 1 0.04
17 4 0.15
18 13 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATAATTTTTAATATATTA
Found at i:294871 original size:14 final size:14
Alignment explanation
Indices: 294847--294979 Score: 51
Period size: 14 Copynumber: 10.1 Consensus size: 14
294837 AATTTTAATA
294847 TATTA-ATAATTTT
1 TATTATATAATTTT
294860 TATTATATAA-TTT
1 TATTATATAATTTT
*
294873 T-TTA-A-AATATT
1 TATTATATAATTTT
*
294884 TA-TATAATAATATCGTG
1 TATTAT-ATAAT-T--TT
*
294901 T-TTATATTATTTT
1 TATTATATAATTTT
*
294914 TAATAT-TATATTTT
1 TATTATATA-ATTTT
*
294928 TATTAT-T--TTTA
1 TATTATATAATTTT
*
294939 TATTATATAA-TTA
1 TATTATATAATTTT
*
294952 TA-TA-ATAATTTA
1 TATTATATAATTTT
294964 TATTATATAAATTTT
1 TATTATAT-AATTTT
294979 T
1 T
294980 TAAAACTTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 36
0.66 0.07 0.26
Matches are distributed among these distances:
10 2 0.02
11 19 0.21
12 11 0.12
13 20 0.22
14 23 0.25
15 7 0.08
16 4 0.04
17 5 0.05
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (14 bp):
TATTATATAATTTT
Found at i:294915 original size:11 final size:11
Alignment explanation
Indices: 294901--294944 Score: 63
Period size: 11 Copynumber: 3.9 Consensus size: 11
294891 TAATATCGTG
294901 TTTATATTATT
1 TTTATATTATT
294912 TTTAATATTATAT
1 TTT-ATATTAT-T
294925 TTT-TATTATT
1 TTTATATTATT
294935 TTTATATTAT
1 TTTATATTAT
294945 ATAATTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.13
11 15 0.50
12 7 0.23
13 4 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTATATTATT
Found at i:294918 original size:23 final size:23
Alignment explanation
Indices: 294891--294946 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
294881 ATTTATATAA
* *
294891 TAATATCGTGTTTATATTATTTT
1 TAATATCATATTTATATTATTTT
* *
294914 TAATATTATATTTTTATTATTTT
1 TAATATCATATTTATATTATTTT
*
294937 T-ATATTATAT
1 TAATATCATAT
294947 AATTATATAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
TAATATCATATTTATATTATTTT
Found at i:294922 original size:17 final size:18
Alignment explanation
Indices: 294902--294944 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
294892 AATATCGTGT
294902 TTATATTATTT-TTAATA
1 TTATATTATTTATTAATA
* *
294919 TTATATT-TTTATTATTT
1 TTATATTATTTATTAATA
294936 TTATATTAT
1 TTATATTAT
294945 ATAATTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATTATTTATTAATA
Found at i:294977 original size:15 final size:14
Alignment explanation
Indices: 294935--294973 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
294925 TTTTATTATT
294935 TTTATATTATATAA
1 TTTATATTATATAA
294949 -TTATA-TA-ATAA
1 TTTATATTATATAA
294960 TTTATATTATATAA
1 TTTATATTATATAA
294974 ATTTTTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
11 4 0.18
12 7 0.32
13 7 0.32
14 4 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTTATATTATATAA
Found at i:309406 original size:17 final size:18
Alignment explanation
Indices: 309370--309410 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
309360 ATGTTTAAAT
*
309370 ATTAAA-AATAATTTTTA
1 ATTAAATAATAATTTTAA
309387 ATTAAATAATAA-TTTAA
1 ATTAAATAATAATTTTAA
309404 ATTAAAT
1 ATTAAAT
309411 CAAGATCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAATAATAATTTTAA
Found at i:310142 original size:16 final size:16
Alignment explanation
Indices: 310123--310153 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
310113 TATAATATGT
310123 ATAAAATAATTAAAAC
1 ATAAAATAATTAAAAC
*
310139 ATAACATAATTAAAA
1 ATAAAATAATTAAAA
310154 TTTATATAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAAAATAATTAAAAC
Found at i:310244 original size:24 final size:23
Alignment explanation
Indices: 310217--310262 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
310207 TTAATATTTT
*
310217 TATATTATAATAATTAAATAAATA
1 TATATTAT-ATAAATAAATAAATA
*
310241 TATATTATATAAATATATAAAT
1 TATATTATATAAATAAATAAAT
310263 TATTCCGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TATATTATATAAATAAATAAATA
Found at i:310252 original size:15 final size:15
Alignment explanation
Indices: 310229--310259 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
310219 TATTATAATA
310229 ATTAAATAAATATAT
1 ATTAAATAAATATAT
*
310244 ATTATATAAATATAT
1 ATTAAATAAATATAT
310259 A
1 A
310260 AATTATTCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATTAAATAAATATAT
Found at i:311531 original size:14 final size:15
Alignment explanation
Indices: 311492--311531 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
311482 TATATTTTTA
311492 TTAATTTAAAAATAT
1 TTAATTTAAAAATAT
*
311507 TTATATATAAAAAT-T
1 TTA-ATTTAAAAATAT
311522 TTAATTTAAA
1 TTAATTTAAA
311532 TTCAAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.27
15 7 0.32
16 9 0.41
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATTTAAAAATAT
Found at i:312534 original size:30 final size:30
Alignment explanation
Indices: 312455--312539 Score: 75
Period size: 30 Copynumber: 2.8 Consensus size: 30
312445 GTTTTTAAAT
** * *
312455 TTTAAAATAAATATAGTAAAATGAT-ACATA
1 TTTAAAATAAATAT-GTAAAATTTTAAAAAA
* *
312485 TTTATAAA-ATATATTTAAAATTTTAAAAAA
1 TTTA-AAATAAATATGTAAAATTTTAAAAAA
*
312515 TTTAAAATAAATATGTAAAAATTTA
1 TTTAAAATAAATATGTAAAATTTTA
312540 TTAACTTTAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
29 10 0.23
30 30 0.70
31 3 0.07
ACGTcount: A:0.56, C:0.01, G:0.04, T:0.39
Consensus pattern (30 bp):
TTTAAAATAAATATGTAAAATTTTAAAAAA
Found at i:313645 original size:2 final size:2
Alignment explanation
Indices: 313638--313669 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
313628 ATTTTTCTTC
313638 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
313670 CTAGAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314598 original size:36 final size:33
Alignment explanation
Indices: 314532--314610 Score: 97
Period size: 36 Copynumber: 2.3 Consensus size: 33
314522 ATTAATTTAA
*
314532 TTAAAAATAAAAAATTTATTTGATTTATTATTATT
1 TTAAAAATAAAAAATTTATTT-ATTAATTATT-TT
314567 TATAAAAATAAAAAATTTTAATTT-TTAATTATTTT
1 T-TAAAAATAAAAAA-TTT-ATTTATTAATTATTTT
314602 TTAAAAATA
1 TTAAAAATA
314611 TATTTTTATG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
34 8 0.20
35 4 0.10
36 21 0.52
37 3 0.08
38 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (33 bp):
TTAAAAATAAAAAATTTATTTATTAATTATTTT
Found at i:315040 original size:13 final size:13
Alignment explanation
Indices: 315022--315046 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
315012 TAATTTAAAC
315022 TTAAATAAATTAT
1 TTAAATAAATTAT
315035 TTAAATAAATTA
1 TTAAATAAATTA
315047 ATGTTTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TTAAATAAATTAT
Found at i:316337 original size:15 final size:17
Alignment explanation
Indices: 316313--316349 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
316303 GTATTGAATG
316313 AAAA-TATTTTT-TT-T
1 AAAATTATTTTTATTAT
316327 AAAATTATTTTTATTAT
1 AAAATTATTTTTATTAT
316344 AAAATT
1 AAAATT
316350 TTTAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 2 0.10
17 7 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AAAATTATTTTTATTAT
Found at i:316352 original size:15 final size:16
Alignment explanation
Indices: 316313--316357 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
316303 GTATTGAATG
316313 AAAATATTTTT-TT-T
1 AAAATATTTTTATTAT
316327 AAAATTATTTTTATTAT
1 AAAA-TATTTTTATTAT
*
316344 AAAAT-TTTTAATTA
1 AAAATATTTTTATTA
316358 AATTTAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.15
15 15 0.56
16 3 0.11
17 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
AAAATATTTTTATTAT
Found at i:316770 original size:20 final size:22
Alignment explanation
Indices: 316724--316779 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
316714 AATTACAAAA
316724 TTTATATATTTATAATTCTATT
1 TTTATATATTTATAATTCTATT
*
316746 ATTATA-ATTT-TAATT-TAATT
1 TTTATATATTTATAATTCT-ATT
316766 TTTATATAATTTAT
1 TTTATAT-ATTTAT
316780 TCAATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 1 0.04
20 13 0.46
21 4 0.14
22 9 0.32
23 1 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTATATATTTATAATTCTATT
Found at i:318345 original size:3 final size:3
Alignment explanation
Indices: 318337--318376 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
318327 TAAGTTGAAA
*
318337 ATT ATT ATT ATT ATT ATT AAT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
318377 AAAAGCACTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:319459 original size:19 final size:19
Alignment explanation
Indices: 319420--319474 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
319410 AAAAAAAAGC
**
319420 TTTTTATAAAATT-AATTA
1 TTTTTATAAAATTAAAAAA
319438 TTTTTATAAAATTAAAAAA
1 TTTTTATAAAATTAAAAAA
319457 --TTTATAATAATTAAAAAA
1 TTTTTATAA-AATTAAAAAA
319475 GCTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.21
18 23 0.70
19 3 0.09
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTTTTATAAAATTAAAAAA
Found at i:319460 original size:17 final size:18
Alignment explanation
Indices: 319440--319474 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
319430 ATTAATTATT
319440 TTTATAA-AATTAAAAAA
1 TTTATAATAATTAAAAAA
319457 TTTATAATAATTAAAAAA
1 TTTATAATAATTAAAAAA
319475 GCTTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
TTTATAATAATTAAAAAA
Found at i:319737 original size:18 final size:18
Alignment explanation
Indices: 319710--319756 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
319700 TTTTAATATA
*
319710 TATTTAATAATTAAATTT
1 TATTTAATAAATAAATTT
*
319728 T-TTTACATAAATATATTT
1 TATTTA-ATAAATAAATTT
*
319746 TATTTATTAAA
1 TATTTAATAAA
319757 ATTATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 4 0.17
18 16 0.67
19 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (18 bp):
TATTTAATAAATAAATTT
Found at i:320497 original size:20 final size:21
Alignment explanation
Indices: 320467--320530 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 21
320457 AAATATATAT
*
320467 TAATATTTTTAAATAATAAAA
1 TAATATATTTAAATAATAAAA
*
320488 TAA-ATATTTAAAAAATTTAAAA
1 TAATATATTTAAATAA--TAAAA
**
320510 TAATATAAATAAATAA-AAAA
1 TAATATATTTAAATAATAAAA
320530 T
1 T
320531 TTAGAAGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
20 15 0.43
21 3 0.09
22 8 0.23
23 9 0.26
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (21 bp):
TAATATATTTAAATAATAAAA
Found at i:320518 original size:27 final size:27
Alignment explanation
Indices: 320481--320533 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
320471 ATTTTTAAAT
**
320481 AATAAAATAAATATTTAAAAAATTTAA
1 AATAAAATAAATAAATAAAAAATTTAA
*
320508 AATAATATAAATAAATAAAAAATTTA
1 AATAAAATAAATAAATAAAAAATTTA
320534 GAAGAAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
AATAAAATAAATAAATAAAAAATTTAA
Found at i:323652 original size:30 final size:28
Alignment explanation
Indices: 323616--323695 Score: 91
Period size: 24 Copynumber: 3.0 Consensus size: 28
323606 AGTTCTATGT
323616 AATATAATTATATGATATAAAAATAATTAA
1 AATATAATTATAT-A-ATAAAAATAATTAA
323646 AATATAA-TATA-AATAAAAA-AA-T-A
1 AATATAATTATATAATAAAAATAATTAA
*
323669 TATA-AATTATATAATAAAAATAATTAA
1 AATATAATTATATAATAAAAATAATTAA
323696 TATGTAAAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.05
23 8 0.18
24 9 0.20
25 4 0.09
26 8 0.18
27 2 0.05
29 4 0.09
30 7 0.16
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (28 bp):
AATATAATTATATAATAAAAATAATTAA
Found at i:323771 original size:27 final size:27
Alignment explanation
Indices: 323616--323792 Score: 103
Period size: 27 Copynumber: 6.3 Consensus size: 27
323606 AGTTCTATGT
*
323616 AATATAATTATATGATATAAAAATA-ATTAA
1 AATATAA-TATA-AATATAAAAATATA-T-A
*
323646 AATATAATATAAATAAAAAAATATATA
1 AATATAATATAAATATAAAAATATATA
* * *
323673 AAT-TATATAATAAAAATAATTAATATGTAA
1 AATATA-AT-ATAAATATAA-AAATATAT-A
* * * *
323703 AATTTTATATAAATAT-ATAATATTTTA
1 AATATAATATAAATATAAAAATA-TATA
323730 AA-ATAAT-TATAATATAAAAATATATA
1 AATATAATATA-AATATAAAAATATATA
* * *
323756 AATATAATATAGATATATAAATTTATTA
1 AATATAATATAAATATAAAAATATA-TA
*
323784 AATCTAATA
1 AATATAATA
323793 AGAAGGACCA
Statistics
Matches: 118, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
25 2 0.02
26 15 0.13
27 35 0.30
28 34 0.29
29 18 0.15
30 13 0.11
31 1 0.01
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (27 bp):
AATATAATATAAATATAAAAATATATA
Done.