Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold41
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: 2798036
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Warning! 10448 characters in sequence are not A, C, G, or T
File 9 of 21
Found at i:868983 original size:13 final size:13
Alignment explanation
Indices: 868952--868985 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
868942 AATTATAAAA
*
868952 TTAAAAAAATATT
1 TTAAATAAATATT
868965 TT-AATAAATATT
1 TTAAATAAATATT
868977 TTAAATAAA
1 TTAAATAAA
868986 ATAAGTAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
TTAAATAAATATT
Found at i:869317 original size:18 final size:18
Alignment explanation
Indices: 869280--869315 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
869270 TATTTATTAA
869280 TATAATATATTTAATATT
1 TATAATATATTTAATATT
*
869298 TATATTATATTT-ATATT
1 TATAATATATTTAATATT
869315 T
1 T
869316 TAAACTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATAATATATTTAATATT
Found at i:871225 original size:22 final size:21
Alignment explanation
Indices: 871192--871243 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
871182 TAGTTTCAAC
**
871192 AAATATAAAAATTAATTAATTA
1 AAATA-AAAAATTAACAAATTA
871214 AAATAAATAAATTAACAAATTA
1 AAATAAA-AAATTAACAAATTA
871236 AAATAAAA
1 AAATAAAA
871244 TGAATTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 3 0.11
22 24 0.89
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (21 bp):
AAATAAAAAATTAACAAATTA
Found at i:871474 original size:18 final size:17
Alignment explanation
Indices: 871426--871474 Score: 50
Period size: 16 Copynumber: 3.0 Consensus size: 17
871416 AACATAAATA
*
871426 TATAAATTAAAATTTA-
1 TATAAAATAAAATTTAT
871442 TATAAAAT-AAA-TTAT
1 TATAAAATAAAATTTAT
*
871457 TAATATAATAAAATTTAT
1 T-ATAAAATAAAATTTAT
871475 GAAAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 3 0.11
15 4 0.15
16 13 0.48
17 3 0.11
18 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TATAAAATAAAATTTAT
Found at i:872193 original size:16 final size:16
Alignment explanation
Indices: 872152--872299 Score: 71
Period size: 16 Copynumber: 9.2 Consensus size: 16
872142 AAACTGAATT
*
872152 AATTTTAATT-TTTAA
1 AATTTTAATTATTTTA
872167 AAGTTTTAATTATTTTA
1 AA-TTTTAATTATTTTA
* *
872184 AATTTGAATTAATTAAATTT
1 AATTTTAATT-ATT---TTA
*
872204 AATATTTATATTA-ATTA
1 AAT-TTTA-ATTATTTTA
*
872221 AA-TTTAAGTT-TATTA
1 AATTTTAA-TTATTTTA
*
872236 AGTTTT-ATT-TTTT-
1 AATTTTAATTATTTTA
*
872249 -ATTTAAATTATTTTA
1 AATTTTAATTATTTTA
*
872264 AATTTAAATTATTTTAA
1 AATTTTAATTATTTT-A
872281 AATTTTAATT-TTATTA
1 AATTTTAATTATT-TTA
872297 AAT
1 AAT
872300 AAAATAAAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 33
0.70 0.07 0.22
Matches are distributed among these distances:
12 3 0.03
13 3 0.03
14 10 0.10
15 14 0.13
16 38 0.36
17 25 0.24
20 5 0.05
21 4 0.04
22 3 0.03
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
AATTTTAATTATTTTA
Found at i:872210 original size:22 final size:21
Alignment explanation
Indices: 872172--872233 Score: 74
Period size: 22 Copynumber: 3.0 Consensus size: 21
872162 TTTAAAAGTT
*
872172 TTAATT-ATTTTAAATTTGA-A
1 TTAATTAAATTTAAATTT-ATA
872192 TTAATTAAATTTAATATTTATA
1 TTAATTAAATTTAA-ATTTATA
*
872214 TTAATTAAATTTAAGTTTAT
1 TTAATTAAATTTAAATTTAT
872234 TAAGTTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
20 6 0.16
21 12 0.32
22 19 0.51
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TTAATTAAATTTAAATTTATA
Found at i:872325 original size:16 final size:16
Alignment explanation
Indices: 872249--872320 Score: 58
Period size: 16 Copynumber: 4.6 Consensus size: 16
872239 TTTATTTTTT
*
872249 ATTTAAATTATTTTAA
1 ATTTAAATTATATTAA
*
872265 ATTTAAATTATTTTAAA
1 ATTTAAATTATATT-AA
* *
872282 ATTTTAATTTTATTAA
1 ATTTAAATTATATTAA
* * *
872298 A-TAAAATAAAATTAA
1 ATTTAAATTATATTAA
872313 A-TTAAATT
1 ATTTAAATT
872321 TAAATGAATT
Statistics
Matches: 45, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
15 15 0.33
16 17 0.38
17 13 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTAAATTATATTAA
Found at i:872394 original size:15 final size:15
Alignment explanation
Indices: 872374--872403 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
872364 ATATCATGTC
872374 AAATTAATTTAAATT
1 AAATTAATTTAAATT
*
872389 AAATTAATTTTAATT
1 AAATTAATTTAAATT
872404 TTTAAATTTT
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:0.00, T:0.50
Consensus pattern (15 bp):
AAATTAATTTAAATT
Found at i:872476 original size:233 final size:236
Alignment explanation
Indices: 872068--872578 Score: 830
Period size: 233 Copynumber: 2.2 Consensus size: 236
872058 TTTTATTAAA
*
872068 TAAATTAAATTTAAATAAATTCAACGTGCTTTTCAACATTAATTAGAGTTAGATATATCATGTCA
1 TAAATTAAATTTAAATGAATTCAACGTGCTTTTCAACATTAATTAGAGTTAGATATATCATGTCA
* *
872133 AATTAATTTAAACTGAATTAATTTTAATTTTTAAAAGTTTTAATTATTTTAAATTTGAATTAATT
66 AATTAATTTAAACTAAATTAATTTTAATTTTT--AA----TAATTATTTTAAATTTGAATCAATT
872198 AAATTTAATATTTATATTAATTAAATTTAAGTTTATTAAGTTTTATTTTTTATTTAAATTATTTT
125 AAATTTAATATTTATATTAATTAAATTTAAGTTTATTAAGTTTTATTTTTTATTTAAATTATTTT
872263 AAATTTAAATTATTTTAAAATTTTAATTTTATTAAATAAAATAAAAT
190 AAATTTAAATTATTTTAAAATTTTAATTTTATTAAATAAAATAAAAT
* * *
872310 TAAATTAAATTTAAATGAATTTAACGTGCTTTTCAATATTAGTTAGAGTTAGATATATCATGTCA
1 TAAATTAAATTTAAATGAATTCAACGTGCTTTTCAACATTAATTAGAGTTAGATATATCATGTCA
*
872375 AATTAATTTAAATTAAATTAATTTTAATTTTT-A-AATT-TTTTAAATTTGAATCAATTAAATTT
66 AATTAATTTAAACTAAATTAATTTTAATTTTTAATAATTATTTTAAATTTGAATCAATTAAATTT
*
872437 AATATTTATATTAATTAGATTTAAGTTTATTAAGTTTTATTTTTTATTTAAATTATTTTAAATTT
131 AATATTTATATTAATTAAATTTAAGTTTATTAAGTTTTATTTTTTATTTAAATTATTTTAAATTT
* * *
872502 TAATTATTTTAAAATTTTAATTTTATTAAATTAAATTAAAT
196 AAATTATTTTAAAATTTTAATTTTATTAAATAAAATAAAAT
* *
872543 TAATTTAAATTTAAATGAATTCAACGTACTTTTCAA
1 TAAATTAAATTTAAATGAATTCAACGTGCTTTTCAA
872579 GATAGGTCTT
Statistics
Matches: 255, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
233 159 0.62
234 4 0.02
239 1 0.00
242 91 0.36
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (236 bp):
TAAATTAAATTTAAATGAATTCAACGTGCTTTTCAACATTAATTAGAGTTAGATATATCATGTCA
AATTAATTTAAACTAAATTAATTTTAATTTTTAATAATTATTTTAAATTTGAATCAATTAAATTT
AATATTTATATTAATTAAATTTAAGTTTATTAAGTTTTATTTTTTATTTAAATTATTTTAAATTT
AAATTATTTTAAAATTTTAATTTTATTAAATAAAATAAAAT
Found at i:872492 original size:16 final size:16
Alignment explanation
Indices: 872482--872553 Score: 69
Period size: 16 Copynumber: 4.6 Consensus size: 16
872472 TTTATTTTTT
872482 ATTTAAATTATTTTAA
1 ATTTAAATTATTTTAA
*
872498 ATTTTAATTATTTTAAA
1 ATTTAAATTATTTT-AA
*
872515 ATTTTAATT-TTATTAA
1 ATTTAAATTATT-TTAA
**
872531 A-TTAAATTAAATT-A
1 ATTTAAATTATTTTAA
872545 ATTTAAATT
1 ATTTAAATT
872554 TAAATGAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
14 2 0.04
15 15 0.31
16 18 0.38
17 13 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATTATTTTAA
Found at i:872496 original size:10 final size:10
Alignment explanation
Indices: 872483--872553 Score: 50
Period size: 10 Copynumber: 7.8 Consensus size: 10
872473 TTATTTTTTA
872483 TTTAAATTAT
1 TTTAAATTAT
872493 TTT-AA--AT
1 TTTAAATTAT
872500 TTT-AATTAT
1 TTTAAATTAT
872509 TTTAAA--AT
1 TTTAAATTAT
872517 TTT-AATT-T
1 TTTAAATTAT
*
872525 TATTAAATTAA
1 T-TTAAATTAT
* *
872536 ATTAAATTAA
1 TTTAAATTAT
872546 TTTAAATT
1 TTTAAATT
872554 TAAATGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
7 9 0.18
8 7 0.14
9 9 0.18
10 25 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTTAAATTAT
Found at i:872544 original size:15 final size:16
Alignment explanation
Indices: 872526--872558 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
872516 TTTTAATTTT
872526 ATTAAATTAAA-TTAA
1 ATTAAATTAAATTTAA
*
872541 ATTAATTTAAATTTAA
1 ATTAAATTAAATTTAA
872557 AT
1 AT
872559 GAATTCAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAATTAAATTTAA
Found at i:872558 original size:16 final size:16
Alignment explanation
Indices: 872374--872563 Score: 65
Period size: 16 Copynumber: 11.6 Consensus size: 16
872364 ATATCATGTC
872374 AAATTAATTTAAA-TT
1 AAATTAATTTAAATTT
*
872389 AAATTAATTTTAATTTTT
1 AAATTAA-TTTAA-ATTT
*
872407 AAATT-TTTTAAATTT
1 AAATTAATTTAAATTT
* *
872422 GAATCAA-TTAAATTT
1 AAATTAATTTAAATTT
*
872437 -AA-T-ATTTATA-TT
1 AAATTAATTTAAATTT
*
872449 -AATTAGATTTAAGTTT
1 AAATTA-ATTTAAATTT
* **
872465 ATTAAGTTTTATTTTTTATTT
1 A--AA---TTAATTTAAATTT
*
872486 AAATTATTTTAAATTT
1 AAATTAATTTAAATTT
* *
872502 TAATTATTTTAAAATTTT
1 AAATTAATTT-AAA-TTT
*
872520 AATTTTATTAAATTAAA-TT
1 AA----ATTAATTTAAATTT
872539 AAATTAATTTAAATTT
1 AAATTAATTTAAATTT
*
872555 AAATGAATT
1 AAATTAATT
872564 CAACGTACTT
Statistics
Matches: 131, Mismatches: 22, Indels: 43
0.67 0.11 0.22
Matches are distributed among these distances:
12 5 0.04
13 5 0.04
14 2 0.02
15 36 0.27
16 42 0.32
17 3 0.02
18 11 0.08
19 8 0.06
21 10 0.08
22 9 0.07
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (16 bp):
AAATTAATTTAAATTT
Found at i:875479 original size:21 final size:21
Alignment explanation
Indices: 875453--875499 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
875443 GTATAAAATG
875453 ATATATTAGTTGAATGAAAAA
1 ATATATTAGTTGAATGAAAAA
** * *
875474 ATATATTTTTTGGATGAAATA
1 ATATATTAGTTGAATGAAAAA
875495 ATATA
1 ATATA
875500 ATTTTTAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (21 bp):
ATATATTAGTTGAATGAAAAA
Found at i:875504 original size:21 final size:21
Alignment explanation
Indices: 875466--875505 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
875456 TATTAGTTGA
*
875466 ATGAAAAAATATATTTTTTGG
1 ATGAAAAAATATAATTTTTGG
*
875487 ATGAAATAATATAATTTTT
1 ATGAAAAAATATAATTTTT
875506 AATAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.10, T:0.45
Consensus pattern (21 bp):
ATGAAAAAATATAATTTTTGG
Found at i:879650 original size:11 final size:11
Alignment explanation
Indices: 879636--879695 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
879626 TGGACCGAGT
879636 GTGGGGTGGGG
1 GTGGGGTGGGG
*
879647 GTGGGGTGGGT
1 GTGGGGTGGGG
*
879658 GT-GGGT-TGG
1 GTGGGGTGGGG
**
879667 GTGTTGTGGGG
1 GTGGGGTGGGG
*
879678 TGTGGGGGGGGG
1 -GTGGGGTGGGG
879690 GTGGGG
1 GTGGGG
879696 GTTTTTGTTG
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
9 3 0.08
10 6 0.16
11 20 0.54
12 8 0.22
ACGTcount: A:0.00, C:0.00, G:0.75, T:0.25
Consensus pattern (11 bp):
GTGGGGTGGGG
Found at i:880148 original size:18 final size:19
Alignment explanation
Indices: 880125--880169 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
880115 GGGTTGTGTA
* *
880125 GTGGGGTTGTGGTG-GGGG
1 GTGGGGTGGGGGTGTGGGG
880143 GTGGGGTGGGGGTGTGGGG
1 GTGGGGTGGGGGTGTGGGG
*
880162 GGGGGGTG
1 GTGGGGTG
880170 TCCCCACCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.00, C:0.00, G:0.78, T:0.22
Consensus pattern (19 bp):
GTGGGGTGGGGGTGTGGGG
Found at i:880151 original size:23 final size:23
Alignment explanation
Indices: 880090--880166 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
880080 GTGGGAGGTG
880090 GGGGGGTTGGGGGTGGGGGTTGT-GT
1 GGGGGG-T-GGGGT-GGGGTTGTGGT
** **
880115 GGGTTGTGTAGTGGGGTTGTGGT
1 GGGGGGTGGGGTGGGGTTGTGGT
* *
880138 GGGGGGTGGGGTGGGGGTGTGGG
1 GGGGGGTGGGGTGGGGTTGTGGT
880161 GGGGGG
1 GGGGGG
880167 GTGTCCCCAC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
22 8 0.20
23 28 0.68
24 1 0.02
25 4 0.10
ACGTcount: A:0.01, C:0.00, G:0.73, T:0.26
Consensus pattern (23 bp):
GGGGGGTGGGGTGGGGTTGTGGT
Found at i:880166 original size:13 final size:13
Alignment explanation
Indices: 880138--880170 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
880128 GGGTTGTGGT
*
880138 GGGGG-GTGGGGT
1 GGGGGTGTGGGGG
880150 GGGGGTGTGGGGG
1 GGGGGTGTGGGGG
880163 GGGGGTGT
1 GGGGGTGT
880171 CCCCACCCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.00, C:0.00, G:0.82, T:0.18
Consensus pattern (13 bp):
GGGGGTGTGGGGG
Found at i:880257 original size:26 final size:28
Alignment explanation
Indices: 880219--880273 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
880209 CACAAACACA
*
880219 CCCCACAACCCCCCCACCCCCCCCCCCC
1 CCCCACAACCCCCCCACCACCCCCCCCC
880247 CCCCAC-A-CCCCCCACCACCCCCCCCC
1 CCCCACAACCCCCCCACCACCCCCCCCC
880273 C
1 C
880274 ACACCACCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 19 0.73
27 1 0.04
28 6 0.23
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (28 bp):
CCCCACAACCCCCCCACCACCCCCCCCC
Found at i:880259 original size:28 final size:29
Alignment explanation
Indices: 880219--880273 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
880209 CACAAACACA
880219 CCCCACAACCCCC-CCACCCCCCCCCCCC
1 CCCCACAACCCCCACCACCCCCCCCCCCC
*
880247 CCCCACACCCCCCACCACCCCCCCCCC
1 CCCCACAACCCCCACCACCCCCCCCCC
880274 ACACCACCAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (29 bp):
CCCCACAACCCCCACCACCCCCCCCCCCC
Found at i:880281 original size:26 final size:26
Alignment explanation
Indices: 880219--880291 Score: 80
Period size: 26 Copynumber: 2.9 Consensus size: 26
880209 CACAAACACA
*
880219 CCCCACAAC-CCCCCCACC-CCCCCC
1 CCCCACACCACCCCCCACCACCCCCC
* *
880243 CCCCCCCCACACCCCCCACCACCCCCC
1 CCCCACAC-CACCCCCCACCACCCCCC
*
880270 CCCCACACCACCACCCA-CACCC
1 CCCCACACCACCCCCCACCACCC
880292 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
24 5 0.12
25 6 0.15
26 17 0.43
27 12 0.30
ACGTcount: A:0.19, C:0.81, G:0.00, T:0.00
Consensus pattern (26 bp):
CCCCACACCACCCCCCACCACCCCCC
Found at i:880284 original size:29 final size:26
Alignment explanation
Indices: 880219--880285 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
880209 CACAAACACA
*
880219 CCCCACAAC-CCCCCCACCCCCCCCC
1 CCCCACCACACCCCCCACCCCCCCCC
*
880244 CCCCCCCACACCCCCCACCACCCCCCC
1 CCCCACCACACCCCCCACC-CCCCCCC
880271 CCCACACCACCACCC
1 CCC-CACCA-CACCC
880286 ACACCCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.20
26 9 0.26
27 10 0.29
28 4 0.11
29 5 0.14
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (26 bp):
CCCCACCACACCCCCCACCCCCCCCC
Found at i:880287 original size:23 final size:22
Alignment explanation
Indices: 880232--880287 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
880222 CACAACCCCC
*
880232 CCACCCCCCCCCCCCCCCCACA
1 CCACCCCCACCCCCCCCCCACA
*
880254 CCCCCCACCACCCCCCCCCCACA
1 CCACCC-CCACCCCCCCCCCACA
880277 CCACCACCCAC
1 CCACC-CCCAC
880288 ACCCAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.17
23 23 0.79
24 1 0.03
ACGTcount: A:0.18, C:0.82, G:0.00, T:0.00
Consensus pattern (22 bp):
CCACCCCCACCCCCCCCCCACA
Found at i:880290 original size:28 final size:28
Alignment explanation
Indices: 880228--880290 Score: 69
Period size: 28 Copynumber: 2.3 Consensus size: 28
880218 ACCCCACAAC
* *
880228 CCCCCCACC-CCCCCCCCCC-CCCCACA
1 CCCCACACCACCCCCCCCCCACACCACA
*
880254 CCCCCCACCACCCCCCCCCCACACCAC-
1 CCCCACACCACCCCCCCCCCACACCACA
880281 CACCCACACC
1 C-CCCACACC
880291 CAAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 9 0.28
27 11 0.34
28 12 0.38
ACGTcount: A:0.17, C:0.83, G:0.00, T:0.00
Consensus pattern (28 bp):
CCCCACACCACCCCCCCCCCACACCACA
Found at i:880335 original size:10 final size:9
Alignment explanation
Indices: 880326--880420 Score: 57
Period size: 8 Copynumber: 11.6 Consensus size: 9
880316 CCCCCCCCCA
880326 ACCCCACCC
1 ACCCCACCC
*
880335 ACCCCA-AC
1 ACCCCACCC
880343 ACCCC-CCC
1 ACCCCACCC
*
880351 ACACC-CCC
1 ACCCCACCC
*
880359 AACCC-CCC
1 ACCCCACCC
*
880367 ACCCCCCCCC
1 A-CCCCACCC
880377 ACCCC-CCC
1 ACCCCACCC
*
880385 ACCCAACCC
1 ACCCCACCC
880394 -CCCC-CCC
1 ACCCCACCC
880401 -CCCC-CCC
1 ACCCCACCC
*
880408 -CCGCACCC
1 ACCCCACCC
880416 ACCCC
1 ACCCC
880421 CCCCCACCGT
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
7 13 0.19
8 34 0.49
9 19 0.27
10 4 0.06
ACGTcount: A:0.18, C:0.81, G:0.01, T:0.00
Consensus pattern (9 bp):
ACCCCACCC
Found at i:880346 original size:17 final size:17
Alignment explanation
Indices: 880326--880388 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 17
880316 CCCCCCCCCA
880326 ACCCCACCCACCCCAAC
1 ACCCCACCCACCCCAAC
*
880343 ACCCCCCCACACCCCCAAC
1 ACCCCACC-CA-CCCCAAC
* *
880362 CCCCCACCC-CCCC-CC
1 ACCCCACCCACCCCAAC
880377 ACCCC-CCCACCC
1 ACCCCACCCACCC
880389 AACCCCCCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
14 3 0.08
15 8 0.21
16 4 0.11
17 7 0.18
18 3 0.08
19 13 0.34
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (17 bp):
ACCCCACCCACCCCAAC
Found at i:880348 original size:18 final size:17
Alignment explanation
Indices: 880327--880420 Score: 71
Period size: 15 Copynumber: 5.8 Consensus size: 17
880317 CCCCCCCCAA
880327 CCCCACCCACCCCAACAC
1 CCCCACCCACCCCAAC-C
880345 CCCC-CCACACCCCCAACC
1 CCCCACC-CA-CCCCAACC
880363 CCCCACCC-CCCC--CC
1 CCCCACCCACCCCAACC
880377 ACCCC-CCCA-CCCAACC
1 -CCCCACCCACCCCAACC
*
880393 CCCC-CCC-CCCC-CCC
1 CCCCACCCACCCCAACC
880407 CCCGCACCCACCCC
1 CCC-CACCCACCCC
880421 CCCCCACCGT
Statistics
Matches: 64, Mismatches: 1, Indels: 23
0.73 0.01 0.26
Matches are distributed among these distances:
14 13 0.20
15 15 0.23
16 9 0.14
17 6 0.09
18 12 0.19
19 9 0.14
ACGTcount: A:0.17, C:0.82, G:0.01, T:0.00
Consensus pattern (17 bp):
CCCCACCCACCCCAACC
Found at i:880358 original size:34 final size:33
Alignment explanation
Indices: 880320--880386 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
880310 AAGAAACCCC
880320 CCCCCAA-CCCCACCCACCCCAACACCCCCCCACA
1 CCCCCAACCCCCACCC-CCCC-ACACCCCCCCACA
*
880354 CCCCCAACCCCCCACCCCCCCCCACCCCCCCAC
1 CCCCCAA-CCCCCACCCCCCCACACCCCCCCAC
880387 CCAACCCCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 18 0.60
35 4 0.13
36 8 0.27
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (33 bp):
CCCCCAACCCCCACCCCCCCACACCCCCCCACA
Found at i:880365 original size:1 final size:1
Alignment explanation
Indices: 880361--880425 Score: 58
Period size: 1 Copynumber: 65.0 Consensus size: 1
880351 ACACCCCCAA
* * * ** * * *
880361 CCCCCCACCCCCCCCCACCCCCCCACCCAACCCCCCCCCCCCCCCCCCCGCACCCACCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
880426 ACCGTTTTTT
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.11, C:0.88, G:0.02, T:0.00
Consensus pattern (1 bp):
C
Found at i:880407 original size:49 final size:51
Alignment explanation
Indices: 880315--880428 Score: 146
Period size: 49 Copynumber: 2.3 Consensus size: 51
880305 GAAGGAAGAA
880315 ACCCCCCCCCAACCCCACCCACCCCAACACCCCCCCACACCCCCAACC-C-CCC
1 ACCCCCCCCC-ACCCCACCCACCCCAACACCCCCCCACACCCCC--CCGCACCC
* * *
880367 ACCCCCCCCCACCCC-CCCA-CCCAACCCCCCCCCCCCCCCCCCCGCACCC
1 ACCCCCCCCCACCCCACCCACCCCAACACCCCCCCACACCCCCCCGCACCC
880416 ACCCCCCCCCACC
1 ACCCCCCCCCACC
880429 GTTTTTTTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
47 2 0.04
48 1 0.02
49 35 0.61
50 4 0.07
51 5 0.09
52 10 0.18
ACGTcount: A:0.18, C:0.82, G:0.01, T:0.00
Consensus pattern (51 bp):
ACCCCCCCCCACCCCACCCACCCCAACACCCCCCCACACCCCCCCGCACCC
Found at i:880424 original size:26 final size:25
Alignment explanation
Indices: 880316--880425 Score: 105
Period size: 26 Copynumber: 4.2 Consensus size: 25
880306 AAGGAAGAAA
**
880316 CCCCCCCCCAACCCCACCCACCCCAAC
1 CCCCCCCCCCCCCCCACCCACCCC--C
* *
880343 ACCCCCCCACACCCCCAACCC-CCCACC
1 -CCCCCCC-CCCCCCCCACCCACCC-CC
*
880370 CCCCCCCACCCCCCCACCCAACCCCC
1 CCCCCCCCCCCCCCCACCC-ACCCCC
880396 CCCCCCCCCCCCCCGCACCCACCCCC
1 CCCCCCCCCCCCCC-CACCCACCCCC
880422 CCCC
1 CCCC
880426 ACCGTTTTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
25 9 0.13
26 32 0.46
27 9 0.13
28 10 0.14
29 9 0.13
ACGTcount: A:0.16, C:0.83, G:0.01, T:0.00
Consensus pattern (25 bp):
CCCCCCCCCCCCCCCACCCACCCCC
Found at i:880462 original size:24 final size:25
Alignment explanation
Indices: 880431--880541 Score: 100
Period size: 24 Copynumber: 4.3 Consensus size: 25
880421 CCCCCACCGT
880431 TTTTTTTTGTGTGTTTGG-TGTGTG
1 TTTTTTTTGTGTGTTTGGTTGTGTG
* *
880455 TTTTTTTTTTGTGTTTGGTTTTG-G
1 TTTTTTTTGTGTGTTTGGTTGTGTG
* * * *
880479 TTTTTTTTTTGGGTGTCGTTGTGTG
1 TTTTTTTTGTGTGTTTGGTTGTGTG
880504 TTTTTTTTGTTGTGGTGTTTGTGTTGTGTTG
1 --TTTTTT-TTGT-GTGTTTG-GTTGTG-TG
880535 TTTTTTT
1 TTTTTTT
880542 GGGGTTGGTT
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
24 37 0.54
25 4 0.06
27 6 0.09
28 4 0.06
29 10 0.14
30 6 0.09
31 2 0.03
ACGTcount: A:0.00, C:0.01, G:0.29, T:0.70
Consensus pattern (25 bp):
TTTTTTTTGTGTGTTTGGTTGTGTG
Found at i:880734 original size:42 final size:43
Alignment explanation
Indices: 880682--880768 Score: 117
Period size: 42 Copynumber: 2.0 Consensus size: 43
880672 TTGAGTGGGT
* *
880682 GTTGTTTGGGGTTGGTTGG-GTAGGTTGGGGTT-GT-GGGGTGTG
1 GTTGTGTGGGGGTGGTTGGTG-AGG-TGGGGTTAGTGGGGGTGTG
880724 GTTGTGTGGGGGTGGTTGGTGAGGTGGGGTTAGTGGGGGTGTG
1 GTTGTGTGGGGGTGGTTGGTGAGGTGGGGTTAGTGGGGGTGTG
880767 GT
1 GT
880769 GGGATGGTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
41 7 0.17
42 22 0.55
43 11 0.28
ACGTcount: A:0.03, C:0.00, G:0.60, T:0.37
Consensus pattern (43 bp):
GTTGTGTGGGGGTGGTTGGTGAGGTGGGGTTAGTGGGGGTGTG
Found at i:880740 original size:14 final size:15
Alignment explanation
Indices: 880713--880768 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
880703 AGGTTGGGGT
880713 TGTGGGGTGTGGTTG
1 TGTGGGGTGTGGTTG
880728 TGTGGGG-GTGGTTG
1 TGTGGGGTGTGGTTG
* *
880742 -GTGAGGTGGGGTTAG
1 TGTGGGGTGTGGTT-G
880757 TG-GGGGTGTGGT
1 TGTGGGGTGTGGT
880769 GGGATGGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 5 0.15
14 12 0.35
15 16 0.47
16 1 0.03
ACGTcount: A:0.04, C:0.00, G:0.62, T:0.34
Consensus pattern (15 bp):
TGTGGGGTGTGGTTG
Found at i:880749 original size:28 final size:26
Alignment explanation
Indices: 880710--880764 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
880700 GGTAGGTTGG
* * *
880710 GGTTGTGGGGTGTGGTTGTGTGGGGGT
1 GGTTGTGAGGTGGGGTT-AGTGGGGGT
880737 GGTTGGTGAGGTGGGGTTAGTGGGGGT
1 GGTT-GTGAGGTGGGGTTAGTGGGGGT
880764 G
1 G
880765 TGGTGGGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.04, C:0.00, G:0.64, T:0.33
Consensus pattern (26 bp):
GGTTGTGAGGTGGGGTTAGTGGGGGT
Found at i:880870 original size:17 final size:18
Alignment explanation
Indices: 880833--880871 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
880823 TGGTTTTTTT
*
880833 GTGGGGGGTGTGTGGCTG
1 GTGGGGGGTGTGTGGCGG
*
880851 GTGGGGGGTGT-TGTCGG
1 GTGGGGGGTGTGTGGCGG
880868 GTGG
1 GTGG
880872 TTTGGGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.00, C:0.05, G:0.67, T:0.28
Consensus pattern (18 bp):
GTGGGGGGTGTGTGGCGG
Found at i:882525 original size:24 final size:26
Alignment explanation
Indices: 882479--882530 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
882469 ATTAATATTT
*
882479 ATATATTTTATTATTAAATTTAAATAA
1 ATATATATTATTATTAAATTTAAA-AA
882506 ATATATATTATT-TT-AA-TTAAAAA
1 ATATATATTATTATTAAATTTAAAAA
882529 AT
1 AT
882531 TGTTCTTGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
23 4 0.17
24 5 0.21
25 2 0.08
26 2 0.08
27 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
ATATATATTATTATTAAATTTAAAAA
Found at i:883125 original size:22 final size:23
Alignment explanation
Indices: 883073--883130 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
883063 ATATAATACG
*
883073 ATATAATTTAAATATAATTTTTAA
1 ATAT-ATTTAAATATAATTATTAA
*
883097 ATTTATTT-AATATACATTATTAA
1 ATATATTTAAATATA-ATTATTAA
*
883120 A-ATATTAAAAT
1 ATATATTTAAAT
883131 TTATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
22 10 0.36
23 15 0.54
24 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATATATTTAAATATAATTATTAA
Found at i:883399 original size:11 final size:12
Alignment explanation
Indices: 883371--883413 Score: 63
Period size: 11 Copynumber: 3.8 Consensus size: 12
883361 TGATATAATT
883371 ATATAATATAAA
1 ATATAATATAAA
*
883383 AAATAAT-TAAA
1 ATATAATATAAA
883394 ATATAATATAAA
1 ATATAATATAAA
883406 A-ATAATAT
1 ATATAATAT
883414 TTTATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 17 0.61
12 11 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
ATATAATATAAA
Found at i:883422 original size:18 final size:20
Alignment explanation
Indices: 883399--883437 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
883389 TTAAAATATA
883399 ATATAAA-A-ATAATATTTT
1 ATATAAATATATAATATTTT
883417 ATATAAATATATAATATTTT
1 ATATAAATATATAATATTTT
883437 A
1 A
883438 AATATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 1 0.05
20 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATAAATATATAATATTTT
Found at i:883452 original size:20 final size:20
Alignment explanation
Indices: 883398--883453 Score: 62
Period size: 20 Copynumber: 2.8 Consensus size: 20
883388 ATTAAAATAT
883398 AATATAA-AAATAATATTTTA
1 AATATAATAAA-AATATTTTA
* *
883418 TATA-AATATATAATATTTTA
1 AATATAATA-AAAATATTTTA
883438 AATATAATAAAAATAT
1 AATATAATAAAAATAT
883454 ATAAATTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 2 0.07
20 22 0.76
21 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATAATAAAAATATTTTA
Found at i:884413 original size:16 final size:15
Alignment explanation
Indices: 884392--884439 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
884382 AATTTTTAAA
884392 AAAATTTATAAATATT
1 AAAATTT-TAAATATT
*
884408 AAAA-TTTAAATTTT
1 AAAATTTTAAATATT
*
884422 AAATTTTTTAAATATT
1 AAA-ATTTTAAATATT
884438 AA
1 AA
884440 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 10 0.37
15 2 0.07
16 15 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAATTTTAAATATT
Found at i:884785 original size:26 final size:27
Alignment explanation
Indices: 884730--884804 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 27
884720 TTTAAATATG
* *
884730 AATTAAAATTTTTTAATATTAATTAAA
1 AATTAAAATATTTTAATATAAATTAAA
*
884757 AATTAAAA-ATTTTAAT-TAAATTTATA
1 AATTAAAATATTTTAATATAAA-TTAAA
*
884783 AATTAAATTAAATTTTAATATA
1 AATTAAA--ATATTTTAATATA
884805 TTTAAATTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.08
26 18 0.45
27 8 0.20
28 1 0.03
29 8 0.20
30 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (27 bp):
AATTAAAATATTTTAATATAAATTAAA
Found at i:884811 original size:21 final size:19
Alignment explanation
Indices: 884759--884891 Score: 99
Period size: 21 Copynumber: 6.6 Consensus size: 19
884749 TAATTAAAAA
* *
884759 TTAAAAATTTTAATTAAAT
1 TTAATAATTTAAATTAAAT
*
884778 TT-ATAAATTAAATTAAATT
1 TTAATAATTTAAATTAAA-T
884797 TTAATATATTTAAATTTAAAT
1 TTAATA-ATTTAAA-TTAAAT
*
884818 CACTT-ATAATTTAAATTTAAT
1 ---TTAATAATTTAAATTAAAT
* *
884839 TAAATAATAATTAAATTTAAT
1 TTAATAAT--TTAAATTAAAT
*
884860 TTAATTATTTTAAATTAAAT
1 TTAA-TAATTTAAATTAAAT
884880 TTAAATAATTTA
1 TT-AATAATTTA
884892 CGAATACATA
Statistics
Matches: 92, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
18 13 0.14
19 10 0.11
20 21 0.23
21 28 0.30
22 15 0.16
23 3 0.03
24 2 0.02
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAATAATTTAAATTAAAT
Found at i:884815 original size:6 final size:6
Alignment explanation
Indices: 884763--884885 Score: 50
Period size: 6 Copynumber: 20.7 Consensus size: 6
884753 TAAAAATTAA
* * * *
884763 AAATTT TAA-TT AAATTT ATAAATT AAA-TT AAATTT TAA--T ATATTT
1 AAATTT AAATTT AAATTT A-AATTT AAATTT AAATTT AAATTT AAATTT
*
884808 AAATTT AAATCACTT ATAATTT AAATTT -AA-TT AAA--T AATAATT AAATTT
1 AAATTT AAAT---TT A-AATTT AAATTT AAATTT AAATTT AA-ATTT AAATTT
884857 -AATTT AATTATTTT AAA-TT AAATTT AAAT
1 AAATTT AA--A-TTT AAATTT AAATTT AAAT
884886 AATTTACGAA
Statistics
Matches: 91, Mismatches: 8, Indels: 36
0.67 0.06 0.27
Matches are distributed among these distances:
4 7 0.08
5 24 0.26
6 36 0.40
7 12 0.13
8 1 0.01
9 8 0.09
10 3 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (6 bp):
AAATTT
Found at i:884841 original size:26 final size:23
Alignment explanation
Indices: 884781--884883 Score: 72
Period size: 22 Copynumber: 4.4 Consensus size: 23
884771 ATTAAATTTA
*
884781 TAAATTAAATTAAAT-TT-TAA-
1 TAAATTTAATTAAATATTATAAT
*
884801 TATATTTAAATTTAAATCACTTATAATT
1 TAAATTT-AA-TTAAAT-A-TTATAA-T
884829 TAAATTTAATTAAATA--ATAAT
1 TAAATTTAATTAAATATTATAAT
* *
884850 TAAATTTAATTTAATTATTTTAAAT
1 TAAATTTAA-TTAAATATTAT-AAT
884875 TAAATTTAA
1 TAAATTTAA
884884 ATAATTTACG
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
20 5 0.08
21 12 0.18
22 16 0.24
24 1 0.02
25 15 0.23
26 9 0.14
27 2 0.03
28 6 0.09
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATTTAATTAAATATTATAAT
Found at i:885463 original size:35 final size:36
Alignment explanation
Indices: 885401--885468 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 36
885391 TTAAAAATAT
* * *
885401 TTTATATTTATATAAATTTTGATATATTAATATTTA
1 TTTATATTTAAATAAATTTTAAAATATTAATATTTA
*
885437 TTTATA-TTAAATAAATTTTAAAATATTTATAT
1 TTTATATTTAAATAAATTTTAAAATATTAATAT
885469 ATTCATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 22 0.79
36 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (36 bp):
TTTATATTTAAATAAATTTTAAAATATTAATATTTA
Found at i:885762 original size:18 final size:18
Alignment explanation
Indices: 885708--885762 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
885698 ATATAAAAAT
*
885708 ATATCAAAATTTATATTA
1 ATATCAAAATTTATATAA
*
885726 ACAT--AAA-TTAT-TAA
1 ATATCAAAATTTATATAA
885740 TATATCAAAATTTATATAA
1 -ATATCAAAATTTATATAA
885759 ATAT
1 ATAT
885763 ATATTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
14 2 0.07
15 7 0.24
16 3 0.10
17 3 0.10
18 11 0.38
19 3 0.10
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
ATATCAAAATTTATATAA
Found at i:885765 original size:10 final size:10
Alignment explanation
Indices: 885671--885766 Score: 51
Period size: 10 Copynumber: 9.6 Consensus size: 10
885661 ATTAGAGATA
885671 ATATA-AAAT
1 ATATATAAAT
885680 A-ATATAAAT
1 ATATATAAAT
*
885689 ATGATATTAAT
1 AT-ATATAAAT
885700 ATA-A-AAAT
1 ATATATAAAT
885708 ATATCA-AAAT
1 ATAT-ATAAAT
*
885718 TTATATTAACAT
1 ATATA-TAA-AT
* *
885730 AAATTATTAAT
1 ATA-TATAAAT
885741 ATATCA-AAAT
1 ATAT-ATAAAT
*
885751 TTATATAAAT
1 ATATATAAAT
885761 ATATAT
1 ATATAT
885767 TTTAAACATA
Statistics
Matches: 66, Mismatches: 10, Indels: 21
0.68 0.10 0.22
Matches are distributed among these distances:
8 9 0.14
9 9 0.14
10 25 0.38
11 16 0.24
12 5 0.08
13 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (10 bp):
ATATATAAAT
Found at i:886014 original size:20 final size:20
Alignment explanation
Indices: 885991--886032 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
885981 TTATTTAAAT
885991 ATAAATAATATAAA-TATTAA
1 ATAAAT-ATATAAATTATTAA
886011 ATAAATATATAAATTATTAA
1 ATAAATATATAAATTATTAA
886031 AT
1 AT
886033 TAATTTTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAATATATAAATTATTAA
Found at i:890415 original size:15 final size:16
Alignment explanation
Indices: 890395--890440 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
890385 TTTATGCAAA
890395 TATAAATTTTAAAAT-
1 TATAAATTTTAAAATC
*
890410 TATAAATATTTAATATC
1 TATAAAT-TTTAAAATC
*
890427 TA-AAATTTTTAAAT
1 TATAAATTTTAAAAT
890441 ATCAAATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.50
16 11 0.42
17 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
TATAAATTTTAAAATC
Found at i:890433 original size:31 final size:31
Alignment explanation
Indices: 890398--890482 Score: 86
Period size: 31 Copynumber: 2.7 Consensus size: 31
890388 ATGCAAATAT
* *
890398 AAATTTTAAAATTATAAAT-ATTTAATATCTA
1 AAATTTTAAAATTATAAATAAATAAAT-TCTA
* *
890429 AAATTTTTAAA-TATCAAATAAATAAATTTTA
1 AAATTTTAAAATTAT-AAATAAATAAATTCTA
890460 AAATTTTAAAA-TATATAATAAAT
1 AAATTTTAAAATTATA-AATAAAT
890483 TATTAATTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
30 4 0.09
31 37 0.80
32 5 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (31 bp):
AAATTTTAAAATTATAAATAAATAAATTCTA
Found at i:893775 original size:18 final size:18
Alignment explanation
Indices: 893729--893804 Score: 56
Period size: 17 Copynumber: 4.4 Consensus size: 18
893719 AAAAATATAA
* *
893729 TATAAAATATGATGTAAATA
1 TATATAATATG-T-TAAATT
893749 TAT-TAATATGTTAAATT
1 TATATAATATGTTAAATT
893766 TATATAATA---TAAA-T
1 TATATAATATGTTAAATT
*
893780 TAT-TAATATTTTAAAATT
1 TATATAATATGTT-AAATT
893798 TATATAA
1 TATATAA
893805 ATATATAATA
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
13 5 0.11
14 4 0.09
15 4 0.09
16 1 0.02
17 11 0.23
18 10 0.21
19 9 0.19
20 3 0.06
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (18 bp):
TATATAATATGTTAAATT
Found at i:893784 original size:31 final size:34
Alignment explanation
Indices: 893743--893820 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 34
893733 AAATATGATG
893743 TAAATATATTAATATGTT-AAATTTATAT-AATA
1 TAAATATATTAATATGTTAAAATTTATATAAATA
*
893775 TAAAT-TATTAATATTTTAAAATTTATATAAATA
1 TAAATATATTAATATGTTAAAATTTATATAAATA
*
893808 TATAATATTTTAA
1 TA-AATATATTAA
893821 ATATAATTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 11 0.28
32 15 0.38
33 6 0.15
34 3 0.08
35 5 0.12
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
TAAATATATTAATATGTTAAAATTTATATAAATA
Found at i:893836 original size:33 final size:34
Alignment explanation
Indices: 893743--893848 Score: 106
Period size: 27 Copynumber: 3.4 Consensus size: 34
893733 AAATATGATG
* *
893743 TAAATATATTAATATGTTAAAT-TTA-TATAATA
1 TAAATATATTAATATTTTAAATATAATTATAATA
893775 TAAAT-TATTAATATTTT--A-A-AATT-T-ATA
1 TAAATATATTAATATTTTAAATATAATTATAATA
893802 TAAATATA-TAATATTTTAAATATAATTATAATA
1 TAAATATATTAATATTTTAAATATAATTATAATA
* *
893835 TAAAAATATAAATA
1 TAAATATATTAATA
893849 CAATATATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
27 17 0.28
28 4 0.07
29 3 0.05
30 1 0.02
31 15 0.25
32 6 0.10
33 10 0.17
34 4 0.07
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (34 bp):
TAAATATATTAATATTTTAAATATAATTATAATA
Found at i:893863 original size:19 final size:19
Alignment explanation
Indices: 893819--893855 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
893809 ATAATATTTT
* *
893819 AAATATAATTATAATATAA
1 AAATATAAATACAATATAA
893838 AAATATAAATACAATATA
1 AAATATAAATACAATATA
893856 TATATATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATATAAATACAATATAA
Found at i:896856 original size:122 final size:124
Alignment explanation
Indices: 896609--896860 Score: 312
Period size: 131 Copynumber: 2.0 Consensus size: 124
896599 TTAATAATTC
** **
896609 ATTTCTATTGTTTAATGTTTATTTATTTATTTTTAGTTTTTCTTCTCTTAGTCTGCTATTTATGC
1 ATTTCTATTGTTTAATGTTTATTTATTTATTTTTAG-TTTTCTTCTCTTAAACTGCTATTTACAC
* *
896674 TATTATTGCTTGTATGCTTGGCTTTTAAATTTAATTTTGATTTTACAACTTACAATGGTAATTTT
65 TATTATTGCTTGTATGCTTAGC-------TTTAATTTTGATTTTACAACTTACAAAGGTAATTTT
896739 GT
123 GT
896741 ATTTCTATTGTTTAATGTTTATTTATTTATTTTTAG-TTTCATTCTCTTAAACTGCTATTTACAC
1 ATTTCTATTGTTTAATGTTTATTTATTTATTTTTAGTTTTC-TTCTCTTAAACTGCTATTTACAC
* ** *
896805 TATTATTGCTTGTATGCTTAGC-TTAA-TTTGGTTTTACGTCTTAGAAAGGTAATTTT
65 TATTATTGCTTGTATGCTTAGCTTTAATTTTGATTTTACAACTTACAAAGGTAATTTT
896861 TTCATGTTTA
Statistics
Matches: 109, Mismatches: 10, Indels: 12
0.83 0.08 0.09
Matches are distributed among these distances:
122 25 0.23
123 4 0.04
130 4 0.04
131 40 0.37
132 36 0.33
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (124 bp):
ATTTCTATTGTTTAATGTTTATTTATTTATTTTTAGTTTTCTTCTCTTAAACTGCTATTTACACT
ATTATTGCTTGTATGCTTAGCTTTAATTTTGATTTTACAACTTACAAAGGTAATTTTGT
Found at i:897543 original size:50 final size:50
Alignment explanation
Indices: 897484--897585 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 50
897474 CATCCTTGAT
*
897484 TTCATTTTCCTCCAACAACTGATTTTTGTTACTTATCAGTGTTTGCCAAG
1 TTCATTTTCCCCCAACAACTGATTTTTGTTACTTATCAGTGTTTGCCAAG
897534 TTCATTTTCCCCCAACAACTGATTTTTGTTACTTATCAGTGTTTGCCAAG
1 TTCATTTTCCCCCAACAACTGATTTTTGTTACTTATCAGTGTTTGCCAAG
897584 TT
1 TT
897586 TAAACTTATC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.22, C:0.23, G:0.12, T:0.44
Consensus pattern (50 bp):
TTCATTTTCCCCCAACAACTGATTTTTGTTACTTATCAGTGTTTGCCAAG
Found at i:901545 original size:7 final size:7
Alignment explanation
Indices: 901533--901559 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
901523 ATAATTTTAA
901533 AATATAT
1 AATATAT
901540 AATATAT
1 AATATAT
901547 AATATAT
1 AATATAT
901554 AATATA
1 AATATA
901560 CAATTATTTT
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:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:901590 original size:26 final size:24
Alignment explanation
Indices: 901548--901598 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 24
901538 ATAATATATA
901548 ATATATAATATACAA-TTATTTTT
1 ATATATAATATACAATTTATTTTT
901571 ATATAATAATATAACTAATTTATTTTT
1 ATAT-ATAATAT-AC-AATTTATTTTT
901598 A
1 A
901599 AAATCTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 4 0.17
24 7 0.29
25 2 0.08
26 2 0.08
27 9 0.38
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
ATATATAATATACAATTTATTTTT
Found at i:902248 original size:3 final size:3
Alignment explanation
Indices: 902240--902272 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
902230 AATTTCTTTT
902240 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
902273 AGTGTAAGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:903359 original size:42 final size:41
Alignment explanation
Indices: 903259--903368 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 41
903249 TATTATAAAA
* *
903259 AATAAAATAAAATTTAATTATAATAATTATAATTTTTTACTT
1 AATAAAATTAAATTAAATT-TAATAATTATAATTTTTTACTT
*
903301 TAT-AAATTAAAAATTAAATTTAATATATT-TAA-TTTTTACTT
1 AATAAAATT--AAATTAAATTTAATA-ATTATAATTTTTTACTT
903342 AAATTAAAATTAAATTAAATTTAATAA
1 -AA-TAAAATTAAATTAAATTTAATAA
903369 AAACCAAATC
Statistics
Matches: 58, Mismatches: 4, Indels: 13
0.77 0.05 0.17
Matches are distributed among these distances:
41 14 0.24
42 26 0.45
43 13 0.22
44 5 0.09
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (41 bp):
AATAAAATTAAATTAAATTTAATAATTATAATTTTTTACTT
Found at i:908112 original size:36 final size:33
Alignment explanation
Indices: 908042--908112 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 33
908032 TTATTTATAT
* *
908042 TTTTTTATTATCAATGTATAAAATAATTATATA
1 TTTTTTATTATCAATGTATAAAATAAATAAATA
* *
908075 TTTTTTATTATTAATTTAATTAAAATAAAATAAATA
1 TTTTTTATTATCAATGT-A-TAAAAT-AAATAAATA
908111 TT
1 TT
908113 ACGTAGTTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
33 15 0.48
34 1 0.03
35 6 0.19
36 9 0.29
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (33 bp):
TTTTTTATTATCAATGTATAAAATAAATAAATA
Found at i:909069 original size:3 final size:3
Alignment explanation
Indices: 909061--909091 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
909051 GTGCATTGCA
909061 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
909092 TAAGAGTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:912686 original size:21 final size:21
Alignment explanation
Indices: 912662--912702 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
912652 GAACAAAAGC
*
912662 ACCAAATCATGCACTAACATG
1 ACCAAATCATACACTAACATG
912683 ACCAAATCATACACTAACAT
1 ACCAAATCATACACTAACAT
912703 AAACACATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.46, C:0.29, G:0.05, T:0.20
Consensus pattern (21 bp):
ACCAAATCATACACTAACATG
Found at i:913146 original size:29 final size:29
Alignment explanation
Indices: 913114--913201 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 29
913104 TATGTAAAAA
913114 TTAAAAATTAAAAATTATTTTAATATAAT
1 TTAAAAATTAAAAATTATTTTAATATAAT
* ** *
913143 TTAAAAGTTAAATGTT-TATTTAATATTAT
1 TTAAAAATTAAAAATTAT-TTTAATATAAT
913172 TTAAAAATTAAAAAATTATTTTTAA-ATAAT
1 TTAAAAATT-AAAAATTA-TTTTAATATAAT
913202 AAAATATAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
28 1 0.02
29 31 0.66
30 9 0.19
31 5 0.11
32 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (29 bp):
TTAAAAATTAAAAATTATTTTAATATAAT
Found at i:916592 original size:50 final size:48
Alignment explanation
Indices: 916537--916645 Score: 155
Period size: 50 Copynumber: 2.2 Consensus size: 48
916527 AAATGGAAGG
* *
916537 AAGCAAGAAAGTGAGATAAGTAAGAGAAGAACCAGGATGAAAAAAGGAC
1 AAGCAAGAAAGAGAGATAAGTAAGAGAAGAACCAGGAAGAAAAAA-GAC
* *
916586 AGAGCAAGAGAGAGAGATAAGTAAGAGAAGAACCGGGAAGAAAAAAGAC
1 A-AGCAAGAAAGAGAGATAAGTAAGAGAAGAACCAGGAAGAAAAAAGAC
*
916635 AAGGAAGAAAG
1 AAGCAAGAAAG
916646 GCGCTGCTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
48 8 0.15
49 5 0.09
50 40 0.75
ACGTcount: A:0.56, C:0.07, G:0.31, T:0.06
Consensus pattern (48 bp):
AAGCAAGAAAGAGAGATAAGTAAGAGAAGAACCAGGAAGAAAAAAGAC
Found at i:918105 original size:2 final size:2
Alignment explanation
Indices: 918098--918126 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
918088 AACTTATCGA
918098 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
918127 TCACGAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:921886 original size:3 final size:3
Alignment explanation
Indices: 921878--921919 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
921868 TTAGTACCTA
921878 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
921920 GCGTACATCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:922240 original size:19 final size:19
Alignment explanation
Indices: 922192--922230 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
922182 ATCAAGTACC
922192 TTAAAATTT-TA--ATATA
1 TTAAAATTTATATTATATA
922208 TTAAAATTTATATTATATA
1 TTAAAATTTATATTATATA
922227 TTAA
1 TTAA
922231 TTATTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
19 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAAATTTATATTATATA
Found at i:925092 original size:3 final size:3
Alignment explanation
Indices: 925084--925125 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
925074 AATGTGGCAG
925084 TAT TAT TAT TAT TAT TAT T-T TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
925126 TGGATAAGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:925109 original size:20 final size:20
Alignment explanation
Indices: 925084--925122 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
925074 AATGTGGCAG
925084 TATTATTATTATTATTATTT
1 TATTATTATTATTATTATTT
925104 TATTATTATTATTATTATT
1 TATTATTATTATTATTATT
925123 ATTTGGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTATTATTATTATTATTT
Found at i:926654 original size:2 final size:2
Alignment explanation
Indices: 926647--926681 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
926637 ACAGGGACAC
926647 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
926682 AGGAGAAGGA
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:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:928573 original size:32 final size:28
Alignment explanation
Indices: 928518--928579 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 28
928508 TGAACTGACC
928518 ATAATATTTATTATTTATTTATTATATGA
1 ATAATATTTATTATTTATTTATTATA-GA
*
928547 ATAATATTTTTTATTATATTTATATTATAGA
1 ATAATATTTATTATT-TA-TT-TATTATAGA
928578 AT
1 AT
928580 TAAAATTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.48
30 2 0.07
31 6 0.21
32 7 0.24
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (28 bp):
ATAATATTTATTATTTATTTATTATAGA
Found at i:929823 original size:24 final size:25
Alignment explanation
Indices: 929780--929827 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
929770 TCAATTAATT
*
929780 TATTATTTTCATAAAGTAAAAAATA
1 TATTATTTTAATAAAGTAAAAAATA
*
929805 TATTA-TTTAATAAATTAAAAAAT
1 TATTATTTTAATAAAGTAAAAAAT
929828 TAAAAGCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (25 bp):
TATTATTTTAATAAAGTAAAAAATA
Found at i:931545 original size:17 final size:18
Alignment explanation
Indices: 931517--931552 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
931507 TTACTAAAAT
*
931517 TATTTTTATAATAATTAA
1 TATTTTTATAATAAATAA
931535 TATTTTT-TAATAAATAA
1 TATTTTTATAATAAATAA
931552 T
1 T
931553 TAAAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TATTTTTATAATAAATAA
Found at i:932881 original size:17 final size:17
Alignment explanation
Indices: 932861--932893 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
932851 AACTGACTTG
932861 TTAATTT-TATAATTATT
1 TTAATTTAT-TAATTATT
932878 TTAATTTATTAATTAT
1 TTAATTTATTAATTAT
932894 CATTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTAATTTATTAATTATT
Found at i:933148 original size:25 final size:23
Alignment explanation
Indices: 933115--933185 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 23
933105 GAGTTTAGAA
*
933115 TAAAATATTTTAAATTTAAGTTAAT
1 TAAATTATTTT-AATTTAA-TTAAT
933140 TAAATTA--TT-ATTTAATTAAT
1 TAAATTATTTTAATTTAATTAAT
* * *
933160 AAAATTATTTTATTTTTATTTAAT
1 TAAATTATTTTA-ATTTAATTAAT
933184 TA
1 TA
933186 TAAATATGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 11 0.30
21 6 0.16
22 2 0.05
23 2 0.05
24 10 0.27
25 6 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (23 bp):
TAAATTATTTTAATTTAATTAAT
Found at i:933164 original size:20 final size:21
Alignment explanation
Indices: 933128--933168 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
933118 AATATTTTAA
*
933128 ATTTAAGTTAATTAAATTATT
1 ATTTAAGTTAATAAAATTATT
933149 ATTTAA-TTAATAAAATTATT
1 ATTTAAGTTAATAAAATTATT
933169 TTATTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTTAAGTTAATAAAATTATT
Found at i:933178 original size:28 final size:28
Alignment explanation
Indices: 933147--933206 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 28
933137 AATTAAATTA
*
933147 TTATTTAATTAATAAA-AT-TATTTTATTT
1 TTATTTAATT-ATAAATATGTA-ATTATTT
933175 TTATTTAATTATAAATATGTAATTATTT
1 TTATTTAATTATAAATATGTAATTATTT
933203 TTAT
1 TTAT
933207 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 5 0.17
28 22 0.76
29 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTATTTAATTATAAATATGTAATTATTT
Found at i:933439 original size:22 final size:22
Alignment explanation
Indices: 933382--933446 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
933372 AAATTGATTC
*
933382 ATATAATTAATTTAAAATAATTAA
1 ATATAATTAATTT-AAAT-ATCAA
* *
933406 ATTTAATAAATTTAAATATCAA
1 ATATAATTAATTTAAATATCAA
933428 ATATAATTAATTTAAATAT
1 ATATAATTAATTTAAATAT
933447 GATTAATTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
22 21 0.58
23 4 0.11
24 11 0.31
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATATAATTAATTTAAATATCAA
Found at i:933464 original size:22 final size:22
Alignment explanation
Indices: 933386--933480 Score: 71
Period size: 22 Copynumber: 4.5 Consensus size: 22
933376 TGATTCATAT
*
933386 AATTAATTTAAAATAATTAAATTT
1 AATTAATTT-AAAT-ATTAAATTA
* *
933410 AATAAATTTAAATATCAAA-T-
1 AATTAATTTAAATATTAAATTA
933430 -A-TAA-TT-AAT-TTAAATAT-
1 AATTAATTTAAATATTAAAT-TA
*
933447 GATTAATTTAAATATTAAATTA
1 AATTAATTTAAATATTAAATTA
933469 AATTAATTTAAA
1 AATTAATTTAAA
933481 CTTCATATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
15 4 0.07
16 3 0.05
17 3 0.05
18 3 0.05
19 4 0.07
20 2 0.03
21 5 0.09
22 22 0.38
23 4 0.07
24 8 0.14
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (22 bp):
AATTAATTTAAATATTAAATTA
Found at i:933519 original size:16 final size:15
Alignment explanation
Indices: 933384--933545 Score: 65
Period size: 15 Copynumber: 10.7 Consensus size: 15
933374 ATTGATTCAT
*
933384 ATAA-TTAATTTAAA
1 ATAATTTAAATTAAA
*
933398 ATAA-TTAAATT-TA
1 ATAATTTAAATTAAA
933411 ATAAATTTAAATATCAAA
1 AT-AATTTAAAT-T-AAA
*
933429 TATAA-TTAATTTAAA
1 -ATAATTTAAATTAAA
* *
933444 TATGA-TT-AATTTAA
1 -ATAATTTAAATTAAA
933458 AT-A-TTAAATTAAA
1 ATAATTTAAATTAAA
* * *
933471 TTAATTTAAACTTCAT
1 ATAATTTAAA-TTAAA
*
933487 ATAATTTAAAATAAAA
1 ATAATTT-AAATTAAA
933503 ATAATTTAAATGT-AA
1 ATAATTTAAAT-TAAA
933518 A-AATTTAAAAATTTAAA
1 ATAATTT--AAA-TTAAA
933535 ATAATATTAAA
1 ATAAT-TTAAA
933546 AACAATTTAA
Statistics
Matches: 114, Mismatches: 16, Indels: 33
0.70 0.10 0.20
Matches are distributed among these distances:
12 3 0.03
13 12 0.11
14 23 0.20
15 27 0.24
16 24 0.21
17 15 0.13
18 6 0.05
19 4 0.04
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (15 bp):
ATAATTTAAATTAAA
Found at i:934767 original size:10 final size:10
Alignment explanation
Indices: 934752--934776 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
934742 AATTGCATCA
934752 TTATTGTAAT
1 TTATTGTAAT
934762 TTATTGTAAT
1 TTATTGTAAT
934772 TTATT
1 TTATT
934777 AAAAGATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (10 bp):
TTATTGTAAT
Found at i:935656 original size:84 final size:84
Alignment explanation
Indices: 935496--935657 Score: 184
Period size: 84 Copynumber: 1.9 Consensus size: 84
935486 TTTAATTAAT
* * * * * *
935496 TTTTTATATTGTGTTTGTATCATATATCAATTCATCCATATTTTACATAATTTATCATCGTAATT
1 TTTTTATATTATATTTATATCATATATCAATTCATCCATAATTTAAATAATTTATCAACGTAATT
*
935561 TAATTTAGAAAAATTTATG
66 CAATTTAGAAAAATTTATG
* ** *
935580 TTTTTATATTATATTTATATCATATCTCAATTTGT-GATAATTTAAATAATTTATCAAAC-TAAT
1 TTTTTATATTATATTTATATCATATATCAATTCATCCATAATTTAAATAATTTATC-AACGTAAT
*
935643 TCGATTTAGGAAAAA
65 TCAATTTA-GAAAAA
935658 ACTGTGCTCT
Statistics
Matches: 64, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
83 27 0.42
84 37 0.58
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (84 bp):
TTTTTATATTATATTTATATCATATATCAATTCATCCATAATTTAAATAATTTATCAACGTAATT
CAATTTAGAAAAATTTATG
Found at i:935765 original size:32 final size:33
Alignment explanation
Indices: 935712--935774 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
935702 ATACTATAAA
*
935712 TTTATATAGATTTTTACATATTAATA-ATTTAT
1 TTTATATAGATTTTAACATATTAATATATTTAT
* *
935744 TTTATAT-GAATTTTAATATATTTATATATTT
1 TTTATATAG-ATTTTAACATATTAATATATTT
935775 TTATTATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
31 1 0.04
32 21 0.81
33 4 0.15
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.59
Consensus pattern (33 bp):
TTTATATAGATTTTAACATATTAATATATTTAT
Found at i:935786 original size:19 final size:19
Alignment explanation
Indices: 935740--935787 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
935730 TATTAATAAT
935740 TTATTTTATATGAATTTTA
1 TTATTTTATATGAATTTTA
* *
935759 ATATATTTATAT-ATTTTTA
1 TTAT-TTTATATGAATTTTA
935778 TTATCTTTAT
1 TTAT-TTTAT
935788 TCATTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTTTATATGAATTTTA
Found at i:935827 original size:20 final size:22
Alignment explanation
Indices: 935802--935841 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
935792 TTTTCATGTC
935802 ATGTTG-ATTTAA-TTATTTTT
1 ATGTTGTATTTAATTTATTTTT
935822 ATGTTGTATTTAATTTATTT
1 ATGTTGTATTTAATTTATTT
935842 AATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 6 0.33
22 6 0.33
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (22 bp):
ATGTTGTATTTAATTTATTTTT
Found at i:935860 original size:24 final size:21
Alignment explanation
Indices: 935831--935889 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 21
935821 TATGTTGTAT
935831 TTAATTTATTTAATATTTTTATAA
1 TTAATTTATTT--TATTTTTA-AA
*
935855 TTAATTAATTTTATTTTTAAA
1 TTAATTTATTTTATTTTTAAA
*
935876 TTATATTTTTTTTA
1 TTA-ATTTATTTTA
935890 AAGTTATTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 5 0.16
22 16 0.52
24 10 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTAATTTATTTTATTTTTAAA
Found at i:935867 original size:29 final size:30
Alignment explanation
Indices: 935808--935870 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 30
935798 TGTCATGTTG
** *
935808 ATTTAATTATTTTTATGTTGTATTTAATTT
1 ATTTAATTATTTTTATAATGTAATTAATTT
935838 ATTTAA-TATTTTTATAAT-TAATTAATTTT
1 ATTTAATTATTTTTATAATGTAATTAA-TTT
935867 ATTT
1 ATTT
935871 TTAAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 6 0.21
29 17 0.59
30 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (30 bp):
ATTTAATTATTTTTATAATGTAATTAATTT
Found at i:935889 original size:22 final size:22
Alignment explanation
Indices: 935810--935878 Score: 63
Period size: 21 Copynumber: 3.1 Consensus size: 22
935800 TCATGTTGAT
* *
935810 TTAATTATTTTTATGTTGTAT--
1 TTAATTAATTTTAT-TTTTATAA
*
935831 TTAATTTATTTAATATTTTTATAA
1 TTAATTAATTT--TATTTTTATAA
935855 TTAATTAATTTTATTTTTA-AA
1 TTAATTAATTTTATTTTTATAA
935876 TTA
1 TTA
935879 TATTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
21 14 0.35
22 13 0.32
23 3 0.08
24 10 0.25
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (22 bp):
TTAATTAATTTTATTTTTATAA
Found at i:936038 original size:2 final size:2
Alignment explanation
Indices: 936033--936072 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
936023 TTTAACATAA
936033 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
936073 GCATGCTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:940293 original size:21 final size:20
Alignment explanation
Indices: 940269--940353 Score: 58
Period size: 19 Copynumber: 4.3 Consensus size: 20
940259 TTGTTGATTC
940269 ATATATTTTTATAATATTTT-
1 ATATATTTTTATAA-ATTTTA
*
940289 -TATA-TTTTATTACAA-TATA
1 ATATATTTTTA-TA-AATTTTA
940308 AT-TATTTTTA-AAATTATT-
1 ATATATTTTTATAAATT-TTA
*
940326 TTATATTTTATATAAATTTTA
1 ATATATTTT-TATAAATTTTA
940347 ATATATT
1 ATATATT
940354 AATAATTTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 21
0.67 0.05 0.28
Matches are distributed among these distances:
17 2 0.04
18 10 0.20
19 16 0.32
20 11 0.22
21 11 0.22
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (20 bp):
ATATATTTTTATAAATTTTA
Found at i:940369 original size:32 final size:33
Alignment explanation
Indices: 940333--940404 Score: 110
Period size: 32 Copynumber: 2.2 Consensus size: 33
940323 ATTTTATATT
* *
940333 TTATATAAATTTTAATATATTAATA-ATTTATA
1 TTATATAAATTTTAAAATATTAATATATTTAAA
*
940365 TTATATAAATTTTAAAATATTTATATATTTAAA
1 TTATATAAATTTTAAAATATTAATATATTTAAA
940398 TTATATA
1 TTATATA
940405 TATTAATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
32 23 0.64
33 13 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TTATATAAATTTTAAAATATTAATATATTTAAA
Found at i:940397 original size:17 final size:17
Alignment explanation
Indices: 940366--940407 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
940356 TAATTTATAT
*
940366 TATATAAAT-TTTAAAA
1 TATATATATATTTAAAA
* *
940382 TATTTATATATTTAAAT
1 TATATATATATTTAAAA
940399 TATATATAT
1 TATATATAT
940408 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATTTAAAA
Found at i:942072 original size:25 final size:24
Alignment explanation
Indices: 942044--942098 Score: 85
Period size: 23 Copynumber: 2.3 Consensus size: 24
942034 TATTTTTACT
942044 TATATCATAATTTAAAACTATATAA
1 TATATCA-AATTTAAAACTATATAA
*
942069 TATATC-ACTTTAAAACTATATAA
1 TATATCAAATTTAAAACTATATAA
942092 TATATCA
1 TATATCA
942099 CTGATATTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 22 0.79
25 6 0.21
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (24 bp):
TATATCAAATTTAAAACTATATAA
Found at i:942099 original size:23 final size:23
Alignment explanation
Indices: 942054--942100 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
942044 TATATCATAA
942054 TTTAAAACTATATAATATATCAC
1 TTTAAAACTATATAATATATCAC
942077 TTTAAAACTATATAATATATCAC
1 TTTAAAACTATATAATATATCAC
942100 T
1 T
942101 GATATTAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTAAAACTATATAATATATCAC
Found at i:946671 original size:21 final size:21
Alignment explanation
Indices: 946636--946691 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
946626 ATCGATAAAG
*
946636 TAATTAAAATAAA-ATATAATT
1 TAATTAATATAAATATAT-ATT
946657 TAAATTAATATAAATATATATT
1 T-AATTAATATAAATATATATT
*
946679 TTATTAAT-TAAAT
1 TAATTAATATAAAT
946692 TTTTTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
20 5 0.16
21 7 0.23
22 15 0.48
23 4 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATTAATATAAATATATATT
Found at i:947599 original size:31 final size:33
Alignment explanation
Indices: 947533--947648 Score: 91
Period size: 31 Copynumber: 3.5 Consensus size: 33
947523 AACATAAAAA
* *
947533 ATAATAAATATATATAAATATATTAAAATTTAT
1 ATAATAAAAATATATAAATATATCAAAATTTAT
* *
947566 ATAATAAAAATA-AT-AATTTATCAAATTTTAT
1 ATAATAAAAATATATAAATATATCAAAATTTAT
*
947597 ATAA-ATATAAT-TAT-AATATAT-AAAATATATAAAT
1 ATAATA-AAAATATATAAATATATCAAAAT-T-T--AT
*
947631 ATAATATAAATATATAAA
1 ATAATAAAAATATATAAA
947649 GTATTAAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
30 5 0.08
31 31 0.48
32 3 0.05
33 11 0.17
34 9 0.14
35 4 0.06
36 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (33 bp):
ATAATAAAAATATATAAATATATCAAAATTTAT
Found at i:947606 original size:6 final size:6
Alignment explanation
Indices: 947595--947644 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
947585 ATCAAATTTT
*
947595 ATATAA ATATAA TTATAA TATATAA A-AT-- ATATAA ATAT-A ATATAA
1 ATATAA ATATAA ATATAA -ATATAA ATATAA ATATAA ATATAA ATATAA
947640 ATATA
1 ATATA
947645 TAAAGTATTA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
3 1 0.03
4 2 0.05
5 7 0.19
6 22 0.59
7 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:947614 original size:11 final size:11
Alignment explanation
Indices: 947595--947644 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
947585 ATCAAATTTT
947595 ATATAAATATAA
1 ATAT-AATATAA
*
947607 TTATAATATATA
1 ATATAATATA-A
*
947619 AAAT-ATATAA
1 ATATAATATAA
947629 ATATAATATAA
1 ATATAATATAA
947640 ATATA
1 ATATA
947645 TAAAGTATTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
10 4 0.12
11 22 0.69
12 6 0.19
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATATAA
Found at i:947625 original size:28 final size:27
Alignment explanation
Indices: 947519--947657 Score: 104
Period size: 28 Copynumber: 4.9 Consensus size: 27
947509 ATCAATTTAT
* *
947519 ATATAACATAAAAAATA-ATAAATAT-
1 ATATAATATATAAAATATATAAATATA
* *
947544 ATATAAATATATTAAAATTTATATAATAAAA
1 ATAT-AATATA-TAAAATATATA-AAT-ATA
* *
947575 ATAATAATTTATCAAATTTTATATAAATATA
1 AT-ATAATATAT-AAA--ATATATAAATATA
947606 ATTATAATATATAAAATATATAAATATA
1 A-TATAATATATAAAATATATAAATATA
*
947634 ATATAAATATATAAAGTAT-TAAAT
1 ATAT-AATATATAAAATATATAAAT
947658 TTATTAAATT
Statistics
Matches: 91, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
25 4 0.04
26 5 0.05
27 13 0.14
28 29 0.32
29 3 0.03
30 5 0.05
31 21 0.23
32 6 0.07
33 5 0.05
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (27 bp):
ATATAATATATAAAATATATAAATATA
Found at i:947645 original size:19 final size:18
Alignment explanation
Indices: 947533--947648 Score: 81
Period size: 19 Copynumber: 5.9 Consensus size: 18
947523 AACATAAAAA
947533 ATAATAAATATATATAAAT
1 ATAATAAA-ATATATAAAT
* *
947552 ATATTAAAATTTATATAAT
1 ATAATAAAATATATA-AAT
* *
947571 AAAAATAATAATTTATCAAAT
1 -ATAATAA-AATATAT-AAAT
* *
947592 TTTATATAAATATAATTATAAT
1 ATAATA-AAATAT-A-TA-AAT
947614 AT-ATAAAATATATAAAT
1 ATAATAAAATATATAAAT
947631 ATAATATAAATATATAAA
1 ATAATA-AAATATATAAA
947649 GTATTAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
17 5 0.06
18 11 0.14
19 22 0.28
20 18 0.23
21 16 0.21
22 6 0.08
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAAAATATATAAAT
Found at i:947863 original size:17 final size:17
Alignment explanation
Indices: 947843--947880 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
947833 AATGAGACTT
*
947843 TATTTTATTTTATTTTA
1 TATTTTAATTTATTTTA
947860 TATTTTAATTTATTTTA
1 TATTTTAATTTATTTTA
947877 -ATTT
1 TATTT
947881 GGGTTCACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (17 bp):
TATTTTAATTTATTTTA
Found at i:947877 original size:10 final size:10
Alignment explanation
Indices: 947841--947880 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
947831 ATAATGAGAC
*
947841 TTTATTTTAT
1 TTTATTTTAA
947851 TTTATTTT-A
1 TTTATTTTAA
947860 --TATTTTAA
1 TTTATTTTAA
947868 TTTATTTTAA
1 TTTATTTTAA
947878 TTT
1 TTT
947881 GGGTTCACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
7 6 0.23
8 1 0.04
10 19 0.73
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTATTTTAA
Found at i:948037 original size:5 final size:5
Alignment explanation
Indices: 948027--948063 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
948017 TTACCATGCA
*
948027 CCTCC CCTCC CCTCC CCTCC CCTCC CCTCC CTTCC CC
1 CCTCC CCTCC CCTCC CCTCC CCTCC CCTCC CCTCC CC
948064 CACTTCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.00, C:0.78, G:0.00, T:0.22
Consensus pattern (5 bp):
CCTCC
Found at i:948144 original size:17 final size:17
Alignment explanation
Indices: 948124--948169 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
948114 AAATAATAAT
948124 TAAAATATAATATTAAA
1 TAAAATATAATATTAAA
*
948141 TAAAAAATAATA-TAAA
1 TAAAATATAATATTAAA
*
948157 T-ATATATAATATT
1 TAAAATATAATATT
948170 TTAAATGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
15 8 0.32
16 6 0.24
17 11 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TAAAATATAATATTAAA
Found at i:948374 original size:19 final size:19
Alignment explanation
Indices: 948310--948374 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
948300 ATTATTATTT
948310 TATAAAATT-TATAAAATAA
1 TATAAAATTATA-AAAATAA
*
948329 -A-ATAA-TATAAAAATAA
1 TATAAAATTATAAAAATAA
* **
948345 TATTATTTTATAAAAATAA
1 TATAAAATTATAAAAATAA
948364 TATAAAATTAT
1 TATAAAATTAT
948375 TTTTATATTA
Statistics
Matches: 34, Mismatches: 8, Indels: 8
0.68 0.16 0.16
Matches are distributed among these distances:
16 8 0.24
17 6 0.18
18 1 0.03
19 19 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TATAAAATTATAAAAATAA
Found at i:948387 original size:14 final size:14
Alignment explanation
Indices: 948370--948399 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
948360 ATAATATAAA
*
948370 ATTATTTTTATATT
1 ATTATTTATATATT
948384 ATTATTTATATATT
1 ATTATTTATATATT
948398 AT
1 AT
948400 AATTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTATTTATATATT
Found at i:949259 original size:31 final size:30
Alignment explanation
Indices: 949199--949259 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
949189 ATGGTCAACT
* * *
949199 TAAAAATATTTTAAAGTTAAGTGATTAAAA
1 TAAAAATATTTTAAAATTAAGTAAATAAAA
*
949229 TAAAAATTTTTATAAAATTAAGTAAATAAAA
1 TAAAAATATTT-TAAAATTAAGTAAATAAAA
949260 ACGTAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAAAATATTTTAAAATTAAGTAAATAAAA
Found at i:949965 original size:19 final size:20
Alignment explanation
Indices: 949933--949972 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
949923 TAACTTCAAA
*
949933 AAAAAAGTTGAAAAAAAATT
1 AAAAAAGTTAAAAAAAAATT
949953 AAAAAAG-TAAAAAAAAATT
1 AAAAAAGTTAAAAAAAAATT
949972 A
1 A
949973 TTTTTATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (20 bp):
AAAAAAGTTAAAAAAAAATT
Found at i:953219 original size:19 final size:17
Alignment explanation
Indices: 953195--953236 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 17
953185 CGTATATATG
953195 TAAATATAACATAAATTTT
1 TAAATATAACA-AAA-TTT
*
953214 TAAATATATCAAAATTT
1 TAAATATAACAAAATTT
953231 TAAATA
1 TAAATA
953237 ATATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 3 0.14
19 10 0.45
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATATAACAAAATTT
Found at i:953233 original size:17 final size:18
Alignment explanation
Indices: 953195--953253 Score: 70
Period size: 16 Copynumber: 3.4 Consensus size: 18
953185 CGTATATATG
*
953195 TAAATATAACATAAATTTT
1 TAAATATATCATAAA-TTT
953214 TAAATATATCA-AAATTT
1 TAAATATATCATAAATTT
*
953231 TAAATA-AT-ATATATTT
1 TAAATATATCATAAATTT
953247 TAAATAT
1 TAAATAT
953254 TTTATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 1 0.03
16 13 0.36
17 9 0.25
18 3 0.08
19 10 0.28
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATATATCATAAATTT
Found at i:953940 original size:17 final size:18
Alignment explanation
Indices: 953918--953957 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
953908 AAATTGAAAA
*
953918 TTGATAGATTAT-TTAAT
1 TTGATAGAGTATATTAAT
*
953935 TTGATATAGTATATTAAT
1 TTGATAGAGTATATTAAT
953953 TTGAT
1 TTGAT
953958 GAAATTTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (18 bp):
TTGATAGAGTATATTAAT
Found at i:954102 original size:12 final size:13
Alignment explanation
Indices: 954085--954163 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 13
954075 TCTATTAATT
954085 TTATATTA-TAAA
1 TTATATTATTAAA
954097 TTATATTATTAAA
1 TTATATTATTAAA
**
954110 TTAAATATATATTTTTA
1 TT--ATAT-TA-TTAAA
954127 TTA-ATTA-TAAA
1 TTATATTATTAAA
*
954138 TTATAATATTAAAA
1 TTATATTATT-AAA
954152 TTAT-TT-TTAAA
1 TTATATTATTAAA
954163 T
1 T
954164 ATTATAAAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 17
0.70 0.08 0.22
Matches are distributed among these distances:
11 9 0.17
12 13 0.25
13 10 0.19
14 9 0.17
15 5 0.09
16 2 0.04
17 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTATATTATTAAA
Found at i:954122 original size:19 final size:19
Alignment explanation
Indices: 954093--954163 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 19
954083 TTTTATATTA
954093 TAAAT-TATATTATTAAAT
1 TAAATATATATTATTAAAT
*
954111 TAAATATATATT-TT-TAT
1 TAAATATATATTATTAAAT
* *
954128 TAATTATAAATTA-TAATAT
1 TAAATATATATTATTAA-AT
*
954147 TAAA-AT-TATTTTTAAAT
1 TAAATATATATTATTAAAT
954164 ATTATAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
17 18 0.44
18 12 0.29
19 11 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TAAATATATATTATTAAAT
Found at i:954142 original size:22 final size:19
Alignment explanation
Indices: 954089--954149 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
954079 TTAATTTTAT
954089 ATTATAAATTATATTATTAA
1 ATTATAAATTATATTATT-A
*
954109 ATTA-AATATATATTTTTATTA
1 ATTATAA-AT-TA-TATTATTA
*
954130 ATTATAAATTATAATATTA
1 ATTATAAATTATATTATTA
954149 A
1 A
954150 AATTATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
19 9 0.26
20 8 0.24
21 9 0.26
22 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATTATAAATTATATTATTA
Found at i:956148 original size:23 final size:22
Alignment explanation
Indices: 956120--956173 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
956110 TATTAGATAA
956120 TATAATTATATATTTTATATTAT
1 TATAATTATATATTTTATA-TAT
* *
956143 TTTAA-TAT-TATTTTTTATAT
1 TATAATTATATATTTTATATAT
956163 TATAATTATAT
1 TATAATTATAT
956174 TTAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 4 0.15
23 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
TATAATTATATATTTTATATAT
Found at i:956150 original size:20 final size:19
Alignment explanation
Indices: 956127--956186 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 19
956117 TAATATAATT
*
956127 ATATATTTTATATTATTTTA
1 ATATATTTTATA-TATTATA
*
956147 ATATTATTTTTTATATTATA
1 ATA-TATTTTATATATTATA
* *
956167 ATTATATTTAAAATATTATA
1 A-TATATTTTATATATTATA
956187 TATTTAAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 23 0.70
21 10 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATATATTTTATATATTATA
Done.