Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 110 of 199
Found at i:33430144 original size:331 final size:327
Alignment explanation
Indices: 33429488--33430619 Score: 1175
Period size: 331 Copynumber: 3.4 Consensus size: 327
33429478 ATACAGGGGA
* * * * *
33429488 AAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTATGT-AA------TTTTTT
1 AAAAAAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTTT
* * **
33429546 TTTACATTTTGAGTTGTCATTGGCTGGCACCAGTATAC-AAAAAATTCAAAAAACGAAAATTTTG
66 TTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAAAATT-AAAAAA--AAAATTTTG
* ** **** *
33429610 GTGGTGGCCTGGCAATGGTCGGCACCACCTTTATGTAAAAAAAAAAATTTACATTTTGGGTTGTC
128 GTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAATTATTTTTTTACATTTTGGGCTGTC
* * * *
33429675 ATTGGTCGGCACCAGTATAC-AAAAAATTCAAAAAAAAAAATTTTTTTGGTGGTGGCCTGCCAAT
193 ATTGGTTGGCACCAGTATACAAAAAAATTC------AAAAATTTTTTTTGAGGTGGCCTGGCAAT
* * *
33429739 GGCCGACACCACCTTTATGCAATTTTTTTTTTACATTTTGGGCTGTCATTAGCCGGCACCAGTAT
252 GGCCG-CACCACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACTAGTAT
*
33429804 ACAAAAAAATT-
316 ACGAAAAAATTC
* * *
33429815 AAAAAAAAATTTTGGTGGTGGCTTGGTAATAGCCGGCACCACCTTTATGTAAATTGGTTTTTTTT
1 AAAAAAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAA-T--TTTTTTTT
* ******
33429880 TTTTTTACATTTTGGGCTGTCATTGGCCAACACCAGTATACGAAAACAATTCAAAATTTTTTTTT
63 TTTTTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAA-AATT-AAAAAAAAAATTT
* * *
33429945 TGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT-AATTTTTTTTTTTACATTTTGGGCTA
126 TGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAATTATTTTTTTACATTTTGGGCTG
* *
33430009 TAATTGGTTGGCACCAGTATACAAAAAAATTCAAAATTTTTTTTTGAGGTGGCCTGGCAATGGCC
191 TCATTGGTTGGCACCAGTATACAAAAAAATTCAAAAATTTTTTTTGAGGTGGCCTGGCAATGGCC
* * * *
33430074 TGCACCACCTTTAAGTAATTTTTTTTTTACATTTTGGACTGTCATTGGCTGACACTAGTATACGA
256 -GCACCACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACTAGTATACGA
33430139 AAAAATTC
320 AAAAATTC
**** * * **
33430147 AAAATTTTTTTTTTGGTGGTGGCTTGGCAATGGACAGCATGACCTTTATGTAAA---TTTTTTTT
1 AAAA-AAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTT
* *
33430209 TTTTACATTTTGGGCTATCATTGG-CAGGCACCAGTATACGAAAAAGTTAAAAAAAAAATTTTGG
65 TTTTACATTTTGGGCTGTCATTGGCCA-GCACCAGTATACGAAAAAATTAAAAAAAAAATTTTGG
33430273 TGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTACATTTTGGGCTG
129 TGGTGGCCTGGCAATGGCCGGCACCACCTTTATGT---AAAATTATTTTTTTACATTTTGGGCTG
* * * * *** *
33430338 TCATTGGCCT-GCACTAGTATATGAAAAAAATTAAAAAAAAATTTTTCATGGTGGCCTGGCAATG
191 TCATTGG-TTGGCACCAGTATA-CAAAAAAATTCAAAAATTTTTTTTGA-GGTGGCCTGGCAATG
* ******* * *
33430402 GCCGGCACCACTTTTATGTAAAAAAAAATTTACATTTTGGGCTATCATTGGCCGGCA-TCAATAT
253 GCC-GCACCACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACT-AGTAT
33430466 ACGAAAAAATTC
316 ACGAAAAAATTC
33430478 AAAAAAAATTTTTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATG-AAATTTTTTTTT
1 AAAAAAAA---TTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTT
* * *
33430542 CTTTTTACATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTGAAAAAAAAAACTTT
63 TTTTTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAAAATT-AAAAAAAAAA-TTT
33430607 TAGGTGGTGGCCT
126 T-GGTGGTGGCCT
33430620 AAAAATTGCC
Statistics
Matches: 665, Mismatches: 105, Indels: 59
0.80 0.13 0.07
Matches are distributed among these distances:
325 45 0.07
326 5 0.01
327 89 0.13
328 2 0.00
329 39 0.06
330 21 0.03
331 169 0.25
332 8 0.01
333 75 0.11
335 49 0.07
336 47 0.07
337 92 0.14
338 15 0.02
339 9 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (327 bp):
AAAAAAAATTTTTGGTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTTT
TTTACATTTTGGGCTGTCATTGGCCAGCACCAGTATACGAAAAAATTAAAAAAAAAATTTTGGTG
GTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAATTATTTTTTTACATTTTGGGCTGTCATT
GGTTGGCACCAGTATACAAAAAAATTCAAAAATTTTTTTTGAGGTGGCCTGGCAATGGCCGCACC
ACCTTTATGTAATTTTTTTTTTACATTTTGGGCTGTCATTGGCCGGCACTAGTATACGAAAAAAT
TC
Found at i:33430392 original size:223 final size:221
Alignment explanation
Indices: 33429487--33430619 Score: 1141
Period size: 223 Copynumber: 5.1 Consensus size: 221
33429477 TATACAGGGG
* * * *
33429487 AAAAAAAAATTTTGGGTGCTGGCCTGTCAATGGCCGACACCACCTTTATGT-AA-TTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * * *
33429550 CATTTTGAGTTGTCATTGGCTGGCACCAGTATAC-AAAAAATTCAAAAAACGAAAATTTTGGTGG
66 CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATT-AAAAAA--AAAATTTTGGTGG
* **** *
33429614 TGGCCTGGCAATGGTCGGCACCACCTTTATGTAAAAAAA---AAAATTTACATTTTGGGTTGTCA
128 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCA
*
33429676 TTGGTCGGCACCAGTATAC-AAAAAATTC
193 TTGGCCGGCACCAGTATACGAAAAAATTC
* * *
33429704 AAAAAAAAAAATTTTTTTGGTGGTGGCCTGCCAATGGCCGACACCACCTTTATG-CAATTTTTTT
1 --AAAAAAAAA--TTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTT
* *
33429768 TTTACATTTTGGGCTGTCATTAGCCGGCACCAGTATACAAAAAAATT-AAAAAAAAATTTTGGTG
62 TTTACATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTG
* * * ****
33429832 GTGGCTTGGTAATAGCCGGCACCACCTTTATGTAAATTGGTTTTTTTTTTTTTTACATTTTGGGC
127 GTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA----AAAATTTTTTTTTTACATTTTGGGC
**
33429897 TGTCATTGGCCAACACCAGTATACGAAAACAATTC
188 TGTCATTGGCCGGCACCAGTATACGAAAA-AATTC
***** *
33429932 AAAATTTTTTTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAATTTTTTTTTTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* ** * **** * *
33429997 CATTTTGGGCTATAATTGGTTGGCACCAGTATACAAAAAAATT-CAAAATTTTTTTTTGAGGTGG
66 CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTGGTGG
* * *
33430061 CCTGGCAATGGCCTGCACCACCTTTAAGT-----AATTTTTTTTTTACATTTTGGACTGTCATTG
131 CCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCATTG
* * *
33430121 GCTGACACTAGTATACGAAAAAATTC
196 GCCGGCACCAGTATACGAAAAAATTC
***** * * * **
33430147 AAAATTTTTTTTTTGGTGGTGGCTTGGCAATGGACAGCATGACCTTTATGTAAATTTTTTTTTTT
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAA--TTTTTTTTT
* * *
33430212 TACATTTTGGGCTATCATTGGCAGGCACCAGTATACGAAAAAGTTAAAAAAAAAATTTTGGTGGT
64 TACATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTGGT
*
33430277 GGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTATTTTTTTACATTTTGGGCTGTCAT
129 GGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCAT
* * *
33430342 TGGCCTGCACTAGTATATGAAAAAAATT-
194 TGGCCGGCACCAGTATACG-AAAAAATTC
** * ******
33430370 AAAAAAAAATTTTTCATGGTGGCCTGGCAATGGCCGGCACCACTTTTATGTAAA-AAAAAATTTA
1 AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
* * * **
33430434 CATTTTGGGCTATCATTGGCCGGCATCAATATACGAAAAAATTCAAAAAAAATTTTTTTTGGTGG
66 CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATT-AAAAAAAA--AATTTTGGTGG
* ****
33430499 TGGCTTGGCAATGGCCGGCACCACCTTTATG-AAATTTTTTTTTCTTTTTACATTTTGGGCTGTC
128 TGGCCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTT-TTTTTACATTTTGGGCTGTC
* *
33430563 ATTGGCCGGTACCAGTATACGAAAAAATTGA
192 ATTGGCCGGCACCAGTATACGAAAAAATT-C
*
33430594 AAAAAAAAACTTTTAGGTGGTGGCCT
1 AAAAAAAAA-TTTTTGGTGGTGGCCT
33430620 AAAAATTGCC
Statistics
Matches: 764, Mismatches: 119, Indels: 56
0.81 0.13 0.06
Matches are distributed among these distances:
215 53 0.07
216 46 0.06
217 49 0.06
218 41 0.05
219 53 0.07
220 43 0.06
221 53 0.07
222 55 0.07
223 167 0.22
224 56 0.07
225 101 0.13
226 38 0.05
227 4 0.01
228 5 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (221 bp):
AAAAAAAAATTTTTGGTGGTGGCCTGGCAATGGCCGGCACCACCTTTATGTAAATTTTTTTTTTA
CATTTTGGGCTATCATTGGCCGGCACCAGTATACAAAAAAATTAAAAAAAAAATTTTGGTGGTGG
CCTGGCAATGGCCGGCACCACCTTTATGTAAAAAAATTTTTTTTTTACATTTTGGGCTGTCATTG
GCCGGCACCAGTATACGAAAAAATTC
Found at i:33430636 original size:115 final size:115
Alignment explanation
Indices: 33430430--33430636 Score: 279
Period size: 115 Copynumber: 1.8 Consensus size: 115
33430420 TAAAAAAAAA
* *** *
33430430 TTTACATTTTGGGCTATCATTGGCCGGCATCAATATACGAAAAAATTCAAAAAAAATTTTTTTTG
1 TTTACATTTTGGGCTATCATTGGCCGGCACCAATATACGAAAAAATTCAAAAAAAAAACTTTTAG
* *** *
33430495 GTGGTGGCTTGGCAATGGCCGGCACCACCTTTATGAAATTTTTTTTTCTT
66 GTGGTGGCCTAAAAATGGCCGACACCACCTTTATGAAATTTTTTTTTCTT
* * * *
33430545 TTTACATTTTGGGCTGTCATTGGCCGGTACCAGTATACGAAAAAATTGAAAAAAAAAACTTTTAG
1 TTTACATTTTGGGCTATCATTGGCCGGCACCAATATACGAAAAAATTCAAAAAAAAAACTTTTAG
*
33430610 GTGGTGGCCTAAAAATTGCCGACACCA
66 GTGGTGGCCTAAAAATGGCCGACACCA
33430637 AATTTATCAA
Statistics
Matches: 77, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
115 77 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (115 bp):
TTTACATTTTGGGCTATCATTGGCCGGCACCAATATACGAAAAAATTCAAAAAAAAAACTTTTAG
GTGGTGGCCTAAAAATGGCCGACACCACCTTTATGAAATTTTTTTTTCTT
Found at i:33433589 original size:54 final size:55
Alignment explanation
Indices: 33433510--33433628 Score: 152
Period size: 56 Copynumber: 2.2 Consensus size: 55
33433500 ATATTCTTGT
* *
33433510 AAAAATAAATTTGCATTGAAAATAG-AAAT-TTTAAATATAAAATGAAATGAGAA
1 AAAAATAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATGAAATGAGAA
* * * **
33433563 AAAAATTAAATTTCCTTTGGAAATAGAAAATATGTAGATATAAAATGAAATGAGGT
1 AAAAA-TAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATGAAATGAGAA
33433619 AAAAATAAAT
1 AAAAATAAAT
33433629 GTTATCAGGC
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
53 5 0.09
54 17 0.30
55 9 0.16
56 25 0.45
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.29
Consensus pattern (55 bp):
AAAAATAAATTTCCATTGAAAATAGAAAATATGTAAATATAAAATGAAATGAGAA
Found at i:33437819 original size:33 final size:33
Alignment explanation
Indices: 33437772--33437839 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
33437762 AAGCTGCACA
* *
33437772 TAAGGTATCTGGGCACCAAAGACCTGACGAGCC
1 TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
33437805 TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
1 TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
33437838 TA
1 TA
33437840 TTCGGAGTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.32, C:0.26, G:0.26, T:0.15
Consensus pattern (33 bp):
TAAGGTATCCGGGCAACAAAGACCTGACGAGCC
Found at i:33441258 original size:28 final size:28
Alignment explanation
Indices: 33441218--33441272 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
33441208 TTTTTTTTAC
33441218 TTTTTTTTTATAATTGG-ATATAAGTAGA
1 TTTTTTTTTATAA-TGGAATATAAGTAGA
33441246 TTTTTTTTTATAATGGAATATAAGTAG
1 TTTTTTTTTATAATGGAATATAAGTAG
33441273 TGAGATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 3 0.12
28 23 0.88
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (28 bp):
TTTTTTTTTATAATGGAATATAAGTAGA
Found at i:33441844 original size:28 final size:28
Alignment explanation
Indices: 33441804--33441858 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
33441794 GTGTAGAGGC
*
33441804 GGCATTGCTTTATATGAGTAAAAAATAT
1 GGCACTGCTTTATATGAGTAAAAAATAT
33441832 GGCACTGCTTTATATGAGTAAAAAATA
1 GGCACTGCTTTATATGAGTAAAAAATA
33441859 CGGGATACGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (28 bp):
GGCACTGCTTTATATGAGTAAAAAATAT
Found at i:33452781 original size:32 final size:32
Alignment explanation
Indices: 33452745--33452809 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
33452735 TTTGTTAGAT
*
33452745 ATTTATTATGTTTTAAGCTTGTTAGATTTTGA
1 ATTTATTATGTTTTAAGCTTGTTAGATATTGA
*
33452777 ATTTATTATGTTTTAAGCTTGTTGGATATTGA
1 ATTTATTATGTTTTAAGCTTGTTAGATATTGA
33452809 A
1 A
33452810 ATGATTGACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.26, C:0.03, G:0.17, T:0.54
Consensus pattern (32 bp):
ATTTATTATGTTTTAAGCTTGTTAGATATTGA
Found at i:33454112 original size:20 final size:20
Alignment explanation
Indices: 33454063--33454112 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
33454053 ACAATTTAAA
* *
33454063 ATATATAAATTTATTAATTT
1 ATATAAAAATTTATTAATAT
* *
33454083 TTATATAAATTTATTAATAT
1 ATATAAAAATTTATTAATAT
*
33454103 ATGTAAAAAT
1 ATATAAAAAT
33454113 AACTTTTCCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATAAAAATTTATTAATAT
Found at i:33458268 original size:18 final size:18
Alignment explanation
Indices: 33458247--33458286 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
33458237 AAAATATTTA
*
33458247 TTTTGATGT-TTTTAGTAT
1 TTTTGATGTATTATA-TAT
33458265 TTTTGATGTATTATATAT
1 TTTTGATGTATTATATAT
33458283 TTTT
1 TTTT
33458287 TTAAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTTTGATGTATTATATAT
Found at i:33461502 original size:37 final size:33
Alignment explanation
Indices: 33461460--33461563 Score: 82
Period size: 37 Copynumber: 2.8 Consensus size: 33
33461450 CAAGATAAAC
33461460 ATTAAATTTAATTTAATATTAAGATAATCACTTTAA
1 ATTAAATTTAATTTAATATTAAGATAAT--C-TTAA
** *
33461496 TATTAAATTAATAAAATACTATTAAGATAAGTCTTAA
1 -ATTAAATT--TAATTTAATATTAAGATAA-TCTTAA
*
33461533 ATTAAATTTAATATTAAACTATTAAAATAAT
1 ATTAAATTTAAT-TT-AA-TATTAAGATAAT
33461564 ATTATTTTTG
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
34 3 0.06
35 1 0.02
36 10 0.19
37 22 0.41
38 1 0.02
39 16 0.30
40 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (33 bp):
ATTAAATTTAATTTAATATTAAGATAATCTTAA
Found at i:33461520 original size:25 final size:25
Alignment explanation
Indices: 33461466--33461520 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
33461456 AAACATTAAA
*
33461466 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
33461491 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
33461515 TATTAA
1 T-TTAA
33461521 GATAAGTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:33462454 original size:22 final size:20
Alignment explanation
Indices: 33462418--33462476 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 20
33462408 AGCCCGGCCC
33462418 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
33462440 ATTTATTTTAAAAATGAAAAA
1 ATTTATTTTAAAAAT-AAAAA
**
33462461 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
33462477 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 17 0.52
22 8 0.24
23 7 0.21
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:33462498 original size:18 final size:17
Alignment explanation
Indices: 33462468--33462594 Score: 60
Period size: 17 Copynumber: 7.7 Consensus size: 17
33462458 AAAAAGTATT
33462468 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
33462485 TTAAAAATTTTTTTAAAAAGTA
1 TTAAAAA-TATTTT--AAA--A
33462507 TTTAAAAAATATTTTAAAA
1 -TT-AAAAATATTTTAAAA
**
33462526 TTAAAAA-ATAAT-AAA
1 TTAAAAATATTTTAAAA
33462541 --AAAAATA--TT----
1 TTAAAAATATTTTAAAA
33462550 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
*
33462567 TTAAAAA-AATTTAAAA
1 TTAAAAATATTTTAAAA
* *
33462583 ATAAATATATTT
1 TTAAAAATATTT
33462595 ATTATATCAA
Statistics
Matches: 84, Mismatches: 9, Indels: 34
0.66 0.07 0.27
Matches are distributed among these distances:
11 7 0.08
12 1 0.01
13 7 0.08
14 1 0.01
15 3 0.04
16 16 0.19
17 22 0.26
18 7 0.08
19 1 0.01
20 3 0.04
21 3 0.04
22 1 0.01
23 7 0.08
24 5 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:33462515 original size:41 final size:41
Alignment explanation
Indices: 33462456--33462574 Score: 175
Period size: 41 Copynumber: 2.9 Consensus size: 41
33462446 TTTAAAAATG
* **
33462456 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAATTTTT
1 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAT
** *
33462497 TTAAAAAGTATTTAAAAAATATTTTAAAATTAAAAAATAAT
1 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAT
*
33462538 AAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAA
1 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAA
33462575 ATTTAAAAAT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (41 bp):
AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATAAT
Found at i:33462567 original size:10 final size:11
Alignment explanation
Indices: 33462458--33462566 Score: 65
Period size: 11 Copynumber: 10.4 Consensus size: 11
33462448 TAAAAATGAA
33462458 AAAAAGTATTTT
1 AAAAA-TATTTT
33462470 AAAAATATTTT
1 AAAAATATTTT
33462481 --AAA-A--TT
1 AAAAATATTTT
*
33462487 AAAAATTTTTTT
1 AAAAA-TATTTT
*
33462499 AAAAAGTATTTA
1 AAAAA-TATTTT
33462511 AAAAATATTTT
1 AAAAATATTTT
*
33462522 --AAA-A-TTA
1 AAAAATATTTT
***
33462529 AAAAATAATAAA
1 AAAAAT-ATTTT
33462541 AAAAATATTTT
1 AAAAATATTTT
33462552 AAAAATATTTT
1 AAAAATATTTT
33462563 AAAA
1 AAAA
33462567 TTAAAAAAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
6 2 0.03
7 2 0.03
8 5 0.07
9 9 0.12
11 29 0.39
12 28 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:33462579 original size:16 final size:17
Alignment explanation
Indices: 33462550--33462587 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
33462540 AAAAAATATT
*
33462550 TTAAAAATATTTTAAAA
1 TTAAAAATAATTTAAAA
33462567 TTAAAAA-AATTTAAAA
1 TTAAAAATAATTTAAAA
*
33462583 ATAAA
1 TTAAA
33462588 TATATTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TTAAAAATAATTTAAAA
Found at i:33462582 original size:41 final size:41
Alignment explanation
Indices: 33462456--33462595 Score: 174
Period size: 41 Copynumber: 3.4 Consensus size: 41
33462446 TTTAAAAATG
* **
33462456 AAAAAAAGTATTTTAAAAATATTTTAAAATTAAAAATTTTT
1 AAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTT
** * * *
33462497 TTAAAAAGTATTTAAAAAATATTTTAAAATT-AAAAAATAAT
1 AAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAAT-TT
33462538 AAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTT
1 AAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTT
33462579 AAAAATAAATATATTTA
1 AAAAA-AAATAT-TTTA
33462596 TTATATCAAG
Statistics
Matches: 84, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
40 5 0.06
41 62 0.74
42 13 0.15
43 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (41 bp):
AAAAAAAATATTTTAAAAATATTTTAAAATTAAAAAAATTT
Found at i:33462594 original size:16 final size:16
Alignment explanation
Indices: 33462554--33462595 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
33462544 AATATTTTAA
*
33462554 AAATAT-TTTAAAATT
1 AAATATATTTAAAAAT
* *
33462569 AAAAAAATTTAAAAAT
1 AAATATATTTAAAAAT
33462585 AAATATATTTA
1 AAATATATTTA
33462596 TTATATCAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAATATATTTAAAAAT
Found at i:33463956 original size:20 final size:20
Alignment explanation
Indices: 33463931--33463973 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
33463921 AGGAGCACAT
33463931 CGTAGGATGCAACCTTTACC
1 CGTAGGATGCAACCTTTACC
*
33463951 CGTAGGATGTAACCTTTACC
1 CGTAGGATGCAACCTTTACC
33463971 CGT
1 CGT
33463974 TTGTGTGCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (20 bp):
CGTAGGATGCAACCTTTACC
Found at i:33479861 original size:14 final size:14
Alignment explanation
Indices: 33479835--33479893 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
33479825 ACTGTTGAAC
33479835 TTAAAATATAAAATT
1 TTAAAA-ATAAAATT
33479850 TTAAAAATAAAATT
1 TTAAAAATAAAATT
33479864 TATAAAAATAAGAA-T
1 T-TAAAAATAA-AATT
* *
33479879 ATAAAAATTAAATT
1 TTAAAAATAAAATT
33479893 T
1 T
33479894 CAAATATGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 2 0.05
14 18 0.47
15 16 0.42
16 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
TTAAAAATAAAATT
Found at i:33480196 original size:26 final size:27
Alignment explanation
Indices: 33480161--33480212 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
33480151 ATAAAAAATA
33480161 ATCAAAATATTATAATT-TTTTTATTT
1 ATCAAAATATTATAATTATTTTTATTT
33480187 ATCAAAATATTATAATTATTTTTATT
1 ATCAAAATATTATAATTATTTTTATT
33480213 ATTTACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (27 bp):
ATCAAAATATTATAATTATTTTTATTT
Found at i:33480229 original size:29 final size:29
Alignment explanation
Indices: 33480161--33480230 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 29
33480151 ATAAAAAATA
33480161 ATCAAAATATTAT-A--ATTTTTTTATTT
1 ATCAAAATATTATAATTATTTTTTTATTT
33480187 ATCAAAATATTATAATTATTTTTATTATTT
1 ATCAAAATATTATAATTATTTTT-TTATTT
33480217 A-CTAAAATA-TATAA
1 ATC-AAAATATTATAA
33480231 AAAACAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
26 13 0.33
27 1 0.03
29 12 0.31
30 13 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (29 bp):
ATCAAAATATTATAATTATTTTTTTATTT
Found at i:33480321 original size:27 final size:27
Alignment explanation
Indices: 33480291--33480342 Score: 88
Period size: 27 Copynumber: 1.9 Consensus size: 27
33480281 AGGCCAATGG
33480291 CATTGGCGGCACCAGA-GGTGCCAAAGC
1 CATTGGCGGCACCA-ATGGTGCCAAAGC
33480318 CATTGGCGGCACCAATGGTGCCAAA
1 CATTGGCGGCACCAATGGTGCCAAA
33480343 AATCATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 1 0.04
27 23 0.96
ACGTcount: A:0.27, C:0.29, G:0.31, T:0.13
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAGC
Found at i:33480420 original size:33 final size:34
Alignment explanation
Indices: 33480381--33480445 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
33480371 AGGGGGGGTC
33480381 GGTGGTGGGGGGG-AGAAGGAGAGGGAAAGAAGG
1 GGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAGG
33480414 GGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAA
1 GGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAA
33480446 AGAAAGGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.31, C:0.02, G:0.62, T:0.06
Consensus pattern (34 bp):
GGTGGTGGGGGGGCAGAAGGAGAGGGAAAGAAGG
Found at i:33480459 original size:13 final size:14
Alignment explanation
Indices: 33480438--33480470 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
33480428 AGAAGGAGAG
33480438 GGAAAGAAAG-AAA
1 GGAAAGAAAGAAAA
*
33480451 GGAAGGAAAGAAAA
1 GGAAAGAAAGAAAA
33480465 GGAAAG
1 GGAAAG
33480471 GGAGAGGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (14 bp):
GGAAAGAAAGAAAA
Found at i:33480492 original size:30 final size:30
Alignment explanation
Indices: 33480456--33480564 Score: 89
Period size: 30 Copynumber: 3.5 Consensus size: 30
33480446 AGAAAGGAAG
33480456 GAAAGAAAAGGAAAGGGAGAGGAGAAAAAA
1 GAAAGAAAAGGAAAGGGAGAGGAGAAAAAA
* * *
33480486 GAAAGAAAGGGAGGAGAGGA-AGAAAGAAAAAGA
1 GAAAGAAAAGGA-AAG-GGAGAG-GAGAAAAA-A
* *
33480519 GGAAAGAAAAGGAAA-GGTGATGAG-AAAAA
1 -GAAAGAAAAGGAAAGGGAGAGGAGAAAAAA
33480548 GAAAGAAAGAAGGAAAG
1 GAAAG-AA-AAGGAAAG
33480565 AAAAGGAAAG
Statistics
Matches: 62, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
28 5 0.08
29 3 0.05
30 22 0.35
31 8 0.13
32 11 0.18
33 2 0.03
34 11 0.18
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (30 bp):
GAAAGAAAAGGAAAGGGAGAGGAGAAAAAA
Found at i:33480514 original size:64 final size:64
Alignment explanation
Indices: 33480431--33480556 Score: 177
Period size: 64 Copynumber: 2.0 Consensus size: 64
33480421 GGGGGGCAGA
*
33480431 AGGAGAGGGAAAGAAAG-AAAGGAAGGAAAGAAAAGGAAAGGGAGAGGAGAAAAAAGAAAGAAAG
1 AGGAGAGGGAAAGAAAGAAAAAG-AGGAAAGAAAAGGAAA-GGAGAGGAG-AAAAAGAAAGAAAG
33480495 GG
63 GG
* *
33480497 AGGAGA-GG-AAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGTGATGAGAAAAAGAAAGAAAG
1 AGGAGAGGGAAAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGAGAGGAGAAAAAGAAAGAAAG
33480557 AAGGAAAGAA
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
62 14 0.25
63 7 0.12
64 23 0.41
65 6 0.11
66 6 0.11
ACGTcount: A:0.60, C:0.00, G:0.38, T:0.02
Consensus pattern (64 bp):
AGGAGAGGGAAAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGAGAGGAGAAAAAGAAAGAAAGGG
Found at i:33480562 original size:40 final size:40
Alignment explanation
Indices: 33480505--33480597 Score: 136
Period size: 40 Copynumber: 2.4 Consensus size: 40
33480495 GGAGGAGAGG
* * *
33480505 AAGAAAGAAAAAGAGGAAAGAAAAGGAAAGGTGATGAGAAA
1 AAGAAAGAAAGA-AGGAAAGAAAAGGAAAGGAGAAGAGAAA
33480546 AAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
1 AAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
33480586 AA-AAAG-AAGAAG
1 AAGAAAGAAAGAAG
33480598 AGGGAAGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
38 6 0.12
39 4 0.08
40 28 0.57
41 11 0.22
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (40 bp):
AAGAAAGAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA
Found at i:33480593 original size:35 final size:35
Alignment explanation
Indices: 33480430--33480625 Score: 116
Period size: 40 Copynumber: 5.8 Consensus size: 35
33480420 GGGGGGGCAG
* * *
33480430 AAGGAGAGG-GAA-AGAAAGAAAGGAAGGAAAGAA
1 AAGGAAAGGAGAAGAGAAAAAAAAGAAGGAAAGAA
* *
33480463 AAGGAAAGG-G-AGAG-GAGAAAA-AA-GAAAG-A
1 AAGGAAAGGAGAAGAGAAAAAAAAGAAGGAAAGAA
* *
33480492 AAGG-GAGGAGAGGAAGAAAGAAAAAG-AGGAAAGAA
1 AAGGAAAGGAGAAG-AGAAA-AAAAAGAAGGAAAGAA
* *
33480527 AAGGAAAGGTGATGAGAAAAAGAAAGAAAGAAGGAAAGAA
1 AAGGAAAGGAGA--AG-AGAA-AAA-AAAGAAGGAAAGAA
**
33480567 AAGGAAAGGAGAAGAGAAAAAAAAGAA-GAAGAGGG
1 AAGGAAAGGAGAAGAGAAAAAAAAGAAGGAA-AGAA
33480602 AAGG-AA-GAG-AGA-AAAAAAAAGAAG
1 AAGGAAAGGAGAAGAGAAAAAAAAGAAG
33480626 AGAGGAAAAG
Statistics
Matches: 131, Mismatches: 15, Indels: 35
0.72 0.08 0.19
Matches are distributed among these distances:
28 3 0.02
29 6 0.05
30 6 0.05
31 15 0.11
32 10 0.08
33 19 0.15
34 10 0.08
35 17 0.13
36 8 0.06
37 3 0.02
38 9 0.07
39 5 0.04
40 20 0.15
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (35 bp):
AAGGAAAGGAGAAGAGAAAAAAAAGAAGGAAAGAA
Found at i:33480596 original size:17 final size:18
Alignment explanation
Indices: 33480549--33480599 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 18
33480539 TGAGAAAAAG
33480549 AAAG-AAAGAAGGAA-AGA
1 AAAGAAAAGAA-GAAGAGA
* *
33480566 AAAGGAAAGGAGAAGAGA
1 AAAGAAAAGAAGAAGAGA
33480584 AAA-AAAAGAAGAAGAG
1 AAAGAAAAGAAGAAGAG
33480600 GGAAGGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 18 0.62
18 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAGAAGAGA
Found at i:33480596 original size:30 final size:31
Alignment explanation
Indices: 33480562--33480626 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
33480552 GAAAGAAGGA
33480562 AAGAAAAGGAAAGG-AGA-AGAGAAAAAAAAG
1 AAGAAAAGGAAAGGAAGAGAGA-AAAAAAAAG
* *
33480592 AAGAAGAGGGAAGGAAGAGAGAAAAAAAAAG
1 AAGAAAAGGAAAGGAAGAGAGAAAAAAAAAG
33480623 AAGA
1 AAGA
33480627 GAGGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 12 0.39
31 16 0.52
32 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (31 bp):
AAGAAAAGGAAAGGAAGAGAGAAAAAAAAAG
Found at i:33480617 original size:28 final size:29
Alignment explanation
Indices: 33480577--33480632 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
33480567 AAGGAAAGGA
*
33480577 GAAGAGAAAAAAAAGAAGAAGAG-GGAAG
1 GAAGAGAAAAAAAAAAAGAAGAGAGGAAG
*
33480605 GAAGAGAGAAAAAAAAAGAAGAGAGGAA
1 GAAGAGAAAAAAAAAAAGAAGAGAGGAA
33480633 AAGGTAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (29 bp):
GAAGAGAAAAAAAAAAAGAAGAGAGGAAG
Found at i:33480660 original size:15 final size:15
Alignment explanation
Indices: 33480640--33480669 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
33480630 GAAAAGGTAA
33480640 TTTTTTTTATAAATT
1 TTTTTTTTATAAATT
33480655 TTTTTTTTATAAATT
1 TTTTTTTTATAAATT
33480670 AATTTTTTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTTTTTTATAAATT
Found at i:33480673 original size:19 final size:18
Alignment explanation
Indices: 33480651--33480687 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
33480641 TTTTTTTATA
*
33480651 AATTTTTTTTTTATAAATT
1 AATTTTTTGTTTA-AAATT
33480670 AATTTTTTGTTTAAAATT
1 AATTTTTTGTTTAAAATT
33480688 TATATTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
AATTTTTTGTTTAAAATT
Found at i:33480675 original size:15 final size:15
Alignment explanation
Indices: 33480642--33480677 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
33480632 AAAGGTAATT
**
33480642 TTTTTTATAAATTTT
1 TTTTTTATAAATTAA
33480657 TTTTTTATAAATTAA
1 TTTTTTATAAATTAA
33480672 TTTTTT
1 TTTTTT
33480678 GTTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTATAAATTAA
Found at i:33489057 original size:3 final size:3
Alignment explanation
Indices: 33489049--33489172 Score: 130
Period size: 3 Copynumber: 41.7 Consensus size: 3
33489039 TATTAATACT
* * *
33489049 AAC AAC AAC AAC AAC AAC AAC AAC AAC TAA- AAC TAT AAC AAC AAT
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC -AAC AAC AAC AAC AAC AAC
* * * *
33489094 ATA- ATC AAC AAT ATA- AAC AA- TAT AAC AAC AAC AAC AAC AAC AAC
1 A-AC AAC AAC AAC A-AC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
33489138 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
33489173 TAATAATAAT
Statistics
Matches: 103, Mismatches: 11, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
2 4 0.04
3 95 0.92
4 4 0.04
ACGTcount: A:0.65, C:0.27, G:0.00, T:0.08
Consensus pattern (3 bp):
AAC
Found at i:33489177 original size:3 final size:3
Alignment explanation
Indices: 33489171--33489204 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
33489161 CAACAACAAC
33489171 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33489205 CTAACTAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:33489339 original size:10 final size:11
Alignment explanation
Indices: 33489322--33489350 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
33489312 TAAAAATTAC
33489322 CTTCTTTTTCT
1 CTTCTTTTTCT
33489333 C-TCTTTTTCT
1 CTTCTTTTTCT
33489343 CTTCTTTT
1 CTTCTTTT
33489351 CCGCAGCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:33489480 original size:27 final size:27
Alignment explanation
Indices: 33489450--33489535 Score: 109
Period size: 27 Copynumber: 3.2 Consensus size: 27
33489440 CCAATCTGTA
*
33489450 TGGCCCCATTGGTGTCGCCAATGGCTT
1 TGGCCCCATTGGTGCCGCCAATGGCTT
*
33489477 TGGCACCATTGGTGCCGCCAATGGCTT
1 TGGCCCCATTGGTGCCGCCAATGGCTT
* * * * *
33489504 TGGCGCCTTTGGTGCCGGCAATGCCAT
1 TGGCCCCATTGGTGCCGCCAATGGCTT
33489531 TGGCC
1 TGGCC
33489536 TGATCAGACT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.12, C:0.30, G:0.31, T:0.27
Consensus pattern (27 bp):
TGGCCCCATTGGTGCCGCCAATGGCTT
Found at i:33489620 original size:30 final size:27
Alignment explanation
Indices: 33489582--33489652 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
33489572 CAGGTTTTTT
33489582 TTAT-ATATTTTGGTAAATAATAAAAATAA
1 TTATAATATTTTGGTAAAT-A-AAAAA-AA
*
33489611 TTATAATATTTTGGTAAATAAAAAAAG
1 TTATAATATTTTGGTAAATAAAAAAAA
33489638 TTATAATATTTTGGT
1 TTATAATATTTTGGT
33489653 TATTTTTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 16 0.40
28 5 0.12
29 5 0.12
30 14 0.35
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (27 bp):
TTATAATATTTTGGTAAATAAAAAAAA
Found at i:33492338 original size:20 final size:19
Alignment explanation
Indices: 33492306--33492359 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
33492296 TCTCTCAACA
33492306 AAAAATTACAAAATAATTTT
1 AAAAATT-CAAAATAATTTT
* *
33492326 CAAAAATTTAAAATCATTTT
1 -AAAAATTCAAAATAATTTT
*
33492346 TAAAATTCAAAATA
1 AAAAATTCAAAATA
33492360 TTTATATAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 11 0.39
20 10 0.36
21 7 0.25
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:33492519 original size:3 final size:3
Alignment explanation
Indices: 33492511--33492545 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
33492501 AGTATCTTAT
33492511 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
33492546 TTGCTTTGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:33495922 original size:30 final size:30
Alignment explanation
Indices: 33495860--33495948 Score: 106
Period size: 30 Copynumber: 3.0 Consensus size: 30
33495850 ATAGGTTGGC
* * * *
33495860 ACATGGGCGTGTGTCCAGCCCGTGTGGCTT
1 ACATAGGCATGTGCCCAACCCGTGTGGCTT
* *
33495890 ACATAGGCATGTGCCCAACCCTTGTGGGTT
1 ACATAGGCATGTGCCCAACCCGTGTGGCTT
* *
33495920 ACATGGGCATGTGCCCAGCCCGTGTGGCT
1 ACATAGGCATGTGCCCAACCCGTGTGGCT
33495949 CTTGAAATCT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.15, C:0.28, G:0.33, T:0.25
Consensus pattern (30 bp):
ACATAGGCATGTGCCCAACCCGTGTGGCTT
Found at i:33496771 original size:11 final size:11
Alignment explanation
Indices: 33496755--33496780 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
33496745 ATAATCAATA
33496755 TTTTTTTATTT
1 TTTTTTTATTT
33496766 TTTTTTTATTT
1 TTTTTTTATTT
33496777 TTTT
1 TTTT
33496781 AAGAACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTATTT
Found at i:33497710 original size:6 final size:6
Alignment explanation
Indices: 33497699--33497806 Score: 146
Period size: 6 Copynumber: 18.0 Consensus size: 6
33497689 AGAAACAACC
33497699 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
* * * * *
33497747 ATAAAA ATAAAA CTAAAA CTAAAA CTAAAA CTAAAA CTAAAA A-AAAGA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA-A
*
33497795 AAAAAA ATAAAA
1 ATAAAA ATAAAA
33497807 TCAATGATCC
Statistics
Matches: 97, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
5 3 0.03
6 91 0.94
7 3 0.03
ACGTcount: A:0.80, C:0.05, G:0.01, T:0.15
Consensus pattern (6 bp):
ATAAAA
Found at i:33499462 original size:15 final size:15
Alignment explanation
Indices: 33499421--33499548 Score: 64
Period size: 15 Copynumber: 8.9 Consensus size: 15
33499411 ATAGTTAAAT
*
33499421 AACATAACAATAATAA
1 AACATAATAATAAT-A
33499437 GAACA-AA-AATAATA
1 -AACATAATAATAATA
33499451 AACATAATAATAA-A
1 AACATAATAATAATA
*
33499465 AACA-AAT-AGAA-A
1 AACATAATAATAATA
*
33499477 GA-ATAATAATAA-A
1 AACATAATAATAATA
* *
33499490 ACAAATGATAATAAATA
1 A-ACATAATAAT-AATA
33499507 AA-ATAATAAATAATAA
1 AACATAAT-AATAAT-A
33499523 AACA-AATAATAATTA
1 AACATAATAATAA-TA
33499538 AA-ATAA-AATAA
1 AACATAATAATAA
33499549 AAATAAAGAG
Statistics
Matches: 92, Mismatches: 6, Indels: 29
0.72 0.05 0.23
Matches are distributed among these distances:
11 1 0.01
12 8 0.09
13 11 0.12
14 15 0.16
15 35 0.38
16 15 0.16
17 7 0.08
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.20
Consensus pattern (15 bp):
AACATAATAATAATA
Found at i:33499506 original size:34 final size:34
Alignment explanation
Indices: 33499459--33499554 Score: 106
Period size: 34 Copynumber: 2.8 Consensus size: 34
33499449 TAAACATAAT
* *
33499459 AATAAAAACAAATAGAAAGAAT-AATAATAAAACA
1 AATAATAATAAATA-AAAGAATAAATAATAAAACA
* *
33499493 AATGATAATAAATAAAATAATAAATAATAAAACA
1 AATAATAATAAATAAAAGAATAAATAATAAAACA
*
33499527 AATAATAATTAAAATAAAATAA-AAATAA
1 AATAATAA-T-AAATAAAAGAATAAATAA
33499555 AGAGCACGGG
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
33 6 0.11
34 30 0.56
35 7 0.13
36 11 0.20
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.21
Consensus pattern (34 bp):
AATAATAATAAATAAAAGAATAAATAATAAAACA
Found at i:33499508 original size:19 final size:17
Alignment explanation
Indices: 33499479--33499555 Score: 65
Period size: 15 Copynumber: 4.6 Consensus size: 17
33499469 AATAGAAAGA
33499479 ATAATAATAAAACAAAT
1 ATAATAATAAAACAAAT
*
33499496 GATAATAAATAAAA-TAAT
1 -ATAAT-AATAAAACAAAT
33499514 A-AATAATAAAAC-AA-
1 ATAATAATAAAACAAAT
*
33499528 ATAATAATTAAAATAAA-
1 ATAATAA-TAAAACAAAT
*
33499545 ATAAAAATAAA
1 ATAATAATAAA
33499556 GAGCACGGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
14 1 0.02
15 14 0.27
16 12 0.24
17 9 0.18
18 8 0.16
19 7 0.14
ACGTcount: A:0.73, C:0.03, G:0.01, T:0.23
Consensus pattern (17 bp):
ATAATAATAAAACAAAT
Found at i:33499512 original size:12 final size:12
Alignment explanation
Indices: 33499442--33499555 Score: 65
Period size: 12 Copynumber: 9.2 Consensus size: 12
33499432 AATAAGAACA
*
33499442 AAAATAATAAAC
1 AAAATAATAAAT
* *
33499454 ATAATAATAAAA
1 AAAATAATAAAT
* *
33499466 ACAAAT-AGAAAG
1 A-AAATAATAAAT
*
33499478 AATAATAATAAAAC
1 AA-AATAAT-AAAT
33499492 AAATGATAATAAAT
1 AAA--ATAATAAAT
33499506 AAAATAATAAAT
1 AAAATAATAAAT
*
33499518 AATAA-AACAAAT
1 AA-AATAATAAAT
*
33499530 AATAATTA-AAAT
1 AA-AATAATAAAT
33499542 AAAATAA-AAAT
1 AAAATAATAAAT
33499553 AAA
1 AAA
33499556 GAGCACGGGT
Statistics
Matches: 83, Mismatches: 11, Indels: 17
0.75 0.10 0.15
Matches are distributed among these distances:
11 12 0.14
12 47 0.57
13 8 0.10
14 11 0.13
15 5 0.06
ACGTcount: A:0.73, C:0.04, G:0.03, T:0.21
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:33503357 original size:5 final size:5
Alignment explanation
Indices: 33503349--33503390 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
33503339 AACTAAAAAC
33503349 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AA
33503391 ATGGCTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:33508021 original size:19 final size:19
Alignment explanation
Indices: 33507989--33508030 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
33507979 TCTTATTTAT
33507989 TATATGTTATTTTTAAATA
1 TATATGTTATTTTTAAATA
*
33508008 TATAT-TTATATTTTAAATT
1 TATATGTTAT-TTTTAAATA
33508027 TATA
1 TATA
33508031 ATTTCAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATGTTATTTTTAAATA
Found at i:33508577 original size:12 final size:13
Alignment explanation
Indices: 33508562--33508594 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
33508552 TTTGAAATAT
33508562 TTTTATTTTTC-A
1 TTTTATTTTTCTA
33508574 TTTTATTTTTCTA
1 TTTTATTTTTCTA
*
33508587 TTTAATTT
1 TTTTATTT
33508595 CTAATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTATTTTTCTA
Found at i:33518362 original size:18 final size:21
Alignment explanation
Indices: 33518339--33518376 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
33518329 TGGGAGTAAA
33518339 TTTAGG-TTT-TA-TTAAATT
1 TTTAGGATTTGTAGTTAAATT
33518357 TTTAGGATTTGTAGTTAAAT
1 TTTAGGATTTGTAGTTAAAT
33518377 CATGGGCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 3 0.18
20 2 0.12
21 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTAGGATTTGTAGTTAAATT
Found at i:33527129 original size:27 final size:27
Alignment explanation
Indices: 33527087--33527339 Score: 321
Period size: 27 Copynumber: 9.4 Consensus size: 27
33527077 CCCTAAAATA
*
33527087 GGTAAAATGACTGAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
*
33527114 GGTAAAATAACCGAAATATCCCC-ATAG
1 GGTAAAATGACCGAAATA-CCCCTATAG
** * *
33527141 GGTAAAATGACTAAAATGCCCCCATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* *
33527168 GGTAAAATGAACAAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* * *
33527195 GGTAAAATGATCGAAGTACCCCTATAT
1 GGTAAAATGACCGAAATACCCCTATAG
*
33527222 GGTAAAATGACCTAAATACCCCTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* *
33527249 GATAAAATGACCGAAATACCCTTATAG
1 GGTAAAATGACCGAAATACCCCTATAG
* *
33527276 GGTAAAATGACCGAAATACCCCCATAA
1 GGTAAAATGACCGAAATACCCCTATAG
*
33527303 GGTAAAATGATCGAAATACCCC-ATAG
1 GGTAAAATGACCGAAATACCCCTATAG
*
33527329 GGTAAGATGAC
1 GGTAAAATGAC
33527340 TATTATACCC
Statistics
Matches: 195, Mismatches: 29, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
26 16 0.08
27 175 0.90
28 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGAAATACCCCTATAG
Found at i:33534418 original size:59 final size:59
Alignment explanation
Indices: 33534355--33534504 Score: 194
Period size: 59 Copynumber: 2.5 Consensus size: 59
33534345 GCCAGAAACA
* * *
33534355 CATCCTTTTCTTTCAATACTCGCCATAAAGGCTTTCCATTAAAAAATTTTCTATAAAGG
1 CATCCTTTTCTTTCAGTACTCGCCACAAAGGCTTTCCATTAAAAAATTTTCAATAAAGG
* * * *
33534414 CATCCTTTTCATTT-AGTACTCGCCACAAAGGCTTTCCTTTTAGAGATTTTCAATAAAGG
1 CATCCTTTTC-TTTCAGTACTCGCCACAAAGGCTTTCCATTAAAAAATTTTCAATAAAGG
* * *
33534473 AATCATTTTCTTTCAGTACTCGACACAAAGGC
1 CATCCTTTTCTTTCAGTACTCGCCACAAAGGC
33534505 ATCCTTCGTC
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 3 0.04
59 73 0.92
60 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (59 bp):
CATCCTTTTCTTTCAGTACTCGCCACAAAGGCTTTCCATTAAAAAATTTTCAATAAAGG
Found at i:33538353 original size:19 final size:21
Alignment explanation
Indices: 33538329--33538371 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
33538319 GCACCTAGGA
33538329 TGATTGT-TTTGA-CATGTTT
1 TGATTGTATTTGATCATGTTT
*
33538348 TGATTGTATTTGATCGTGTTT
1 TGATTGTATTTGATCATGTTT
33538369 TGA
1 TGA
33538372 ACTGGTTAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.16, C:0.05, G:0.23, T:0.56
Consensus pattern (21 bp):
TGATTGTATTTGATCATGTTT
Found at i:33560681 original size:24 final size:25
Alignment explanation
Indices: 33560645--33560692 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
33560635 TTTCTTTCCA
33560645 TTTTCTTTCTATT-TCTTTATTATG
1 TTTTCTTTCTATTATCTTTATTATG
33560669 TTTTCATTT-TATTATCTTTATTAT
1 TTTTC-TTTCTATTATCTTTATTAT
33560693 TATCATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.17, C:0.10, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTCTTTCTATTATCTTTATTATG
Found at i:33560694 original size:12 final size:12
Alignment explanation
Indices: 33560672--33560706 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
33560662 TATTATGTTT
33560672 TCATT-TTATTA
1 TCATTATTATTA
*
33560683 TCTTTATTATTA
1 TCATTATTATTA
33560695 TCATTATTATTA
1 TCATTATTATTA
33560707 AAGTTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.29, C:0.09, G:0.00, T:0.63
Consensus pattern (12 bp):
TCATTATTATTA
Found at i:33561806 original size:85 final size:85
Alignment explanation
Indices: 33561663--33561832 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
33561653 AAACTACCCC
33561663 TATAAGAACTAAATTGAATGACAATCAAAAGTACACAAGAAAAAATGGTCGGTCGATATCTATGT
1 TATAAGAACTAAATTGAATGACAATCAAAAGTACACAAGAAAAAATGGTCGGTCGATATCTATGT
33561728 TGCTAATTAATTCTTGGATT
66 TGCTAATTAATTCTTGGATT
33561748 TATAAGAACTAAATTGAATGACAATCAAAAGTACACAAGAAAAAATGGTCGGTCGATATCTATGT
1 TATAAGAACTAAATTGAATGACAATCAAAAGTACACAAGAAAAAATGGTCGGTCGATATCTATGT
33561813 TGCTAATTAATTCTTGGATT
66 TGCTAATTAATTCTTGGATT
33561833 GGGGATATAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (85 bp):
TATAAGAACTAAATTGAATGACAATCAAAAGTACACAAGAAAAAATGGTCGGTCGATATCTATGT
TGCTAATTAATTCTTGGATT
Found at i:33577079 original size:20 final size:20
Alignment explanation
Indices: 33577050--33577093 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
33577040 ATTAGAATTT
*
33577050 AAAA-ATTAAATTAAAAACA
1 AAAATATTAAAATAAAAACA
*
33577069 AAAATATTAAAATAAAAAGA
1 AAAATATTAAAATAAAAACA
33577089 AAAAT
1 AAAAT
33577094 GGCTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (20 bp):
AAAATATTAAAATAAAAACA
Found at i:33582570 original size:50 final size:49
Alignment explanation
Indices: 33582460--33582574 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 49
33582450 GCAAACACAC
* * *
33582460 CATAGCTCGTATGAGCTTACCAATTTTAGCTTGTGAGAGCTTACCAATT
1 CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
* * *
33582509 C-TCAACTCGTATGAGCTTACCGATTTCCAGCTCGTGAGAGCATACCGATT
1 CAT-AGCTCGTATGAGCTTACCAATTT-CAGCTCGTGAGAGCATACCAATT
33582559 CATAGCTCGTATGAGC
1 CATAGCTCGTATGAGC
33582575 ATACATGTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
48 1 0.02
49 22 0.39
50 32 0.57
51 1 0.02
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (49 bp):
CATAGCTCGTATGAGCTTACCAATTTCAGCTCGTGAGAGCATACCAATT
Found at i:33582578 original size:25 final size:24
Alignment explanation
Indices: 33582462--33582574 Score: 104
Period size: 25 Copynumber: 4.6 Consensus size: 24
33582452 AAACACACCA
*
33582462 TAGCTCGTATGAGCTTACCAATTT
1 TAGCTCGTATGAGCTTACCAATTC
*
33582486 TAGCTTGTGA-GAGCTTACCAATTC
1 TAGCTCGT-ATGAGCTTACCAATTC
* *
33582510 TCAACTCGTATGAGCTTACCGATTTC
1 T-AGCTCGTATGAGCTTACC-AATTC
* * *
33582536 CAGCTCGTGA-GAGCATACCGATTC
1 TAGCTCGT-ATGAGCTTACCAATTC
33582560 ATAGCTCGTATGAGC
1 -TAGCTCGTATGAGC
33582575 ATACATGTAC
Statistics
Matches: 71, Mismatches: 11, Indels: 13
0.75 0.12 0.14
Matches are distributed among these distances:
24 26 0.37
25 40 0.56
26 5 0.07
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (24 bp):
TAGCTCGTATGAGCTTACCAATTC
Found at i:33585298 original size:18 final size:18
Alignment explanation
Indices: 33585270--33585304 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
33585260 ATATATTAAT
33585270 AAATAAATTATT-TAGTA
1 AAATAAATTATTATAGTA
33585287 AAATATAATTATTATAGT
1 AAATA-AATTATTATAGT
33585305 TGCAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 7 0.44
19 4 0.25
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (18 bp):
AAATAAATTATTATAGTA
Found at i:33590999 original size:25 final size:25
Alignment explanation
Indices: 33590932--33591001 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
33590922 GAGGATACTC
*
33590932 CACAGCTTGTGTGAGCACACCGATT
1 CACAGCTTGTGTGAGCATACCGATT
* *
33590957 CACAGCTCGTGTGAGCATATCGATT
1 CACAGCTTGTGTGAGCATACCGATT
*
33590982 CATAGCTTGTGTGAGCATAC
1 CACAGCTTGTGTGAGCATAC
33591002 ATGTACAGGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.27
Consensus pattern (25 bp):
CACAGCTTGTGTGAGCATACCGATT
Found at i:33599629 original size:41 final size:41
Alignment explanation
Indices: 33599507--33599637 Score: 158
Period size: 41 Copynumber: 3.2 Consensus size: 41
33599497 TACCTAATAA
* *
33599507 AATACACC-GACACGAAGCTTGCTAGGCTCAAAGCTTGATAT
1 AATACACCAG-CACGAAGCTTGCTAGGCACAAAGCCTGATAT
* * * *
33599548 AACACACCAGCACGAAGCCTGCTTGG-ATAAAGCCTGATAT
1 AATACACCAGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
***
33599588 AATACATTGGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
1 AATACACCAGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
33599629 AATACACCA
1 AATACACCA
33599638 CAACATCACG
Statistics
Matches: 72, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
40 31 0.43
41 40 0.56
42 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (41 bp):
AATACACCAGCACGAAGCTTGCTAGGCACAAAGCCTGATAT
Found at i:33601112 original size:29 final size:29
Alignment explanation
Indices: 33601079--33601277 Score: 220
Period size: 29 Copynumber: 6.8 Consensus size: 29
33601069 ATCAAATAAA
*
33601079 GAAAAGGGAAGGTTTCGACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
*
33601108 GAAAAGGGATGGCTTCGACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
** ** *
33601137 GAGTAGGGATGACTTCGACCAACGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
** *
33601166 GAAAAGGGATGACTTCAACCATCGAATAT
1 GAAAAGGGATGGTTTCGACCATCGAATAT
*
33601195 GAAAAGGGATGACTTT-GACCATCGAATAT
1 GAAAAGGGATG-GTTTCGACCATCGAATAT
* * * *
33601224 GAAAATGGATGGTTTCAACCATCGATTAAA
1 GAAAAGGGATGGTTTCGACCATCGAAT-AT
* *
33601254 GAGAAGGGATGGTTTCGACTATCG
1 GAAAAGGGATGGTTTCGACCATCG
33601278 TTTAGCACAC
Statistics
Matches: 145, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
28 3 0.02
29 119 0.82
30 23 0.16
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (29 bp):
GAAAAGGGATGGTTTCGACCATCGAATAT
Found at i:33604660 original size:40 final size:40
Alignment explanation
Indices: 33604616--33604751 Score: 173
Period size: 40 Copynumber: 3.4 Consensus size: 40
33604606 TTATTTATAA
* * ** * *
33604616 TAGATTCAGTTGGTATGGCTTGAGGGCACATACGTTTTAG
1 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
33604656 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
1 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
* ** *
33604696 TAGATTCAGTAGGTATGGATCGAAAGTGCATACGTTTCAG
1 TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
*
33604736 TAGATTCGGTAGGTAT
1 TAGATTCAGTAGGTAT
33604752 CACTCGATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 85 1.00
ACGTcount: A:0.28, C:0.13, G:0.27, T:0.32
Consensus pattern (40 bp):
TAGATTCAGTAGGTATGGCTCGAAAGCACATACATTTCAG
Found at i:33606796 original size:45 final size:44
Alignment explanation
Indices: 33606701--33606908 Score: 141
Period size: 45 Copynumber: 4.6 Consensus size: 44
33606691 ATGTCATGGT
* * ** **
33606701 GTCTTTCAACCATTGTCTTATTCATTTCCTGTCATGTTGCCATAGC
1 GTCTTTCAACTATGGTCTTATTCATTTGAT-TCATG-ACCCATAGC
*
33606747 GTCTTTCAACTATGGTCTTATTCATTTGATTCATGACGTCATAGC
1 GTCTTTCAACTATGGTCTTATTCATTTGATTCATGAC-CCATAGC
* * * * * *
33606792 GTCTTTCAGCTATGGTCTTACTCGA-TAGAATCGTGATCCCATAAC
1 GTCTTTCAACTATGGTCTTATTC-ATTTGATTCATGA-CCCATAGC
* * * * * * * *
33606837 GTCTTTCAACTATGGTCTCACTCGTTTCTAGTC-TGGTCTCATAGT
1 GTCTTTCAACTATGGTCTTATTCATTT-GATTCAT-GACCCATAGC
*
33606882 GTCTTTCAACTATGGTCTTATTTATTT
1 GTCTTTCAACTATGGTCTTATTCATTT
33606909 TCGATATAGT
Statistics
Matches: 128, Mismatches: 28, Indels: 13
0.76 0.17 0.08
Matches are distributed among these distances:
45 96 0.75
46 32 0.25
ACGTcount: A:0.20, C:0.23, G:0.15, T:0.42
Consensus pattern (44 bp):
GTCTTTCAACTATGGTCTTATTCATTTGATTCATGACCCATAGC
Found at i:33606897 original size:24 final size:24
Alignment explanation
Indices: 33606870--33606942 Score: 62
Period size: 24 Copynumber: 3.2 Consensus size: 24
33606860 GTTTCTAGTC
*
33606870 TGGTCTCATAGTGTCTTTCAACTA
1 TGGTCTCATAATGTCTTTCAACTA
* * * *
33606894 TGGTCTTAT-TTAT-TTTCGA-TA
1 TGGTCTCATAATGTCTTTCAACTA
* *
33606915 TAGTGTCATAATGTCTTTCAACTA
1 TGGTCTCATAATGTCTTTCAACTA
33606939 TGGT
1 TGGT
33606943 TTTAATCATT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
21 8 0.23
22 7 0.20
23 7 0.20
24 13 0.37
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.47
Consensus pattern (24 bp):
TGGTCTCATAATGTCTTTCAACTA
Found at i:33612404 original size:41 final size:41
Alignment explanation
Indices: 33612343--33612469 Score: 130
Period size: 41 Copynumber: 3.1 Consensus size: 41
33612333 TTACAACTTA
* * *
33612343 CCTGATACAACACACTGGCACGAAGCCTGATAAGCTCAAAG
1 CCTGATATAACACACAGGCACGAAGCCTGATAAGCACAAAG
* * *
33612384 CTTGATATAACACACAGGCACGAAGCCTGCTAGGCACAAAG
1 CCTGATATAACACACAGGCACGAAGCCTGATAAGCACAAAG
* ** * * *
33612425 CCTGATATAATAGTTCA-GCATGAAGCCTGCTAGGCACAAAG
1 CCTGATATAACA-CACAGGCACGAAGCCTGATAAGCACAAAG
33612466 CCTG
1 CCTG
33612470 CTATGCACAA
Statistics
Matches: 74, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 72 0.97
42 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (41 bp):
CCTGATATAACACACAGGCACGAAGCCTGATAAGCACAAAG
Found at i:33612468 original size:16 final size:16
Alignment explanation
Indices: 33612447--33612484 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
33612437 GTTCAGCATG
33612447 AAGCCTGCTAGGCACA
1 AAGCCTGCTAGGCACA
*
33612463 AAGCCTGCTATGCACA
1 AAGCCTGCTAGGCACA
33612479 AAGCCT
1 AAGCCT
33612485 AATATACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.32, G:0.21, T:0.16
Consensus pattern (16 bp):
AAGCCTGCTAGGCACA
Found at i:33612778 original size:45 final size:45
Alignment explanation
Indices: 33612718--33612879 Score: 161
Period size: 45 Copynumber: 3.6 Consensus size: 45
33612708 TTGTCACAGT
* * * * *
33612718 GTCTTTCAACTATGGTCTTATTC-ATTTGATTTGTTATGCTATAGC
1 GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCATA-C
* *
33612763 GTCTTTCAGCTATGGTCTTACTCGA-TAGAATCGTAATGCCATTAC
1 GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCA-TAC
* * * *
33612808 ATCTTTCAGCTATAGTCTTACTCGATAT-AATTGTGATGCCATAAC
1 GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCAT-AC
*
33612853 GTCTTTCAGCTATGGTTTTACTC-ATTT
1 GTCTTTCAGCTATGGTCTTACTCGATTT
33612880 CTGGTATGGT
Statistics
Matches: 96, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
44 4 0.04
45 89 0.93
46 3 0.03
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.43
Consensus pattern (45 bp):
GTCTTTCAGCTATGGTCTTACTCGATTTGAATTGTAATGCCATAC
Found at i:33612893 original size:45 final size:44
Alignment explanation
Indices: 33612844--33612969 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 44
33612834 ATAATTGTGA
* * * * *
33612844 TGCCATAACGTCTTTCAGCTATGGTTTTACTCATTTCTGGTATGG
1 TGCCATAA-GTCTTTCAACTATGGTCTTAATCATTTCCGGTATAG
* * *
33612889 TGCCATAGTGTCTTTCAACTATGGTCTTATTTATTTCCGGTATAG
1 TGCCATA-AGTCTTTCAACTATGGTCTTAATCATTTCCGGTATAG
*
33612934 TGCCATAGATTCTTTCAACTATGGTCTTAATCATTT
1 TGCCATA-AGTCTTTCAACTATGGTCTTAATCATTT
33612970 TCTTCAAGCC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.44
Consensus pattern (44 bp):
TGCCATAAGTCTTTCAACTATGGTCTTAATCATTTCCGGTATAG
Found at i:33622114 original size:74 final size:74
Alignment explanation
Indices: 33621969--33622116 Score: 217
Period size: 74 Copynumber: 2.0 Consensus size: 74
33621959 CCATATAAGC
* * *
33621969 ACTAATTAAATAGAAGTTTGAACCCCTTTAGACATAATAAATATTTTGTAATTTTTCATACCTAA
1 ACTAATCAAATAGAAGTTTAAACCCCTTTAGACATAATAAATATTTTCTAATTTTTCATACCTAA
33622034 GTTAAAAAG
66 GTTAAAAAG
* *
33622043 ACTAATCAAATAGAAGTTTAAACCCCTTTAGAC-TAAATAACTATTTTTCTAGTTTTTCATACCT
1 ACTAATCAAATAGAAGTTTAAACCCCTTTAGACAT-AATAAATA-TTTTCTAATTTTTCATACCT
*
33622107 AAGTAAAAAA
64 AAGTTAAAAA
33622117 AGGGTATCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
73 1 0.02
74 38 0.58
75 27 0.41
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (74 bp):
ACTAATCAAATAGAAGTTTAAACCCCTTTAGACATAATAAATATTTTCTAATTTTTCATACCTAA
GTTAAAAAG
Found at i:33624587 original size:6 final size:6
Alignment explanation
Indices: 33624573--33624606 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
33624563 AGGATTGCAA
*
33624573 ATTTCC ATTTTC ATTTCC ATTTCC ATTTCC ATTT
1 ATTTCC ATTTCC ATTTCC ATTTCC ATTTCC ATTT
33624607 TTAGAAACCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (6 bp):
ATTTCC
Found at i:33632370 original size:13 final size:13
Alignment explanation
Indices: 33632352--33632391 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
33632342 CATGAAAATT
*
33632352 AAAAGAAAGGAAG
1 AAAAGAAAGAAAG
33632365 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
* *
33632378 CAAAGAGAGAAAG
1 AAAAGAAAGAAAG
33632391 A
1 A
33632392 GACGCACGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:33633545 original size:43 final size:43
Alignment explanation
Indices: 33633484--33633569 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
33633474 TATATGATTG
* *
33633484 ATATTGGAATGACAAAGATGAGAAATGAATATGAGATGAGAAA
1 ATATTGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
*
33633527 ATATTGAAATGGCAAAGATGAGAAACGAATATGAGATGAGAAA
1 ATATTGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
33633570 TGAAATATGA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.51, C:0.03, G:0.26, T:0.20
Consensus pattern (43 bp):
ATATTGAAATGACAAAGATGAGAAACGAATATGAGATGAGAAA
Found at i:33633578 original size:19 final size:19
Alignment explanation
Indices: 33633542--33633592 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
33633532 GAAATGGCAA
*
33633542 AGATGAGAAACG-AATATG
1 AGATGAGAAATGAAATATG
33633560 AGATGAGAAATGAAATATG
1 AGATGAGAAATGAAATATG
*
33633579 AAATGATGAAATGA
1 AGATGA-GAAATGA
33633593 GATGTGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.38
19 11 0.38
20 7 0.24
ACGTcount: A:0.53, C:0.02, G:0.25, T:0.20
Consensus pattern (19 bp):
AGATGAGAAATGAAATATG
Found at i:33633587 original size:27 final size:27
Alignment explanation
Indices: 33633557--33633611 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
33633547 AGAAACGAAT
*
33633557 ATGAGATGAGAAATGAAA-TATGAAATG
1 ATGAAATGAGAAATGAAACT-TGAAATG
**
33633584 ATGAAATGAGATGTGAAACTTGAAATG
1 ATGAAATGAGAAATGAAACTTGAAATG
33633611 A
1 A
33633612 ATTCAAGTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.25, T:0.24
Consensus pattern (27 bp):
ATGAAATGAGAAATGAAACTTGAAATG
Found at i:33633601 original size:20 final size:19
Alignment explanation
Indices: 33633544--33633592 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
33633534 AATGGCAAAG
* *
33633544 ATGAGAAACG-AATATGAG
1 ATGAGAAATGAAATATGAA
33633562 ATGAGAAATGAAATATGAA
1 ATGAGAAATGAAATATGAA
33633581 ATGATGAAATGA
1 ATGA-GAAATGA
33633593 GATGTGAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 9 0.33
19 11 0.41
20 7 0.26
ACGTcount: A:0.53, C:0.02, G:0.24, T:0.20
Consensus pattern (19 bp):
ATGAGAAATGAAATATGAA
Found at i:33634107 original size:25 final size:22
Alignment explanation
Indices: 33634075--33634119 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 22
33634065 TAGTTGAGGC
33634075 AATGTTGGTATGGTAGCTTAGCAT
1 AATGTTGGTAT-GT-GCTTAGCAT
33634099 AATGCTTGGTATGTGCTTAGC
1 AATG-TTGGTATGTGCTTAGC
33634120 TTCAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 6 0.30
25 7 0.35
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (22 bp):
AATGTTGGTATGTGCTTAGCAT
Found at i:33634509 original size:54 final size:54
Alignment explanation
Indices: 33634434--33634553 Score: 152
Period size: 54 Copynumber: 2.2 Consensus size: 54
33634424 CACACGCGGG
* * ***
33634434 CGTGTGACCCAAGTCAGTGAGTTACACGA-GCTGAGACACGGGCTGGGACACGGC
1 CGTGTGTCCCAAGTCAGTGAGTTACA-GAGGCTGAGACACAGGCAAAGACACGGC
* * *
33634488 CGTGTGTCTCAAGTCAGTGAGTTACATAGGCTGAGACATAGGCAAAGACACGGC
1 CGTGTGTCCCAAGTCAGTGAGTTACAGAGGCTGAGACACAGGCAAAGACACGGC
33634542 CGTGTGTCCCAA
1 CGTGTGTCCCAA
33634554 CTTCGAGAGT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
53 1 0.02
54 55 0.98
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (54 bp):
CGTGTGTCCCAAGTCAGTGAGTTACAGAGGCTGAGACACAGGCAAAGACACGGC
Found at i:33644041 original size:34 final size:34
Alignment explanation
Indices: 33644003--33644067 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
33643993 TTTAAGTCGT
33644003 TTTCTACACCGCCAATAAAGAAATCAATAGATGA
1 TTTCTACACCGCCAATAAAGAAATCAATAGATGA
* *
33644037 TTTCTGCACCGCCGATAAAGAAATCAATAGA
1 TTTCTACACCGCCAATAAAGAAATCAATAGA
33644068 CCGGTGTACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.42, C:0.22, G:0.14, T:0.23
Consensus pattern (34 bp):
TTTCTACACCGCCAATAAAGAAATCAATAGATGA
Found at i:33646094 original size:42 final size:42
Alignment explanation
Indices: 33646041--33646131 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
33646031 ATAGTTGAAA
* *
33646041 GATAGAACGTTGTTTCTACAACAAATCCGAGAGTTGCAAAAT
1 GATAGACCGTTGTTTCTACAACAAATCCAAGAGTTGCAAAAT
*
33646083 GATAGACCGTTGTTTCTACAACAAATGCAAGAGTTGCAAAAT
1 GATAGACCGTTGTTTCTACAACAAATCCAAGAGTTGCAAAAT
33646125 GAT-GACC
1 GATAGACC
33646132 CGAAGCTAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (42 bp):
GATAGACCGTTGTTTCTACAACAAATCCAAGAGTTGCAAAAT
Found at i:33649354 original size:28 final size:28
Alignment explanation
Indices: 33649319--33649449 Score: 127
Period size: 28 Copynumber: 4.7 Consensus size: 28
33649309 CAGTAATAGT
33649319 ACAGTGTGGGCCTTAGCCCAATACAGCA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
** * *
33649347 ATGGTGTGGGCCTTATCCCAATACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
* * **
33649375 ACAATGTGGGCCTTAGCCCAAAACAATA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
* * * *
33649403 ACAATGTGAGCCTTAGCCCAATAGAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGCA
* * *
33649431 ACAATATAGGCCTTAGCCC
1 ACAGTGTGGGCCTTAGCCC
33649450 TAAACAATAT
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGCA
Found at i:33649391 original size:56 final size:56
Alignment explanation
Indices: 33649323--33649456 Score: 160
Period size: 56 Copynumber: 2.4 Consensus size: 56
33649313 AATAGTACAG
* * *** * *
33649323 TGTGGGCCTTAGCCCAATACAGCAATGGTGTGGGCCTTATCCCAATACAGTAACAA
1 TGTGGGCCTTAGCCCAAAACAACAACAATGTGAGCCTTAGCCCAATACAGTAACAA
* *
33649379 TGTGGGCCTTAGCCCAAAACAATAACAATGTGAGCCTTAGCCCAATAGAGTAACAA
1 TGTGGGCCTTAGCCCAAAACAACAACAATGTGAGCCTTAGCCCAATACAGTAACAA
* * *
33649435 TATAGGCCTTAGCCCTAAACAA
1 TGTGGGCCTTAGCCCAAAACAA
33649457 TATCAGTACA
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 66 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.22
Consensus pattern (56 bp):
TGTGGGCCTTAGCCCAAAACAACAACAATGTGAGCCTTAGCCCAATACAGTAACAA
Found at i:33649457 original size:56 final size:56
Alignment explanation
Indices: 33649351--33649458 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
33649341 ACAGCAATGG
* * * *
33649351 TGTGGGCCTTATCCCAATACAGTAACAATGTGGGCCTTAGCCCAAAACAATAACAA
1 TGTGAGCCTTAGCCCAATACAGTAACAATATAGGCCTTAGCCCAAAACAATAACAA
* *
33649407 TGTGAGCCTTAGCCCAATAGAGTAACAATATAGGCCTTAGCCCTAAACAATA
1 TGTGAGCCTTAGCCCAATACAGTAACAATATAGGCCTTAGCCCAAAACAATA
33649459 TCAGTACAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (56 bp):
TGTGAGCCTTAGCCCAATACAGTAACAATATAGGCCTTAGCCCAAAACAATAACAA
Found at i:33649600 original size:26 final size:26
Alignment explanation
Indices: 33649566--33649645 Score: 117
Period size: 26 Copynumber: 3.1 Consensus size: 26
33649556 AACACACCAA
33649566 TATCGCAGCAAAGCTGCCAATAATAG
1 TATCGCAGCAAAGCTGCCAATAATAG
* *
33649592 TATCACAGCAAAGCTGCCAATAACA-
1 TATCGCAGCAAAGCTGCCAATAATAG
* *
33649617 TATCGCAGCAAAACTACCAATAATAG
1 TATCGCAGCAAAGCTGCCAATAATAG
33649643 TAT
1 TAT
33649646 ACTGCCTCCA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 21 0.45
26 26 0.55
ACGTcount: A:0.42, C:0.24, G:0.14, T:0.20
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAATAATAG
Found at i:33650035 original size:28 final size:27
Alignment explanation
Indices: 33649791--33650202 Score: 286
Period size: 27 Copynumber: 15.3 Consensus size: 27
33649781 GGGTTATAAT
*
33649791 AGTCATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
* * *
33649818 -GATCATTTTACCCTATGGTGGTAATTC
1 AG-TCATTTTACCCTTTGGGGGTATTTC
* * *
33649845 GGTCATTTTACCCTATGAGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
* * * *
33649872 -GATCATTTCACGCTTCGAGGGTATTTC
1 AG-TCATTTTACCCTTTGGGGGTATTTC
* * **
33649899 GGTCATTTCA-CC-TTCAGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
*
33649924 AGTCATTTTA-CCTTATGGGGGTAATTC
1 AGTCATTTTACCCTT-TGGGGGTATTTC
* * *
33649951 GGTGATTTTACCCTATGGGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
**
33649978 -GATCATTTCT-CCCTTCAGGGGTATTTC
1 AG-TCATTT-TACCCTTTGGGGGTATTTC
* *
33650005 AGTTATTTCACCCTTTGGGGGGTATTTC
1 AGTCATTTTACCCTTT-GGGGGTATTTC
* *** *
33650033 AGTCATTTTACCCATCAAGGGTATTTT
1 AGTCATTTTACCCTTTGGGGGTATTTC
* * * * *
33650060 GGTCATTTTACCCTTCGAGGGAATTTT
1 AGTCATTTTACCCTTTGGGGGTATTTC
* ** *
33650087 GGTCATTTTA-CCTTGTATGGGTATTTT
1 AGTCATTTTACCCTT-TGGGGGTATTTC
* * * *
33650114 GGTTATTTTACCCTGTAGGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
*
33650141 AGTCATTTTATCCTTT-GGGGTATTTC
1 AGTCATTTTACCCTTTGGGGGTATTTC
* *
33650167 -GATCATTTTACCCTTCGGGGGCATTTC
1 AG-TCATTTTACCCTTTGGGGGTATTTC
33650194 AGTCATTTT
1 AGTCATTTT
33650203 CCCACAAATC
Statistics
Matches: 313, Mismatches: 55, Indels: 34
0.78 0.14 0.08
Matches are distributed among these distances:
25 22 0.07
26 31 0.10
27 227 0.73
28 33 0.11
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (27 bp):
AGTCATTTTACCCTTTGGGGGTATTTC
Found at i:33656683 original size:18 final size:18
Alignment explanation
Indices: 33656643--33656676 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33656633 CCATGAGGTC
33656643 TGCCCGTGTGGGCCCACA
1 TGCCCGTGTGGGCCCACA
33656661 TGCCCGTGT-GGCCCAC
1 TGCCCGTGTGGGCCCAC
33656677 TTAGCCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.41, G:0.32, T:0.18
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:33658565 original size:43 final size:43
Alignment explanation
Indices: 33658487--33658636 Score: 160
Period size: 43 Copynumber: 3.5 Consensus size: 43
33658477 TGTCTCAAAC
* * *
33658487 ATGGTCTTACATGGAAATCTCATATCAATGGCAATATTCCAACT
1 ATGGTCTTACA-CGAAATCTCATATCAATGCCAATATCCCAACT
* * * * *
33658531 ATGGTCTTACACGAAGTCTCATATCGATGCCAATAGCCTAGCT
1 ATGGTCTTACACGAAATCTCATATCAATGCCAATATCCCAACT
* * *
33658574 ATGGTCTTACAAGAAGTCTTATATCAATGCC-ATATCCCAGA-T
1 ATGGTCTTACACGAAATCTCATATCAATGCCAATATCCCA-ACT
*
33658616 ATGGTCTTATACGAAATCTCA
1 ATGGTCTTACACGAAATCTCA
33658637 AATGCCAATG
Statistics
Matches: 87, Mismatches: 18, Indels: 4
0.80 0.17 0.04
Matches are distributed among these distances:
42 24 0.28
43 52 0.60
44 11 0.13
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCATATCAATGCCAATATCCCAACT
Found at i:33658652 original size:44 final size:44
Alignment explanation
Indices: 33658598--33658731 Score: 169
Period size: 48 Copynumber: 3.0 Consensus size: 44
33658588 AGTCTTATAT
**
33658598 CAATGCCATATCCCAGATATGGTCTTATACGAAATCTCAAATGC
1 CAATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATGC
* * *
33658642 CAATGGCATATCCCAGATATGGCCTTATACGGGATTTCAAATCGATGC
1 CAATGCCATATCCCAGATATGGTCTTATACGGGATCTC-AA---ATGC
* *
33658690 CGATGCCATATCCCAAATATGGTCTTATACGGGATCTCAAAT
1 CAATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAAT
33658732 CAATTCGGCA
Statistics
Matches: 76, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
44 35 0.46
45 2 0.03
47 2 0.03
48 37 0.49
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (44 bp):
CAATGCCATATCCCAGATATGGTCTTATACGGGATCTCAAATGC
Found at i:33664976 original size:42 final size:43
Alignment explanation
Indices: 33664833--33664980 Score: 199
Period size: 43 Copynumber: 3.4 Consensus size: 43
33664823 TGTCCCAAAC
*
33664833 ATGGTCTTACATGGAAATCTCATATCGATGCCAATATCCCAGCT
1 ATGGTCTTACA-CGAAATCTCATATCGATGCCAATATCCCAGCT
* *
33664877 ATGGTCTTACACGAAGTCTCATATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACACGAAATCTCATATCGATGCCAATATCCCAGCT
* * * *
33664920 ATGGTCTTACACGAAATTTCATATCAATGAC-ATATCCCAGAT
1 ATGGTCTTACACGAAATCTCATATCGATGCCAATATCCCAGCT
* *
33664962 ATTGTCTTATACGAAATCT
1 ATGGTCTTACACGAAATCT
33664981 TAAATCAATG
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
42 25 0.27
43 56 0.61
44 11 0.12
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCATATCGATGCCAATATCCCAGCT
Found at i:33664992 original size:85 final size:87
Alignment explanation
Indices: 33664833--33664992 Score: 207
Period size: 85 Copynumber: 1.9 Consensus size: 87
33664823 TGTCCCAAAC
* * * * *
33664833 ATGGTCTTACATGGAAATCTCATATCGATGCCAATATCCCAGCTATGGTCTTACACGAAGTCTCA
1 ATGGTCTTACATCGAAATCTCATATCAATGACAATATCCCAGATATGGTCTTACACGAAATCTCA
* *
33664898 TATCGATGCCAATAGCCCAGCT
66 AATCAATGCCAATAGCCCAGCT
* * * *
33664920 ATGGTCTTACA-CGAAATTTCATATCAATGAC-ATATCCCAGATATTGTCTTATACGAAATCTTA
1 ATGGTCTTACATCGAAATCTCATATCAATGACAATATCCCAGATATGGTCTTACACGAAATCTCA
33664983 AATCAATGCC
66 AATCAATGCC
33664993 GATGCCATAT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
85 35 0.56
86 16 0.26
87 11 0.18
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (87 bp):
ATGGTCTTACATCGAAATCTCATATCAATGACAATATCCCAGATATGGTCTTACACGAAATCTCA
AATCAATGCCAATAGCCCAGCT
Found at i:33665021 original size:48 final size:48
Alignment explanation
Indices: 33664950--33665130 Score: 202
Period size: 48 Copynumber: 3.8 Consensus size: 48
33664940 ATATCAATGA
* * * *
33664950 CATATCCCAGATATTGTCTTATACGAAATCTTAAATCAATGCCGATGC
1 CATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGCCGATGC
* * * * **
33664998 CATATCCTATATCTGGTCTTATAC-AGGATCTCAAATGGATGTTGATGC
1 CATATCCCAGATATGGTCTTATACGA-GATCTCAAATCGATGCCGATGC
* *
33665046 CATATCCCAGATATGGTCTTATACGGGATCTCAAAACGATGCCGATGC
1 CATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGCCGATGC
** * *
33665094 CATATTTCAGATATGGTCTTATATGGGATCTCAAATC
1 CATATCCCAGATATGGTCTTATACGAGATCTCAAATC
33665131 AATCCGGCAA
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 108 0.99
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (48 bp):
CATATCCCAGATATGGTCTTATACGAGATCTCAAATCGATGCCGATGC
Found at i:33665065 original size:96 final size:96
Alignment explanation
Indices: 33664950--33665129 Score: 245
Period size: 96 Copynumber: 1.9 Consensus size: 96
33664940 ATATCAATGA
* * * * *
33664950 CATATCCCAGATATTGTCTTATACGAAATCTTAAATCAATGCCGATGCCATATC-CTATATCTGG
1 CATATCCCAGATATGGTCTTATACGAAATCTCAAAACAATGCCGATGCCATATCTC-AGATATGG
33665014 TCTTATACAGGATCTCAAATGGATGTTGATGC
65 TCTTATACAGGATCTCAAATGGATGTTGATGC
** * *
33665046 CATATCCCAGATATGGTCTTATACGGGATCTCAAAACGATGCCGATGCCATATTTCAGATATGGT
1 CATATCCCAGATATGGTCTTATACGAAATCTCAAAACAATGCCGATGCCATATCTCAGATATGGT
**
33665111 CTTATATGGGATCTCAAAT
66 CTTATACAGGATCTCAAAT
33665130 CAATCCGGCA
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
96 71 0.99
97 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (96 bp):
CATATCCCAGATATGGTCTTATACGAAATCTCAAAACAATGCCGATGCCATATCTCAGATATGGT
CTTATACAGGATCTCAAATGGATGTTGATGC
Found at i:33665159 original size:30 final size:30
Alignment explanation
Indices: 33665125--33665219 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 30
33665115 TATGGGATCT
*
33665125 CAAATCAATCCGGCAATATATATACATATA
1 CAAATCAATTCGGCAATATATATACATATA
** * *
33665155 CAAATCAATTCGAAAATGTATATATCTACATA
1 CAAATCAATTCGGCAATATATATA-C-ATATA
*
33665187 TAAATCAATTCGGCAATATATAATACATATA
1 CAAATCAATTCGGCAATATAT-ATACATATA
33665218 CA
1 CA
33665220 TTTGAATTCA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
30 20 0.39
31 6 0.12
32 22 0.43
33 3 0.06
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.29
Consensus pattern (30 bp):
CAAATCAATTCGGCAATATATATACATATA
Found at i:33674654 original size:9 final size:10
Alignment explanation
Indices: 33674634--33674662 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
33674624 ATTGCGTGTT
33674634 TGAATAGAAA
1 TGAATAGAAA
33674644 TGAAT-GAAA
1 TGAATAGAAA
33674653 TGAATAGAAA
1 TGAATAGAAA
33674663 ATGAGAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.59, C:0.00, G:0.21, T:0.21
Consensus pattern (10 bp):
TGAATAGAAA
Found at i:33675396 original size:24 final size:24
Alignment explanation
Indices: 33675369--33675417 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
33675359 TGTTTCTATT
*
33675369 AAAGAAGAGAAAACTTTCATTTTC
1 AAAGAAAAGAAAACTTTCATTTTC
* *
33675393 AAAGAAAAGAGAATTTTCATTTTC
1 AAAGAAAAGAAAACTTTCATTTTC
33675417 A
1 A
33675418 CCCCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (24 bp):
AAAGAAAAGAAAACTTTCATTTTC
Found at i:33678431 original size:20 final size:19
Alignment explanation
Indices: 33678406--33678450 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
33678396 CGGGACTAAA
* *
33678406 TCAAAAATTTAGAGAATTTT
1 TCAAAAAATTAGA-AAATTT
*
33678426 TCAAAAAATTATAAAATTT
1 TCAAAAAATTAGAAAATTT
33678445 TCAAAA
1 TCAAAA
33678451 CTGCAAGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (19 bp):
TCAAAAAATTAGAAAATTT
Found at i:33679971 original size:25 final size:25
Alignment explanation
Indices: 33679920--33680009 Score: 110
Period size: 25 Copynumber: 3.6 Consensus size: 25
33679910 GTACATGTAT
* *
33679920 GCTCATACGAGCTGTA-AATGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
33679944 GCTCCTCCGAGCTGAATAACGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
* *
33679969 GCTCATACGAGCTGAGTATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
*
33679994 GCTCATAAGAGCTGAA
1 GCTCATACGAGCTGAA
33680010 ATCGATAACC
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 13 0.24
25 42 0.76
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.22
Consensus pattern (25 bp):
GCTCATACGAGCTGAATAACGGTAA
Found at i:33681285 original size:22 final size:22
Alignment explanation
Indices: 33681257--33681338 Score: 119
Period size: 22 Copynumber: 3.7 Consensus size: 22
33681247 GTGCCAATCT
33681257 ATGAGAGCTTAGTACGTTAGCC
1 ATGAGAGCTTAGTACGTTAGCC
33681279 ATGAGAGCTTAGTACGTTAGCC
1 ATGAGAGCTTAGTACGTTAGCC
* * * **
33681301 ATGAGGGTTTAGTTCGTTAAAC
1 ATGAGAGCTTAGTACGTTAGCC
33681323 ATGAGAGCTTAGTACG
1 ATGAGAGCTTAGTACG
33681339 ACTATAGACA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (22 bp):
ATGAGAGCTTAGTACGTTAGCC
Found at i:33687505 original size:15 final size:15
Alignment explanation
Indices: 33687464--33687512 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
33687454 AAGAAAATAA
33687464 ATAAAAGATAT-AAAT
1 ATAAAA-ATATAAAAT
* *
33687479 ATAAGGATTATAAAAT
1 ATAA-AAATATAAAAT
33687495 ATAAAAATATAAAAT
1 ATAAAAATATAAAAT
33687510 ATA
1 ATA
33687513 GGTACGTACG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 19 0.68
16 9 0.32
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
ATAAAAATATAAAAT
Found at i:33687948 original size:3 final size:3
Alignment explanation
Indices: 33687913--33688002 Score: 67
Period size: 3 Copynumber: 29.3 Consensus size: 3
33687903 ATAAGAAAAC
* * * * * *
33687913 ATA ATA CTA ACA ATA GTA TTA ATA A-A TATA ATA ATA AAA ATA GTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
*
33687958 A-A GATA ATA ATG ATA ATA ATA ATA ATA ACTAA ATA ATA ATA ATA A
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA A-T-A ATA ATA ATA ATA A
33688003 AAAATGCTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
2 2 0.03
3 60 0.88
4 4 0.06
5 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:33688905 original size:20 final size:20
Alignment explanation
Indices: 33688880--33688918 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
33688870 GACGGCGCAA
**
33688880 GTGGTGGTGGTGACGTGACC
1 GTGGTGGTGACGACGTGACC
33688900 GTGGTGGTGACGACGTGAC
1 GTGGTGGTGACGACGTGAC
33688919 GTTGGCGGCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.15, G:0.49, T:0.23
Consensus pattern (20 bp):
GTGGTGGTGACGACGTGACC
Found at i:33694953 original size:70 final size:70
Alignment explanation
Indices: 33694874--33695016 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
33694864 ATACAATATC
33694874 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
1 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
33694939 AAATA
66 AAATA
*
33694944 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGTT
1 TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
33695009 AAATA
66 AAATA
33695014 TAA
1 TAA
33695017 GTCTTGATAC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (70 bp):
TAAAAATTATTTATATCATAATTTAATTCTTATTAACATAATATTTTATATTTTAAATAAAAGCT
AAATA
Found at i:33694992 original size:35 final size:35
Alignment explanation
Indices: 33694883--33694994 Score: 113
Period size: 35 Copynumber: 3.2 Consensus size: 35
33694873 CTAAAAATTA
33694883 TTTATATCATAATTTAATTCTTATTAACATAATAT
1 TTTATATCATAATTTAATTCTTATTAACATAATAT
** * * ** *
33694918 TTTATATTTTAAATAAAAGCTAAATATAA-A-AAT-T
1 TTTATATCATAATTTAATTCT-TAT-TAACATAATAT
33694952 ATTTATATCATAATTTAATTCTTATTAACATAATAT
1 -TTTATATCATAATTTAATTCTTATTAACATAATAT
33694988 TTTATAT
1 TTTATAT
33694995 TTTAAATAAA
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
33 3 0.05
34 4 0.07
35 43 0.75
36 4 0.07
37 3 0.05
ACGTcount: A:0.44, C:0.06, G:0.01, T:0.49
Consensus pattern (35 bp):
TTTATATCATAATTTAATTCTTATTAACATAATAT
Found at i:33697361 original size:26 final size:27
Alignment explanation
Indices: 33697322--33697373 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
33697312 AGTTTTTCAT
33697322 TGCTTTTGAAAAGTGC-TGTGAAAAAG
1 TGCTTTTGAAAAGTGCTTGTGAAAAAG
*
33697348 TGCTTTT-AAGAAGTGCTTTTGAAAAA
1 TGCTTTTGAA-AAGTGCTTGTGAAAAA
33697374 TTTGAGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 2 0.09
26 13 0.57
27 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (27 bp):
TGCTTTTGAAAAGTGCTTGTGAAAAAG
Found at i:33697652 original size:27 final size:29
Alignment explanation
Indices: 33697585--33697653 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 29
33697575 CTAAGTAATT
33697585 AATAT-TAATTATTTATTAAATTTAATTAG
1 AATATATAATTATTTATTAAA-TTAATTAG
*
33697614 AATATATAAATTATTT-TTAAA-TATTTA-
1 AATATAT-AATTATTTATTAAATTAATTAG
33697641 AATATAATAATTA
1 AATAT-ATAATTA
33697654 AATATTTGTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
27 10 0.28
28 7 0.19
29 5 0.14
30 6 0.17
31 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
AATATATAATTATTTATTAAATTAATTAG
Found at i:33697656 original size:32 final size:30
Alignment explanation
Indices: 33697584--33697660 Score: 79
Period size: 31 Copynumber: 2.5 Consensus size: 30
33697574 TCTAAGTAAT
*
33697584 TAATATT-AATTATTTATTAAATTTAATTA
1 TAATATTAAATTATTTATTAAATTTAAATA
*
33697613 GAATATATAAATTATTT-TTAAATATTTAAATA
1 TAATAT-TAAATTATTTATT-AA-ATTTAAATA
33697645 TAATAATTAAA-TATTT
1 TAAT-ATTAAATTATTT
33697661 GTAATTAGAT
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
29 5 0.12
30 3 0.08
31 15 0.38
32 15 0.38
33 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (30 bp):
TAATATTAAATTATTTATTAAATTTAAATA
Found at i:33700501 original size:24 final size:24
Alignment explanation
Indices: 33700472--33700540 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 24
33700462 AAATAAAAGT
33700472 AATAATAATACAGT-ATAACTTTTA-
1 AATAATAATACA-TAATAA-TTTTAG
*
33700496 AGTAATAATACATAATAATTTTAG
1 AATAATAATACATAATAATTTTAG
*
33700520 AATAATAATACACAATAATTT
1 AATAATAATACATAATAATTT
33700541 CAAAAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
23 6 0.15
24 34 0.85
ACGTcount: A:0.52, C:0.07, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATAATACATAATAATTTTAG
Found at i:33702884 original size:20 final size:20
Alignment explanation
Indices: 33702841--33702884 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
33702831 GACAGAGATT
* **
33702841 AAACAGAAGAGGAACTAATT
1 AAACAGAAGAAGAACTAAAG
*
33702861 AAACAGAAGAAGAAGTAAAG
1 AAACAGAAGAAGAACTAAAG
33702881 AAAC
1 AAAC
33702885 TCTCACCTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.61, C:0.09, G:0.20, T:0.09
Consensus pattern (20 bp):
AAACAGAAGAAGAACTAAAG
Found at i:33703004 original size:29 final size:29
Alignment explanation
Indices: 33702971--33703027 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
33702961 CTCCAATTTC
33702971 ACCAGCAGA-GGAAAAAGAACGTTTGGGGA
1 ACCAGCAGAGGGAAAAA-AACGTTTGGGGA
*
33703000 ACCAGCAGAGGGGAAAAAACGTTTGGGG
1 ACCAGCAGAGGGAAAAAAACGTTTGGGG
33703028 GAGAAGACAG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 20 0.77
30 6 0.23
ACGTcount: A:0.39, C:0.14, G:0.37, T:0.11
Consensus pattern (29 bp):
ACCAGCAGAGGGAAAAAAACGTTTGGGGA
Found at i:33703461 original size:9 final size:9
Alignment explanation
Indices: 33703447--33703532 Score: 120
Period size: 9 Copynumber: 9.4 Consensus size: 9
33703437 TTTGGTTAAA
33703447 AATTACCCG
1 AATTACCCG
33703456 AATTACCCG
1 AATTACCCG
33703465 AATTACCCG
1 AATTACCCG
33703474 AATTACCCG
1 AATTACCCG
*
33703483 AATTAACCG
1 AATTACCCG
*
33703492 AATTAACCG
1 AATTACCCG
33703501 AATTA-CCG
1 AATTACCCG
*
33703509 AAAAATACCCG
1 --AATTACCCG
33703520 AATTACCCG
1 AATTACCCG
33703529 AATT
1 AATT
33703533 TTTTTATTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 6
0.89 0.04 0.08
Matches are distributed among these distances:
8 3 0.04
9 61 0.86
10 4 0.06
11 3 0.04
ACGTcount: A:0.40, C:0.28, G:0.10, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:33703690 original size:13 final size:13
Alignment explanation
Indices: 33703672--33703701 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33703662 TTTTAGTTTT
33703672 ATTGGGTTGAGTA
1 ATTGGGTTGAGTA
*
33703685 ATTGGGTTGGGTA
1 ATTGGGTTGAGTA
33703698 ATTG
1 ATTG
33703702 AGTTTGGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGAGTA
Found at i:33708277 original size:23 final size:22
Alignment explanation
Indices: 33708223--33708273 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
33708213 AATAAAAACA
33708223 AAAACATATGTATAAAATATAT
1 AAAACATATGTATAAAATATAT
* **
33708245 ATAAGCATATGTATACTATATAT
1 A-AAACATATGTATAAAATATAT
33708268 AAAACA
1 AAAACA
33708274 ATATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (22 bp):
AAAACATATGTATAAAATATAT
Found at i:33708342 original size:3 final size:3
Alignment explanation
Indices: 33708310--33708370 Score: 79
Period size: 3 Copynumber: 20.7 Consensus size: 3
33708300 GCGCATGAAT
* * * *
33708310 ATA AAA ATA AAA ATA ATA A-A AAA ATG ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
33708357 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
33708371 GATGATGATG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:33708375 original size:3 final size:3
Alignment explanation
Indices: 33708369--33708403 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
33708359 AATAATAATA
33708369 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
33708404 ACAAGATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:33708873 original size:22 final size:21
Alignment explanation
Indices: 33708838--33708914 Score: 68
Period size: 19 Copynumber: 3.7 Consensus size: 21
33708828 AAAAGGTATC
* *
33708838 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAGAT
33708859 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATC-TCTAAGAT
* *
33708882 TGCATATCATA--TCTAAGAT
1 TACAAATCATATCTCTAAGAT
* *
33708901 TATATATCATATCT
1 TACAAATCATATCT
33708915 AAGATTGCAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
19 17 0.37
21 4 0.09
22 15 0.33
23 10 0.22
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (21 bp):
TACAAATCATATCTCTAAGAT
Done.