Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 135 of 204
Found at i:41091479 original size:22 final size:22
Alignment explanation
Indices: 41091436--41091505 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
41091426 GATATATTAG
41091436 TATG-TATATTA-TGT-T-TGT
1 TATGATATATTAGTGTGTATGT
41091454 TATGATATATTAGTGTGTATGT
1 TATGATATATTAGTGTGTATGT
* *
41091476 TATGATATGTTAGTATGTATAG-
1 TATGATATATTAGTGTGTAT-GT
41091498 TATGATAT
1 TATGATAT
41091506 TTTTTTTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.09
19 7 0.16
20 3 0.07
21 1 0.02
22 29 0.64
23 1 0.02
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.51
Consensus pattern (22 bp):
TATGATATATTAGTGTGTATGT
Found at i:41107294 original size:26 final size:27
Alignment explanation
Indices: 41107246--41107306 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
41107236 TAGGTTAATT
* *
41107246 TTAAAAT-AAGTAATATGTAAAATAAC
1 TTAAAATAAAATAATATATAAAATAAC
*
41107272 TTTAAATAAAATAATATAT-AAATAAC
1 TTAAAATAAAATAATATATAAAATAAC
41107298 TTAAAATAA
1 TTAAAATAA
41107307 TTAGCCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (27 bp):
TTAAAATAAAATAATATATAAAATAAC
Found at i:41109586 original size:132 final size:132
Alignment explanation
Indices: 41109314--41109586 Score: 388
Period size: 132 Copynumber: 2.1 Consensus size: 132
41109304 TGCAACCTCG
* * *
41109314 GGGAGATAAAATTACAGGCTTCAATGTACTCCACTGTAATCACAGGGAGGTAAAATTCACCATCT
1 GGGAGATAGAATTACAGGCTTCAATGTACTCCACTATAATCACAAGGAGGTAAAATTCACCATCT
* * * * *
41109379 TTGATCTACTCGACTATTACTTAGGGAGATGAGATCTGAAATCTTCAATCTATTCCGCTGCTGCC
66 TTGATCTACTCCACTATTACGTAGGGAGATGAGATCTGAAATCTTCAACCTATTCCACTGCTGAC
41109444 CA
131 CA
* * **
41109446 GGGAGATAGAATTACTGGCTTCAATGTATTCCACTATAATCACAAGGAGGTAAAATAT-GTCATC
1 GGGAGATAGAATTACAGGCTTCAATGTACTCCACTATAATCACAAGGAGGTAAAAT-TCACCATC
* *
41109510 TTTGATCTGCTCCACTATTGCGTAGGGAGATGAGATCTGAAAT-TTCCAACCTATTCCACTGCTG
65 TTTGATCTACTCCACTATTACGTAGGGAGATGAGATCTGAAATCTT-CAACCTATTCCACTGCTG
41109574 ACCA
129 ACCA
41109578 GGGAGATAG
1 GGGAGATAG
41109587 GACTTGTGGC
Statistics
Matches: 125, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
131 2 0.02
132 122 0.98
133 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (132 bp):
GGGAGATAGAATTACAGGCTTCAATGTACTCCACTATAATCACAAGGAGGTAAAATTCACCATCT
TTGATCTACTCCACTATTACGTAGGGAGATGAGATCTGAAATCTTCAACCTATTCCACTGCTGAC
CA
Found at i:41109857 original size:257 final size:257
Alignment explanation
Indices: 41109508--41110327 Score: 1250
Period size: 257 Copynumber: 3.2 Consensus size: 257
41109498 AAATATGTCA
* * * ** *
41109508 TCTTTGATCTGCTCCACTATTGCGTAGGGAGATGAGATCTGAAATTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
41109573 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTC
66 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTC
*
41109638 TTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-TCAACCTATTCCACTGCTG
131 TTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTG
*
41109702 ACCAAGGAGATAGAACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCTG
196 ACCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCTG
* *
41109764 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTCAACCTATTCCACTGC
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTC-CAACCTATTCCACTGC
* * *
41109829 TGACCAGGGATATAGGACTTGTGGCTTAAATTTGCTTCCTTACTCTTGAAGATAAGATTTGCCGT
65 TGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGT
* * * *
41109894 CTTCGATCTGATCCGCTACTGCTTATGGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGCT
130 CTTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCT
* *
41109959 GACC-AGGAATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTG-TCG
195 GACCAAGG-AGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCT-G
* * * *
41110022 TCTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCAACCTATTCCACTACT
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
* * *
41110087 GACCAGGGAGATAGGACTTGTGGCATAAATCTGCTTTCTTACACTTGAAGATAAGATTCGCCGTC
66 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTC
* * * *
41110152 TTTGATCTACTCCGCTAGTGCTTAGGGAGACAAGATCTGTAATTTCCCAACTTATTCCACTACTG
131 TTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTG
* * * * *
41110217 GCCAAGGAGATAGGACTTTTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCG
196 ACCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCTG
* * *
41110279 TCTTCGATCTACTCCACTATTGCTTAGAGAGACAAGATCTGTAATTTCC
1 TCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCC
41110328 CTGATCTGTT
Statistics
Matches: 510, Mismatches: 48, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
256 40 0.08
257 349 0.68
258 121 0.24
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (257 bp):
TCTTCGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTC
TTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTGCTG
ACCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCTG
Found at i:41109896 original size:129 final size:128
Alignment explanation
Indices: 41109508--41110327 Score: 1226
Period size: 129 Copynumber: 6.4 Consensus size: 128
41109498 AAATATGTCA
* * * * ** *
41109508 TCTTTGATCTGCTCCACTATTGCGTAGGGAGATGAGATCTGAAATTTCCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
41109573 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
66 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
* *
41109636 TCTTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTTCAACCTATTCCACTGCT
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
* * *
41109701 GACCAAGGAGATAGAACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCTG
66 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
*
41109764 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTCAACCTATTCCACTGC
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTC-CAACCTATTCCACTGC
* * *
41109829 TGACCAGGGATATAGGACTTGTGGCTTAAATTTGCTTCCTTACTCTTGAAGATAAGATTTGCCG
65 TGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
* * *
41109893 TCTTCGATCTGATCCGCTACTGCTTATGGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGC
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGC
* * * *
41109958 TGACCAGGAATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTCG
65 TGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
* * *
41110022 TCTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCAACCTATTCCACTACT
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
* * *
41110087 GACCAGGGAGATAGGACTTGTGGCATAAATCTGCTTTCTTACACTTGAAGATAAGATTCGCCG
66 GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
* * * * *
41110150 TCTTTGATCTACTCCGCTAGTGCTTAGGGAGACAAGATCTGTAATTTCCCAACTTATTCCACTAC
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTT-CCAACCTATTCCACTGC
* * * * *
41110215 TGGCCAAGGAGATAGGACTTTTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCG
65 TGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
* * * *
41110279 TCTTCGATCTACTCCACTATTGCTTAGAGAGACAAGATCTGTAATTTCC
1 TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCC
41110328 CTGATCTGTT
Statistics
Matches: 634, Mismatches: 55, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
128 280 0.44
129 353 0.56
130 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (128 bp):
TCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTGCT
GACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCG
Found at i:41110002 original size:386 final size:385
Alignment explanation
Indices: 41109508--41110328 Score: 1250
Period size: 386 Copynumber: 2.1 Consensus size: 385
41109498 AAATATGTCA
* * * * *
41109508 TCTTTGATCTGCTCCACTATTGCGTAGGGAGATGAGATCTGAAATTT-CCAACCTATTCCACTGC
1 TCTTCGATCTGATCCACTATTGCTTA-GGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGC
*
41109572 TGACCAGGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGT
65 TGACCAGGAAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGT
** * *
41109637 CTTTGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTTCAACCTATTCCACTGCTG
130 CTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTACTG
* * *
41109702 ACCAAGGAGATAGAACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCTGTCT
195 ACCAAGGAGATAGAACTTGTGGCATAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCT
* * * *
41109767 TCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCTCAACCTATTCCACTGCTGA
260 TCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGA
* * * * **
41109832 CCAGGGATATAGGACTTGTGGCTTAAATTTGCTTCCTTACTCTTGAAGATAAGATTTGCCG
325 CCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCG
* *
41109893 TCTTCGATCTGATCCGCTACTGCTTATGGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGC
1 TCTTCGATCTGATCCACTATTGCTTA-GGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGC
* * *
41109958 TGACCAGGAATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTTGTCGT
65 TGACCAGGAAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGT
*
41110023 CTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTGTAATTTCCAACCTATTCCACTACTG
130 CTTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTACTG
* * *
41110088 ACCAGGGAGATAGGACTTGTGGCATAAATCTGCTTTCTTACACTTGAAGATAAGATTCGCCGTCT
195 ACCAAGGAGATAGAACTTGTGGCATAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCT
* * * *
41110153 TTGATCTACTCCGCTAGTGCTTAGGGAGACAAGATCTGTAATTTCCCAACTTATTCCACTACTGG
260 TCGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGA
*
41110218 CCAAGGAGATAGGACTTTTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCG
325 CCAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCG
*
41110279 TCTTCGATCT-ACTCCACTATTGCTTAGAGAGACAAGATCTGTAATTTCCC
1 TCTTCGATCTGA-TCCACTATTGCTTAG-GAGATAAGATCTGTAATTTCCC
41110329 TGATCTGTTC
Statistics
Matches: 392, Mismatches: 41, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
385 41 0.10
386 351 0.90
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (385 bp):
TCTTCGATCTGATCCACTATTGCTTAGGAGATAAGATCTGTAATTTCCCAACCTATTCCACTGCT
GACCAGGAAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCTTGAAGATAAGATTCGCCGTC
TTCAATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCAACCTATTCCACTACTGA
CCAAGGAGATAGAACTTGTGGCATAAATCTGCTTCCTTACACTTGAAGATAAGATTCGCCGTCTT
CGATCTACTCCGCTACTGCTTAGGGAGACAAGATCTGTAATTTCCCAACCTATTCCACTACTGAC
CAAGGAGATAGGACTTGTGGCTTAAATCTGCTTCCTTACACTTGAAGATAAGATTCACCG
Found at i:41111574 original size:7 final size:7
Alignment explanation
Indices: 41111555--41111606 Score: 63
Period size: 7 Copynumber: 7.3 Consensus size: 7
41111545 TTAGCCTCTC
41111555 CATTTTT
1 CATTTTT
41111562 -ACTTTTT
1 CA-TTTTT
41111569 CATTTTTT
1 CA-TTTTT
41111577 CATTTTT
1 CATTTTT
41111584 CA-TTTT
1 CATTTTT
41111590 CATTTTTT
1 CA-TTTTT
41111598 CATTTTT
1 CATTTTT
41111605 CA
1 CA
41111607 CAATTTTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
6 7 0.17
7 19 0.47
8 14 0.35
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (7 bp):
CATTTTT
Found at i:41111575 original size:8 final size:8
Alignment explanation
Indices: 41111564--41111604 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
41111554 CCATTTTTAC
41111564 TTTTTCAT
1 TTTTTCAT
41111572 TTTTTCA-
1 TTTTTCAT
41111579 TTTTTCA-
1 TTTTTCAT
41111586 -TTTTCAT
1 TTTTTCAT
41111593 TTTTTCAT
1 TTTTTCAT
41111601 TTTT
1 TTTT
41111605 CACAATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 7 0.23
8 18 0.58
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCAT
Found at i:41111589 original size:21 final size:21
Alignment explanation
Indices: 41111555--41111606 Score: 86
Period size: 21 Copynumber: 2.4 Consensus size: 21
41111545 TTAGCCTCTC
*
41111555 CATTTTTACTTTTTCATTTTTT
1 CATTTTT-CATTTTCATTTTTT
41111577 CATTTTTCATTTTCATTTTTT
1 CATTTTTCATTTTCATTTTTT
41111598 CATTTTTCA
1 CATTTTTCA
41111607 CAATTTTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 22 0.76
22 7 0.24
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (21 bp):
CATTTTTCATTTTCATTTTTT
Found at i:41117105 original size:26 final size:27
Alignment explanation
Indices: 41117057--41117117 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
41117047 TAGGTTAATT
* *
41117057 TTAAAAT-AAGTAATATGTAAAATAAC
1 TTAAAATAAAATAATATATAAAATAAC
*
41117083 TTTAAATAAAATAATATAT-AAATAAC
1 TTAAAATAAAATAATATATAAAATAAC
41117109 TTAAAATAA
1 TTAAAATAA
41117118 TTAGCCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 21 0.70
27 9 0.30
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (27 bp):
TTAAAATAAAATAATATATAAAATAAC
Found at i:41118937 original size:29 final size:31
Alignment explanation
Indices: 41118891--41118957 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
41118881 TATGAATTTG
* *
41118891 GAATTTAGTCTGTATA-TTTTTA-TTTTTAA
1 GAATTTAGTCTCTATATTTTTTAGATTTTAA
* *
41118920 GAATTTAGTTTCTCTATTTTTTAGATTTTAA
1 GAATTTAGTCTCTATATTTTTTAGATTTTAA
41118951 -AATTTAG
1 GAATTTAG
41118958 GTTCAAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 13 0.41
30 13 0.41
31 6 0.19
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.57
Consensus pattern (31 bp):
GAATTTAGTCTCTATATTTTTTAGATTTTAA
Found at i:41118941 original size:30 final size:30
Alignment explanation
Indices: 41118891--41118957 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
41118881 TATGAATTTG
* *
41118891 GAATTTAGTCTGTATATTTTTA-TTTTTAA
1 GAATTTAGTCTCTATATTTTTAGATTTTAA
41118920 GAATTTAGTTTCTCTAT-TTTTTAGATTTTAA
1 GAATTTAG--TCTCTATATTTTTAGATTTTAA
41118951 -AATTTAG
1 GAATTTAG
41118958 GTTCAAATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 8 0.24
30 13 0.39
31 12 0.36
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.57
Consensus pattern (30 bp):
GAATTTAGTCTCTATATTTTTAGATTTTAA
Found at i:41119407 original size:17 final size:17
Alignment explanation
Indices: 41119385--41119418 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41119375 GTCCATTTAC
41119385 ATAGTCCAATATCGATT
1 ATAGTCCAATATCGATT
41119402 ATAGTCCAATATCGATT
1 ATAGTCCAATATCGATT
41119419 TTAATTACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (17 bp):
ATAGTCCAATATCGATT
Found at i:41120560 original size:3 final size:3
Alignment explanation
Indices: 41120552--41120609 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
41120542 GTTAATACTC
*
41120552 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41120600 TTA TTA TTA T
1 TTA TTA TTA T
41120610 AACCATGTAC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41120741 original size:22 final size:22
Alignment explanation
Indices: 41120714--41120755 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41120704 ATAATTCAAA
41120714 ATATACATACATTTTCTATAAT
1 ATATACATACATTTTCTATAAT
* *
41120736 ATATACGTACATTTTTTATA
1 ATATACATACATTTTCTATA
41120756 TTTTCAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATACATACATTTTCTATAAT
Found at i:41127792 original size:44 final size:43
Alignment explanation
Indices: 41127728--41128148 Score: 504
Period size: 44 Copynumber: 10.1 Consensus size: 43
41127718 GAAGCAAATC
*
41127728 GAAGATTGTGAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
1 GAAGATTGT-AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
41127772 AAAGATTGTAAGTCCTATCTCCCTGGTCAGCAATGGAATA----
1 GAAGATTGTAA-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
41127812 G--G--TG-AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
1 GAAGATTGTAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* * *
41127850 GAAGATTATGAGTCCTATCTCCCTGGTCAGCAGTGGAATTGGTT
1 GAAGATTGT-AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
*
41127894 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATTGGTT
1 GAAGATTGTAA-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
41127938 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATA----
1 GAAGATTGTAA-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
*
41127978 G--G--TG-AATCATATCTCCCTGGTCAGCAGTGGAAT--GTT
1 GAAGATTGTAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
*
41128014 GTAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
1 GAAGATTGT-AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
41128058 GAAGATTGTGAATCCTATCTCCCTGGTCAGTAGTGGAATAAGTT
1 GAAGATTGT-AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* * *
41128102 GAAGATTGTGAATCCTATCTCCCTGGTCAGCAATGGAGTATGTT
1 GAAGATTGT-AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
41128146 GAA
1 GAA
41128149 AATTACAGAT
Statistics
Matches: 334, Mismatches: 20, Indels: 46
0.83 0.05 0.12
Matches are distributed among these distances:
34 53 0.16
35 4 0.01
36 5 0.01
38 4 0.01
40 4 0.01
42 29 0.09
43 2 0.01
44 233 0.70
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (43 bp):
GAAGATTGTAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
Found at i:41127932 original size:166 final size:164
Alignment explanation
Indices: 41127728--41128138 Score: 673
Period size: 164 Copynumber: 2.5 Consensus size: 164
41127718 GAAGCAAATC
* *
41127728 GAAGATTGTGAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTAAAGATTGTAAGTCCTATCTC
1 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTC
*
41127793 CCTGGTCAGCAATGGAATAGGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTA
66 CCTGGTCAGCAATGGAATAGGTGAATCATATCTCCCTGGTCAGCAGTGGAAT--GTTGAAGATTA
* *
41127858 TGAGTCCTATCTCCCTGGTCAGCAGTGGAATTGGTT
129 TGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
*
41127894 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGTAAGTCCTATCTC
1 GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTC
* * *
41127959 CCTGGTCAGCAGTGGAATAGGTGAATCATATCTCCCTGGTCAGCAGTGGAATGTTGTAGATTGTG
66 CCTGGTCAGCAATGGAATAGGTGAATCATATCTCCCTGGTCAGCAGTGGAATGTTGAAGATTATG
41128024 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
131 AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
41128058 GAAGATTGTGAA-TCCTATCTCCCTGGTCAGTAGTGGAATAAGTTGAAGATTGTGAA-TCCTATC
1 GAAGATTGT-AAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTCCTATC
41128121 TCCCTGGTCAGCAATGGA
64 TCCCTGGTCAGCAATGGA
41128139 GTATGTTGAA
Statistics
Matches: 230, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
164 114 0.50
165 4 0.02
166 112 0.49
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (164 bp):
GAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTCCTATCTC
CCTGGTCAGCAATGGAATAGGTGAATCATATCTCCCTGGTCAGCAGTGGAATGTTGAAGATTATG
AATCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
Found at i:41128048 original size:120 final size:122
Alignment explanation
Indices: 41127865--41128097 Score: 393
Period size: 120 Copynumber: 1.9 Consensus size: 122
41127855 TTATGAGTCC
41127865 TATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
1 TATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
*
41127930 AATTGGTTGAAGATTGT-AAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCA
66 AATAGGTTGAAGATTGTGAA-TCCTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCA
*
41127987 TATCTCCCTGGTCAGCAGTGGAA-T-GTTGTAGATTGTGAA-TCCTATCTCCCTGGTCAGCAGTG
1 TATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGT-AAGTCCTATCTCCCTGGTCAGCAGTG
*
41128049 GAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGTAGTGGAATA
65 GAATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATA
41128098 AGTTGAAGAT
Statistics
Matches: 106, Mismatches: 3, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
120 78 0.74
121 5 0.05
122 23 0.22
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (122 bp):
TATCTCCCTGGTCAGCAGTGGAATTGGTTGAAGATTGTAAGTCCTATCTCCCTGGTCAGCAGTGG
AATAGGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTGAATCA
Found at i:41128165 original size:88 final size:86
Alignment explanation
Indices: 41127981--41128182 Score: 255
Period size: 88 Copynumber: 2.3 Consensus size: 86
41127971 TGGAATAGGT
* * *
41127981 GAATCATATCTCCCTGGTCAGCAGTGGAATGTTGTAGATTGTGAATCCTATCTCCCTGGTCAGCA
1 GAATCCTATCTCCCTGGTCAGTAGTGGAATGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCA
* * **
41128046 GTGGAATAGGTTGAAGATTGT
66 ATGGAATAGGTTGAAAATTCA
41128067 GAATCCTATCTCCCTGGTCAGTAGTGGAATAAGTTGAAGATTGTGAATCCTATCTCCCTGGTCAG
1 GAATCCTATCTCCCTGGTCAGTAGTGGAAT--GTTGAAGATTGTGAATCCTATCTCCCTGGTCAG
* *
41128132 CAATGGAGTATGTTGAAAATTACA
64 CAATGGAATAGGTTGAAAATT-CA
* *
41128156 G-ATCTTATCTCCCTAAG-CAGTAGTGGA
1 GAATCCTATCTCCCT-GGTCAGTAGTGGA
41128183 GCAGATCGAA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 28 0.28
88 71 0.70
89 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (86 bp):
GAATCCTATCTCCCTGGTCAGTAGTGGAATGTTGAAGATTGTGAATCCTATCTCCCTGGTCAGCA
ATGGAATAGGTTGAAAATTCA
Found at i:41128194 original size:88 final size:87
Alignment explanation
Indices: 41128016--41128366 Score: 224
Period size: 88 Copynumber: 4.0 Consensus size: 87
41128006 GGAATGTTGT
* * * ** *
41128016 AGATTGTGAATCCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATT-GTGAATCCTATCTCC
1 AGATTGTGAATCCTATCTCCCTGGTCAGCAATGGAGTA-GTTGAAAATTACAG-ATCTTATCTCC
* ** *
41128080 CT-GGTCAGTAGTGGAATA-AGTTGA
64 CTAAG-CAGTAGTGGAGCAGA-TCGA
41128104 AGATTGTGAATCCTATCTCCCTGGTCAGCAATGGAGTATGTTGAAAATTACAGATCTTATCTCCC
1 AGATTGTGAATCCTATCTCCCTGGTCAGCAATGGAGTA-GTTGAAAATTACAGATCTTATCTCCC
41128169 TAAGCAGTAGTGGAGCAGATCGA
65 TAAGCAGTAGTGGAGCAGATCGA
* * * * * * * *** *
41128192 AGATGGTAAATCTTATCTTTCCATGGT-AG-TAGGGAAGTAGATT-TAAGCCACTAG-CCTTATC
1 AGATTGTGAATCCTATC--TCCCTGGTCAGCAATGG-AGTAG-TTGAAAATTAC-AGATCTTATC
* * * * *
41128253 TCCCTGAGCAGCAGTGGAGTAGGTTGA
61 TCCCTAAGCAGTAGTGGAGCAGATCGA
* * * *
41128280 AGATTAT-AGA-CCTTATCTCCCTAAG-CAGTAGTGGAGTAG--G-AAATTACAGATCTTATCTC
1 AGATTGTGA-ATCC-TATCTCCCT-GGTCAGCAATGGAGTAGTTGAAAATTACAGATCTTATCTC
41128339 CCTAAGCAGTAGTGGAGCAGATCGA
63 CCTAAGCAGTAGTGGAGCAGATCGA
41128364 AGA
1 AGA
41128367 CAGCGAATCT
Statistics
Matches: 204, Mismatches: 44, Indels: 34
0.72 0.16 0.12
Matches are distributed among these distances:
83 2 0.01
84 35 0.17
86 4 0.02
87 10 0.05
88 133 0.65
89 13 0.06
90 7 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (87 bp):
AGATTGTGAATCCTATCTCCCTGGTCAGCAATGGAGTAGTTGAAAATTACAGATCTTATCTCCCT
AAGCAGTAGTGGAGCAGATCGA
Found at i:41128205 original size:44 final size:42
Alignment explanation
Indices: 41128157--41128366 Score: 137
Period size: 44 Copynumber: 4.9 Consensus size: 42
41128147 AAAATTACAG
*
41128157 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGAT--TAA
* * * ** *
41128201 ATCTTATCTTTCC-ATGGTAGTAG-GGAAGTAGATTTAAGCCACT-A
1 ATCTTATC-TCCCTA-AGCAGTAGTGG-AGTAGATCGAAG--ATTAA
** * * * *
41128245 GCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATTA-A
*
41128288 GACCTTATCTCCCTAAGCAGTAGTGGAGTAG---GAA-ATTACA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATTA-A
*
41128328 GATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGA
41128367 CAGCGAATCT
Statistics
Matches: 129, Mismatches: 23, Indels: 28
0.72 0.13 0.16
Matches are distributed among these distances:
40 34 0.26
41 5 0.04
43 22 0.17
44 48 0.37
45 19 0.15
47 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (42 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCGAAGATTAA
Found at i:41128346 original size:40 final size:43
Alignment explanation
Indices: 41128246--41128355 Score: 154
Period size: 40 Copynumber: 2.6 Consensus size: 43
41128236 AAGCCACTAG
* * *
41128246 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAGA
1 CCTTATCTCCCTAAGCAGTAGTGGAGTAGG-TGAAGATTACAGA
41128290 CCTTATCTCCCTAAGCAGTAGTGGAGTA-G-GAA-ATTACAGA
1 CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTGAAGATTACAGA
*
41128330 TCTTATCTCCCTAAGCAGTAGTGGAG
1 CCTTATCTCCCTAAGCAGTAGTGGAG
41128356 CAGATCGAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
40 32 0.52
41 3 0.05
43 1 0.02
44 26 0.42
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (43 bp):
CCTTATCTCCCTAAGCAGTAGTGGAGTAGGTGAAGATTACAGA
Found at i:41128379 original size:84 final size:83
Alignment explanation
Indices: 41128148--41128388 Score: 206
Period size: 84 Copynumber: 2.8 Consensus size: 83
41128138 AGTATGTTGA
*
41128148 AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTA-AATCTTATCTTT
1 AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAG-AGAATCTTATC-TT
* *
41128212 CC-ATGGTAGTAGGGAAGTAG
64 CCTA-AGCAGTAGGGAAGTAG
* * * * * * * *
41128232 -ATTTA-AGCCACTAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAG-ACCTT
1 AAATTACAG--A-T---CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TAGAGAATCTT
*
41128294 ATCTCCCTAAGCAGTAGTGG-AGTAGG
59 ATCTTCCTAAGCAGTAG-GGAAGTA-G
* *
41128320 AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTCC
1 AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGAGAATCTTATCTTCC
41128385 TAAG
66 TAAG
41128389 GTAATAGGGA
Statistics
Matches: 120, Mismatches: 23, Indels: 28
0.70 0.13 0.16
Matches are distributed among these distances:
82 2 0.02
83 6 0.05
84 46 0.38
85 1 0.01
87 14 0.12
88 44 0.37
89 5 0.04
90 2 0.02
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (83 bp):
AAATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATAGAGAATCTTATCTTCC
TAAGCAGTAGGGAAGTAG
Found at i:41128443 original size:88 final size:88
Alignment explanation
Indices: 41128159--41128443 Score: 248
Period size: 88 Copynumber: 3.3 Consensus size: 88
41128149 AATTACAGAT
* * *
41128159 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGTA-AATCTTATCTTTCC-ATGGTAGT
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATAG-AGAATCTTATC-TTCCTAAGGTAGT
* *
41128222 AGGGAAGTAGATTTAAGCCACTAGC
64 AGGGAAGCAGATTAAAGCCACTAGC
* * * * * * *
41128247 CTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTATAG-ACCTTATCTCCCTAAGCAGTAG
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGA-TAGAGAATCTTATCTTCCTAAG--GTAG
* * * *
41128311 T-GGAGTAGGAAATTACAG--A-T---
63 TAGG-GAAGCAGATTAAAGCCACTAGC
* * * *
41128331 CTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACAGCGAATCTTATCTTCCTAAGGTAATAG
1 CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATAGAGAATCTTATCTTCCTAAGGTAGTAG
41128396 GGAAGCAGATTAAAGCCACTAGC
66 GGAAGCAGATTAAAGCCACTAGC
* *
41128419 CTTATCTCCCTCAGCAACAGTGGAG
1 CTTATCTCCCTAAGCAGCAGTGGAG
41128444 TATTTTTTTA
Statistics
Matches: 150, Mismatches: 33, Indels: 28
0.71 0.16 0.13
Matches are distributed among these distances:
82 14 0.09
83 4 0.03
84 46 0.31
85 1 0.01
87 4 0.03
88 64 0.43
89 3 0.02
90 14 0.09
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (88 bp):
CTTATCTCCCTAAGCAGCAGTGGAGCAGATCGAAGATAGAGAATCTTATCTTCCTAAGGTAGTAG
GGAAGCAGATTAAAGCCACTAGC
Found at i:41130815 original size:24 final size:26
Alignment explanation
Indices: 41130767--41130817 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
41130757 TAGATTTTTT
*
41130767 TAAATTATTATAATTCTTTAAAAATA
1 TAAATTATTAGAATTCTTTAAAAATA
*
41130793 TAAATT-TTAGAATT-TTTATAAATA
1 TAAATTATTAGAATTCTTTAAAAATA
41130817 T
1 T
41130818 TTTGAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 10 0.43
25 7 0.30
26 6 0.26
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (26 bp):
TAAATTATTAGAATTCTTTAAAAATA
Found at i:41130826 original size:19 final size:19
Alignment explanation
Indices: 41130791--41130846 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
41130781 TCTTTAAAAA
*
41130791 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAATTTT
41130809 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
41130827 TAAAAATTATTTTG-ATTTT
1 TATAAA-TATTTTGAATTTT
41130846 T
1 T
41130847 TTTAATTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 16 0.48
19 17 0.52
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:41130828 original size:18 final size:18
Alignment explanation
Indices: 41130791--41130845 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
41130781 TCTTTAAAAA
*
41130791 TATAAAT-TTTAGAATTTT
1 TATAAATATTTTGAA-TTT
41130809 TATAAATATTTTGAATTT
1 TATAAATATTTTGAATTT
*
41130827 TAAAAATTATTTTG-ATTT
1 TATAAA-TATTTTGAATTT
41130845 T
1 T
41130846 TTTTAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 20 0.61
19 13 0.39
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TATAAATATTTTGAATTT
Found at i:41137464 original size:27 final size:27
Alignment explanation
Indices: 41137434--41137599 Score: 115
Period size: 27 Copynumber: 6.1 Consensus size: 27
41137424 CTAATATTTA
41137434 TAAAATGACCGTAATACCCCTGTAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
* * * * *
41137461 TAAAATTACC-AAAAAACCCTCATAGGG
1 TAAAATGACCGTAATACCCCT-GTAGGG
* *
41137488 TAAAATGATCGTAAT-GCCCTAGTAGGG
1 TAAAATGACCGTAATACCCCT-GTAGGG
** ** *
41137515 TAAAATGATTGTAATACCCCCATAGGA
1 TAAAATGACCGTAATACCCCTGTAGGG
* *
41137542 TTAAATGACCGAAATA-CCCT-TATGAGG
1 TAAAATGACCGTAATACCCCTGTA-G-GG
* * *
41137569 TAAAATGACCATAATGCCCCTGGAGGG
1 TAAAATGACCGTAATACCCCTGTAGGG
41137596 TAAA
1 TAAA
41137600 TAACTATTTT
Statistics
Matches: 104, Mismatches: 28, Indels: 14
0.71 0.19 0.10
Matches are distributed among these distances:
25 2 0.02
26 11 0.11
27 80 0.77
28 10 0.10
29 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (27 bp):
TAAAATGACCGTAATACCCCTGTAGGG
Found at i:41137693 original size:24 final size:24
Alignment explanation
Indices: 41137622--41137730 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
41137612 CCATTGAGTG
* *
41137622 TAAATGATTGATTTGTCTGTGATG
1 TAAATGACTGATTTGTCTGTGATT
* *
41137646 TAAATGACTAATTTATCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
41137670 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*** * *
41137694 GGTATGATTGATTTGTGTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
**
41137718 TGTATGACTGATT
1 TAAATGACTGATT
41137731 CTGAGCATGG
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 72 1.00
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.47
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:41138110 original size:32 final size:32
Alignment explanation
Indices: 41137899--41138111 Score: 162
Period size: 32 Copynumber: 6.7 Consensus size: 32
41137889 TTTGCTGTGA
* *
41137899 TGTTACTGATGGCTTTGTGTCAATCATAGT-AC
1 TGTTACTGATGGCTTTGTGCCGATCATA-TCAC
** * * *
41137931 TACTACTGATGGCTTTGTACCGATCGTATTAC
1 TGTTACTGATGGCTTTGTGCCGATCATATCAC
* * *
41137963 CGTTA-TCGATGGCTGTGTGCTGATCATATCAC
1 TGTTACT-GATGGCTTTGTGCCGATCATATCAC
* * * *
41137995 CGTTACTGGTGG-TTGTGTACCGATCATATCAT
1 TGTTACTGATGGCTT-TGTGCCGATCATATCAC
* * *
41138027 TGTTACTGATGGCTTTGTACCGATCATGTTAC
1 TGTTACTGATGGCTTTGTGCCGATCATATCAC
** * * **
41138059 CATTACTAATGGCTGTGTGCCGATTGTATCAC
1 TGTTACTGATGGCTTTGTGCCGATCATATCAC
*
41138091 TGCTACTGATGGCTTTGTGCC
1 TGTTACTGATGGCTTTGTGCC
41138112 AATGACATTA
Statistics
Matches: 138, Mismatches: 38, Indels: 10
0.74 0.20 0.05
Matches are distributed among these distances:
31 3 0.02
32 132 0.96
33 3 0.02
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (32 bp):
TGTTACTGATGGCTTTGTGCCGATCATATCAC
Found at i:41145085 original size:24 final size:24
Alignment explanation
Indices: 41145034--41145086 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
41145024 TTTACTATTT
* *
41145034 ATTAGTATAATATATTTAGCATTT
1 ATTAGCATAATATATTTAGCATTG
41145058 ATTAGCATAATATATTT-GACATTG
1 ATTAGCATAATATATTTAG-CATTG
41145082 ATTAG
1 ATTAG
41145087 AATTAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATTAGCATAATATATTTAGCATTG
Found at i:41149018 original size:16 final size:16
Alignment explanation
Indices: 41148987--41149016 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41148977 TGACATGTGT
41148987 TTTTTTTAAATATTTA
1 TTTTTTTAAATATTTA
41149003 TTTTTTT-AATATTT
1 TTTTTTTAAATATTT
41149017 TACTATACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTTTAAATATTTA
Found at i:41159220 original size:26 final size:26
Alignment explanation
Indices: 41159184--41159239 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
41159174 TGAAAAAGAA
41159184 AAAAGATGAATATATTTATAAGGTTT
1 AAAAGATGAATATATTTATAAGGTTT
41159210 AAAAGATGAATATATTTATAAGGTTT
1 AAAAGATGAATATATTTATAAGGTTT
41159236 AAAA
1 AAAA
41159240 TTTGCCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (26 bp):
AAAAGATGAATATATTTATAAGGTTT
Found at i:41161935 original size:32 final size:34
Alignment explanation
Indices: 41161835--41161940 Score: 92
Period size: 37 Copynumber: 3.1 Consensus size: 34
41161825 ATTTTATTGA
*
41161835 AAATGAAAATTTTCACAGTTTATCAAATACACCGT
1 AAAT-AAAACTTTCACAGTTTATCAAATACACCGT
* * **
41161870 AAATTAAAACTTTTCA-ATTTTTTTACACTTACACCGT
1 AAA-TAAAAC-TTTCACA-GTTTAT-CAAATACACCGT
*
41161907 AAA-AGAA-TTTCACAGTTTATCAAATACACCGT
1 AAATAAAACTTTCACAGTTTATCAAATACACCGT
41161939 AA
1 AA
41161941 CTTTTTTAGC
Statistics
Matches: 56, Mismatches: 10, Indels: 13
0.71 0.13 0.16
Matches are distributed among these distances:
32 12 0.21
33 9 0.16
34 1 0.02
35 11 0.20
36 10 0.18
37 13 0.23
ACGTcount: A:0.42, C:0.18, G:0.07, T:0.34
Consensus pattern (34 bp):
AAATAAAACTTTCACAGTTTATCAAATACACCGT
Found at i:41163021 original size:8 final size:8
Alignment explanation
Indices: 41163008--41163034 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
41162998 ATTTTTTGTG
41163008 TAATTTTA
1 TAATTTTA
41163016 TAATTTTA
1 TAATTTTA
41163024 TAATTTTA
1 TAATTTTA
41163032 TAA
1 TAA
41163035 AATAAATGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TAATTTTA
Found at i:41163473 original size:41 final size:40
Alignment explanation
Indices: 41163428--41163553 Score: 173
Period size: 40 Copynumber: 3.1 Consensus size: 40
41163418 TTTTATTTTT
*
41163428 ATTTTTTTAATTTTAAAATACTTTTAAAATACTTTTTTTAA
1 ATTTTTTTAATTTTAAAATAATTTTAAAATAC-TTTTTTAA
* * *
41163469 ATTTTTTTAATTTTAAAATATTTTTAAAATACTTTGTAAA
1 ATTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTAA
* *
41163509 ATTTTTTTAATTTAAAAATAATTTTAAAATAAATTTTTT-A
1 ATTTTTTTAATTTTAAAATAATTTTAAAAT-ACTTTTTTAA
41163549 ATTTT
1 ATTTT
41163554 AAAATAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
40 40 0.53
41 36 0.47
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (40 bp):
ATTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTAA
Found at i:41163493 original size:11 final size:11
Alignment explanation
Indices: 41163438--41163518 Score: 55
Period size: 11 Copynumber: 7.5 Consensus size: 11
41163428 ATTTTTTTAA
*
41163438 TTTTAAAATAC
1 TTTTAAAATAT
41163449 TTTTAAAATACTT
1 TTTTAAAATA--T
*
41163462 TTTTTAAAT-T
1 TTTTAAAATAT
*
41163472 TTTT----TAA
1 TTTTAAAATAT
41163479 TTTTAAAATAT
1 TTTTAAAATAT
41163490 TTTTAAAATACT
1 TTTTAAAATA-T
* *
41163502 TTGTAAAATTT
1 TTTTAAAATAT
41163513 TTTTAA
1 TTTTAA
41163519 TTTAAAAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
6 1 0.02
7 4 0.07
10 5 0.09
11 28 0.51
12 9 0.16
13 8 0.15
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41163563 original size:11 final size:11
Alignment explanation
Indices: 41163476--41163564 Score: 59
Period size: 11 Copynumber: 8.6 Consensus size: 11
41163466 TAAATTTTTT
41163476 TAATTTTAAAA
1 TAATTTTAAAA
*
41163487 TATTTTTAAAA
1 TAATTTTAAAA
*
41163498 TACTTTGTAAAA
1 TAATTT-TAAAA
*
41163510 T--TTTT---T
1 TAATTTTAAAA
*
41163516 TAATTTAAAAA
1 TAATTTTAAAA
41163527 TAATTTTAAAA
1 TAATTTTAAAA
*
41163538 TAAATTTT---T
1 T-AATTTTAAAA
41163547 TAATTTTAAAA
1 TAATTTTAAAA
41163558 TAATTTT
1 TAATTTT
41163565 TTGGTATTTA
Statistics
Matches: 60, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
6 1 0.02
8 9 0.15
9 2 0.03
10 3 0.05
11 33 0.55
12 12 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (11 bp):
TAATTTTAAAA
Found at i:41163574 original size:20 final size:20
Alignment explanation
Indices: 41163527--41163566 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
41163517 AATTTAAAAA
41163527 TAATTTTAAAATAAATTTTT
1 TAATTTTAAAATAAATTTTT
41163547 TAATTTTAAAAT-AATTTTT
1 TAATTTTAAAATAAATTTTT
41163566 T
1 T
41163567 GGTATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATTTTAAAATAAATTTTT
Found at i:41174195 original size:18 final size:19
Alignment explanation
Indices: 41174174--41174209 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41174164 AAAATCACAA
41174174 AGAC-GTGCAAAAAAGCAG
1 AGACTGTGCAAAAAAGCAG
*
41174192 AGACTGTGCTAAAAAGCA
1 AGACTGTGCAAAAAAGCA
41174210 TAAAAATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.17, G:0.25, T:0.11
Consensus pattern (19 bp):
AGACTGTGCAAAAAAGCAG
Found at i:41175403 original size:30 final size:29
Alignment explanation
Indices: 41175369--41175448 Score: 90
Period size: 31 Copynumber: 2.7 Consensus size: 29
41175359 TTTTCAAATT
*
41175369 TTCAAAAGTATAGGGACTAAAATTGAACAA
1 TTCAAAAGTATAAGGACTAAAA-TGAACAA
* *
41175399 TTCAAAAAGTACAAGGACTAAAATGATCAA
1 TTC-AAAAGTATAAGGACTAAAATGAACAA
* *
41175429 AT-AAAAGTATATGGACTAAA
1 TTCAAAAGTATAAGGACTAAA
41175449 TCTATAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.37
30 10 0.23
31 17 0.40
ACGTcount: A:0.53, C:0.10, G:0.15, T:0.23
Consensus pattern (29 bp):
TTCAAAAGTATAAGGACTAAAATGAACAA
Found at i:41178764 original size:21 final size:21
Alignment explanation
Indices: 41178709--41178764 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
41178699 ATATAATACT
*
41178709 AAAATT-TATTATACTCATATA
1 AAAATTATATT-TACACATATA
*
41178730 AAAA-TAAATATTACACATATA
1 AAAATTATAT-TTACACATATA
41178751 AAAATTATATTTAC
1 AAAATTATATTTAC
41178765 TAAAAATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.03
21 23 0.79
22 5 0.17
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTATATTTACACATATA
Found at i:41178834 original size:13 final size:13
Alignment explanation
Indices: 41178816--41178840 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41178806 TAAAAGAGTT
41178816 ATTAATTAAAAAG
1 ATTAATTAAAAAG
41178829 ATTAATTAAAAA
1 ATTAATTAAAAA
41178841 ACTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (13 bp):
ATTAATTAAAAAG
Found at i:41179959 original size:75 final size:76
Alignment explanation
Indices: 41179808--41179959 Score: 200
Period size: 76 Copynumber: 2.0 Consensus size: 76
41179798 TTCATCGAAA
* * **
41179808 GGAGGAGGACCCCCCTGATGGTAATATTGATCCCATTGGATTGGGAGATTGAACAACCAAGATCT
1 GGAGGAGGACCCCCCTAATGGTAATACTGATCCCATTGGAACGGGAGATTGAACAACCAAGATCT
41179873 TTCAAGGATAT
66 TTCAAGGATAT
* * * * *
41179884 GGAGTAGGATCCCCCTAATGGTAATACTGATCCCA-TGGAACGGGGGATTGAGCCAA-CGAGATC
1 GGAGGAGGACCCCCCTAATGGTAATACTGATCCCATTGGAACGGGAGATTGA-ACAACCAAGATC
41179947 TTTCAAGGATAT
65 TTTCAAGGATAT
41179959 G
1 G
41179960 CTTCTTGGAA
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
75 32 0.48
76 34 0.52
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (76 bp):
GGAGGAGGACCCCCCTAATGGTAATACTGATCCCATTGGAACGGGAGATTGAACAACCAAGATCT
TTCAAGGATAT
Found at i:41181511 original size:44 final size:44
Alignment explanation
Indices: 41181448--41181537 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
41181438 AATGGATTGG
* *
41181448 TACATAGGTTGCAAGCTCAATGTTTGATGATGTGTGGCATTTTT
1 TACATAGGTTGCAAGCTCAATGTTCGATGATGTGTAGCATTTTT
* *
41181492 TACATAGGTTGGAAGCTCAATGTTCGATGATTTGTAGCATTTTT
1 TACATAGGTTGCAAGCTCAATGTTCGATGATGTGTAGCATTTTT
41181536 TA
1 TA
41181538 TAAAATTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.24, C:0.11, G:0.23, T:0.41
Consensus pattern (44 bp):
TACATAGGTTGCAAGCTCAATGTTCGATGATGTGTAGCATTTTT
Found at i:41182717 original size:17 final size:17
Alignment explanation
Indices: 41182695--41182744 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
41182685 TCTCAGATTT
41182695 TGATACCCATATCTTTC
1 TGATACCCATATCTTTC
*
41182712 TGATACCTATATCTTTC
1 TGATACCCATATCTTTC
41182729 TGATACCCATATCTTT
1 TGATACCCATATCTTT
41182745 GACTTTCTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.24, C:0.26, G:0.06, T:0.44
Consensus pattern (17 bp):
TGATACCCATATCTTTC
Found at i:41183207 original size:36 final size:35
Alignment explanation
Indices: 41183167--41183240 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
41183157 TTTTAGAATG
*
41183167 TTTGAA-ATGTAAAATTATATTTTGTAAAATATAATT
1 TTTGAATATGT-AAATT-TATTTTGTAAAATAAAATT
*
41183203 TTTGAATTATGTACATTTATTTTGTAAAATAAAATT
1 TTTGAA-TATGTAAATTTATTTTGTAAAATAAAATT
41183239 TT
1 TT
41183241 CATTAAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 26 0.76
37 4 0.12
38 4 0.12
ACGTcount: A:0.41, C:0.01, G:0.08, T:0.50
Consensus pattern (35 bp):
TTTGAATATGTAAATTTATTTTGTAAAATAAAATT
Found at i:41183704 original size:22 final size:23
Alignment explanation
Indices: 41183674--41183719 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
41183664 TTAAAATTTT
* *
41183674 GAAGTAGAAGAAGAGGAAGAAGA
1 GAAGTAGAAAAAGAAGAAGAAGA
41183697 GAAG-AGAAAAAGAAGAAGAAGA
1 GAAGTAGAAAAAGAAGAAGAAGA
41183719 G
1 G
41183720 TTGTATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (23 bp):
GAAGTAGAAAAAGAAGAAGAAGA
Found at i:41184127 original size:22 final size:24
Alignment explanation
Indices: 41184088--41184134 Score: 80
Period size: 22 Copynumber: 2.0 Consensus size: 24
41184078 AGACATTAAA
41184088 ATTTTATGTTAAAATAGTTATTAT
1 ATTTTATGTTAAAATAGTTATTAT
41184112 ATTTT-TGTT-AAATAGTTATTAT
1 ATTTTATGTTAAAATAGTTATTAT
41184134 A
1 A
41184135 CGCAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 14 0.61
23 4 0.17
24 5 0.22
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (24 bp):
ATTTTATGTTAAAATAGTTATTAT
Found at i:41188133 original size:15 final size:14
Alignment explanation
Indices: 41188111--41188140 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
41188101 TTTCTTCCAA
41188111 CTTCACAATTTCAC
1 CTTCACAATTTCAC
41188125 CTTCTACAATTTCAC
1 CTTC-ACAATTTCAC
41188140 C
1 C
41188141 ATAAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.27, C:0.37, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTCACAATTTCAC
Found at i:41188812 original size:42 final size:42
Alignment explanation
Indices: 41188748--41188864 Score: 180
Period size: 42 Copynumber: 2.8 Consensus size: 42
41188738 TTTTACAACC
* * *
41188748 AAAAACGCCGTTAAAGATCATGTTCTTTAGTGGCGCTTAGAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAG
41188790 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAG
* * *
41188832 AAAAACGCCACTGAAGAACATGGTCTTTAGCGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGG
41188865 TGTTTTTATC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAG
Found at i:41188888 original size:42 final size:43
Alignment explanation
Indices: 41188837--41189029 Score: 252
Period size: 42 Copynumber: 4.6 Consensus size: 43
41188827 TAGAGAAAAA
* *
41188837 CGCCACTGAAGAACATGGTCTTTAGCGGTG-TTTTTATCTAAG
1 CGCCGCTGAAGAACATGGTCTTTAGCGGCGTTTTTTATCTAAG
* *
41188879 CGCCGCTGAAGAACATGGTCTTTAGCGGTGTTTTTTTTCTAAG
1 CGCCGCTGAAGAACATGGTCTTTAGCGGCGTTTTTTATCTAAG
*
41188922 CGCCGCTGAAGAACATGTTCTTTAGCGGCG-TTTTT-TCATAAG
1 CGCCGCTGAAGAACATGGTCTTTAGCGGCGTTTTTTATC-TAAG
* *
41188964 CGCCGC-GAAAGAACATGATCTTTAGTGGCGTTTTTTAT-TAAG
1 CGCCGCTG-AAGAACATGGTCTTTAGCGGCGTTTTTTATCTAAG
* *
41189006 CGCCGCTAAAGAACATGTTCTTTA
1 CGCCGCTGAAGAACATGGTCTTTA
41189030 ACGACGCTTT
Statistics
Matches: 137, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
41 3 0.02
42 89 0.65
43 44 0.32
44 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (43 bp):
CGCCGCTGAAGAACATGGTCTTTAGCGGCGTTTTTTATCTAAG
Found at i:41188955 original size:85 final size:84
Alignment explanation
Indices: 41188837--41189029 Score: 273
Period size: 85 Copynumber: 2.3 Consensus size: 84
41188827 TAGAGAAAAA
* * * *
41188837 CGCCACTGAAGAACATGGTCTTTAGCGGTGTTTTTATC-TAAGCGCCGCTG-AAGAACATGGTCT
1 CGCCGCTGAAGAACATGTTCTTTAGCGGCGTTTTT-TCATAAGCGCCGC-GAAAGAACATGATCT
* *
41188900 TTAGCGGTGTTTTTTTTCTAAG
64 TTAGCGGCGTTTTTTAT-TAAG
41188922 CGCCGCTGAAGAACATGTTCTTTAGCGGCGTTTTTTCATAAGCGCCGCGAAAGAACATGATCTTT
1 CGCCGCTGAAGAACATGTTCTTTAGCGGCGTTTTTTCATAAGCGCCGCGAAAGAACATGATCTTT
*
41188987 AGTGGCGTTTTTTATTAAG
66 AGCGGCGTTTTTTATTAAG
*
41189006 CGCCGCTAAAGAACATGTTCTTTA
1 CGCCGCTGAAGAACATGTTCTTTA
41189030 ACGACGCTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
84 30 0.31
85 68 0.69
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (84 bp):
CGCCGCTGAAGAACATGTTCTTTAGCGGCGTTTTTTCATAAGCGCCGCGAAAGAACATGATCTTT
AGCGGCGTTTTTTATTAAG
Found at i:41188978 original size:127 final size:127
Alignment explanation
Indices: 41188795--41189029 Score: 312
Period size: 127 Copynumber: 1.9 Consensus size: 127
41188785 TAGAGAAAAA
* *
41188795 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAGAAAAACGCCACTGAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGACAAAAACGCCACTGAAGAACATGATCTTT
* *
41188860 AGCGGTG-TTTTTATCTAAGCGCCGCTGAAGAACATGGTCTTTAGCGGTGTTTTTTTTCTAAG
66 AGCGGCGTTTTTTAT-TAAGCGCCGCTAAAGAACATGGTCTTTAGCGGTGTTTTTTTTCTAAG
* * *** * * *
41188922 CGCCGCTGAAGAACATGTTCTTTAGCGGCGTTTTTTCATAAGCGCCGC-GAAAGAACATGATCTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGACAAAAACGCCACTG-AAGAACATGATCTT
* *
41188986 TAGTGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGTTCTTTA
65 TAGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGGTCTTTA
41189030 ACGACGCTTT
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
126 1 0.01
127 84 0.91
128 7 0.08
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.31
Consensus pattern (127 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGACAAAAACGCCACTGAAGAACATGATCTTT
AGCGGCGTTTTTTATTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGTGTTTTTTTTCTAAG
Found at i:41194347 original size:14 final size:15
Alignment explanation
Indices: 41194316--41194350 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
41194306 TCTGACCGCA
*
41194316 AAATCCCTAAACCTT
1 AAATCCCTAAACCCT
41194331 AAATCCC-AAACCCT
1 AAATCCCTAAACCCT
41194345 AAATCC
1 AAATCC
41194351 ATACAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.37, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATCCCTAAACCCT
Found at i:41195144 original size:21 final size:21
Alignment explanation
Indices: 41195120--41195204 Score: 64
Period size: 21 Copynumber: 4.0 Consensus size: 21
41195110 ACTAGTTAAT
41195120 CTAAACTTTAAACCATAAACC
1 CTAAACTTTAAACCATAAACC
* * * * *
41195141 CTAAAATCATAAACCTTTAACA
1 CTAAACT-TTAAACCATAAACC
* *
41195163 C-ATAACCTTAAACCTTAAACC
1 CTA-AACTTTAAACCATAAACC
* *
41195184 CCAACCTTTAAACCATAAACC
1 CTAAACTTTAAACCATAAACC
41195205 ATAGACCAAA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
21 34 0.71
22 14 0.29
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAAACTTTAAACCATAAACC
Found at i:41195478 original size:115 final size:113
Alignment explanation
Indices: 41195270--41195823 Score: 434
Period size: 115 Copynumber: 4.8 Consensus size: 113
41195260 GGTTAAGACC
* * *
41195270 AAAACTCTGCGTTTTGGTTAAAATATTTTCCGGCGCTTCTCAAAAAGCGCCGCTAACACTATGCT
1 AAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCT
* * *
41195335 TTAGCGGCGATTTCTCGT-GGACGCCACTAATTCCAGTATACATCAAGAA
66 TTAGCGGCG-TTTCCCATAAG-CGCCACTAATTCCAGTATACATCAAGAA
* * * * * * *
41195384 TTAAACACTGCGTTTTTGTTAATATATTTTACAGCGCTTCTCAAAAAGCGCCGCTAATAGTATGC
1 -AAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGC
* * * *
41195449 TTTAGCGGCGTTCTCCCATAAGCGCCACTAATTCTAATATACCTCATGAA
65 TTTAGCGGCGTT-TCCCATAAGCGCCACTAATTCCAGTATACATCAAGAA
*** * **** * *
41195499 AAAACTCTGCGTTTTGGTGGGCATATTTTGCGGCGCTTTTTTCCAAGTGCCGCTAATACTATGAT
1 AAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCT
** *** ** *
41195564 TTAGCGATGTTTTTTAATATA-CGCCACTAATAACTGTATACATCAAGACAAA
66 TTAGCGGCG-TTTCCCATA-AGCGCCACTAATTCCAGTATACATCAAG---AA
* * ** * * ** * *
41195616 AAAACGCTGCATTTTGGTTGCCAAATATTGCGGCGCTTCTCCGAAAGCGTCGCTAATAGTATGAC
1 AAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATG-C
** ** * *
41195681 -TTAGCGGCGTGTTCCC-TTTGCGCCACTAATTCTTGTATACCTCAAGAC
65 TTTAGCGGCGT-TTCCCATAAGCGCCACTAATTCCAGTATACATCAAGAA
* * *
41195729 CAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAA-CGCCGCTAATATTATGC
1 AAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCA-AAAAGCGCCGCTAATACTATGC
* * **
41195793 TTTAGCGGTGTTTTCCCTTAAATGCCACTAA
65 TTTAGCGGCG-TTTCCCATAAGCGCCACTAA
41195824 CTGTAACATA
Statistics
Matches: 337, Mismatches: 88, Indels: 29
0.74 0.19 0.06
Matches are distributed among these distances:
112 1 0.00
113 61 0.18
114 93 0.28
115 97 0.29
116 25 0.07
117 60 0.18
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (113 bp):
AAAACTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAAAAAGCGCCGCTAATACTATGCT
TTAGCGGCGTTTCCCATAAGCGCCACTAATTCCAGTATACATCAAGAA
Found at i:41195783 original size:230 final size:229
Alignment explanation
Indices: 41195264--41195807 Score: 576
Period size: 230 Copynumber: 2.4 Consensus size: 229
41195254 ATGCACGGTT
* * *
41195264 AAGACCAAAACTCTGCGTTTTGGTTAAAATATTTTCCGGCGCTTCTCA-AAAAGCGCCGCTAACA
1 AAGACC-AAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAA-CGCCGCTAATA
* * ** * ** **
41195328 CTATGCTTTAGCGGCGATTTCTCGTGGACGCCACTAATTCCAGTATACATCAAGAATTAAACACT
64 CTATGCTTTAGCGGTGTTTTCTAATAGACGCCACTAATAACAGTATACATCAAGAAAAAAACACT
* * * * *
41195393 GCGTTTTTGTTAATATATTTTACAGCGCTTCTCAAAAAGCGCCGCTAATAGTATGCTTTAGCGGC
129 GCATTTTGGTTAACAAATATTACAGCGCTTCTCAAAAAGCGCCGCTAATAGTATGCTTTAGCGGC
41195458 GTTCTCCCATAAGCGCCACTAATTCTAATATACCTC
194 GTTCTCCCATAAGCGCCACTAATTCTAATATACCTC
* ** ** * ** * **
41195494 ATGAAAAAACTCTGCGTTTTGG-TGGGCATATTTTGCGGCGCTTTTTTCCAAGTGCCGCTAATAC
1 AAGACCAAACTCTGCGTTTTGGTTAAG-ATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATAC
* * * * * *
41195558 TATGATTTAGCGATGTTTTTTAATATACGCCACTAATAACTGTATACATCAAGACAAAAAAACGC
65 TATGCTTTAGCGGTGTTTTCTAATAGACGCCACTAATAACAGTATACATCAAG--AAAAAAACAC
** * * ** *
41195623 TGCATTTTGGTTGCCAAATATTGCGGCGCTTCTCCGAAAGCGTCGCTAATAGTATGAC-TTAGCG
128 TGCATTTTGGTTAACAAATATTACAGCGCTTCTCAAAAAGCGCCGCTAATAGTATG-CTTTAGCG
** **
41195687 GCGTGT-TCCC-TTTGCGCCACTAATTCTTGTATACCTC
192 GCGT-TCTCCCATAAGCGCCACTAATTCTAATATACCTC
*
41195724 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATATT
1 AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATACT
41195789 ATGCTTTAGCGGTGTTTTC
66 ATGCTTTAGCGGTGTTTTC
41195808 CCTTAAATGC
Statistics
Matches: 247, Mismatches: 60, Indels: 14
0.77 0.19 0.04
Matches are distributed among these distances:
228 1 0.00
229 83 0.34
230 94 0.38
231 67 0.27
232 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.32
Consensus pattern (229 bp):
AAGACCAAACTCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTCTCACAAAACGCCGCTAATACT
ATGCTTTAGCGGTGTTTTCTAATAGACGCCACTAATAACAGTATACATCAAGAAAAAAACACTGC
ATTTTGGTTAACAAATATTACAGCGCTTCTCAAAAAGCGCCGCTAATAGTATGCTTTAGCGGCGT
TCTCCCATAAGCGCCACTAATTCTAATATACCTC
Found at i:41202086 original size:24 final size:24
Alignment explanation
Indices: 41202059--41202106 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
41202049 AGGAACATTG
41202059 AAAAAATAAAGTAATAC-TTTTTTT
1 AAAAAAT-AAGTAATACATTTTTTT
**
41202083 AAAAAATTGGTAATACATTTTTTT
1 AAAAAATAAGTAATACATTTTTTT
41202107 TTTGTCTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (24 bp):
AAAAAATAAGTAATACATTTTTTT
Found at i:41213276 original size:13 final size:13
Alignment explanation
Indices: 41213258--41213287 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41213248 TTGAGATTGT
*
41213258 ATTTGAAAAGAAA
1 ATTTGAAAAAAAA
41213271 ATTTGAAAAAAAA
1 ATTTGAAAAAAAA
41213284 ATTT
1 ATTT
41213288 AGCAACTTTG
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:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (13 bp):
ATTTGAAAAAAAA
Found at i:41214230 original size:21 final size:21
Alignment explanation
Indices: 41214200--41214261 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
41214190 AAGAGTTGTT
* *
41214200 AATAAGAGAAAATGAGCGAAA
1 AATAAAAGAAAATGAGAGAAA
* *
41214221 AATAAAAGAAATTGAGAG-AT
1 AATAAAAGAAAATGAGAGAAA
41214241 AA-AAAAG-AAATGAGAGAAA
1 AATAAAAGAAAATGAGAGAAA
41214260 AA
1 AA
41214262 AAATTGAAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.24
19 8 0.24
20 3 0.09
21 15 0.44
ACGTcount: A:0.66, C:0.02, G:0.21, T:0.11
Consensus pattern (21 bp):
AATAAAAGAAAATGAGAGAAA
Found at i:41214254 original size:18 final size:18
Alignment explanation
Indices: 41214224--41214263 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 18
41214214 AGCGAAAAAT
41214224 AAAAGAAATTGAGAGATAA
1 AAAAGAAATTGAGAGA-AA
41214243 AAAAGAAA-TGAGAGAAA
1 AAAAGAAATTGAGAGAAA
41214260 AAAA
1 AAAA
41214264 ATTGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.29
18 7 0.33
19 8 0.38
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAGAAATTGAGAGAAA
Found at i:41214270 original size:20 final size:18
Alignment explanation
Indices: 41214209--41214264 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 18
41214199 TAATAAGAGA
*
41214209 AAATGAGCGAAAAATAAAAG
1 AAATGAGAG-AAAA-AAAAG
*
41214229 AAATTGAGAGATAAAAAAG
1 AAA-TGAGAGAAAAAAAAG
41214248 AAATGAGAGAAAAAAAA
1 AAATGAGAGAAAAAAAA
41214265 TTGAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 13 0.41
19 8 0.25
20 6 0.19
21 5 0.16
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.11
Consensus pattern (18 bp):
AAATGAGAGAAAAAAAAG
Found at i:41216175 original size:39 final size:39
Alignment explanation
Indices: 41216121--41216237 Score: 128
Period size: 39 Copynumber: 3.0 Consensus size: 39
41216111 TAATTTAGTT
* *
41216121 TGAGTCTTTAATTATGTTATAATTTGAACATCATTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
* * *
41216160 TGAGTTTTTAATTATGTCATAATCTAAACAACATTAATA
1 TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
* * * * *
41216199 AG-GGTTTTAATTATGTCATAGTTTAGGACATCTTTAATA
1 TGAGTTTTTAATTATGTCATAATTT-GAACATCATTAATA
41216238 CATGTTTTAA
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
38 19 0.30
39 45 0.70
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.44
Consensus pattern (39 bp):
TGAGTTTTTAATTATGTCATAATTTGAACATCATTAATA
Found at i:41222463 original size:43 final size:43
Alignment explanation
Indices: 41222401--41222487 Score: 165
Period size: 43 Copynumber: 2.0 Consensus size: 43
41222391 CTAGTAAGGG
*
41222401 TCTGATTCACCACTGCATCATTGGGTCCCCCTCACCCAAACAT
1 TCTGATTCACCACTACATCATTGGGTCCCCCTCACCCAAACAT
41222444 TCTGATTCACCACTACATCATTGGGTCCCCCTCACCCAAACAT
1 TCTGATTCACCACTACATCATTGGGTCCCCCTCACCCAAACAT
41222487 T
1 T
41222488 TTCCCAAGTC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.24, C:0.39, G:0.10, T:0.26
Consensus pattern (43 bp):
TCTGATTCACCACTACATCATTGGGTCCCCCTCACCCAAACAT
Found at i:41223295 original size:13 final size:14
Alignment explanation
Indices: 41223271--41223299 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41223261 AATTTCAAAC
41223271 TTTTAAATTGAAAT
1 TTTTAAATTGAAAT
41223285 TTTTAAA-TGAAAT
1 TTTTAAATTGAAAT
41223298 TT
1 TT
41223300 GTCTCCAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTAAATTGAAAT
Found at i:41225733 original size:3 final size:3
Alignment explanation
Indices: 41225719--41225758 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
41225709 GTATTAGCAT
* *
41225719 TTA TTA TCA TTA TTA TTA TTA TTAA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA
41225759 GTTTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:41225739 original size:25 final size:25
Alignment explanation
Indices: 41225710--41225758 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41225700 ATTAATTTTG
*
41225710 TATTAGCATTTATTATCATTATTAT
1 TATTAGCAATTATTATCATTATTAT
**
41225735 TATTATTAATTATTATCATTATTA
1 TATTAGCAATTATTATCATTATTA
41225759 GTTTTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (25 bp):
TATTAGCAATTATTATCATTATTAT
Found at i:41225746 original size:16 final size:16
Alignment explanation
Indices: 41225727--41225758 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
41225717 ATTTATTATC
*
41225727 ATTATTATTATTATTA
1 ATTATTATCATTATTA
41225743 ATTATTATCATTATTA
1 ATTATTATCATTATTA
41225759 GTTTTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTATTATCATTATTA
Found at i:41225765 original size:25 final size:25
Alignment explanation
Indices: 41225719--41225766 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
41225709 GTATTAGCAT
41225719 TTATTATCATTATTATTATTATTAA
1 TTATTATCATTATTATTATTATTAA
41225744 TTATTATCATTATTAGTT-TTATT
1 TTATTATCATTATTA-TTATTATT
41225767 TTCCCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (25 bp):
TTATTATCATTATTATTATTATTAA
Found at i:41225836 original size:2 final size:2
Alignment explanation
Indices: 41225831--41225869 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
41225821 TTTTTTATTC
*
41225831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
41225870 GCATTATGCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41225991 original size:6 final size:6
Alignment explanation
Indices: 41225980--41226005 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41225970 TTATTTTCCT
41225980 ATATAC ATATAC ATATAC ATATAC AT
1 ATATAC ATATAC ATATAC ATATAC AT
41226006 CCATACATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (6 bp):
ATATAC
Found at i:41226152 original size:40 final size:40
Alignment explanation
Indices: 41226097--41226217 Score: 109
Period size: 46 Copynumber: 2.9 Consensus size: 40
41226087 ATACACACTT
* *
41226097 TTTTATAA-CGTATATACTTATATTTTATATATTTTTTGTA
1 TTTTATAATC-TATATACTTATATTTTATTTATTTTTTATA
* *
41226137 TTTTATAATCTATATACCTTTATATGTAAATATTTATGCTTTTATA
1 TTTTATAATCTATATA-C-TTATAT-T--TTATTTAT-TTTTTATA
* * *
41226183 TTTTATAATCCATATACATATCTTTTATTTATTTT
1 TTTTATAATCTATATACTTATATTTTATTTATTTT
41226218 CCTCATTTAT
Statistics
Matches: 65, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
40 16 0.25
41 9 0.14
42 6 0.09
43 2 0.03
44 4 0.06
45 7 0.11
46 21 0.32
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (40 bp):
TTTTATAATCTATATACTTATATTTTATTTATTTTTTATA
Found at i:41230013 original size:24 final size:24
Alignment explanation
Indices: 41229986--41230036 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
41229976 TCTCCATCTA
41229986 TATCTAAATCTATGCT-TGCATTTG
1 TATCTAAATCTAT-CTATGCATTTG
* * *
41230010 TATCTGAATTTATTTATGCATTTG
1 TATCTAAATCTATCTATGCATTTG
41230034 TAT
1 TAT
41230037 TTGATTATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
TATCTAAATCTATCTATGCATTTG
Found at i:41234287 original size:51 final size:51
Alignment explanation
Indices: 41234222--41234353 Score: 210
Period size: 51 Copynumber: 2.6 Consensus size: 51
41234212 ACTATAATTT
* *
41234222 CCTTTTGGCTAAAGATAAAGATAATTTCAGCATTAATGTTTAATAATGCAA
1 CCTTTTGGCTAAAGATGAAGATAATTTCAGCATTAAAGTTTAATAATGCAA
*
41234273 CCTTTTGGCAAAAGATGAAGATAATTTCAGCATTAAAGTTTAATAATGCAA
1 CCTTTTGGCTAAAGATGAAGATAATTTCAGCATTAAAGTTTAATAATGCAA
** *
41234324 CCTTCCGGCTAAAGACGAAGATAATTTCAG
1 CCTTTTGGCTAAAGATGAAGATAATTTCAG
41234354 TGGTGCAAGA
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (51 bp):
CCTTTTGGCTAAAGATGAAGATAATTTCAGCATTAAAGTTTAATAATGCAA
Found at i:41242047 original size:10 final size:11
Alignment explanation
Indices: 41242024--41242070 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
41242014 AGTAACTAAC
41242024 AAAATAACATT
1 AAAATAACATT
41242035 AAAATAA-ATT
1 AAAATAACATT
* *
41242045 AAAAACAACATA
1 -AAAATAACATT
*
41242057 AAAATAACAAT
1 AAAATAACATT
41242068 AAA
1 AAA
41242071 CAAACTACAC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
10 3 0.10
11 24 0.83
12 2 0.07
ACGTcount: A:0.72, C:0.09, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAACATT
Found at i:41243600 original size:43 final size:43
Alignment explanation
Indices: 41243539--41243626 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
41243529 AATTTCACGT
*
41243539 TAGATCTCTGTGTATCATTTTAACAGGAGTGAT-TAAACTGATC
1 TAGATCTCTATGTATCATTTTAACAGGAGTG-TGTAAACTGATC
* *
41243582 TAGATCTCTATTTATCATTTTCACAGGAGTGTGTAAACTGATC
1 TAGATCTCTATGTATCATTTTAACAGGAGTGTGTAAACTGATC
41243625 TA
1 TA
41243627 ACAGGTGTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (43 bp):
TAGATCTCTATGTATCATTTTAACAGGAGTGTGTAAACTGATC
Found at i:41246917 original size:16 final size:16
Alignment explanation
Indices: 41246880--41246917 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
41246870 TTTGGTTCAG
41246880 TATAATGGAATAGAGC
1 TATAATGGAATAGAGC
* *
41246896 TGTAATGGAATAGAGT
1 TATAATGGAATAGAGC
41246912 TATAAT
1 TATAAT
41246918 AGAACAAAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.32
Consensus pattern (16 bp):
TATAATGGAATAGAGC
Found at i:41247206 original size:21 final size:21
Alignment explanation
Indices: 41247182--41247294 Score: 67
Period size: 21 Copynumber: 5.5 Consensus size: 21
41247172 TTATTATTAA
41247182 ATATAATTTAACAATAATAAT
1 ATATAATTTAACAATAATAAT
*
41247203 ATATAATTT---AATAATATT
1 ATATAATTTAACAATAATAAT
* * * *
41247221 CT-TAATATAACAATTACTAAA
1 ATATAATTTAACAA-TAATAAT
* *
41247242 ATATGAA-TTAATAAAAATAAT
1 ATAT-AATTTAACAATAATAAT
*
41247263 ATATAATATT-ACAAAAAATAAT
1 ATATAAT-TTAAC-AATAATAAT
*
41247285 ATAAAATTTA
1 ATATAATTTA
41247295 CTTTATTATT
Statistics
Matches: 68, Mismatches: 14, Indels: 19
0.67 0.14 0.19
Matches are distributed among these distances:
17 5 0.07
18 9 0.13
20 4 0.06
21 25 0.37
22 23 0.34
23 2 0.03
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (21 bp):
ATATAATTTAACAATAATAAT
Found at i:41247279 original size:22 final size:21
Alignment explanation
Indices: 41247254--41247295 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
41247244 ATGAATTAAT
*
41247254 AAAAATAATATATAATATTACA
1 AAAAATAATATAAAAT-TTACA
41247276 AAAAATAATATAAAATTTAC
1 AAAAATAATATAAAATTTAC
41247296 TTTATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATAATATAAAATTTACA
Found at i:41261656 original size:33 final size:33
Alignment explanation
Indices: 41261614--41261816 Score: 163
Period size: 33 Copynumber: 5.6 Consensus size: 33
41261604 TCCCCCAAGG
*
41261614 GGTTGCTAAGTGTTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
41261647 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CC-GA--TT-CAT-T---GGT
* *
41261689 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
41261722 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
41261764 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
41261797 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
41261817 ACTATATTTT
Statistics
Matches: 135, Mismatches: 17, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
33 61 0.45
34 4 0.03
35 2 0.01
36 3 0.02
37 7 0.05
38 7 0.05
39 3 0.02
40 2 0.01
41 4 0.03
42 42 0.31
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:41261706 original size:42 final size:39
Alignment explanation
Indices: 41261647--41261860 Score: 121
Period size: 33 Copynumber: 5.5 Consensus size: 39
41261637 ATTCATTGGT
41261647 GGTTGCTAAGTGCTGATTCCACCATATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACC-TA-TTT-AATGTGAAGGG
* * *
41261689 GGTTGCTAAGTGCTGATT-C-CCTGA-ATCAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCT-ATTTAATGTGAAGGG
* *
41261722 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACC-TAT-TT-AATGTGAAGGG
* * *
41261764 GGTTGCTAAGTGCTGATTCC-CCGA-TTCAT-T---GGT
1 GGTTGCTAAGTGCTGATTCCACCTATTTAATGTGAAGGG
* *
41261797 GGTTGCTAAGTGCTGATTCCACTATATTTTTGAATGTGAAAAGG
1 GGTTGCTAAGTGCTGATTCCAC-CTA--TTT-AATGTG-AAGGG
**
41261841 GGTTGCTAAGTTTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
41261861 CCGAATCATT
Statistics
Matches: 130, Mismatches: 20, Indels: 42
0.68 0.10 0.22
Matches are distributed among these distances:
33 40 0.31
34 2 0.02
35 4 0.03
36 3 0.02
37 5 0.04
38 7 0.05
39 4 0.03
40 5 0.04
41 3 0.02
42 38 0.29
44 19 0.15
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.35
Consensus pattern (39 bp):
GGTTGCTAAGTGCTGATTCCACCTATTTAATGTGAAGGG
Found at i:41261735 original size:75 final size:75
Alignment explanation
Indices: 41261610--41261897 Score: 432
Period size: 75 Copynumber: 3.8 Consensus size: 75
41261600 AGTTTCCCCC
* *
41261610 AAGGGGTTGCTAAGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
41261675 TTAAATGTGA
66 TTAAATGTGA
* * * * *
41261685 AGGGGGTTGCTAAGTGCTGATTCCCTGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
41261750 TTAAATGTGA
66 TTAAATGTGA
* *
41261760 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACTATATT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATA-T
*
41261825 TTTGAATGTGAA
65 TTTAAATGTG-A
** * *
41261837 AAGGGGTTGCTAAGTTTTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGAATCCACCA
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCA
41261898 ATAACGGATA
Statistics
Matches: 190, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
75 125 0.66
76 9 0.05
77 56 0.29
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
TTAAATGTGA
Found at i:41270612 original size:25 final size:25
Alignment explanation
Indices: 41270556--41270673 Score: 105
Period size: 25 Copynumber: 4.7 Consensus size: 25
41270546 GGTTACCGAT
** *
41270556 TTCAGCTCTTATGAGCTTCCCGATA
1 TTCAGCTCGCATGAGCTTCCTGATA
*
41270581 CTT-AGCTCGCATGAGCTTCCTGCTA
1 -TTCAGCTCGCATGAGCTTCCTGATA
* * *
41270606 TTCAGCTTGCATAAGCTT-CTCGTTA
1 TTCAGCTCGCATGAGCTTCCT-GATA
* *
41270631 TTCAGCTCACATGAGCTTCCTGGTA
1 TTCAGCTCGCATGAGCTTCCTGATA
* *
41270656 TTCAGCTCGGAGGAGCTT
1 TTCAGCTCGCATGAGCTT
41270674 ACTGTTTACA
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
24 4 0.05
25 67 0.89
26 4 0.05
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (25 bp):
TTCAGCTCGCATGAGCTTCCTGATA
Found at i:41275020 original size:25 final size:25
Alignment explanation
Indices: 41274992--41275083 Score: 132
Period size: 25 Copynumber: 3.7 Consensus size: 25
41274982 TTCAGCTTTT
**
41274992 ATGAGCTTCCCAATACTT-AGCTCGC
1 ATGAGCTTCCCGTTA-TTCAGCTCGC
41275017 ATGAGCTTCCCGTTATTCAGCTCGC
1 ATGAGCTTCCCGTTATTCAGCTCGC
* *
41275042 ATAAGCTTCCCGTTATTCAGCTCAC
1 ATGAGCTTCCCGTTATTCAGCTCGC
41275067 ATGAGCTTCCCGTTATT
1 ATGAGCTTCCCGTTATT
41275084 GAACTGAGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
24 2 0.03
25 59 0.97
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATTCAGCTCGC
Found at i:41275097 original size:25 final size:25
Alignment explanation
Indices: 41275019--41275099 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
41275009 TAGCTCGCAT
* * *
41275019 GAGCTTCCCGTTATTCAGCTCGCAT
1 GAGCTTCCCGTTATTCAACTCACAG
* * *
41275044 AAGCTTCCCGTTATTCAGCTCACAT
1 GAGCTTCCCGTTATTCAACTCACAG
* * *
41275069 GAGCTTCCCGTTATTGAACTGAGAG
1 GAGCTTCCCGTTATTCAACTCACAG
41275094 GAGCTT
1 GAGCTT
41275100 ATCGTTTACA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGTTATTCAACTCACAG
Found at i:41285075 original size:51 final size:51
Alignment explanation
Indices: 41285015--41285159 Score: 227
Period size: 51 Copynumber: 2.8 Consensus size: 51
41285005 TAAAAAGGAA
* *
41285015 TTTAATAATGCAACCTTTTGGCTAAAGATAAAGATAATTTCAGCATTAATG
1 TTTAATAATGCAACCTTTTGGCTAAAGATGAAGATAATTTCAGCATTAAAG
* *
41285066 TTTAATAATGCAACCTTCTGGCAAAAGATGAAGATAATTTCAGCATTAAAG
1 TTTAATAATGCAACCTTTTGGCTAAAGATGAAGATAATTTCAGCATTAAAG
* * *
41285117 TTTAATAATGCAACCATTCGGCTAAAGACGAAGATAATTTCAG
1 TTTAATAATGCAACCTTTTGGCTAAAGATGAAGATAATTTCAG
41285160 TGGTGCAAGA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
51 85 1.00
ACGTcount: A:0.40, C:0.14, G:0.15, T:0.31
Consensus pattern (51 bp):
TTTAATAATGCAACCTTTTGGCTAAAGATGAAGATAATTTCAGCATTAAAG
Found at i:41290725 original size:42 final size:42
Alignment explanation
Indices: 41290666--41290864 Score: 344
Period size: 42 Copynumber: 4.7 Consensus size: 42
41290656 GCCGCTAAAG
*
41290666 TTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCT
41290708 TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCT
*
41290750 TTAGCGGCGCTTAGAAAAAAACGCCTCTAAAGACCATGTTCT
1 TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCT
* *
41290792 TTAGCGGCGCTTAGAAAAGAAATGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGACCATGTTCT
*
41290835 TTAGCGGCGCTTAGATAAAAACGCCGCTAA
1 TTAGCGGCGCTTAGAAAAAAACGCCGCTAA
41290865 GGAACATGAA
Statistics
Matches: 148, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 110 0.74
43 38 0.26
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (42 bp):
TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCT
Found at i:41290916 original size:127 final size:126
Alignment explanation
Indices: 41290666--41290925 Score: 306
Period size: 127 Copynumber: 2.1 Consensus size: 126
41290656 GCCGCTAAAG
*
41290666 TTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACG
1 TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACG
* ***** * * *
41290731 CCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCCTCTAAAGACCATGTTCT
66 CCGCTAAAGAACATGAAAAATAGCGGCACTTAGAAAAAAACGACTCTAAAGAACATGTTCT
* * *
41290792 TTAGCGGCGCTTAGAAAAGAAATGTCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGATAAAAAC
1 TTAGCGGCGCTTAGAAAA-AAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAAC
* * * *****
41290857 GCCGCTAAGGAACATGAAAAATAGTGGCATTTTTTTTAAAAC-ACTGCTAAAGAACATGTTCT
65 GCCGCTAAAGAACATGAAAAATAGCGGCACTTAGAAAAAAACGACT-CTAAAGAACATGTTCT
41290919 TTAGCGG
1 TTAGCGG
41290926 TGTTTTTATA
Statistics
Matches: 111, Mismatches: 21, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
126 19 0.17
127 92 0.83
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (126 bp):
TTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACG
CCGCTAAAGAACATGAAAAATAGCGGCACTTAGAAAAAAACGACTCTAAAGAACATGTTCT
Found at i:41296809 original size:9 final size:9
Alignment explanation
Indices: 41296795--41297115 Score: 141
Period size: 9 Copynumber: 37.9 Consensus size: 9
41296785 AAGTTATACA
41296795 TTATGTAAG
1 TTATGTAAG
41296804 TTATGTAAG
1 TTATGTAAG
41296813 TTATGTAAG
1 TTATGTAAG
*
41296822 TTGTGTAAG
1 TTATGTAAG
**
41296831 TTGCGTAAG
1 TTATGTAAG
*
41296840 TTGTGT-A-
1 TTATGTAAG
* *
41296847 TTATGAAAC
1 TTATGTAAG
41296856 TTATGTAAG
1 TTATGTAAG
*
41296865 TTATGT--C
1 TTATGTAAG
41296872 TTATGTAAG
1 TTATGTAAG
*
41296881 TTATGTAAA
1 TTATGTAAG
41296890 TTATGT-A-
1 TTATGTAAG
*
41296897 TTATTTACA-
1 TTATGTA-AG
*
41296906 -CATGTAAG
1 TTATGTAAG
*
41296914 TTATGT--C
1 TTATGTAAG
41296921 TTATGTAAG
1 TTATGTAAG
**
41296930 TTGCGTAAG
1 TTATGTAAG
*
41296939 TTGTGT-A-
1 TTATGTAAG
* *
41296946 TTATGAAAC
1 TTATGTAAG
41296955 TTATGTAAG
1 TTATGTAAG
**
41296964 TTGCGTAAG
1 TTATGTAAG
*
41296973 TTGTGT-A-
1 TTATGTAAG
* * *
41296980 TAATAGCAAAC
1 TTAT-G-TAAG
* *
41296991 TTATTTAAT
1 TTATGTAAG
*
41297000 TTATGTAGG
1 TTATGTAAG
*
41297009 GTATGTAAG
1 TTATGTAAG
41297018 TTATGTAAG
1 TTATGTAAG
*
41297027 TTCTGT-A-
1 TTATGTAAG
*
41297034 TTATTTACA-
1 TTATGTA-AG
*
41297043 -CATGTAAG
1 TTATGTAAG
*
41297051 TTGTGT-A-
1 TTATGTAAG
41297058 TTATGTAAG
1 TTATGTAAG
*
41297067 TTATGCAAG
1 TTATGTAAG
41297076 TTATGT-A-
1 TTATGTAAG
* *
41297083 TTAAGTAGG
1 TTATGTAAG
41297092 TTATGTAAG
1 TTATGTAAG
41297101 TTATGT--G
1 TTATGTAAG
41297108 TTATGTAA
1 TTATGTAA
41297116 ATGAATATAT
Statistics
Matches: 233, Mismatches: 53, Indels: 52
0.69 0.16 0.15
Matches are distributed among these distances:
7 50 0.21
8 19 0.08
9 160 0.69
10 1 0.00
11 3 0.01
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (9 bp):
TTATGTAAG
Found at i:41296874 original size:16 final size:17
Alignment explanation
Indices: 41296854--41296931 Score: 83
Period size: 16 Copynumber: 4.8 Consensus size: 17
41296844 GTATTATGAA
41296854 ACTTATGTAAGTTATGT
1 ACTTATGTAAGTTATGT
41296871 -CTTATGTAAGTTATGT
1 ACTTATGTAAGTTATGT
* *
41296887 AAATTATGT-A-TTATTT
1 -ACTTATGTAAGTTATGT
**
41296903 ACACATGTAAGTTATGT
1 ACTTATGTAAGTTATGT
41296920 -CTTATGTAAGTT
1 ACTTATGTAAGTT
41296932 GCGTAAGTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
15 5 0.10
16 32 0.65
17 6 0.12
18 6 0.12
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.47
Consensus pattern (17 bp):
ACTTATGTAAGTTATGT
Found at i:41296894 original size:25 final size:25
Alignment explanation
Indices: 41296784--41297115 Score: 177
Period size: 25 Copynumber: 12.8 Consensus size: 25
41296774 GATTTAGGAA
**
41296784 TAAGTTATACATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* **
41296809 TAAGTTATGTAAGTTGTGTAAGTTGCG
1 TAAGTTATGT-A-TTATGTAAGTTATG
* * *
41296836 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
41296861 TAAGTTATGTCTTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
41296886 TAAATTATGTATTATTTACA--CATG
1 TAAGTTATGTATTATGTA-AGTTATG
* **
41296910 TAAGTTATGTCTTATGTAAGTTGCG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
41296935 TAAGTTGTGTATTATGAAACTTATG
1 TAAGTTATGTATTATGTAAGTTATG
** * *
41296960 TAAGTTGCGTAAGTTGTGT-A-TAATAG
1 TAAGTTATGT-A-TTATGTAAGTTAT-G
* * * * *
41296986 CAAACTTATTTAATTTATGTAGGGTATG
1 -TAAGTTATGT-A-TTATGTAAGTTATG
* *
41297014 TAAGTTATGTAAGTTCTGTATTATTTACACATG
1 TAAGTTATGT-A-TTATGTA--AGTT----ATG
*
41297047 TAAGTTGTGTATTATGTAAGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
* * *
41297072 CAAGTTATGTATTAAGTAGGTTATG
1 TAAGTTATGTATTATGTAAGTTATG
*
41297097 TAAGTTATGTGTTATGTAA
1 TAAGTTATGTATTATGTAA
41297116 ATGAATATAT
Statistics
Matches: 226, Mismatches: 64, Indels: 34
0.70 0.20 0.10
Matches are distributed among these distances:
23 1 0.00
24 18 0.08
25 124 0.55
26 6 0.03
27 51 0.23
28 1 0.00
29 6 0.03
31 6 0.03
32 1 0.00
33 12 0.05
ACGTcount: A:0.31, C:0.05, G:0.20, T:0.44
Consensus pattern (25 bp):
TAAGTTATGTATTATGTAAGTTATG
Found at i:41296958 original size:34 final size:36
Alignment explanation
Indices: 41296920--41296994 Score: 127
Period size: 34 Copynumber: 2.1 Consensus size: 36
41296910 TAAGTTATGT
*
41296920 CTTATGTAAGTTGCGTAAGTTGTGTATTAT-G-AAA
1 CTTATGTAAGTTGCGTAAGTTGTGTATAATAGCAAA
41296954 CTTATGTAAGTTGCGTAAGTTGTGTATAATAGCAAA
1 CTTATGTAAGTTGCGTAAGTTGTGTATAATAGCAAA
41296990 CTTAT
1 CTTAT
41296995 TTAATTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 29 0.76
35 1 0.03
36 8 0.21
ACGTcount: A:0.31, C:0.08, G:0.21, T:0.40
Consensus pattern (36 bp):
CTTATGTAAGTTGCGTAAGTTGTGTATAATAGCAAA
Found at i:41297096 original size:137 final size:133
Alignment explanation
Indices: 41296795--41297102 Score: 400
Period size: 137 Copynumber: 2.3 Consensus size: 133
41296785 AAGTTATACA
* *
41296795 TTATGTAAGTTATGTAAGTTATGTAAGTTGTGTAAGTTGCGTAAGTTGTGTATTATGAAACTTAT
1 TTATGTAAGTTATGT-A-TTATGTAAGTTATGTAAGTTGCGTAAGTTGTGTATAATGAAACTTAT
* *
41296860 GTAAGTTATGTCTTATGTAAGTTATGTAAATTATGTATTATTTACACATGTAAGTTATGTCTTAT
64 GTAAGTTATGTCGTATGTAAGTTATGTAAATTATGTATTATTTACACATGTAAGTTATGTATTAT
41296925 GTAAG
129 GTAAG
** * * *
41296930 TTGCGTAAGTTGTGTATTATGAAACTTATGTAAGTTGCGTAAGTTGTGTATAATAGCAAACTTAT
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGCGTAAGTTGTGTATAAT-G-AAACTTAT
* * * * * *
41296995 TTAATTTATGTAGGGTATGTAAGTTATGTAAGTTCTGTATTATTTACACATGTAAGTTGTGTATT
64 GTAAGTTATGT--CGTATGTAAGTTATGTAAATTATGTATTATTTACACATGTAAGTTATGTATT
41297060 ATGTAAG
127 ATGTAAG
* * *
41297067 TTATGCAAGTTATGTATTAAGTAGGTTATGTAAGTT
1 TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTT
41297103 ATGTGTTATG
Statistics
Matches: 146, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
133 34 0.23
134 2 0.01
135 29 0.20
137 81 0.55
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (133 bp):
TTATGTAAGTTATGTATTATGTAAGTTATGTAAGTTGCGTAAGTTGTGTATAATGAAACTTATGT
AAGTTATGTCGTATGTAAGTTATGTAAATTATGTATTATTTACACATGTAAGTTATGTATTATGT
AAG
Found at i:41297110 original size:16 final size:16
Alignment explanation
Indices: 41297044--41297115 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
41297034 TTATTTACAC
* *
41297044 ATGTAAGTTGTGTATT
1 ATGTAAGTTATGTGTT
*
41297060 ATGTAAGTTATGCAAGTT
1 ATGTAAGTTATG--TGTT
*
41297078 ATGT-A-TTAAGTAGGTT
1 ATGTAAGTTATGT--GTT
41297094 ATGTAAGTTATGTGTT
1 ATGTAAGTTATGTGTT
41297110 ATGTAA
1 ATGTAA
41297116 ATGAATATAT
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
16 31 0.70
17 2 0.05
18 11 0.25
ACGTcount: A:0.31, C:0.01, G:0.24, T:0.44
Consensus pattern (16 bp):
ATGTAAGTTATGTGTT
Found at i:41297233 original size:49 final size:48
Alignment explanation
Indices: 41297180--41297325 Score: 133
Period size: 49 Copynumber: 3.1 Consensus size: 48
41297170 TATTATTAAT
41297180 AAAATTTAAATATAGCTTACATACGTAAATGAATATATGTATCATATTA
1 AAAATTTAAATATAGCTTACATACGTAAATGAATATATGTAT-ATATTA
* * ** * ** * * *
41297229 AAAATAT-AGTAATA-CTTATTTAAGT-TGTCAATTTAT-TAT-TAAT-
1 AAAATTTAAAT-ATAGCTTACATACGTAAATGAATATATGTATATATTA
41297272 AAAATTTAAATATAGCTTACATACGTAAATGAATATATGTATAATATTA
1 AAAATTTAAATATAGCTTACATACGTAAATGAATATATGTAT-ATATTA
41297321 AAAAT
1 AAAAT
41297326 ATAGTAATAC
Statistics
Matches: 69, Mismatches: 20, Indels: 16
0.66 0.19 0.15
Matches are distributed among these distances:
43 9 0.13
44 13 0.19
45 7 0.10
46 6 0.09
47 7 0.10
48 13 0.19
49 14 0.20
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (48 bp):
AAAATTTAAATATAGCTTACATACGTAAATGAATATATGTATATATTA
Found at i:41297276 original size:43 final size:43
Alignment explanation
Indices: 41297137--41297368 Score: 144
Period size: 43 Copynumber: 5.1 Consensus size: 43
41297127 TATAATATTA
41297137 AAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
1 AAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
* * ** * ** * * *
41297180 AAAATTTA-AATATAGCTTACATACGTAAATGAATATATGTATCATATT
1 AAAATATAGTA-ATA-CTTATTTAAGT-TGTCAATTTAT-TAT--TAAT
41297228 AAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
1 -AAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
* * ** * ** * * *
41297272 AAAATTTA-AATATAGCTTACATACGTAAATGAATATATGTATAATATT
1 AAAATATAGTA-ATA-CTTATTTAAGT-TGTCAATTTAT-TAT--TAAT
41297320 AAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
1 -AAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
41297364 AAAAT
1 AAAAT
41297369 TTAAATATAG
Statistics
Matches: 133, Mismatches: 40, Indels: 32
0.65 0.20 0.16
Matches are distributed among these distances:
42 2 0.02
43 25 0.19
44 22 0.17
45 14 0.11
46 12 0.09
47 14 0.11
48 22 0.17
49 20 0.15
50 2 0.02
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (43 bp):
AAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATTAAT
Found at i:41297383 original size:92 final size:92
Alignment explanation
Indices: 41297112--41297386 Score: 541
Period size: 92 Copynumber: 3.0 Consensus size: 92
41297102 TATGTGTTAT
41297112 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
41297177 AATAAAATTTAAATATAGCTTACATAC
66 AATAAAATTTAAATATAGCTTACATAC
*
41297204 GTAAATGAATATATGTATCATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
41297269 AATAAAATTTAAATATAGCTTACATAC
66 AATAAAATTTAAATATAGCTTACATAC
41297296 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
1 GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
41297361 AATAAAATTTAAATATAGCTTACATA
66 AATAAAATTTAAATATAGCTTACATA
41297387 AGCAATTTTT
Statistics
Matches: 181, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 181 1.00
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.41
Consensus pattern (92 bp):
GTAAATGAATATATGTATAATATTAAAAATATAGTAATACTTATTTAAGTTGTCAATTTATTATT
AATAAAATTTAAATATAGCTTACATAC
Found at i:41304746 original size:41 final size:41
Alignment explanation
Indices: 41304642--41304750 Score: 141
Period size: 41 Copynumber: 2.7 Consensus size: 41
41304632 ACCGACTTTT
* * * * *
41304642 AGCCTGCTAGAC-TTATAGTCCGAATAATTTCACCGGCATTA
1 AGCCTGCTAGACAATA-AGTCTGAATTATATCACCGGCATCA
41304683 AGCCTGCTAGACAATGAA-TCTGAATTATATCACCGGCATCA
1 AGCCTGCTAGACAAT-AAGTCTGAATTATATCACCGGCATCA
41304724 AGCCTGCTAGACAATAAGTCTGAATTA
1 AGCCTGCTAGACAATAAGTCTGAATTA
41304751 CATTCAATCA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
40 2 0.03
41 55 0.92
42 2 0.03
43 1 0.02
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (41 bp):
AGCCTGCTAGACAATAAGTCTGAATTATATCACCGGCATCA
Found at i:41306423 original size:13 final size:13
Alignment explanation
Indices: 41306405--41306429 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41306395 TCAACCGATT
41306405 AAATTTTCACACG
1 AAATTTTCACACG
41306418 AAATTTTCACAC
1 AAATTTTCACAC
41306430 ATATAACCTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:41309643 original size:23 final size:22
Alignment explanation
Indices: 41309609--41309653 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
41309599 AATAGGTTTT
* * *
41309609 GCATGTATAACATGTACGGTTC
1 GCATGAATAACATATAAGGTTC
41309631 GCATGAATAAACATATAAGGTTC
1 GCATGAAT-AACATATAAGGTTC
41309654 ACACATTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (22 bp):
GCATGAATAACATATAAGGTTC
Found at i:41309857 original size:29 final size:28
Alignment explanation
Indices: 41309815--41309892 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 28
41309805 GTTTTCATTC
* *
41309815 ATAATGGTTTGCATACAAGGGTTCGCCT
1 ATAAGGGTTCGCATACAAGGGTTCGCCT
* * *
41309843 ATAGGGGGTTCGCATACATGGGTTCTCCT
1 ATA-AGGGTTCGCATACAAGGGTTCGCCT
41309872 ATAAGGGTTCGCATACAAGGG
1 ATAAGGGTTCGCATACAAGGG
41309893 GGTCATACAT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
28 19 0.45
29 23 0.55
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (28 bp):
ATAAGGGTTCGCATACAAGGGTTCGCCT
Found at i:41309867 original size:14 final size:14
Alignment explanation
Indices: 41309820--41309892 Score: 65
Period size: 14 Copynumber: 5.1 Consensus size: 14
41309810 CATTCATAAT
*
41309820 GGTTTGCATACAAG
1 GGTTCGCATACAAG
* * *
41309834 GGTTCGCCTATAGGG
1 GGTTCGCATACA-AG
*
41309849 GGTTCGCATACATG
1 GGTTCGCATACAAG
* * *
41309863 GGTTCTCCTATAAG
1 GGTTCGCATACAAG
41309877 GGTTCGCATACAAG
1 GGTTCGCATACAAG
41309891 GG
1 GG
41309893 GGTCATACAT
Statistics
Matches: 44, Mismatches: 14, Indels: 2
0.73 0.23 0.03
Matches are distributed among these distances:
14 33 0.75
15 11 0.25
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (14 bp):
GGTTCGCATACAAG
Found at i:41309978 original size:15 final size:15
Alignment explanation
Indices: 41309958--41309991 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
41309948 TTTAGATCCC
*
41309958 ACACCTGATTTGAGG
1 ACACCTGATTTGAAG
41309973 ACACCTGATTTGAAG
1 ACACCTGATTTGAAG
41309988 ACAC
1 ACAC
41309992 AAAAAACCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (15 bp):
ACACCTGATTTGAAG
Found at i:41318555 original size:20 final size:20
Alignment explanation
Indices: 41318530--41318567 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41318520 ACTATTTTAT
41318530 TTTATATAAATATTTGTTTC
1 TTTATATAAATATTTGTTTC
**
41318550 TTTATATTTATATTTGTT
1 TTTATATAAATATTTGTT
41318568 CGCTAACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (20 bp):
TTTATATAAATATTTGTTTC
Found at i:41318836 original size:85 final size:85
Alignment explanation
Indices: 41318693--41319004 Score: 382
Period size: 85 Copynumber: 3.7 Consensus size: 85
41318683 TGAAAATAAA
* * * * *
41318693 AATTAAAATTGAATAAAATTTGTTTTGGGATTTATTCCCGCCGTTCAATAGATTTTATTTCATTT
1 AATT-AAATTAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTTCATTT
*
41318758 TTTATTTT-TTTCTAAGCGAG
65 TTTATTTTATTTCTAAACGAG
* *
41318778 AATTAAAATTAAGTAAAATATGTTTTGGGATTTATTCCCGCCGTTTAACAGATTTTA-TTCTATT
1 AATT-AAATTAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTTC-ATT
* *
41318842 TTTTATTTTATTTGTAAACAAG
64 TTTTATTTTATTTCTAAACGAG
* * *
41318864 AATTAAATTAAATAAAATCTGTTTCGGGATTTATTCCAGCCGTTTAACAGATTTTATTCCA-TTT
1 AATTAAATTAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTTCATTTT
* * *
41318928 TGATTTTGTTTCCAAACGAG
66 TTATTTTATTTCTAAACGAG
* * * *
41318948 AATT-AATCAAAT-AATTATGTTTCGGGATTTATTCCTGCCGTTTAACAAATTTTATTT
1 AATTAAATTAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTT
41319005 TGATTTTGTT
Statistics
Matches: 200, Mismatches: 24, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
82 40 0.20
83 7 0.04
84 25 0.12
85 113 0.56
86 15 0.08
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.46
Consensus pattern (85 bp):
AATTAAATTAAATAAAATATGTTTCGGGATTTATTCCCGCCGTTTAACAGATTTTATTTCATTTT
TTATTTTATTTCTAAACGAG
Found at i:41320007 original size:28 final size:28
Alignment explanation
Indices: 41319932--41320185 Score: 236
Period size: 28 Copynumber: 9.1 Consensus size: 28
41319922 GACCATGTGT
41319932 CCCCTATTTTTTAGATTTTACAATTTTA
1 CCCCTATTTTTTAGATTTTACAATTTTA
* * *
41319960 TCCCCTA-CTTTAAAATTTTTACAATTTTA
1 -CCCCTATTTTTTAGA-TTTTACAATTTTA
*
41319989 CCCCTATTTTTCTA-ATTTTATAATTTT-
1 CCCCTATTTTT-TAGATTTTACAATTTTA
* * *
41320016 CACCTATTTTTTAAATTTTACAATTTTG
1 CCCCTATTTTTTAGATTTTACAATTTTA
* * * *
41320044 CTCATATTTTTTAGATTTTATAATTTTGC
1 CCCCTATTTTTTAGATTTTACAATTTT-A
41320073 CCCCTATTTTTTAGATTTTACAATATTT-
1 CCCCTATTTTTTAGATTTTACAAT-TTTA
* * *
41320101 -CTC-ATTTTTTAAAATTTTACAATTTTT
1 CCCCTATTTTTT-AGATTTTACAATTTTA
* *
41320128 CCCATATTTTTTAGATTTTA-AAGTTTTG
1 CCCCTATTTTTTAGATTTTACAA-TTTTA
*
41320156 CCCTTA-TTTTTAGATTTTACAATTTTA
1 CCCCTATTTTTTAGATTTTACAATTTTA
41320183 CCC
1 CCC
41320186 AAAATTTTAA
Statistics
Matches: 188, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
26 12 0.06
27 57 0.30
28 64 0.34
29 51 0.27
30 4 0.02
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (28 bp):
CCCCTATTTTTTAGATTTTACAATTTTA
Found at i:41320062 original size:55 final size:55
Alignment explanation
Indices: 41319936--41320181 Score: 234
Period size: 55 Copynumber: 4.4 Consensus size: 55
41319926 ATGTGTCCCC
* * * *
41319936 TATTTTTTAGATTTTACAATTTTATCCCCTA-CTTTAAAATTTTTACAATTTTACCCC
1 TATTTTTTAGATTTTACAA-TTT-TCCCCTATTTTTTAAA-TTTTACAATTTTGCCCA
* * *
41319993 TATTTTTCTA-ATTTTATAATTTTCACCTATTTTTTAAATTTTACAATTTTGCTCA
1 TATTTTT-TAGATTTTACAATTTTCCCCTATTTTTTAAATTTTACAATTTTGCCCA
* * *
41320048 TATTTTTTAGATTTTATAATTTTGCCCCCTATTTTTTAGATTTTACAATATTT-CTCA
1 TATTTTTTAGATTTTACAATTTT--CCCCTATTTTTTAAATTTTACAAT-TTTGCCCA
* * * * *
41320105 T-TTTTTAAAATTTTACAATTTTTCCCATATTTTTTAGATTTTA-AAGTTTTGCCCT
1 TATTTTTTAGATTTTACAA-TTTTCCCCTATTTTTTAAATTTTACAA-TTTTGCCCA
41320160 TA-TTTTTAGATTTTACAATTTT
1 TATTTTTTAGATTTTACAATTTT
41320182 ACCCAAAATT
Statistics
Matches: 162, Mismatches: 17, Indels: 23
0.80 0.08 0.11
Matches are distributed among these distances:
54 11 0.07
55 77 0.48
56 23 0.14
57 46 0.28
58 5 0.03
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (55 bp):
TATTTTTTAGATTTTACAATTTTCCCCTATTTTTTAAATTTTACAATTTTGCCCA
Found at i:41320077 original size:84 final size:82
Alignment explanation
Indices: 41319976--41320186 Score: 261
Period size: 84 Copynumber: 2.5 Consensus size: 82
41319966 ACTTTAAAAT
* *
41319976 TTTTACAATTTTACCCCTATTTTTCTA-ATTTTATAAT-TTTCACCTATTTTTT-AAATTTTACA
1 TTTTA-AATTTTGCCCCTATTTTT-TAGATTTTACAATATTTC-CC-ATTTTTTAAAATTTTACA
*
41320038 ATTTTGCTCATATTTTTTAGA
62 ATTTTGCCCATATTTTTTAGA
*
41320059 TTTTATAATTTTGCCCCCTATTTTTTAGATTTTACAATATTTCTCATTTTTTAAAATTTTACAAT
1 TTTTA-AATTTTG-CCCCTATTTTTTAGATTTTACAATATTTCCCATTTTTTAAAATTTTACAAT
*
41320124 TTTTCCCATATTTTTTAGA
64 TTTGCCCATATTTTTTAGA
*
41320143 TTTTAAAGTTTTGCCCTTA-TTTTTAGATTTTACAAT-TTTACCCA
1 TTTTAAA-TTTTGCCCCTATTTTTTAGATTTTACAATATTT-CCCA
41320187 AAATTTTAAG
Statistics
Matches: 114, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
81 3 0.03
82 20 0.18
83 27 0.24
84 60 0.53
85 4 0.04
ACGTcount: A:0.26, C:0.15, G:0.04, T:0.55
Consensus pattern (82 bp):
TTTTAAATTTTGCCCCTATTTTTTAGATTTTACAATATTTCCCATTTTTTAAAATTTTACAATTT
TGCCCATATTTTTTAGA
Found at i:41320511 original size:33 final size:34
Alignment explanation
Indices: 41320471--41320549 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 34
41320461 AGCACAATAC
** *
41320471 TTGCTACTATATTGAACTGCTATAAGTATA-TAA
1 TTGCTACTATACCGAACTGCTATAAGCATATTAA
* *
41320504 TTGCTACTATACCGAACTGTTATAAGCATATTGA
1 TTGCTACTATACCGAACTGCTATAAGCATATTAA
41320538 TTGCTACTATAC
1 TTGCTACTATAC
41320550 TACTTTGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
33 26 0.65
34 14 0.35
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (34 bp):
TTGCTACTATACCGAACTGCTATAAGCATATTAA
Found at i:41320709 original size:45 final size:45
Alignment explanation
Indices: 41320659--41320752 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
41320649 GCAATTTGTC
41320659 TGCACT-ATTTAGCGGTTTATCCACACCATATTAGCAACTTTTATT
1 TGCACTGA-TTAGCGGTTTATCCACACCATATTAGCAACTTTTATT
*
41320704 TGCACTGATTAGCGGTTTATCCACACTATATTAGCAACTTTTATT
1 TGCACTGATTAGCGGTTTATCCACACCATATTAGCAACTTTTATT
41320749 TGCA
1 TGCA
41320753 TCGAATTAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 46 0.98
46 1 0.02
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (45 bp):
TGCACTGATTAGCGGTTTATCCACACCATATTAGCAACTTTTATT
Found at i:41320793 original size:46 final size:45
Alignment explanation
Indices: 41320659--41320783 Score: 155
Period size: 45 Copynumber: 2.8 Consensus size: 45
41320649 GCAATTTGTC
* *
41320659 TGCACT-ATTTAGCGGTTTATCCACACCATATTAGCAACTTTTATT
1 TGCACTGA-TTAGCGGTTTACCCACACTATATTAGCAACTTTTATT
*
41320704 TGCACTGATTAGCGGTTTATCCACACTATATTAGCAACTTTTATT
1 TGCACTGATTAGCGGTTTACCCACACTATATTAGCAACTTTTATT
* * *
41320749 TGCA-TCGAATTAGTGGTTTACCCTCACTGTATTAG
1 TGCACT-G-ATTAGCGGTTTACCCACACTATATTAG
41320784 TAGTTTTTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
44 1 0.01
45 47 0.65
46 24 0.33
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (45 bp):
TGCACTGATTAGCGGTTTACCCACACTATATTAGCAACTTTTATT
Found at i:41323627 original size:25 final size:24
Alignment explanation
Indices: 41323599--41323662 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
41323589 ATAGGTAGTA
41323599 TATACTGAGACTATTAAAGATAGAC
1 TATACTGAGACTATTAAA-ATAGAC
* **
41323624 TATACTGAAAAC-ACTTAAAATAGTG
1 TATACTG-AGACTA-TTAAAATAGAC
41323649 TATACTGAGACTAT
1 TATACTGAGACTAT
41323663 AGTAAAAGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
24 4 0.12
25 20 0.62
26 8 0.25
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (24 bp):
TATACTGAGACTATTAAAATAGAC
Found at i:41330030 original size:18 final size:18
Alignment explanation
Indices: 41330004--41330041 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
41329994 ATAAAATAAA
*
41330004 AACGTTTTG-AAATTGAAT
1 AACGATTTGTAAA-TGAAT
41330022 AACGATTTGTAAATGAAT
1 AACGATTTGTAAATGAAT
41330040 AA
1 AA
41330042 TTTTTTGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.45, C:0.05, G:0.16, T:0.34
Consensus pattern (18 bp):
AACGATTTGTAAATGAAT
Found at i:41331356 original size:17 final size:17
Alignment explanation
Indices: 41331334--41331370 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
41331324 CGACATATAA
41331334 ATATTGAGTTACATTTT
1 ATATTGAGTTACATTTT
41331351 ATATTGAGTTACATTTT
1 ATATTGAGTTACATTTT
41331368 ATA
1 ATA
41331371 GCTAATGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (17 bp):
ATATTGAGTTACATTTT
Found at i:41336648 original size:51 final size:52
Alignment explanation
Indices: 41336458--41336635 Score: 188
Period size: 51 Copynumber: 3.5 Consensus size: 52
41336448 TGAAAGTGAA
* * *
41336458 AGTGAT-GGTCACGTGTGTAGTACTGTGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * * * * *
41336508 A-AGATAGGTCGCATATGTAGTACTATGTGCAAGCTACTATGCGTACCGGAT
1 AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
* * * *
41336559 AGCT--TCGATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
41336610 AGTGAT-GGTCACATGTGTAGTACTAT
1 AGTGATAGGTCACATGTGTAGTACTAT
41336636 ACGTAGGCTA
Statistics
Matches: 101, Mismatches: 21, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
49 3 0.03
50 38 0.38
51 59 0.58
52 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (52 bp):
AGTGATAGGTCACATGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGAT
Found at i:41336744 original size:42 final size:42
Alignment explanation
Indices: 41336657--41336997 Score: 381
Period size: 42 Copynumber: 8.1 Consensus size: 42
41336647 TATGTGAACT
41336657 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
* * *
41336699 CGTATCCTTGATTATGAAAGG-GGTTGCTATGTGTTGATTCC-C
1 CGTATCATTGATTAT--AAGGTGGTTGCTAAGTGCTGATTCCAC
*
41336741 CGTATCATTGATTATAAGGTGGTTGTTAAGTGCTGATTCCAC
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
* * * *
41336783 CGTATCCTTGATTGTGAAAGG-GGTTGCTATGTGTTGATTCC-C
1 CGTATCATTGATTAT--AAGGTGGTTGCTAAGTGCTGATTCCAC
*
41336825 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAT
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
* *
41336867 CGTATCCTTGATTGTGAAAGG-GGTTGCTATA-TGCTGATTCC-C
1 CGTATCATTGATTAT--AAGGTGGTTGCTA-AGTGCTGATTCCAC
41336909 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
* * * ** * * *
41336951 TGGGATCCTTTGAACATGAGGCGGTTACTAAGTGCTGATTCCAC
1 -CGTAT-CATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
41336995 CGT
1 CGT
41336998 GTAACGGTTA
Statistics
Matches: 251, Mismatches: 32, Indels: 31
0.80 0.10 0.10
Matches are distributed among these distances:
40 13 0.05
41 53 0.21
42 84 0.33
43 57 0.23
44 44 0.18
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (42 bp):
CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
Found at i:41336801 original size:84 final size:84
Alignment explanation
Indices: 41336657--41336950 Score: 543
Period size: 84 Copynumber: 3.5 Consensus size: 84
41336647 TATGTGAACT
*
41336657 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTATGAAAGGGG
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGG
41336722 TTGCTATGTGTTGATTCCC
66 TTGCTATGTGTTGATTCCC
*
41336741 CGTATCATTGATTATAAGGTGGTTGTTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGG
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGG
41336806 TTGCTATGTGTTGATTCCC
66 TTGCTATGTGTTGATTCCC
*
41336825 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCATCGTATCCTTGATTGTGAAAGGGG
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGG
* *
41336890 TTGCTATATGCTGATTCCC
66 TTGCTATGTGTTGATTCCC
41336909 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
1 CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCAC
41336951 TGGGATCCTT
Statistics
Matches: 203, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 203 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.37
Consensus pattern (84 bp):
CGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTATCCTTGATTGTGAAAGGGG
TTGCTATGTGTTGATTCCC
Found at i:41347858 original size:22 final size:22
Alignment explanation
Indices: 41347819--41347860 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41347809 ATTTTAAATA
* *
41347819 GTGTGTTTATTGGGTCCTAATG
1 GTGTATTTATTGGATCCTAATG
*
41347841 GTGTATTTATTGTATCCTAA
1 GTGTATTTATTGGATCCTAA
41347861 GAGTACCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.48
Consensus pattern (22 bp):
GTGTATTTATTGGATCCTAATG
Found at i:41355934 original size:7 final size:6
Alignment explanation
Indices: 41355900--41355933 Score: 59
Period size: 6 Copynumber: 5.5 Consensus size: 6
41355890 TTTTTGGCTG
41355900 TTTCTTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTT
41355934 TTACTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Done.