Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1532
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1715538
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 192937 characters in sequence are not A, C, G, or T
File 5 of 5
Found at i:1331581 original size:58 final size:58
Alignment explanation
Indices: 1331508--1331644 Score: 256
Period size: 58 Copynumber: 2.4 Consensus size: 58
1331498 CTTGGTGAGA
1331508 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC
1 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC
*
1331566 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTCTCTATAGCTTGGAGAAAAC
1 ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC
*
1331624 ACAGTTTCTCTATAGTTTGGT
1 ACAGTTTCTCTATAGCTTGGT
1331645 GATAAAACAG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 77 1.00
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (58 bp):
ACAGTTTCTCTATAGCTTGGTAAGACCACCTAAAATTTATCTATAGCTTGGAGAAAAC
Found at i:1331654 original size:27 final size:27
Alignment explanation
Indices: 1331547--1331643 Score: 113
Period size: 27 Copynumber: 3.4 Consensus size: 27
1331537 CTAAAATTTA
1331547 TCTATAGCTTGGAGAAAACACAGTTTC
1 TCTATAGCTTGGAGAAAACACAGTTTC
* * * *
1331574 TCTATAGCTTGGTAAGACCACCTAAAATTTC
1 TCTATAGCTTGG--AGA-AAAC-ACAGTTTC
1331605 TCTATAGCTTGGAGAAAACACAGTTTC
1 TCTATAGCTTGGAGAAAACACAGTTTC
*
1331632 TCTATAGTTTGG
1 TCTATAGCTTGG
1331644 TGATAAAACA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
27 29 0.51
28 2 0.04
29 6 0.11
30 2 0.04
31 18 0.32
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (27 bp):
TCTATAGCTTGGAGAAAACACAGTTTC
Found at i:1332482 original size:2 final size:2
Alignment explanation
Indices: 1332475--1332529 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1332465 AATGAAAGAA
1332475 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1332517 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
1332530 ACATGACAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1335860 original size:2 final size:2
Alignment explanation
Indices: 1335853--1335890 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1335843 GCACCTACAG
1335853 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1335891 CAAGAAGAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1337078 original size:16 final size:16
Alignment explanation
Indices: 1337057--1337091 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
1337047 TTTATTCATT
1337057 TTTTTTGGTATATATA
1 TTTTTTGGTATATATA
*
1337073 TTTTTTTGTATATATA
1 TTTTTTGGTATATATA
1337089 TTT
1 TTT
1337092 ATAGGCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (16 bp):
TTTTTTGGTATATATA
Found at i:1340767 original size:28 final size:28
Alignment explanation
Indices: 1340732--1340788 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1340722 AGAAATACGG
1340732 CTAGGCATGTACTGTGTTTGACCATGCA
1 CTAGGCATGTACTGTGTTTGACCATGCA
1340760 CTAGGCATGTACTGTGTTTGACCATGCA
1 CTAGGCATGTACTGTGTTTGACCATGCA
1340788 C
1 C
1340789 CTACAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (28 bp):
CTAGGCATGTACTGTGTTTGACCATGCA
Found at i:1346644 original size:23 final size:24
Alignment explanation
Indices: 1346596--1346645 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
1346586 TTTAATAACC
*
1346596 AAAAAACACCAAAAATCTAATTTA
1 AAAAAACACCAAAAATCTAATATA
*
1346620 AAAAAAC-CCAAACAATTTAA-ATA
1 AAAAAACACCAAA-AATCTAATATA
1346643 AAA
1 AAA
1346646 TTTTCATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.66, C:0.16, G:0.00, T:0.18
Consensus pattern (24 bp):
AAAAAACACCAAAAATCTAATATA
Found at i:1350535 original size:24 final size:24
Alignment explanation
Indices: 1350501--1350550 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
1350491 TTATTAAAGG
*
1350501 GATTCCTTATGGAGTGAGCAGTTT
1 GATTCCCTATGGAGTGAGCAGTTT
1350525 GATTCCCTATGGAGTGAGCAGTTT
1 GATTCCCTATGGAGTGAGCAGTTT
1350549 GA
1 GA
1350551 GGGGAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.14, G:0.30, T:0.34
Consensus pattern (24 bp):
GATTCCCTATGGAGTGAGCAGTTT
Found at i:1352709 original size:32 final size:32
Alignment explanation
Indices: 1352668--1352761 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
1352658 TTCAGGCAAA
1352668 GGGGTCATTTTTCTACGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
**
1352700 GGGGTCATTTTTCGGCGTAGAATAATGACCGG
1 GGGGTCATTTTTCTACGTAGAATAATGACCGG
* *
1352732 GGGGTCATTATTCTACGTAGAAAAATGACC
1 GGGGTCATTTTTCTACGTAGAATAATGACC
1352762 CCCGGTCATT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (32 bp):
GGGGTCATTTTTCTACGTAGAATAATGACCGG
Found at i:1352772 original size:31 final size:32
Alignment explanation
Indices: 1352668--1352779 Score: 145
Period size: 32 Copynumber: 3.5 Consensus size: 32
1352658 TTCAGGCAAA
*
1352668 GGGGTCATTTTTCTACGTAGAATAATGACCGG
1 GGGGTCATTATTCTACGTAGAATAATGACCGG
* **
1352700 GGGGTCATTTTTCGGCGTAGAATAATGACCGG
1 GGGGTCATTATTCTACGTAGAATAATGACCGG
* *
1352732 GGGGTCATTATTCTACGTAGAAAAATGACC-C
1 GGGGTCATTATTCTACGTAGAATAATGACCGG
**
1352763 CCGGTCATTATTCTACG
1 GGGGTCATTATTCTACG
1352780 GGGGTCATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 15 0.21
32 56 0.79
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.29
Consensus pattern (32 bp):
GGGGTCATTATTCTACGTAGAATAATGACCGG
Found at i:1354520 original size:12 final size:12
Alignment explanation
Indices: 1354503--1354528 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1354493 ATTTCAGCAG
1354503 CATTATCATCAT
1 CATTATCATCAT
1354515 CATTATCATCAT
1 CATTATCATCAT
1354527 CA
1 CA
1354529 AAGACAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.27, G:0.00, T:0.38
Consensus pattern (12 bp):
CATTATCATCAT
Found at i:1373311 original size:13 final size:13
Alignment explanation
Indices: 1373293--1373318 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1373283 ATGGGGTTCA
1373293 TATAATTAATAAT
1 TATAATTAATAAT
1373306 TATAATTAATAAT
1 TATAATTAATAAT
1373319 AATCCTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TATAATTAATAAT
Found at i:1380130 original size:15 final size:15
Alignment explanation
Indices: 1380092--1380270 Score: 126
Period size: 15 Copynumber: 11.3 Consensus size: 15
1380082 TCATTTCACT
**
1380092 CTACACTACACTACA
1 CTACACTATGCTACA
* * *
1380107 CTTCGCTATGCAACA
1 CTACACTATGCTACA
1380122 CTACACTATGCTACA
1 CTACACTATGCTACA
* *
1380137 CTGA-ACTACGCTTCA
1 CT-ACACTATGCTACA
1380152 CTACACTATGCTACGCAACA
1 CTACACTATGCT-----ACA
1380172 CTACACTATGCTACGTTA
1 CTACACTATGCTAC---A
* *
1380190 CCATACACTTTGCTACG
1 -C-TACACTATGCTACA
1380207 CTACACTATGCTACA
1 CTACACTATGCTACA
1380222 CTACACTATGCTACA
1 CTACACTATGCTACA
* *
1380237 CTACGCTACGCTACA
1 CTACACTATGCTACA
* **
1380252 CTACATTACACTACA
1 CTACACTATGCTACA
1380267 CTAC
1 CTAC
1380271 CCTAAATCAC
Statistics
Matches: 131, Mismatches: 21, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
14 1 0.01
15 100 0.76
16 2 0.02
18 1 0.01
19 1 0.01
20 26 0.20
ACGTcount: A:0.31, C:0.35, G:0.08, T:0.26
Consensus pattern (15 bp):
CTACACTATGCTACA
Found at i:1380165 original size:20 final size:20
Alignment explanation
Indices: 1380142--1380256 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
1380132 CTACACTGAA
*
1380142 CTACGCTTCACTACACTATG
1 CTACGCTACACTACACTATG
*
1380162 CTACGCAACACTACACTATG
1 CTACGCTACACTACACTATG
* *
1380182 CTACGTTAC-CATACACTTTG
1 CTACGCTACAC-TACACTATG
** **
1380202 CTACGCTACACTATGCTACA
1 CTACGCTACACTACACTATG
* ** *
1380222 CTACACTATGCTACACTACG
1 CTACGCTACACTACACTATG
1380242 CTACGCTACACTACA
1 CTACGCTACACTACA
1380257 TTACACTACA
Statistics
Matches: 73, Mismatches: 20, Indels: 4
0.75 0.21 0.04
Matches are distributed among these distances:
19 1 0.01
20 71 0.97
21 1 0.01
ACGTcount: A:0.30, C:0.35, G:0.10, T:0.26
Consensus pattern (20 bp):
CTACGCTACACTACACTATG
Found at i:1380345 original size:20 final size:20
Alignment explanation
Indices: 1380320--1380368 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1380310 TCATTTCACT
**
1380320 CTACACTTCACTATGCTACG
1 CTACACTTCACTAAACTACG
*
1380340 CTACACTACACTAAACTACG
1 CTACACTTCACTAAACTACG
*
1380360 CTACGCTTC
1 CTACACTTC
1380369 GCTACAATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.37, G:0.08, T:0.27
Consensus pattern (20 bp):
CTACACTTCACTAAACTACG
Found at i:1380373 original size:25 final size:25
Alignment explanation
Indices: 1380329--1380383 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
1380319 TCTACACTTC
* *
1380329 ACTATGCTACGCTACACTACACTAA
1 ACTACGCTACGCTACACTACAATAA
* * *
1380354 ACTACGCTACGCTTCGCTACAATAC
1 ACTACGCTACGCTACACTACAATAA
1380379 ACTAC
1 ACTAC
1380384 CCTAAATCAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.33, C:0.35, G:0.09, T:0.24
Consensus pattern (25 bp):
ACTACGCTACGCTACACTACAATAA
Found at i:1380405 original size:113 final size:116
Alignment explanation
Indices: 1380202--1380486 Score: 432
Period size: 113 Copynumber: 2.5 Consensus size: 116
1380192 ATACACTTTG
* **
1380202 CTACGCTACACTATGCTACACTACACTATGCTACACTACGCTACGCTACACTACATTACACTACA
1 CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTAC--TACACTACA
1380267 CTACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT
64 CTACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT
* * * * *
1380320 CTACACTTCACTATGCTACGCTACACTACACTAAACTACGCTACGCTTCGCTAC-A-A-TACACT
1 CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTACTACACTACACT
1380382 ACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT
66 ACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT
** *
1380433 CTACACTACACTACACTACACTACACTACACTACACTACACTACGCTACACTAC
1 CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTAC
1380487 ACTACATTGC
Statistics
Matches: 151, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
113 103 0.68
114 1 0.01
115 1 0.01
118 46 0.30
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.27
Consensus pattern (116 bp):
CTACACTACACTATGCTACACTACACTACACTACACTACGCTACGCTACACTACTACACTACACT
ACCCTAAATCACAATACACAATGTCCTTGAAATACTCTACTTCATTTCACT
Found at i:1380441 original size:5 final size:5
Alignment explanation
Indices: 1380433--1380622 Score: 326
Period size: 5 Copynumber: 38.0 Consensus size: 5
1380423 TCATTTCACT
*
1380433 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACG CTACA
1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
* * * *
1380483 CTACA CTACA TTGCA CTACA CTATA CTACA CTACA CTACA CTACA TTACA
1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
*
1380533 TTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
1380583 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
1 CTACA CTACA CTACA CTACA CTACA CTACA CTACA CTACA
1380623 AGTCACAATT
Statistics
Matches: 175, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 175 1.00
ACGTcount: A:0.39, C:0.38, G:0.01, T:0.22
Consensus pattern (5 bp):
CTACA
Found at i:1381773 original size:18 final size:18
Alignment explanation
Indices: 1381746--1381800 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
1381736 TCTTTCTTTC
1381746 TTTC-TTTTTTTTTGTCT
1 TTTCTTTTTTTTTTGTCT
1381763 TTTCTTTTTTTTTTGGTC-
1 TTTCTTTTTTTTTT-GTCT
*
1381781 TTTCTATTTTTTTT-TCT
1 TTTCTTTTTTTTTTGTCT
1381798 TTT
1 TTT
1381801 TCAGTCAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
16 2 0.06
17 7 0.21
18 22 0.65
19 3 0.09
ACGTcount: A:0.02, C:0.11, G:0.05, T:0.82
Consensus pattern (18 bp):
TTTCTTTTTTTTTTGTCT
Found at i:1381774 original size:19 final size:19
Alignment explanation
Indices: 1381740--1381795 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1381730 ATCTCTTCTT
* *
1381740 TCTTTCTTTCTTTTTTTTTG
1 TCTTTCTAT-TTTTTTTTGG
1381760 TCTTTTCT-TTTTTTTTTGG
1 TC-TTTCTATTTTTTTTTGG
1381779 TCTTTCTATTTTTTTTT
1 TCTTTCTATTTTTTTTT
1381796 CTTTTTCAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
18 5 0.15
19 20 0.61
20 3 0.09
21 5 0.15
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.80
Consensus pattern (19 bp):
TCTTTCTATTTTTTTTTGG
Found at i:1381802 original size:18 final size:17
Alignment explanation
Indices: 1381746--1381802 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 17
1381736 TCTTTCTTTC
1381746 TTTCTTTTTTTTTGTC-T
1 TTTCTTTTTTTTT-TCTT
* *
1381763 TTTCTTTTTTTTTTGGTC
1 TTTCTTTTTTTTTT-CTT
1381781 TTTCTATTTTTTTTTCTT
1 TTTCT-TTTTTTTTTCTT
1381799 TTTC
1 TTTC
1381803 AGTCAAAAGC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
16 1 0.03
17 13 0.39
18 10 0.30
19 9 0.27
ACGTcount: A:0.02, C:0.12, G:0.05, T:0.81
Consensus pattern (17 bp):
TTTCTTTTTTTTTTCTT
Found at i:1382462 original size:126 final size:126
Alignment explanation
Indices: 1382237--1382485 Score: 392
Period size: 126 Copynumber: 2.0 Consensus size: 126
1382227 GATAAACGAG
* * *
1382237 TAACTATTAAATATCCGTTGTATTATATTCTAAAACTAAGGTATTTCTTAAAGGAAATTCCAGGT
1 TAACTATCAAATATCCGTTGTAATATATTCTAAAACTAAGGTATTTCTTAAAGGAAATGCCAGGT
* * * *
1382302 ATTGTACATGTAATGTATTTGGTTGGTACTAGAAGTCGCCACACGTCATCCATATACTGAA
66 ATTGTACATGTAACGTATTTGATTGGTACTAGAAGTCGCCACAAGTCATCCAAATACTGAA
* *
1382363 TAACTATCAAATATCCGTTGTAATATATTTTAGAA-TGAAGGTATTTCTTAAAGGAAATGCCAGG
1 TAACTATCAAATATCCGTTGTAATATATTCTAAAACT-AAGGTATTTCTTAAAGGAAATGCCAGG
*
1382427 TATTGTACATGTAACGTATTTGATTGGTATTAGAAGTCGCCACAAGTCATCCAAATACT
65 TATTGTACATGTAACGTATTTGATTGGTACTAGAAGTCGCCACAAGTCATCCAAATACT
1382486 TTTGTAAATA
Statistics
Matches: 112, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
125 1 0.01
126 111 0.99
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (126 bp):
TAACTATCAAATATCCGTTGTAATATATTCTAAAACTAAGGTATTTCTTAAAGGAAATGCCAGGT
ATTGTACATGTAACGTATTTGATTGGTACTAGAAGTCGCCACAAGTCATCCAAATACTGAA
Found at i:1382522 original size:37 final size:37
Alignment explanation
Indices: 1382472--1382545 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
1382462 GTCGCCACAA
* *
1382472 GTCATCCAAATACTTTTGTAAATATGATACTGTTTAC
1 GTCATCCAAATACTTTTGTAAATATCAGACTGTTTAC
*
1382509 GTCATCCATATACTTTTGTAAATATCAGACTGTTTAC
1 GTCATCCAAATACTTTTGTAAATATCAGACTGTTTAC
1382546 TTTAATTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (37 bp):
GTCATCCAAATACTTTTGTAAATATCAGACTGTTTAC
Found at i:1383249 original size:19 final size:19
Alignment explanation
Indices: 1383225--1383263 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1383215 CAGAAGAACA
1383225 AATGTAGCTTATTGTGTCC
1 AATGTAGCTTATTGTGTCC
*
1383244 AATGTAGCTTGTTGTGTCC
1 AATGTAGCTTATTGTGTCC
1383263 A
1 A
1383264 TCCTATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.23, T:0.41
Consensus pattern (19 bp):
AATGTAGCTTATTGTGTCC
Found at i:1385639 original size:16 final size:16
Alignment explanation
Indices: 1385620--1385651 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1385610 TGTATGGATG
*
1385620 AATGAATGAGTAAATA
1 AATGAATGACTAAATA
1385636 AATGAATGACTAAATA
1 AATGAATGACTAAATA
1385652 CTGAATTATA
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:0.56, C:0.03, G:0.16, T:0.25
Consensus pattern (16 bp):
AATGAATGACTAAATA
Found at i:1387534 original size:52 final size:50
Alignment explanation
Indices: 1387443--1387542 Score: 150
Period size: 52 Copynumber: 2.0 Consensus size: 50
1387433 CTATTAATAT
*
1387443 CCACGTAGACTAAAAATTTCCACGACCATCAAGCACCCCCACCCCCCCCCC
1 CCACGTAGACTAAAAATTTCCACGACCATCAACCACCCCC-CCCCCCCCCC
*
1387494 NCCACGTAGACTAAAAATTTCCACGACCATC-ACC-CCCCCCCCCTCCCCC
1 -CCACGTAGACTAAAAATTTCCACGACCATCAACCACCCCCCCCCCCCCCC
1387543 AATAATCGAC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
49 9 0.20
50 5 0.11
51 2 0.04
52 30 0.65
ACGTcount: A:0.27, C:0.52, G:0.07, T:0.13
Consensus pattern (50 bp):
CCACGTAGACTAAAAATTTCCACGACCATCAACCACCCCCCCCCCCCCCC
Found at i:1390970 original size:15 final size:15
Alignment explanation
Indices: 1390950--1390981 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1390940 TTTCCTTTTG
1390950 TGCTTCATGCGGTTA
1 TGCTTCATGCGGTTA
1390965 TGCTTCATGCGGTTA
1 TGCTTCATGCGGTTA
1390980 TG
1 TG
1390982 AAGGTTAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.19, G:0.28, T:0.41
Consensus pattern (15 bp):
TGCTTCATGCGGTTA
Found at i:1396721 original size:2 final size:2
Alignment explanation
Indices: 1396714--1396740 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1396704 CCGAGCCGCA
1396714 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1396741 NNNNNNNNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1398800 original size:2 final size:2
Alignment explanation
Indices: 1398795--1398842 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1398785 AGAAGTATAT
1398795 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1398837 AG AG AG
1 AG AG AG
1398843 CACACAACAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1402075 original size:32 final size:32
Alignment explanation
Indices: 1402038--1402099 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
1402028 AATGCTATTC
*
1402038 ATTCTTTAGAATATTCCAAGATGATAAGATCA
1 ATTCTTTAGAATATTCCAAGATGACAAGATCA
1402070 ATTCTTTAGAATATTCCAAGATGACAAGAT
1 ATTCTTTAGAATATTCCAAGATGACAAGAT
1402100 AGATTTTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (32 bp):
ATTCTTTAGAATATTCCAAGATGACAAGATCA
Found at i:1407138 original size:4 final size:4
Alignment explanation
Indices: 1407092--1407130 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
1407082 AAGAGTTGGG
* *
1407092 GTTT -TTT GTTT GTTT GTTT GTTT GTTT TTTT TTTT GTTT
1 GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT GTTT
1407131 TTTTTTTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.09
4 29 0.91
ACGTcount: A:0.00, C:0.00, G:0.18, T:0.82
Consensus pattern (4 bp):
GTTT
Found at i:1407138 original size:12 final size:12
Alignment explanation
Indices: 1407093--1407134 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
1407083 AGAGTTGGGG
1407093 TTTTTTGTTTGT
1 TTTTTTGTTTGT
*
1407105 TTGTTTGTTTGT
1 TTTTTTGTTTGT
*
1407117 TTTTTTTTTTGT
1 TTTTTTGTTTGT
1407129 TTTTTT
1 TTTTTT
1407135 TTTTACAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTTTTGTTTGT
Found at i:1407162 original size:19 final size:19
Alignment explanation
Indices: 1407138--1407180 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1407128 TTTTTTTTTT
*
1407138 TACAAAAATTGAACACTTG
1 TACAAAAACTGAACACTTG
1407157 TACAAAAACTGAACACTTG
1 TACAAAAACTGAACACTTG
1407176 TACAA
1 TACAA
1407181 TTTTACAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (19 bp):
TACAAAAACTGAACACTTG
Found at i:1409440 original size:2 final size:2
Alignment explanation
Indices: 1409433--1409471 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1409423 GACTGGCTCT
1409433 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1409472 TTATTCAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1413524 original size:2 final size:2
Alignment explanation
Indices: 1413517--1413572 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
1413507 GTCAGTTTAT
1413517 GA GA GA GA GA GA GA GA GA GA GA GA GNA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA G-A GA GA GA GA GA GA GA GA
1413560 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
1413573 TTGTACATGT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1420271 original size:2 final size:2
Alignment explanation
Indices: 1420264--1420300 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1420254 AGATAAATAT
1420264 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1420301 TGACCACATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1424293 original size:2 final size:2
Alignment explanation
Indices: 1424286--1424370 Score: 163
Period size: 2 Copynumber: 43.0 Consensus size: 2
1424276 TAGAATAATA
1424286 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1424328 CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1424369 CT
1 CT
1424371 ACGTGTATGA
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1426455 original size:2 final size:2
Alignment explanation
Indices: 1426448--1426479 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1426438 GGCGTAATAT
1426448 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1426480 NCTACGACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1428783 original size:2 final size:2
Alignment explanation
Indices: 1428776--1428827 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1428766 TTGGTGTAAT
1428776 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1428818 GA GA GA GA GA
1 GA GA GA GA GA
1428828 ATTGTTTTAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1431154 original size:21 final size:21
Alignment explanation
Indices: 1431128--1431176 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1431118 GCATCGTCCA
1431128 CAAACAATTGTCGTAAAATTG
1 CAAACAATTGTCGTAAAATTG
1431149 CAAACAATTGTCGTAAAATTG
1 CAAACAATTGTCGTAAAATTG
1431170 CAAACAA
1 CAAACAA
1431177 AGGTCGTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.24
Consensus pattern (21 bp):
CAAACAATTGTCGTAAAATTG
Found at i:1431182 original size:21 final size:21
Alignment explanation
Indices: 1431137--1431184 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1431127 ACAAACAATT
**
1431137 GTCGTAAAATTGCAAACAATT
1 GTCGTAAAATTGCAAACAAAG
1431158 GTCGTAAAATTGCAAACAAAG
1 GTCGTAAAATTGCAAACAAAG
1431179 GTCGTA
1 GTCGTA
1431185 TTTCCGAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.25
Consensus pattern (21 bp):
GTCGTAAAATTGCAAACAAAG
Found at i:1450270 original size:58 final size:58
Alignment explanation
Indices: 1450189--1450304 Score: 160
Period size: 58 Copynumber: 2.0 Consensus size: 58
1450179 AAAATTCTAA
* * **
1450189 TTAGTTTTCTGCACCATTTATTGCAGAGGGTGAAAAATTCTGACCTCACAAATTTTGT
1 TTAGTTTTCCGCACCATTTATTGCAAAAAGTGAAAAATTCTGACCTCACAAATTTTGT
* * * *
1450247 TTAGTTTTCCGCACTATTTATTGCAAAAAGTGAGAAATTCTGTCCTCGCAAATTTTGT
1 TTAGTTTTCCGCACCATTTATTGCAAAAAGTGAAAAATTCTGACCTCACAAATTTTGT
1450305 AGCAAACCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (58 bp):
TTAGTTTTCCGCACCATTTATTGCAAAAAGTGAAAAATTCTGACCTCACAAATTTTGT
Found at i:1459671 original size:191 final size:190
Alignment explanation
Indices: 1459347--1459727 Score: 744
Period size: 191 Copynumber: 2.0 Consensus size: 190
1459337 TTAAGTACCC
1459347 TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTTT
1 TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTTT
1459412 GTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAACC
66 GTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAACC
*
1459477 CGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTTTGTGCTGGTGG
131 CGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG
1459537 NTTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTT
1 -TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTT
1459602 TGTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAAC
65 TGTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAAC
1459667 CCGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG
130 CCGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG
1459728 GGGAGGAAGA
Statistics
Matches: 189, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 189 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (190 bp):
TTTATGTTACGAGCCCCTGATAAGGAAGAAACTTTAATGTATGATTTGATTAATTGTGTACCTTT
GTTACGCCGATTGCGCCAATGTTTCCTCCATACGTTGTCGTTGCATGTCCACATCCGACGAAACC
CGCTATCAGACTACAGAACCCCTCAATGGCTATTCCTCGATTAACACTATGTGCTGGTGG
Found at i:1461508 original size:2 final size:2
Alignment explanation
Indices: 1461501--1461549 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1461491 TGTTGTTAAA
1461501 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1461543 AG AG AG A
1 AG AG AG A
1461550 TTTATTTTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1463966 original size:2 final size:2
Alignment explanation
Indices: 1463959--1464024 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
1463949 AAGCATGAAT
1463959 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1464001 GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA
1464025 TTTTCAGTCT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1472942 original size:250 final size:244
Alignment explanation
Indices: 1472501--1473049 Score: 752
Period size: 250 Copynumber: 2.2 Consensus size: 244
1472491 ATCAACACCA
* *
1472501 GCATAGAGAGAACCAGACAAACCAGATACTGTAATGTAAC-A-AAAACATTATTACAAATGGCAT
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATGGCAT
* ** * *
1472564 AAAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAG
66 AAAGAGAACCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAAAGAG
* * * *
1472629 AGAATCAGACAAACACGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGAA
131 AGAACCAGACAAACACGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAGAGAA
1472694 CCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATGGTA-A-ATG
196 CCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTAT--TACATATG
*
1472743 GCATAGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCAT
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATGGCAT
* * *
1472808 AGAGAGTACCAGACAAACAAGGTACCAGTACTATTACATAACAACGAAACATTATTACAAATGAC
66 AAAGAGAACCAGACAAACAAGGT---AGT-CTA--ACATAACAACAAAACATTATTACAAATGAC
1472873 AAAGAGAGAACCAGACAAAC-CAGGTACTGTAATGTAACAACAAAACATTATAACAAA-GGACAA
125 AAAGAGAGAACCAGACAAACAC-GGTACTGTAATGTAACAACAAAACATTATAACAAATGG-CAA
* * * *
1472936 AGAGAGAACCAGACAACCAATGTATTGTAATGTAACAACCAAACATTATTACATATG
188 AGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACATATG
* * *
1472993 ACATAGAGAGAACCAGACAAACAAGG-ATCTGTAATATAACAACCAAACATTATTACA
1 GCATAGAGAGAACCAGACAAACAAGGTA-CTGTAATGTAACAACAAAACATTATTACA
1473050 TTGTACAACC
Statistics
Matches: 271, Mismatches: 23, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
242 37 0.14
243 1 0.00
244 43 0.16
247 3 0.01
248 4 0.01
249 5 0.02
250 178 0.66
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (244 bp):
GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATGGCAT
AAAGAGAACCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAAAGAG
AGAACCAGACAAACACGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAGAGAA
CCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACATATG
Found at i:1472944 original size:189 final size:183
Alignment explanation
Indices: 1472505--1473049 Score: 733
Period size: 189 Copynumber: 3.0 Consensus size: 183
1472495 ACACCAGCAT
* *
1472505 AGAGAGAACCAGACAAACCAGATACTGTAATGTAAC-A-AAAACATTATTACAAATGGCATAA-A
1 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCA-AAGA
1472567 GAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGA
65 GAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGA
* * * ** * *
1472632 ATCAGACAAACACGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCAT
130 ACCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAA
* * *** *
1472686 AGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATGGTAAATGGCATAGAG
1 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAG
*
1472751 AGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGTA
66 AGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGAA
*
1472816 CCAGACAAACAAGGTACCAGTACTATTACATAACAACGAAACATTATTACAAATGACAA
131 CCAGACAAACAAGGT---AGT-CTA--ACATAACAACAAAACATTATTACAAATGACAA
1472875 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAA-GGACAAAGA
1 AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGG-CAAAGA
* * * * * *
1472939 GAGAACCAGACAACCAATGTATTGTAATGTAACAACCAAACATTATTACATATGACATAGAGAGA
65 GAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGA
* *
1473004 ACCAGACAAACAAGG-A-TCTGTAATATAACAACCAAACATTATTACA
130 ACCAGACAAACAAGGTAGTC--TAACATAACAACAAAACATTATTACA
1473050 TTGTACAACC
Statistics
Matches: 321, Mismatches: 31, Indels: 22
0.86 0.08 0.06
Matches are distributed among these distances:
181 33 0.10
182 2 0.01
183 120 0.37
184 1 0.00
185 3 0.01
186 3 0.01
187 2 0.01
188 2 0.01
189 155 0.48
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (183 bp):
AGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAATGGCAAAGAG
AGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATGGCATAGAGAGAA
CCAGACAAACAAGGTAGTCTAACATAACAACAAAACATTATTACAAATGACAA
Found at i:1473050 original size:61 final size:61
Alignment explanation
Indices: 1472501--1473049 Score: 737
Period size: 61 Copynumber: 8.9 Consensus size: 61
1472491 ATCAACACCA
* *
1472501 GCATAGAGAGAACCAGACAAACCAGATACTGTAATGTAAC-A-AAAACATTATTACAAATG
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
* *
1472560 GCATAAAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATG
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
* * *
1472621 GCATAGAGAGAATCAGACAAACACGGTAGTGTAATGTAACAACAAAACATTATTACAAATG
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
* ***
1472682 GCATAGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATGGTAAATG
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
*
1472743 GCATAGAGAGAACCAGACAAACAAGGTAGTGTAATGTAACAACAAAACATTATTACAAATG
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
* * * *
1472804 GCATAGAGAGTACCAGACAAACAAGGTACCAGTACTATTACATAACAACGAAACATTATTACAAA
1 GCATAGAGAGAACCAGACAAACAAGGTA-CTGTA--A-T--GTAACAACAAAACATTATTACAAA
1472869 TG
60 TG
* * * *
1472871 ACAAAGAGAGAACCAGACAAACCAGGTACTGTAATGTAACAACAAAACATTATAACAAA-G
1 GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
* * * * * *
1472931 GACAAAGAGAGAACCAGACAACCAATGTATTGTAATGTAACAACCAAACATTATTACATATG
1 G-CATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
* * *
1472993 ACATAGAGAGAACCAGACAAACAAGG-ATCTGTAATATAACAACCAAACATTATTACA
1 GCATAGAGAGAACCAGACAAACAAGGTA-CTGTAATGTAACAACAAAACATTATTACA
1473050 TTGTACAACC
Statistics
Matches: 437, Mismatches: 42, Indels: 20
0.88 0.08 0.04
Matches are distributed among these distances:
59 36 0.08
60 3 0.01
61 338 0.77
62 4 0.01
63 1 0.00
64 2 0.00
65 1 0.00
66 4 0.01
67 48 0.11
ACGTcount: A:0.49, C:0.17, G:0.16, T:0.18
Consensus pattern (61 bp):
GCATAGAGAGAACCAGACAAACAAGGTACTGTAATGTAACAACAAAACATTATTACAAATG
Found at i:1477935 original size:10 final size:9
Alignment explanation
Indices: 1477915--1477939 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1477905 ACTTCCATAC
1477915 AAAAAACAA
1 AAAAAACAA
1477924 AAAAAACAA
1 AAAAAACAA
1477933 AAAAAAC
1 AAAAAAC
1477940 TAACGCCACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAACAA
Found at i:1487662 original size:20 final size:21
Alignment explanation
Indices: 1487637--1487680 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1487627 TCTGATATTA
1487637 AATAAAATTTGC-TTCCCAAC
1 AATAAAATTTGCATTCCCAAC
* *
1487657 AATAAAATTTTCATTGCCAAC
1 AATAAAATTTGCATTCCCAAC
1487678 AAT
1 AAT
1487681 GCAGCTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.32
Consensus pattern (21 bp):
AATAAAATTTGCATTCCCAAC
Found at i:1494192 original size:48 final size:48
Alignment explanation
Indices: 1494129--1494230 Score: 161
Period size: 48 Copynumber: 2.1 Consensus size: 48
1494119 ATTTTTACAG
1494129 CTTTGAAATTTTTATGAAGTGTTAAGCT-AAAACAAAAAGACATTTGCT
1 CTTTGAAATTTTTATGAAGTGTTAAGCTAAAAACAAAAA-ACATTTGCT
1494177 CTTTGAAATTTTTATGAAGTGTTAAGCTAAAAAAAACAAAAAACATTTGCT
1 CTTTGAAATTTTTATGAAGTGTTAAGCT---AAAAACAAAAAACATTTGCT
1494228 CTT
1 CTT
1494231 ATAAACAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 5
0.91 0.00 0.09
Matches are distributed among these distances:
48 28 0.56
51 12 0.24
52 10 0.20
ACGTcount: A:0.41, C:0.11, G:0.13, T:0.35
Consensus pattern (48 bp):
CTTTGAAATTTTTATGAAGTGTTAAGCTAAAAACAAAAAACATTTGCT
Found at i:1500063 original size:24 final size:23
Alignment explanation
Indices: 1500031--1500079 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
1500021 AGAAAAGAGA
1500031 AATTGACAAAAATTATTAAAA-TTT
1 AATTGAC-AAAATT-TTAAAAGTTT
*
1500055 AATTTACAAAATTTTAAAAGTTT
1 AATTGACAAAATTTTAAAAGTTT
1500078 AA
1 AA
1500080 CAAATTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 11 0.48
24 6 0.26
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
AATTGACAAAATTTTAAAAGTTT
Found at i:1504908 original size:42 final size:43
Alignment explanation
Indices: 1504849--1504930 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 43
1504839 ACTATAATAA
*
1504849 TTGTAGTTCCATCAATAATTGA-GATGCGTAAGAGAATATCTT
1 TTGTAGTTCCATCAATAATTGATGATACGTAAGAGAATATCTT
* * *
1504891 TTGTAGTTCCGTCAATAATTGATGATATGTAGGAGAATAT
1 TTGTAGTTCCATCAATAATTGATGATACGTAAGAGAATAT
1504931 TTATAATAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
42 21 0.60
43 14 0.40
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.37
Consensus pattern (43 bp):
TTGTAGTTCCATCAATAATTGATGATACGTAAGAGAATATCTT
Found at i:1504981 original size:45 final size:45
Alignment explanation
Indices: 1504845--1505080 Score: 212
Period size: 46 Copynumber: 5.3 Consensus size: 45
1504835 AATAACTATA
* * ** *
1504845 ATAATTGTAGTTCCATCAATAATTGAGATGCGTAAGAGAATATCT
1 ATAATTGTAGTTCCATCAATAATCGGGATATGTAGGAGAATATCT
* * * *
1504890 -T--TTGTAGTTCCGTCAATAATTGATGATATGTAGGAGAATATTT
1 ATAATTGTAGTTCCATCAATAATCG-GGATATGTAGGAGAATATCT
* * *
1504933 ATAATAGTAGTTCCTTCAGTAATCAGGGATAT-TAGGAGAATATCT
1 ATAATTGTAGTTCCATCAATAATC-GGGATATGTAGGAGAATATCT
* * * * *
1504978 ATAATTGTATTTCCGTCAATGATCGGGAATGTGTTGGAGAATATCT
1 ATAATTGTAGTTCCATCAATAATCGGG-ATATGTAGGAGAATATCT
* * *
1505024 ATAATTGTAGTTCCATCAATAATCGTGGATATGTGGGAAAATATAT
1 ATAATTGTAGTTCCATCAATAATCG-GGATATGTAGGAGAATATCT
*
1505070 AT-TTTGTAGTT
1 ATAATTGTAGTT
1505081 TCATTGACAT
Statistics
Matches: 156, Mismatches: 27, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
42 20 0.13
43 15 0.10
44 5 0.03
45 42 0.27
46 71 0.46
47 3 0.02
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (45 bp):
ATAATTGTAGTTCCATCAATAATCGGGATATGTAGGAGAATATCT
Found at i:1504986 original size:91 final size:88
Alignment explanation
Indices: 1504827--1505055 Score: 214
Period size: 91 Copynumber: 2.5 Consensus size: 88
1504817 CTAACGGGTT
* ** *
1504827 TGTAGGAGAATAACTATAATAATTGTAGTTCCATCAATAAT--TGAGATGCGTAAGAGAATATCT
1 TGTAGGAGAATATCTATAAT-A--GTAGTTCCATCAATAATCGTG-GAT-ATTAGGAGAATATCT
* *
1504890 TTTGTAGTTCCGTCAATAATTGATG-ATA
61 TTTGTAGTTCCGTCAATAATCG-GGAATA
* * *
1504918 TGTAGGAGAATATTTATAATAGTAGTTCCTTCAGTAATCAG-GGATATTAGGAGAATATCTATAA
1 TGTAGGAGAATATCTATAATAGTAGTTCCATCAATAATC-GTGGATATTAGGAGAATATCT-T--
* * *
1504982 TTGTATTTCCGTCAATGATCGGGAATG
62 TTGTAGTTCCGTCAATAATCGGGAATA
* *
1505009 TGTTGGAGAATATCTATAATTGTAGTTCCATCAATAATCGTGGATAT
1 TGTAGGAGAATATCTATAATAGTAGTTCCATCAATAATCGTGGATAT
1505056 GTGGGAAAAT
Statistics
Matches: 113, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
88 27 0.24
89 4 0.04
90 4 0.04
91 78 0.69
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (88 bp):
TGTAGGAGAATATCTATAATAGTAGTTCCATCAATAATCGTGGATATTAGGAGAATATCTTTTGT
AGTTCCGTCAATAATCGGGAATA
Found at i:1506799 original size:62 final size:62
Alignment explanation
Indices: 1506702--1506823 Score: 244
Period size: 62 Copynumber: 2.0 Consensus size: 62
1506692 AAATCAGGAA
1506702 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTATAT
1 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTATAT
1506764 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTAT
1 AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTAT
1506824 TTATAAAAGT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.30
Consensus pattern (62 bp):
AACAGCTTGAATTGAATCAGGTGAGGCAGAATTTATATCTATCAATTACAGAAAGATTATAT
Found at i:1515361 original size:172 final size:166
Alignment explanation
Indices: 1515135--1515738 Score: 784
Period size: 167 Copynumber: 3.6 Consensus size: 166
1515125 TCCAAGAGGG
* * * * * *
1515135 TCATGATTTTCACAAATTTGAATCTACATTACCCGAGGAAGCTTCCAAACAAGTTTCAGCTTTTC
1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* * * * *
1515200 TGGCTGAATAATTTTTTAGAAGAAGATTTTTAAAGATTTACTCAATATATTCCCATGTTAAACTT
66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAAC-T
* **
1515265 TGACCCCCCCCCCCCAGTAAGGCCCCACCCTACCCCTGGGGA
130 TGA----CCCCCCCCATTGTGGCCCCACCCTACCCC-GGGGA
* * * * * *
1515307 TCTTGTTTTTCACTACTTTGAATCTACACTACCTAAGGATGCTTCCCCACAAGTTTCATCTTTCC
1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
*
1515372 TGGCTGACTAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT
66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT
* * ** * *
1515437 CAACCCCTTCATTGTGGCCCCACCTTACCCCCGGGGG
131 GACCCCCCCCATTGTGGCCCCACCCTA-CCCCGGGGA
*
1515474 TCATGATTTTCACAACTTTGAATCTACACTACCTGATGATGCTTCCACACAAGTTTCAGCTTTCC
1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* *
1515539 TGGCTGATTAGTTTTTGAGAGGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT
66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT
* *
1515604 GA---CCCCCATTGTGGCCCCACCCTATCCCC-AGAA
131 GACCCCCCCCATTGTGGCCCCACCCTA-CCCCGGGGA
1515637 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
1 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
* * * *
1515702 TGGCTTAATGGTTCTTGAGAAGAAGATTTTTGAAGAT
66 TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGAT
1515739 GACTCTCAAA
Statistics
Matches: 380, Mismatches: 51, Indels: 11
0.86 0.12 0.02
Matches are distributed among these distances:
163 96 0.25
164 23 0.06
167 144 0.38
168 4 0.01
171 3 0.01
172 110 0.29
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (166 bp):
TCATGATTTTCACAACTTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTCC
TGGCTGAATAGTTTTTGAGAAGAAGATTTTTAAAGATTTACTCTATATATTCCAATGTAAAACTT
GACCCCCCCCATTGTGGCCCCACCCTACCCCGGGGA
Found at i:1533820 original size:26 final size:25
Alignment explanation
Indices: 1533770--1533848 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 25
1533760 GTGCCACATG
*
1533770 ATATATATAAAGAAAA-C-TACA-T
1 ATATATATAAAGAAAATCGTATATT
1533792 ATATATATAAAGAAAATCGTATATTT
1 ATATATATAAAGAAAATCGTATA-TT
1533818 ATATATATAAAGAAAAT-G-ATA-T
1 ATATATATAAAGAAAATCGTATATT
1533840 ATATATATA
1 ATATATATA
1533849 NNNNNNNNNN
Statistics
Matches: 52, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
22 26 0.50
23 1 0.02
24 6 0.12
25 1 0.02
26 18 0.35
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (25 bp):
ATATATATAAAGAAAATCGTATATT
Found at i:1535260 original size:20 final size:20
Alignment explanation
Indices: 1535237--1535326 Score: 85
Period size: 20 Copynumber: 4.4 Consensus size: 20
1535227 TGGTTATATA
1535237 TATATATACA-CGATTTTCTT
1 TATATATACATCG-TTTTCTT
*
1535257 TATATATA-TTCAGTTTTCTT
1 TATATATACATC-GTTTTCTT
* *
1535277 TATATATATATCGTATTCATT
1 TATATATACATCGTTTTC-TT
* *
1535298 ATATATATATATCATTTTCTT
1 -TATATATACATCGTTTTCTT
1535319 TATATATA
1 TATATATA
1535327 TAAATATACG
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
20 37 0.62
21 7 0.12
22 16 0.27
ACGTcount: A:0.32, C:0.10, G:0.03, T:0.54
Consensus pattern (20 bp):
TATATATACATCGTTTTCTT
Found at i:1535327 original size:20 final size:20
Alignment explanation
Indices: 1535205--1535375 Score: 137
Period size: 22 Copynumber: 7.8 Consensus size: 20
1535195 ATATATCGCG
1535205 ATTTTCTTTATATATATATC
1 ATTTTCTTTATATATATATC
* * * *
1535225 AGTGGTTATATATATATATACAC
1 A-T-TTTCTTTATATATATA-TC
1535248 GATTTTCTTTATATATAT-TC
1 -ATTTTCTTTATATATATATC
1535268 AGTTTTCTTTATATATATATC
1 A-TTTTCTTTATATATATATC
* *
1535289 GTATTCATTATATATATATATC
1 ATTTTC-TT-TATATATATATC
1535311 ATTTTCTTTATATATATAAATATAC
1 ATTTTC-TT-TATATAT--ATAT-C
*
1535336 GATTTTCTTTATATATATATGT
1 -ATTTTCTTTATATATATAT-C
1535358 AGTTTTCTTTATATATAT
1 A-TTTTCTTTATATATAT
1535376 CATGTGGCAC
Statistics
Matches: 123, Mismatches: 15, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
19 1 0.01
20 22 0.18
21 6 0.05
22 71 0.58
23 2 0.02
24 12 0.10
25 3 0.02
26 6 0.05
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.54
Consensus pattern (20 bp):
ATTTTCTTTATATATATATC
Found at i:1542511 original size:85 final size:86
Alignment explanation
Indices: 1542352--1542523 Score: 265
Period size: 85 Copynumber: 2.0 Consensus size: 86
1542342 ACAATATCAA
* * *
1542352 AACCAATAAAAATGTAGTAACAAACCAGCTTCCTTTTCCATATTTGATCGGAGGTTGACGTTCGA
1 AACCAATAAAAATATAGTAACAAACCAGCTTCCTTTTACATATTTGATCGGAGCTTGACGTTCGA
1542417 AGTTATGCTATTTATACTTTT
66 AGTTATGCTATTTATACTTTT
* ** *
1542438 AACCAATAAAAATATAGTAACAAATCATTTTCCTTTTACAT-TTTGATCGGAGCTTGACGTTGGA
1 AACCAATAAAAATATAGTAACAAACCAGCTTCCTTTTACATATTTGATCGGAGCTTGACGTTCGA
*
1542502 AGTTATGCTATTTCTACTTTT
66 AGTTATGCTATTTATACTTTT
1542523 A
1 A
1542524 TCAATAGTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
85 42 0.54
86 36 0.46
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (86 bp):
AACCAATAAAAATATAGTAACAAACCAGCTTCCTTTTACATATTTGATCGGAGCTTGACGTTCGA
AGTTATGCTATTTATACTTTT
Found at i:1547017 original size:8 final size:8
Alignment explanation
Indices: 1547004--1547048 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
1546994 TGCGTCTACA
1547004 GACAGACG
1 GACAGACG
1547012 GACAGACG
1 GACAGACG
* *
1547020 GACGGACA
1 GACAGACG
1547028 GACAGACG
1 GACAGACG
*
1547036 GACGGACG
1 GACAGACG
1547044 GACAG
1 GACAG
1547049 GGTGAAACCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.36, C:0.24, G:0.40, T:0.00
Consensus pattern (8 bp):
GACAGACG
Found at i:1547018 original size:12 final size:12
Alignment explanation
Indices: 1547001--1547038 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
1546991 AGTTGCGTCT
1547001 ACAGACAGACGG
1 ACAGACAGACGG
*
1547013 ACAGACGGACGG
1 ACAGACAGACGG
1547025 ACAGACAGACGG
1 ACAGACAGACGG
1547037 AC
1 AC
1547039 GGACGGACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.39, C:0.26, G:0.34, T:0.00
Consensus pattern (12 bp):
ACAGACAGACGG
Found at i:1549811 original size:1 final size:1
Alignment explanation
Indices: 1549807--1549850 Score: 88
Period size: 1 Copynumber: 44.0 Consensus size: 1
1549797 CCCCCCCCCC
1549807 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1549851 TATNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1549905 original size:12 final size:12
Alignment explanation
Indices: 1549891--1549930 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
1549881 CCCCCCCCAA
*
1549891 AAAAAAAAACAAA
1 AAAAAAAAA-AAC
1549904 AAAAAAAAAAAC
1 AAAAAAAAAAAC
*
1549916 AAAACAAAAAAC
1 AAAAAAAAAAAC
1549928 AAA
1 AAA
1549931 GTTATTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAC
Found at i:1549909 original size:15 final size:15
Alignment explanation
Indices: 1549889--1549926 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1549879 CCCCCCCCCC
1549889 AAAAAAAAAAACAAA
1 AAAAAAAAAAACAAA
1549904 AAAAAAAAAAACAAA
1 AAAAAAAAAAACAAA
1549919 ACAAAAAA
1 A-AAAAAA
1549927 CAAAGTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAACAAA
Found at i:1549914 original size:20 final size:20
Alignment explanation
Indices: 1549889--1549926 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1549879 CCCCCCCCCC
1549889 AAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAACAAAAAAAA
*
1549909 AAAAAACAAAACAAAAAA
1 AAAAAAAAAAACAAAAAA
1549927 CAAAGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAAAA
Found at i:1569840 original size:2 final size:2
Alignment explanation
Indices: 1569835--1569868 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1569825 CGCGCGCGCG
*
1569835 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CC CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1569869 TACGTGTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.53, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:1570109 original size:27 final size:27
Alignment explanation
Indices: 1570079--1570131 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1570069 CACATCCAAT
*
1570079 TGAACACCTCTTAAACACACGTTCAAG
1 TGAACACCTCATAAACACACGTTCAAG
* * *
1570106 TGAACATCTCATATACACACTTTCAA
1 TGAACACCTCATAAACACACGTTCAA
1570132 TACAACTCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.38, C:0.28, G:0.08, T:0.26
Consensus pattern (27 bp):
TGAACACCTCATAAACACACGTTCAAG
Found at i:1573506 original size:22 final size:22
Alignment explanation
Indices: 1573453--1573514 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 22
1573443 GGCGAAGGAG
* * *
1573453 CGAAAGTGCGAGGATGTGACGG
1 CGAAAGTGCGAAGATGCGACGA
*
1573475 C-AAAGCGCGAAGATGCGACGA
1 CGAAAGTGCGAAGATGCGACGA
*
1573496 CGAAAGTGCGAAGTTGCGA
1 CGAAAGTGCGAAGATGCGA
1573515 AGGCAAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.32, C:0.18, G:0.39, T:0.11
Consensus pattern (22 bp):
CGAAAGTGCGAAGATGCGACGA
Found at i:1578633 original size:2 final size:2
Alignment explanation
Indices: 1578628--1578671 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1578618 CAGTCTGTGT
1578628 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1578670 GA
1 GA
1578672 TATCCTTTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1579220 original size:19 final size:19
Alignment explanation
Indices: 1579196--1579236 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
1579186 TAAATCTTTT
1579196 TATCAATTTCATAGATATA
1 TATCAATTTCATAGATATA
1579215 TATCAATTTCATAGATATA
1 TATCAATTTCATAGATATA
1579234 TAT
1 TAT
1579237 ATAGATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (19 bp):
TATCAATTTCATAGATATA
Found at i:1579234 original size:2 final size:2
Alignment explanation
Indices: 1579229--1579296 Score: 100
Period size: 2 Copynumber: 34.0 Consensus size: 2
1579219 AATTTCATAG
* * *
1579229 AT AT AT AT AT AG AT AT AT AT AT AG AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1579271 AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1579297 TTATCAAGAA
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1579242 original size:12 final size:12
Alignment explanation
Indices: 1579225--1579296 Score: 121
Period size: 12 Copynumber: 6.2 Consensus size: 12
1579215 TATCAATTTC
1579225 ATAGATATATAT
1 ATAGATATATAT
1579237 ATAGATATATAT
1 ATAGATATATAT
1579249 ATAGATATATAT
1 ATAGATATATAT
1579261 ATAG--ATATAT
1 ATAGATATATAT
1579271 ATAGATATATAT
1 ATAGATATATAT
*
1579283 ATATATATATAT
1 ATAGATATATAT
1579295 AT
1 AT
1579297 TTATCAAGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
10 10 0.18
12 47 0.82
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
ATAGATATATAT
Found at i:1580775 original size:3 final size:3
Alignment explanation
Indices: 1580767--1580804 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1580757 TCCATTTCAA
1580767 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA
1580805 GACTTGTACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:1585842 original size:20 final size:20
Alignment explanation
Indices: 1585819--1585864 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
1585809 ACAATACTGA
1585819 ATCATAGGATACAATACAAT
1 ATCATAGGATACAATACAAT
**
1585839 ATCATATTATACAATACAAT
1 ATCATAGGATACAATACAAT
1585859 ATCATA
1 ATCATA
1585865 CTTTACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.30
Consensus pattern (20 bp):
ATCATAGGATACAATACAAT
Found at i:1585871 original size:20 final size:20
Alignment explanation
Indices: 1585827--1585877 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
1585817 GAATCATAGG
1585827 ATACAATACAATATCATATT
1 ATACAATACAATATCATATT
1585847 ATACAATACAATATCATACTT
1 ATACAATACAATATCATA-TT
*
1585868 -TACAAAACAA
1 ATACAATACAA
1585878 ATAAGTTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (20 bp):
ATACAATACAATATCATATT
Found at i:1593857 original size:176 final size:176
Alignment explanation
Indices: 1591819--1594503 Score: 3530
Period size: 176 Copynumber: 15.1 Consensus size: 176
1591809 TCCCATCCCA
** *
1591819 ATGTATCACAAGAGTTTTATAAATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * * *
1591884 GCTATTGAGGAATGGTGGGTCAATGCAAGAGGTGTCTTCCACCTGAATATCCTCTTTACCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* *
1591949 TGAAAAGAAAAAAGGACAAAATGTCTTATATGGTTAACCGAAGTAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* * *
1591995 ATGCATCACAAGAGTTTTATTTATAAATCAATATATTGTACATACCAGCAACTTGTCCACAGGAA
1 ATGTATCACAAGAGTTTTATTGATAAA-CTA-ATATTGTACATACCAGCAACTTGTCCACAGGAA
* * * * * *
1592060 GCGCTATTGAGGAACGGTGGGTCGATTCGAGAAGTGTCTTCCACCTGAGTATCATCTTCAGCTTT
64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT
*
1592125 ATTGAAGAGAAAAAAGGAC--AATGTCTCATATGGTTAACAGATTGAAGTAC
129 ATTGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAAC--A--GAAGTAC
* * * *
1592175 ATGTATCACAAGAGCTTT-TTAAGTAAACTGATATTGTACATACCAGCAACTTGTCCACCGGAAG
1 ATGTATCACAAGAGTTTTATTGA-TAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAG
* * *
1592239 CGCTATTGAGGAATGGTGGGTCAATGCAAGAAGTGTCTTCCACCTGAGTATCATCTTCATCTTTA
65 CGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTA
* * *
1592304 TTGAGGAGAAAAAAAGGACAAAATGTCTAATATGGTTTACAGAAGTAC
130 TTGAAGAG-AAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* *
1592352 ATGTATCACAAGAGTTTTATTGATGAACTAGTATTGTACATACCAGCAACTTGTCCACAGGAAGC
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* *
1592417 GCTATTGAGGAATGGTGGGTCAATGCAAGAAGTGTCTTCCACCTGAGTATCCTCTTCATCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* * * * * *
1592482 TGAAGAGAAATAAGAACAAAATGTCTTAAAT-ATTAAACGGATGTAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTT-AACAGAAGTAC
* * * * *
1592528 ATGAATCATAAGAGTTTTATTAATAAACTAATATATTGTACATACCAGCAAGTTTTCCACAGGAA
1 ATGTATCACAAGAGTTTTATTGATAAACT-A-ATATTGTACATACCAGCAACTTGTCCACAGGAA
* * * * *
1592593 GCGCTATTGAGGAATGGTGGGTCATTGCAAGAGGTGTCTTCCACCTGAATATCCTCTTTACCTTT
64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT
* *
1592658 ATTGAAAAGAAAAAAGGACAAATTTAATGACTTATATGGTTAACAGAAGTAC
129 ATTGAAGAGAAAAAAGGAC-AA---AATGTCTTATATGGTTAACAGAAGTAC
* * * *
1592710 ATGTATCACAAGAGTTTTATTGATTAACTGATATTGTACATACCAGCAACTTGTCCACCGGAAGA
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * *
1592775 GCTATTGAGGAACGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAGTATCCTCTCCATCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* * * * *
1592840 TGACGAGAAAAAAAGGACAAAATGTGTAATATGGTTTACAGAAGAAC
131 TGAAGAG-AAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* *
1592887 ATGTAGCACAAGAGTTTTATTGATAAACTAGTATTGTACATACCAGCAACTTGTCCACAGGAAGC
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* *
1592952 GCTATTGAGGAATGGTGGGTCAATGCAAGAAGTGTCTTCCACCTGAGTATCCTCTTCATCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* * * * * *
1593017 TGAAGAGAAATAAGAACAAAATGTCTTAAAT-ATTAAACGGATGTAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTT-AACAGAAGTAC
* * * * * *
1593063 ATGAATCATAAGAGTTTTATTAATAAACTAATATATTGTACATACGAGCAAGTTTTCCACAGGAA
1 ATGTATCACAAGAGTTTTATTGATAAACT-A-ATATTGTACATACCAGCAACTTGTCCACAGGAA
* * * * *
1593128 GCGCTATTGAGGAATGGTGGGTCATTGCAAGAAGTGTCCTCCACCTGAATATCCTCTTTACCTTT
64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT
* *
1593193 ATTGAAAAGAAAAAAGGACAAATTTAATGACTTATATGGTTAACAGAAGTAC
129 ATTGAAGAGAAAAAAGGAC-AA---AATGTCTTATATGGTTAACAGAAGTAC
* *
1593245 ATGTATCACAAGAGTTTCATTGATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * * * * *
1593310 GCTATTGAGGAATGGTGGGTCAATTCGAGAGGTGTCTTCCATCTGAATATCATCATCAGCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* * * *
1593375 TGAAGAGAAAATAGGACAAAGTGTCTTATATGGTTTACAGATTGAAATAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGG-TTA-ACA--GAAGTAC
* * * * *
1593425 ATGTAGCACAAGAGTTTTATTGATTAACTGATATTGTACATACCAGCAACTTGTCCACCGGAAGA
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * *
1593490 GCTATTGAGGAACGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAGTATCCTCTCCATCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* * * * *
1593555 TGACGAGAAAAAAAGGACAAAATGTGTAATATGGTTTACAGAAGAAC
131 TGAAGAG-AAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* *
1593602 ATGTAGCACAAGAGTTTTATTGATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * * * * *
1593667 GCTATTGAGGAATGGAT-GGTCGATTCGAGAAGTGTCTTCCATCTCAATATCTTCTTCAGCTTTA
66 GCTATTGAGGAATGG-TGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTA
* *
1593731 TTGAAGAGAAAAAAGGACAAAGTGTCTTATATGGTTAACAGAAGTGC
130 TTGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
** *
1593778 ATGTATCACAAGAGTTTTATAAATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGA
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * *
1593843 GCTATTGAGGAATGGTGGGTCAATGCGAGAGGTGTCTTCCACCTGAATATCCTCTTTACCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* *
1593908 TGAAAAGAAAAAAGGACAAAGTGTCTTATATGGTTAACAGAAGTAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* *
1593954 ATGTATCACAAGAGTTTTATCGATAAACTGATATTGTACATACCAGCAACTTGTCCACAGGAAGC
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* * ** * *
1594019 GCTATTGAGGAATGGTGGGTCAATTCGAGAAGTGTCTTCCATCACAATATCATCTTCAGCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
* * *
1594084 TGAAGGGAAAAAAGGACAAAATGTCTAATATGGTTTACAGAAGTAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* * *
1594130 ATGTATCACAAGAGTTTTATTGATAAACTAGTATTGTACATACCAGCAACTTGTCCACGGGAAGA
1 ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
* ** ** *
1594195 GCTATTGAGGAATGGTGGGTCAATGCAAGAAGTCCCTTCCACCTGCGTATCATCTTCATCTTTAT
66 GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
***
1594260 TGAAGAGAAAAAAACCCAAAATGTCTTATATGGTTAACAGAAGTAC
131 TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
* *
1594306 ATGTATCACAAGAGTTTTATTAATAAATTAATATATTGTACATACCAGCAACTTGTCCACAGGAA
1 ATGTATCACAAGAGTTTTATTGATAAACT-A-ATATTGTACATACCAGCAACTTGTCCACAGGAA
* * ** * * * *
1594371 GCGCTTTTGAGGAATGGTGGGTCGATTTGAGAAGTGTCTTCCATCAGAATATCATCTTCAGCTTT
64 GCGCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTT
* * * *
1594436 ATTGAAGAGAAAAAAAGACATAATGACTTATTTGGTTAACAGATA-TAC
129 ATTGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGA-AGTAC
*
1594484 ATGCATCACAAGAGTTTTAT
1 ATGTATCACAAGAGTTTTAT
1594504 AAATAAGGCC
Statistics
Matches: 2197, Mismatches: 274, Indels: 74
0.86 0.11 0.03
Matches are distributed among these distances:
175 5 0.00
176 691 0.31
177 415 0.19
178 567 0.26
179 24 0.01
180 354 0.16
181 49 0.02
182 88 0.04
183 4 0.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (176 bp):
ATGTATCACAAGAGTTTTATTGATAAACTAATATTGTACATACCAGCAACTTGTCCACAGGAAGC
GCTATTGAGGAATGGTGGGTCAATGCGAGAAGTGTCTTCCACCTGAATATCCTCTTCATCTTTAT
TGAAGAGAAAAAAGGACAAAATGTCTTATATGGTTAACAGAAGTAC
Found at i:1599741 original size:24 final size:24
Alignment explanation
Indices: 1599714--1599761 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1599704 CAACGAAATC
1599714 ACTGCCACTTTTAACACCTTGTTT
1 ACTGCCACTTTTAACACCTTGTTT
*
1599738 ACTGCCACTTTTAACATCTTGTTT
1 ACTGCCACTTTTAACACCTTGTTT
1599762 GAAAATTCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.21, C:0.27, G:0.08, T:0.44
Consensus pattern (24 bp):
ACTGCCACTTTTAACACCTTGTTT
Found at i:1600450 original size:16 final size:16
Alignment explanation
Indices: 1600429--1600468 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1600419 ATTACAGTCA
*
1600429 ACTCGTAACCAAACTG
1 ACTCGTAACCAAACAG
*
1600445 ACTCGTACCCAAACAG
1 ACTCGTAACCAAACAG
*
1600461 ACTTGTAA
1 ACTCGTAA
1600469 TCAGATTGTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.38, C:0.30, G:0.12, T:0.20
Consensus pattern (16 bp):
ACTCGTAACCAAACAG
Found at i:1604942 original size:2 final size:2
Alignment explanation
Indices: 1604899--1604931 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1604889 GGGCTTACAA
1604899 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1604932 GGATGCACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1608251 original size:12 final size:12
Alignment explanation
Indices: 1608234--1608260 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1608224 ATACACACAC
1608234 GTACATAAACTA
1 GTACATAAACTA
1608246 GTACATAAACTA
1 GTACATAAACTA
1608258 GTA
1 GTA
1608261 ATTACATTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.26
Consensus pattern (12 bp):
GTACATAAACTA
Found at i:1608750 original size:2 final size:2
Alignment explanation
Indices: 1608743--1608783 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1608733 TACAAACTAA
1608743 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1608784 ATTCAGAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1615768 original size:2 final size:2
Alignment explanation
Indices: 1615761--1615822 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
1615751 NNNNNNNNNN
1615761 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1615803 TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC
1615823 AATATGTGTT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1616055 original size:21 final size:20
Alignment explanation
Indices: 1616018--1616059 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
1616008 CCCATGAGTC
*
1616018 TTTGTTTAGTTTTTAAACATG
1 TTTGTTTAGTTTATAAA-ATG
1616039 TTTGTTTA-TCTTATAAAATG
1 TTTGTTTAGT-TTATAAAATG
1616059 T
1 T
1616060 ATGCATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.26, C:0.05, G:0.12, T:0.57
Consensus pattern (20 bp):
TTTGTTTAGTTTATAAAATG
Found at i:1618847 original size:4 final size:4
Alignment explanation
Indices: 1618838--1618873 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1618828 TACCCTTGTG
* *
1618838 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
1618874 CGTCCGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (4 bp):
TGTC
Found at i:1618860 original size:12 final size:12
Alignment explanation
Indices: 1618843--1618880 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1618833 TTGTGTGTCT
1618843 GTCTGTCCGTCC
1 GTCTGTCCGTCC
* *
1618855 GTCTGTCTGTCT
1 GTCTGTCCGTCC
1618867 GTCTGTCCGTCC
1 GTCTGTCCGTCC
1618879 GT
1 GT
1618881 AACAAAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.00, C:0.34, G:0.26, T:0.39
Consensus pattern (12 bp):
GTCTGTCCGTCC
Found at i:1618863 original size:20 final size:20
Alignment explanation
Indices: 1618838--1618877 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1618828 TACCCTTGTG
1618838 TGTCTGTCTGTCCGTCCGTC
1 TGTCTGTCTGTCCGTCCGTC
*
1618858 TGTCTGTCTGTCTGTCCGTC
1 TGTCTGTCTGTCCGTCCGTC
1618878 CGTAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.33, G:0.25, T:0.42
Consensus pattern (20 bp):
TGTCTGTCTGTCCGTCCGTC
Found at i:1619306 original size:166 final size:167
Alignment explanation
Indices: 1618904--1619444 Score: 890
Period size: 166 Copynumber: 3.3 Consensus size: 167
1618894 GTTGCATTTA
* *
1618904 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTGTTTGTTAAGGCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
1618969 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
1619034 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * * *
1619071 TCTCAGCAA-TGGTATATCGCAGATGCTTGAAATTTTTACACAGTATTTGTATAGGCATGCCATA
1 TCTCAGCAACT-ATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATA
* *
1619135 TCGTGGGATCTATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGTTTATTT
65 TCGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTT
* * *
1619200 TTT-GCCAAAATTTTCAAACAAATTTCCGTCAAAGAAT
130 TTTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* * *
1619237 TCTCAGCAACTATTTATCGGAGATGCTTGAAATTTTAACACACTATTTGTTTAGTCATGCCATAT
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
* *
1619302 CGTGGGATATATTTTTGTATCAATCGGACGTCAACTTCCTGTT-AATGACGACTTTGCTTATTTT
66 CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
1619366 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
131 TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
* *
1619403 TCTCAGCAACTGTTTATCGCAGATGCTTGAAATTTTTACACA
1 TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACA
1619445 NNNNNNNNNN
Statistics
Matches: 343, Mismatches: 28, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
165 22 0.06
166 198 0.58
167 123 0.36
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (167 bp):
TCTCAGCAACTATTTATCGCAGATGCTTGAAATTTTAACACAGTATTTGTTTAGGCATGCCATAT
CGTGGGATATATTTTTGTACCAATCAGACGTCAACTTCCTGTTAAATGACGACTTTGCTTATTTT
TTAACCAAAATTTTCAAACAAATTTTCGTCAAAGATT
Found at i:1621298 original size:34 final size:34
Alignment explanation
Indices: 1621253--1621320 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
1621243 TAGGCATTTG
* *
1621253 AAATGCTTTATGCTCCACAGATGTTTCAGTATTC
1 AAATGCATTATGCTCCACAGATATTTCAGTATTC
*
1621287 AAATGCATTATGCTCTACAGATATTTCAGTATTC
1 AAATGCATTATGCTCCACAGATATTTCAGTATTC
1621321 CTTTCAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (34 bp):
AAATGCATTATGCTCCACAGATATTTCAGTATTC
Found at i:1624368 original size:39 final size:39
Alignment explanation
Indices: 1624310--1625049 Score: 1063
Period size: 39 Copynumber: 19.0 Consensus size: 39
1624300 TCCTGCCAGA
*
1624310 CTGTGTGGAGTTATTAACAGGTAGGATGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
*
1624349 CAGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
** *
1624388 CAATGTGGAGTTATAAACAGGTAGGATGACTGTATCTGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
** * * *
1624427 CAATGTGGAGTTATAAACAGGTAGGGTGACTGTAACAGA
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* * *
1624466 CTGTGTGGAGTTATAAACATGTAGGGTGACTGTATCAGA
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* *
1624505 CTCTGTGGAGTTATAAACAGGTAGGATGACTGTATC-CT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* * *
1624543 ACTGTGTGGAGTTATTAACAGGAAGGATGACTGTATC-CT
1 -CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
*
1624582 ACTGTGTGGAGTTATAAACAGGTAGGATGACTGTATC-CT
1 -CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* *
1624621 ACTGTGTGGAGTTATAAACAGGTAGGGTGACTGTATCAGA
1 -CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* *
1624661 CTGTGTGGAGTTGTTAACAGGTAGGATGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* *
1624700 CTGTGGGGAGTTATAAAGAGGTAGGATGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* * *
1624739 CTGTGGGGAGTTATAGACAGGTAGGGTGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* * *
1624778 CAGTGGGGAGTTATAAACAGGTAGGGTGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* * *
1624817 CTGTGTGGAGTTGTTAACAGGTAGGATGACTGTATCAGA
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
1624856 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* * *
1624895 CTGTGGGGAGTTATAAACAGGTAGGGTGACTGTATCAGA
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* *
1624934 CTGTGTGGAGTTATTAACAGGTAGGATGACTGTATCAGA
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
1624973 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
* *
1625012 CTGTGGGGAGTTATAAACAGGTAGGGTGACTGTATCAG
1 CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAG
1625050 NNNNNNNNNN
Statistics
Matches: 642, Mismatches: 57, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
39 642 1.00
ACGTcount: A:0.28, C:0.11, G:0.32, T:0.29
Consensus pattern (39 bp):
CTGTGTGGAGTTATAAACAGGTAGGATGACTGTATCAGT
Found at i:1625424 original size:39 final size:39
Alignment explanation
Indices: 1625366--1626580 Score: 1878
Period size: 39 Copynumber: 31.2 Consensus size: 39
1625356 NNNNNNNNNN
*
1625366 TCAGTCTGTG-GGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* * *
1625404 TCAGTCTGTGTGGAGTTATAAAGAGGAAGGAGGGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGG-GTGACTGTA
*
1625444 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1625483 TCAGTCTGTGGGGAGTTATAAACAGGCAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* * *
1625522 TCAGTCTGTGGGGAGTTATAAAGAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1625561 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1625600 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* * *
1625639 TCAGTCTGTGGGGAGTTATAAAGAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1625678 TCAGTCTGTGTGGAGTTATAGACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1625717 TCAGTCTGTGGGGAGTTATAAACAGGCAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* **
1625756 TCAGTCAGTGTGGAGTTATAAAGGGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1625795 TCAGTCTGTGGGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1625834 TCAGACTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1625873 TCAGTCAGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1625912 TCAGTCAGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
**
1625951 TCAGTCAATGTGGAGTTATAAACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
** *
1625990 TCAGTCAATGTGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1626029 TCAGTCTGTGGGGAGTTATAAACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1626068 TCAGTCTGTGGGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1626107 TC-CTACTGTGTGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGT-CTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* * *
1626146 TCAGTCTGTGGGGAGTTATAAACAGTTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1626185 TCAGTCTGTGTGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1626224 TC-CTACTGTGTGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGT-CTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1626263 TCAGTCTGTGGGGAGTTATAAACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* * *
1626302 TCAGTCTGTGGGGAGTTATAGACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
1626341 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* * * *
1626380 TCAGTCTATGGGGAGTTATTAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1626419 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1626458 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
*
1626497 TCAGTCTGTGTGGAGTTATAAAGAGGTAGGGTGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
* *
1626536 TCAGTCTGTGGGGAGTTATAAACAGGTAGGATGACTGTA
1 TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
1626575 TCAGTC
1 TCAGTC
1626581 AGTGGAGATA
Statistics
Matches: 1096, Mismatches: 75, Indels: 11
0.93 0.06 0.01
Matches are distributed among these distances:
38 12 0.01
39 1046 0.95
40 38 0.03
ACGTcount: A:0.27, C:0.10, G:0.34, T:0.29
Consensus pattern (39 bp):
TCAGTCTGTGTGGAGTTATAAACAGGTAGGGTGACTGTA
Found at i:1631135 original size:24 final size:24
Alignment explanation
Indices: 1631107--1631156 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1631097 TTCTATCAGT
1631107 TTAAGGAAATAAATAATATCATTA
1 TTAAGGAAATAAATAATATCATTA
1631131 TTAAGGAAATAAATAATATCATTA
1 TTAAGGAAATAAATAATATCATTA
1631155 TT
1 TT
1631157 GATAAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.52, C:0.04, G:0.08, T:0.36
Consensus pattern (24 bp):
TTAAGGAAATAAATAATATCATTA
Found at i:1632293 original size:22 final size:22
Alignment explanation
Indices: 1632268--1632321 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1632258 AATCGCACCT
*
1632268 TCGCCATCGCAACTTCGCACTC
1 TCGCCTTCGCAACTTCGCACTC
* *
1632290 TCGCCTTCGCATCTTCGCACTT
1 TCGCCTTCGCAACTTCGCACTC
1632312 TCGCCTTCGC
1 TCGCCTTCGC
1632322 CTTTTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.11, C:0.44, G:0.15, T:0.30
Consensus pattern (22 bp):
TCGCCTTCGCAACTTCGCACTC
Found at i:1645153 original size:32 final size:33
Alignment explanation
Indices: 1645087--1645163 Score: 138
Period size: 33 Copynumber: 2.4 Consensus size: 33
1645077 GATTTTGGTC
1645087 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
*
1645120 TCAATATTCAACGTTGAAAAATGA-CCCCCGGG
1 TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
1645152 TCAATTTTCAAC
1 TCAATTTTCAAC
1645164 CCGGGTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
32 19 0.45
33 23 0.55
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (33 bp):
TCAATTTTCAACGTTGAAAAATGACCCCCCGGG
Found at i:1645775 original size:21 final size:20
Alignment explanation
Indices: 1645751--1645815 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
1645741 TGAATGGGTG
1645751 ATATCACCTATTCGAATTTGA
1 ATATCACCTATTC-AATTTGA
* *
1645772 ATATCACCT-TTACAAATTGGGG
1 ATATCACCTATT-C-AATT-TGA
*
1645794 ATATCACTTATTCAATTTGA
1 ATATCACCTATTCAATTTGA
1645814 AT
1 AT
1645816 GAGTGTTATC
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
20 5 0.14
21 18 0.51
22 10 0.29
23 2 0.06
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (20 bp):
ATATCACCTATTCAATTTGA
Found at i:1646250 original size:10 final size:10
Alignment explanation
Indices: 1646222--1646252 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
1646212 AAATAGATAA
1646222 ATTTTCTTAT
1 ATTTTCTTAT
1646232 ATTTT-TTAT
1 ATTTTCTTAT
1646241 ATTTTCTTAT
1 ATTTTCTTAT
1646251 AT
1 AT
1646253 ATATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (10 bp):
ATTTTCTTAT
Found at i:1646352 original size:2 final size:2
Alignment explanation
Indices: 1646345--1646419 Score: 105
Period size: 2 Copynumber: 37.5 Consensus size: 2
1646335 CACTTTGATA
** ** *
1646345 CT CT CT CT CT CT CT CT CT CT CT CT NN NN NT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1646387 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1646420 ATATTTAACA
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1648034 original size:13 final size:14
Alignment explanation
Indices: 1648005--1648038 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1647995 GGGTCTATAC
*
1648005 TCAATATTAATAAA
1 TCAATAATAATAAA
1648019 TCAATAATAA-AAA
1 TCAATAATAATAAA
1648032 TCAATAA
1 TCAATAA
1648039 AAACTTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (14 bp):
TCAATAATAATAAA
Found at i:1648295 original size:12 final size:13
Alignment explanation
Indices: 1648268--1648299 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
1648258 TCTTCTTTTA
1648268 TTAAATTTTAAAC
1 TTAAATTTTAAAC
1648281 TTAAATTTT-AAC
1 TTAAATTTTAAAC
1648293 TTAAATT
1 TTAAATT
1648300 GTTTCGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
TTAAATTTTAAAC
Found at i:1650856 original size:15 final size:15
Alignment explanation
Indices: 1650836--1650866 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1650826 TGCTTCATAT
1650836 ATTGAGTAAAGGAAA
1 ATTGAGTAAAGGAAA
1650851 ATTGAGTAAAGGAAA
1 ATTGAGTAAAGGAAA
1650866 A
1 A
1650867 GCTAGCTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (15 bp):
ATTGAGTAAAGGAAA
Found at i:1654641 original size:10 final size:10
Alignment explanation
Indices: 1654626--1654656 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1654616 TGTGGCTCTG
1654626 AAACATACAC
1 AAACATACAC
*
1654636 AAACATACAT
1 AAACATACAC
1654646 AAACATACAC
1 AAACATACAC
1654656 A
1 A
1654657 TTACAAGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (10 bp):
AAACATACAC
Found at i:1658553 original size:2 final size:2
Alignment explanation
Indices: 1658546--1658603 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
1658536 TACAAATAAA
1658546 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1658588 CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT
1658604 GTAGCAACTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1662624 original size:134 final size:134
Alignment explanation
Indices: 1662402--1662732 Score: 374
Period size: 134 Copynumber: 2.5 Consensus size: 134
1662392 TATAATCATG
* * * * * * *
1662402 ACCCCTCAACCATATATATTCATGTTTCTGATGTCAAGGGGCATCAAATGTTATGTAGGTTATGG
1 ACCCCTTAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATGG
* * *
1662467 GCCCTGTGGGTGGTCCTGACCCCCTCAAACACCAAGTCCCTTAATATCTTC-AAAACTGTTGAGA
66 GCCCTGTGGGTGGTCCTGACCCCCTCAAACACCAAGTCCATGAATATC-TCGAAAACGGTTGAGA
1662531 TCCCC
130 TCCCC
* * *
1662536 A-CCCTTAAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAACGGTATGTACGTCATG
1 ACCCCTT-AACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATG
* * ** *
1662600 GGCCC-G-GGGATGGTCGTGACCCCCCTCGAACAGGAAGTGCATGAATATCTCGAAAACGGTTGA
65 GGCCCTGTGGG-TGGTCCTGA-CCCCCTCAAACACCAAGTCCATGAATATCTCGAAAACGGTTGA
1662663 GATCCCC
128 GATCCCC
* * *
1662670 ACCCCTTAACCGTATGTATTCTTGATCCTTA----AA-GGGCATCAAAAGGTATGTAGGTAATGG
1 ACCCCTTAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATGG
1662730 GCC
66 GCC
1662733 TCAGGGTTAA
Statistics
Matches: 170, Mismatches: 22, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
129 27 0.16
130 2 0.01
132 3 0.02
133 15 0.09
134 118 0.69
135 5 0.03
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (134 bp):
ACCCCTTAACCATATATATTCTTGTTCCTTATGTCAAGGGGCATCAAAAGGTATGTAGGTAATGG
GCCCTGTGGGTGGTCCTGACCCCCTCAAACACCAAGTCCATGAATATCTCGAAAACGGTTGAGAT
CCCC
Found at i:1663879 original size:2 final size:2
Alignment explanation
Indices: 1663872--1663935 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
1663862 TGTATGCATA
1663872 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1663914 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
1663936 ATTAAAGTGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1668072 original size:30 final size:29
Alignment explanation
Indices: 1668030--1668116 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 29
1668020 CCATTGCATC
*
1668030 TTCGCTCTTCGCCGTCGCA-TCTTCGCACT
1 TTCGCTCTTCGCCGTCGCACTC-TCGCACA
*
1668059 TTCGCTCCTTCGCCGTTGCACTCTCGCACA
1 TTCGCT-CTTCGCCGTCGCACTCTCGCACA
*
1668089 TTCGCT-TTCGCAACTTCGCACTCTCGCA
1 TTCGCTCTTCGC--CGTCGCACTCTCGCA
1668117 TCTCCGACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
28 5 0.10
29 6 0.12
30 37 0.74
31 2 0.04
ACGTcount: A:0.10, C:0.41, G:0.16, T:0.32
Consensus pattern (29 bp):
TTCGCTCTTCGCCGTCGCACTCTCGCACA
Found at i:1673282 original size:166 final size:165
Alignment explanation
Indices: 1672853--1674358 Score: 1897
Period size: 166 Copynumber: 9.2 Consensus size: 165
1672843 CTTCTACTCA
* *
1672853 AATAG-TTTTGAGAAGAAGATTTTTAAAAAATTTT-TCTATATA----TA---AAAA-TTTAT-C
1 AATAGTTTTTGAGAAGAAGATTTTT-AAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
* * * * *
1672907 CCCCATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTTAAAACTACATTATCT
65 CCCCATTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT
* *** * *
1672972 GAGGATGCTTACACGCCAATTTGAGCTTTCTTGGCCA
129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
* * * * *
1673009 AAAAGTTTTT-A-AA-AAGATTTTTAAAGATTTTGTCTATATATTCCTGTATAATAA-TTTATCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAA-AACTTGATCC
* * *
1673070 CCCAATTGTGGCCCCACCCTACCCCTGGGGACCATGATTTGAACAAACTTGAATCTACATTACCT
65 CCCCATTGTGGCCCCACCCTACCCC-AGGGACCATGATTTGAACAAACTTGAATCTACACTACCT
*
1673135 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCA
129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
*
1673172 AATAGATTTTGAGAAGAAGATTTTTAAAGATTTTCT-TAATATATTCCTATGTAAAACTTGATCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCT-ATATATTCCTATGTAAAACTTGATCC
* * * * *
1673236 CCCTATTGTTGCCCCACCCTACCTCCTGGGACTATGATTTGAACAAACTTGAATCTACACTACCA
65 CCCCATTGTGGCCCCACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT
1673301 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
*
1673338 TATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCT-TAATATATTCCTATGTAAAACTTGATCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCT-ATATATTCCTATGTAAAACTTGATCC
* * *
1673402 CCCCATTGTGGCCCCACCCTACCCCCTGGGACCATGATTTGAACATACTTGAATCTACACTACTT
65 CCCCATTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT
* * *
1673467 GAGGATGCTTCCACTCAAATTTAAGCTTTCCTGGTCT
129 GAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
* * * * ** *
1673504 AACAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCCATTTATTCCTATGTAAAAATCCATTCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC
* * * * * *
1673569 CCCATTGTAGCCCCACCATACCACAAGGGACTATGATTTCAACAAACTGGAATCTACACTACCTG
66 CCCATTGTGGCCCCACCCTACC-CCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTG
* * * *
1673634 AGGATGCTTCCATTTTAATTTGAGCTTTTCTAGCCT
130 AGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
*
1673670 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC
* * *
1673735 CCCATTGTTGCCCCACCCTACTCACAGGCACCATGATTTGAACAAACTTGAATCTACACTACCTG
66 CCCATTGTGGCCCCACCCTAC-CCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTG
* * * *
1673800 AGGATGCTTTCATTTTAATTTGAGCTTTCCTGACCT
130 AGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
1673836 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC
* * * *
1673901 CCCATTGTTGCCCCACCCTATCCCCAGGGACTATGATTTGAACAAACTTGAATCTACACTATCTA
66 CCCATTGTGGCCCCACCCTA-CCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTG
* * *
1673966 AGGATGCTTCCATTTTAATTTGAGCTTTTCTGGCCT
130 AGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
* *
1674002 GATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATATAAAACTTGATCCC
1 AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGAT-CC
* *
1674067 CCCCATTGTTGCCCCACCCTACCCACAGGGACCATGATTTGAACAAACTTGAATCTACACTATCT
65 CCCCATTGTGGCCCCACCCTACCC-CAGGGACCATGATTTGAACAAACTTGAATCTACACTACCT
* * *
1674132 AAGGATGCTTCCATTTTAATTTGAGC-TTCTCTGGCCT
129 GAGGATGCTTCCACTTAAATTTGAGCTTTC-CTGGCCT
* * *
1674169 GATACTTTTTGAGAAGAAGATTTATT-AAGATTTTCTCTAAATATTCCTATGTAAAACTTGATCC
1 AATAGTTTTTGAGAAGAAGATTT-TTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCC
*
1674233 CCCTC-TTGTGGCCCTCA--CTACCCCCGGGGACCATGATTTGAACAAACCTT-AATCTACACTA
65 CCC-CATTGTGGCCC-CACCCTA-CCCCAGGGACCATGATTTGAACAAA-CTTGAATCTACACTA
* * ** * * * * *
1674294 CCTGAGGATGCCTCAACACAAGTTTAAGCTTTTCAGGCCG
126 CCTGAGGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
1674334 AATAGTTTTTGAGAAGAAGATTTTT
1 AATAGTTTTTGAGAAGAAGATTTTT
1674359 GAAAAATACC
Statistics
Matches: 1203, Mismatches: 115, Indels: 56
0.88 0.08 0.04
Matches are distributed among these distances:
153 8 0.01
154 17 0.01
155 2 0.00
156 5 0.00
157 4 0.00
158 1 0.00
161 2 0.00
162 11 0.01
163 95 0.08
164 3 0.00
165 87 0.07
166 806 0.67
167 160 0.13
168 2 0.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (165 bp):
AATAGTTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTCCTATGTAAAACTTGATCCC
CCCATTGTGGCCCCACCCTACCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTACCTGA
GGATGCTTCCACTTAAATTTGAGCTTTCCTGGCCT
Found at i:1676215 original size:2 final size:2
Alignment explanation
Indices: 1676208--1676256 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1676198 GGTATGCATA
1676208 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1676250 CT CT CT C
1 CT CT CT C
1676257 AAAATAACGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:1677590 original size:11 final size:11
Alignment explanation
Indices: 1677560--1677591 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
1677550 TAAAGACGAT
*
1677560 CTTTAAGCCAC
1 CTTTAAGCTAC
1677571 CTTTAAGCTAC
1 CTTTAAGCTAC
1677582 CTTTAAGCTA
1 CTTTAAGCTA
1677592 TAAGTATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.34
Consensus pattern (11 bp):
CTTTAAGCTAC
Found at i:1677650 original size:22 final size:22
Alignment explanation
Indices: 1677600--1677652 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1677590 TATAAGTATT
*
1677600 GCTTAAAGGTGGCTTAAAGAAA
1 GCTTAAAGATGGCTTAAAGAAA
* **
1677622 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCTTAAAGAAA
1677644 GCTTAAAGA
1 GCTTAAAGA
1677653 CTATCTTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (22 bp):
GCTTAAAGATGGCTTAAAGAAA
Found at i:1677673 original size:11 final size:11
Alignment explanation
Indices: 1677657--1677685 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1677647 TAAAGACTAT
1677657 CTTTAAGCCAC
1 CTTTAAGCCAC
1677668 CTTTAAGCCAC
1 CTTTAAGCCAC
1677679 CTTTAAG
1 CTTTAAG
1677686 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1677733 original size:11 final size:11
Alignment explanation
Indices: 1677717--1677745 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1677707 GTCCAAACTT
1677717 CTTTAAGCCAC
1 CTTTAAGCCAC
1677728 CTTTAAGCCAC
1 CTTTAAGCCAC
1677739 CTTTAAG
1 CTTTAAG
1677746 GACAACTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1677749 original size:60 final size:60
Alignment explanation
Indices: 1677656--1677805 Score: 300
Period size: 60 Copynumber: 2.5 Consensus size: 60
1677646 TTAAAGACTA
1677656 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT
1 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT
1677716 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT
1 TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT
1677776 TCTTTAAGCCACCTTTAAGCCACCTTTAAG
1 TCTTTAAGCCACCTTTAAGCCACCTTTAAG
1677806 CCACCTTTAA
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 90 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.32
Consensus pattern (60 bp):
TCTTTAAGCCACCTTTAAGCCACCTTTAAGGACAACTTATAGGTCCTTAATGTCCAAACT
Found at i:1677793 original size:11 final size:11
Alignment explanation
Indices: 1677777--1677841 Score: 121
Period size: 11 Copynumber: 5.9 Consensus size: 11
1677767 GTCCAAACTT
1677777 CTTTAAGCCAC
1 CTTTAAGCCAC
1677788 CTTTAAGCCAC
1 CTTTAAGCCAC
1677799 CTTTAAGCCAC
1 CTTTAAGCCAC
*
1677810 CTTTAAGCTAC
1 CTTTAAGCCAC
1677821 CTTTAAGCCAC
1 CTTTAAGCCAC
1677832 CTTTAAGCCA
1 CTTTAAGCCA
1677842 TTAAAAAAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 52 1.00
ACGTcount: A:0.28, C:0.34, G:0.09, T:0.29
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:1679056 original size:112 final size:112
Alignment explanation
Indices: 1678859--1679081 Score: 401
Period size: 112 Copynumber: 2.0 Consensus size: 112
1678849 AACCCTGACG
** * *
1678859 TGCACCTGGGCACACGACACACCTGTTGTGTATATCTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT
*
1678924 TTCTTAAGTTGGACAAACAATAGACTTTAATTAGATATACACAAACA
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
1678971 TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT
1 TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT
1679036 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAAC
66 TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAAC
1679082 GAACAAAACT
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
112 106 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (112 bp):
TGCACCTGGGCACACGACACAAATGCTGTGTATAACTTGTATATTCTGTGTTAGTTCCAGGGGTT
TTCTTAAGTTGGACAAACAATAGACTCTAATTAGATATACACAAACA
Found at i:1679302 original size:2 final size:2
Alignment explanation
Indices: 1679295--1679344 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1679285 CGGATGAACT
*
1679295 GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1679337 GA GA GA GA
1 GA GA GA GA
1679345 TTTTTTTCAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1679701 original size:22 final size:22
Alignment explanation
Indices: 1679673--1679733 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
1679663 AATATTGACT
*
1679673 TAAAGGCCACTTAAAGACAGTG
1 TAAAGGCCACTTAAAGACAGCG
* *
1679695 TAAAGG-CAGTGTAAAGAGAGCG
1 TAAAGGCCACT-TAAAGACAGCG
*
1679717 TAAATGCCACTTAAAGA
1 TAAAGGCCACTTAAAGA
1679734 TGCTTAAAGG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 26 0.81
23 3 0.09
ACGTcount: A:0.43, C:0.15, G:0.25, T:0.18
Consensus pattern (22 bp):
TAAAGGCCACTTAAAGACAGCG
Found at i:1679749 original size:11 final size:11
Alignment explanation
Indices: 1679726--1679775 Score: 75
Period size: 11 Copynumber: 4.6 Consensus size: 11
1679716 GTAAATGCCA
*
1679726 CTTAAAGAT-G
1 CTTAAAGGTGG
1679736 CTTAAAGGTGG
1 CTTAAAGGTGG
1679747 CTTAAAGGTGG
1 CTTAAAGGTGG
*
1679758 CTTAAAGGTAG
1 CTTAAAGGTGG
1679769 CTTAAAG
1 CTTAAAG
1679776 AAGTTTGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
10 8 0.22
11 29 0.78
ACGTcount: A:0.34, C:0.10, G:0.28, T:0.28
Consensus pattern (11 bp):
CTTAAAGGTGG
Found at i:1679872 original size:11 final size:11
Alignment explanation
Indices: 1679856--1679885 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1679846 CCTTTTAGCT
*
1679856 CCTTTAAGTCA
1 CCTTTAAGCCA
1679867 CCTTTAAGCCA
1 CCTTTAAGCCA
1679878 CCTTTAAG
1 CCTTTAAG
1679886 GACTTGCTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.27, C:0.30, G:0.10, T:0.33
Consensus pattern (11 bp):
CCTTTAAGCCA
Found at i:1681071 original size:4 final size:4
Alignment explanation
Indices: 1681062--1681097 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
1681052 TCTAGCCTTG
* *
1681062 TGTC TGTC TGTC CGTC CGTC TGTC TGTC TGTC TGTC
1 TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC TGTC
1681098 CGTCCGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.31, G:0.25, T:0.44
Consensus pattern (4 bp):
TGTC
Done.