Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 2 of 378
Found at i:398050 original size:30 final size:32
Alignment explanation
Indices: 397987--398061 Score: 93
Period size: 30 Copynumber: 2.4 Consensus size: 32
397977 TTTGTATATA
*
397987 TTTATTATATTT-AAATTATTATTTATAGTTGT
1 TTTAATATATTTGAAATTATTA-TTATAGTTGT
*
398019 TTTAATATATTTGAAATT-TTA-TATTGTTGT
1 TTTAATATATTTGAAATTATTATTATAGTTGT
*
398049 TTTAATAAATTTG
1 TTTAATATATTTG
398062 TCAATTGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 20 0.51
32 14 0.36
33 5 0.13
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (32 bp):
TTTAATATATTTGAAATTATTATTATAGTTGT
Found at i:404493 original size:21 final size:21
Alignment explanation
Indices: 404468--404508 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
404458 AAAATTGATC
*
404468 AATTTTAATTCAGATAAATTT
1 AATTTTAATTAAGATAAATTT
*
404489 AATTTTAATTAAGTTAAATT
1 AATTTTAATTAAGATAAATT
404509 ATGTTATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (21 bp):
AATTTTAATTAAGATAAATTT
Found at i:405964 original size:37 final size:38
Alignment explanation
Indices: 405898--405979 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
405888 GATTTTTAAT
405898 AAAAAAGACTAACTTTGCTCTTTAATCTAATATAAAA-AA
1 AAAAAAGACTAACTTTGCTCTTT-ATCTAA-ATAAAAGAA
405937 AAAAAAGACTAA-TTT-CTCCGTTT-TCTAAATAAAAGAA
1 AAAAAAGACTAACTTTGCT-C-TTTATCTAAATAAAAGAA
*
405974 ACAAAA
1 AAAAAA
405980 TGCAATCCGA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
36 6 0.15
37 14 0.36
38 4 0.10
39 15 0.38
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.28
Consensus pattern (38 bp):
AAAAAAGACTAACTTTGCTCTTTATCTAAATAAAAGAA
Found at i:407448 original size:14 final size:14
Alignment explanation
Indices: 407429--407458 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
407419 GTTTTAAAAG
407429 TATATGTGTGTATA
1 TATATGTGTGTATA
*
407443 TATATGTGTGTGTA
1 TATATGTGTGTATA
407457 TA
1 TA
407459 GCACAGTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (14 bp):
TATATGTGTGTATA
Found at i:411113 original size:34 final size:34
Alignment explanation
Indices: 411075--411143 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
411065 GTGGAATTCT
411075 TGTTTTGGTCCCTCTAATTAAATTTTAGATTTAG
1 TGTTTTGGTCCCTCTAATTAAATTTTAGATTTAG
411109 TGTTTTGGTCCCTCTAATTAAATTTTAGATTTAG
1 TGTTTTGGTCCCTCTAATTAAATTTTAGATTTAG
411143 T
1 T
411144 CCATTAATCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (34 bp):
TGTTTTGGTCCCTCTAATTAAATTTTAGATTTAG
Found at i:412027 original size:48 final size:48
Alignment explanation
Indices: 411958--412051 Score: 188
Period size: 48 Copynumber: 2.0 Consensus size: 48
411948 GTCGCAAGTT
411958 AGTCTAGGTGCTTTTAAGAAAAAAAATCTACGACTAACTAATGATACA
1 AGTCTAGGTGCTTTTAAGAAAAAAAATCTACGACTAACTAATGATACA
412006 AGTCTAGGTGCTTTTAAGAAAAAAAATCTACGACTAACTAATGATA
1 AGTCTAGGTGCTTTTAAGAAAAAAAATCTACGACTAACTAATGATA
412052 TAAAAGTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.28
Consensus pattern (48 bp):
AGTCTAGGTGCTTTTAAGAAAAAAAATCTACGACTAACTAATGATACA
Found at i:416500 original size:16 final size:16
Alignment explanation
Indices: 416479--416510 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
416469 TTGGGGAAGA
416479 AAAATCCAAGGTAAGT
1 AAAATCCAAGGTAAGT
416495 AAAATCCAAGGTAAGT
1 AAAATCCAAGGTAAGT
416511 TCATGATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (16 bp):
AAAATCCAAGGTAAGT
Found at i:417826 original size:38 final size:38
Alignment explanation
Indices: 417664--417825 Score: 252
Period size: 38 Copynumber: 4.3 Consensus size: 38
417654 ATATTCGATG
417664 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
417702 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
**
417740 TATATCCTAGTTAAATCCCGCAGGCTTCGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
* * * *
417778 TATATCCGGGATAAATCCCGCAAGCCTAGTGCTGGTAT
1 TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
*
417816 TATATTCGGG
1 TATATCCGGG
417826 ACTTCGTGCC
Statistics
Matches: 113, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 113 1.00
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (38 bp):
TATATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAT
Found at i:419694 original size:3 final size:3
Alignment explanation
Indices: 419686--419714 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
419676 TATTTTTAAA
419686 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
419715 AAAATAAGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:423410 original size:22 final size:21
Alignment explanation
Indices: 423368--423412 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
423358 CTTCGAGATA
*
423368 CTAGTTTAGTCTCGATTTATT
1 CTAGTTTAGTCTCGATATATT
423389 CTAGTTTAAGTC-CAGATATATT
1 CTAGTTT-AGTCTC-GATATATT
423411 CT
1 CT
423413 GATTTTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.24, C:0.16, G:0.13, T:0.47
Consensus pattern (21 bp):
CTAGTTTAGTCTCGATATATT
Found at i:424372 original size:74 final size:74
Alignment explanation
Indices: 424287--424434 Score: 269
Period size: 74 Copynumber: 2.0 Consensus size: 74
424277 AAGTCCACTC
*
424287 AACTTTTAAATAATTTTATGATGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
1 AACTTTCAAATAATTTTATGATGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
*
424352 ACTAATTTA
66 ACCAATTTA
*
424361 AACTTTCAAATAATTTTATGGTGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
1 AACTTTCAAATAATTTTATGATGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
424426 ACCAATTTA
66 ACCAATTTA
424435 CACTAATTAT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (74 bp):
AACTTTCAAATAATTTTATGATGATTTTATAATATTTTAAAATTAAATGACTAATAATTTAATAA
ACCAATTTA
Found at i:426816 original size:23 final size:23
Alignment explanation
Indices: 426790--426837 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
426780 ACATAGTTTG
426790 TATCATATAGAAAAATATGCTTT
1 TATCATATAGAAAAATATGCTTT
*
426813 TATCATATGGAAAAATATGCTTT
1 TATCATATAGAAAAATATGCTTT
426836 TA
1 TA
426838 GTATTTCTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.40
Consensus pattern (23 bp):
TATCATATAGAAAAATATGCTTT
Found at i:431361 original size:30 final size:31
Alignment explanation
Indices: 431304--431363 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
431294 TTACAAAATG
*
431304 GTCATTTAACTATTCGAAAGTTTTCATTTAT
1 GTCATTTAACTATTCGAAAGCTTTCATTTAT
431335 GTCATTTAACTATTCGAAA-CTTTCATTTA
1 GTCATTTAACTATTCGAAAGCTTTCATTTA
431364 GGTTATTGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.30, C:0.15, G:0.08, T:0.47
Consensus pattern (31 bp):
GTCATTTAACTATTCGAAAGCTTTCATTTAT
Found at i:431873 original size:31 final size:32
Alignment explanation
Indices: 431837--431928 Score: 102
Period size: 31 Copynumber: 3.0 Consensus size: 32
431827 CTATTTAGTG
*
431837 CTTGAGTTTGATTTTAATGTTTGATTTGGTAT
1 CTTGAGTTTGATTTTAATGTTTAATTTGGTAT
* *
431869 -TTGAGTTTTATTTT--TGTTTCAAATTGGTAT
1 CTTGAGTTTGATTTTAATGTTT-AATTTGGTAT
* *
431899 CTT-AGTTTGGTTTTAATGTTCAATTTGGTA
1 CTTGAGTTTGATTTTAATGTTTAATTTGGTA
431929 CCTAGGCCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
29 5 0.10
30 17 0.35
31 23 0.47
32 4 0.08
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.57
Consensus pattern (32 bp):
CTTGAGTTTGATTTTAATGTTTAATTTGGTAT
Found at i:433023 original size:31 final size:31
Alignment explanation
Indices: 432983--433046 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
432973 GTAAACAACC
* *
432983 TAGTAACTTAAATAAATACTTTTGAATAATT
1 TAGTAACTTAAATAAAGACTTTCGAATAATT
*
433014 TAGTGACTTAAATAAAGACTTTCGAATAATT
1 TAGTAACTTAAATAAAGACTTTCGAATAATT
433045 TA
1 TA
433047 ATCATCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (31 bp):
TAGTAACTTAAATAAAGACTTTCGAATAATT
Found at i:434368 original size:193 final size:192
Alignment explanation
Indices: 434115--434663 Score: 721
Period size: 194 Copynumber: 2.8 Consensus size: 192
434105 GAAATTTCCT
* **
434115 AAGCTATGAAA-CTTTGATTCCTTACTGATTCTGCTATGTTGTGTTTATGATTGTTGATATATGC
1 AAGCTATAAAATC-TTGATTCCTTACTGATTCTGCTAAATTGTGTTTATGATTGTTGATATATGC
* *
434179 TGTTTGTTGCTGTATATTGC-TTTGAGTTTTTCAAAAATCGAAGAGAAATGTCTTTGAAAAACGG
65 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAATGTCTTT-AAGAACGG
* * *
434243 GAATACGGGTTTTGTTTAACTGTCTGAATTGCTTCTCGACAAAA-CCCAGTTTACAACATTTCCG
129 GAAT-CGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCAGTTTACAACATATCCG
* * *
434307 ACGTTATAAAATCTTGATTTCTTACTGATTCTGCTAAAATTGTGTTTATGATTGTTGATATATGC
1 AAGCTATAAAATCTTGATTCCTTACTGATTCTGCT-AAATTGTGTTTATGATTGTTGATATATGC
*
434372 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAGCAT-T-TTTAAGAATG
65 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAA--ATGTCTTTAAGAACG
* **
434435 GGAATTCGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCATTTTATGACATATCC
128 GGAA-TCGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCAGTTTACAACATATCC
434500 G
192 G
* * * * *
434501 AAGCTATGACATCTTGATTCCTTAATGATTCTGCTGGATTTGTGTTTATGATTGTTGATATATGC
1 AAGCTATAAAATCTTGATTCCTTACTGATTCTGCT-AAATTGTGTTTATGATTGTTGATATATGC
* * * * *
434566 TGTTTGTTGCTATATATTGCTTTTGAGTTTTTCAAGAGTCGAAGAAAAACGACTTTTAAGAACGG
65 TGTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAATGTC-TTTAAGAACGG
* **
434631 GAATCTGTGTGTTGTTTAACCATCTGAATTGCT
129 GAATC-GGGTGTTGTTTAACTGTCTGAATTGCT
434664 GCTCTGGTCG
Statistics
Matches: 313, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
192 30 0.10
193 94 0.30
194 149 0.48
195 38 0.12
196 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (192 bp):
AAGCTATAAAATCTTGATTCCTTACTGATTCTGCTAAATTGTGTTTATGATTGTTGATATATGCT
GTTTGTTGCTGTATATTGCTTTTGAGTTTTTCAAAAGTCGAAGAGAAATGTCTTTAAGAACGGGA
ATCGGGTGTTGTTTAACTGTCTGAATTGCTTCTCAACAAAACCCCAGTTTACAACATATCCG
Found at i:436637 original size:72 final size:72
Alignment explanation
Indices: 436554--436692 Score: 224
Period size: 72 Copynumber: 1.9 Consensus size: 72
436544 CGATTCCGAT
* *
436554 GAAAAGGGTTCTTCCGATTGTAGCGAAGACCTTAATCCATAAGGCTTACACAAGTAAAAGTGCCA
1 GAAAAGGGTTCTTCCGATTATAGCGAAGACCATAATCCATAAGGCTTACACAAGTAAAAGTGCCA
436619 TTGAAAA
66 TTGAAAA
* ** *
436626 GAAAAGTGTTCTTCCGATTATAGCGAAGATGATAATCCATATGGCTTACACAAGTAAAAGTGCCA
1 GAAAAGGGTTCTTCCGATTATAGCGAAGACCATAATCCATAAGGCTTACACAAGTAAAAGTGCCA
436691 TT
66 TT
436693 CTTTGGTATA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 61 1.00
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (72 bp):
GAAAAGGGTTCTTCCGATTATAGCGAAGACCATAATCCATAAGGCTTACACAAGTAAAAGTGCCA
TTGAAAA
Found at i:438669 original size:22 final size:22
Alignment explanation
Indices: 438642--438683 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
438632 CATATCGAAT
438642 ATATATAATTATTTTAAAATCG
1 ATATATAATTATTTTAAAATCG
438664 ATATATAATTATTTTAAAAT
1 ATATATAATTATTTTAAAAT
438684 GAAAAGTCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATATAATTATTTTAAAATCG
Found at i:440409 original size:16 final size:16
Alignment explanation
Indices: 440388--440425 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
440378 GATCACTTTT
440388 AAGTTCAAG-TCATTTC
1 AAGTTCAAGCT-ATTTC
*
440404 AAGTTCATGCTATTTC
1 AAGTTCAAGCTATTTC
440420 AAGTTC
1 AAGTTC
440426 TGATCATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 19 0.95
17 1 0.05
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (16 bp):
AAGTTCAAGCTATTTC
Found at i:443516 original size:26 final size:26
Alignment explanation
Indices: 443480--443534 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
443470 ATTCAAGATG
443480 TATAATTTAGTATTTTTCTTAAAAAC
1 TATAATTTAGTATTTTTCTTAAAAAC
443506 TATAATTTAGTATTTTTCTTAAAAAC
1 TATAATTTAGTATTTTTCTTAAAAAC
443532 TAT
1 TAT
443535 CTGATAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.38, C:0.07, G:0.04, T:0.51
Consensus pattern (26 bp):
TATAATTTAGTATTTTTCTTAAAAAC
Found at i:446786 original size:16 final size:17
Alignment explanation
Indices: 446751--446789 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
446741 TAAGTCCCAT
446751 ATTTAAATTCAAAAATA
1 ATTTAAATTCAAAAATA
446768 ATTTAAATAT-AAAAA-A
1 ATTTAAAT-TCAAAAATA
446784 ATTTAA
1 ATTTAA
446790 GTATTATATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 13 0.62
18 1 0.05
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTTAAATTCAAAAATA
Found at i:453444 original size:17 final size:18
Alignment explanation
Indices: 453422--453464 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
453412 TATAAAAAAA
453422 TTATTTTAATTT-TTTAT
1 TTATTTTAATTTATTTAT
453439 TTATTTT-ATTTATTTAT
1 TTATTTTAATTTATTTAT
453456 TTATTTTAA
1 TTATTTTAA
453465 CTCTTAAACT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.79
18 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTATTTTAATTTATTTAT
Found at i:459504 original size:29 final size:28
Alignment explanation
Indices: 459437--459508 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
459427 AAAATTGTAC
* * *
459437 AGCACTAAGTGTGCGAGTTTGATTCTAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
459465 AGCACTAAGTGTGCGAG-CTGAAAATATAT
1 AGCACTAAGTGTGCGAGTCTG--AATATAT
459494 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
459509 GATTCACTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 2 0.05
28 17 0.44
29 20 0.51
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:461090 original size:8 final size:8
Alignment explanation
Indices: 461077--461136 Score: 66
Period size: 8 Copynumber: 7.5 Consensus size: 8
461067 CATTCAATAG
461077 GGCAGTTT
1 GGCAGTTT
461085 GGCAGTTT
1 GGCAGTTT
*
461093 GGTAGTTT
1 GGCAGTTT
*
461101 GGCAGCTT
1 GGCAGTTT
*
461109 GGCAATTT
1 GGCAGTTT
*
461117 GGTAGTTT
1 GGCAGTTT
* *
461125 GACATTTT
1 GGCAGTTT
461133 GGCA
1 GGCA
461137 TGACAATCAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
8 41 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (8 bp):
GGCAGTTT
Found at i:461104 original size:24 final size:24
Alignment explanation
Indices: 461077--461136 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
461067 CATTCAATAG
*
461077 GGCAGTTTGGCAGTTTGGTAGTTT
1 GGCAGTTTGGCAATTTGGTAGTTT
*
461101 GGCAGCTTGGCAATTTGGTAGTTT
1 GGCAGTTTGGCAATTTGGTAGTTT
* *
461125 GACATTTTGGCA
1 GGCAGTTTGGCA
461137 TGACAATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.17, C:0.12, G:0.33, T:0.38
Consensus pattern (24 bp):
GGCAGTTTGGCAATTTGGTAGTTT
Found at i:465979 original size:2 final size:2
Alignment explanation
Indices: 465967--466003 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
465957 TGGAAATTGG
*
465967 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
466004 GTGTTGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:468494 original size:18 final size:20
Alignment explanation
Indices: 468457--468498 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
468447 CTATATATGC
*
468457 ATTTTTCAAATATATAAATA
1 ATTTTTCAAAAATATAAATA
468477 ATTTTT-AAAAAT-TAAATA
1 ATTTTTCAAAAATATAAATA
468495 ATTT
1 ATTT
468499 ATGTCTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 5 0.24
20 6 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTTTCAAAAATATAAATA
Found at i:478531 original size:16 final size:16
Alignment explanation
Indices: 478510--478543 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
478500 TTTTAAAATT
478510 TAAAATTTAGTTCTTG
1 TAAAATTTAGTTCTTG
478526 TAAAATTTAGTTCTTG
1 TAAAATTTAGTTCTTG
478542 TA
1 TA
478544 TATCGATTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.32, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
TAAAATTTAGTTCTTG
Found at i:483462 original size:16 final size:16
Alignment explanation
Indices: 483441--483474 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
483431 ATCAAAGTCA
*
483441 AATATATTATGCTAAT
1 AATATATCATGCTAAT
*
483457 AATATATCATTCTAAT
1 AATATATCATGCTAAT
483473 AA
1 AA
483475 ATGCTAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (16 bp):
AATATATCATGCTAAT
Found at i:483487 original size:24 final size:24
Alignment explanation
Indices: 483457--483507 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
483447 TTATGCTAAT
* *
483457 AATATATCATTCTAATAAATGCTA
1 AATATATCATACTAATAAATACTA
* *
483481 AATATATTATACTTATAAATACTA
1 AATATATCATACTAATAAATACTA
483505 AAT
1 AAT
483508 CTTCTAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (24 bp):
AATATATCATACTAATAAATACTA
Found at i:486343 original size:143 final size:137
Alignment explanation
Indices: 486172--487795 Score: 728
Period size: 145 Copynumber: 11.8 Consensus size: 137
486162 ATGACAAAAT
486172 TATATATTTTGTTGTTTGGTTA-GTTAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTAT
1 TATATATTTTGTTGTTTGGTTACG-TAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTAT
* * * *
486236 TTTAATTGTCTAAATTTGGTCATTTAGCTG-AAAATTTTAGTGTTCTTTTGTTATTAATAAGTTT
65 TTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTC---T-TT-TTAAT--GGTT
*
486300 CTTTATGAATATATG
123 CTTTATGAATATAAG
* * * *
486315 TATATATTTTATTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTAAGTTTAATTTAACCATT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTATT
* * **
486380 TTAATTGTCTCAATTTAGTAATTTAGGTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGA
66 TTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
486445 ATATAAG
131 ATATAAG
* * * *
486452 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATATAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGCTTAATTTAGCTAT
* * ***** *
486516 TTTAGTTGTTGTGAAA---A--AATTTAG-TG-TTCTTTTTGGTGGTTC---TT--T--------
65 TTTAATTG-TCT-AAATTTAGTAATTTAGCTGAAAAAATTTAGT-GTTCTTTTTAATGGTTCTTT
486561 ATGAATATAAG
127 ATGAATATAAG
* * * * *
486572 TATATATTTTGTTCTTTGGTTACTTAGAAAGTAAATT-ATAGTGGATTAAGCTTAATATAGATAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGCTTAATTTAGCTAT
* * ***** *
486636 TTTAGTTGTCGGGAAA---A--AATTTAG-TG-TTGTTTTTGGTGGTTC---TT--T--------
65 TTTAATTGTC--TAAATTTAGTAATTTAGCTGAAAAAATTTAGT-GTTCTTTTTAATGGTTCTTT
486681 ATGAATATAAG
127 ATGAATATAAG
* * ** *
486692 TATATTTTTTGTTGTTTGGTTACTTAGAAAGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTATT
* * * * * * * **
486757 TTAATCGTCTCAATTTCGTCATTTAGGTGAAAAATTTTAGTGTTCATTTTGGTGGTTCTTTATGA
66 TTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
486822 ATATAAG
131 ATATAAG
* * * *
486829 TATATAATTTGTTGTTGGGTTACTTAGAAAGTAAATT-ATAGTGGAATAAGCTT-ATGTTAGCTA
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGCTTAAT-TTAGCTA
* * * * * *
486892 CTTTAATT-TCTAAGTTTGGTCATTTAGGTGAAAAACA-TTAGTGTTCTTCTGCTTTTTTTTTAT
64 TTTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAA-ATTTAGTG----T-T-C---TTTTTAAT
*
486955 GGTTCTTTATGAATATATG
119 GGTTCTTTATGAATATAAG
* * * *
486974 TATATAATTTGTTGTTTGTTTACTTAGAAAGTAAATT-ATAGTGGGA-TAAGCTTAATTTACACT
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGT-GGATTAAGCTTAATTTA-GCT
* * * * * * ** *
487037 ACTTTAATTGTCTAAAGTTCGTCATTTAGGTGAAAAAA--T--TGTTATTAGTAA-GTTTCTTTA
63 ATTTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTA
**
487097 TGAATATATC
128 TGAATATAAG
* * * * **
487107 TATATGTTTTGTTGTTTGGTTACTTAGAAAGTAAATGGTAGTGGGA-TAAGCTTAA-GAATGCTA
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGT-GGATTAAGCTTAATTTA-GCTA
* * * * * * * * * *
487170 CTTTAGTTTTCTAAATTTCGTTACTTAGGTGACAAAAGTTAGTGTTCTTATGCTATTTTTTATGG
64 TTTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTG----T-T-C--TTTTTAATGG
* * *
487235 TTCATTATGGATATATG
121 TTCTTTATGAATATAAG
* * * * *
487252 TATATAATTTATTGTTTGGTTACCTACAAAGTAAATT-ACAGTGGGA-TAACCTTAATTTAGCTA
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGT-GGATTAAGCTTAATTTAGCTA
* * * ** * * *
487315 CTTTACTTTTCTAAATTTCTTCATTTAGGTGAAAAAATTTAGTG-TCTTTTGTTATTTTTTTATA
64 TTTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTC-TTT-TTA-------ATG
*
487379 GTTCTTTATGAATAT--C
120 GTTCTTTATGAATATAAG
* * * *
487395 TTTATA-TTTGTTGTTTGGTTACTTAGAAAGTAAATT-ATAATGGATTGAGCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGCTTAATTTAGCTA-
* * * ** * *
487458 TTTT-ATTGTCTAAATTTCGTCATTTAGGTGAAAATTTTTTGTGTTCTTTTGTTATTAGCAAGTT
64 TTTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTC-TTT-TTAAT-G---G-T
**
487522 TCTTTATGAATATGTG
122 TCTTTATGAATATAAG
* * * * *
487538 TATATATTTTGTTGTTTGGTTTCTTAGAAAGCAAATTGTAGTGGGA-TAAGCTTAATTTAGCTAC
1 TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGT-GGATTAAGCTTAATTTAGCTAT
** * * * * * **
487602 TTTAATTGTCTAAATTTCA-TCGTTTAGGTAAAAAAATTTCGTGTTTCTTTTGTTATTAGTAAGT
65 TTTAATTGTCTAAATTT-AGTAATTTAGCTGAAAAAATTTAGTG-TTC-TTT-TTAATGGT-TCT
* *
487666 TTATGCACAAACATATG
125 TTATG----AATATAAG
* * * *
487683 TATATA--TTGCTT-TTTGGTTGCTTAGAAAGTAAATT-ATGGTGGAATAAGCTTAATTTAGCTA
1 TATATATTTTG-TTGTTTGGTTACGTAGAAAGTAAATTGA-AGTGGATTAAGCTTAATTTAGCTA
* * * * * *
487744 CTTTAATTGTCCAAATTTCGTTATTTAGGTG-AAAAATTTAAATGTTCTTTTT
64 TTTTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTT-AGTGTTCTTTTT
487796 GTTTTTTTGG
Statistics
Matches: 1218, Mismatches: 168, Indels: 193
0.77 0.11 0.12
Matches are distributed among these distances:
118 2 0.00
119 1 0.00
120 190 0.16
123 6 0.00
124 6 0.00
125 6 0.00
127 2 0.00
128 1 0.00
129 1 0.00
130 2 0.00
132 40 0.03
133 72 0.06
134 12 0.01
136 37 0.03
137 153 0.13
138 6 0.00
139 7 0.01
140 8 0.01
141 30 0.02
142 93 0.08
143 182 0.15
144 99 0.08
145 220 0.18
146 18 0.01
147 24 0.02
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (137 bp):
TATATATTTTGTTGTTTGGTTACGTAGAAAGTAAATTGAAGTGGATTAAGCTTAATTTAGCTATT
TTAATTGTCTAAATTTAGTAATTTAGCTGAAAAAATTTAGTGTTCTTTTTAATGGTTCTTTATGA
ATATAAG
Found at i:486619 original size:120 final size:120
Alignment explanation
Indices: 486406--486759 Score: 636
Period size: 120 Copynumber: 3.0 Consensus size: 120
486396 AGTAATTTAG
486406 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
1 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
*
486471 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTT
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
486526 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
1 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
*
486591 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGATACTTTAGTTGTC
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
* * * *
486646 GGGAAAAAATTTAGTGTTGTTTTTGGTGGTTCTTTATGAATATAAGTATATTTTTTGTTGTTTGG
1 GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
* *
486711 TTACTTAGAAAGTAAATTTTAGTGGATTAAGCTTAATTTAGCTACTTTA
66 TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTA
486760 ATCGTCTCAA
Statistics
Matches: 225, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 225 1.00
ACGTcount: A:0.29, C:0.05, G:0.19, T:0.47
Consensus pattern (120 bp):
GTGAAAAAATTTAGTGTTCTTTTTGGTGGTTCTTTATGAATATAAGTATATATTTTGTTCTTTGG
TTACTTAGAAAGTAAATTATAGTGGATTAAGCTTAATATAGCTACTTTAGTTGTC
Found at i:487640 original size:286 final size:283
Alignment explanation
Indices: 487075--487779 Score: 740
Period size: 287 Copynumber: 2.4 Consensus size: 283
487065 GGTGAAAAAA
*
487075 TTGTTATTAGTAAGTTTCTTTATGAATATATCTATATGTTTTGTTGTTTGGTTACTTAGAAAGTA
1 TTGTTATTAGTAAG-TTCTTTATG-A-ATATCTATAT-ATTTGTTGTTTGGTTACTTAGAAAGTA
** ** * *
487140 AATGGTAGTGGGATAAGCTTAA-GAATGCTAC-TTTAGTTTTCTAAATTTCGTTACTTAGGTGAC
62 AATTATAGT-GGATAAGCTTAATTTA-GCTACTTTTA-TTGTCTAAATTTCGTTATTTAGGTGA-
*** * *
487203 AAAAGTTAGTGTTCTTATGCTATTTTTTATGGTTCATTATGGATATATGTATATAATTTATTGTT
123 AAAAGTTAGTGTTCTTATGCTATTTAGCAAGGTTCATTATGAATATATGTATATAATTTATTGTT
* * *
487268 TGGTTACCTACAAAGTAAATTACAGTGGGATAACCTTAATTTAGCTACTTTACTTTTCTAAATTT
188 TGGTTACCTACAAAGCAAATTACAGTGGGATAACCTTAATTTAGCTACTTTAATTGTCTAAATTT
* *
487333 CTTCATTTAGGTGAAAAAATTTAGTG-TCTT
253 CATCATTTAGGTAAAAAAATTTAGTGTTCTT
** *
487363 TTGTTATTTTTTTATAGTTCTTTATGAATATCTTTATATTTGTTGTTTGGTTACTTAGAAAGTAA
1 TTGTTA--TTAGTA-AGTTCTTTATGAATATCTATATATTTGTTGTTTGGTTACTTAGAAAGTAA
* * *
487428 ATTATAATGGATTGAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTCATTTAGGTGAAAAT
63 ATTATAGTGGA-TAAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTTATTTAGGTGAAAA-
** * * * * * * * *
487493 TTTTTGTGTTCTTTTGTTA-TTAGCAAGTTTCTTTATGAATATGTGTATATATTTTGTTGTTTGG
126 AGTTAGTGTTCTTATGCTATTTAGCAAGGTTCATTATGAATATATGTATATAATTTATTGTTTGG
* * * ** *
487557 TTTCTTAGAAAGCAAATTGTAGTGGGATAAGCTTAATTTAGCTACTTTAATTGTCTAAATTTCAT
191 TTACCTACAAAGCAAATTACAGTGGGATAACCTTAATTTAGCTACTTTAATTGTCTAAATTTCAT
* *
487622 CGTTTAGGTAAAAAAATTTCGTGTTTCTT
256 CATTTAGGTAAAAAAATTTAGTG-TTCTT
* ** * *
487651 TTGTTATTAGTAAGTT-TATGCACAAACATATGTATATA-TTGCTT-TTTGGTTGCTTAGAAAGT
1 TTGTTATTAGTAAGTTCT-T-TA-TGA-ATATCTATATATTTG-TTGTTTGGTTACTTAGAAAGT
* * *
487713 AAATTATGGTGGAATAAGCTTAATTTAGCTACTTTAATTGTCCAAATTTCGTTATTTAGGTGAAA
61 AAATTATAGTGG-ATAAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTTATTTAGGTGAAA
487778 AA
125 AA
487780 TTTAAATGTT
Statistics
Matches: 346, Mismatches: 56, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
284 1 0.00
285 5 0.01
286 121 0.35
287 161 0.47
288 42 0.12
289 1 0.00
290 13 0.04
291 2 0.01
ACGTcount: A:0.29, C:0.08, G:0.16, T:0.47
Consensus pattern (283 bp):
TTGTTATTAGTAAGTTCTTTATGAATATCTATATATTTGTTGTTTGGTTACTTAGAAAGTAAATT
ATAGTGGATAAGCTTAATTTAGCTACTTTTATTGTCTAAATTTCGTTATTTAGGTGAAAAAGTTA
GTGTTCTTATGCTATTTAGCAAGGTTCATTATGAATATATGTATATAATTTATTGTTTGGTTACC
TACAAAGCAAATTACAGTGGGATAACCTTAATTTAGCTACTTTAATTGTCTAAATTTCATCATTT
AGGTAAAAAAATTTAGTGTTCTT
Found at i:491231 original size:4 final size:4
Alignment explanation
Indices: 491222--491298 Score: 57
Period size: 4 Copynumber: 19.0 Consensus size: 4
491212 TGCATAGGAT
* * ** * *
491222 TGTA TGTA TGTA TGTA TGTA TGTA TTTT TGGTA -AAA TGTA TGTA TATG
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA T-GTA TGTA TGTA TGTA TGTA
* *
491270 TGTTA TGTA TGTA TGCA TGCA TGTA TGTA
1 TG-TA TGTA TGTA TGTA TGTA TGTA TGTA
491299 CATAAGAGGA
Statistics
Matches: 56, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
3 1 0.02
4 51 0.91
5 4 0.07
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (4 bp):
TGTA
Found at i:493131 original size:15 final size:16
Alignment explanation
Indices: 493097--493141 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
493087 ATTAAACTCC
493097 AAAAGTGGAAGAAACAA
1 AAAAG-GGAAGAAACAA
*
493114 AAAAGGGAAGAAAGAA
1 AAAAGGGAAGAAACAA
493130 AAAA-GGAAGAAA
1 AAAAGGGAAGAAA
493142 TGCTTTTCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
15 8 0.30
16 14 0.52
17 5 0.19
ACGTcount: A:0.69, C:0.02, G:0.27, T:0.02
Consensus pattern (16 bp):
AAAAGGGAAGAAACAA
Found at i:493980 original size:4 final size:4
Alignment explanation
Indices: 493971--494025 Score: 101
Period size: 4 Copynumber: 13.8 Consensus size: 4
493961 TTCCTCTTTT
*
493971 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ACAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
494019 ATAC ATA
1 ATAC ATA
494026 AGCATCATCA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 49 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:494111 original size:2 final size:2
Alignment explanation
Indices: 494106--494144 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
494096 GGGGTTATGA
* * *
494106 AT AT AT AT AT AT AT AC AT AC AT AC AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
494145 GCAGGTTAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:494350 original size:30 final size:31
Alignment explanation
Indices: 494310--494368 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
494300 CAATACGGTG
494310 GGTACTCGAGCTCGGGTGTAAATATCGGAAA
1 GGTACTCGAGCTCGGGTGTAAATATCGGAAA
* *
494341 GGTAC-CGAGCTCGTGTGTAAATTTCGGA
1 GGTACTCGAGCTCGGGTGTAAATATCGGA
494369 TACAGGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.25
Consensus pattern (31 bp):
GGTACTCGAGCTCGGGTGTAAATATCGGAAA
Found at i:500099 original size:34 final size:34
Alignment explanation
Indices: 500061--500130 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
500051 AGATATCAAA
500061 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
1 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
*
500095 AGTTTGGTGCAGAGTAGAATTAATTAAAGAAAAG
1 AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
500129 AG
1 AG
500131 AAAACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.27, T:0.24
Consensus pattern (34 bp):
AGTTTGGTGCAGAGAAGAATTAATTAAAGAAAAG
Found at i:504522 original size:23 final size:23
Alignment explanation
Indices: 504496--504540 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
504486 CTAAAACCAT
504496 ATTA-TCCCTAAAAAATAGGTTTC
1 ATTATTCCCTAAAAAA-AGGTTTC
* *
504519 ATTATTCTCTATAAAAAGGTTT
1 ATTATTCCCTAAAAAAAGGTTT
504541 AATTTTGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (23 bp):
ATTATTCCCTAAAAAAAGGTTTC
Found at i:507397 original size:22 final size:22
Alignment explanation
Indices: 507372--507428 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
507362 CTTATTATTG
* *
507372 TTTTGCTGTTGTTTTGCTAATA
1 TTTTGTTGTTATTTTGCTAATA
* *
507394 TTTTGTTATTATTTTGCTAATT
1 TTTTGTTGTTATTTTGCTAATA
507416 TTTTGTTGTTATT
1 TTTTGTTGTTATT
507429 ATTTAAATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.14, C:0.05, G:0.14, T:0.67
Consensus pattern (22 bp):
TTTTGTTGTTATTTTGCTAATA
Found at i:514514 original size:24 final size:24
Alignment explanation
Indices: 514460--514526 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
514450 TAGTTAATCC
*
514460 ATTTAAA-AATAATAAAATATTAATA
1 ATTTAAAGAATAAT--AATAATAATA
514485 ATTTTAAAGAATAATAATAATAATA
1 A-TTTAAAGAATAATAATAATAATA
**
514510 ATTTATTGAATAATAAT
1 ATTTAAAGAATAATAAT
514527 TCAAAGTAGA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.38
25 11 0.30
26 6 0.16
27 6 0.16
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (24 bp):
ATTTAAAGAATAATAATAATAATA
Found at i:520402 original size:22 final size:22
Alignment explanation
Indices: 520372--520422 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
520362 ATAAATTTAT
*
520372 TAGTCAATTAAAATAGTTAAAA
1 TAGTTAATTAAAATAGTTAAAA
***
520394 TAGTTAATTATTCTAGTTAAAA
1 TAGTTAATTAAAATAGTTAAAA
520416 TA-TTAAT
1 TAGTTAAT
520423 GTGGATTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (22 bp):
TAGTTAATTAAAATAGTTAAAA
Found at i:532762 original size:75 final size:75
Alignment explanation
Indices: 532672--532822 Score: 293
Period size: 75 Copynumber: 2.0 Consensus size: 75
532662 GCAAAGACGG
532672 TGTCGATAAATTAGTAGTAGTGTTATTTTTTTAACGCGTCAAATTCAAATTATCTATACAAAAGT
1 TGTCGATAAATTAGTAGTAGTGTTATTTTTTTAACGCGTCAAATTCAAATTATCTATACAAAAGT
532737 TCACATTAGT
66 TCACATTAGT
*
532747 TGTCGATAAATTAGTAGTAGTGTTATTTTTTTAACGCGTCAAATTCAAATTATCTATACCAAAGT
1 TGTCGATAAATTAGTAGTAGTGTTATTTTTTTAACGCGTCAAATTCAAATTATCTATACAAAAGT
532812 TCACATTAGT
66 TCACATTAGT
532822 T
1 T
532823 TTCAATTAGA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 75 1.00
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (75 bp):
TGTCGATAAATTAGTAGTAGTGTTATTTTTTTAACGCGTCAAATTCAAATTATCTATACAAAAGT
TCACATTAGT
Found at i:541413 original size:237 final size:238
Alignment explanation
Indices: 540939--541473 Score: 694
Period size: 237 Copynumber: 2.3 Consensus size: 238
540929 ATAGTCCGAT
* * *
540939 GGGGGAATATCAGGTTCATTTATA--ACAAACGTGTCCAAAAGAGAAGCACATTAGAAGTATGTG
1 GGGGGAATATCGGGTTCATTTATACCTCAAA--TATCCAAAAGAGAAGCACATTAGAAGTATGTG
* * * * *
541002 TTAAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTTGGAACATGTTTTTGTTGAAG
64 CTAAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTAGAAACATGTTGTCGTTGAAG
* *
541067 CATCACATCGAGTTTATTATCCATAGATTATAGCTTCTAAGAGTAATCACAGCAAATATCACATT
129 CATCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAATCACAGCAAATATCACATT
541132 TAACTAGAACCCACTTCGGATTACGAACATATTCAACAGTTTGAA
194 TAACTAGAACCCACTTCGGATTACGAACATATTCAACAGTTTGAA
* * * *
541177 GGGGGAATATTGGGTTCATTTAGT-CC-GAACATATCCGAAAGAGAAGTACATTAGAAGTATG-G
1 GGGGGAATATCGGGTTCATTTA-TACCTCAA-ATATCCAAAAGAGAAGCACATTAGAAGTATGTG
* * * *
541239 CTAGAATCTTATAGCGG-CAAAGCCATGTCAATGAGCCTAGATGCTCAGAAACGTGTTGTCGTTG
64 CTA-AATCTCATAACGGTC-AAGCCATGTCAACGAGCCTAGATGCT-AGAAACATGTTGTCGTTG
* * * *
541303 AAGCA-C-CATCGAGTTTATTGTCCATGGATCATACCTTCTAAGAGTAATTCACAG-GAATATCG
126 AAGCATCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAA-TCACAGCAAATATCA
*
541365 CATTTAACTAGAACCCACTTCGGATTA-GTAACATATTCAACGGTTTGAA
190 CATTTAACTAGAACCCACTTCGGATTACG-AACATATTCAACAGTTTGAA
* *
541414 GGGGGAATATCGGGTTCTTTTATACCTCAAATATCCAAAAGATAAGCACATTAGAAGTAT
1 GGGGGAATATCGGGTTCATTTATACCTCAAATATCCAAAAGAGAAGCACATTAGAAGTAT
541474 AATGGTAAAG
Statistics
Matches: 258, Mismatches: 28, Indels: 23
0.83 0.09 0.07
Matches are distributed among these distances:
236 2 0.01
237 142 0.55
238 92 0.36
239 21 0.08
240 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (238 bp):
GGGGGAATATCGGGTTCATTTATACCTCAAATATCCAAAAGAGAAGCACATTAGAAGTATGTGCT
AAATCTCATAACGGTCAAGCCATGTCAACGAGCCTAGATGCTAGAAACATGTTGTCGTTGAAGCA
TCACATCGAGTTTATTATCCATAGATCATACCTTCTAAGAGTAATCACAGCAAATATCACATTTA
ACTAGAACCCACTTCGGATTACGAACATATTCAACAGTTTGAA
Found at i:542190 original size:109 final size:115
Alignment explanation
Indices: 542071--542325 Score: 315
Period size: 109 Copynumber: 2.2 Consensus size: 115
542061 TATATACACT
* **
542071 TATATATAGGAAACCACTAGGATTAATAAATGTATATATATGACTTCCAAGATAGTTC-C-A-CT
1 TATATATAGGAAACCTCTAGGATTAATAAATAAATATATATGACTTCCAAGATAGTTCTCTACCT
*
542133 AACAGATACTATGAAGACATAT-GTATATAGGCAATG-C-GATAAACTTA
66 AACAGATACTATGAAGACATATAGTATATAGGCAATGTCAGATAAACATA
** *
542180 TATATATAGGAAACCTCTAGGATTAATTTATAAATGTATATGACTTCCAAGATAGTTCTTCTAGC
1 TATATATAGGAAACCTCTAGGATTAATAAATAAATATATATGACTTCCAAGATAGTTC-TCTA--
* * *
542245 CCTAACAGATGCTATGAAGACATATATTATATAGGCAATGTCTAGGATAAACATG
63 CCTAACAGATACTATGAAGACATATAGTATATAGGCAATGTC-A-GATAAACATA
* *
542300 TATATATAAGAAATCTCTAGGATTAA
1 TATATATAGGAAACCTCTAGGATTAA
542326 CTTAACCTAT
Statistics
Matches: 123, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
109 52 0.42
111 1 0.01
112 1 0.01
115 23 0.19
116 13 0.11
117 1 0.01
120 32 0.26
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (115 bp):
TATATATAGGAAACCTCTAGGATTAATAAATAAATATATATGACTTCCAAGATAGTTCTCTACCT
AACAGATACTATGAAGACATATAGTATATAGGCAATGTCAGATAAACATA
Found at i:542675 original size:16 final size:16
Alignment explanation
Indices: 542654--542693 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
542644 AAGATACATG
542654 CATGCATACATCCATC
1 CATGCATACATCCATC
*
542670 CATGCATCCATCCATC
1 CATGCATACATCCATC
*
542686 CATACATA
1 CATGCATA
542694 TACACACAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.33, C:0.38, G:0.05, T:0.25
Consensus pattern (16 bp):
CATGCATACATCCATC
Found at i:553155 original size:26 final size:26
Alignment explanation
Indices: 553126--553184 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
553116 TTCTTATTTC
*
553126 TTATTATT-GA-GCTTATAATATATAAT
1 TTATTATTAGATG-TTAGAATAT-TAAT
553152 TTA-TATTAGATGTTAGAATATTAAT
1 TTATTATTAGATGTTAGAATATTAAT
553177 TCTATTAT
1 T-TATTAT
553185 ATATATATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
25 9 0.32
26 15 0.54
27 4 0.14
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.51
Consensus pattern (26 bp):
TTATTATTAGATGTTAGAATATTAAT
Found at i:555084 original size:18 final size:18
Alignment explanation
Indices: 555061--555095 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
555051 GAAACCCAAC
555061 AAAATAAATC-AAACATGA
1 AAAATAAA-CGAAACATGA
555079 AAAATAAACGAAACATG
1 AAAATAAACGAAACATG
555096 GGAAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.66, C:0.11, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAATAAACGAAACATGA
Found at i:557420 original size:96 final size:96
Alignment explanation
Indices: 557252--557454 Score: 230
Period size: 96 Copynumber: 2.1 Consensus size: 96
557242 GGTTTCACCT
* * * *
557252 CCTTCAAAAGCGGTGGTCTCGATGTTCGAAGCAACTGTGGAACTTAGAACATTGAGTTCATTATA
1 CCTTCAAAAGCGGTCGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGAGTTCATTATA
*
557317 AAAATTTTCATCCTGCGAGAAGAACTGATCA
66 AAAATTTTCATCCTGCGAGAAGAACTGACCA
* * * **
557348 CCTTCAAAAGCGG-CGACGTCGATGTTCGAAGCAACTGTAGAATTTAGAACGCT-ATTTTGGTTA
1 CCTTCAAAAGCGGTCGAC-TCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGA-GTTCATTA
* * * *
557411 TAAATATTTTCCTCCTGCGTGAAGAATTGACCA
64 TAAAAATTTTCATCCTGCGAGAAGAACTGACCA
* *
557444 ACTTCATAAGC
1 CCTTCAAAAGC
557455 AGTGGCGCCG
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
95 3 0.03
96 86 0.97
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (96 bp):
CCTTCAAAAGCGGTCGACTCGATGTTCGAAGCAACTGTAGAACTTAGAACACTGAGTTCATTATA
AAAATTTTCATCCTGCGAGAAGAACTGACCA
Found at i:559299 original size:23 final size:22
Alignment explanation
Indices: 559268--559315 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
559258 TAGTCTCTAG
559268 TTTTTA-TTTTTAAGAATTTAAT
1 TTTTTATTTTTTAA-AATTTAAT
*
559290 TTTTCTATTTTTTAAATTTTAAT
1 TTTT-TATTTTTTAAAATTTAAT
559313 TTT
1 TTT
559316 CAAGTTCAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 4 0.17
23 12 0.52
24 7 0.30
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTATTTTTTAAAATTTAAT
Found at i:562357 original size:19 final size:19
Alignment explanation
Indices: 562333--562375 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
562323 TTATTAATAG
* *
562333 TATTATTTTATAAATAAAT
1 TATTATTTAATAAAAAAAT
562352 TATTATTTAATAAAAAAAT
1 TATTATTTAATAAAAAAAT
562371 T-TTAT
1 TATTAT
562376 GTTAGAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTATTTAATAAAAAAAT
Found at i:567590 original size:21 final size:22
Alignment explanation
Indices: 567552--567594 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
567542 ATTTAAAAAC
*
567552 ATAAAAACTAATATTAAAACAA
1 ATAAAAACTAATACTAAAACAA
*
567574 ATAAAAA-TGATACTAAAACAA
1 ATAAAAACTAATACTAAAACAA
567595 TTTTTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.67, C:0.09, G:0.02, T:0.21
Consensus pattern (22 bp):
ATAAAAACTAATACTAAAACAA
Found at i:569934 original size:102 final size:102
Alignment explanation
Indices: 569735--569927 Score: 282
Period size: 102 Copynumber: 1.9 Consensus size: 102
569725 ATTTATTACG
* * * *
569735 AATTGAATGTAGACTTTTGATTTTTAGATTGAAAAATCAGTGATTATTAATTTTTAATTAGCTAA
1 AATTGAATGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATTAATTTTTAATTAGCTAA
*
569800 TAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
66 CAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
* *
569837 AATTGAATGTAGTCTTTTGATCTCTAGAGTGAAAAATCAGTGACTA-TCATTTGTTAATTAGCTA
1 AATTGAATGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATTAATTT-TTAATTAGCTA
*
569901 CCAATCAGAGT-ATTAAGCAGATAATTT
65 ACAATCAGAGTGA-TAAGCAGATAATTT
569928 TGTTATTTGG
Statistics
Matches: 81, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
101 6 0.07
102 75 0.93
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.39
Consensus pattern (102 bp):
AATTGAATGTAGACTTTTGATCTCTAGAGTGAAAAATCAGTGACTATTAATTTTTAATTAGCTAA
CAATCAGAGTGATAAGCAGATAATTTGTTTATTCCAC
Found at i:574784 original size:32 final size:32
Alignment explanation
Indices: 574739--574802 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
574729 TTTTAGGATT
574739 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
1 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
* *
574771 TTCTAGGGGAACTGGGAATCCTGAAATGGCTA
1 TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
574803 AGGAAGAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (32 bp):
TTCTAGGGAAACTGAGAATCCTGAAATGGCTA
Found at i:579404 original size:69 final size:69
Alignment explanation
Indices: 579293--579432 Score: 217
Period size: 69 Copynumber: 2.0 Consensus size: 69
579283 CCGGAAGGTA
* ** *
579293 AACAAATTGAAAACTGAAATCGAAGTGTCATATTTTGCATGTACTAGGGTAAGATATGTTTTGAT
1 AACAAATCGAAAACCAAAATCGAAGTGTCATATTTTGCATGTACTAGGATAAGATATGTTTTGAT
579358 GAAT
66 GAAT
* * *
579362 AACAAATCGAAAACCAAAATCGAATTGTCATTTTTTGCATGTACTAGGATGAGATATGTTTTGAT
1 AACAAATCGAAAACCAAAATCGAAGTGTCATATTTTGCATGTACTAGGATAAGATATGTTTTGAT
579427 GAAT
66 GAAT
579431 AA
1 AA
579433 TCTCTAGCGG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.33
Consensus pattern (69 bp):
AACAAATCGAAAACCAAAATCGAAGTGTCATATTTTGCATGTACTAGGATAAGATATGTTTTGAT
GAAT
Found at i:580505 original size:21 final size:21
Alignment explanation
Indices: 580436--580533 Score: 97
Period size: 21 Copynumber: 4.7 Consensus size: 21
580426 TCCTTCATCT
* *
580436 GCATACCCTCCTCCACCTTCG
1 GCATACCCTCCACCACCTTCC
* * ** * * *
580457 GCTTATCCTCCGTCGCATTCA
1 GCATACCCTCCACCACCTTCC
*
580478 GCTTACCCTCCACCACCTTCC
1 GCATACCCTCCACCACCTTCC
580499 GCATACCCTCCACCACCTTCC
1 GCATACCCTCCACCACCTTCC
*
580520 ACATACCCTCCACC
1 GCATACCCTCCACC
580534 TCCGCCACAT
Statistics
Matches: 62, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 62 1.00
ACGTcount: A:0.17, C:0.52, G:0.07, T:0.23
Consensus pattern (21 bp):
GCATACCCTCCACCACCTTCC
Found at i:580804 original size:25 final size:25
Alignment explanation
Indices: 580770--580819 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
580760 CCAAGGGTTT
*
580770 CACATGTCAACCAAATGCAAAAATG
1 CACATGTCAACCAAAAGCAAAAATG
*
580795 CACATGTCAACCAAAAGCTAAAATG
1 CACATGTCAACCAAAAGCAAAAATG
580820 AGAAGTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.48, C:0.24, G:0.12, T:0.16
Consensus pattern (25 bp):
CACATGTCAACCAAAAGCAAAAATG
Found at i:581050 original size:18 final size:18
Alignment explanation
Indices: 581027--581062 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
581017 TTGACCTAAG
581027 GCAGACTATTTATTATCC
1 GCAGACTATTTATTATCC
581045 GCAGACTATTTATTATCC
1 GCAGACTATTTATTATCC
581063 TAACTTGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.11, T:0.39
Consensus pattern (18 bp):
GCAGACTATTTATTATCC
Found at i:606701 original size:14 final size:14
Alignment explanation
Indices: 606682--606718 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
606672 ATTTTTTTTA
606682 ATTAAAATAAAACT
1 ATTAAAATAAAACT
606696 ATTAAAAATAAAACT
1 ATT-AAAATAAAACT
*
606711 ATTGAAAT
1 ATTAAAAT
606719 TTAAAAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (14 bp):
ATTAAAATAAAACT
Found at i:606705 original size:15 final size:15
Alignment explanation
Indices: 606685--606713 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
606675 TTTTTTAATT
606685 AAAATAAAACTATTA
1 AAAATAAAACTATTA
606700 AAAATAAAACTATT
1 AAAATAAAACTATT
606714 GAAATTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAAACTATTA
Found at i:610260 original size:2 final size:2
Alignment explanation
Indices: 610253--610279 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
610243 CTGTGAGCAG
610253 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
610280 CATGATATGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:618199 original size:13 final size:12
Alignment explanation
Indices: 618181--618214 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
618171 ATATAAATTC
618181 AAACAAATAAGGA
1 AAACAAAT-AGGA
618194 AAACAAATAGGA
1 AAACAAATAGGA
618206 ACAACAAAT
1 A-AACAAAT
618215 TAAAAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 5 0.25
13 15 0.75
ACGTcount: A:0.68, C:0.12, G:0.12, T:0.09
Consensus pattern (12 bp):
AAACAAATAGGA
Found at i:619083 original size:121 final size:117
Alignment explanation
Indices: 618940--619195 Score: 300
Period size: 117 Copynumber: 2.2 Consensus size: 117
618930 TTTATTTTTA
* *
618940 AGCTCAAGCTCGGCTTGAGATATAATC-AAGCTATTCGAGCAAGCTCAATTAAGCTCATTTATCT
1 AGCTCAAGCTCAGCTTGAGATATAATCGAA-C---T-GAGCAAGCTCAATTAAGCTCATTTATCA
* *
619004 ATTTTTGTACTCAATCTTGAACTTCAGCTCAATTAAGCTCATA-TGTATTAAATCTTG
61 ATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACT-TATTAAAGCTTG
** * * *
619061 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGCTCAAGCTCGATTCAGCTTATTTATCAATTTT
1 AGCTCAAGCTCAGCTTGAGATATAATCGAACTGAGCAAGCTCAATTAAGCTCATTTATCAATTTT
* * * * * *
619126 TGTACTCTAGCTTGAGCTTTAGCTCGATTACGCTCGTACTTATTAAAGCTTG
66 TGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACTTATTAAAGCTTG
*
619178 AGCTCGAGCTCAGCTTGA
1 AGCTCAAGCTCAGCTTGA
619196 TAATTAAGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
117 86 0.74
118 2 0.02
121 27 0.23
122 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (117 bp):
AGCTCAAGCTCAGCTTGAGATATAATCGAACTGAGCAAGCTCAATTAAGCTCATTTATCAATTTT
TGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTCATACTTATTAAAGCTTG
Found at i:619150 original size:117 final size:117
Alignment explanation
Indices: 618979--619195 Score: 301
Period size: 117 Copynumber: 1.9 Consensus size: 117
618969 GCTATTCGAG
* *
618979 CAAGCTCAATTAAGCTCATTTATCTATTTTTGTACTCAATCTTGAACTTCAGCTCAATTAAGCTC
1 CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
*
619044 ATA-TGTATTAAATCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
66 ATACT-TATTAAAGCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
* * * * * * * *
619096 CAAGCTCGATTCAGCTTATTTATCAATTTTTGTACTCTAGCTTGAGCTTTAGCTCGATTACGCTC
1 CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
* *
619161 GTACTTATTAAAGCTTGAGCTCGAGCTCAGCTTGA
66 ATACTTATTAAAGCTTGAGCTCAAGCTCAGCTTGA
619196 TAATTAAGCT
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
117 85 0.99
118 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.36
Consensus pattern (117 bp):
CAAGCTCAATTAAGCTCATTTATCAATTTTTGTACTCAAGCTTGAACTTCAGCTCAATTAAGCTC
ATACTTATTAAAGCTTGAGCTCAAGCTCAGCTTGAGATATAATCGAACTGCT
Found at i:623550 original size:22 final size:22
Alignment explanation
Indices: 623524--623568 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
623514 TACTATGATT
*
623524 TTTTATTTATTTTAATTTATTA
1 TTTTATTTATTTTAAATTATTA
*
623546 TTTTATTTCTTTTAAATTATTA
1 TTTTATTTATTTTAAATTATTA
623568 T
1 T
623569 AGGAGCTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTATTTATTTTAAATTATTA
Found at i:623695 original size:21 final size:20
Alignment explanation
Indices: 623671--623708 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
623661 ATTAAGCTTT
*
623671 TTATTTTTTTGAATATTTTAA
1 TTATATTTTT-AATATTTTAA
623692 TTATATTTTTAAT-TTTT
1 TTATATTTTTAATATTTT
623709 TTGAAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 3 0.19
21 9 0.56
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTATATTTTTAATATTTTAA
Found at i:627182 original size:13 final size:13
Alignment explanation
Indices: 627164--627195 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
627154 ATAGTTTAAT
627164 AATAAAATAAAGA
1 AATAAAATAAAGA
627177 AATAAAATAAAGA
1 AATAAAATAAAGA
627190 AATAAA
1 AATAAA
627196 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (13 bp):
AATAAAATAAAGA
Found at i:628505 original size:15 final size:15
Alignment explanation
Indices: 628482--628529 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
628472 TATCAAATTT
628482 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
628497 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
628512 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
628526 ATAT
1 ATAT
628530 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:629064 original size:25 final size:23
Alignment explanation
Indices: 629012--629069 Score: 107
Period size: 23 Copynumber: 2.5 Consensus size: 23
629002 TAATATTCCG
629012 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
629035 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
*
629058 GATGTGTTTGGG
1 GGTGTGTTTGGG
629070 AGGAATCCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.09, C:0.03, G:0.41, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:629195 original size:18 final size:19
Alignment explanation
Indices: 629174--629214 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
629164 AATGAAATGA
629174 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
629192 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
629211 GAAA
1 GAAA
629215 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:636742 original size:19 final size:18
Alignment explanation
Indices: 636708--636765 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
636698 ATTTTAAAAA
*
636708 TATAAATTTTAGATTTTT
1 TATAAATTTTAAATTTTT
636726 TATAAATATTTAAATTTTT
1 TATAAAT-TTTAAATTTTT
*
636745 TATTTAAATTTTTAATTTTT
1 TA--TAAATTTTAAATTTTT
636765 T
1 T
636766 TTTGTAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.20
19 12 0.34
20 11 0.31
21 5 0.14
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TATAAATTTTAAATTTTT
Found at i:636758 original size:12 final size:13
Alignment explanation
Indices: 636732--636762 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
636722 TTTTTATAAA
636732 TATTTAAATTTTT
1 TATTTAAATTTTT
636745 TATTTAAATTTTT
1 TATTTAAATTTTT
*
636758 AATTT
1 TATTT
636763 TTTTTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTAAATTTTT
Found at i:636777 original size:20 final size:20
Alignment explanation
Indices: 636710--636765 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
636700 TTTAAAAATA
636710 TAAA-TTTTAGATTTTTTA--
1 TAAATTTTTA-ATTTTTTATT
*
636728 TAAATATTTAAATTTTTTATT
1 TAAAT-TTTTAATTTTTTATT
636749 TAAATTTTTAATTTTTT
1 TAAATTTTTAATTTTTT
636766 TTTGTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.12
19 8 0.25
20 15 0.47
21 5 0.16
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (20 bp):
TAAATTTTTAATTTTTTATT
Found at i:647852 original size:2 final size:2
Alignment explanation
Indices: 647847--647885 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
647837 AAGGAAATTA
647847 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
647886 AAATTAACGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:658785 original size:16 final size:17
Alignment explanation
Indices: 658764--658809 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
658754 ATAATATTTT
658764 TATTTTTG-AATTTATA
1 TATTTTTGAAATTTATA
*
658780 TATTTTAGAAATTTATA
1 TATTTTTGAAATTTATA
*
658797 T-TTTTTAAAATTT
1 TATTTTTGAAATTT
658810 TCAATTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (17 bp):
TATTTTTGAAATTTATA
Found at i:658794 original size:17 final size:16
Alignment explanation
Indices: 658772--658809 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
658762 TTTATTTTTG
658772 AATTTATATATTTTAGA
1 AATTTATATATTTTA-A
*
658789 AATTTATATTTTTTAA
1 AATTTATATATTTTAA
658805 AATTT
1 AATTT
658810 TCAATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AATTTATATATTTTAA
Found at i:667677 original size:132 final size:129
Alignment explanation
Indices: 667439--667828 Score: 557
Period size: 132 Copynumber: 3.0 Consensus size: 129
667429 AATTGCATTC
*
667439 CCTGTATGTCACGAATTTGGGTTTTATGTGTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
1 CCTGTATGTCACGAATCTGGGTTTTA--TGTTCTTTTACCTGACTGCTAACTCATATCATTTTGC
* **
667504 TCGTCCTATCTTGTATCAAGAATCATAGACTTAGGATGTCTTTGTACTGCTTATATCGGTTAATA
64 TCGTCC-ATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTAATA
667569 TA
128 TA
*
667571 TCTGTATGTCACGAATCTGGGTTTTATCCGTTCTTTTACCTGACTGCTAACTC-TAATCATTTTG
1 CCTGTATGTCACGAATCTGGGTTTTAT--GTTCTTTTACCTGACTGCTAACTCAT-ATCATTTTG
* *
667635 CTCATGCCATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGATTATATCGGTTAAT
63 CTCGT-CCATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTAAT
667700 ATA
127 ATA
* *
667703 CCTATATGTCACGAATCTTGGTTTTATGTTTCTTTTACCTGACTGCTAACTCATATCATTTTGCT
1 CCTGTATGTCACGAATCTGGGTTTTATG-TTCTTTTACCTGACTGCTAACTCATATCATTTTGCT
* * * * * *
667768 CGTCCCGTTTCGTATTAAGAATCATAGACTGCAGATGTCTTTGTACTGCATATATCTGTTA
65 CGT-CCATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTA
667829 TTCAAAAACT
Statistics
Matches: 233, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
130 2 0.01
131 87 0.37
132 142 0.61
133 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (129 bp):
CCTGTATGTCACGAATCTGGGTTTTATGTTCTTTTACCTGACTGCTAACTCATATCATTTTGCTC
GTCCATCTCGTATCAAGAATCATAGACTGCGGATGTCTTTGTACTGCTTATATCGGTTAATATA
Found at i:671601 original size:18 final size:18
Alignment explanation
Indices: 671578--671612 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
671568 AGTCAAAAAA
671578 ACAAATCAAACTTTTCTC
1 ACAAATCAAACTTTTCTC
671596 ACAAATCAAACTTTTCT
1 ACAAATCAAACTTTTCT
671613 AAGTTTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (18 bp):
ACAAATCAAACTTTTCTC
Found at i:674663 original size:12 final size:12
Alignment explanation
Indices: 674646--674687 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
674636 AGCCGAAAAG
674646 AAATAAATTAAT
1 AAATAAATTAAT
*
674658 AAATAAATGAAT
1 AAATAAATTAAT
*
674670 GAATAAA-TATAT
1 AAATAAATTA-AT
674682 AAATAA
1 AAATAA
674688 TGATAATGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
11 1 0.04
12 24 0.96
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.29
Consensus pattern (12 bp):
AAATAAATTAAT
Found at i:675570 original size:22 final size:22
Alignment explanation
Indices: 675544--675594 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
675534 GTTTTAAATG
675544 ATTTTAGAACAC-AGCTTGTGAA
1 ATTTTAG-ACACGAGCTTGTGAA
675566 ATTTT-GACACGTAGCTTGTGAA
1 ATTTTAGACACG-AGCTTGTGAA
*
675588 ATCTTAG
1 ATTTTAG
675595 TCATTCATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 4 0.16
21 1 0.04
22 19 0.76
23 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (22 bp):
ATTTTAGACACGAGCTTGTGAA
Found at i:675724 original size:31 final size:28
Alignment explanation
Indices: 675672--675733 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 28
675662 AAATTGGTCG
675672 TTAAATTTTAAAATATTTAATTACA-TCC
1 TTAAATTTTAAAATATTTAATTA-AGTCC
*
675700 TTAAACTTTTAAGATTATGTTAATTAAGTCC
1 TTAAA-TTTTAA-AATAT-TTAATTAAGTCC
675731 TTA
1 TTA
675734 TGATACTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.17
29 6 0.21
30 5 0.17
31 13 0.45
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.47
Consensus pattern (28 bp):
TTAAATTTTAAAATATTTAATTAAGTCC
Found at i:678656 original size:171 final size:171
Alignment explanation
Indices: 678357--678675 Score: 539
Period size: 171 Copynumber: 1.9 Consensus size: 171
678347 AAAGCACCAA
**
678357 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTCCCTTTGGACAAGAAAAT
1 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
* * *
678422 GACCTTCGGGCATAATCTTGGAGTCAAGGTGGCTTCTAAAGTTAACGGTGAAAAATACACCATGA
66 GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
678487 TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
131 TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
* * * *
678528 AAAGTTTGAACTTTGAACATGACAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAACAT
1 AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
*
678593 GACCTTCAGGCCTAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
66 GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
*
678658 TGAGAGCACTAAAATGTA
131 TAAGAGCACTAAAATGTA
678676 TTATGCTGCT
Statistics
Matches: 137, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
171 137 1.00
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.26
Consensus pattern (171 bp):
AAAGTTCGAACTTAGAACATGAAAACCTATATTTCTATAAACTATTTAACTTTGGACAAGAAAAT
GACCTTCAGGCATAATCTTGGAGTCAAGGTGGCTTCAAAAGTTAACGGGGAAAAATACACCATGA
TAAGAGCACTAAAATGTAAAGCATCATAAGAAAAATAAAAT
Found at i:683715 original size:14 final size:14
Alignment explanation
Indices: 683693--683726 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
683683 GCCGTTTCGC
*
683693 TATTATATTGTTAT
1 TATTTTATTGTTAT
683707 TATTTTATTGTTAT
1 TATTTTATTGTTAT
683721 TATTTT
1 TATTTT
683727 GATATTGCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (14 bp):
TATTTTATTGTTAT
Found at i:684153 original size:20 final size:20
Alignment explanation
Indices: 684120--684159 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
684110 ATATATTTAC
*
684120 TATATATTATAAAATATAAA
1 TATATATTAGAAAATATAAA
* *
684140 TATATTTTAGAAAATTTAAA
1 TATATATTAGAAAATATAAA
684160 AAATATGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (20 bp):
TATATATTAGAAAATATAAA
Found at i:688807 original size:13 final size:13
Alignment explanation
Indices: 688789--688815 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
688779 AGTTTTTCAT
688789 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
688802 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
688815 T
1 T
688816 AAAATGTCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.22, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:692307 original size:46 final size:46
Alignment explanation
Indices: 692241--692514 Score: 424
Period size: 46 Copynumber: 6.0 Consensus size: 46
692231 GAGTGTGCTT
692241 CCTGATAT-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
692286 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
692332 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
*
692378 CCTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * ***
692424 CGTGATATGAAATGAACAAGACCATGGTTGAAAGATACCATGGCAA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
* * * * * * *
692470 CATGACAGAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
692515 TCATGTCAAA
Statistics
Matches: 214, Mismatches: 14, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
45 8 0.04
46 206 0.96
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (46 bp):
CCTGATATAAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAA
Found at i:700412 original size:57 final size:57
Alignment explanation
Indices: 700344--700511 Score: 282
Period size: 57 Copynumber: 2.9 Consensus size: 57
700334 TCGGACATAA
*
700344 CGAGTTCTGGGGATGCCGCCTCATTCTCGTTTTGTCCTACCACAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* *
700401 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTTCTACAACAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* * *
700458 CGAGTTCTGGGGATACCTCCTCATCCTCGTTTTGTCCAACCACAAATTGGATTG
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTG
700512 AGAGCAACAA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 103 1.00
ACGTcount: A:0.18, C:0.27, G:0.22, T:0.33
Consensus pattern (57 bp):
CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
Found at i:702890 original size:29 final size:30
Alignment explanation
Indices: 702872--702935 Score: 105
Period size: 29 Copynumber: 2.2 Consensus size: 30
702862 AATTGGTCCT
702872 TAAACTTCAAAATGTTTT-AATTACATCCC
1 TAAACTTCAAAATGTTTTAAATTACATCCC
702901 TAAACTTCAAAATGTTTT-AATTACATCCC
1 TAAACTTCAAAATGTTTTAAATTACATCCC
*
702930 GAAACT
1 TAAACT
702936 ATCGATCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.05, T:0.36
Consensus pattern (30 bp):
TAAACTTCAAAATGTTTTAAATTACATCCC
Found at i:704357 original size:57 final size:57
Alignment explanation
Indices: 704289--704456 Score: 282
Period size: 57 Copynumber: 2.9 Consensus size: 57
704279 TCGGACATAA
*
704289 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTT
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* * *
704346 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTTCTACAAAAAATTGGATTGCTC
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
* *
704403 CGAGTTCTGGGGATGCCTCCTCATCCTCGTTTTGTCCAACCACAAATTGGATTG
1 CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTG
704457 AGAGCAACAA
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 102 1.00
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.33
Consensus pattern (57 bp):
CGAGTTCTGGGGATGCCGCCTCATCCTCGTTTTGTCCTACCACAAATTGGATTGCTC
Found at i:705259 original size:16 final size:17
Alignment explanation
Indices: 705233--705265 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
705223 TTTCTTATTT
705233 AATGGTATGAAATGTTA
1 AATGGTATGAAATGTTA
705250 AATGGT-TGAAATGTTA
1 AATGGTATGAAATGTTA
705266 TCGTAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.36
Consensus pattern (17 bp):
AATGGTATGAAATGTTA
Found at i:719146 original size:20 final size:19
Alignment explanation
Indices: 719112--719167 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
719102 AAATGGTAGC
*
719112 AAAATAGTAAAAAAAAGAA
1 AAAATAGCAAAAAAAAGAA
719131 GAAAATAGCAACAAAATAA-AA
1 -AAAATAGCAA-AAAA-AAGAA
*
719152 AAAA-AGCAAGAAAAAG
1 AAAATAGCAAAAAAAAG
719168 TAATAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 2 0.06
18 3 0.10
19 5 0.16
20 13 0.42
21 6 0.19
22 2 0.06
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAATAGCAAAAAAAAGAA
Found at i:719177 original size:30 final size:29
Alignment explanation
Indices: 719120--719179 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
719110 GCAAAATAGT
*
719120 AAAAAAAAGAAGAAAATAGCAACAAAATA
1 AAAAAAAAGAAGAAAATAGCAAAAAAATA
*
719149 AAAAAAAAGCAAGAAAA-AGTAATAAAAATA
1 AAAAAAAAG-AAGAAAATAGCAA-AAAAATA
719179 A
1 A
719180 CAGTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (29 bp):
AAAAAAAAGAAGAAAATAGCAAAAAAATA
Found at i:724765 original size:44 final size:44
Alignment explanation
Indices: 724702--724812 Score: 206
Period size: 44 Copynumber: 2.5 Consensus size: 44
724692 AGAGTCATGC
724702 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
1 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
*
724746 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTTTTTGGGT
1 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
724790 TACTATGCGAATTTGTC-ATTTTC
1 TACTATGCGAATTTGTCAATTTTC
724813 CATTTTCAAC
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
43 6 0.09
44 60 0.91
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (44 bp):
TACTATGCGAATTTGTCAATTTTCTACCAACCCATTGTTTGGGT
Found at i:729124 original size:5 final size:5
Alignment explanation
Indices: 729114--729142 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
729104 ATTTTTAAAC
729114 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
729143 GAATATTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:730706 original size:44 final size:44
Alignment explanation
Indices: 730643--730753 Score: 197
Period size: 44 Copynumber: 2.5 Consensus size: 44
730633 AGAGTCATGC
* *
730643 TACTATGCGAATTTGTCAATTTTCTATCAACCCATTGTTTGGGT
1 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTATTTGGGT
730687 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTATTTGGGT
1 TACTATGCGAATTTGTCAATTTTCTACCAACCCATTATTTGGGT
730731 TACTATGCGAATTTGTC-ATTTTC
1 TACTATGCGAATTTGTCAATTTTC
730754 CATTTTCAAC
Statistics
Matches: 65, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 6 0.09
44 59 0.91
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (44 bp):
TACTATGCGAATTTGTCAATTTTCTACCAACCCATTATTTGGGT
Found at i:734170 original size:30 final size:30
Alignment explanation
Indices: 734097--734300 Score: 185
Period size: 30 Copynumber: 6.8 Consensus size: 30
734087 TACTACAACT
* *
734097 GCCGTTGGGTGAATTACCATAACCACCGCC
1 GCCGCTGGGTGAATAACCATAACCACCGCC
* *
734127 GCTGCTAGGGTGAATTACCATAACCACCGCC
1 GCCGCT-GGGTGAATAACCATAACCACCGCC
* * **
734158 ACCGCTGGGTGAATTACCATAACCACTACC
1 GCCGCTGGGTGAATAACCATAACCACCGCC
* * * ** *
734188 ACCGCTAGGTGAATAACCATAACTATTGCT
1 GCCGCTGGGTGAATAACCATAACCACCGCC
* **** *
734218 GCCACTGGGTGAATAACCATAACTGTTGCT
1 GCCGCTGGGTGAATAACCATAACCACCGCC
734248 GCCG-TGGGGTGAATAACCATAACCACCGCC
1 GCCGCT-GGGTGAATAACCATAACCACCGCC
* *
734278 GCTGCTAGGTGAATAACCATAAC
1 GCCGCTGGGTGAATAACCATAAC
734301 TAAACCCATG
Statistics
Matches: 147, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
29 1 0.01
30 117 0.80
31 29 0.20
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (30 bp):
GCCGCTGGGTGAATAACCATAACCACCGCC
Found at i:734237 original size:90 final size:90
Alignment explanation
Indices: 734134--734302 Score: 214
Period size: 90 Copynumber: 1.9 Consensus size: 90
734124 GCCGCTGCTA
* * *
734134 GGGTGAATTACCATAACCACCGCCACCGCT-GGGTGAATTACCATAACCACTACCACCGCTAGGT
1 GGGTGAATAACCATAACCACCGCCACCG-TGGGGTGAATAACCATAACCACCACCACCGCTAGGT
734198 GAATAACCATAACTATTGCTGCCACT
65 GAATAACCATAACTATTGCTGCCACT
**** ** * * *
734224 GGGTGAATAACCATAACTGTTGCTGCCGTGGGGTGAATAACCATAACCACCGCCGCTGCTAGGTG
1 GGGTGAATAACCATAACCACCGCCACCGTGGGGTGAATAACCATAACCACCACCACCGCTAGGTG
734289 AATAACCATAACTA
66 AATAACCATAACTA
734303 AACCCATGTG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
89 1 0.02
90 65 0.98
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (90 bp):
GGGTGAATAACCATAACCACCGCCACCGTGGGGTGAATAACCATAACCACCACCACCGCTAGGTG
AATAACCATAACTATTGCTGCCACT
Found at i:738146 original size:25 final size:25
Alignment explanation
Indices: 738112--738161 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
738102 CAACCTCTTC
738112 GTTTGAGCAAGTATACTAGTCAATT
1 GTTTGAGCAAGTATACTAGTCAATT
738137 GTTTGAGCAAGTATACTAGTCAATT
1 GTTTGAGCAAGTATACTAGTCAATT
738162 CCCAATCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (25 bp):
GTTTGAGCAAGTATACTAGTCAATT
Found at i:745589 original size:66 final size:69
Alignment explanation
Indices: 745457--745594 Score: 194
Period size: 66 Copynumber: 2.0 Consensus size: 69
745447 TCTGTTCTCG
* ** *
745457 TGATTGTTCAAAGGTTGTGCATTACTCCTCTTAATCTGAACGGAGGGATTGCAGGGAGGCATTGT
1 TGATTGTTCAAAGGCTGTGCATTACTCCTCTTAATCCAAACAGAGGGATTGCAGGGAGGCATTGT
745522 AAAC
66 AAAC
745526 TGATTGTTCAAAGGCTGTGCATTACT-C-C-TAATCCAAACAGAGGGATTGC-GAGGAGGCATTG
1 TGATTGTTCAAAGGCTGTGCATTACTCCTCTTAATCCAAACAGAGGGATTGCAG-GGAGGCATTG
*
745587 TAACC
65 TAAAC
745592 TGA
1 TGA
745595 AGTTGCATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
65 1 0.02
66 35 0.56
67 1 0.02
68 1 0.02
69 25 0.40
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (69 bp):
TGATTGTTCAAAGGCTGTGCATTACTCCTCTTAATCCAAACAGAGGGATTGCAGGGAGGCATTGT
AAAC
Found at i:747652 original size:38 final size:34
Alignment explanation
Indices: 747604--747698 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 34
747594 TTAAAATTTT
*
747604 AAATTCATAAAAATAAAATTACACTTTAATTCCTCTTAA
1 AAATT-ATAAAAATAAAATTA-A-TTTAATT-AT-TTAA
747643 AAATTATAAAAAT----TTAATTTAATTATTTAA
1 AAATTATAAAAATAAAATTAATTTAATTATTTAA
747673 AAATTATAAAAATATAAATT-ATTTAA
1 AAATTATAAAAATA-AAATTAATTTAA
747699 ATTTACTATC
Statistics
Matches: 50, Mismatches: 1, Indels: 15
0.76 0.02 0.23
Matches are distributed among these distances:
30 17 0.34
31 1 0.02
32 7 0.14
33 1 0.02
34 9 0.18
35 2 0.04
38 8 0.16
39 5 0.10
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (34 bp):
AAATTATAAAAATAAAATTAATTTAATTATTTAA
Found at i:748342 original size:35 final size:35
Alignment explanation
Indices: 748303--748370 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
748293 ATTAAATACC
* *
748303 AAAGTTTCCTCATTAATTATCGATTGAGTCTTACT
1 AAAGTTTCCTCACTAATCATCGATTGAGTCTTACT
748338 AAAGTTTCCTCACTAATCATCGATTGAGTCTTA
1 AAAGTTTCCTCACTAATCATCGATTGAGTCTTA
748371 ACTCGATTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (35 bp):
AAAGTTTCCTCACTAATCATCGATTGAGTCTTACT
Found at i:768733 original size:3 final size:3
Alignment explanation
Indices: 768725--768756 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
768715 GCAAACTTCA
*
768725 AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
768757 AAAAAACCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:771795 original size:40 final size:40
Alignment explanation
Indices: 771740--771820 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
771730 TTAGTTATTT
771740 ACTATAATTCCATCTATTTTCCCCACTATTAACCCAAACC
1 ACTATAATTCCATCTATTTTCCCCACTATTAACCCAAACC
771780 ACTATAATTCCATCTATTTTCCCCACTATTAACCCAAACC
1 ACTATAATTCCATCTATTTTCCCCACTATTAACCCAAACC
771820 A
1 A
771821 AACTTGGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.35, G:0.00, T:0.32
Consensus pattern (40 bp):
ACTATAATTCCATCTATTTTCCCCACTATTAACCCAAACC
Found at i:780008 original size:21 final size:22
Alignment explanation
Indices: 779970--780011 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
779960 TTCACCCCAT
779970 ATGGCATTTTGCTTTACTTCCG
1 ATGGCATTTTGCTTTACTTCCG
779992 ATGGC-TTTT-CTTCTACTTCC
1 ATGGCATTTTGCTT-TACTTCC
780012 AGTGAAGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.16
21 11 0.58
22 5 0.26
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.48
Consensus pattern (22 bp):
ATGGCATTTTGCTTTACTTCCG
Found at i:781625 original size:377 final size:374
Alignment explanation
Indices: 780876--781770 Score: 1087
Period size: 377 Copynumber: 2.4 Consensus size: 374
780866 ATATTAAACC
*
780876 AAAATTTAATGTTAAAAATGCAAAATTTGAATTACAAA-TTTCTAGGAGGGGTCAAAAATGAAAT
1 AAAATTTAATGTT-AAAATGCAAAATCTGAATTACAAATTTTC-AGGAGGGGTCAAAAATGAAAT
* * * *
780940 TTCACCGTTTTATCCAAGGTGCCAAATCCAAAGCCTCTAG-TCCCTTTGGATTGGCCCTTTATCT
64 TTCACCATTTTAT-CATGGTGCCAAATCCAAAGCCTCTAGCTCCCTTTGGGTTGGCCCTTTCTCT
*** * * *
781004 ATCCTA-TTTT-ACCGA-CTGTTTTCGGACATGGCGTATGAGATATGATCGGTCAAATTTGATCT
128 ATCCTATTTTTGTTTGACCTGTTTTCGGACATGGCGTATGAGATATAATCAGTCAAATTCGATCT
* * * **
781066 TGGTCCTTCTTATTATACTTAAATTTGATTTTAGTCTTTATACTTTAATTTGATATTATTGGTTT
193 TGGTCCTTCTTATTATACTAAAATTTGATTTTAGTCTTTATAATTTAATTTGATATAATTAATTT
* * * ** *
781131 TTCTTCTTTTATAATATCAGTTGTCGGTTCAAATCATTAATTATTTTGATTAAAACATTATGATA
258 TTCTACTTTTATAATATCAGTTGTCAGTTCAAATCATTAACTATTCAGATTAAAACATTACGATA
* * **
781196 AATATTCTTTTGGGAATCGAGGTAAAAATATAAATTCAACTGGCTGAAGCTA
323 AATATTCTTTTGGGAATCAAGGTAAAAATATAAATTCAACTGACCAAAGCTA
*
781248 AAAATTTAATGTTAAAATTCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTT
1 AAAATTTAATGTTAAAATGCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTT
* * * *
781313 CACCATTTTATGTATCGTACCAAATCCAAAGCTTCTAGCTCCC-TTGGGTTGGCCCTTTCTCTAT
66 CACCATTTTAT-CATGGTGCCAAATCCAAAGCCTCTAGCTCCCTTTGGGTTGGCCCTTTCTCTAT
* * *
781377 CCTATTTTTTGTTTGACCTGTTTTGGGACGTGG-GTATGAGATATAATCAGTCAAATTACGGTCT
130 CCTA-TTTTTGTTTGACCTGTTTTCGGACATGGCGTATGAGATATAATCAGTCAAATT-CGATCT
* *
781441 TGGTCCTTCTTATTGTACTAAAATTTGATATTTAGTCTTTATAATTTATTTTGATATAATTTAAT
193 TGGTCCTTCTTATTATACTAAAATTTGAT-TTTAGTCTTTATAATTTAATTTGATATAA-TTAAT
* *
781506 CTTTT-TACTTTTATAATAT-TGTTAGTTAGTTCAAATCATTAACTATTCCAG-TTAAAACATTA
256 -TTTTCTACTTTTATAATATCAGTT-GTCAGTTCAAATCATTAACTATT-CAGATTAAAACATTA
* *
781568 CGATAAATATT-TTATTGGGAATCAAGGTAAATATATATATTCAACTGACCAAAGCTA
318 CGATAAATATTCTT-TTGGGAATCAAGGTAAAAATATAAATTCAACTGACCAAAGCTA
* * * * * ** *
781625 AAAATTTGATGTTAAAAGGCAAAA-CTTAAATTATAAATTTTTAAAAGGGGCCAAAAATGAAATT
1 AAAATTTAATGTTAAAATGCAAAATC-TGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATT
* * ** *
781689 TCACTATTTTATCCTGGTGCCAAATCCAAAGCCAGTAGC-CCCTTTGGGTTGGTCCTTTCTCTAT
65 TCACCATTTTATCATGGTGCCAAATCCAAAGCCTCTAGCTCCCTTTGGGTTGGCCCTTTCTCTAT
* *
781753 ACTGTTTTTGTTTGACCT
130 CCTATTTTTGTTTGACCT
781771 ATTTCTAGGC
Statistics
Matches: 447, Mismatches: 61, Indels: 27
0.84 0.11 0.05
Matches are distributed among these distances:
371 99 0.22
372 21 0.05
373 4 0.01
374 24 0.05
375 62 0.14
376 74 0.17
377 158 0.35
378 5 0.01
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (374 bp):
AAAATTTAATGTTAAAATGCAAAATCTGAATTACAAATTTTCAGGAGGGGTCAAAAATGAAATTT
CACCATTTTATCATGGTGCCAAATCCAAAGCCTCTAGCTCCCTTTGGGTTGGCCCTTTCTCTATC
CTATTTTTGTTTGACCTGTTTTCGGACATGGCGTATGAGATATAATCAGTCAAATTCGATCTTGG
TCCTTCTTATTATACTAAAATTTGATTTTAGTCTTTATAATTTAATTTGATATAATTAATTTTTC
TACTTTTATAATATCAGTTGTCAGTTCAAATCATTAACTATTCAGATTAAAACATTACGATAAAT
ATTCTTTTGGGAATCAAGGTAAAAATATAAATTCAACTGACCAAAGCTA
Found at i:781844 original size:14 final size:14
Alignment explanation
Indices: 781821--781860 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
781811 TTAATGACAT
781821 TATAAAATTAAAAA
1 TATAAAATTAAAAA
*
781835 TATCAAATT-AAAA
1 TATAAAATTAAAAA
781848 TATAAAGATTAAA
1 TATAAA-ATTAAA
781861 TCATCGGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 11 0.50
15 2 0.09
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (14 bp):
TATAAAATTAAAAA
Found at i:793848 original size:3 final size:3
Alignment explanation
Indices: 793840--793866 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
793830 GGGGACCTGT
793840 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
793867 AAATGGGTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:794564 original size:3 final size:3
Alignment explanation
Indices: 794558--794587 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
794548 TTTTAATTTC
794558 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
794588 AGTTGACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:802790 original size:20 final size:19
Alignment explanation
Indices: 802767--802818 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 19
802757 AAATTATAAA
* *
802767 AAAAAATCAAAATGTTTTT
1 AAAAAATCAAAATATTTAT
*
802786 CAAAAATTCAAAATATTTAT
1 -AAAAAATCAAAATATTTAT
*
802806 AAAAAATAAAAAT
1 AAAAAATCAAAAT
802819 TCTAAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.62, C:0.06, G:0.02, T:0.31
Consensus pattern (19 bp):
AAAAAATCAAAATATTTAT
Found at i:802817 original size:27 final size:27
Alignment explanation
Indices: 802787--802838 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
802777 AATGTTTTTC
*
802787 AAAAATTCAAAAT-ATTTATAAAAAAT
1 AAAAATTCAAAATAATATATAAAAAAT
*
802813 AAAAATTCTAAATAATATATAAAAAA
1 AAAAATTCAAAATAATATATAAAAAA
802839 GTTGAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (27 bp):
AAAAATTCAAAATAATATATAAAAAAT
Found at i:803409 original size:16 final size:16
Alignment explanation
Indices: 803388--803419 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
803378 TTTTCTCTCC
*
803388 CTCTTTCTAAGCTTTT
1 CTCTTTCCAAGCTTTT
803404 CTCTTTCCAAGCTTTT
1 CTCTTTCCAAGCTTTT
803420 AAAAATTTCG
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:0.12, C:0.28, G:0.06, T:0.53
Consensus pattern (16 bp):
CTCTTTCCAAGCTTTT
Found at i:817634 original size:78 final size:78
Alignment explanation
Indices: 817545--817779 Score: 380
Period size: 78 Copynumber: 3.0 Consensus size: 78
817535 GTCAGGCAGA
* **
817545 GCCAACTAGTGTGACTCAGAAAACCAATTTAACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
817610 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
*
817623 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTATTGAGTCAGAGGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
817688 CGGCTTTCTGGAC
66 CGGCTTTCTGGAC
* * * * *
817701 ACCAACTAGTGTGACTCAGAAAACAAATTCGGCTCGTCCTAATCAAGCTACTGAGTCGGAAGGAC
1 GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
*
817766 CAGCTTTCTGGAC
66 CGGCTTTCTGGAC
817779 G
1 G
817780 GCATGTCCGT
Statistics
Matches: 145, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
78 145 1.00
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (78 bp):
GCCAACTAGTGTGACTCAGAAAACAAATTCGACTCGTCCTAATGAAGCTACTGAGTCAGAGGGAC
CGGCTTTCTGGAC
Found at i:818885 original size:192 final size:189
Alignment explanation
Indices: 818558--818933 Score: 515
Period size: 192 Copynumber: 2.0 Consensus size: 189
818548 AGTTTTTTGG
*
818558 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATTTTCACTGA
1 AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
* * * *
818623 TATTCTGTCAATTTTGGGCTGGTATTGCAATTTGACTTGCCATTTTTGCTTGCATTGTGGTTTTA
66 TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
* **
818688 TTATTTGGGGTTGTGCCGTAGTTTAATTTCCATACCATAGTAAAAAGCTTCTTTATTGTAGC
131 TTATTT--AGTCATGCCGTAGTTTAATTTCCATACCATAGT-AAAAGCTTCTTTATTGTAGC
*
818750 AATTAAAAAGATGTT-GG-TTATTGTTGTATAGCAAGGGTTTTACTTCAGGTTTTTATATTCACT
1 AATT-AAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGG-TTTTATATTCACT
* * * * *
818813 GATATTCTGTCTATTTCGATCTGGTATTGCATTTTGAATTGCTACTTTTGCTTG-TTTCGTGGTT
64 GATATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATT-GTGGTT
* ** *
818877 TTATTATTTAGTCATGCCGTAGTTTATTTTCCATTTCATAGTAGAAGCTTCTTTATT
128 TTATTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATT
818934 ATATATAATC
Statistics
Matches: 163, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
189 14 0.09
190 27 0.17
191 33 0.20
192 79 0.48
193 10 0.06
ACGTcount: A:0.23, C:0.12, G:0.19, T:0.47
Consensus pattern (189 bp):
AATTAAAAGATGTTAGGATTATTATTGTATAGCAAGGGTTTTACTTCAGGTTTTATATTCACTGA
TATTCTGTCAATTTCGAGCTGGTATTGCAATTTGAATTGCCACTTTTGCTTGCATTGTGGTTTTA
TTATTTAGTCATGCCGTAGTTTAATTTCCATACCATAGTAAAAGCTTCTTTATTGTAGC
Found at i:820374 original size:31 final size:31
Alignment explanation
Indices: 820339--820410 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
820329 TGCAAAATTT
* *
820339 TTATTGAGTTTTTTGAAAGTTTTCA-TTTAAA
1 TTATTGAGTTATTTGAAAGTTAT-ATTTTAAA
* *
820370 TTATTGAATTATTTGAAAGTTATATTTTAAG
1 TTATTGAGTTATTTGAAAGTTATATTTTAAA
820401 TTATTGAGTT
1 TTATTGAGTT
820411 GTTAAGTTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (31 bp):
TTATTGAGTTATTTGAAAGTTATATTTTAAA
Found at i:820800 original size:41 final size:41
Alignment explanation
Indices: 820754--820879 Score: 185
Period size: 35 Copynumber: 3.2 Consensus size: 41
820744 ACTAAATCAT
*
820754 AATATCTCATATAATACACTTAGATTTGTATGCTTCTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
820795 AATATCTC-----ATA-ACTTAGATTTGTATGCTTGTGATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
*
820830 AATATCTCATATAATACACTTATATTTGTATGCTTGT-ATA
1 AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
820870 AATATCTCAT
1 AATATCTCAT
820880 TTAGTAAGAA
Statistics
Matches: 77, Mismatches: 2, Indels: 13
0.84 0.02 0.14
Matches are distributed among these distances:
35 31 0.40
36 3 0.04
40 16 0.21
41 27 0.35
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (41 bp):
AATATCTCATATAATACACTTAGATTTGTATGCTTGTGATA
Found at i:823489 original size:55 final size:55
Alignment explanation
Indices: 823405--823514 Score: 193
Period size: 55 Copynumber: 2.0 Consensus size: 55
823395 ACGTATATCT
**
823405 CCTATTGATGTATAAAAACTAGTTTTTCAATTGTAGAAATTGATAAAATTTTTAA
1 CCTATTGATGTATAAAAACTAGTTTTTCAACCGTAGAAATTGATAAAATTTTTAA
*
823460 CCTATTGATGTATAAAAACTAGTTTTTCAACCGTAGAAATTGATAGAATTTTTAA
1 CCTATTGATGTATAAAAACTAGTTTTTCAACCGTAGAAATTGATAAAATTTTTAA
823515 TGAAGAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (55 bp):
CCTATTGATGTATAAAAACTAGTTTTTCAACCGTAGAAATTGATAAAATTTTTAA
Found at i:828800 original size:123 final size:123
Alignment explanation
Indices: 828647--828875 Score: 318
Period size: 123 Copynumber: 1.9 Consensus size: 123
828637 TTTGCCTCAT
* * * *
828647 CTGGATTGTTGATGAAATTTGGGTTTGAAACTAAAAGCTTATCCAAGTTAGTAAGCGAAAGGTTC
1 CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATCCAAGTTAGTAAGCGAAAGGTTC
*
828712 AAGTCC-TTTCCATTCGTGTTTTAGCTT-TGTTCATCTTGTTTTTCCTCATATGTATTGC
66 AAGTCCTTTTCCATT-GTGTTGTAG-TTCTGTTCATCTTGTTTTTCCTCATATGTATTGC
* * * **
828770 CTGGATTGTTGACGAAATTCGGGTTTGAAACCGAAAGCTCATTCGAGTTAGTAATTGAAAGGTTC
1 CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATCCAAGTTAGTAAGCGAAAGGTTC
**
828835 AAGTCCTTTTTGATTGTGTTGTAGTTCTGTTCATCTTGTTT
66 AAGTCCTTTTCCATTGTGTTGTAGTTCTGTTCATCTTGTTT
828876 AGATTGCTGT
Statistics
Matches: 92, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
122 2 0.02
123 84 0.91
124 6 0.07
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (123 bp):
CTGGATTGTTGACGAAATTCGGGTTTGAAACCAAAAGCTCATCCAAGTTAGTAAGCGAAAGGTTC
AAGTCCTTTTCCATTGTGTTGTAGTTCTGTTCATCTTGTTTTTCCTCATATGTATTGC
Found at i:832628 original size:6 final size:6
Alignment explanation
Indices: 832613--832668 Score: 58
Period size: 6 Copynumber: 9.3 Consensus size: 6
832603 TATGCTCCTT
* * * * *
832613 AGTAGG AGTAGT AGTAGG AGTAGG AGCAGG AGCAGG AGCAGG AGCAGG
1 AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG AGTAGG
*
832661 AGCAGG AG
1 AGTAGG AG
832669 CTGCTGAGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.34, C:0.09, G:0.48, T:0.09
Consensus pattern (6 bp):
AGTAGG
Found at i:832649 original size:18 final size:18
Alignment explanation
Indices: 832613--832668 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
832603 TATGCTCCTT
* * *
832613 AGTAGGAGTAGTAGTAGG
1 AGTAGGAGCAGGAGCAGG
832631 AGTAGGAGCAGGAGCAGG
1 AGTAGGAGCAGGAGCAGG
*
832649 AGCAGGAGCAGGAGCAGG
1 AGTAGGAGCAGGAGCAGG
832667 AG
1 AG
832669 CTGCTGAGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.34, C:0.09, G:0.48, T:0.09
Consensus pattern (18 bp):
AGTAGGAGCAGGAGCAGG
Done.