Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 141 of 230
Found at i:41436620 original size:31 final size:32
Alignment explanation
Indices: 41436371--41436670 Score: 128
Period size: 32 Copynumber: 9.3 Consensus size: 32
41436361 CTTACACAAC
41436371 ACATAACTTACATAATAACTTACATAACTTAT
1 ACATAACTTACATAATAACTTACATAACTTAT
* * *
41436403 ATATAAACTTATAT-ATAACTTACATACATAGCTTAA
1 ACAT-AACTTACATAATAACTTACAT--A-A-CTTAT
* * * * * *
41436439 ATAAAATTTATAT-GTAAACTTACACAAC----
1 ACATAACTTACATAAT-AACTTACATAACTTAT
*
41436467 AGATAACTTACATAATAACTTACATAACTTAT
1 ACATAACTTACATAATAACTTACATAACTTAT
* *
41436499 ATATAAACTTATAT-ATAACTTACATACATAACTTA-
1 ACAT-AACTTACATAATAAC-T---TACATAACTTAT
* * * *
41436534 ACTAAAATTTATAT-ATAAACTTACACAAC----
1 AC-ATAACTTACATAAT-AACTTACATAACTTAT
41436563 ACATAACTTACATAATAACTTACATAACTTAT
1 ACATAACTTACATAATAACTTACATAACTTAT
* * *
41436595 ACATGACTTATAT-ATAACTTTCATAACTTACTT
1 ACATAACTTACATAATAACTTACATAACTTA--T
* * *
41436628 ATAATAACTTACATAACTTACTTATAATAAC-T-T
1 A-CATAACTTACATAA-TAACTTA-CATAACTTAT
41436661 ACATAACTTA
1 ACATAACTTA
41436671 TTAATATTTT
Statistics
Matches: 206, Mismatches: 33, Indels: 58
0.69 0.11 0.20
Matches are distributed among these distances:
28 39 0.19
29 5 0.02
31 16 0.08
32 49 0.24
33 22 0.11
34 11 0.05
35 23 0.11
36 36 0.17
37 5 0.02
ACGTcount: A:0.47, C:0.16, G:0.01, T:0.36
Consensus pattern (32 bp):
ACATAACTTACATAATAACTTACATAACTTAT
Found at i:41436636 original size:14 final size:14
Alignment explanation
Indices: 41436617--41436662 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
41436607 TATAACTTTC
41436617 ATAACTTACTTATA
1 ATAACTTACTTATA
41436631 ATAACTTAC-----
1 ATAACTTACTTATA
41436640 ATAACTTACTTATA
1 ATAACTTACTTATA
41436654 ATAACTTAC
1 ATAACTTAC
41436663 ATAACTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
9 9 0.33
14 18 0.67
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.39
Consensus pattern (14 bp):
ATAACTTACTTATA
Found at i:41436642 original size:23 final size:23
Alignment explanation
Indices: 41436600--41436670 Score: 124
Period size: 23 Copynumber: 3.0 Consensus size: 23
41436590 CTTATACATG
*
41436600 ACTTATATATAACTTTCATAACTT
1 ACTTATA-ATAACTTACATAACTT
41436624 ACTTATAATAACTTACATAACTT
1 ACTTATAATAACTTACATAACTT
41436647 ACTTATAATAACTTACATAACTT
1 ACTTATAATAACTTACATAACTT
41436670 A
1 A
41436671 TTAATATTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 39 0.85
24 7 0.15
ACGTcount: A:0.42, C:0.17, G:0.00, T:0.41
Consensus pattern (23 bp):
ACTTATAATAACTTACATAACTT
Found at i:41439427 original size:21 final size:21
Alignment explanation
Indices: 41439401--41439471 Score: 97
Period size: 21 Copynumber: 3.4 Consensus size: 21
41439391 CTACAACTTA
*
41439401 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
41439422 AAGCAGCGGCTGCAGCGAAGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
41439443 AAGCAGAGGCTGTAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
41439464 AAGCAGAG
1 AAGCAGAG
41439472 TAGAGCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.32, C:0.18, G:0.45, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:41439855 original size:41 final size:42
Alignment explanation
Indices: 41439798--41439899 Score: 154
Period size: 42 Copynumber: 2.5 Consensus size: 42
41439788 AAAGCGCTGT
*
41439798 TAAAGAACATGTTCTTTAGCAGCGCTT-AGAAAAAATGCCGC
1 TAAAGAACATGTTCTTTAGCAGCGCTTAAGAAAAAACGCCGC
*
41439839 TAAAG-ACTATGTTCTTTAGCGGCGCTTAAGAAAAAACGCCGC
1 TAAAGAAC-ATGTTCTTTAGCAGCGCTTAAGAAAAAACGCCGC
*
41439881 TAAAGAACATGATCTTTAG
1 TAAAGAACATGTTCTTTAG
41439900 TGGTGTTTTT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
40 2 0.04
41 23 0.42
42 28 0.51
43 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (42 bp):
TAAAGAACATGTTCTTTAGCAGCGCTTAAGAAAAAACGCCGC
Found at i:41440050 original size:22 final size:21
Alignment explanation
Indices: 41440020--41440064 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
41440010 TTAGTGGCGT
*
41440020 TAAAAAACGCCGCTAAAGGCC
1 TAAAAAACGCCGCTAAAGACC
41440041 TAAATAAACGCCGCTAAAGACC
1 TAAA-AAACGCCGCTAAAGACC
41440063 TA
1 TA
41440065 TTTTGGTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.44, C:0.27, G:0.16, T:0.13
Consensus pattern (21 bp):
TAAAAAACGCCGCTAAAGACC
Found at i:41440809 original size:50 final size:50
Alignment explanation
Indices: 41440520--41440809 Score: 287
Period size: 50 Copynumber: 5.8 Consensus size: 50
41440510 TGAATATAAC
* * * ** * * *
41440520 GTGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTAC-
1 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CG
* * * * * * ** * *
41440570 -TGCCAATGCCATATCTCAAATATGGTCTTACATGAGAGTTCTCATATAG
1 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * ** * **
41440619 GTGCCCATGCCATGTCCCAAACATGGTCTTACGGGGGACTTCTCATCTTA
1 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
41440669 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCG
1 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
41440719 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATCTCG
1 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
41440769 GTGTCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
1 GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCT
41440810 TTTTACCCAA
Statistics
Matches: 200, Mismatches: 38, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
49 34 0.17
50 166 0.83
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
GTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:41440929 original size:13 final size:13
Alignment explanation
Indices: 41440911--41440937 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41440901 AGTCAACATT
41440911 AAATAAATTCATA
1 AAATAAATTCATA
41440924 AAATAAATTCATA
1 AAATAAATTCATA
41440937 A
1 A
41440938 TTTTTGGAAA
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:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTCATA
Found at i:41446232 original size:21 final size:20
Alignment explanation
Indices: 41446189--41446233 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
41446179 TTTCTAATCA
*
41446189 ATAATTATTACAAAACTATC
1 ATAATTATTACAAAACTACC
41446209 ATAATTTATT-CAAAACTTACC
1 ATAA-TTATTACAAAAC-TACC
41446230 ATAA
1 ATAA
41446234 GGGCAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (20 bp):
ATAATTATTACAAAACTACC
Found at i:41446446 original size:27 final size:27
Alignment explanation
Indices: 41446329--41446480 Score: 98
Period size: 27 Copynumber: 5.6 Consensus size: 27
41446319 GTATACCGTC
* * *
41446329 AAGGCATTCCTTTCAGAGT-TTGCCTCG
1 AAGGCATTCCTTTCATA-TATTGCCACA
* * * *
41446356 AAGGTATTCTTTTCAAAGT-TTTCCACTA
1 AAGGCATTCCTTTCATA-TATTGCCAC-A
*
41446384 AA-GCATTCCTTTCGTATATTGCCACA
1 AAGGCATTCCTTTCATATATTGCCACA
*
41446410 GAGGCATTCC-TTCTATATATTGCCACA
1 AAGGCATTCCTTTC-ATATATTGCCACA
* * ** *
41446437 AATGCGTTCCTTTCATATATT-ATAGTA
1 AAGGCATTCCTTTCATATATTGCCA-CA
41446464 AAGGCATTCCTTTCATA
1 AAGGCATTCCTTTCATA
41446481 ACATTTTTAC
Statistics
Matches: 98, Mismatches: 21, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
26 7 0.07
27 86 0.88
28 5 0.05
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (27 bp):
AAGGCATTCCTTTCATATATTGCCACA
Found at i:41450938 original size:34 final size:34
Alignment explanation
Indices: 41450881--41450947 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
41450871 TCCTACCCCG
* * *
41450881 CATGCAATTTAATCAAAACATTTCAAGCAATTCT
1 CATGCAATTCAAACAAAACATTTCAAACAATTCT
**
41450915 CATGCAATTCAAACAAATTATTTCAAACAATTC
1 CATGCAATTCAAACAAAACATTTCAAACAATTC
41450948 AACTATCCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.43, C:0.21, G:0.04, T:0.31
Consensus pattern (34 bp):
CATGCAATTCAAACAAAACATTTCAAACAATTCT
Found at i:41452526 original size:13 final size:13
Alignment explanation
Indices: 41452508--41452539 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
41452498 TACTGATTTT
41452508 TGCACACTTTCAC
1 TGCACACTTTCAC
41452521 TGCACACTTTCAC
1 TGCACACTTTCAC
*
41452534 TACACA
1 TGCACA
41452540 TCCTAAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.28, C:0.38, G:0.06, T:0.28
Consensus pattern (13 bp):
TGCACACTTTCAC
Found at i:41456533 original size:16 final size:16
Alignment explanation
Indices: 41456513--41456565 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 16
41456503 AAAAATTATG
* *
41456513 TTTTCCATCCTTCTAG
1 TTTTCCATCATTCTAA
* * *
41456529 TTTTCTATCTTTTTAA
1 TTTTCCATCATTCTAA
41456545 TTTTCCATCATTCTAA
1 TTTTCCATCATTCTAA
41456561 TTTTC
1 TTTTC
41456566 TTTCCACTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTTCCATCATTCTAA
Found at i:41458273 original size:14 final size:13
Alignment explanation
Indices: 41458232--41458265 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
41458222 TTATGCCATT
41458232 TATTTTCTTAATTA
1 TATTTT-TTAATTA
41458246 TATTTTTATAATTA
1 TATTTTT-TAATTA
41458260 TATTTT
1 TATTTT
41458266 ATTTATTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTTTTTAATTA
Found at i:41460616 original size:45 final size:45
Alignment explanation
Indices: 41460542--41460747 Score: 277
Period size: 45 Copynumber: 4.6 Consensus size: 45
41460532 ATATGCCAAG
* * * *
41460542 ATGAGTAAGACCATAGTTGAATGATGCTATGGCATTATGATAAAA
1 ATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATAAAA
* * *
41460587 ATGAGTAAGACTATAGCTGAAAGACGCTATGGCATCGTGACAAAA
1 ATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATAAAA
* * *
41460632 ATGAATAAGACCATAGCTGAAAGATGCTATGGTATCATGATAAAA
1 ATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATAAAA
* * *
41460677 ATGAGTAAGACCATAGTTGAAAGAAGCTATGACATCATGATAAAA
1 ATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATAAAA
* *
41460722 ATCAGAAAGACCATAGCTGAAAGACG
1 ATGAGTAAGACCATAGCTGAAAGACG
41460748 TTAAGACATA
Statistics
Matches: 139, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 139 1.00
ACGTcount: A:0.43, C:0.13, G:0.22, T:0.22
Consensus pattern (45 bp):
ATGAGTAAGACCATAGCTGAAAGACGCTATGGCATCATGATAAAA
Found at i:41460928 original size:27 final size:26
Alignment explanation
Indices: 41460898--41460976 Score: 61
Period size: 27 Copynumber: 3.0 Consensus size: 26
41460888 ACGACATCAT
41460898 AGATAGTTATATGGGATAATAAACAC
1 AGATAGTTATATGGGATAATAAACAC
* * * *
41460924 GAGATTG-TATGATGAGACATTAAACAC
1 -AGATAGTTAT-ATGGGATAATAAACAC
***
41460951 AGGATAGTTCGCTGGGATAATAAACA
1 A-GATAGTTATATGGGATAATAAACA
41460977 TGGGTGGTCA
Statistics
Matches: 38, Mismatches: 11, Indels: 6
0.69 0.20 0.11
Matches are distributed among these distances:
26 4 0.11
27 33 0.87
28 1 0.03
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (26 bp):
AGATAGTTATATGGGATAATAAACAC
Found at i:41467071 original size:35 final size:35
Alignment explanation
Indices: 41467032--41467114 Score: 157
Period size: 35 Copynumber: 2.4 Consensus size: 35
41467022 CTATTTTAAA
41467032 AATAAAAATAAAATAATTTTTATTAATATTTAGGT
1 AATAAAAATAAAATAATTTTTATTAATATTTAGGT
*
41467067 AATAAAAATAAAATAATTTTTATTAATATTTATGT
1 AATAAAAATAAAATAATTTTTATTAATATTTAGGT
41467102 AATAAAAATAAAA
1 AATAAAAATAAAA
41467115 ATAAAAACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.40
Consensus pattern (35 bp):
AATAAAAATAAAATAATTTTTATTAATATTTAGGT
Found at i:41467112 original size:41 final size:38
Alignment explanation
Indices: 41467028--41467120 Score: 129
Period size: 35 Copynumber: 2.4 Consensus size: 38
41467018 TATACTATTT
*
41467028 TAAAAATAAAAATAAAATAATTTTTATTAATATTTAGG
1 TAAAAATAAAAATAAAATAATTTTTATTAATATTTAGA
41467066 T---AATAAAAATAAAATAATTTTTATTAATATTTATGTAA
1 TAAAAATAAAAATAAAATAATTTTTATTAATATTTA-G--A
41467104 TAAAAATAAAAATAAAA
1 TAAAAATAAAAATAAAA
41467121 ACAAAATTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 9
0.83 0.02 0.16
Matches are distributed among these distances:
35 32 0.67
36 1 0.02
38 2 0.04
41 13 0.27
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (38 bp):
TAAAAATAAAAATAAAATAATTTTTATTAATATTTAGA
Found at i:41473416 original size:20 final size:19
Alignment explanation
Indices: 41473393--41473538 Score: 58
Period size: 20 Copynumber: 7.3 Consensus size: 19
41473383 CACATACGTG
41473393 CCCCTGTTTGTACTTTGATA
1 CCCCTGTTTGTACTTTG-TA
* * * *
41473413 CCCCTGATTGCACATATGTG
1 CCCCTGTTTGTAC-TTTGTA
* *
41473433 CCCCTGTATGTACTTTGGTG
1 CCCCTGTTTGTACTTT-GTA
* * * * *
41473453 CCCTTGATTGCACATATGTG
1 CCCCTGTTTGTAC-TTTGTA
*
41473473 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTT-TGTA
* * * * *
41473493 CCTCTGATTGCACATATGTG
1 CCCCTGTTTGTAC-TTTGTA
* *
41473513 CCCCTATTTTTACTTTGGTA
1 CCCCTGTTTGTACTTT-GTA
41473533 CCCCTG
1 CCCCTG
41473539 ATTGCACATA
Statistics
Matches: 87, Mismatches: 33, Indels: 12
0.66 0.25 0.09
Matches are distributed among these distances:
19 5 0.06
20 76 0.87
21 6 0.07
ACGTcount: A:0.15, C:0.28, G:0.18, T:0.38
Consensus pattern (19 bp):
CCCCTGTTTGTACTTTGTA
Found at i:41473425 original size:40 final size:40
Alignment explanation
Indices: 41473375--41473691 Score: 366
Period size: 40 Copynumber: 8.0 Consensus size: 40
41473365 GTTAATTATA
*
41473375 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGATACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
* * *
41473415 CCTGATTGCACATATGTGCCCCTGTATGTACTTTGGTGCC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
* * *
41473455 CTTGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
* * * *
41473495 TCTGATTGCACATATGTGCCCCTATTTTTACTTTGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
* ** ** *
41473535 CCTGATTGCACATATGTGTGCCTGTTTGTACTTCAGTAGC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
* * * * *
41473575 CTTGATTGCACATACCTGTCCCTATTTGTACTTCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
* * *
41473615 CCTAATTGCACATACATGCCCCTGTTTGTACTTCGGTACC
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
** * *
41473655 TTTGATTGCA-ATACGTGCCCCTTTTTGTACTTCGGTA
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTA
41473692 TACGTGCCGC
Statistics
Matches: 239, Mismatches: 38, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
39 25 0.10
40 214 0.90
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (40 bp):
CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACC
Found at i:41473510 original size:80 final size:80
Alignment explanation
Indices: 41473375--41473691 Score: 404
Period size: 80 Copynumber: 4.0 Consensus size: 80
41473365 GTTAATTATA
* * * * *
41473375 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCCTGATTGCACATATGTGCCCCTGT
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCTCTGATTGCACATACGTGCCCCTAT
* *
41473440 ATGTACTTTGGTGCC
66 TTGTACTTTGGTACC
* * *
41473455 CTTGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACCTCTGATTGCACATATGTGCCCCTAT
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCTCTGATTGCACATACGTGCCCCTAT
*
41473520 TTTTACTTTGGTACC
66 TTGTACTTTGGTACC
* ** * * *
41473535 CCTGATTGCACATATGTGTGCCTGTTTGTACTTCAGTAGCCT-TGATTGCACATACCTGTCCCTA
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTA-CCTCTGATTGCACATACGTGCCCCTA
*
41473599 TTTGTACTTCGGTACC
65 TTTGTACTTTGGTACC
* * * *
41473615 CCTAATTGCACATACATGCCCCTGTTTGTACTTCGGTACCTTTGATTGCA-ATACGTGCCCCTTT
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCTCTGATTGCACATACGTGCCCCTAT
*
41473679 TTGTACTTCGGTA
66 TTGTACTTTGGTA
41473692 TACGTGCCGC
Statistics
Matches: 208, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
79 27 0.13
80 178 0.86
81 3 0.01
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (80 bp):
CCTGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCTCTGATTGCACATACGTGCCCCTAT
TTGTACTTTGGTACC
Found at i:41473603 original size:120 final size:120
Alignment explanation
Indices: 41473375--41473687 Score: 414
Period size: 120 Copynumber: 2.6 Consensus size: 120
41473365 GTTAATTATA
*
41473375 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGATACCCCTGATTGCACATATGTGCCCCTGT
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATATGTGCCCCTGT
* ** ** *
41473440 ATGTACTTTGGTGCCCTTGATTGCACATATGTGCCCCTGTTTGTACTTCGGTACC
66 TTGTACTTCAGTGCCCTTGATTGCACATACCTGCCCCTATTTGTACTTCGGTACC
* * * * **
41473495 TCTGATTGCACATATGTGCCCCTATTTTTACTTTGGTACCCCTGATTGCACATATGTGTGCCTGT
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATATGTGCCCCTGT
*
41473560 TTGTACTTCAGTAG-CCTTGATTGCACATACCTGTCCCTATTTGTACTTCGGTACC
66 TTGTACTTCAGT-GCCCTTGATTGCACATACCTGCCCCTATTTGTACTTCGGTACC
* * * ** * *
41473615 CCTAATTGCACATACATGCCCCTGTTTGTACTTCGGTACCTTTGATTGCA-ATACGTGCCCCTTT
1 CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATATGTGCCCCTGT
41473679 TTGTACTTC
66 TTGTACTTC
41473688 GGTATACGTG
Statistics
Matches: 165, Mismatches: 27, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
119 19 0.12
120 145 0.88
121 1 0.01
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (120 bp):
CCTGATTGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATATGTGCCCCTGT
TTGTACTTCAGTGCCCTTGATTGCACATACCTGCCCCTATTTGTACTTCGGTACC
Found at i:41473714 original size:26 final size:26
Alignment explanation
Indices: 41473665--41473714 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
41473655 TTTGATTGCA
* *
41473665 ATACGTGCCCCTTTTTGTACTTCGGT
1 ATACGTGCCCCTGTTTATACTTCGGT
* *
41473691 ATACGTGCCGCTGTTTATAGTTCG
1 ATACGTGCCCCTGTTTATACTTCG
41473715 ATAATTTCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.14, C:0.24, G:0.22, T:0.40
Consensus pattern (26 bp):
ATACGTGCCCCTGTTTATACTTCGGT
Found at i:41481889 original size:40 final size:40
Alignment explanation
Indices: 41481829--41481995 Score: 210
Period size: 40 Copynumber: 4.2 Consensus size: 40
41481819 CGAAATTTAG
* * * *
41481829 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
41481869 CCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
*
41481909 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* *
41481949 CCGGATAAAATCACTAGCACAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
41481989 CCGGATA
1 CCGGATA
41481996 TCATTCAAAT
Statistics
Matches: 108, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 103 0.95
41 3 0.03
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.22
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:41485666 original size:30 final size:31
Alignment explanation
Indices: 41485627--41485687 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
41485617 TATTAGTACA
* *
41485627 GTGTAGGCCTTAGACCATTATAGT-AATAGT
1 GTGTAGGCCTTAGACCAATACAGTAAATAGT
* *
41485657 GTGTGGGCCTTAGCCCAATACAGTAAATAGT
1 GTGTAGGCCTTAGACCAATACAGTAAATAGT
41485688 ACAATTCAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (31 bp):
GTGTAGGCCTTAGACCAATACAGTAAATAGT
Found at i:41487423 original size:33 final size:33
Alignment explanation
Indices: 41487366--41487464 Score: 114
Period size: 33 Copynumber: 3.1 Consensus size: 33
41487356 CTTGTAGAAT
* * ** *
41487366 CAGTCTGGGCCTGAGCCTTATACAGTATTAGTA
1 CAGTGTGGGCCTTAGCCCAATACAGTAATAGTA
*
41487399 CAGTGTGGGCCTTAGCCCATTACAGTAATAGT-
1 CAGTGTGGGCCTTAGCCCAATACAGTAATAGTA
41487431 --GTGTGGGCCTTAGCCCAATACAGTAAGTAGTA
1 CAGTGTGGGCCTTAGCCCAATACAGTAA-TAGTA
41487463 CA
1 CA
41487465 ATTCAGTAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
30 25 0.45
31 4 0.07
33 26 0.47
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.27
Consensus pattern (33 bp):
CAGTGTGGGCCTTAGCCCAATACAGTAATAGTA
Found at i:41487437 original size:30 final size:31
Alignment explanation
Indices: 41487401--41487461 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
41487391 TATTAGTACA
*
41487401 GTGTGGGCCTTAGCCCATTACAGTAA-TAGT
1 GTGTGGGCCTTAGCCCAATACAGTAAGTAGT
41487431 GTGTGGGCCTTAGCCCAATACAGTAAGTAGT
1 GTGTGGGCCTTAGCCCAATACAGTAAGTAGT
41487462 ACAATTCAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (31 bp):
GTGTGGGCCTTAGCCCAATACAGTAAGTAGT
Found at i:41487840 original size:27 final size:27
Alignment explanation
Indices: 41487810--41488020 Score: 182
Period size: 27 Copynumber: 7.8 Consensus size: 27
41487800 TACCTTATGA
*
41487810 GGGTAGTTCATTCATTTTACCCTTCAG
1 GGGTATTTCATTCATTTTACCCTTCAG
**
41487837 GGGTATTTCGGTCATTTTACCCTTCAG
1 GGGTATTTCATTCATTTTACCCTTCAG
*** **
41487864 GGGTATTTTGGTCATTTTA-CCTTTTG
1 GGGTATTTCATTCATTTTACCCTTCAG
*
41487890 GGGATATTTCGGTT-ATTTTACCCTTCAG
1 GGG-TATTTC-ATTCATTTTACCCTTCAG
* * *
41487918 GGGTATTTCAATCATTTTATCCTT-TG
1 GGGTATTTCATTCATTTTACCCTTCAG
*
41487944 AGGGTATTTCGATT-ATTTTACCCTTCGG
1 -GGGTATTTC-ATTCATTTTACCCTTCAG
*
41487972 GGGTATTTCGA-TCATTTTACCCTT-TG
1 GGGTATTTC-ATTCATTTTACCCTTCAG
**
41487998 AGGGTATTTCAGCCATTTTACCC
1 -GGGTATTTCATTCATTTTACCC
41488021 ACAAATTGCA
Statistics
Matches: 155, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
26 13 0.08
27 129 0.83
28 13 0.08
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (27 bp):
GGGTATTTCATTCATTTTACCCTTCAG
Found at i:41487868 original size:54 final size:53
Alignment explanation
Indices: 41487810--41488020 Score: 246
Period size: 54 Copynumber: 3.9 Consensus size: 53
41487800 TACCTTATGA
* *
41487810 GGGTAGTTCATTCATTTTACCC-TTCAGGGGTATTTCGGTCATTTTACCCTTCAG
1 GGGTATTTCA-TCATTTTACCCTTTGA-GGGTATTTCGGTCATTTTACCCTTCAG
** * *
41487864 GGGTATTTTGGTCATTTTACCTTTTG-GGGATATTTCGGTTATTTTACCCTTCAG
1 GGGTA-TTTCATCATTTTACCCTTTGAGGG-TATTTCGGTCATTTTACCCTTCAG
* * * *
41487918 GGGTATTTCAATCATTTTATCCTTTGAGGGTATTTCGATTATTTTACCCTTCGG
1 GGGTATTTC-ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTTCAG
* *
41487972 GGGTATTTCGATCATTTTACCCTTTGAGGGTATTTCAGCCATTTTACCC
1 GGGTATTTC-ATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCC
41488021 ACAAATTGCA
Statistics
Matches: 134, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
53 6 0.04
54 121 0.90
55 7 0.05
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (53 bp):
GGGTATTTCATCATTTTACCCTTTGAGGGTATTTCGGTCATTTTACCCTTCAG
Found at i:41487909 original size:81 final size:81
Alignment explanation
Indices: 41487821--41488020 Score: 242
Period size: 81 Copynumber: 2.5 Consensus size: 81
41487811 GGTAGTTCAT
* * *
41487821 TCATTTTACCCTTCAGGGGTATTTCGGTCATTTTACCCTTCAG-GGGTATTTTGGTCATTTTACC
1 TCATTTTACCCTTCAGGGGTATTTCAGTCATTTTACCCTT-AGAGGGTATTTCGATCATTTTACC
* * *
41487885 TTTTGGGGATATTTCGG
65 CTTCGGGGATATTTCGA
* * * * *
41487902 TTATTTTACCCTTCAGGGGTATTTCAATCATTTTATCCTTTGAGGGTATTTCGATTATTTTACCC
1 TCATTTTACCCTTCAGGGGTATTTCAGTCATTTTACCCTTAGAGGGTATTTCGATCATTTTACCC
*
41487967 TTCGGGGGTATTTCGA
66 TTCGGGGATATTTCGA
* *
41487983 TCATTTTACCCTT-TGAGGGTATTTCAGCCATTTTACCC
1 TCATTTTACCCTTCAG-GGGTATTTCAGTCATTTTACCC
41488021 ACAAATTGCA
Statistics
Matches: 100, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
80 2 0.02
81 98 0.98
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.45
Consensus pattern (81 bp):
TCATTTTACCCTTCAGGGGTATTTCAGTCATTTTACCCTTAGAGGGTATTTCGATCATTTTACCC
TTCGGGGATATTTCGA
Found at i:41491378 original size:13 final size:13
Alignment explanation
Indices: 41491360--41491384 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41491350 TAATGGTATA
41491360 TTGAATCCATGAC
1 TTGAATCCATGAC
41491373 TTGAATCCATGA
1 TTGAATCCATGA
41491385 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:41493051 original size:47 final size:47
Alignment explanation
Indices: 41492964--41493261 Score: 431
Period size: 47 Copynumber: 6.4 Consensus size: 47
41492954 TAATTGAATA
* *
41492964 AATGTGAA-AGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATG
1 AATGTGAACA-TGTGTATGTGTG-ATAAGGCCGAATGGCCAATGTGATG
*
41493012 AAAGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
** * *
41493059 AATGTGAACATGCATATATGAGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
41493106 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * *
41493153 AAAGTGAACAGGTGTATGTGTGATAAGGCCGAGTGGCCAATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
* * * *
41493200 AATGTGAGCATGTGTATGTGAGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
41493247 AATGTGAA-A-GTGTAT
1 AATGTGAACATGTGTAT
41493262 AAATGTGATA
Statistics
Matches: 226, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
45 6 0.03
46 1 0.00
47 200 0.88
48 18 0.08
49 1 0.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (47 bp):
AATGTGAACATGTGTATGTGTGATAAGGCCGAATGGCCAATGTGATG
Found at i:41493269 original size:141 final size:140
Alignment explanation
Indices: 41492964--41493273 Score: 478
Period size: 141 Copynumber: 2.2 Consensus size: 140
41492954 TAATTGAATA
* *
41492964 AATGTGAAAGTGTATATGTGTGAATAGGGCCGAATGGCCAATGTGATGAAAGTGAACATGTGTAT
1 AATGTGAAAGTGTATA-GTGTG-ATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAGGTGTAT
41493029 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATG
64 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATG
41493094 GCCAATGTGATG
129 GCCAATGTGATG
41493106 AATGTGAACATGTGTAT-GTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAGGTGTAT
1 AATGTGAA-A-GTGTATAGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAGGTGTAT
* * ** * *
41493170 GTGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAGCATGTGTATGTGAGATAAGGCCTAATG
64 GTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATG
*
41493235 GCCGATGTGATG
129 GCCAATGTGATG
*
41493247 AATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTAT-AGTGTGATAAG
41493274 TCCCGAAGGG
Statistics
Matches: 154, Mismatches: 10, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
139 6 0.04
140 1 0.01
141 127 0.82
142 13 0.08
143 1 0.01
144 6 0.04
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.26
Consensus pattern (140 bp):
AATGTGAAAGTGTATAGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAGGTGTATGT
GTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGC
CAATGTGATG
Found at i:41494381 original size:20 final size:20
Alignment explanation
Indices: 41494356--41494395 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
41494346 TCCGACTTTG
41494356 GAGATTTATTATAAATTAAC
1 GAGATTTATTATAAATTAAC
41494376 GAGATTTATTATAAATTAAC
1 GAGATTTATTATAAATTAAC
41494396 CAGAGATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
GAGATTTATTATAAATTAAC
Found at i:41495355 original size:43 final size:43
Alignment explanation
Indices: 41495294--41495467 Score: 303
Period size: 43 Copynumber: 4.0 Consensus size: 43
41495284 TTGGTTTTCA
* *
41495294 GCAATCAGTGTTAACGGTTGCGAGATTGGCACTAAGTGTGCGG
1 GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
*
41495337 GCAATCAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
1 GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
41495380 GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
1 GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
* *
41495423 GCAATAAGTATTCACGGTTGTGAGATTGGCACTAAGTGTGCGG
1 GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
41495466 GC
1 GC
41495468 TTGAAATGCA
Statistics
Matches: 127, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 127 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (43 bp):
GCAATAAGTGTTCACGGTTGCGAGATTGGCACTAAGTGTGCGG
Found at i:41495482 original size:29 final size:29
Alignment explanation
Indices: 41495449--41495522 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
41495439 GTTGTGAGAT
* *
41495449 TGGCACTAAGTGTGCGGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
*
41495478 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
41495507 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41495523 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.12
29 36 0.88
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:41495600 original size:40 final size:40
Alignment explanation
Indices: 41495545--41495899 Score: 575
Period size: 40 Copynumber: 8.9 Consensus size: 40
41495535 AAGCACTATG
*
41495545 TGTGCGAATTGATATATCCGGGTTAAGACCCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
41495585 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
41495625 TGTGCGAATTGATATATCCGGGCTAAGACCTGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
* *
41495665 TGTGCGAATTGATATATCCGGGCTAAAACCTGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
41495705 TGTGCGAATTGATATATCCGGGTTAAGACCCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
*
41495745 TGTGCGAATTGATATATCCGGGCTAAGACCTGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
* * *
41495785 TGTGTGAATTGATATATCTGGGATAAGACCCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
41495825 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
* * * * * *
41495865 CGTACGAGTTGCTATACCCGGGTTAAGACCCGAAG
1 TGTGCGAATTGATATATCCGGGCTAAGACCCGAAG
41495900 TCAATTGAGC
Statistics
Matches: 294, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 294 1.00
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.26
Consensus pattern (40 bp):
TGTGCGAATTGATATATCCGGGCTAAGACCCGAAGGCATT
Found at i:41495983 original size:40 final size:40
Alignment explanation
Indices: 41495915--41495995 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
41495905 TGAGCTTGTG
* * * *
41495915 GTTATATCCAGACTAAGTTCCGACGAGCATTCGTGCTGGT
1 GTTATATCCAGACTAAGTCCCGAAGAGCAATCATGCTGGT
* * *
41495955 GTTATATCCGGGCTAGGTCCCGAAGAGCAATCATGCTGGT
1 GTTATATCCAGACTAAGTCCCGAAGAGCAATCATGCTGGT
41495995 G
1 G
41495996 ACATGTATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
GTTATATCCAGACTAAGTCCCGAAGAGCAATCATGCTGGT
Found at i:41497736 original size:13 final size:13
Alignment explanation
Indices: 41497718--41497742 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41497708 TAATGGTATA
41497718 TTGAATCCATGAC
1 TTGAATCCATGAC
41497731 TTGAATCCATGA
1 TTGAATCCATGA
41497743 AAATTTAGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TTGAATCCATGAC
Found at i:41499406 original size:47 final size:47
Alignment explanation
Indices: 41499336--41499619 Score: 437
Period size: 47 Copynumber: 6.1 Consensus size: 47
41499326 TGAAAGTGTA
* *
41499336 TATGTGTGAATAGGGCCGAATGGCCAATGTGATGAAAATGAACATGTG
1 TATGTGTG-ATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
*
41499384 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTA
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
*
41499431 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGTG
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
*
41499478 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACAGGTG
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
* * *
41499525 TATGTGTGATAAGGCCGAGTGGCCAATGTGATGAATGTGAGCATGTG
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
* * * *
41499572 TATGTGAGATAAGGCCTAATGGCCGATGTGATGAATGTGAA-A-GTG
1 TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
41499617 TAT
1 TAT
41499620 AAATGTGATA
Statistics
Matches: 220, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
45 6 0.03
46 1 0.00
47 205 0.93
48 8 0.04
ACGTcount: A:0.31, C:0.10, G:0.32, T:0.26
Consensus pattern (47 bp):
TATGTGTGATAAGGCCGAATGGCCAATGTGATGAAAGTGAACATGTG
Found at i:41504663 original size:29 final size:28
Alignment explanation
Indices: 41504610--41504665 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
41504600 ATGATTTATA
* *
41504610 AAAATTGACTATTCTTTTTGTAAATATT
1 AAAATTAACTATTCTTTTTGCAAATATT
41504638 AAAATTAACTA-TCTTTTTCTGCAAATAT
1 AAAATTAACTATTC-TTTT-TGCAAATAT
41504666 ATTAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 2 0.08
28 14 0.58
29 8 0.33
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (28 bp):
AAAATTAACTATTCTTTTTGCAAATATT
Found at i:41504744 original size:15 final size:16
Alignment explanation
Indices: 41504726--41504755 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
41504716 TAACAACTAA
41504726 TATATAAT-TATATTT
1 TATATAATATATATTT
41504741 TATATAATATATATT
1 TATATAATATATATT
41504756 AATTGTTATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:41508653 original size:29 final size:29
Alignment explanation
Indices: 41508418--41508643 Score: 138
Period size: 29 Copynumber: 7.8 Consensus size: 29
41508408 TATCGGTGAT
* * *
41508418 CATCGAATATAAAAAGGGACAGCTTCGGC
1 CATCGAATATGAAAAGGGATAGCTTCGAC
* * * *
41508447 TATCGATTATGAAAAGGGAT-GGTGACGAC
1 CATCGAATATGAAAAGGGATAGCT-TCGAC
* ** * * *
41508476 CAT-TAGCCATGGAAAGGGAT-GGTGACGAC
1 CATCGA-ATATGAAAAGGGATAGCT-TCGAC
* *
41508505 CATCTAATATGAAGAGGGATAGCTTCGAC
1 CATCGAATATGAAAAGGGATAGCTTCGAC
* *
41508534 TATCGAATATAAAAAGGGATAGCTTCGAC
1 CATCGAATATGAAAAGGGATAGCTTCGAC
* * *
41508563 TATCGATTATGAAAAGGGAT-GGTGAT-GAC
1 CATCGAATATGAAAAGGGATAGCT--TCGAC
* * * *
41508592 CATCGATTAATGAAAAGAGATGGCTTCAAC
1 CATCGAAT-ATGAAAAGGGATAGCTTCGAC
*
41508622 CATTGAATATGAAAAGGGATAG
1 CATCGAATATGAAAAGGGATAG
41508644 TTACAACCAT
Statistics
Matches: 155, Mismatches: 33, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
28 5 0.03
29 124 0.80
30 24 0.15
31 2 0.01
ACGTcount: A:0.37, C:0.14, G:0.27, T:0.23
Consensus pattern (29 bp):
CATCGAATATGAAAAGGGATAGCTTCGAC
Found at i:41512294 original size:554 final size:554
Alignment explanation
Indices: 41511238--41512350 Score: 2136
Period size: 554 Copynumber: 2.0 Consensus size: 554
41511228 CGAGTAATCG
41511238 ATTTATTCAAGTATGGTATTTAAAGAACGTATTAAACAAAATTTCTGCTGAATTGATTTCTTTAG
1 ATTTATTCAAGTATGGTATTTAAAGAACGTATTAAACAAAATTTCTGCTGAATTGATTTCTTTAG
41511303 TGAATGGGATAATGTGGGATTGTTGGTGACTGTAGTAGCCAGTGGAATAATGTTTGAATTGCCAA
66 TGAATGGGATAATGTGGGATTGTTGGTGACTGTAGTAGCCAGTGGAATAATGTTTGAATTGCCAA
41511368 GATATCTAAATGCAGCGGTTATAGTTGAGTAGCTTACGGCGATCTCTTTTGAGTATTTTATATGT
131 GATATCTAAATGCAGCGGTTATAGTTGAGTAGCTTACGGCGATCTCTTTTGAGTATTTTATATGT
*
41511433 TCTTTTGTCCACAGAGGTATATGTAGTTGTTGATTTTCTGATGTGATTCTTATCGTATGAGAACG
196 TCTTTTGTCCACAGAGGTATATGTAGTTGTTGATTGTCTGATGTGATTCTTATCGTATGAGAACG
*
41511498 TTAGCTAATCATAATGTTAGACAAAAATATTGTTAGGCTGGTTGATTTCTGATAAACATTACTTT
261 TTAGCTAATCATAATGTTAGACAAAAATATTGTTAGGCTGGTTGATTTCTAATAAACATTACTTT
41511563 GTCTTTCTTTAGCATTCTATTCCATTAAGTTTGGTAAAAAATTGAATGATAAAACTCATATGATG
326 GTCTTTCTTTAGCATTCTATTCCATTAAGTTTGGTAAAAAATTGAATGATAAAACTCATATGATG
* *
41511628 CTACTATTTTGTTTCTACTGGTTGTTGTTGTACTTTATATATATGCAAATTATGTTGTCTCTGTC
391 CTACTATTCTGTTTCTACTAGTTGTTGTTGTACTTTATATATATGCAAATTATGTTGTCTCTGTC
* *
41511693 ACAACTGATTCCAGTGCATATGAGTGATGTTTTTCTTCGGGATTTTCTTTGAGGAATCATCGAGC
456 ACAACTGATTCCAATGCATATGAGTGATGTTTTTCTTCGGAATTTTCTTTGAGGAATCATCGAGC
41511758 TCTTTATCATTCAATATGGGTTGTATTCTCAAAA
521 TCTTTATCATTCAATATGGGTTGTATTCTCAAAA
*
41511792 ATTTATTCAAGTATGGTATTTAAAGAACGTATTAACCAAAATTTCTGCTGAATTGATTTCTTTAG
1 ATTTATTCAAGTATGGTATTTAAAGAACGTATTAAACAAAATTTCTGCTGAATTGATTTCTTTAG
41511857 TGAATGGGATAATGTGGGATTGTTGGTGACTGTAGTAGCCAGTGGAATAATGTTTGAATTGCCAA
66 TGAATGGGATAATGTGGGATTGTTGGTGACTGTAGTAGCCAGTGGAATAATGTTTGAATTGCCAA
41511922 GATATCTAAATGCAGCGGTTATAGTTGAGTAGCTTACGGCGATCTCTTTTGAGTATTTTATATGT
131 GATATCTAAATGCAGCGGTTATAGTTGAGTAGCTTACGGCGATCTCTTTTGAGTATTTTATATGT
41511987 TCTTTTGTCCACAGAGGTATATGTAGTTGTTGATTGTCTGATGTGATTCTTATCGTATGAGAACG
196 TCTTTTGTCCACAGAGGTATATGTAGTTGTTGATTGTCTGATGTGATTCTTATCGTATGAGAACG
*
41512052 TTAGCTAATCATAATGTTAGACAAAAATATTGTTAGGCTGGTTGATTTCTAATAGACATTACTTT
261 TTAGCTAATCATAATGTTAGACAAAAATATTGTTAGGCTGGTTGATTTCTAATAAACATTACTTT
* *
41512117 TTCTTTCTTTAGCATTCTATTCCATTAAGTTTGGTAAAAAATTGGATGATAAAACTCATATGATG
326 GTCTTTCTTTAGCATTCTATTCCATTAAGTTTGGTAAAAAATTGAATGATAAAACTCATATGATG
41512182 CTACTATTCTGTTTCTACTAGTTGTTGTTGTACTTTATATATATGCAAATTATGTTGTCTCTGTC
391 CTACTATTCTGTTTCTACTAGTTGTTGTTGTACTTTATATATATGCAAATTATGTTGTCTCTGTC
41512247 ACAACTGATTCCAATGCATATGAGTGATGTTTTTCTTCGGAATTTTCTTTGAGGAATCATCGAGC
456 ACAACTGATTCCAATGCATATGAGTGATGTTTTTCTTCGGAATTTTCTTTGAGGAATCATCGAGC
41512312 TCTTTATCATTCAATATGGGTTGTATTCTCAAAA
521 TCTTTATCATTCAATATGGGTTGTATTCTCAAAA
41512346 ATTTA
1 ATTTA
41512351 GTATAGCTTC
Statistics
Matches: 549, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
554 549 1.00
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (554 bp):
ATTTATTCAAGTATGGTATTTAAAGAACGTATTAAACAAAATTTCTGCTGAATTGATTTCTTTAG
TGAATGGGATAATGTGGGATTGTTGGTGACTGTAGTAGCCAGTGGAATAATGTTTGAATTGCCAA
GATATCTAAATGCAGCGGTTATAGTTGAGTAGCTTACGGCGATCTCTTTTGAGTATTTTATATGT
TCTTTTGTCCACAGAGGTATATGTAGTTGTTGATTGTCTGATGTGATTCTTATCGTATGAGAACG
TTAGCTAATCATAATGTTAGACAAAAATATTGTTAGGCTGGTTGATTTCTAATAAACATTACTTT
GTCTTTCTTTAGCATTCTATTCCATTAAGTTTGGTAAAAAATTGAATGATAAAACTCATATGATG
CTACTATTCTGTTTCTACTAGTTGTTGTTGTACTTTATATATATGCAAATTATGTTGTCTCTGTC
ACAACTGATTCCAATGCATATGAGTGATGTTTTTCTTCGGAATTTTCTTTGAGGAATCATCGAGC
TCTTTATCATTCAATATGGGTTGTATTCTCAAAA
Found at i:41512883 original size:29 final size:29
Alignment explanation
Indices: 41512844--41512902 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
41512834 TAATCTCGAT
41512844 TTATGTCAACGAGTTAAAATAGGATGTTA
1 TTATGTCAACGAGTTAAAATAGGATGTTA
41512873 TTATGTCAACGAGTTAAAATAGGATGTTA
1 TTATGTCAACGAGTTAAAATAGGATGTTA
41512902 T
1 T
41512903 GTTTCGTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.36
Consensus pattern (29 bp):
TTATGTCAACGAGTTAAAATAGGATGTTA
Found at i:41514928 original size:29 final size:29
Alignment explanation
Indices: 41514882--41515039 Score: 165
Period size: 29 Copynumber: 5.4 Consensus size: 29
41514872 GATCATTGAG
* *
41514882 TATGAAAAAGGATAGCTTCGGGTATCGAA
1 TATGAAAAGGGATAGCTTCGGCTATCGAA
* * * *
41514911 TATGAAAAGGGATTGCTTCAGATATCGAT
1 TATGAAAAGGGATAGCTTCGGCTATCGAA
* * * *
41514940 TATGAAAAGGGAT-GGTGACGACTATCAAA
1 TATGAAAAGGGATAGCT-TCGGCTATCGAA
* *
41514969 TATGAAGAGGGATAGCTTCGACTATCGAA
1 TATGAAAAGGGATAGCTTCGGCTATCGAA
* *
41514998 TATGAAAAGGGATAGCTTCGGCTATTGAT
1 TATGAAAAGGGATAGCTTCGGCTATCGAA
*
41515027 TATGAAAAAGGAT
1 TATGAAAAGGGAT
41515040 GGTGACGACC
Statistics
Matches: 106, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
28 2 0.02
29 102 0.96
30 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (29 bp):
TATGAAAAGGGATAGCTTCGGCTATCGAA
Found at i:41515028 original size:87 final size:87
Alignment explanation
Indices: 41514882--41515048 Score: 253
Period size: 87 Copynumber: 1.9 Consensus size: 87
41514872 GATCATTGAG
** *
41514882 TATGAAAAAGGATAGCTTCGGGTATCGAATATGAAAAGGGATTGCTTCAGATATCGATTATGAAA
1 TATGAAAAAGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCAGATATCGATTATGAAA
*
41514947 AGGGATGGTGACGACTATCAAA
66 AAGGATGGTGACGACTATCAAA
* * * * *
41514969 TATGAAGAGGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCGGCTATTGATTATGAAA
1 TATGAAAAAGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCAGATATCGATTATGAAA
41515034 AAGGATGGTGACGAC
66 AAGGATGGTGACGAC
41515049 CATCGATTAA
Statistics
Matches: 71, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.25
Consensus pattern (87 bp):
TATGAAAAAGGATAGCTTCGACTATCGAATATGAAAAGGGATAGCTTCAGATATCGATTATGAAA
AAGGATGGTGACGACTATCAAA
Found at i:41515056 original size:29 final size:28
Alignment explanation
Indices: 41514904--41515072 Score: 133
Period size: 29 Copynumber: 5.8 Consensus size: 28
41514894 TAGCTTCGGG
* * *
41514904 TATCGAATATGAAAAGGGATTGCTTCAGA-
1 TATCGATTATGAAAAGGGA-TGGTAC-GAC
41514933 TATCGATTATGAAAAGGGATGGTGACGAC
1 TATCGATTATGAAAAGGGATGGT-ACGAC
* * * * *
41514962 TATCAAATATGAAGAGGGATAGCTTCGAC
1 TATCGATTATGAAAAGGGAT-GGTACGAC
* * * *
41514991 TATCGAATATGAAAAGGGATAGCTTCGGC
1 TATCGATTATGAAAAGGGAT-GGTACGAC
* *
41515020 TATTGATTATGAAAAAGGATGGTGACGAC
1 TATCGATTATGAAAAGGGATGGT-ACGAC
*
41515049 CATCGATTAATGAAAAGGGATGGT
1 TATCGATT-ATGAAAAGGGATGGT
41515073 TTCAACCATC
Statistics
Matches: 115, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
28 7 0.06
29 92 0.80
30 16 0.14
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (28 bp):
TATCGATTATGAAAAGGGATGGTACGAC
Found at i:41515081 original size:30 final size:29
Alignment explanation
Indices: 41515024--41515082 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
41515014 TTCGGCTATT
*
41515024 GATTATGAAAAAGGATGGTGACGACCATC
1 GATTATGAAAAAGGATGGTGACAACCATC
* **
41515053 GATTAATGAAAAGGGATGGTTTCAACCATC
1 GATT-ATGAAAAAGGATGGTGACAACCATC
41515083 AAATACGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.37, C:0.14, G:0.25, T:0.24
Consensus pattern (29 bp):
GATTATGAAAAAGGATGGTGACAACCATC
Found at i:41517778 original size:171 final size:169
Alignment explanation
Indices: 41517489--41517830 Score: 594
Period size: 171 Copynumber: 2.0 Consensus size: 169
41517479 TTATAATACA
*
41517489 TTATTCTTATAATTTTGATTAAGTTATATTTTGTTCAAAATTTGAATTTTTTTAATTATGCTAAA
1 TTATTCTTATAATTATGATTAAGTTATATTTTGTTCAAAATTTGAATTTTTTTAATTATGCTAAA
41517554 CTCTAGTATAAATAAAGTTTTAATATCTCAATAATTGCTATGTTAGCTGAACTATGACATAAATG
66 CTCTAGTATAAATAAAGTTTTAATATCTCAATAATTGCTATGTTAGCTGAACTATGACATAAATG
*
41517619 TTACTCTTAATAAAGTGTGTAAATCAAACCATAAAATTT
131 TTACTCTTAATAAAGTGTGAAAATCAAACCATAAAATTT
*
41517658 TTATTCTTCTAATTATGATTAAGTTATATTTTGTTCAAAAATTTGAATTTTTGTTAATTATGCTA
1 TTATTCTTATAATTATGATTAAGTTATATTTTGTTC-AAAATTTGAATTTTT-TTAATTATGCTA
* * ** *
41517723 AACTCTAGTATAAATAAAGTTTTATTATCTTAATAATTGCTATGTTATTTGAACTATGATATAAA
64 AACTCTAGTATAAATAAAGTTTTAATATCTCAATAATTGCTATGTTAGCTGAACTATGACATAAA
41517788 TGTTACTCTTAATAAAGTGTGAAAATCAAACCATAAAATTT
129 TGTTACTCTTAATAAAGTGTGAAAATCAAACCATAAAATTT
41517829 TT
1 TT
41517831 TAATTCCTTA
Statistics
Matches: 163, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
169 34 0.21
170 15 0.09
171 114 0.70
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (169 bp):
TTATTCTTATAATTATGATTAAGTTATATTTTGTTCAAAATTTGAATTTTTTTAATTATGCTAAA
CTCTAGTATAAATAAAGTTTTAATATCTCAATAATTGCTATGTTAGCTGAACTATGACATAAATG
TTACTCTTAATAAAGTGTGAAAATCAAACCATAAAATTT
Found at i:41537330 original size:25 final size:25
Alignment explanation
Indices: 41537302--41537387 Score: 111
Period size: 25 Copynumber: 3.4 Consensus size: 25
41537292 ATGTAGATCG
*
41537302 GTATGCTCTCGCGAGCTATAAATCC
1 GTATGCTCTCACGAGCTATAAATCC
* *
41537327 GTATGCTCTCATGAGCTATAAATCT
1 GTATGCTCTCACGAGCTATAAATCC
* *
41537352 GTATGCTCTCACGAGATATAAAT-T
1 GTATGCTCTCACGAGCTATAAATCC
41537376 GATATGCTCTCA
1 G-TATGCTCTCA
41537388 TGAGTTGTGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
24 2 0.04
25 53 0.96
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (25 bp):
GTATGCTCTCACGAGCTATAAATCC
Found at i:41537331 original size:50 final size:50
Alignment explanation
Indices: 41537288--41537391 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
41537278 TATGCTCATT
* * * *
41537288 TGAGATGTAGATCGGTATGCTCTCGCGAGCTATAAATCCGTATGCTCTCA
1 TGAGATATAAATCGGTATGCTCTCACGAGATATAAATCCGTATGCTCTCA
* * *
41537338 TGAGCTATAAATCTGTATGCTCTCACGAGATATAAAT-TGATATGCTCTCA
1 TGAGATATAAATCGGTATGCTCTCACGAGATATAAATCCG-TATGCTCTCA
41537388 TGAG
1 TGAG
41537392 TTGTGGAGTA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
49 1 0.02
50 45 0.98
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (50 bp):
TGAGATATAAATCGGTATGCTCTCACGAGATATAAATCCGTATGCTCTCA
Found at i:41539041 original size:35 final size:33
Alignment explanation
Indices: 41539000--41539064 Score: 103
Period size: 35 Copynumber: 1.9 Consensus size: 33
41538990 GAATTTTGCA
*
41539000 TATATATATGTTATATTAATAAATAATAAGAAATG
1 TATATATATGTTATATT-AT-AATAAAAAGAAATG
41539035 TATATATATGTTATATTATAATAAAAAGAA
1 TATATATATGTTATATTATAATAAAAAGAA
41539065 TTAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 10 0.34
34 2 0.07
35 17 0.59
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (33 bp):
TATATATATGTTATATTATAATAAAAAGAAATG
Found at i:41542690 original size:720 final size:715
Alignment explanation
Indices: 41541381--41542812 Score: 2490
Period size: 720 Copynumber: 2.0 Consensus size: 715
41541371 ATGTGTAAAT
*
41541381 GGCTAACACGTTTGGTGTAATGCTTAGGCTTTGGCCAAATTGTGATTGAAATATGCCATGTTAAC
1 GGCTAACACGTTTGGTGTAATGCTTAGGCTTTGGCCAAATTGTGATTGAAATATGCCATGTGAAC
*
41541446 TTACCTATTATTGGATTCAATGGTAAGTTGTGTTTTACATTATACGAACTAAGCATTTATGCTTA
66 TTACCTATTATTGGATTAAATGGTAAGTTGTGTTTTACATTATACGAACTAAGCATTTATGCTTA
* *
41541511 CACTATGTTATTTTCTATGTTTTATAGTGAATCGAAAGCTCGTTCGGGTTGGAAGCTTGTCAGGG
131 CACTATGTTATTTTCTATGTTTTATAATGAATCGAAAGCTCGTTCAGGTTGGAAGCTTGTCAGGG
*
41541576 TTATATCACACTATCCATCGGCTATATTGGTACTTTTGGATGTTTCTAAGTTTGGTTATAATGGC
196 TTATATCACACTATCCATCGACTATATTGGTACTTTTGGATGTTTCTAAGTTTGGTTATAATGGC
* * *
41541641 ATGTATAGGTATTTTGGTTGTTGAAGTAGCCATTTGTTTTGGCCAATATGTTTTGGCTTGAGAGT
261 ATGTATAGGTATTTTGGTTGTTGAAGTAGCCATTTGTTTTGGCCAATATGTTTTCGCTTAAGAAT
* * * *
41541706 TTGGTATTTAGAATGTTTGAAATGGTTGAATATATTGTTATATGCATGTGGCCTTATAATGGTTG
326 TTAGTATTTAGAATGTTTGAAATGGTTGAATATATTGTTATACGCATGTGGCCCTATAATGATTG
* *
41541771 AATTTATAGTTCGTGGATGCTTAGATGATGGATGAGAATATAGTCAGTTAGGTATGAAAGTGTAG
391 AATTTATAGTTCATGGATGCTTAGATGATGGATGAGAATATAGTCAGTTAGCTATGAAAGTGTAG
*
41541836 ATGGCATATATGAGTTATGATGTTATTTGGTAAATGGTAAATTTGGTATTTGTGGATGTGAATTT
456 ATGGCATATATGAGTTATGATGCTATTTGGTAAATGGTAAATTTGGTATTTGTGGATGTGAATTT
* *
41541901 GGTATGTGATCAAAGTGATAATTGTTGGTTAAATGATGCACATGGTTATATATATTTATATGTTG
521 GGTATGTGATCAAACTGATAACTGTTGGTTAAATGATGCACATGGTTATATATATTTATATGTTG
* *
41541966 TCATAGAGA-TGCCTTTGGGCATATGGGTTGTATGCAAATGTACCATATTTGGTTAGCTTGATTA
586 TCATAGAGACT-CCTCTGGGCATATGGGTTGTATGCAAATGTACCATATTCGGTTAGCTTGATTA
*
41542030 TGTATGGTTTTGGTGCATTTTGATGGCTTGTTGAATTGTGCAAAAATGATTATATGTACATGCTT
650 TGTATGGTTTTGATGCATTTTGATGGCTTGTTGAATTGTGCAAAAATGATTATATGTACATGCTT
41542095 A
715 A
*
41542096 GGCTAACATGTTTGGTGTACATGCTTAGGCTTTGGCCAAATTGTGATTGAAATATGCCATGTGAA
1 GGCTAACACGTTTGGTGTA-ATGCTTAGGCTTTGGCCAAATTGTGATTGAAATATGCCATGTGAA
41542161 CTTACCTATTATTGGATTAAATGGTAAGTTGTGTTTTACATTATACGAACTTACTAAGCATTTAT
65 CTTACCTATTATTGGATTAAATGGTAAGTTGTGTTTTACATTATACG-A---ACTAAGCATTTAT
* * *
41542226 GCTTACACTCTGTTATTTTTTGTGTTTTATAATGAATCGAAAGCTCGTTCAGGTTGGAAGCTTGT
126 GCTTACACTATGTTATTTTCTATGTTTTATAATGAATCGAAAGCTCGTTCAGGTTGGAAGCTTGT
**
41542291 CAGGGTTATATCACACTATCTTTCGACTATATTGGTACTTTTGGATGTTTCTAAGTTTGGTTATA
191 CAGGGTTATATCACACTATCCATCGACTATATTGGTACTTTTGGATGTTTCTAAGTTTGGTTATA
*
41542356 ATGGCATGTATAGGTATTTTGGTTGTTGAAGTAGCCGTTTGTTTTGGCCAATATGTTTTCGCTTA
256 ATGGCATGTATAGGTATTTTGGTTGTTGAAGTAGCCATTTGTTTTGGCCAATATGTTTTCGCTTA
41542421 AGAATTTAGTATTTAGAATGTTTGAAATGGTTGAATATATTGTTATACGCATGTGGCCCTATAAT
321 AGAATTTAGTATTTAGAATGTTTGAAATGGTTGAATATATTGTTATACGCATGTGGCCCTATAAT
* * *
41542486 GATTGATTTTATAGTTCATGGATGCTTAGATGATGGATGAGAATATAGTCATTTTGCTATGAAAG
386 GATTGAATTTATAGTTCATGGATGCTTAGATGATGGATGAGAATATAGTCAGTTAGCTATGAAAG
41542551 TGTAGATGGCATATATGAGTTATGATGCTATTTGGTAAATGGTAAATTTGGTATTTGTGGATGTG
451 TGTAGATGGCATATATGAGTTATGATGCTATTTGGTAAATGGTAAATTTGGTATTTGTGGATGTG
*
41542616 AATTTGGTATGTGATCAAACTGATAACTGTTGGTTAAATGATGCACATGGTTATATATGTTTATA
516 AATTTGGTATGTGATCAAACTGATAACTGTTGGTTAAATGATGCACATGGTTATATATATTTATA
*
41542681 TAG-TGTCATAGAGACTCCTCTGGGCATATTGGTTGTATGCAAATGTACCATATTCGGTTAGCTT
581 T-GTTGTCATAGAGACTCCTCTGGGCATATGGGTTGTATGCAAATGTACCATATTCGGTTAGCTT
*
41542745 GATTATGTATGGTTTTGATGCATTTTGATGGCTTGTTGAATTGTGCAAAAATGGTTATATGTACA
645 GATTATGTATGGTTTTGATGCATTTTGATGGCTTGTTGAATTGTGCAAAAATGATTATATGTACA
41542810 TGC
710 TGC
41542813 ATGAAGGGTG
Statistics
Matches: 677, Mismatches: 33, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
715 18 0.03
716 90 0.13
717 1 0.00
720 566 0.84
721 2 0.00
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (715 bp):
GGCTAACACGTTTGGTGTAATGCTTAGGCTTTGGCCAAATTGTGATTGAAATATGCCATGTGAAC
TTACCTATTATTGGATTAAATGGTAAGTTGTGTTTTACATTATACGAACTAAGCATTTATGCTTA
CACTATGTTATTTTCTATGTTTTATAATGAATCGAAAGCTCGTTCAGGTTGGAAGCTTGTCAGGG
TTATATCACACTATCCATCGACTATATTGGTACTTTTGGATGTTTCTAAGTTTGGTTATAATGGC
ATGTATAGGTATTTTGGTTGTTGAAGTAGCCATTTGTTTTGGCCAATATGTTTTCGCTTAAGAAT
TTAGTATTTAGAATGTTTGAAATGGTTGAATATATTGTTATACGCATGTGGCCCTATAATGATTG
AATTTATAGTTCATGGATGCTTAGATGATGGATGAGAATATAGTCAGTTAGCTATGAAAGTGTAG
ATGGCATATATGAGTTATGATGCTATTTGGTAAATGGTAAATTTGGTATTTGTGGATGTGAATTT
GGTATGTGATCAAACTGATAACTGTTGGTTAAATGATGCACATGGTTATATATATTTATATGTTG
TCATAGAGACTCCTCTGGGCATATGGGTTGTATGCAAATGTACCATATTCGGTTAGCTTGATTAT
GTATGGTTTTGATGCATTTTGATGGCTTGTTGAATTGTGCAAAAATGATTATATGTACATGCTTA
Found at i:41542926 original size:13 final size:13
Alignment explanation
Indices: 41542908--41542932 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41542898 AGAGCCTGTA
41542908 TCTTAGCCGTGTC
1 TCTTAGCCGTGTC
41542921 TCTTAGCCGTGT
1 TCTTAGCCGTGT
41542933 GACCCTGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.28, G:0.24, T:0.40
Consensus pattern (13 bp):
TCTTAGCCGTGTC
Found at i:41549681 original size:56 final size:51
Alignment explanation
Indices: 41549593--41549776 Score: 226
Period size: 51 Copynumber: 3.5 Consensus size: 51
41549583 GATGAGATCT
* *
41549593 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGTTGAGATTATAAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCATC---GAGATGA-AAG-GGTCC
* *
41549649 CATGTAAGACCATGTCAGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAAAGGGTCC
* * *
41549700 CATTTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGA-GGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAAAGGGTCC
** *
41549750 CCCGTAAGACCATGTCTAGGACATGGC
1 CATGTAAGACCATGTCTGGGACATGGC
41549777 ATGGACACCT
Statistics
Matches: 117, Mismatches: 11, Indels: 6
0.87 0.08 0.04
Matches are distributed among these distances:
50 28 0.24
51 47 0.40
52 2 0.02
53 6 0.05
56 34 0.29
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (51 bp):
CATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAAAGGGTCC
Found at i:41549721 original size:51 final size:51
Alignment explanation
Indices: 41549593--41549833 Score: 236
Period size: 50 Copynumber: 4.7 Consensus size: 51
41549583 GATGAGATCT
* * *
41549593 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGTTGAGATTATAAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCATC---GAGATGA-GAG-GGTCC
*
41549649 CATGTAAGACCATGTCAGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
* *
41549700 CATTTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGA-GGTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
** * * * * * **
41549750 CCCGTAAGACCATGTCTAGGACATGGC-ATGGACACCTATATGAGA-ACTCC
1 CATGTAAGACCATGTCTGGGACATGGCGTTGG-CATCGAGATGAGAGGGTCC
* * * *
41549800 CATGTAAGACCATATCTTGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCGTTGGCA
41549834 GTACAAGAAA
Statistics
Matches: 161, Mismatches: 22, Indels: 10
0.83 0.11 0.05
Matches are distributed among these distances:
49 3 0.02
50 66 0.41
51 50 0.31
52 2 0.01
53 6 0.04
56 34 0.21
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (51 bp):
CATGTAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
Found at i:41549772 original size:50 final size:50
Alignment explanation
Indices: 41549593--41549882 Score: 228
Period size: 50 Copynumber: 5.7 Consensus size: 50
41549583 GATGAGATCT
* * * *
41549593 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGTTGAGATTATAAGAGGTCC
1 CATGTAAGACCATGTCTAGGACATGGCGTTGGCA-C--CGAG---ATGAGAGGTCC
*
41549649 CATGTAAGACCATGTC-AGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
1 CATGTAAGACCATGTCTA-GGACATGGCGTTGGCACCGAGATGAGA-GGTCC
* *
41549700 CATTTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCC
** * * * **
41549750 CCCGTAAGACCATGTCTAGGACATGGC-ATGGACACCTATATGAGAACTCC
1 CATGTAAGACCATGTCTAGGACATGGCGTTGG-CACCGAGATGAGAGGTCC
* * * * * * * **
41549800 CATGTAAGACCATATCTTGGATATGGCATTGGCA--GTACAAGAAACATCC
1 CATGTAAGACCATGTCTAGGACATGGCGTTGGCACCG-AGATGAGAGGTCC
* * *
41549849 CATGTAAGACTATGTCTAGGACATAGCTTTGGCA
1 CATGTAAGACCATGTCTAGGACATGGCGTTGGCA
41549883 TGTTATATTC
Statistics
Matches: 193, Mismatches: 35, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
49 39 0.20
50 71 0.37
51 49 0.25
53 3 0.02
56 31 0.16
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (50 bp):
CATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCC
Found at i:41549793 original size:101 final size:103
Alignment explanation
Indices: 41549593--41549833 Score: 258
Period size: 101 Copynumber: 2.3 Consensus size: 103
41549583 GATGAGATCT
* *
41549593 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGTTGAGATTATAAGAGGTCCCATGTAAGA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCG-CGAG--TATAAGAGGTCCCACGTAAGA
* * **
41549658 CCATGTCAGGGACATGGCGTTGGCATCGAGATGAGAGGGTCC
63 CCATGTCAGGGACATGGCGATGGCACCGAGATGAGA-ACTCC
* * * *
41549700 CATTTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGAG-ATGAGAGGTCCCCCGTAAGACCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGCGAGTATAAGAGGTCCCACGTAAGACCA
* *
41549762 TGTCTA-GGACATGGC-ATGGACACCTATATGAGAACTCC
66 TGTC-AGGGACATGGCGATGG-CACCGAGATGAGAACTCC
* * *
41549800 CATGTAAGACCATATCTTGGATATGGCATTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
41549834 GTACAAGAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
100 35 0.30
101 43 0.37
102 1 0.01
104 3 0.03
106 1 0.01
107 32 0.28
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (103 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCATCGCGAGTATAAGAGGTCCCACGTAAGACCA
TGTCAGGGACATGGCGATGGCACCGAGATGAGAACTCC
Found at i:41556036 original size:50 final size:49
Alignment explanation
Indices: 41555936--41556226 Score: 285
Period size: 50 Copynumber: 5.7 Consensus size: 49
41555926 GGATGAGATC
** *
41555936 CCATGTAAGACCATGTCTGGGTTATGGCATTGGCATCATTGAGATTATGAGAGGT
1 CCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGGT
*
41555991 CTCATGTAAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGGT
1 C-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
** *
41556041 CCTATGTAAGACCATGTCTGGGACATGGCGCTGGCACCGAGATAAGAGGT
1 CC-ATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * *
41556091 CCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACTGAGATGAGAGGT
1 -CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
** * * * * **
41556141 CCCCCGTATGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACT
1 -CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
* * * *
41556191 CCAATGTAAGACCATATCTAGGATATGACATTGGCA
1 CC-ATGTAAGACCATGTCTGGGACATGGCATTGGCA
41556227 GTACAAGAAA
Statistics
Matches: 201, Mismatches: 31, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
49 3 0.01
50 160 0.80
51 2 0.01
53 3 0.01
55 2 0.01
56 31 0.15
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.24
Consensus pattern (49 bp):
CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGT
Found at i:41556226 original size:150 final size:151
Alignment explanation
Indices: 41555933--41556276 Score: 354
Period size: 150 Copynumber: 2.3 Consensus size: 151
41555923 AGAGGATGAG
* ** * *
41555933 ATCCCATGTAAGACCATGTCTGGGTTATGGCATTGGCATCATTGAGATTATGAGAGGTCTCATGT
1 ATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCA-TGAG--TATGAGAGGTCCCACGT
* ** * * *
41555998 AAGACCATGTCTGAGACATGGCATTGGCACCGAGATGAGAGGTCCTATGTAAGACCATGTCTGGG
63 AAGACCATGTCTGAGACATGGCATGGGCACCGAGATGAGAACTCCAATGTAAGACCATATCTAGG
* * * * *
41556063 ACATGGCGCTGGCA-CCGAGATAAG
128 ACATGACACTGGCAGACAAGA-AAC
* *
41556087 AGGTCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCA-C-TGAG-ATGAGAGGTCCCCCGTA
1 A--TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATGAGTATGAGAGGTCCCACGTA
* * * *
41556149 TGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAACTCCAATGTAAGACCATATCTAGGA
64 AGACCATGTCTGAGACATGGCATGGGCACCGAGATGAGAACTCCAATGTAAGACCATATCTAGGA
* *
41556214 TATGACATTGGCAGTACAAGAAAC
129 CATGACACTGGCAG-ACAAGAAAC
* * *
41556238 ATCCCATGTAAGACTATGTCTAGGACATAGCTTTGGCAT
1 ATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCAT
41556277 GTTATGTTCA
Statistics
Matches: 158, Mismatches: 27, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
149 34 0.22
150 78 0.49
151 3 0.02
152 4 0.03
153 4 0.03
154 1 0.01
155 1 0.01
156 33 0.21
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (151 bp):
ATCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATGAGTATGAGAGGTCCCACGTAAG
ACCATGTCTGAGACATGGCATGGGCACCGAGATGAGAACTCCAATGTAAGACCATATCTAGGACA
TGACACTGGCAGACAAGAAAC
Found at i:41560477 original size:26 final size:26
Alignment explanation
Indices: 41560434--41560483 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
41560424 AAATGTGAAC
*
41560434 GGGGTTGCTAAGTGCTGATTCCCCAA
1 GGGGTTGCTAAGTCCTGATTCCCCAA
**
41560460 GGGGTTGCTGTGTCCTGATTCCCC
1 GGGGTTGCTAAGTCCTGATTCCCC
41560484 GATTCATTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.12, C:0.26, G:0.32, T:0.30
Consensus pattern (26 bp):
GGGGTTGCTAAGTCCTGATTCCCCAA
Found at i:41560532 original size:101 final size:100
Alignment explanation
Indices: 41560357--41560719 Score: 548
Period size: 101 Copynumber: 3.6 Consensus size: 100
41560347 ATTGCATATA
* *
41560357 AAGGGGTTCCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
41560422 TAAAATGTGAACGGGGTTGCTAAGTGCTGATTCCCC
66 TAAAATGTGAA-GGGGTTGCTAAGTGCTGATTCCCC
* * *
41560458 AAGGGGTTGCTGTGTCCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
41560523 TTAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCC
* ** * *
41560558 GAGGGGTTGCTAAGTGCTAATT-CCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
* *
41560622 TGAAATGTGAAGGGGGTTGATAAGTGCTGATTCGCCC
66 TAAAATGTGAA-GGGGTTGCTAAGTGCTGATTC-CCC
* * *
41560659 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGATGGTTGCTAAGTGCGGAATCCACCG
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
41560720 ATAATGGTTA
Statistics
Matches: 235, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
99 49 0.21
100 61 0.26
101 91 0.39
102 34 0.14
ACGTcount: A:0.19, C:0.20, G:0.29, T:0.32
Consensus pattern (100 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TAAAATGTGAAGGGGTTGCTAAGTGCTGATTCCCC
Found at i:41560569 original size:26 final size:26
Alignment explanation
Indices: 41560533--41560582 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
41560523 TTAAATGTGA
*
41560533 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTAATTCCCCG
41560559 AGGGGTTGCTAAGTGCTAATTCCC
1 AGGGGTTGCTAAGTGCTAATTCCC
41560583 TATTCATTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.32, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTAATTCCCCG
Found at i:41572594 original size:4 final size:4
Alignment explanation
Indices: 41572585--41572618 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
41572575 TTAATTACAT
* *
41572585 TAAA TAAA TAAA TAAT TAAA TAAA TAAA AAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
41572619 TGTTTTTGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:41573578 original size:3 final size:3
Alignment explanation
Indices: 41573570--41573622 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
41573560 GTCATTTTAC
*
41573570 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41573618 TAT TA
1 TAT TA
41573623 CCATTGATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:41573800 original size:22 final size:21
Alignment explanation
Indices: 41573769--41573829 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 21
41573759 TATTTGGTTT
41573769 TGTTTCTTTTTATTAGTTTTTAC
1 TGTTT-TTTTTA-TAGTTTTTAC
41573792 T-TTTATTTTTAT-GTTTTTAC
1 TGTTT-TTTTTATAGTTTTTAC
*
41573812 TGTTTTTATTACTAGTTT
1 TGTTTTTTTTA-TAGTTT
41573830 AGTTATTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
20 14 0.42
21 5 0.15
22 13 0.39
23 1 0.03
ACGTcount: A:0.15, C:0.07, G:0.08, T:0.70
Consensus pattern (21 bp):
TGTTTTTTTTATAGTTTTTAC
Found at i:41576592 original size:79 final size:81
Alignment explanation
Indices: 41576492--41576676 Score: 218
Period size: 79 Copynumber: 2.3 Consensus size: 81
41576482 GCTCCTCGTT
* * *
41576492 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAATTGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
41576555 AGATTTAGTAAC-TCGCA
64 AGATATAGTAACTTAGCA
* ** *
41576572 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCAG
* *
41576636 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
41576652 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41576677 CATCATTCAA
Statistics
Matches: 90, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
78 3 0.03
79 53 0.59
80 34 0.38
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCAG
ATATAGTAACTTAGCA
Found at i:41576676 original size:40 final size:40
Alignment explanation
Indices: 41576492--41576676 Score: 216
Period size: 40 Copynumber: 4.7 Consensus size: 40
41576482 GCTCCTCGTT
* *
41576492 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * * *
41576532 CAATTGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
41576572 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
41576611 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
41576652 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41576677 CATCATTCAA
Statistics
Matches: 122, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
38 2 0.02
39 31 0.25
40 77 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41579411 original size:27 final size:27
Alignment explanation
Indices: 41579372--41579549 Score: 160
Period size: 27 Copynumber: 6.6 Consensus size: 27
41579362 ATGTTGAGCC
* *
41579372 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
41579399 CACACACTTAGTGCTACGTAATAAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41579426 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
41579454 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
41579481 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* * *
41579508 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41579535 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
41579550 GTACAATTTA
Statistics
Matches: 124, Mismatches: 24, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 24 0.19
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41579532 original size:54 final size:55
Alignment explanation
Indices: 41579372--41579549 Score: 182
Period size: 54 Copynumber: 3.3 Consensus size: 55
41579362 ATGTTGAGCC
* * * * * * * *
41579372 CGCACACTCAGTGCTATATAATC-AACTCACACACTTAGTGCTACGTAATAAAAT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
** * *
41579426 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
* **
41579481 CGCACACTTAGTGC-ATCATATTC-ATTTCGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTA-CATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
*
41579535 CGCACCCTTAGTGCT
1 CGCACACTTAGTGCT
41579550 GTACAATTTA
Statistics
Matches: 102, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
54 59 0.58
55 43 0.42
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (55 bp):
CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:41587376 original size:27 final size:27
Alignment explanation
Indices: 41587346--41587523 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
41587336 ATATTGAGCC
* *
41587346 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
41587373 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
41587400 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
41587428 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
41587455 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
41587482 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
41587509 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41587524 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:41587485 original size:82 final size:81
Alignment explanation
Indices: 41587367--41587522 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
41587357 TGCTATATAA
* *
41587367 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
41587432 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
41587449 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
41587513 CACTTAGTGC
65 CACTTAGTGC
41587523 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:41595352 original size:27 final size:27
Alignment explanation
Indices: 41595322--41595498 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
41595312 ATATTGAGCC
* * *
41595322 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAACT
* * *
41595349 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAACT
41595376 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTC-AACT
** * *
41595404 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAACT
* **
41595431 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAACT
*
41595458 CGCACACTTAGTGCAACATAGTCAA-T
1 CGCACACTTAGTGCTACATAGTCAACT
41595484 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41595499 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 7
0.84 0.12 0.05
Matches are distributed among these distances:
26 15 0.12
27 90 0.70
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAACT
Found at i:41595414 original size:55 final size:54
Alignment explanation
Indices: 41595322--41595498 Score: 205
Period size: 55 Copynumber: 3.3 Consensus size: 54
41595312 ATATTGAGCC
* * * * *
41595322 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
* ** * *
41595376 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCAACATAGTCAAAT
* **
41595431 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTC-AAT
1 CGCACACTTAGTGCTA-CATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
41595484 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
41595499 GTACAATTTA
Statistics
Matches: 104, Mismatches: 16, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
53 16 0.15
54 43 0.41
55 45 0.43
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCAACATAGTCAAAT
Found at i:41595461 original size:82 final size:80
Alignment explanation
Indices: 41595343--41595497 Score: 222
Period size: 82 Copynumber: 1.9 Consensus size: 80
41595333 TGCTATATAA
* *
41595343 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTC-AA-TCGCA
41595408 CACTTAGTGCCGCATGG
64 CACTTAGTGCCGCATGG
* * **
41595425 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAATCGCAC
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAATCGCAC
41595489 ACTTAGTGC
65 ACTTAGTGC
41595498 TGTACAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
80 15 0.23
81 3 0.05
82 48 0.73
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (80 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAATCGCACA
CTTAGTGCCGCATGG
Found at i:41603994 original size:13 final size:13
Alignment explanation
Indices: 41603978--41604043 Score: 71
Period size: 13 Copynumber: 5.1 Consensus size: 13
41603968 TTTAAACCAA
41603978 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
41603991 ACTTCTCAAAATC
1 ACTTTTCAAAAGC
*
41604004 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
**
41604017 ACTTTTCAAAAAT
1 ACTTTTCAAAAGC
41604030 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
41604043 A
1 A
41604044 ATGAAGAACT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
12 4 0.09
13 35 0.81
14 4 0.09
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41615334 original size:15 final size:15
Alignment explanation
Indices: 41615309--41615341 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41615299 ATCAATTGAA
41615309 AAAATCATAGAAAATG
1 AAAATCATAGAAAA-G
41615325 AAAA-CATAGAAAAG
1 AAAATCATAGAAAAG
41615339 AAA
1 AAA
41615342 GAAAGACCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 9 0.53
16 4 0.24
ACGTcount: A:0.70, C:0.06, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAATCATAGAAAAG
Found at i:41615735 original size:13 final size:14
Alignment explanation
Indices: 41615719--41615751 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
41615709 TGGGTTCGAA
41615719 TTTGATA-AATTTT
1 TTTGATATAATTTT
41615732 TTTGA-ATAATTTT
1 TTTGATATAATTTT
41615745 TTTGATA
1 TTTGATA
41615752 GATAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.06
13 16 0.89
14 1 0.06
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (14 bp):
TTTGATATAATTTT
Found at i:41618357 original size:113 final size:111
Alignment explanation
Indices: 41618190--41618647 Score: 372
Period size: 113 Copynumber: 4.0 Consensus size: 111
41618180 AGAATAAGAA
* * * * * *
41618190 TTAGTGGCGTTTTAT-AGAAAGCGCCGCAAAAAACCTAATCCGAACGACGTCGTTTGCCGAGCTT
1 TTAGCGGCGTTTT-TGAAAAAGCACCGCAAAAAACCTAATCCCAACGA-GCCGTTT-CTGAGCTT
* *
41618254 TCGGGGATTTAGCGGCGTTTCTAATAAAGAGCCGTTAATGCTCAGGGAT
63 TCGGGGATTTAGCGGCGTTTCTAATAAAGCGCCGCTAATGCTCAGGGAT
* ** * * *
41618303 TTAGCGACGTTTTTGAGTAAGCATCGTAAAAAGCCTAATCCCAACGATGCCGTTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAAAAAGCACCGCAAAAAACCTAATCCCAACGA-GCCG--TTTCTGAGCTT
* * * * * * *
41618368 TCGAGTGA-TTAGTGGCGTTTTTAGTAAAGCGCCGCTAATTCTTAGGGCT
63 TCG-GGGATTTAGCGGCGTTTCTAATAAAGCGCCGCTAATGCTCAGGGAT
* *
41618417 TTAGCGGCGTTTTTGAAAAAGCGCCGCAAAAAACCTAAGT-ACAACG-GCAGCGTTTCTGAGCTT
1 TTAGCGGCGTTTTTGAAAAAGCACCGCAAAAAACCTAA-TCCCAACGAGC--CGTTTCTGAGC-T
* *
41618480 TTCGGGAATTTAGCGGCGTTTCTAGA-GAAGCGCCGCTAATGCTCAGGGAT
62 TTCGGGGATTTAGCGGCGTTTCTA-ATAAAGCGCCGCTAATGCTCAGGGAT
* ** * * * * * *
41618530 TTAGTGGCGTTTTTGGTATAGCGCCGCAAAAAAAAACTAAGCCCAACGTCGTCGTTTTCT-ATGC
1 TTAGCGGCGTTTTTGAAAAAGCACCGC--AAAAAACCTAATCCCAACG-AGCCG-TTTCTGA-GC
* * *
41618594 TTTCAGGGATTTAGCGGTGTTTTTAGA-AAAGCGCCGCTAATGCTCAGGGAT
61 TTTCGGGGATTTAGCGGCGTTTCTA-ATAAAGCGCCGCTAATGCTCAGGGAT
41618645 TTA
1 TTA
41618648 AAATAATTTA
Statistics
Matches: 278, Mismatches: 50, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
112 14 0.05
113 101 0.36
114 81 0.29
115 74 0.27
116 7 0.03
117 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (111 bp):
TTAGCGGCGTTTTTGAAAAAGCACCGCAAAAAACCTAATCCCAACGAGCCGTTTCTGAGCTTTCG
GGGATTTAGCGGCGTTTCTAATAAAGCGCCGCTAATGCTCAGGGAT
Found at i:41618428 original size:114 final size:113
Alignment explanation
Indices: 41618217--41618647 Score: 329
Period size: 114 Copynumber: 3.8 Consensus size: 113
41618207 AAAGCGCCGC
* *
41618217 AAAAAACCTAATCCGAACGACGTCGTTTGCCGAGCTTTCGGGGATTTAGCGGCGTTTCTAATAAA
1 AAAAAACCTAATCCCAACGACGCCGTTTGCCGAGCTTTCGGGGATTTAGCGGCGTTTCTAATAAA
*
41618282 GAGCCGTTAATGCTCAGGGATTTAGCGACGTTTTTGAGTAAGCATCGT
66 GAGCCGCTAATGCTCAGGGATTTAGCGACGTTTTTGAGTAAGCATCGT
* * * * * * * *
41618330 AAAAAGCCTAATCCCAACGATGCCGTTTTTCTGAGCTTTCGAGTGA-TTAGTGGCGTTTTTAGTA
1 AAAAAACCTAATCCCAACGACGCCG-TTTGCCGAGCTTTCG-GGGATTTAGCGGCGTTTCTAATA
* * * * * ** ** *
41618394 AAGCGCCGCTAATTCTTAGGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
64 AAGAGCCGCTAATGCTCAGGGATTTAGCGACGTTTTTGAGTAAGCATCGT
* * * *
41618444 AAAAAACCTAAGT-ACAACGGCAG-CGTTT-CTGAGCTTTTCGGGAATTTAGCGGCGTTTCTAGA
1 AAAAAACCTAA-TCCCAACGAC-GCCGTTTGCCGAGC-TTTCGGGGATTTAGCGGCGTTTCTA-A
* * * * ** *
41618506 -GAAGCGCCGCTAATGCTCAGGGATTTAGTGGCGTTTTTG-GTATAGCGCCGCAA
62 TAAAGAGCCGCTAATGCTCAGGGATTTAGCGACGTTTTTGAGTA-AGCATCG--T
* * * * * * * * *
41618559 AAAAAAACTAAGCCCAACGTCGTCGTTT-TCTATGCTTTCAGGGATTTAGCGGTGTTTTTAGA-A
1 AAAAAACCTAATCCCAACGACGCCGTTTGCCGA-GCTTTCGGGGATTTAGCGGCGTTTCTA-ATA
*
41618622 AAGCGCCGCTAATGCTCAGGGATTTA
64 AAGAGCCGCTAATGCTCAGGGATTTA
41618648 AAATAATTTA
Statistics
Matches: 255, Mismatches: 50, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
112 9 0.04
113 83 0.33
114 85 0.33
115 76 0.30
116 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (113 bp):
AAAAAACCTAATCCCAACGACGCCGTTTGCCGAGCTTTCGGGGATTTAGCGGCGTTTCTAATAAA
GAGCCGCTAATGCTCAGGGATTTAGCGACGTTTTTGAGTAAGCATCGT
Found at i:41619293 original size:39 final size:40
Alignment explanation
Indices: 41619238--41619318 Score: 110
Period size: 39 Copynumber: 2.0 Consensus size: 40
41619228 TAATAAAACT
* *
41619238 TTTAGGGGTTACGCTTTAGGGGTT-TAGGAGATTTAGGGG
1 TTTAGGGGTTACGCTTTAAGGGTTAAAGGAGATTTAGGGG
* * *
41619277 TTTAGGGTTTATGCTTTAAGGGTTAAAGGGGATTTAGGGG
1 TTTAGGGGTTACGCTTTAAGGGTTAAAGGAGATTTAGGGG
41619317 TT
1 TT
41619319 GTGGGTTAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 21 0.58
40 15 0.42
ACGTcount: A:0.20, C:0.04, G:0.38, T:0.38
Consensus pattern (40 bp):
TTTAGGGGTTACGCTTTAAGGGTTAAAGGAGATTTAGGGG
Found at i:41620082 original size:39 final size:40
Alignment explanation
Indices: 41620028--41620116 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 40
41620018 AATAAAATTT
*
41620028 TTTAGGGGTTATGCTTTAGGGGTTAA-GGAGATTTAGGGG
1 TTTAGGGGTTATGCTTTAAGGGTTAAGGGAGATTTAGGGG
* *
41620067 TTTAGGGTTTATGCTTTAAGGGTTAAGGGGGATTTAGGGG
1 TTTAGGGGTTATGCTTTAAGGGTTAAGGGAGATTTAGGGG
*
41620107 -TTATGGGTTA
1 TTTAGGGGTTA
41620117 GGAATTTGGG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
39 32 0.73
40 12 0.27
ACGTcount: A:0.20, C:0.02, G:0.39, T:0.38
Consensus pattern (40 bp):
TTTAGGGGTTATGCTTTAAGGGTTAAGGGAGATTTAGGGG
Found at i:41620708 original size:789 final size:789
Alignment explanation
Indices: 41619189--41620770 Score: 2914
Period size: 789 Copynumber: 2.0 Consensus size: 789
41619179 TATTTTTAAA
41619189 TAATATTTATTTACGTAAAATTTAAATAGTAAAATTATATAATAAAACTTTTAGGGGTTACGCTT
1 TAATATTTATTTACGTAAAATTTAAATAGTAAAATTATATAATAAAACTTTTAGGGGTTACGCTT
*
41619254 TAGGGGTTTAGGAGATTTAGGGGTTTAGGGTTTATGCTTTAAGGGTTAAAGGGGATTTAGGGGTT
66 TAGGGGTTAAGGAGATTTAGGGGTTTAGGGTTTATGCTTTAAGGGTTAAAGGGGATTTAGGGGTT
*
41619319 GTGGGTTAGGAATTTGGGAATTAGGGGTTATTAATTTTTATATTAAATACTTTTAAATATTACTT
131 ATGGGTTAGGAATTTGGGAATTAGGGGTTATTAATTTTTATATTAAATACTTTTAAATATTACTT
41619384 AAAATTTTAATAATTATTTATGTAAAATTTAAATTAAATATACAATAGATAAATAAATAAATAAT
196 AAAATTTTAATAATTATTTATGTAAAATTTAAATTAAATATACAATAGATAAATAAATAAATAAT
*
41619449 AAAATTTATTCAAATTTTAGCAAATATTTACTGCATTTTTATTTGTGGCATTTTTCGAAAAACGC
261 AAAATTTATTCAAATTTTAGCAAATATTAACTGCATTTTTATTTGTGGCATTTTTCGAAAAACGC
* *
41619514 CGTAAATTATCTTTAAACTGGAAAACGGCATTGTTTCAGCAAATATATTTGTGGCGTTTTTTATG
326 CGTAAATTATCTTTAAACTGGAAAACAGCATTGTTTCAGCAAATACATTTGTGGCGTTTTTTATG
*
41619579 AAAACGCTAGAAAATTTACTTATATTTTAACAAAACGGCACCGTCTCTCTCTGTACATGAAATTT
391 AAAACGCTAGAAAATTTACTTATATTTTAACAAAACAGCACCGTCTCTCTCTGTACATGAAATTT
41619644 TAGTGGCGTTTTTTACTAAAACGCCGCAAATATGGATACAATATCCGCAAATACTTATAAATAAA
456 TAGTGGCGTTTTTTACTAAAACGCCGCAAATATGGATACAATATCCGCAAATACTTATAAATAAA
*
41619709 GTAAATATTTAGTGGCGTTTCTATGGAAAACGCCGCAAATAATATTTGAAAAATTGAATAAAACG
521 GTAAATATTTAGTGGCGTTTCTATGAAAAACGCCGCAAATAATATTTGAAAAATTGAATAAAACG
41619774 GAGCCGTTTCATTGACGAGTTCAATTGACCCTCAAAATTTGTAAAATTTGTGGCGTTTTCTTTAA
586 GAGCCGTTTCATTGACGAGTTCAATTGACCCTCAAAATTTGTAAAATTTGTGGCGTTTTCTTTAA
*
41619839 GCGGCGCTTCATGAAATGAAATTATACCGGCATATCTCCATCAACCCAATTTAACTTAAAAATAG
651 GCGGCGCTTCATGAAATGAAATTATAACGGCATATCTCCATCAACCCAATTTAACTTAAAAATAG
41619904 AGCATAAATTTAAAATTGTAATACATTATTTGAATAATATCAATAATTTATAAATTCGAATGTTG
716 AGCATAAATTTAAAATTGTAATACATTATTTGAATAATATCAATAATTTATAAATTCGAATGTTG
41619969 ATAAAATTT
781 ATAAAATTT
* * *
41619978 TAATATTTATTTATGTAAAATTTAAATAGTAAAATTATATAATAAAATTTTTTAGGGGTTATGCT
1 TAATATTTATTTACGTAAAATTTAAATAGTAAAATTATATAATAAAA-CTTTTAGGGGTTACGCT
*
41620043 TTAGGGGTTAAGGAGATTTAGGGGTTTAGGGTTTATGCTTTAAGGGTTAAGGGGGATTTAGGGGT
65 TTAGGGGTTAAGGAGATTTAGGGGTTTAGGGTTTATGCTTTAAGGGTTAAAGGGGATTTAGGGGT
41620108 TATGGGTTAGGAATTTGGGAATTAGGGGTTATTAATTTTTATATTAAATACTTTTAAATATTACT
130 TATGGGTTAGGAATTTGGGAATTAGGGGTTATTAATTTTTATATTAAATACTTTTAAATATTACT
41620173 TAAAATTTTAATAATTATTTATGTAAAATTTAAATTAAATATACAATAGATAAATAAATAAATAA
195 TAAAATTTTAATAATTATTTATGTAAAATTTAAATTAAATATACAATAGATAAATAAATAAATAA
* *
41620238 TAAAATTTATTCAAATTTTAGCAAATATTAATTGCATTTTTATTTGTGGCGTTTTTCGAAAAACG
260 TAAAATTTATTCAAATTTTAGCAAATATTAACTGCATTTTTATTTGTGGCATTTTTCGAAAAACG
* **
41620303 CCGTAAATTATCTTTAAACTGGAAAACAGCGTTGTTTCAGTTAAT-CATTTGTGGCGTTTTTTAT
325 CCGTAAATTATCTTTAAACTGGAAAACAGCATTGTTTCAGCAAATACATTTGTGGCGTTTTTTAT
* * *
41620367 GAAAACGCTAGAAAATTTACTTATATTTTAATAAAACAGCACCGTCTCTTTCTGTATATGAAATT
390 GAAAACGCTAGAAAATTTACTTATATTTTAACAAAACAGCACCGTCTCTCTCTGTACATGAAATT
* *
41620432 TTAGTGGCGTTTTTTACTAAAACGCCGCAAATATGGATATAATATCCGCAAATACTTTTAAATAA
455 TTAGTGGCGTTTTTTACTAAAACGCCGCAAATATGGATACAATATCCGCAAATACTTATAAATAA
*
41620497 AGTGAATATTTAGTGGCGTTTCTATGAAAAACGCCGCAAATAATATTTGAAAAATTGAATAAAAC
520 AGTAAATATTTAGTGGCGTTTCTATGAAAAACGCCGCAAATAATATTTGAAAAATTGAATAAAAC
* *
41620562 GGAGCCGTTTCATTGACGAGTTCAGTTGACCCTCAAAATTTGTAAGATTTGTGGCGTTTTCTTTA
585 GGAGCCGTTTCATTGACGAGTTCAATTGACCCTCAAAATTTGTAAAATTTGTGGCGTTTTCTTTA
*
41620627 AGCGGCGCTTCATGAAATGAAATTATAATGGCATATCTCCATCAACCCAATTTAACTTAAAAATA
650 AGCGGCGCTTCATGAAATGAAATTATAACGGCATATCTCCATCAACCCAATTTAACTTAAAAATA
41620692 GAGCATAAATTTAAAATTGTAATACATTATTTGAATAATATCAATAATTTATAAATTCGAATGTT
715 GAGCATAAATTTAAAATTGTAATACATTATTTGAATAATATCAATAATTTATAAATTCGAATGTT
41620757 GATAAAATTT
780 GATAAAATTT
41620767 TAAT
1 TAAT
41620771 TATACACTCT
Statistics
Matches: 766, Mismatches: 26, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
789 456 0.60
790 310 0.40
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (789 bp):
TAATATTTATTTACGTAAAATTTAAATAGTAAAATTATATAATAAAACTTTTAGGGGTTACGCTT
TAGGGGTTAAGGAGATTTAGGGGTTTAGGGTTTATGCTTTAAGGGTTAAAGGGGATTTAGGGGTT
ATGGGTTAGGAATTTGGGAATTAGGGGTTATTAATTTTTATATTAAATACTTTTAAATATTACTT
AAAATTTTAATAATTATTTATGTAAAATTTAAATTAAATATACAATAGATAAATAAATAAATAAT
AAAATTTATTCAAATTTTAGCAAATATTAACTGCATTTTTATTTGTGGCATTTTTCGAAAAACGC
CGTAAATTATCTTTAAACTGGAAAACAGCATTGTTTCAGCAAATACATTTGTGGCGTTTTTTATG
AAAACGCTAGAAAATTTACTTATATTTTAACAAAACAGCACCGTCTCTCTCTGTACATGAAATTT
TAGTGGCGTTTTTTACTAAAACGCCGCAAATATGGATACAATATCCGCAAATACTTATAAATAAA
GTAAATATTTAGTGGCGTTTCTATGAAAAACGCCGCAAATAATATTTGAAAAATTGAATAAAACG
GAGCCGTTTCATTGACGAGTTCAATTGACCCTCAAAATTTGTAAAATTTGTGGCGTTTTCTTTAA
GCGGCGCTTCATGAAATGAAATTATAACGGCATATCTCCATCAACCCAATTTAACTTAAAAATAG
AGCATAAATTTAAAATTGTAATACATTATTTGAATAATATCAATAATTTATAAATTCGAATGTTG
ATAAAATTT
Found at i:41622143 original size:33 final size:31
Alignment explanation
Indices: 41622079--41622151 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
41622069 GGTTTTTGCA
* *
41622079 GCTAAGATGGTACCTTCTATGCGTTTTTGCT
1 GCTAAGATGGTACCTTCTATGCATTTCTGCT
41622110 GCTAAGATGGTACCGCTTCTATTG-ATTTCTGCT
1 GCTAAGATGGTA-C-CTTCTA-TGCATTTCTGCT
41622143 GCTAA-ATGG
1 GCTAAGATGG
41622152 GAAATAGCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 12 0.32
32 5 0.14
33 18 0.49
34 2 0.05
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
GCTAAGATGGTACCTTCTATGCATTTCTGCT
Found at i:41623177 original size:9 final size:9
Alignment explanation
Indices: 41623155--41623489 Score: 281
Period size: 9 Copynumber: 38.3 Consensus size: 9
41623145 CACTTGTACA
*
41623155 TTACAAAAC
1 TTACATAAC
41623164 TTACATAAC
1 TTACATAAC
*
41623173 CTACATAAC
1 TTACATAAC
41623182 TTACATAAC
1 TTACATAAC
41623191 TTACATAA-
1 TTACATAAC
*
41623199 -TACAAAAC
1 TTACATAAC
*
41623207 TCACATAAC
1 TTACATAAC
* *
41623216 TTAAATATC
1 TTACATAAC
*
41623225 TTACACAAC
1 TTACATAAC
41623234 TTACATAAC
1 TTACATAAC
*
41623243 CTACATAA-
1 TTACATAAC
*
41623251 -TACATTTACC
1 TTACA--TAAC
41623261 TTACATAAC
1 TTACATAAC
41623270 TTACATAAC
1 TTACATAAC
41623279 TTACATAATAC
1 TTACAT-A-AC
*
41623290 ATA-ATAAC
1 TTACATAAC
41623298 TTAC--AAC
1 TTACATAAC
41623305 TTACATAAC
1 TTACATAAC
* *
41623314 ATACATTAC
1 TTACATAAC
**
41623323 TTTGATAAC
1 TTACATAAC
41623332 TTACATAAC
1 TTACATAAC
41623341 TTACATAA-
1 TTACATAAC
*
41623349 -TACACAAC
1 TTACATAAC
41623357 TTACATAAC
1 TTACATAAC
*
41623366 TTACTTAA-
1 TTACATAAC
*
41623374 -TACACAAC
1 TTACATAAC
41623382 TTACATAAC
1 TTACATAAC
*
41623391 TTACTTAA-
1 TTACATAAC
41623399 -TACATAAC
1 TTACATAAC
41623407 TTACATAAC
1 TTACATAAC
41623416 TT--ATACAC
1 TTACATA-AC
*
41623424 GTACATAAC
1 TTACATAAC
*
41623433 TTACA-AAA
1 TTACATAAC
*
41623441 TT-TATACAC
1 TTACATA-AC
*
41623450 GTACATAAC
1 TTACATAAC
41623459 TTACATACAC
1 TTACATA-AC
*
41623469 GTACATAAC
1 TTACATAAC
41623478 TTACATAAC
1 TTACATAAC
41623487 TTA
1 TTA
41623490 TACCCTTGTA
Statistics
Matches: 258, Mismatches: 44, Indels: 48
0.74 0.13 0.14
Matches are distributed among these distances:
7 38 0.15
8 12 0.05
9 183 0.71
10 17 0.07
11 8 0.03
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.31
Consensus pattern (9 bp):
TTACATAAC
Found at i:41623204 original size:43 final size:43
Alignment explanation
Indices: 41623156--41623489 Score: 240
Period size: 43 Copynumber: 7.7 Consensus size: 43
41623146 ACTTGTACAT
*
41623156 TACAAAACTTACATAACCTACATAACTTACATAACTTACATAA
1 TACAAAACTTACATAACTTACATAACTTACATAACTTACATAA
* * * *
41623199 TACAAAACTCACATAACTTAAATATCTTACACAACTTACATAA
1 TACAAAACTTACATAACTTACATAACTTACATAACTTACATAA
* *
41623242 CCTACATAA--TACATTTACCTTACATAACTTACATAACTTACATAA
1 --TACAAAACTTACA--TAACTTACATAACTTACATAACTTACATAA
* * **
41623287 TACATAATAACTTAC--AACTTACATAACATACATTACTTTGATAA
1 TAC--AA-AACTTACATAACTTACATAACTTACATAACTTACATAA
* * *
41623331 CTTACATAACTTACATAA--TACACAACTTACATAACTTACTTAA
1 --TACAAAACTTACATAACTTACATAACTTACATAACTTACATAA
* *
41623374 TACACAACTTACATAACTTACTTAA--TACATAACTTACATAA
1 TACAAAACTTACATAACTTACATAACTTACATAACTTACATAA
* * * * * *
41623415 CTTA-TACACGTACATAACTTACA-AAATT-TATACACGTACATAA
1 --TACAAAACTTACATAACTTACATAACTTACATA-ACTTACATAA
* *
41623458 CTTACATACACGTACATAACTTACATAACTTA
1 --TACA-AAACTTACATAACTTACATAACTTA
41623490 TACCCTTGTA
Statistics
Matches: 230, Mismatches: 37, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
41 32 0.14
42 17 0.07
43 91 0.40
44 25 0.11
45 53 0.23
46 9 0.04
48 3 0.01
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.31
Consensus pattern (43 bp):
TACAAAACTTACATAACTTACATAACTTACATAACTTACATAA
Found at i:41623360 original size:25 final size:26
Alignment explanation
Indices: 41623156--41623489 Score: 196
Period size: 25 Copynumber: 12.8 Consensus size: 26
41623146 ACTTGTACAT
* *
41623156 TACAAAACTTACATAACCTACATAACT
1 TACATAACTTACATAACTTACATAA-T
*
41623183 TACATAACTTACATAA--TACAAAACT
1 TACATAACTTACATAACTTACATAA-T
* * * *
41623208 CACATAACTTAAATATCTTACACAACT
1 TACATAACTTACATAACTTACATAA-T
* *
41623235 TACATAACCTACATAA--TACATTTACCT
1 TACATAACTTACATAACTTACA--TA-AT
41623262 TACATAACTTACATAACTTACATAA-
1 TACATAACTTACATAACTTACATAAT
*
41623287 TACATAATAACTTAC--AACTTACATAACA
1 TAC---ATAACTTACATAACTTACATAA-T
* **
41623315 TACATTACTTTGATAACTTACATAACT
1 TACATAACTTACATAACTTACATAA-T
*
41623342 TACATAA--TACACAACTTACATAACT
1 TACATAACTTACATAACTTACATAA-T
* *
41623367 TACTTAA--TACACAACTTACATAACT
1 TACATAACTTACATAACTTACATAA-T
*
41623392 TACTTAA--TACATAACTTACATAACT
1 TACATAACTTACATAACTTACATAA-T
* *
41623417 T--ATACACGTACATAACTTACAAAAT
1 TACATA-ACTTACATAACTTACATAAT
* * *
41623442 T-TATACACGTACATAACTTACATACACG
1 TACATA-ACTTACATAACTTACATA-A-T
41623470 TACATAACTTACATAACTTA
1 TACATAACTTACATAACTTA
41623490 TACCCTTGTA
Statistics
Matches: 256, Mismatches: 30, Indels: 41
0.78 0.09 0.13
Matches are distributed among these distances:
23 2 0.01
24 1 0.00
25 100 0.39
26 47 0.18
27 73 0.29
28 26 0.10
29 7 0.03
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.31
Consensus pattern (26 bp):
TACATAACTTACATAACTTACATAAT
Found at i:41623482 original size:15 final size:17
Alignment explanation
Indices: 41623408--41623480 Score: 63
Period size: 19 Copynumber: 4.6 Consensus size: 17
41623398 ATACATAACT
41623408 TACATAACTTATACACG
1 TACATAACTTATACACG
41623425 TACATAAC-T-T--AC-
1 TACATAACTTATACACG
*
41623437 -A-A-AATTTATACACG
1 TACATAACTTATACACG
41623451 TACATAACTTACATACACG
1 TACATAACTT--ATACACG
41623470 TACATAACTTA
1 TACATAACTTA
41623481 CATAACTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 20
0.67 0.03 0.30
Matches are distributed among these distances:
9 2 0.05
10 2 0.05
11 2 0.05
13 4 0.09
15 2 0.05
16 2 0.05
17 13 0.30
19 17 0.39
ACGTcount: A:0.44, C:0.22, G:0.04, T:0.30
Consensus pattern (17 bp):
TACATAACTTATACACG
Found at i:41629006 original size:21 final size:20
Alignment explanation
Indices: 41628982--41629024 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
41628972 GGAAGCAGCG
*
41628982 GCTGCAGCGAGGGAAGCGAAA
1 GCTGCAGCGAGAGAAGC-AAA
*
41629003 GCTGTAGCGAGAGAAGCAAA
1 GCTGCAGCGAGAGAAGCAAA
41629023 GC
1 GC
41629025 AGAGCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.35, C:0.19, G:0.40, T:0.07
Consensus pattern (20 bp):
GCTGCAGCGAGAGAAGCAAA
Found at i:41629595 original size:20 final size:19
Alignment explanation
Indices: 41629570--41629621 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
41629560 AGCAATGAAT
41629570 CTGTTCACCAAGAGATACAA
1 CTGTTCA-CAAGAGATACAA
*
41629590 CTGTTCA-AA-ACATACAA
1 CTGTTCACAAGAGATACAA
*
41629607 CTGTTTATCAAGAGA
1 CTGTTCA-CAAGAGA
41629622 CAGAACTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 13 0.50
18 2 0.08
19 2 0.08
20 9 0.35
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.25
Consensus pattern (19 bp):
CTGTTCACAAGAGATACAA
Found at i:41633239 original size:30 final size:30
Alignment explanation
Indices: 41633198--41633258 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
41633188 GCCAAGTTTA
41633198 ATCAATCTCATACACATATAAAATCATCTT
1 ATCAATCTCATACACATATAAAATCATCTT
*
41633228 ATCAATTTCATACACATATAAAATCATCTT
1 ATCAATCTCATACACATATAAAATCATCTT
41633258 A
1 A
41633259 CTTATATAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.34
Consensus pattern (30 bp):
ATCAATCTCATACACATATAAAATCATCTT
Found at i:41638111 original size:15 final size:15
Alignment explanation
Indices: 41638070--41638111 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
41638060 TATTATATAT
* *
41638070 TGAAACTACAGGCTG
1 TGAAACTATAGACTG
41638085 TGAAACTATAGACTG
1 TGAAACTATAGACTG
*
41638100 TGAAACTGTAGA
1 TGAAACTATAGA
41638112 TAATGAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (15 bp):
TGAAACTATAGACTG
Found at i:41641751 original size:18 final size:18
Alignment explanation
Indices: 41641729--41641776 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
41641719 GGAAATTACA
41641729 AAAAAAAAGAGTACGAAGT
1 AAAAAAAA-AGTACGAAGT
* *
41641748 AAAAAAAAATTTCGAAGT
1 AAAAAAAAAGTACGAAGT
41641766 ATAAAAAAAAG
1 A-AAAAAAAAG
41641777 AAGAAGTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.04, G:0.15, T:0.15
Consensus pattern (18 bp):
AAAAAAAAAGTACGAAGT
Found at i:41641751 original size:20 final size:20
Alignment explanation
Indices: 41641728--41641777 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
41641718 AGGAAATTAC
41641728 AAAAAAAAAGAGTACGAAGT
1 AAAAAAAAAGAGTACGAAGT
* *
41641748 -AAAAAAAA-ATTTCGAAGT
1 AAAAAAAAAGAGTACGAAGT
41641766 ATAAAAAAAAGA
1 A-AAAAAAAAGA
41641778 AGAAGTGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.32
19 8 0.32
20 8 0.32
21 1 0.04
ACGTcount: A:0.68, C:0.04, G:0.14, T:0.14
Consensus pattern (20 bp):
AAAAAAAAAGAGTACGAAGT
Found at i:41642680 original size:5 final size:6
Alignment explanation
Indices: 41642638--41642736 Score: 56
Period size: 6 Copynumber: 16.0 Consensus size: 6
41642628 AATGAAAAAG
** ** *
41642638 AAGAAA AAGAAA GTGAAA AAGAAA AAGAAA TTGCAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** * * * *
41642686 TCGAAA AA-ATGA GAGAAA AAGAAA ATGAAGAA AAGAAA ATTGAAA AAGAAA
1 AAGAAA AAGA-AA AAGAAA AAGAAA AAG-A-AA AAGAAA A-AGAAA AAGAAA
41642737 TTGAGATTCA
Statistics
Matches: 66, Mismatches: 22, Indels: 10
0.67 0.22 0.10
Matches are distributed among these distances:
5 1 0.02
6 53 0.80
7 8 0.12
8 4 0.06
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (6 bp):
AAGAAA
Found at i:41642686 original size:18 final size:18
Alignment explanation
Indices: 41642638--41642693 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
41642628 AATGAAAAAG
*
41642638 AAGAAAAAGAAAGTGAAA
1 AAGAAAAAGAAATTGAAA
*
41642656 AAGAAAAAGAAATTGCAA
1 AAGAAAAAGAAATTGAAA
*
41642674 AAGAAAAAGAAATCGAAA
1 AAGAAAAAGAAATTGAAA
41642692 AA
1 AA
41642694 ATGAGAGAAA
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:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAGAAAAAGAAATTGAAA
Found at i:41642721 original size:14 final size:16
Alignment explanation
Indices: 41642691--41642725 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
41642681 AGAAATCGAA
41642691 AAAATGAGAGAAAAAG
1 AAAATGAGAGAAAAAG
41642707 AAAATGA-AG-AAAAG
1 AAAATGAGAGAAAAAG
41642721 AAAAT
1 AAAAT
41642726 TGAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.53
15 2 0.11
16 7 0.37
ACGTcount: A:0.71, C:0.00, G:0.20, T:0.09
Consensus pattern (16 bp):
AAAATGAGAGAAAAAG
Found at i:41642768 original size:14 final size:14
Alignment explanation
Indices: 41642701--41642768 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 14
41642691 AAAATGAGAG
41642701 AAAAAGAAAA-TGA
1 AAAAAGAAAATTGA
41642714 AGAAAAGAAAATTG-
1 A-AAAAGAAAATTGA
41642728 AAAAAG-AAATTGA
1 AAAAAGAAAATTGA
41642741 GATTCAGAAA-AAAATTGA
1 -A---A-AAAGAAAATTGA
41642759 AAAAAGAAAA
1 AAAAAGAAAA
41642769 AGATGTTGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 19
0.70 0.00 0.30
Matches are distributed among these distances:
12 6 0.13
13 9 0.20
14 16 0.36
15 2 0.04
17 2 0.04
18 10 0.22
ACGTcount: A:0.69, C:0.01, G:0.16, T:0.13
Consensus pattern (14 bp):
AAAAAGAAAATTGA
Found at i:41646315 original size:28 final size:27
Alignment explanation
Indices: 41646258--41646409 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
41646248 TAAATTGTGC
*
41646258 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
41646285 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
41646313 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
41646340 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
41646368 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
41646395 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
41646410 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:41646342 original size:55 final size:55
Alignment explanation
Indices: 41646258--41646409 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
41646248 TAAATTGTGC
*
41646258 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
41646313 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
41646368 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
41646410 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:41664870 original size:120 final size:119
Alignment explanation
Indices: 41664648--41664910 Score: 298
Period size: 120 Copynumber: 2.2 Consensus size: 119
41664638 TCCTCGTTCA
* * * **
41664648 AATGCCTTCAGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACTTAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
* * * * *
41664713 TAACAACTCGCACGAATGCTTTCGGGACTTAACCCGGATTTA-ACAAC-TCGCAC
66 TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATAC-ACTTAGCAC
* *
41664766 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACAC-AATGCCTTCGGGACTTAACCCGGA
** * ** *
41664831 TTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
64 TTTAACAACTCGCACAAAGGCCTTCGGGA-CTTAACCCGGATATATACACTTAGCAC
*
41664887 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41664911 CAGCATTCAA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 35 0.29
120 79 0.66
121 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAACAACTCACACAATGCCTTCGGGACTTAACCCGGATT
TAACAACTCGCACAAAGGCCTTCGGGACTTAACCCGGATATATACACTTAGCAC
Found at i:41664871 original size:40 final size:40
Alignment explanation
Indices: 41664648--41664857 Score: 296
Period size: 40 Copynumber: 5.3 Consensus size: 40
41664638 TCCTCGTTCA
* * * * ** *
41664648 AATGCCTTCAGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41664687 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
41664727 AATGCTTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
41664767 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
41664807 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
41664847 AAGGCCTTCGG
1 AATGCCTTCGG
41664858 ATCTTAGTCC
Statistics
Matches: 156, Mismatches: 14, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 32 0.21
40 124 0.79
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:41664894 original size:80 final size:80
Alignment explanation
Indices: 41664690--41664910 Score: 250
Period size: 80 Copynumber: 2.8 Consensus size: 80
41664680 CTCACACAAT
* * * *
41664690 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCTTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATATAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTA
* *
41664755 ACAACTCGCACGAAT
66 ACAACTCGCACAAAG
* * *
41664770 GCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTA
1 GCCTTCGGGACTTAACCCGGATATAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTA
** *
41664835 GTATCTCGCACAAAG
66 ACAACTCGCACAAAG
** * *
41664850 GCCTTC-GGATCTTAGTCCGGATATATTC-ACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGA-CTTAACCCGGATATA-ACAAC-TAGCACGAAAGCCTTCGGGACTTAACCCGGA
41664911 CAGCATTCAA
Statistics
Matches: 125, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
79 3 0.02
80 116 0.93
81 6 0.05
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATAACAACTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTA
ACAACTCGCACAAAG
Found at i:41664919 original size:41 final size:41
Alignment explanation
Indices: 41664842--41664919 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
41664832 TTAGTATCTC
* * *
41664842 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
41664883 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
41664920 ATTAATATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:41668453 original size:21 final size:21
Alignment explanation
Indices: 41668419--41668463 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
41668409 GATATGTAGA
41668419 AAATGCAATGAAAACA-ATTAT
1 AAATGCAATGAAAACACA-TAT
41668440 AAATGC-ATGAAAAACACATAT
1 AAATGCAATG-AAAACACATAT
41668461 AAA
1 AAA
41668464 AATGAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 3 0.14
21 18 0.82
22 1 0.05
ACGTcount: A:0.60, C:0.11, G:0.09, T:0.20
Consensus pattern (21 bp):
AAATGCAATGAAAACACATAT
Found at i:41670955 original size:17 final size:17
Alignment explanation
Indices: 41670933--41670965 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41670923 ACTCTTTGAG
41670933 AATTTCCATAGCATTTC
1 AATTTCCATAGCATTTC
*
41670950 AATTTCCCTAGCATTT
1 AATTTCCATAGCATTT
41670966 TTTCATTCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.42
Consensus pattern (17 bp):
AATTTCCATAGCATTTC
Found at i:41671799 original size:98 final size:98
Alignment explanation
Indices: 41671625--41671821 Score: 331
Period size: 98 Copynumber: 2.0 Consensus size: 98
41671615 GTACAATAAA
* * *
41671625 ACTTTAAAAGAATATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
* **
41671690 CCTCTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
41671723 ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
*
41671788 CCTTTAAAATCCCAAACTCAAAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
41671821 A
1 A
41671822 TGATTTTTAA
Statistics
Matches: 92, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 92 1.00
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTAATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
CCTCTAAAATCCCAAACTCAAAATATTTCCTTT
Found at i:41672517 original size:25 final size:26
Alignment explanation
Indices: 41672487--41672536 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
41672477 ATATAAATAT
41672487 GAAAATATTC-ATTAAAAAAATATAG
1 GAAAATATTCGATTAAAAAAATATAG
*
41672512 GAAAATATTCGTTTAAAAAAATATA
1 GAAAATATTCGATTAAAAAAATATA
41672537 TATATATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (26 bp):
GAAAATATTCGATTAAAAAAATATAG
Found at i:41673183 original size:23 final size:22
Alignment explanation
Indices: 41673140--41673197 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
41673130 AAAGGGTATC
* *
41673140 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
41673161 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
41673184 TACATATCATATCT
1 TACAAATCATATCT
41673198 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:41673200 original size:19 final size:19
Alignment explanation
Indices: 41673176--41673307 Score: 219
Period size: 19 Copynumber: 6.8 Consensus size: 19
41673166 AATCATATCT
*
41673176 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
41673195 TCTAAGATTGCATATATCATA
1 TCTAAGATTGC--ATATCATA
41673216 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
41673235 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41673254 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
41673273 TCTAGGATTGCATATCATA
1 TCTAAGATTGCATATCATA
41673292 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
41673308 CTCAAAAATT
Statistics
Matches: 106, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
19 87 0.82
21 19 0.18
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:41698588 original size:14 final size:14
Alignment explanation
Indices: 41698569--41698601 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
41698559 TTCAACGGTG
41698569 CATGGATGATTTTT
1 CATGGATGATTTTT
41698583 CATGGATGATTTTT
1 CATGGATGATTTTT
*
41698597 AATGG
1 CATGG
41698602 GCAATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (14 bp):
CATGGATGATTTTT
Found at i:41707714 original size:483 final size:483
Alignment explanation
Indices: 41706808--41707777 Score: 1769
Period size: 483 Copynumber: 2.0 Consensus size: 483
41706798 TAATAGCATC
*
41706808 AAATCAGCAAGAAAGTTGCAATCCTGAATCATCAAAAGATAGTTTCTACAAACTTTACCAACTAA
1 AAATCAGCAAGAAAGTTGCAATCCTGAATCATCAAAAGACAGTTTCTACAAACTTTACCAACTAA
*
41706873 CACATACTGGCCTAAATGATTCGTTACTTTAATCACAAATTCAGTTGACTCATAAGGTATTTTCT
66 CACATACTGGCCTAAAGGATTCGTTACTTTAATCACAAATTCAGTTGACTCATAAGGTATTTTCT
* * *
41706938 TATCTGACACTAAGGTCGTGCATATATATGACGGTGTTGACCTCGGGTCAATCAGATCATTAACA
131 TATCTGACACTAAGGTCGTGCATATATATGACGGTGTTGACCTCGAGTCAATCAAAGCATTAACA
*
41707003 TTAGTATCAAAGATAGAAAATGTACCAGTAATCACATCAGGTGCTGAAGCTTCCTCACGAGCTCG
196 TTAGTATCAAAGATAGAAAATGTACCAATAATCACATCAGGTGCTGAAGCTTCCTCACGAGCTCG
*
41707068 AATTGCATATGCCCGAGCCTCAGATCTAACCGTAGAATATTTCATTCCACATCGACTATTACCTG
261 AATTGCATATGCCCGAGCCTCAGATCTAACCGTAGAATATTTCATTCCACATCGACTATTACCCG
*
41707133 TATTTCCACTATTTCTAGATGGTCTCCCTCTCCCAGCCGTGTTACTCGAACGAGTGTTCTGAGCT
326 TATTTCCACTATTTCTAGATGGTCTCCCTCTCCCAGCCGTGTTACTCGAACGACTGTTCTGAGCT
*
41707198 TTCTCCCTATCAGATCTTTCAAGGTAGTCTCGAAGAAAATGGTCATAAGAACCACATTTAAAGCA
391 TTCTCCCTATCAGATCTTTCAAGGCAGTCTCGAAGAAAATGGTCATAAGAACCACATTTAAAGCA
*
41707263 CGATCCATCTCTCAATTTGCATTCTTCG
456 CGATCCATATCTCAATTTGCATTCTTCG
*
41707291 AAATCAGCAAGAAAGTTGCAATCCTGAATCATCAAAAGACAGTTTCTACAAACTTTATCAACTAA
1 AAATCAGCAAGAAAGTTGCAATCCTGAATCATCAAAAGACAGTTTCTACAAACTTTACCAACTAA
* *
41707356 CACATACTGGTCTAAAGGATTCGTTACTTTAATCACAAATTCAGTTGGCTCATAAGGTATTTTCT
66 CACATACTGGCCTAAAGGATTCGTTACTTTAATCACAAATTCAGTTGACTCATAAGGTATTTTCT
* *
41707421 TATCTGACACTAAGGTTGTGCATATATATGAGGGTGTTGACCTCGAGTCAATCAAAGCATTAACA
131 TATCTGACACTAAGGTCGTGCATATATATGACGGTGTTGACCTCGAGTCAATCAAAGCATTAACA
*
41707486 TTAGTATCAAAGATAGAAAATGTACCAATAATCACATCAGGTGCTGAAGCTTTCTCACGAGCTCG
196 TTAGTATCAAAGATAGAAAATGTACCAATAATCACATCAGGTGCTGAAGCTTCCTCACGAGCTCG
41707551 AATTGCATATGCCCGAGCCTCAGATCTAACCGTAGAATATTTCATTCCACATCGACTATTACCCG
261 AATTGCATATGCCCGAGCCTCAGATCTAACCGTAGAATATTTCATTCCACATCGACTATTACCCG
* * *
41707616 TATTTCCACTATTTCTGGATGGTCTCCCTCTCGCAGTCGTGTTACTCGAACGACTGTTCTGAGCT
326 TATTTCCACTATTTCTAGATGGTCTCCCTCTCCCAGCCGTGTTACTCGAACGACTGTTCTGAGCT
41707681 TTCTCCCTATCAGATCTTTCAAGGCAGTCTCGAAGAAAATGGTCATAAGAACCACATTTAAAGCA
391 TTCTCCCTATCAGATCTTTCAAGGCAGTCTCGAAGAAAATGGTCATAAGAACCACATTTAAAGCA
41707746 CGATCCATATCTCAATTTGCATTCTTCG
456 CGATCCATATCTCAATTTGCATTCTTCG
41707774 AAAT
1 AAAT
41707778 AACGCCTATT
Statistics
Matches: 468, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
483 468 1.00
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (483 bp):
AAATCAGCAAGAAAGTTGCAATCCTGAATCATCAAAAGACAGTTTCTACAAACTTTACCAACTAA
CACATACTGGCCTAAAGGATTCGTTACTTTAATCACAAATTCAGTTGACTCATAAGGTATTTTCT
TATCTGACACTAAGGTCGTGCATATATATGACGGTGTTGACCTCGAGTCAATCAAAGCATTAACA
TTAGTATCAAAGATAGAAAATGTACCAATAATCACATCAGGTGCTGAAGCTTCCTCACGAGCTCG
AATTGCATATGCCCGAGCCTCAGATCTAACCGTAGAATATTTCATTCCACATCGACTATTACCCG
TATTTCCACTATTTCTAGATGGTCTCCCTCTCCCAGCCGTGTTACTCGAACGACTGTTCTGAGCT
TTCTCCCTATCAGATCTTTCAAGGCAGTCTCGAAGAAAATGGTCATAAGAACCACATTTAAAGCA
CGATCCATATCTCAATTTGCATTCTTCG
Found at i:41714970 original size:64 final size:64
Alignment explanation
Indices: 41714869--41714994 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 64
41714859 CATCTAAAAT
* * *
41714869 GCAATAAAAGGCTTTTCTCGCTAATCTATCTATCATTTGATCGATGAATGGCAAAAGAAAATTA
1 GCAATAAAAGACTTTTCTCACTAATCTATCTATCATTTGATCGATGAACGGCAAAAGAAAATTA
41714933 GCAATAAAAGACTTTTCTCACTAATCTATCTATCATTTGATCGATGAACGGCAAAAGAAAAT
1 GCAATAAAAGACTTTTCTCACTAATCTATCTATCATTTGATCGATGAACGGCAAAAGAAAAT
41714995 GGTCTTTCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 59 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (64 bp):
GCAATAAAAGACTTTTCTCACTAATCTATCTATCATTTGATCGATGAACGGCAAAAGAAAATTA
Found at i:41719516 original size:47 final size:47
Alignment explanation
Indices: 41719457--41719894 Score: 714
Period size: 47 Copynumber: 9.3 Consensus size: 47
41719447 CAACACAATT
41719457 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41719504 TATATGTGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
41719551 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41719598 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41719645 TATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * *
41719692 CATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
41719739 TATATATGTAATAAGGCCTAATGGCCGATGTGATGAATTTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
*
41719786 TATAAATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* * * * * * *
41719833 TATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTG
1 TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
* *
41719880 CATAAATGTGATAAG
1 TATATATGTGATAAG
41719895 TCCCGAAGGG
Statistics
Matches: 366, Mismatches: 25, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 366 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
TATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG
Found at i:41720069 original size:37 final size:37
Alignment explanation
Indices: 41720017--41720091 Score: 107
Period size: 37 Copynumber: 2.0 Consensus size: 37
41720007 GCTCTAAAGG
* *
41720017 CCCGATGACTACGTGTGG-GACTTTTGTCCGGGTAAGA
1 CCCGATAACTACGTGTGGAGA-TTATGTCCGGGTAAGA
*
41720054 CCCGATAACTTCGTGTGGAGATTATGTCCGGGTAAGA
1 CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGA
41720091 C
1 C
41720092 TTCGTAATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 32 0.94
38 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.31, T:0.27
Consensus pattern (37 bp):
CCCGATAACTACGTGTGGAGATTATGTCCGGGTAAGA
Found at i:41721996 original size:43 final size:43
Alignment explanation
Indices: 41721948--41722089 Score: 275
Period size: 43 Copynumber: 3.3 Consensus size: 43
41721938 TTGGTTTTCA
41721948 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
*
41721991 GCACTAAGTGTGCGGGCAATAAGTGTTCACGATTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
41722034 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
1 GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
41722077 GCACTAAGTGTGC
1 GCACTAAGTGTGC
41722090 AGGCTTGAAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 97 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (43 bp):
GCACTAAGTGTGCGGGCAATAAGTGTTCACGGTTGTGAGATTG
Found at i:41722110 original size:29 final size:29
Alignment explanation
Indices: 41722075--41722148 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
41722065 GTTGTGAGAT
*
41722075 TGGCACTAAGTGTGC-AGGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGA-G-TTGAAAGTACA
*
41722104 TGGCACTAAGTGTGCGAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
41722133 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
41722149 TGGTTGATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 5 0.12
29 35 0.85
30 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:41722584 original size:40 final size:40
Alignment explanation
Indices: 41722461--41722656 Score: 184
Period size: 40 Copynumber: 4.9 Consensus size: 40
41722451 TCGAATGATG
** *
41722461 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGA-TATA
* ** * * *
41722501 TCCGGACTAAGAT-CCGAAG-GCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGAGCATTCATGCTAGTGA-TATA
*
41722541 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATGTA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
*
41722581 TCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
* * * * *
41722621 TCCGTGTTAAATCCCGAAGAGCAATCATGCTGGTGA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA
41722657 CGTGTATTCG
Statistics
Matches: 131, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 1 0.01
40 111 0.85
41 19 0.15
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGATATA
Found at i:41722598 original size:80 final size:81
Alignment explanation
Indices: 41722461--41722657 Score: 206
Period size: 80 Copynumber: 2.5 Consensus size: 81
41722451 TCGAATGATG
**
41722461 TCCGGGCTAAGTCCCGAAG-GC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAG-GCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCT-AGTGACCATATCCGGACTAAGATCCGAAGAGCA
* *
41722523 TTGGTGCGAGTTACTAAA
65 TTCGTGCGAGTGA-TAAA
** *
41722541 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGA-TGTATCCGGGCTAAG-TCCCGAAGAGCA
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGAT-CCGAAGAGCA
* *
41722604 TTCGTGCTAGTGATATA
65 TTCGTGCGAGTGATAAA
* * * * *
41722621 TCCGTGTTAAATCCCGAAGAGCAATCATGCTGGTGAC
1 TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGAC
41722658 GTGTATTCGG
Statistics
Matches: 98, Mismatches: 14, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
79 1 0.01
80 71 0.72
81 20 0.20
82 6 0.06
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGAGCATTCATGCTAGTGACCATATCCGGACTAAGATCCGAAGAGCAT
TCGTGCGAGTGATAAA
Done.