Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 133 of 182
Found at i:41056007 original size:30 final size:31
Alignment explanation
Indices: 41055952--41056019 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
41055942 CACCCTTAAA
** * **
41055952 TATTTACACTATTGGTCCTTCAAATTTTTTG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
41055983 TATTTACACT-TTAATCCCTCAAATTTTGAG
1 TATTTACACTATTAATCCCTCAAATTTTGAG
41056013 TATTTAC
1 TATTTAC
41056020 TCTTGGGCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (31 bp):
TATTTACACTATTAATCCCTCAAATTTTGAG
Found at i:41065335 original size:20 final size:20
Alignment explanation
Indices: 41065312--41065358 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 20
41065302 ATACTTATAA
* **
41065312 AATATATTATTTCATTATGT
1 AATATATTATATCATTACAT
41065332 -A-ATATTATATCATTACAT
1 AATATATTATATCATTACAT
41065350 AATATATTA
1 AATATATTA
41065359 ATTATTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 14 0.64
19 2 0.09
20 6 0.27
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (20 bp):
AATATATTATATCATTACAT
Found at i:41065558 original size:15 final size:15
Alignment explanation
Indices: 41065540--41065569 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41065530 ATGTAATACT
41065540 ATATATATTATTATA
1 ATATATATTATTATA
*
41065555 ATATATTTTATTATA
1 ATATATATTATTATA
41065570 TTATCATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATATTATTATA
Found at i:41065666 original size:16 final size:17
Alignment explanation
Indices: 41065645--41065677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
41065635 ATAATTATAG
41065645 TATTAAA-AATATTTTA
1 TATTAAATAATATTTTA
*
41065661 TATTAAATAATTTTTTA
1 TATTAAATAATATTTTA
41065678 AAAAACATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATTAAATAATATTTTA
Found at i:41066378 original size:16 final size:17
Alignment explanation
Indices: 41066352--41066393 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
41066342 ATATAAAATC
41066352 AAATAAAAATTAATTT-T
1 AAAT-AAAATTAATTTAT
*
41066369 AAATAAAATTTATTTAT
1 AAATAAAATTAATTTAT
*
41066386 AATTAAAA
1 AAATAAAA
41066394 CAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATAAAATTAATTTAT
Found at i:41066413 original size:4 final size:4
Alignment explanation
Indices: 41066406--41066431 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
41066396 AATAAATAAA
41066406 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
41066432 AAATTCAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:41066442 original size:47 final size:47
Alignment explanation
Indices: 41066347--41066451 Score: 115
Period size: 47 Copynumber: 2.2 Consensus size: 47
41066337 AAACAATATA
* * *
41066347 AAATCAAATAAAAATTAATTTTAAATAAAATTTATTTATAATTAAAAC
1 AAAT-AAATAAAAATTAATTTTAAATAAAATTAATTAAAAATTAAAAC
* *
41066395 AAATAAATAAAAATTAATTAATT-AAT-TAATTAATTAAAAATTCAAAC
1 AAATAAATAAAAATTAATT--TTAAATAAAATTAATTAAAAATTAAAAC
41066442 AAATTAAATA
1 AAA-TAAATA
41066452 TAACAATTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
47 34 0.69
48 13 0.27
49 2 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (47 bp):
AAATAAATAAAAATTAATTTTAAATAAAATTAATTAAAAATTAAAAC
Found at i:41067377 original size:28 final size:29
Alignment explanation
Indices: 41067321--41067377 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
41067311 TTATATTTTA
*
41067321 AAAAAATATTAAAAATGTAAATAATATAT
1 AAAAAATATTAAAAATCTAAATAATATAT
41067350 AAAAAAT-TTAAAAATTCTAAAATAATAT
1 AAAAAATATTAAAAA-TCT-AAATAATAT
41067378 TATTTAGGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 7 0.28
29 9 0.36
30 9 0.36
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (29 bp):
AAAAAATATTAAAAATCTAAATAATATAT
Found at i:41068288 original size:12 final size:11
Alignment explanation
Indices: 41068271--41068330 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
41068261 TAATTTTAAA
41068271 TTTTTATAACTT
1 TTTTTATAA-TT
41068283 TTTTTATAATT
1 TTTTTATAATT
*
41068294 TTTTT-TACAAT
1 TTTTTATA-ATT
*
41068305 TTTTTATGATT
1 TTTTTATAATT
41068316 TTTTTGAATAATT
1 TTTTT--ATAATT
41068329 TT
1 TT
41068331 AAATTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
10 2 0.05
11 21 0.52
12 10 0.25
13 7 0.17
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.68
Consensus pattern (11 bp):
TTTTTATAATT
Found at i:41068330 original size:22 final size:22
Alignment explanation
Indices: 41068283--41068337 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
41068273 TTTATAACTT
* *
41068283 TTTTTATAATTTTTTTTACAAT
1 TTTTTATAATTTTTTTGACAAA
*
41068305 TTTTTATGATTTTTTTGA-ATAA
1 TTTTTATAATTTTTTTGACA-AA
41068327 -TTTTA-AATTTT
1 TTTTTATAATTTT
41068338 CAAAAGGGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 17 0.61
ACGTcount: A:0.27, C:0.02, G:0.04, T:0.67
Consensus pattern (22 bp):
TTTTTATAATTTTTTTGACAAA
Found at i:41069058 original size:21 final size:20
Alignment explanation
Indices: 41069034--41069089 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
41069024 CTTCAATCCC
*
41069034 CAATTTTCAATTTTATATTTT
1 CAATTTCCAATTTTA-ATTTT
*
41069055 CAATCTCCAAATTTTAATTTT
1 CAATTTCC-AATTTTAATTTT
41069076 CAATTTCCAATTTT
1 CAATTTCCAATTTT
41069090 CAATCCTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.19
21 18 0.58
22 7 0.23
ACGTcount: A:0.30, C:0.16, G:0.00, T:0.54
Consensus pattern (20 bp):
CAATTTCCAATTTTAATTTT
Found at i:41069075 original size:6 final size:7
Alignment explanation
Indices: 41069034--41069093 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
41069024 CTTCAATCCC
41069034 CAATTTT
1 CAATTTT
41069041 CAATTTT
1 CAATTTT
41069048 -ATATTTT
1 CA-ATTTT
* *
41069055 CAATCTC
1 CAATTTT
41069062 CAAATTTT
1 C-AATTTT
41069070 -AATTTT
1 CAATTTT
*
41069076 CAATTTC
1 CAATTTT
41069083 CAATTTT
1 CAATTTT
41069090 CAAT
1 CAAT
41069094 CCTCAATCCT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
6 7 0.16
7 31 0.72
8 5 0.12
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.52
Consensus pattern (7 bp):
CAATTTT
Found at i:41069081 original size:28 final size:28
Alignment explanation
Indices: 41069014--41069086 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 28
41069004 TTTCTTCCTA
* * *
41069014 AATTCTCAATCTTCAATCCCCAATTTTC
1 AATTTTCAATTTTCAATCCCAAATTTTC
41069042 AATTTT-ATATTTTCAATCTCCAAATTTT-
1 AATTTTCA-ATTTTCAATC-CCAAATTTTC
*
41069070 AATTTTCAATTTCCAAT
1 AATTTTCAATTTTCAAT
41069087 TTTCAATCCT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 28 0.74
29 9 0.24
ACGTcount: A:0.32, C:0.22, G:0.00, T:0.47
Consensus pattern (28 bp):
AATTTTCAATTTTCAATCCCAAATTTTC
Found at i:41071644 original size:19 final size:20
Alignment explanation
Indices: 41071597--41071646 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
41071587 TTTTATATGT
*
41071597 AAAAT-TATAAA-ATTTTCA
1 AAAATATATAAAGATTCTCA
41071615 AAAATAT-TAAAGATTCT-A
1 AAAATATATAAAGATTCTCA
41071633 AAAATATATAAAGA
1 AAAATATATAAAGA
41071647 AAGTTTATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 17 0.61
19 11 0.39
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (20 bp):
AAAATATATAAAGATTCTCA
Found at i:41081709 original size:18 final size:19
Alignment explanation
Indices: 41081686--41081724 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41081676 AAATTCAAAG
41081686 AAATA-TATGAAAATACAT
1 AAATATTATGAAAATACAT
* *
41081704 AAATATTTTTAAAATACAT
1 AAATATTATGAAAATACAT
41081723 AA
1 AA
41081725 TAATAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.33
Consensus pattern (19 bp):
AAATATTATGAAAATACAT
Found at i:41081735 original size:21 final size:19
Alignment explanation
Indices: 41081695--41081737 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
41081685 GAAATATATG
**
41081695 AAAATACATAAATATTTTT
1 AAAATACATAAATAAATTT
41081714 AAAATACATAATAATAAATTT
1 AAAATACAT-A-AATAAATTT
41081735 AAA
1 AAA
41081738 TTTAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.45
20 1 0.05
21 10 0.50
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAATACATAAATAAATTT
Found at i:41081776 original size:19 final size:19
Alignment explanation
Indices: 41081733--41081788 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
41081723 AATAATAAAT
41081733 TTAAATTTAA-ATT-AAT-A
1 TTAAA-TTAATATTAAATAA
41081750 TTAAATTAA-ATATAAATAA
1 TTAAATTAATAT-TAAATAA
*
41081769 TTATATTAATATTAAATAA
1 TTAAATTAATATTAAATAA
41081788 T
1 T
41081789 AATAATAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
16 6 0.18
17 6 0.18
18 3 0.09
19 17 0.50
20 2 0.06
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAAATTAATATTAAATAA
Found at i:41081782 original size:25 final size:25
Alignment explanation
Indices: 41081742--41081794 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 25
41081732 TTTAAATTTA
41081742 AATTAATATTAAATTAAAT-ATAAAT
1 AATTAATATTAAATTAAATAAT-AAT
41081767 AATT-ATATTAATATTAAATAATAAT
1 AATTAATATTAA-ATTAAATAATAAT
41081792 AAT
1 AAT
41081795 AACCAGTCCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 7 0.27
25 17 0.65
26 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AATTAATATTAAATTAAATAATAAT
Found at i:41083836 original size:17 final size:19
Alignment explanation
Indices: 41083814--41083848 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41083804 TGCTATTAAT
41083814 TCTA-TTTA-AGTAATAAC
1 TCTATTTTATAGTAATAAC
41083831 TCTATTTTATAGTAATAA
1 TCTATTTTATAGTAATAA
41083849 AATTAGCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.46
Consensus pattern (19 bp):
TCTATTTTATAGTAATAAC
Found at i:41084745 original size:21 final size:21
Alignment explanation
Indices: 41084706--41084745 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41084696 GAAAAATATT
*
41084706 AAATATATATTTTTATTTTTA
1 AAATATATAGTTTTATTTTTA
41084727 AAATATAATAGTTTT-TTTT
1 AAATAT-ATAGTTTTATTTT
41084746 ATTTTAAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
AAATATATAGTTTTATTTTTA
Found at i:41084861 original size:9 final size:9
Alignment explanation
Indices: 41084847--41084874 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41084837 TTTTGTTACA
41084847 ACAATTAAT
1 ACAATTAAT
41084856 ACAATTAAT
1 ACAATTAAT
41084865 ACAATTAAT
1 ACAATTAAT
41084874 A
1 A
41084875 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41084896 original size:68 final size:68
Alignment explanation
Indices: 41084817--41085017 Score: 298
Period size: 59 Copynumber: 3.1 Consensus size: 68
41084807 TCAAGTTTGT
*
41084817 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41084882 AAA
66 AAA
*
41084885 TTTACTAATCAAATATTAGATTTTATT---AC-----A-ACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41084941 AAA
66 AAA
41084944 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
41085007 AAT
66 AAA
41085010 TTTACTAA
1 TTTACTAA
41085018 CAATTAATTT
Statistics
Matches: 120, Mismatches: 4, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
59 55 0.46
60 1 0.01
62 2 0.02
65 2 0.02
66 27 0.22
67 2 0.02
68 31 0.26
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:41085027 original size:16 final size:16
Alignment explanation
Indices: 41085006--41085047 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41084996 AATAATTTGA
*
41085006 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41085022 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41085038 TAGTTTTAAT
1 TAATTTTAAT
41085048 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41085031 original size:22 final size:22
Alignment explanation
Indices: 41085021--41085075 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
41085011 TTACTAACAA
* * *
41085021 TTAATTTTAATAACAATTAGTT
1 TTAATTTTAATAAAAAATAATT
*
41085043 TTAATTTTATTAAAAAATAATT
1 TTAATTTTAATAAAAAATAATT
41085065 TTAATTTTAAT
1 TTAATTTTAAT
41085076 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (22 bp):
TTAATTTTAATAAAAAATAATT
Found at i:41085418 original size:24 final size:25
Alignment explanation
Indices: 41085372--41085424 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
41085362 TTTCTAAAAG
* **
41085372 ATTTAGTATTTTATTAGTTTAATAT
1 ATTTAGCATTTTATTAGCATAATAT
41085397 ATTTAGCA-TTTATTAGCATAATAT
1 ATTTAGCATTTTATTAGCATAATAT
41085421 ATTT
1 ATTT
41085425 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.55
Consensus pattern (25 bp):
ATTTAGCATTTTATTAGCATAATAT
Found at i:41085435 original size:24 final size:24
Alignment explanation
Indices: 41085391--41085436 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41085381 TTTATTAGTT
*
41085391 TAATATATTTAGCATTTATTAGCA
1 TAATATATTTAGCATTGATTAGCA
41085415 TAATATATTT-GACATTGATTAG
1 TAATATATTTAG-CATTGATTAG
41085437 AATTAGGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (24 bp):
TAATATATTTAGCATTGATTAGCA
Found at i:41088918 original size:29 final size:29
Alignment explanation
Indices: 41088876--41088934 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
41088866 TCGTGGAAGA
*
41088876 GGTGAAGAACTTGTTCATTGAGAGTTCGT
1 GGTGAAGAACTTGTTCATTGAGAATTCGT
*
41088905 GGTGAAGAACTTGTTCGTTGAGAATTCGT
1 GGTGAAGAACTTGTTCATTGAGAATTCGT
41088934 G
1 G
41088935 TCAATGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.10, G:0.32, T:0.34
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCATTGAGAATTCGT
Found at i:41089082 original size:24 final size:24
Alignment explanation
Indices: 41089025--41089076 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
41089015 TTTCTAGAAG
* *
41089025 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
41089049 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
41089073 ATTT
1 ATTT
41089077 GACATTGATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:41089087 original size:24 final size:24
Alignment explanation
Indices: 41089025--41089088 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
41089015 TTTCTAGAAG
* * *
41089025 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTGATTAGCATAATAT
*
41089049 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTGATTAGCATAATAT
41089073 ATTT-GACATTGATTAG
1 ATTTAG-CATTGATTAG
41089089 AATTAGGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
23 1 0.03
24 35 0.97
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (24 bp):
ATTTAGCATTGATTAGCATAATAT
Found at i:41090334 original size:31 final size:31
Alignment explanation
Indices: 41090299--41090358 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
41090289 TTCTAAAAGG
* *
41090299 AAAATCGAATTCAAATTTTAGAAACAATAAA
1 AAAATAGAATTCAAATTTTAAAAACAATAAA
* *
41090330 AAAATAGAATTTAAATTTTAAAAATAATA
1 AAAATAGAATTCAAATTTTAAAAACAATA
41090359 TGGTTAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.30
Consensus pattern (31 bp):
AAAATAGAATTCAAATTTTAAAAACAATAAA
Found at i:41105762 original size:14 final size:13
Alignment explanation
Indices: 41105737--41105766 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
41105727 AAATTTTAAA
41105737 AATAAAAATATAT
1 AATAAAAATATAT
41105750 AATAAATAATATAT
1 AATAAA-AATATAT
41105764 AAT
1 AAT
41105767 TGTTTACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAAAAATATAT
Found at i:41105818 original size:28 final size:29
Alignment explanation
Indices: 41105779--41105848 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
41105769 TTTACAAATT
*
41105779 TAAAAATATATTAGAAA-TTGAAAATACTG
1 TAAAAAT-TATTAGAAATTTGAAAAGACTG
* *
41105808 TAAAAATTATTAGAAATTTTAAAAGATTG
1 TAAAAATTATTAGAAATTTGAAAAGACTG
41105837 TAAAAAATTATT
1 T-AAAAATTATT
41105849 TAAAAAATTT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.25
29 17 0.47
30 10 0.28
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (29 bp):
TAAAAATTATTAGAAATTTGAAAAGACTG
Found at i:41105831 original size:29 final size:26
Alignment explanation
Indices: 41105769--41105874 Score: 86
Period size: 29 Copynumber: 3.7 Consensus size: 26
41105759 TATATAATTG
* *
41105769 TTTACAAATTTAAAAATATATTAGAAA
1 TTTAAAAATGTAAAAAT-TATTAGAAA
*
41105796 TTGAAAATACTGTAAAAATTATTAGAAA
1 TTTAAAA-A-TGTAAAAATTATTAGAAA
*
41105824 TTTTAAAAGATTGTAAAAAATTATTTAAAAAA
1 -TTTAAAA-A-TGT-AAAAATTA-TT-AGAAA
41105856 TTTAAAAATAGTAAAAATT
1 TTTAAAAAT-GTAAAAATT
41105875 GTTATATCTT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
27 5 0.08
28 10 0.15
29 26 0.40
30 11 0.17
31 9 0.14
32 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.07, T:0.36
Consensus pattern (26 bp):
TTTAAAAATGTAAAAATTATTAGAAA
Found at i:41105845 original size:30 final size:28
Alignment explanation
Indices: 41105780--41105872 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 28
41105770 TTACAAATTT
* *
41105780 AAAAATATATTAGAAATTGAAAATACTGT-
1 AAAAAT-TATTAGAAATTTAAAA-ATTGTA
41105809 AAAAATTATTAGAAATTTTAAAAGATTGTA
1 AAAAATTATTAGAAA-TTTAAAA-ATTGTA
* *
41105839 AAAAATTATTTAAAAAATTTAAAAATAGTA
1 AAAAATTA-TT-AGAAATTTAAAAATTGTA
41105869 AAAA
1 AAAA
41105873 TTGTTATATC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
28 9 0.16
29 16 0.29
30 17 0.31
31 9 0.16
32 4 0.07
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (28 bp):
AAAAATTATTAGAAATTTAAAAATTGTA
Found at i:41112105 original size:124 final size:123
Alignment explanation
Indices: 41111833--41112145 Score: 405
Period size: 124 Copynumber: 2.5 Consensus size: 123
41111823 TGAAGCGTTA
* *
41111833 TTGACACTAT-TTTT-ACGTAACCGTCTTCTCAAATTTATTTTCTCAAGAACTACTATAGAAAAA
1 TTGACACTATCTTTTCA-G-AATCGTCTTCTCAAA---ATTTTTTCAAGAACTACTATAGAAAAA
*
41111896 GAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCCTACTTGAAGAGTTT
61 GAGCATCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCCTACTTAAAGAGTTT
* * * * *
41111959 TTTACACTATTTTTTCAGAATCGTCTTCTCAAAATTTTTTCAAGAACTACTGTAGAAAAATAGCG
1 TTGACACTATCTTTTCAGAATCGTCTTCTCAAAATTTTTTCAAGAACTACTATAGAAAAAGAGCA
* * * * *
41112024 TCCACGTGGGAGCTTTTTTTCAGTACTTTTGCTGACAGTGCATCCTGCTTAAAGCGTTT
66 TCCACGTGAGAGC-TTTTTTCAGTAATTTTGCTAACAGTGCATCCTACTTAAAGAGTTT
*
41112083 TTGACATTATCTTTTCAGAATCGTCTTCTCAAAATTAATTTTTCAAGAACTACTATAGAAAAA
1 TTGACACTATCTTTTCAGAATCGTCTTCTCAAAA-T--TTTTTCAAGAACTACTATAGAAAAA
41112146 ACAAAATTCT
Statistics
Matches: 165, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
123 40 0.24
124 71 0.43
125 1 0.01
126 23 0.14
127 29 0.18
128 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (123 bp):
TTGACACTATCTTTTCAGAATCGTCTTCTCAAAATTTTTTCAAGAACTACTATAGAAAAAGAGCA
TCCACGTGAGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATCCTACTTAAAGAGTTT
Found at i:41112305 original size:35 final size:34
Alignment explanation
Indices: 41112224--41112358 Score: 157
Period size: 34 Copynumber: 3.9 Consensus size: 34
41112214 AGCTAAACAC
* * *
41112224 AATTATTTTAAAAAAACCTAAACCTTAATTTAATT
1 AATT-TTTTTAAAAATCCTAAACCCTAATTTAATT
41112259 AATTTTTTTAAAAATCCTAAACCCTAATTTAATT
1 AATTTTTTTAAAAATCCTAAACCCTAATTTAATT
* * * *
41112293 AATTTTACTTAAAACTCCTAAAACCTAATTCAATT
1 AATTTT-TTTAAAAATCCTAAACCCTAATTTAATT
41112328 AATTTTTTTTAAAAAAT--TAAACCCTAATTTA
1 AA-TTTTTTT-AAAAATCCTAAACCCTAATTTA
41112359 TTTTTTAAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
34 45 0.52
35 32 0.37
36 9 0.10
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.41
Consensus pattern (34 bp):
AATTTTTTTAAAAATCCTAAACCCTAATTTAATT
Found at i:41120834 original size:1 final size:1
Alignment explanation
Indices: 41120828--41120859 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
41120818 GGCTTGTAGG
*
41120828 TTTTTTTTTTTTTTTTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
41120860 ATTGATAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:41133955 original size:25 final size:25
Alignment explanation
Indices: 41133927--41133978 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
41133917 GAAAGCTGAT
41133927 AATAACAAACATTCGCTAAGCCAAG
1 AATAACAAACATTCGCTAAGCCAAG
* * * *
41133952 AATAACGAACGTTTGCTAAGCCGAG
1 AATAACAAACATTCGCTAAGCCAAG
41133977 AA
1 AA
41133979 CACAAGTACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.44, C:0.21, G:0.17, T:0.17
Consensus pattern (25 bp):
AATAACAAACATTCGCTAAGCCAAG
Found at i:41144464 original size:20 final size:20
Alignment explanation
Indices: 41144439--41144497 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
41144429 AAGCCATCAA
41144439 TAATGCAGATAAACTGCCAG
1 TAATGCAGATAAACTGCCAG
* * *
41144459 TAATGCAGACAAGCTACCAG
1 TAATGCAGATAAACTGCCAG
* *
41144479 TATTACAGATAAACTGCCA
1 TAATGCAGATAAACTGCCA
41144498 ATGTGGACAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
TAATGCAGATAAACTGCCAG
Found at i:41144470 original size:40 final size:40
Alignment explanation
Indices: 41144392--41144497 Score: 106
Period size: 40 Copynumber: 2.6 Consensus size: 40
41144382 GTGGACGAAA
* * **
41144392 CCACCAA-AATTGCAGACAAGCTGCCAGTAATATGGACAAG
1 CCACCAATAA-TGCAGATAAACTGCCAGTAATACAGACAAG
* *
41144432 CCATCAATAATGCAGATAAACTGCCAGTAATGCAGACAAG
1 CCACCAATAATGCAGATAAACTGCCAGTAATACAGACAAG
* * * *
41144472 CTACCAGTATTACAGATAAACTGCCA
1 CCACCAATAATGCAGATAAACTGCCA
41144498 ATGTGGACAA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 52 0.96
41 2 0.04
ACGTcount: A:0.41, C:0.25, G:0.17, T:0.18
Consensus pattern (40 bp):
CCACCAATAATGCAGATAAACTGCCAGTAATACAGACAAG
Found at i:41148617 original size:40 final size:40
Alignment explanation
Indices: 41148573--41148844 Score: 483
Period size: 40 Copynumber: 6.8 Consensus size: 40
41148563 ATAACCACAA
41148573 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
*
41148613 GCACAAATGCCTTCGGGTCTTAGCCCGGGTATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
41148653 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
41148693 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
41148733 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
* *
41148773 GCACAAATGCCTTCGGGTCTTAGCCCGGATAAAATC-ACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGAT-ATATCAACTC
* *
41148813 GCACAATTGCCTTCGGGACTTAGCCCGGATAT
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAT
41148845 CATTCAAATG
Statistics
Matches: 224, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
39 1 0.00
40 219 0.98
41 4 0.02
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTC
Found at i:41152358 original size:43 final size:43
Alignment explanation
Indices: 41152310--41152444 Score: 150
Period size: 43 Copynumber: 3.2 Consensus size: 43
41152300 CCAGATGTGT
* * *
41152310 TCTTACATGTAATCACATATCGATACCACTGTCCCAGACAGGG
1 TCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGG
* * * *
41152353 TCTTACACG-AATTAAATA-CAATGCCAATGTCCCAGACATGG
1 TCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGG
* * *
41152394 TCTTACACGTAAACACAAATCGATGCCAATGTTCCAGAC-GTGG
1 TCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAG-GG
41152437 TCTTACAC
1 TCTTACAC
41152445 AAAAACACAT
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 28 0.37
42 12 0.16
43 35 0.47
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (43 bp):
TCTTACACGTAATCACATATCGATGCCAATGTCCCAGACAGGG
Found at i:41152431 original size:84 final size:84
Alignment explanation
Indices: 41152285--41152444 Score: 214
Period size: 84 Copynumber: 1.9 Consensus size: 84
41152275 GGAAGGCTCG
** * * * * *
41152285 TACAATGCCAACGTCCCAGATGTGTTCTTACATGTAATCACATATCGATACCACTGTCCCAGACA
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCGATACCAATGTCCCAGAC-
41152350 G-GGTCTTACACGAATTAAA
65 GTGGTCTTACACGAATTAAA
* * *
41152369 TACAATGCCAATGTCCCAGACATGGTCTTACACGTAAACACAAATCGATGCCAATGTTCCAGACG
1 TACAATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCGATACCAATGTCCCAGACG
41152434 TGGTCTTACAC
66 TGGTCTTACAC
41152445 AAAAACACAT
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
83 1 0.02
84 64 0.98
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (84 bp):
TACAATGCCAACGTCCCAGACATGGTCTTACACGTAAACACAAATCGATACCAATGTCCCAGACG
TGGTCTTACACGAATTAAA
Found at i:41157761 original size:11 final size:11
Alignment explanation
Indices: 41157711--41157763 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
41157701 ATAAAAGTTC
41157711 TAAAATA-AAT
1 TAAAATAGAAT
41157721 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
41157734 TCAAAATAGACT
1 T-AAAATAGAAT
*
41157746 CAAAATAGAAT
1 TAAAATAGAAT
41157757 TAAAATA
1 TAAAATA
41157764 ACCATTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:41159493 original size:100 final size:99
Alignment explanation
Indices: 41159369--41159733 Score: 448
Period size: 100 Copynumber: 3.7 Consensus size: 99
41159359 TAACTCGCAA
** * * * * *
41159369 CTTTAAT-CTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 CTTTAATCCT-TTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
* * *
41159433 ACTACACCGCCTAGGAAGTAAGATTTGCTGTTGTAG
65 ACTGCATCGCC-AGGAGGTAAGATTTGCTGTTGTAG
* * **
41159469 CTTTAATCCTTTTAACTGTAATGTCGGGGAAGCAAGATTCACTAATGTGGCTTTAATCTGTTCCA
1 CTTTAATCCTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * *
41159534 CTGCATCGTCAAGGAGGTAAGATTTGCTGCTGTGG
66 CTGCATCG-CCAGGAGGTAAGATTTGCTGTTGTAG
* * *
41159569 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAG-TTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCCTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
*
41159633 CTGCATCGCCAGGGAGGTAAGATTCGCTGTTGTAG
66 CTGCATCGCCA-GGAGGTAAGATTTGCTGTTGTAG
** *
41159668 CTTTAATATTTTTAACTGCAGTGTC-AGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
1 CTTTAATCCTTTTAACTGCAATGTCGA-GGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
41159732 AC
65 AC
41159734 GATGTGGCTT
Statistics
Matches: 234, Mismatches: 26, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
98 2 0.01
99 85 0.36
100 144 0.62
101 3 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (99 bp):
CTTTAATCCTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
CTGCATCGCCAGGAGGTAAGATTTGCTGTTGTAG
Found at i:41159500 original size:50 final size:49
Alignment explanation
Indices: 41159446--41159725 Score: 152
Period size: 50 Copynumber: 5.6 Consensus size: 49
41159436 ACACCGCCTA
* *
41159446 GGAAGTAAGATTTGCTGTTGTAGCTTTAATCCTTTTAACTGTAATGTCGG
1 GGAAGTAAGATTTGCTGATGTGGCTTTAATCCTTTTAACTG-AATGTCGG
* ** * ** * **
41159496 GGAAGCAAGATTCACTAATGTGGCTTTAAT-CTGTTCCACTGCATCGTCAA
1 GGAAGTAAGATTTGCTGATGTGGCTTTAATCCT-TTTAACTGAAT-GTCGG
* * *
41159546 GGAGGTAAGATTTGCTGCTGTGGCTTTAATCTTTTTAACTGCAATGTCGG
1 GGAAGTAAGATTTGCTGATGTGGCTTTAATCCTTTTAACTG-AATGTCGG
* ** * * ** * * *
41159596 GGAAGCAAG-TTCACCGATGTGGCTTTAAT-CTGCTCCACTGCATCGCCAG
1 GGAAGTAAGATTTGCTGATGTGGCTTTAATCCT-TTTAACTGAAT-GTCGG
* * * * ** * *
41159645 GGAGGTAAGATTCGCTGTTGTAGCTTTAATATTTTTAACTGCAGTGTCAG
1 GGAAGTAAGATTTGCTGATGTGGCTTTAATCCTTTTAACTG-AATGTCGG
* ** *
41159695 GGAAGCAAGATTCACCGATGTGGCTTTAATC
1 GGAAGTAAGATTTGCTGATGTGGCTTTAATC
41159726 TGTTCCACGA
Statistics
Matches: 165, Mismatches: 56, Indels: 18
0.69 0.23 0.08
Matches are distributed among these distances:
48 3 0.02
49 35 0.21
50 122 0.74
51 5 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (49 bp):
GGAAGTAAGATTTGCTGATGTGGCTTTAATCCTTTTAACTGAATGTCGG
Found at i:41159718 original size:199 final size:200
Alignment explanation
Indices: 41159369--41159733 Score: 518
Period size: 199 Copynumber: 1.8 Consensus size: 200
41159359 TAACTCGCAA
** * * * *
41159369 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTAGCTTCAATCTGCTCCA
* * * *
41159434 CTACACCGCCTAGGAAGTAAGATTTGCTGTTGTAGCTTTAATCCTTTTAACTGTAATGTCGGGGA
66 CTACACCGCCTAGGAAGTAAGATTCGCTGTTGTAGCTTTAATACTTTTAACTGCAATGTCAGGGA
*
41159499 AGCAAGATTCACTAATGTGGCTTTAATCTGTTCCACTGCATCGTCAAGGAGGTAAGATTTGCTGC
131 AGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGTCAAGGAGGTAAGATTTGCTGC
41159564 TGTGG
196 TGTGG
* * * *
41159569 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAG-TTCACCGATGTGGCTTTAATCTGCTCCA
1 CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTAGCTTCAATCTGCTCCA
* * * * *
41159633 CTGCATCGCC-AGGGAGGTAAGATTCGCTGTTGTAGCTTTAATATTTTTAACTGCAGTGTCAGGG
66 CTACACCGCCTA-GGAAGTAAGATTCGCTGTTGTAGCTTTAATACTTTTAACTGCAATGTCAGGG
*
41159697 AAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCAC
130 AAGCAAGATTCACCAATGTGGCTTTAATCTGTTCCAC
41159734 GATGTGGCTT
Statistics
Matches: 143, Mismatches: 21, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
198 1 0.01
199 110 0.77
200 32 0.22
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (200 bp):
CTTTAATCTGTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTAGCTTCAATCTGCTCCA
CTACACCGCCTAGGAAGTAAGATTCGCTGTTGTAGCTTTAATACTTTTAACTGCAATGTCAGGGA
AGCAAGATTCACCAATGTGGCTTTAATCTGTTCCACTGCATCGTCAAGGAGGTAAGATTTGCTGC
TGTGG
Found at i:41159740 original size:23 final size:23
Alignment explanation
Indices: 41159710--41159755 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
41159700 CAAGATTCAC
*
41159710 CGATGTGGCTTTAATCTGTTCCA
1 CGATGTGGCTTTAATCTGCTCCA
41159733 CGATGTGGCTTTAATCTGCTCCA
1 CGATGTGGCTTTAATCTGCTCCA
41159756 TTGCATCGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (23 bp):
CGATGTGGCTTTAATCTGCTCCA
Found at i:41159994 original size:98 final size:98
Alignment explanation
Indices: 41159825--41160023 Score: 353
Period size: 98 Copynumber: 2.0 Consensus size: 98
41159815 GAGATAAGAC
*
41159825 CTGATGCGACCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
1 CTGATGCGACCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
*
41159890 TAATCTCAGGGAGATAAGATTTCTGGCTTCAAT
66 TAATCTCAGGGAGATAAGATTTCTAGCTTCAAT
* * *
41159923 CTGATGCGACCTACTCCACTGTAACTTCAGAGAGATAATATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGACCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
41159988 TAATCTCAGGGAGATAAGATTTCTAGCTTCAAT
66 TAATCTCAGGGAGATAAGATTTCTAGCTTCAAT
41160021 CTG
1 CTG
41160024 TGGCTTAAAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.33
Consensus pattern (98 bp):
CTGATGCGACCTACTCCACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCACTCCACTA
TAATCTCAGGGAGATAAGATTTCTAGCTTCAAT
Found at i:41161358 original size:14 final size:14
Alignment explanation
Indices: 41161339--41161380 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
41161329 TTAGCCTCTC
41161339 CATTTTTACCTTTT
1 CATTTTTACCTTTT
* *
41161353 CATTTTCA-TTTTT
1 CATTTTTACCTTTT
41161366 CATTTTTCACCTTTT
1 CATTTTT-ACCTTTT
41161381 TTTTTGAGAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.14, C:0.21, G:0.00, T:0.64
Consensus pattern (14 bp):
CATTTTTACCTTTT
Found at i:41162345 original size:15 final size:16
Alignment explanation
Indices: 41162322--41162358 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
41162312 TTTTCTCTCA
41162322 TTTTT-ATTTTGAT-T
1 TTTTTGATTTTGATGT
41162336 TTTTTGATTTTGATGT
1 TTTTTGATTTTGATGT
41162352 TTTTTGA
1 TTTTTGA
41162359 AAGGATCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.24
15 8 0.38
16 8 0.38
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.73
Consensus pattern (16 bp):
TTTTTGATTTTGATGT
Found at i:41165874 original size:31 final size:31
Alignment explanation
Indices: 41165836--41165896 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
41165826 AACTTGTGAG
*
41165836 GGAGTACTAAGTCTGGAACCAAGCTCAGATA
1 GGAGTACTAAGTCTGAAACCAAGCTCAGATA
41165867 GGAGTACTAAGTCTGAAACCAAGCTCAGAT
1 GGAGTACTAAGTCTGAAACCAAGCTCAGAT
41165897 CTTTTGCATC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (31 bp):
GGAGTACTAAGTCTGAAACCAAGCTCAGATA
Found at i:41168633 original size:11 final size:11
Alignment explanation
Indices: 41168583--41168635 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
41168573 ATAAAAGTTC
41168583 TAAAATA-AAT
1 TAAAATAGAAT
41168593 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
41168606 TCAAAATAGACT
1 T-AAAATAGAAT
*
41168618 CAAAATAGAAT
1 TAAAATAGAAT
41168629 TAAAATA
1 TAAAATA
41168636 ACCATTGAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:41174990 original size:16 final size:17
Alignment explanation
Indices: 41174956--41174990 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
41174946 TCATCAAGCT
*
41174956 TTAAAAATAACTTTTAA
1 TTAAAAATAACTTTGAA
41174973 TTAAAAATAA-TTTGAA
1 TTAAAAATAACTTTGAA
41174989 TT
1 TT
41174991 GTGATGTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAAAATAACTTTGAA
Found at i:41177535 original size:45 final size:45
Alignment explanation
Indices: 41177471--41177562 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
41177461 CAAATACTCA
* *
41177471 GTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCCG
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCG
*
41177516 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCG
1 GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCG
41177561 GT
1 GT
41177563 TCACATAGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCG
Found at i:41177626 original size:51 final size:51
Alignment explanation
Indices: 41177559--41177754 Score: 227
Period size: 51 Copynumber: 3.9 Consensus size: 51
41177549 CAATGATGTT
* * * *
41177559 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATC
* * * *
41177610 CGATACACGTAGTAGCCTACACATAGTACTACACACATGATCGA-AACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATAACTATC
* * * * * *
41177661 CGGTACGCATAGTAGCTTGCACATAGTACTACACATGCGACC-TATC-ATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTA-TC
41177711 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
41177755 CACTTTCACT
Statistics
Matches: 118, Mismatches: 23, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
49 1 0.01
50 42 0.36
51 73 0.62
52 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATAACTATC
Found at i:41177774 original size:101 final size:100
Alignment explanation
Indices: 41177565--41177746 Score: 269
Period size: 101 Copynumber: 1.8 Consensus size: 100
41177555 TGTTCGGTTC
* *
41177565 ACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACTATCCGATACACGTAGTAGCCTAC
1 ACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTAC
*
41177630 ACATAGTACTACACACATGATCGAAACTATCCGGT
66 ACATAGTACTACACACATGATCCAAACTATCCGGT
* *
41177665 ACGCATAGTAGCTTGCACATAGTACTACACATGCGACCTATCA-T-TCCGGTACACGTAGTAGCC
1 A--CATAGTAGCCTGCACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCC
*
41177728 TGCACATAGTACTACACAC
63 TACACATAGTACTACACAC
41177747 GTGACCATCA
Statistics
Matches: 74, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
100 1 0.01
101 36 0.49
102 34 0.46
103 3 0.04
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (100 bp):
ACATAGTAGCCTGCACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTAC
ACATAGTACTACACACATGATCCAAACTATCCGGT
Found at i:41179667 original size:26 final size:26
Alignment explanation
Indices: 41179638--41179693 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
41179628 AATTTGTGAG
41179638 AATTGAATCAAATCAAAATT-ATATAT
1 AATT-AATCAAATCAAAATTCATATAT
* *
41179664 AATTACTCAAATCAAAATTCATGTAT
1 AATTAATCAAATCAAAATTCATATAT
41179690 AATT
1 AATT
41179694 TACCTACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.36
Consensus pattern (26 bp):
AATTAATCAAATCAAAATTCATATAT
Found at i:41179723 original size:29 final size:26
Alignment explanation
Indices: 41179645--41179723 Score: 90
Period size: 25 Copynumber: 2.9 Consensus size: 26
41179635 GAGAATTGAA
41179645 TCAAATCAAAATTATATATAA-TTAC
1 TCAAATCAAAATTATATATAATTTAC
*
41179670 TCAAATCAAAATTCATGTATAATTTACC
1 TCAAATCAAAATT-ATATATAATTTA-C
41179698 TACTAAA-CTAAAATTATATATAATTT
1 T-C-AAATC-AAAATTATATATAATTT
41179724 TAAGATTTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 13 0.28
26 7 0.15
27 3 0.07
28 2 0.04
29 12 0.26
30 9 0.20
ACGTcount: A:0.48, C:0.13, G:0.01, T:0.38
Consensus pattern (26 bp):
TCAAATCAAAATTATATATAATTTAC
Found at i:41181738 original size:14 final size:16
Alignment explanation
Indices: 41181711--41181743 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
41181701 TATCAACTGG
41181711 AATCGAAGTGTTGGAA
1 AATCGAAGTGTTGGAA
41181727 AATC-AAGT-TTGGAA
1 AATCGAAGTGTTGGAA
41181741 AAT
1 AAT
41181744 TCAACGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
15 4 0.24
16 4 0.24
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (16 bp):
AATCGAAGTGTTGGAA
Found at i:41187538 original size:23 final size:23
Alignment explanation
Indices: 41187495--41187539 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41187485 ATGGGAAACT
*
41187495 TAAAATAATATTACATAATAAAG
1 TAAAATAATAGTACATAATAAAG
*
41187518 TAAAATAAT-GTATATACATAAA
1 TAAAATAATAGTACATA-ATAAA
41187540 AAAATAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
TAAAATAATAGTACATAATAAAG
Found at i:41189272 original size:44 final size:44
Alignment explanation
Indices: 41188997--41189557 Score: 326
Period size: 44 Copynumber: 12.9 Consensus size: 44
41188987 TAACATTTGC
*
41188997 TATCTTCAGTCTGCTCCACTGCAACTTGAGGGAGATAAGACTTG
1 TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * * * * *
41189041 TAGCTTCCACT-TGCTTCACTGTAATTTC-GAGGAAATAA-AGTCTG
1 TATCTT-CAGTCTGCTCCACTGCAACTTCAG-GGAGATAAGACT-TG
* * * *
41189085 -A--TGC-GATTTGC-CCTACTGCAACTTCAGAGAGATAAGA--TC
1 TATCTTCAG-TCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTTG
* * * * * *
41189124 AATCATTTTAATCCGCTCTACTGCAACTTCAGGGAGATAAGATTTG
1 TATC--TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
*
41189170 TCA-C-T---T-T-CTCCACTGCAACTTCAGGGAGACAAGA-TTCG
1 T-ATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G
* * * * **
41189208 CCATCTTCAGTTTGCCCCACTACAACTTCAAAG-GATAAGACTTG
1 -TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* *
41189252 CTTTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGACTTG
1 -TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * * * *
41189297 TAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTA
1 TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * * *
41189340 T-TGGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTAC
1 TAT--CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-G
* *
41189386 CATCTTCAGTCTGCCCCACTGCAACTTCAGGG-GATAAGACTTG
1 TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * *
41189429 TTTTCTTCAGTCTGCTCCACTGCAACTTTAGAGAGATAAGACTTG
1 -TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
* * * * * *
41189474 TAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAGGATTATTGG
1 TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA--CTT-G
* *
41189521 T-T-TT-AATCTGTTCCACTGCAACTTCAGGGAGATAAGA
1 TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
41189558 TTTGCCATCT
Statistics
Matches: 400, Mismatches: 78, Indels: 78
0.72 0.14 0.14
Matches are distributed among these distances:
37 2 0.00
38 27 0.07
39 2 0.00
40 6 0.01
41 19 0.05
42 2 0.00
43 9 0.02
44 253 0.63
45 72 0.18
46 4 0.01
47 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (44 bp):
TATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG
Found at i:41189423 original size:177 final size:176
Alignment explanation
Indices: 41189099--41189569 Score: 650
Period size: 177 Copynumber: 2.7 Consensus size: 176
41189089 GATTTGCCCT
* ** * * *
41189099 ACTGCAACTTCAGAGAGATAAGA-TCAATCATTTTAATCCGCTCTACTGCAACTTCAGGGAGATA
1 ACTGCAACTTAAGAGAGATAAGACT-TGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
* * * * * * *
41189163 AGA-T-TT-G-TCACT-TTCTCCACTGCAACTTCAGGGAGACAAGATTCGCCATCTTCAGTTTGC
65 GGATTATTGGTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGC
41189223 CCCACTACAACTTCAAAGGATAAGACTTGCTTTCTTCAGTCTGCTCC
130 CCCACTACAACTTCAAAGGATAAGACTTGCTTTCTTCAGTCTGCTCC
41189270 ACTGCAACTTCAAG-GAGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTT-AAGAGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATA
* *
41189334 GGATTATTGGCTTTAATCTGCTCCACTACAACTTCAGGGAGATAAGATTTACCATCTTCAGTCTG
65 GGATTATTGG-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTG
* ** *
41189399 CCCCACTGCAACTTCAGGGGATAAGACTTGTTTTCTTCAGTCTGCTCC
129 CCCCACTACAACTTCAAAGGATAAGACTTGCTTTCTTCAGTCTGCTCC
* * *
41189447 ACTGCAACTTTAGAGAGATAAGACTTGTAACTTTAATCTGCTCCACTACAACTTCAGGGAGATAG
1 ACTGCAACTTAAGAGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
*
41189512 GATTATTGGTTTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTC
66 GATTATTGG-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTC
41189570 TTCAATCCAT
Statistics
Matches: 265, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
171 55 0.21
172 4 0.02
173 2 0.01
174 1 0.00
176 5 0.02
177 198 0.75
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (176 bp):
ACTGCAACTTAAGAGAGATAAGACTTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAG
GATTATTGGTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCC
CCACTACAACTTCAAAGGATAAGACTTGCTTTCTTCAGTCTGCTCC
Found at i:41189569 original size:133 final size:133
Alignment explanation
Indices: 41189103--41189557 Score: 378
Period size: 133 Copynumber: 3.5 Consensus size: 133
41189093 TGCCCTACTG
* ** * * * * *
41189103 CAACTTCAGAGAGATAAGATCAATCAT-TTTAATCCGCTCTACTGCAACTTCAGGGAGATAAGAT
1 CAACTTCAGGGAGATAAGATTTACCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * * * * * * *
41189167 TTGTCA-CTT---T---CTCCACTGCAACTTCAGGGAGACAAGATTCGCCATCTTCAGTTTGCCC
66 TTGT-ATCTTCAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTAG-TAACTTTAATCTGCTC
41189225 CACTA
129 CACTA
** * * ** * *
41189230 CAACTTCAAAG-GATAAGACTTGCTTTCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAGAC
1 CAACTTCAGGGAGATAAGATTTACCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * * * **
41189294 TTGTAACTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCA
66 TTGTATCTTCAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTAGTAACTTTAATCTGCTCCA
41189359 CTA
131 CTA
* *
41189362 CAACTTCAGGGAGATAAGATTTACCATCTTCAGTCTGCCCCACTGCAACTTCAGGG-GATAAGAC
1 CAACTTCAGGGAGATAAGATTTACCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * *
41189426 TTGTTTTCTTCAGTCTGCTCCACTGCAACTTTAGAGAGATAAGACTT-GTAACTTTAATCTGCTC
66 TTG-TATCTTCAATCCGCTCCACTGCAACTTCAGAGAGATAAGA-TTAGTAACTTTAATCTGCTC
41189490 CACTA
129 CACTA
* *** * *
41189495 CAACTTCAGGGAGATAGGA-TTATTGGT-TTTAATCTGTTCCACTGCAACTTCAGGGAGATAAGA
1 CAACTTCAGGGAGATAAGATTTA-CCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
41189558 TTTGCCATCT
Statistics
Matches: 263, Mismatches: 52, Indels: 20
0.79 0.16 0.06
Matches are distributed among these distances:
126 9 0.03
127 48 0.18
130 1 0.00
132 61 0.23
133 142 0.54
134 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (133 bp):
CAACTTCAGGGAGATAAGATTTACCATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
TTGTATCTTCAATCCGCTCCACTGCAACTTCAGAGAGATAAGATTAGTAACTTTAATCTGCTCCA
CTA
Found at i:41191517 original size:18 final size:18
Alignment explanation
Indices: 41191487--41191870 Score: 194
Period size: 18 Copynumber: 21.1 Consensus size: 18
41191477 ATCGAAACAG
41191487 AAATTTTTG-AAACACGA
1 AAATTTTTGAAAACACGA
* *
41191504 GAATTGTTGAAAACACGA
1 AAATTTTTGAAAACACGA
* * *
41191522 ACA-TTTTGAAAAAAAGA
1 AAATTTTTGAAAACACGA
*
41191539 AAATTTTTG-AAATACGA
1 AAATTTTTGAAAACACGA
41191556 GAAATTTTTGAAAACACGA
1 -AAATTTTTGAAAACACGA
*
41191575 AAATTTTTTG-AATCACCG-
1 AAA-TTTTTGAAAACA-CGA
41191593 AAATTTTTGAAAACACGA
1 AAATTTTTGAAAACACGA
*
41191611 AGATTTTTG-AAACACCG-
1 AAATTTTTGAAAACA-CGA
*
41191628 GAATTTTTGAAAACA-GA
1 AAATTTTTGAAAACACGA
* *
41191645 AGGATTTTTG-AAACAAGA
1 A-AATTTTTGAAAACACGA
41191663 AAATTTTTGAAAACACGA
1 AAATTTTTGAAAACACGA
*
41191681 AAATTTATCTTTAAAAACATGCG-
1 AAA--T-T-TTTGAAAACA--CGA
* *
41191704 AATTTTTTAAAAACACGA
1 AAATTTTTGAAAACACGA
* *
41191722 AAATTTTAT-AAAAAATTGTGA
1 AAATTTT-TGAAAACA---CGA
* *
41191743 AAATTCTTGAAAACACGG
1 AAATTTTTGAAAACACGA
*
41191761 AAATCTTTTG-AATCACTG-
1 AAAT-TTTTGAAAACAC-GA
* *
41191779 AAATTCTTGAAAACACAAAAA
1 AAATTTTTGAAAACAC---GA
* *
41191800 AAAATTTTG-AAACGCTG-
1 AAATTTTTGAAAACAC-GA
* *
41191817 GAATTTTGGAAAACA--A
1 AAATTTTTGAAAACACGA
*
41191833 AATTATTTTTG-AAACATGA
1 AA--ATTTTTGAAAACACGA
41191852 AAA-TTTTGAAAACACGA
1 AAATTTTTGAAAACACGA
41191869 AA
1 AA
41191871 GCACGAAAAT
Statistics
Matches: 281, Mismatches: 47, Indels: 78
0.69 0.12 0.19
Matches are distributed among these distances:
16 7 0.02
17 85 0.30
18 112 0.40
19 34 0.12
20 8 0.03
21 22 0.08
22 9 0.03
23 2 0.01
24 2 0.01
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (18 bp):
AAATTTTTGAAAACACGA
Found at i:41191528 original size:35 final size:34
Alignment explanation
Indices: 41191480--41191870 Score: 236
Period size: 35 Copynumber: 10.8 Consensus size: 34
41191470 CGATCCGATC
* *
41191480 GAAACA-GAAATTTTTG-AAACACGAGAATTGTT
1 GAAACACGAAATTTTTGAAAACACGAAAATTTTT
* *
41191512 GAAAACACGAACA-TTTTGAAAAAAAGAAAATTTTT
1 G-AAACACGAA-ATTTTTGAAAACACGAAAATTTTT
*
41191547 GAAATACGAGAAATTTTTGAAAACACGAAAATTTTTT
1 GAAACAC--GAAATTTTTGAAAACACGAAAA-TTTTT
* *
41191584 GAATCACCGAAATTTTTGAAAACACGAAGATTTTT
1 GAAACA-CGAAATTTTTGAAAACACGAAAATTTTT
* *
41191619 GAAACACCGGAATTTTTGAAAACA-GAAGGATTTTT
1 GAAACA-CGAAATTTTTGAAAACACGAA-AATTTTT
*
41191654 GAAACAAGAAAATTTTTGAAAACACGAAAATTTATCTTT
1 GAAACACG-AAATTTTTGAAAACACGAAAA--T-T-TTT
* * *
41191693 AAAAACATGCGAATTTTTTAAAAACACGAAAATTTTAT
1 -GAAACA--CGAAATTTTTGAAAACACGAAAATTTT-T
* * * * *
41191731 AAAAAATTGTGAAAATTCTTGAAAACACGGAAATCTTTT
1 GAAACA---CG-AAATTTTTGAAAACACGAAAAT-TTTT
* * * *
41191770 GAATCACTGAAATTCTTGAAAACACAAAAAAAAATTTT
1 GAAACAC-GAAATTTTTGAAAACAC---GAAAATTTTT
* * *
41191808 GAAACGCTGGAATTTTGGAAAACA--AAATTATTTTT
1 GAAACAC-GAAATTTTTGAAAACACGAAA--ATTTTT
* *
41191843 GAAACATGAAAATTTTGAAAACACGAAA
1 GAAACACGAAATTTTTGAAAACACGAAA
41191871 GCACGAAAAT
Statistics
Matches: 285, Mismatches: 43, Indels: 58
0.74 0.11 0.15
Matches are distributed among these distances:
32 1 0.00
33 8 0.03
34 30 0.11
35 80 0.28
36 61 0.21
37 18 0.06
38 30 0.11
39 29 0.10
40 8 0.03
41 19 0.07
42 1 0.00
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.29
Consensus pattern (34 bp):
GAAACACGAAATTTTTGAAAACACGAAAATTTTT
Found at i:41192400 original size:10 final size:10
Alignment explanation
Indices: 41192381--41192420 Score: 62
Period size: 10 Copynumber: 3.9 Consensus size: 10
41192371 AAATTGAACC
41192381 TTTTTTTCTT
1 TTTTTTTCTT
*
41192391 TTTCTTTCTT
1 TTTTTTTCTT
41192401 CTTTTTTTCTT
1 -TTTTTTTCTT
41192412 TTTTTTTCT
1 TTTTTTTCT
41192421 GGCTTGCCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:41192406 original size:21 final size:21
Alignment explanation
Indices: 41192380--41192420 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41192370 CAAATTGAAC
41192380 CTTTTTTTCTTTTTCTTTCTT
1 CTTTTTTTCTTTTTCTTTCTT
*
41192401 CTTTTTTTCTTTTTTTTTCT
1 CTTTTTTTCTTTTTCTTTCT
41192421 GGCTTGCCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
CTTTTTTTCTTTTTCTTTCTT
Found at i:41192486 original size:12 final size:12
Alignment explanation
Indices: 41192469--41192495 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
41192459 CCTAGCCTGC
41192469 TGGGCCTGCTGG
1 TGGGCCTGCTGG
41192481 TGGGCCTGCTGG
1 TGGGCCTGCTGG
41192493 TGG
1 TGG
41192496 CCTACTGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.22, G:0.52, T:0.26
Consensus pattern (12 bp):
TGGGCCTGCTGG
Found at i:41192724 original size:7 final size:7
Alignment explanation
Indices: 41192712--41192810 Score: 76
Period size: 7 Copynumber: 13.9 Consensus size: 7
41192702 AAAAAAATTA
41192712 TTTTCTT
1 TTTTCTT
41192719 TTTTC-T
1 TTTTCTT
41192725 TTTTCTTT
1 TTTTC-TT
41192733 TTTTCTT
1 TTTTCTT
*
41192740 CTTTCTT
1 TTTTCTT
* * **
41192747 CTTCCCC
1 TTTTCTT
41192754 TTTTCTT
1 TTTTCTT
*
41192761 CTTTCTTT
1 TTTTC-TT
41192769 TTCTTCTT
1 TT-TTCTT
41192777 TCTTTCTT
1 T-TTTCTT
41192785 TTTTCTT
1 TTTTCTT
*
41192792 CTTTC-T
1 TTTTCTT
41192798 TTTTCTT
1 TTTTCTT
*
41192805 CTTTCT
1 TTTTCT
41192811 CGCTTAGCCC
Statistics
Matches: 73, Mismatches: 13, Indels: 12
0.74 0.13 0.12
Matches are distributed among these distances:
6 11 0.15
7 40 0.55
8 18 0.25
9 4 0.05
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCTT
Found at i:41192736 original size:21 final size:21
Alignment explanation
Indices: 41192712--41192808 Score: 95
Period size: 21 Copynumber: 4.4 Consensus size: 21
41192702 AAAAAAATTA
41192712 TTTTCTTTTTTCTTTTTCTTT
1 TTTTCTTTTTTCTTTTTCTTT
* * ***
41192733 TTTTCTTCTTTCTTCTTCCCC
1 TTTTCTTTTTTCTTTTTCTTT
*
41192754 TTTTCTTCTTTCTTTTTCTTCTT
1 TTTTCTTTTTTCTTTTTC-T-TT
41192777 TCTTTCTTTTTTCTTCTTTCTTT
1 T-TTTCTTTTTTCTT-TTTCTTT
41192800 TTCTTCTTT
1 TT-TTCTTT
41192809 CTCGCTTAGC
Statistics
Matches: 61, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
21 33 0.54
22 1 0.02
23 10 0.16
24 13 0.21
25 4 0.07
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTCTTTTTTCTTTTTCTTT
Found at i:41192748 original size:24 final size:24
Alignment explanation
Indices: 41192714--41192804 Score: 80
Period size: 24 Copynumber: 3.8 Consensus size: 24
41192704 AAAAATTATT
*
41192714 TTCTTTTTTCTTTTTCTTTTTTTC
1 TTCTTTCTTCTTTTTCTTTTTTTC
*** *
41192738 TTCTTTCTTCTTCCCCTTTTCTTC
1 TTCTTTCTTCTTTTTCTTTTTTTC
41192762 TTTCTTT-TTCTTCTTTCTTTCTTTT-
1 -TTCTTTCTTCTT-TTTCTTT-TTTTC
41192787 TTC-TTCTTTCTTTTTCTT
1 TTCTTTC-TTCTTTTTCTT
41192805 CTTTCTCGCT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
23 2 0.04
24 33 0.62
25 15 0.28
26 3 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (24 bp):
TTCTTTCTTCTTTTTCTTTTTTTC
Found at i:41192773 original size:31 final size:32
Alignment explanation
Indices: 41192727--41192810 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 32
41192717 TTTTTTCTTT
*
41192727 TTCTTTTTTTCTTCTTTC-TTCTTCCCCTTTTC
1 TTCTTTCTTT-TTCTTTCTTTCTTCCCCTTTTC
* **
41192759 TTCTTTCTTTTTC-TTCTTTCTTTCTTTTTTC
1 TTCTTTCTTTTTCTTTCTTTCTTCCCCTTTTC
41192790 TTCTTTCTTTTTC-TTCTTTCT
1 TTCTTTCTTTTTCTTTCTTTCT
41192811 CGCTTAGCCC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
30 3 0.06
31 35 0.74
32 9 0.19
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (32 bp):
TTCTTTCTTTTTCTTTCTTTCTTCCCCTTTTC
Found at i:41192933 original size:21 final size:22
Alignment explanation
Indices: 41192909--41192950 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
41192899 CTTTTCTTTC
41192909 TTTGCTATTTTTT-ATTTTTTG
1 TTTGCTATTTTTTAATTTTTTG
*
41192930 TTTGCTTTTTTTTAATTTTTT
1 TTTGCTATTTTTTAATTTTTT
41192951 TTGTGTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.79
Consensus pattern (22 bp):
TTTGCTATTTTTTAATTTTTTG
Found at i:41193322 original size:30 final size:29
Alignment explanation
Indices: 41193282--41193412 Score: 129
Period size: 30 Copynumber: 4.4 Consensus size: 29
41193272 CAAAAATTTT
* *
41193282 GGGGTAAAAATGCAATTTTGAGAAAGTGTA
1 GGGGTCAAAATGTAATTTTGA-AAAGTGTA
* *
41193312 GGGGTCAAAATATAATTTAGAAAAGT-TAA
1 GGGGTCAAAATGTAATTTTGAAAAGTGT-A
** * *
41193341 GGGGTTGAAATATAATTTTGAAAAATGTTA
1 GGGGTCAAAATGTAATTTTGAAAAGTG-TA
*
41193371 GGGGTCAAAATGTAATTTTAGAAAAGTTTA
1 GGGGTCAAAATGTAATTTT-GAAAAGTGTA
*
41193401 AGGGTCAAAATG
1 GGGGTCAAAATG
41193413 AAAATTTTTA
Statistics
Matches: 83, Mismatches: 14, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.01
29 28 0.34
30 47 0.57
31 7 0.08
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (29 bp):
GGGGTCAAAATGTAATTTTGAAAAGTGTA
Found at i:41193693 original size:78 final size:76
Alignment explanation
Indices: 41193606--41194440 Score: 1059
Period size: 78 Copynumber: 10.8 Consensus size: 76
41193596 GCGTGCGACT
* * *
41193606 CGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAATAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTG-AAA-AATACC
* *
41193671 TCGGCATGCGACC
64 TCAGCATGTGACC
*
41193684 CGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAAAACAGAAATTGAAAAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTG-AAAAACAGAAATTGAAAAATACC
*
41193749 TCAGCGTGTGACC
64 TCAGCATGTGACC
* *
41193762 CGAGACTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCT-
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC
* *
41193826 TGACGTGTGACC
66 AG-CATGTGACC
* *
41193838 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATT-TAAAATACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC
* ** *
41193902 AGCGTACGGCC
66 AGCATGTGACC
*
41193913 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC-GAAATT-TAAAATACCTC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC
* * *
41193976 AGCGTGCGGCC
66 AGCATGTGACC
* *
41193987 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGGACATAAATTGAAAAGTACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAA--ACAGAAATTGAAAAATACC
41194052 TCAGCATGTGACC
64 TCAGCATGTGACC
* * *
41194065 CGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTTTGAAAAACAGAAACTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-GAA-AAATAC
*
41194130 CTCAGCATGTGACT
63 CTCAGCATGTGACC
* * * * *
41194144 CGAGGCTCAACTCACTTCTAGCAAAATGGGTGGATTTTTGAAAAAGACAGAAATTGAAAAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAA-ACAGAAATTGAAAAATACC
41194209 TCAGCATGTGACC
64 TCAGCATGTGACC
* * * *
41194222 CGAGGCTCAACTTACTTCTAGCAATATGAGTTGATTTTTGAAAAACAGAAACTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-GAA-AAATAC
* *
41194287 ATCGGCATGTGACC
63 CTCAGCATGTGACC
* * *
41194301 CGAGGCTCAGCTCACCTCTCACAATATGAGTTGATTTTTG-AAAACAGAAATTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TT-GAA-AAATAC
* *
41194365 CTCGGCATGTGATC
63 CTCAGCATGTGACC
* *
41194379 CGAGGCTCAACTCACCTCTGGCAATATGAGTTGATTTTTGCAAAAACAGAGATTGAAAAATA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTGAAAAATA
41194441 ATTTGTGAAA
Statistics
Matches: 681, Mismatches: 58, Indels: 37
0.88 0.07 0.05
Matches are distributed among these distances:
74 71 0.10
75 61 0.09
76 99 0.15
77 24 0.04
78 270 0.40
79 121 0.18
80 28 0.04
81 7 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (76 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTGAAAAATACCTC
AGCATGTGACC
Found at i:41194209 original size:157 final size:154
Alignment explanation
Indices: 41193606--41194438 Score: 1056
Period size: 157 Copynumber: 5.4 Consensus size: 154
41193596 GCGTGCGACT
* * * *
41193606 CGAGGCTCAACTCACCTATCGTAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAATAATACC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATT-AAAAAAATACC
* *
41193671 TCGGCATGCGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTTGAAAAAACAGAA
65 TCAGCATGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGA-TTTTTGAAAAAACAGAA
*
41193736 ATTGAAAAATACCTCAGCGTGTGACC
129 ATTGAAAAATACCTCAGCATGTGACC
* * *
41193762 CGAGACTCAACTCACCTCTCGCAACATGAGTTGATTTTTGAAAAACAGAAATT-GAAAAATACCT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAAATACCT
* * * *
41193826 -TGACGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAATAGAAA
66 CAG-CATGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAAACAGAAA
* * ** *
41193889 TT-TAAAATACCTCAGCGTACGGCC
130 TTGAAAAATACCTCAGCATGTGACC
*
41193913 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAAC-GAAATT--TAAAATACCT
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAAATACCT
* * * * * *
41193975 CAGCGTGCGGCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAGGACATAAA
66 CAGCATGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAA-AACAGAAA
*
41194040 TTGAAAAGTACCTCAGCATGTGACC
130 TTGAAAAATACCTCAGCATGTGACC
* *
41194065 CGAGGCTCAACTCACTTCTAGCAATATGAGTTGATTTTTGAAAAACAGAAACTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TTAAAA-AAATAC
* * * * *
41194130 CTCAGCATGTGACTCGAGGCTCAACTCACTTCTAGCAAAATGGGTGGATTTTTGAAAAAGACAGA
64 CTCAGCATGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAA-ACAGA
41194195 AATTGAAAAATACCTCAGCATGTGACC
128 AATTGAAAAATACCTCAGCATGTGACC
* * *
41194222 CGAGGCTCAACTTACTTCTAGCAATATGAGTTGATTTTTGAAAAACAGAAACTTAAAAGAAATAC
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAA-TTAAAA-AAATAC
* * *
41194287 ATCGGCATGTGACCCGAGGCTCAGCTCACCTCTCA-CAATATGAGTTGATTTTTG--AAAACAGA
64 CTCAGCATGTGACCCGAGGCTCAACTCACCTCT-AGCAATATGAGTTGATTTTTGAAAAAACAGA
* * *
41194349 AATTTAAAAGAAATACCTCGGCATGTGATC
128 AA-TT-GAA-AAATACCTCAGCATGTGACC
* * *
41194379 CGAGGCTCAACTCACCTCTGGCAATATGAGTTGATTTTTGCAAAAACAGAGATTGAAAAA
1 CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTG-AAAAACAGAAATTAAAAAA
41194439 TAATTTGTGA
Statistics
Matches: 598, Mismatches: 63, Indels: 32
0.86 0.09 0.05
Matches are distributed among these distances:
149 56 0.09
150 10 0.02
151 69 0.12
152 72 0.12
153 11 0.02
154 58 0.10
155 5 0.01
156 53 0.09
157 253 0.42
158 11 0.02
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (154 bp):
CGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAAAAACAGAAATTAAAAAAATACCT
CAGCATGTGACCCGAGGCTCAACTCACCTCTAGCAATATGAGTTGATTTTTGAAAAAACAGAAAT
TGAAAAATACCTCAGCATGTGACC
Found at i:41199296 original size:4 final size:4
Alignment explanation
Indices: 41199287--41199325 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
41199277 ATGCACATCC
41199287 AATG AATG AATG AATG AATG AATG AATG AATG -ATG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
41199326 TTAGTCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.26, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:41201066 original size:17 final size:17
Alignment explanation
Indices: 41201040--41201443 Score: 201
Period size: 17 Copynumber: 22.5 Consensus size: 17
41201030 GAAGCAAATT
*
41201040 TTTTTAAAACACGAAAA
1 TTTTTGAAACACGAAAA
* *
41201057 ATTTTGAAACACGAGAA
1 TTTTTGAAACACGAAAA
* *
41201074 TTTTAGAAA-ACGAGAA
1 TTTTTGAAACACGAAAA
* * *
41201090 TTGTTGCAAACACCAAGA
1 TTTTTG-AAACACGAAAA
** * *
41201108 TTTTAAAAACAAGAAAT
1 TTTTTGAAACACGAAAA
*
41201125 TTTTTGAAACACGAGAAT
1 TTTTTGAAACACGA-AAA
41201143 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
41201161 TTTTTTGAATCACCG-AAA
1 -TTTTTGAAACA-CGAAAA
41201179 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
*
41201197 TTTTTGAAACACTG-GAA
1 TTTTTGAAACAC-GAAAA
* **
41201214 TTTTTGAAAACAGGAGGA
1 TTTTTG-AAACACGAAAA
*
41201232 TTTTTGAAACAAGAAAA
1 TTTTTGAAACACGAAAA
41201249 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* * *
41201267 TTTATCTTTAAAAACACGGGAAT
1 --T-T-TTT-GAAACAC-GAAAA
*
41201290 TTTTTAAAAACACGAAAA
1 TTTTT-GAAACACGAAAA
* *
41201308 TTTTATAAAAAACGTGAAAA
1 TTTT-TGAAACAC--GAAAA
* *
41201328 TTCTTGAAAACACGGAAAT
1 TTTTTG-AAACAC-GAAAA
*
41201347 TTTTTGAATCATCG-AAA
1 TTTTTGAAACA-CGAAAA
*
41201364 TTCTTGAAAACACGAAAAA
1 TTTTTG-AAACACG-AAAA
* *
41201383 TTTTTTGAAACGCCG-GAA
1 -TTTTTGAAAC-ACGAAAA
* *
41201401 TTTTGGAAA-ACAAAAGGA
1 TTTTTGAAACACGAAA--A
*
41201419 TTTTTGAAACATGAAAA
1 TTTTTGAAACACGAAAA
41201436 -TTTTGAAA
1 TTTTTGAAA
41201444 ACATGAAAGC
Statistics
Matches: 299, Mismatches: 56, Indels: 65
0.71 0.13 0.15
Matches are distributed among these distances:
15 1 0.00
16 20 0.07
17 97 0.32
18 95 0.32
19 50 0.17
20 22 0.07
21 2 0.01
22 9 0.03
23 3 0.01
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:41201445 original size:17 final size:16
Alignment explanation
Indices: 41201420--41201489 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
41201410 ACAAAAGGAT
41201420 TTTTGAAACATGAAAA
1 TTTTGAAACATGAAAA
41201436 TTTTGAAAACATG-AAA
1 TTTTG-AAACATGAAAA
****
41201452 GCACGAAA-AT-AAAA
1 TTTTGAAACATGAAAA
* *
41201466 TTTTTAAACATGAAAT
1 TTTTGAAACATGAAAA
41201482 TTTTGAAA
1 TTTTGAAA
41201490 AAATACGGAT
Statistics
Matches: 39, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
14 8 0.21
15 5 0.13
16 19 0.49
17 7 0.18
ACGTcount: A:0.50, C:0.07, G:0.11, T:0.31
Consensus pattern (16 bp):
TTTTGAAACATGAAAA
Found at i:41202313 original size:21 final size:19
Alignment explanation
Indices: 41202287--41202339 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 19
41202277 TTCTTTTTTC
41202287 TTCTTCTTTCTTCTTCCCCTT
1 TTCTTCTTTCTT-TT-CCCTT
*
41202308 TTCTTCTTTC-TTTCTCTT
1 TTCTTCTTTCTTTTCCCTT
41202326 TTCTTCTTTCTTTT
1 TTCTTCTTTCTTTT
41202340 TCTTCTTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 14 0.47
19 5 0.17
20 1 0.03
21 10 0.33
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
TTCTTCTTTCTTTTCCCTT
Found at i:41202318 original size:31 final size:31
Alignment explanation
Indices: 41202275--41202349 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
41202265 ACAAAAATTA
*
41202275 TTTTCTTTTTTC-TTCT-TCTTTCTTCTTCCCC
1 TTTTCTTCTTTCTTTCTCT-TTTCTTCTT-CCC
* *
41202306 TTTTCTTCTTTCTTTCTCTTTTCTTCTTTCT
1 TTTTCTTCTTTCTTTCTCTTTTCTTCTTCCC
41202337 TTTTCTTCTTTCT
1 TTTTCTTCTTTCT
41202350 CGATCAGCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
31 25 0.64
32 13 0.33
33 1 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (31 bp):
TTTTCTTCTTTCTTTCTCTTTTCTTCTTCCC
Found at i:41202338 original size:18 final size:18
Alignment explanation
Indices: 41202305--41202343 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
41202295 TCTTCTTCCC
41202305 CTTTTCTTCTTTCTTTCT
1 CTTTTCTTCTTTCTTTCT
*
41202323 CTTTTCTTCTTTCTTTTT
1 CTTTTCTTCTTTCTTTCT
41202341 CTT
1 CTT
41202344 CTTTCTCGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (18 bp):
CTTTTCTTCTTTCTTTCT
Found at i:41202347 original size:13 final size:13
Alignment explanation
Indices: 41202277--41202349 Score: 62
Period size: 13 Copynumber: 5.6 Consensus size: 13
41202267 AAAAATTATT
41202277 TTCTTT-TTTCTTC
1 TTCTTTCTTT-TTC
*
41202290 TTCTTTCTTCTTC
1 TTCTTTCTTTTTC
* * *
41202303 -CCCTT-TTCTTC
1 TTCTTTCTTTTTC
41202314 TTTCTTTCTCTTTTC
1 -TTCTTTCT-TTTTC
41202329 TTCTTTCTTTTTC
1 TTCTTTCTTTTTC
41202342 TTCTTTCT
1 TTCTTTCT
41202350 CGATCAGCCC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
11 6 0.12
12 3 0.06
13 25 0.51
14 11 0.22
15 4 0.08
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (13 bp):
TTCTTTCTTTTTC
Found at i:41202471 original size:21 final size:21
Alignment explanation
Indices: 41202432--41202489 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
41202422 CTCTTTCTTC
*
41202432 TTTTTCTTTTCTTTCTTTGCTCT
1 TTTTTC-TTT-TTTGTTTGCTCT
*
41202455 TTTTTCTTTTTTGTTTGCTTT
1 TTTTTCTTTTTTGTTTGCTCT
*
41202476 TTTTTGTTTTTTGT
1 TTTTTCTTTTTTGT
41202490 GTCTTTGCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 23 0.72
22 3 0.09
23 6 0.19
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTTGTTTGCTCT
Found at i:41202495 original size:20 final size:21
Alignment explanation
Indices: 41202449--41202495 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
41202439 TTTCTTTCTT
* *
41202449 TGCTCTTTTTTCTTTTTTGTT
1 TGCTTTTTTTTCTTTTTTGTG
*
41202470 TGCTTTTTTTTGTTTTTTGTG
1 TGCTTTTTTTTCTTTTTTGTG
41202491 T-CTTT
1 TGCTTT
41202496 GCTTTGCTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.77
Consensus pattern (21 bp):
TGCTTTTTTTTCTTTTTTGTG
Found at i:41202506 original size:21 final size:22
Alignment explanation
Indices: 41202460--41202507 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
41202450 GCTCTTTTTT
* **
41202460 CTTTTTTGTTTGCTTTTTTTTG
1 CTTTTTTGTGTGCTTTGCTTTG
41202482 -TTTTTTGTGT-CTTTGCTTTG
1 CTTTTTTGTGTGCTTTGCTTTG
41202502 CTTTTT
1 CTTTTT
41202508 ATTTGTTGGC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.75
Consensus pattern (22 bp):
CTTTTTTGTGTGCTTTGCTTTG
Found at i:41202747 original size:30 final size:31
Alignment explanation
Indices: 41202713--41202787 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
41202703 GGGTAGAAAT
41202713 GTAATTTTGAGAAAGTGT-AGGGGTTAAAAA
1 GTAATTTTGAGAAAGTGTAAGGGGTTAAAAA
* * * *
41202743 GTAA-TTT-AGAAAATTTAAGGGGTTGAAAT
1 GTAATTTTGAGAAAGTGTAAGGGGTTAAAAA
*
41202772 GTAATTTTGAAAAAGT
1 GTAATTTTGAGAAAGT
41202788 TTATGGGTCA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 7 0.19
29 17 0.47
30 7 0.19
31 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.33
Consensus pattern (31 bp):
GTAATTTTGAGAAAGTGTAAGGGGTTAAAAA
Found at i:41202808 original size:59 final size:58
Alignment explanation
Indices: 41202694--41202808 Score: 149
Period size: 59 Copynumber: 2.0 Consensus size: 58
41202684 AATGGCAGCA
* * * *
41202694 AAAATTTTGGGGTAGAAATGTAATTTTGAGAAAGTGTAGGGGTTAAAAAGTAATTTAG
1 AAAATTTAGGGGTAGAAATGTAATTTTGAAAAAGTGTAGGGGTCAAAAAGCAATTTAG
* * * *
41202752 AAAATTTAAGGGGTTGAAATGTAATTTTGAAAAAGTTTATGGGTCAAAATGCAATTT
1 AAAATTT-AGGGGTAGAAATGTAATTTTGAAAAAGTGTAGGGGTCAAAAAGCAATTT
41202809 TTTAATTAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
58 7 0.15
59 41 0.85
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (58 bp):
AAAATTTAGGGGTAGAAATGTAATTTTGAAAAAGTGTAGGGGTCAAAAAGCAATTTAG
Found at i:41213690 original size:23 final size:23
Alignment explanation
Indices: 41213647--41213691 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
41213637 ATGGAAAACT
*
41213647 TAAAATAATATTACATAATAAAG
1 TAAAATAATAGTACATAATAAAG
*
41213670 TAAAATAAT-GTATATACATAAA
1 TAAAATAATAGTACATA-ATAAA
41213692 AAAATAGGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (23 bp):
TAAAATAATAGTACATAATAAAG
Found at i:41213756 original size:18 final size:18
Alignment explanation
Indices: 41213735--41213780 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
41213725 TAACCATATC
*
41213735 AATAATAAATAT-ATTAGT
1 AATAATAAATATGA-TAAT
41213753 AATAA-AAACTATGATAAT
1 AATAATAAA-TATGATAAT
41213771 AATAATAAAT
1 AATAATAAAT
41213781 TAATTAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
17 3 0.12
18 17 0.71
19 4 0.17
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (18 bp):
AATAATAAATATGATAAT
Found at i:41213788 original size:12 final size:12
Alignment explanation
Indices: 41213773--41213804 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
41213763 ATGATAATAA
41213773 TAATAAATTAAT
1 TAATAAATTAAT
*
41213785 TAATAAACTAAT
1 TAATAAATTAAT
41213797 TAATAAAT
1 TAATAAAT
41213805 AACAAATAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAAATTAAT
Found at i:41215382 original size:19 final size:19
Alignment explanation
Indices: 41215356--41215443 Score: 72
Period size: 19 Copynumber: 4.7 Consensus size: 19
41215346 GCGCATCCTG
41215356 ACACAAAGTGTATCCTAGC
1 ACACAAAGTGTATCCTAGC
** * *
41215375 GTACAAAGTGCATTCTAGC
1 ACACAAAGTGTATCCTAGC
* *
41215394 ACACAGAGTGTATCCTGGC
1 ACACAAAGTGTATCCTAGC
** *
41215413 ACATGAGGTGTATCCTA--
1 ACACAAAGTGTATCCTAGC
41215430 ACACATAAGTGTAT
1 ACACA-AAGTGTAT
41215444 AATCTCGTAC
Statistics
Matches: 50, Mismatches: 18, Indels: 3
0.70 0.25 0.04
Matches are distributed among these distances:
17 3 0.06
18 7 0.14
19 40 0.80
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (19 bp):
ACACAAAGTGTATCCTAGC
Found at i:41217153 original size:44 final size:44
Alignment explanation
Indices: 41217103--41217193 Score: 121
Period size: 44 Copynumber: 2.1 Consensus size: 44
41217093 AATAATGTAA
* * * *
41217103 ATTAAATTATAATTAT-TTTTAAATACGTAATTATCAGAACTTCT
1 ATTAAATTACAATT-TGTTTTAAATACATAATTACCACAACTTCT
*
41217147 ATTAAATTACAATTTGTTTTAAATGCATAATTACCACAACTTCT
1 ATTAAATTACAATTTGTTTTAAATACATAATTACCACAACTTCT
41217191 ATT
1 ATT
41217194 TTATTTCACC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
43 1 0.02
44 40 0.98
ACGTcount: A:0.40, C:0.12, G:0.04, T:0.44
Consensus pattern (44 bp):
ATTAAATTACAATTTGTTTTAAATACATAATTACCACAACTTCT
Found at i:41219258 original size:14 final size:15
Alignment explanation
Indices: 41219228--41219262 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
41219218 AATCATAAGT
*
41219228 AAATAAACAAGAAAA
1 AAATAAACAACAAAA
41219243 AAATAAA-AACAAAA
1 AAATAAACAACAAAA
41219257 AAATAA
1 AAATAA
41219263 GAAAAATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.83, C:0.06, G:0.03, T:0.09
Consensus pattern (15 bp):
AAATAAACAACAAAA
Found at i:41219305 original size:3 final size:3
Alignment explanation
Indices: 41219299--41219493 Score: 114
Period size: 3 Copynumber: 66.3 Consensus size: 3
41219289 TGGTAATGAA
* * * *** * *
41219299 AAT AAT ACT TAT AAT TAT AAT AAT AAT GGC AAT AAT AAT ATT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
41219347 ATT AAT AAT AAG AA- AA- AAT AA- AAT AA- AAT AAAT AGT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* ** * ** * **
41219389 ATT AAT AAT AAT TCT AAT AAT GAT GTT AAT AGT AAT AA- AAT AGC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
41219436 AA- AACT AAT AAT AAT ACT AGT AAT GAT AAT AAT AAT AAT AAT AAT
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
41219481 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
41219494 GGACAAAATT
Statistics
Matches: 142, Mismatches: 43, Indels: 14
0.71 0.22 0.07
Matches are distributed among these distances:
2 12 0.08
3 125 0.88
4 5 0.04
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41220970 original size:44 final size:44
Alignment explanation
Indices: 41220945--41221154 Score: 165
Period size: 44 Copynumber: 4.7 Consensus size: 44
41220935 TTTTAATTCG
41220945 CTCCACTACAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTA
1 CTCCACTACAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTA
* * * *
41220989 CTCCACTACAACTTCAGGGAGATAAGG-TTTGTTA-TTTCAACCTG
1 CTCCACTACAACTTCAGGGAGAT-AGGATTAG-TAGCTTCAATCTA
* * * * * * *
41221033 CTCTACTGCAACTTCAGAGAGATAAGGTTTA-TGGCTTTAATCTG
1 CTCCACTACAACTTCAGGGAGAT-AGGATTAGTAGCTTCAATCTA
* * * *
41221077 CTCCACTGCAACTTCAGGGAGATAAGATTCGTAGCCTGTCTTCAATCTG
1 CTCCACTACAACTTCAGGGAGATAGGATTAGTA----G-CTTCAATCTA
* * *
41221126 CTCCACTACAACTTTAAGGAGATAAGATT
1 CTCCACTACAACTTCAGGGAGATAGGATT
41221155 GATTTATTTT
Statistics
Matches: 134, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
43 5 0.04
44 86 0.64
45 7 0.05
48 1 0.01
49 35 0.26
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
CTCCACTACAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTA
Found at i:41221478 original size:137 final size:137
Alignment explanation
Indices: 41221173--41221471 Score: 472
Period size: 137 Copynumber: 2.2 Consensus size: 137
41221163 TTTAACATGT
* * * *
41221173 TCCACTGCAACTTCAAGAAGATAAGGTTTAATATGATCTGCTCTACTGCAACTTCAAAGAGATAA
1 TCCACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAAAGAAATAA
* * * *
41221238 GATCCGTAATTTATAGCTTCAATTTGTTCCACTGTAACATCAAGGAAATAAGATTCGCTATCTTC
66 GATCCATAATTTATAGCTTCAATCTGTTCCACTGCAACATCAAGGAAATAAGATTCACTATCTTC
41221303 AGTCTGC
131 AGTCTGC
* *
41221310 TCCACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTATTGCAACTTCAGAGAAATAA
1 TCCACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAAAGAAATAA
* * *
41221375 GATCTATAATTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTC
66 GATCCATAATTTATAGCTTCAATCTGTTCCACTGCAACATCAAGGAAATAAGATTCACTATCTTC
41221440 AGTCTGC
131 AGTCTGC
*
41221447 TCCACTGCAATTTCAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
41221472 ACTTGATTTA
Statistics
Matches: 148, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
137 148 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (137 bp):
TCCACTGCAACTTCAGGGAGATAAGGTTTGATATGATCTGCTCTACTGCAACTTCAAAGAAATAA
GATCCATAATTTATAGCTTCAATCTGTTCCACTGCAACATCAAGGAAATAAGATTCACTATCTTC
AGTCTGC
Found at i:41221557 original size:89 final size:89
Alignment explanation
Indices: 41221392--41222126 Score: 425
Period size: 89 Copynumber: 8.0 Consensus size: 89
41221382 AATTTATAGC
** ** * * * *
41221392 TTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAA
1 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATT-AGTAGCTTCAATCTGCTCCACTACAA
*
41221457 TTTCAGGGAGATAAGACTTGATTTA
65 CTTCAGGGAGATAAGACTTGATTTA
* * * * * * *
41221482 TTCAATTTACCCCAGTGCAACTTCAGGGGGATAAGATTAGTGGCTTCAATTTTCTCCACTGCAAC
1 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCAATCTGCTCCACTACAAC
* *
41221547 TTCAGGGAGATAAGATTTATAATTTATA
66 TTCAGGGAGATAAGA-CT-TGA-TT-TA
** ** * * *
41221575 GCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCGTTATCTTCAGTCTGCTCCACTAC
1 --TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAG-TAGCTTCAATCTGCTCCACTAC
* *
41221640 AACTTCAAGGAGATAGGACTTGATTTA
63 AACTTCAGGGAGATAAGACTTGATTTA
41221667 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCAATCTGCTCCACTACAAC
1 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCAATCTGCTCCACTACAAC
* ** *
41221732 TTCAGGGAGATAAGATTTGTAACCCATC
66 TTCAGGGAGATAAGACTTG--A--TTTA
* * * * * * ** * * *
41221760 TTCAATCTGCTCTACTGCAACTTTAGGGAGATAAGGTTGATTTATTTTTAACCTGCTCCACTGCA
1 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATT-A-GTAGCTTCAATCTGCTCCACTACA
** *
41221825 ACTTCAAAGAGATAATG-TTTGA--TA
64 ACTTCAGGGAGATAA-GACTTGATTTA
* * * * * * *
41221849 -T-GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATCTATAGCTTCAATCTGTTCCA
1 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGA--T-T-A---GTAGCTTCAATCTGCTCCA
* * * * * *
41221912 CTGCAACTTCAGTGAAATAAGA-TTCGCTATC
59 CTACAACTTCAGGGAGATAAGACTT-GATTTA
* * * * *
41221943 TTCAGTCT-CCTCCACTGCAACTTCAAGGAGATAAGACTTAGTATG-ATCAATCTGC-CCTACTG
1 TTCAATCTGCC-CCACTGCAACTTCAGGGGGATAAGA-TTAGTA-GCTTCAATCTGCTCC-ACTA
* ***
41222005 CAACTTCAGGGGGATAAGA-TT-AGTGGC
62 CAACTTCAGGGAGATAAGACTTGA-TTTA
* * *
41222032 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTA-TAACCCGTCTTCAATCTGCTCTAC
1 TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGA-TTAGT-A---G-CTTCAATCTGCTCCAC
* *
41222096 TGCAACTTCAAGGAGATAAGA-TTGATTTA
60 TACAACTTCAGGGAGATAAGACTTGATTTA
41222125 TT
1 TT
41222127 TTTAACCTGC
Statistics
Matches: 504, Mismatches: 104, Indels: 71
0.74 0.15 0.10
Matches are distributed among these distances:
87 29 0.06
88 2 0.00
89 115 0.23
90 102 0.20
91 8 0.02
92 36 0.07
93 75 0.15
94 7 0.01
95 72 0.14
96 58 0.12
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (89 bp):
TTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCAATCTGCTCCACTACAAC
TTCAGGGAGATAAGACTTGATTTA
Found at i:41221570 original size:185 final size:185
Alignment explanation
Indices: 41221345--41221839 Score: 652
Period size: 185 Copynumber: 2.7 Consensus size: 185
41221335 GTTTGATATG
* * * * *
41221345 ATCTGCTCTATTGCAACTTCAGAGAAATAAGATCTATAATTTATAGCTTCAATCTGTTCCACTGC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGTTCCACTGC
* * *
41221410 AACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAATTTCAGGGAGATAAGACT
66 AACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACT
* * *
41221475 TGATTTATTCAATTTACCCCAGTGCAACTTCAGGGGGATAAGATTAGTGGCTTCA
131 TGATTTATTCAATCTACCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCA
* *
41221530 ATTTTCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGTTCCACTGC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGTTCCACTGC
** *
41221595 AACTTCAGGGAAATAAGATTCGTTATCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAGGACT
66 AACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACT
*
41221660 TGATTTATTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCA
131 TGATTTATTCAATCTACCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCA
* * *** * *
41221715 ATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAACCCAT--CTTCAATCTGCTCTACTGC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGTTCCACTGC
* * * * * * * ** * *
41221778 AACTTTAGGGAGATAAGGTTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAGAGATAA
66 AACTTCAGGGAAATAAGATTCA-CTATCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAA
41221840 TGTTTGATAT
Statistics
Matches: 271, Mismatches: 38, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
183 34 0.13
184 32 0.12
185 205 0.76
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (185 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGTTCCACTGC
AACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTACAACTTCAAGGAGATAAGACT
TGATTTATTCAATCTACCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCA
Found at i:41221931 original size:321 final size:320
Alignment explanation
Indices: 41220946--41222173 Score: 1383
Period size: 321 Copynumber: 3.8 Consensus size: 320
41220936 TTTAATTCGC
* * * * * * * *
41220946 TCCACTACAACTTCAGGGAGATAGGATTAG-TAGCTTCAATCTACTCCACTACAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
* * * * * *
41221010 ATAAGGTTTG-TTATTTCAACCTGCTCTACTGCAACTTCAGAGAGATAAGGTTTA-TGGCTTTAA
66 ATAAGGCTTGATTA-TTCAATCTGCCCTACTGCAACTTCAGAGAGATAA-GATTAGTAGCTTCAA
* * ** *
41221073 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGTAGCCTGTCTTCAATCTGCTCCACTACAAC
129 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCCACTGCAAC
* *
41221138 TTTAAGGAGATAAGATTGATTTATTTTTAACATGTTCCACTGCAACTTC-AAGAAGATAAGGTTT
194 TTTAAGGAGATAAGATTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAG-AGATAAGGTTT
* * * *
41221202 AATATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCCGTAATTTATAGCTTCAATTTGT
258 GATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGT
* * * * *
41221265 TCCACTGTAACATCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
* * * * * *
41221330 ATAAGGTTTGA-TA-T-GATCTGCTCTATTGCAACTTCAGAGAAATAAGATCTATAATTTATAGC
66 ATAAGGCTTGATTATTCAATCTGCCCTACTGCAACTTCAGAGAGATAAGA--T-T-A---GTAGC
* * * * *
41221392 TTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGA--T-TCA-CTATCTTCAGTCTGCTCCACT
124 TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCCACT
* * ** * * * ** *
41221453 GCAA-TTTCAGGGAGATAAGACTTGATTTA--TTCAATTTACCCCAGTGCAACTTCAGGGGGATA
189 GCAACTTT-AAGGAGATAAGA-TTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAGAGATA
* * * * * * * * *
41221515 AGATTAGTGGCT-TCAATTTTCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTT
252 AGGTT--T-GATAT-GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTT
41221579 CAATCTGT
313 CAATCTGT
*
41221587 TCCACTGCAACTTCAGGGAAATAAGATTCGTTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
1 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
* * *
41221652 AT-AGGACTTGATTTATTCAATCTGCCCCACTGCAACTTCAGGGGGATAAGATTAGTAGCTTCAA
66 ATAAGG-CTTGA-TTATTCAATCTGCCCTACTGCAACTTCAGAGAGATAAGATTAGTAGCTTCAA
* *
41221716 TCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCTACTGCAAC
129 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCCACTGCAAC
* * *
41221781 TTTAGGGAGATAAGGTTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAGAGATAATGTTTG
194 TTTAAGGAGATAAGATTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAGAGATAAGGTTTG
*
41221846 ATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATCTATAGCTTCAATCTGT
259 ATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGT
* * *
41221908 TCCACTGCAACTTCAGTGAAATAAGATTCGCTATCTTCAGTCTCCTCCACTGCAACTTCAAGGAG
1 TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
* * * * *
41221973 ATAAGACTT-AGTATGATCAATCTGCCCTACTGCAACTTCAGGGGGATAAGATTAGTGGCTTCAA
66 ATAAGGCTTGATTAT--TCAATCTGCCCTACTGCAACTTCAGAGAGATAAGATTAGTAGCTTCAA
* * *
41222037 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTATAACCCGTCTTCAATCTGCTCTACTGCAAC
129 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCCACTGCAAC
* * * **
41222102 TTCAAGGAGATAAGATTGATTTATTTTTAACCTGCTCCATTGCGACTTCAGGGAGATAAGGTTTG
194 TTTAAGGAGATAAGATTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAGAGATAAGGTTTG
41222167 ATATGAT
259 ATATGAT
41222174 AAGATCCGCT
Statistics
Matches: 764, Mismatches: 112, Indels: 64
0.81 0.12 0.07
Matches are distributed among these distances:
316 1 0.00
317 27 0.04
318 2 0.00
319 92 0.12
320 78 0.10
321 305 0.40
322 129 0.17
323 34 0.04
324 69 0.09
325 1 0.00
326 26 0.03
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.32
Consensus pattern (320 bp):
TCCACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
ATAAGGCTTGATTATTCAATCTGCCCTACTGCAACTTCAGAGAGATAAGATTAGTAGCTTCAATC
TGCTCCACTGCAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCCACTGCAACTT
TAAGGAGATAAGATTGATTTATTTTTAACCTGCTCCACTGCAACTTCAAAGAGATAAGGTTTGAT
ATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGT
Found at i:41222049 original size:44 final size:45
Alignment explanation
Indices: 41220944--41222118 Score: 540
Period size: 45 Copynumber: 25.7 Consensus size: 45
41220934 GTTTTAATTC
* *
41220944 GCTCCACTACAACTTCAGGGAGATAGGATTAGTA-GCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGGCTTCAATCT
* * * * * *
41220988 ACTCCACTACAACTTCAGGGAGATAAGGTTTGTTA--TTTCAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGGCTTCAATCT
* * * *
41221032 GCTCTACTGCAACTTCAGAGAGATAAGGTT--TATGGCTTTAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTA-GGCTTCAATCT
*
41221076 GCTCCACTGCAACTTCAGGGAGATAAGATTCGTAGCCTGTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAG---G-CTTCAATCT
* * * * ** *
41221125 GCTCCACTACAACTTTAAGGAGATAAGATTGATTTA-TTTTTAA-CAT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-A-GTAGGCTTCAATC-T
* * * * * *
41221171 GTTCCACTGCAACTTCAAGAAGATAAGGTT--TA--ATAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGGCT-TCAATCT
* ** * * *
41221212 GCTCTACTGCAACTTCAAAGAGATAAGATCCGTAATTTATAGCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGAT---T-A-GTA-GGCTTCAATCT
* * * * * * * *
41221263 GTTCCACTGTAACATCAAGGAAATAAGATTCGCTA-TCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGGCTTCAATCT
* * *
41221308 GCTCCACTGCAACTTCAGGGAGATAAGGTT--T--GATAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGGCT-TCAATCT
* * * * * *
41221349 GCTCTATTGCAACTTCAGAGAAATAAGATCTATAATTTATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A-GTA-GGCTTCAATCT
* * * * *
41221400 GTTCCACTGCAACTTCAGGGAAATAAGATTCACTA-TCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-AGTAGGCTTCAATCT
* * *
41221445 GCTCCACTGCAATTTCAGGGAGATAAGACTTGATTTA---TTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TT-A-GTAGGCTTCAATCT
* * * * *
41221490 ACCCCAGTGCAACTTCAGGGGGATAAGATTAGT-GGCTTCAATTT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGGCTTCAATCT
* * *
41221534 TCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A-GTA-GGCTTCAATCT
* * * * *
41221585 GTTCCACTGCAACTTCAGGGAAATAAGATTCGTTA-TCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGGCTTCAATCT
* * * *
41221630 GCTCCACTACAACTTCAAGGAGATAGGACTTGATTTA---TTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TT-A-GTAGGCTTCAATCT
* *
41221675 GCCCCACTGCAACTTCAGGGGGATAAGATTAGTA-GCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGGCTTCAATCT
* * **
41221719 GCTCCACTACAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAGT-A---GGCTTCAATCT
* * * * ** * *
41221768 GCTCTACTGCAACTTTAGGGAGATAAGGTTGATTTA-TTTTTAACCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT-A-GTAGGCTTCAATCT
** * *
41221814 GCTCCACTGCAACTTCAAAGAGATAATG-TT--T--GATAT-GATCT
1 GCTCCACTGCAACTTCAGGGAGATAA-GATTAGTAGGCT-TCAATCT
* * * *
41221855 GCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATCTATAGCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA--T-T-A-GTA-GGCTTCAATCT
* * * * * *
41221906 GTTCCACTGCAACTTCAGTGAAATAAGATTCGCTA-TCTTCAGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTAG-TAGGCTTCAATCT
* * * *
41221951 CCTCCACTGCAACTTCAAGGAGATAAGACTTAGTATG-ATCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTAGGCTTCAATCT
*
41221996 GC-CCTACTGCAACTTCAGGGGGATAAGATTAGT-GGCTTCAATCT
1 GCTCC-ACTGCAACTTCAGGGAGATAAGATTAGTAGGCTTCAATCT
*
41222040 GCTCCACTGCAACTTCAGGGAGATAAGATTTA-TAACCCGTCTTCAATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGA-TTAGT-A---GGCTTCAATCT
* *
41222089 GCTCTACTGCAACTTCAAGGAGATAAGATT
1 GCTCCACTGCAACTTCAGGGAGATAAGATT
41222119 GATTTATTTT
Statistics
Matches: 872, Mismatches: 169, Indels: 176
0.72 0.14 0.14
Matches are distributed among these distances:
40 1 0.00
41 84 0.10
42 11 0.01
43 5 0.01
44 209 0.24
45 225 0.26
46 72 0.08
47 14 0.02
48 13 0.01
49 110 0.13
50 4 0.00
51 124 0.14
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (45 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTAGTAGGCTTCAATCT
Found at i:41222123 original size:643 final size:638
Alignment explanation
Indices: 41220946--41222126 Score: 1619
Period size: 643 Copynumber: 1.8 Consensus size: 638
41220936 TTTAATTCGC
* * *
41220946 TCCACTACAACTTCAGGGAGATAGGATTAGTAGCTTCAATCTACTCCACTACAACTTCAGGGAGA
1 TCCACTACAACTTCAGGGAAATAAGATTAGTAGCTTCAATCTACTCCACTACAACTTCAAGGAGA
* * * * * *
41221011 TAAGGTTTGTTATTTCAACCTGCTCTACTGCAACTTCAGAGAGATAAGGTTTATGGCTTTAATCT
66 TAAGGCTTGTTATTTCAACCTGCCCCACTGCAACTTCAGAGAGATAAGGATTATAGCTTCAATCT
* * **
41221076 GCTCCACTGCAACTTCAGGGAGATAAGATTCGTAGCCTGTCTTCAATCTGCTCCACTACAACTTT
131 GCTCCACTACAACTTCAGGGAGATAAGATTCGTAACCCATCTTCAATCTGCTCCACTACAACTTT
*
41221141 AAGGAGATAAGATTGATTTATTTTTAACATGTTCCACTGCAACTTCAAGAAGATAAGGTTTAATA
196 AAGGAGATAAGATTGATTTATTTTTAACATGCTCCACTGCAACTTCAAGAAGATAAGGTTTAATA
* *
41221206 TGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCCGTAATTTATAGCTTCAATTTGTTCCACT
261 TGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCCGTAATCTATAGCTTCAATCTGTTCCACT
* * * *
41221271 GTAACATCAAGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGG
326 GCAACATCAAGGAAATAAGATTCGCTATCTTCAGTCTCCTCCACTGCAACTTCAAGGAGATAAGC
* * * *
41221336 TTTGATATGATCTGCTCTATTGCAACTTCAGAGAAATAAGATCTATAATTTATAGCTTCAATCTG
391 TTAGATATAATCTGCCCTACTGCAACTTCAGAGAAATAAGA-CTATAA--TATAGCTTCAATCTG
* * * *
41221401 TTCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTCAGTCTGCTCCACTGCAATTTCAGGGA
453 CTCCACTGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTTCAAGGA
41221466 GATAAGACTTGATTTATTCAATTTACCCCAGTGCAACTTCAGGGGGATAAGATTAGTGGCTTCAA
518 GATAAGACTTGATTTATTCAATTTACCCCAGTGCAACTTCAGGGGGATAAGATTAGTGGCTTCAA
41221531 TTTTCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGT
583 TTTTCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGT
* * * * *
41221587 TCCACTGCAACTTCAGGGAAATAAGATTCGTTATCTTCAGTCTGCTCCACTACAACTTCAAGGAG
1 TCCACTACAACTTCAGGGAAATAAGATTAG-TAGCTTCAATCTACTCCACTACAACTTCAAGGAG
* * *
41221652 AT-AGGACTTGATT-TATTCAATCTGCCCCACTGCAACTTCAGGGGGATAA-GATTAGTAGCTTC
65 ATAAGG-CTTG-TTAT-TTCAACCTGCCCCACTGCAACTTCAGAGAGATAAGGATTA-TAGCTTC
* * *
41221714 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTTGTAACCCATCTTCAATCTGCTCTACTGCA
126 AATCTGCTCCACTACAACTTCAGGGAGATAAGATTCGTAACCCATCTTCAATCTGCTCCACTACA
* * * *
41221779 ACTTTAGGGAGATAAGGTTGATTTATTTTTAACCTGCTCCACTGCAACTTCAA-AGAGATAATGT
191 ACTTTAAGGAGATAAGATTGATTTATTTTTAACATGCTCCACTGCAACTTCAAGA-AGATAAGGT
* * *
41221843 TTGATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTAATCTATAGCTTCAATCTGT
255 TTAATATGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCCGTAATCTATAGCTTCAATCTGT
*
41221908 TCCACTGCAACTTC-AGTGAAATAAGATTCGCTATCTTCAGTCTCCTCCACTGCAACTTCAAGGA
320 TCCACTGCAACATCAAG-GAAATAAGATTCGCTATCTTCAGTCTCCTCCACTGCAACTTCAAGGA
* ** * *
41221972 GATAAGACTTAGTATGATCAATCTGCCCTACTGCAACTTCAGGGGGATAAGA-T-T-A-GTGGCT
384 GATAAG-CTTAG-AT-AT-AATCTGCCCTACTGCAACTTCAGAGAAATAAGACTATAATATAGCT
* * *
41222033 TCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTA-TAACCCGTCTTCAATCTGCTCTACT
445 TCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTCACT-A----TCTTCAATCTGCTCCACT
41222097 GCAACTTCAAGGAGATAAGA-TTGATTTATT
505 GCAACTTCAAGGAGATAAGACTTGATTTATT
41222127 TTTAACCTGC
Statistics
Matches: 469, Mismatches: 55, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
639 1 0.00
640 41 0.09
641 29 0.06
642 43 0.09
643 285 0.61
644 38 0.08
645 3 0.01
646 2 0.00
647 27 0.06
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (638 bp):
TCCACTACAACTTCAGGGAAATAAGATTAGTAGCTTCAATCTACTCCACTACAACTTCAAGGAGA
TAAGGCTTGTTATTTCAACCTGCCCCACTGCAACTTCAGAGAGATAAGGATTATAGCTTCAATCT
GCTCCACTACAACTTCAGGGAGATAAGATTCGTAACCCATCTTCAATCTGCTCCACTACAACTTT
AAGGAGATAAGATTGATTTATTTTTAACATGCTCCACTGCAACTTCAAGAAGATAAGGTTTAATA
TGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCCGTAATCTATAGCTTCAATCTGTTCCACT
GCAACATCAAGGAAATAAGATTCGCTATCTTCAGTCTCCTCCACTGCAACTTCAAGGAGATAAGC
TTAGATATAATCTGCCCTACTGCAACTTCAGAGAAATAAGACTATAATATAGCTTCAATCTGCTC
CACTGCAACTTCAGGGAAATAAGATTCACTATCTTCAATCTGCTCCACTGCAACTTCAAGGAGAT
AAGACTTGATTTATTCAATTTACCCCAGTGCAACTTCAGGGGGATAAGATTAGTGGCTTCAATTT
TCTCCACTGCAACTTCAGGGAGATAAGATTTATAATTTATAGCTTCAATCTGT
Found at i:41222427 original size:24 final size:24
Alignment explanation
Indices: 41222400--41222447 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
41222390 TTTAGGGGAA
41222400 TAAGGTTTGTTACTTCAACATGCT
1 TAAGGTTTGTTACTTCAACATGCT
41222424 TAAGGTTTGTTACTTCAACATGCT
1 TAAGGTTTGTTACTTCAACATGCT
41222448 CTACTGTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.42
Consensus pattern (24 bp):
TAAGGTTTGTTACTTCAACATGCT
Found at i:41231950 original size:3 final size:3
Alignment explanation
Indices: 41231944--41232124 Score: 86
Period size: 3 Copynumber: 61.7 Consensus size: 3
41231934 TGGTAATGAA
* * *** * * *
41231944 AAT AAT AAT TAT AAT TAT AAT AAT AAT GGC AAT AAC AAT ATT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
41231992 ATT AAT AAT AAG AA- AA- AAT AA- AAT AA- AAT AAAT AGT AAT AAC
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* ** * ** * **
41232034 ATT AAT AAT AAT TCT AAT AAT GAT GTT AAT AGT AAT AA- AAT AGC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
41232081 AA- AACT AAT AAT AAT ACT AGT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41232125 CAACAATAAA
Statistics
Matches: 128, Mismatches: 43, Indels: 14
0.69 0.23 0.08
Matches are distributed among these distances:
2 12 0.09
3 111 0.87
4 5 0.04
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41231950 original size:18 final size:18
Alignment explanation
Indices: 41231927--41231972 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
41231917 CTAAATATAT
41231927 ATAATAATGGTAATGAAA
1 ATAATAATGGTAATGAAA
** * *
41231945 ATAATAATTATAATTATA
1 ATAATAATGGTAATGAAA
41231963 ATAATAATGG
1 ATAATAATGG
41231973 CAATAACAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (18 bp):
ATAATAATGGTAATGAAA
Found at i:41233748 original size:11 final size:11
Alignment explanation
Indices: 41233734--41233774 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41233724 TGTTTTCTCC
41233734 CTATTTTGCTA
1 CTATTTTGCTA
*
41233745 CTATTTTACTA
1 CTATTTTGCTA
* *
41233756 TTATGTTGCTA
1 CTATTTTGCTA
41233767 CTATTTTG
1 CTATTTTG
41233775 TTTTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.20, C:0.15, G:0.10, T:0.56
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:41233845 original size:30 final size:30
Alignment explanation
Indices: 41233811--41233875 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
41233801 ACTTATTTTA
*
41233811 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
*
41233841 TTGTTAATTTTATTATTATTTTAGAGGCAT
1 TTGTTAATTTTATTATTATTTTAAAGGCAT
41233871 TTGTT
1 TTGTT
41233876 TGTTAAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.25, C:0.03, G:0.14, T:0.58
Consensus pattern (30 bp):
TTGTTAATTTTATTATTATTTTAAAGGCAT
Found at i:41234022 original size:12 final size:12
Alignment explanation
Indices: 41234005--41234032 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
41233995 TTTTAAAACT
41234005 ATATAAAAATTA
1 ATATAAAAATTA
41234017 ATATAAAAATTA
1 ATATAAAAATTA
41234029 ATAT
1 ATAT
41234033 GGGTGGGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:41235812 original size:19 final size:19
Alignment explanation
Indices: 41235790--41235830 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
41235780 ATTTTTTTAA
*
41235790 TATTTTATGTAAATTATAT
1 TATTTTATATAAATTATAT
41235809 TATTTTATATAAATTATAT
1 TATTTTATATAAATTATAT
41235828 TAT
1 TAT
41235831 ATAAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TATTTTATATAAATTATAT
Found at i:41235816 original size:5 final size:5
Alignment explanation
Indices: 41235802--41235860 Score: 50
Period size: 5 Copynumber: 12.2 Consensus size: 5
41235792 TTTTATGTAA
* * * * *
41235802 ATTAT ATTAT TTTAT A-TAA ATTAT ATTAT ATAAA ATTA- AATAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
*
41235850 ATTAT AATAT A
1 ATTAT ATTAT A
41235861 AATATTAAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
4 6 0.14
5 36 0.86
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (5 bp):
ATTAT
Found at i:41235845 original size:14 final size:15
Alignment explanation
Indices: 41235814--41235860 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
41235804 TATATTATTT
*
41235814 TATAT-AAATTATAT
1 TATATAAAATTATAA
41235828 TATATAAAATTA-AA
1 TATATAAAATTATAA
* *
41235842 TATATTATATTATAA
1 TATATAAAATTATAA
41235857 TATA
1 TATA
41235861 AATATTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATAAAATTATAA
Found at i:41235845 original size:19 final size:21
Alignment explanation
Indices: 41235815--41235865 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
41235805 ATATTATTTT
41235815 ATATAAATTATATTATA-TAAA
1 ATATAAA-TATATTATATTAAA
*
41235836 AT-TAAATATATTATATTATA
1 ATATAAATATATTATATTAAA
41235856 ATATAAATAT
1 ATATAAATAT
41235866 TAAAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 9 0.33
20 9 0.33
21 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAAATATATTATATTAAA
Found at i:41249545 original size:30 final size:30
Alignment explanation
Indices: 41249502--41249560 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
41249492 CTTAATAAGC
*
41249502 AAATGCCTCTAAAATAATAACAAAATTAAT
1 AAATGCCTCTAAAATAATAAAAAAATTAAT
* * *
41249532 AAATGTCTTTAAAATCATAAAAAAATTAA
1 AAATGCCTCTAAAATAATAAAAAAATTAA
41249561 CAATAAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.58, C:0.10, G:0.03, T:0.29
Consensus pattern (30 bp):
AAATGCCTCTAAAATAATAAAAAAATTAAT
Found at i:41255652 original size:16 final size:15
Alignment explanation
Indices: 41255631--41255662 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
41255621 AATATTTGAT
41255631 AATGACTAGCTAATGG
1 AATGACTAGCT-ATGG
41255647 AATGACTAGCTATGG
1 AATGACTAGCTATGG
41255662 A
1 A
41255663 CATGCTTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.38, C:0.12, G:0.25, T:0.25
Consensus pattern (15 bp):
AATGACTAGCTATGG
Found at i:41257243 original size:20 final size:20
Alignment explanation
Indices: 41257218--41257256 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
41257208 GGTGAAAGAG
*
41257218 TTAGTTCTGAAGAAGTGTCA
1 TTAGTTCTAAAGAAGTGTCA
41257238 TTAGTTCTAAAGAAGTGTC
1 TTAGTTCTAAAGAAGTGTC
41257257 GTTCAATCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.23, T:0.36
Consensus pattern (20 bp):
TTAGTTCTAAAGAAGTGTCA
Found at i:41259026 original size:104 final size:104
Alignment explanation
Indices: 41258846--41259162 Score: 499
Period size: 104 Copynumber: 3.0 Consensus size: 104
41258836 TTGTCAACAT
* * * **
41258846 AGCTCACAAAACTATGTTCCCAGCTGATGTTTAAAGGTTAGATGAGTTATACTCAAAATGTTCAT
1 AGCTCACAGAACTATGTTCCCAGTTGATGTTTAAAGGTTAGATGAGTTATACTCACAACCTTCAT
*
41258911 TTATTTGAGTAAGTTGAGTTAAGCTTGCTACTCTGGAAC
66 TTATTTGAGTAAGCTGAGTTAAGCTTGCTACTCTGGAAC
* * *
41258950 AGCTCACAGAATTATGTTCCCAGTTGATGTTGAAAGGTTAGATGAGTTATACTCACAACCTTTAT
1 AGCTCACAGAACTATGTTCCCAGTTGATGTTTAAAGGTTAGATGAGTTATACTCACAACCTTCAT
41259015 TTATTTGAGTAAGCTGAGTTAAGCTTGCTACTCTGGAAC
66 TTATTTGAGTAAGCTGAGTTAAGCTTGCTACTCTGGAAC
* **
41259054 AGCTCACAGACCTACATTCCCAGTTGATGTTTAAAGGTTAGATGAGTTATACTCACAACCTTCAT
1 AGCTCACAGAACTATGTTCCCAGTTGATGTTTAAAGGTTAGATGAGTTATACTCACAACCTTCAT
* * *
41259119 TTATTTGAGTAAGCTGAGTTAAGCTCGCTACTTTGGAAT
66 TTATTTGAGTAAGCTGAGTTAAGCTTGCTACTCTGGAAC
41259158 AGCTC
1 AGCTC
41259163 GCGGACCTAT
Statistics
Matches: 195, Mismatches: 18, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
104 195 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (104 bp):
AGCTCACAGAACTATGTTCCCAGTTGATGTTTAAAGGTTAGATGAGTTATACTCACAACCTTCAT
TTATTTGAGTAAGCTGAGTTAAGCTTGCTACTCTGGAAC
Found at i:41264621 original size:39 final size:41
Alignment explanation
Indices: 41264507--41264690 Score: 199
Period size: 40 Copynumber: 4.6 Consensus size: 41
41264497 GCTCCTCGTT
* *
41264507 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAATCTCGCA
* *
41264547 CAAATGCCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
41264587 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGT-ATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
* * *
41264626 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGTAATC-TCGCA
41264667 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41264691 CATCATTCAA
Statistics
Matches: 129, Mismatches: 7, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
38 2 0.02
39 52 0.40
40 64 0.50
41 11 0.09
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (41 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAATCTCGCA
Found at i:41264651 original size:79 final size:82
Alignment explanation
Indices: 41264507--41264690 Score: 217
Period size: 79 Copynumber: 2.3 Consensus size: 82
41264497 GCTCCTCGTT
* *
41264507 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
*
41264571 GAT-TTAGT-A-TCTCGCA
66 GATATT-GTCACT-TAGCA
**
41264587 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTC-GGATCTTAGTC
1 CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAAT-TCGCACAAATGCCTTCGGGA-CTTAACC
41264648 CGGATATTGTCACTTAGCA
64 CGGATATTGTCACTTAGCA
41264667 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41264691 CATCATTCAA
Statistics
Matches: 92, Mismatches: 5, Indels: 15
0.82 0.04 0.13
Matches are distributed among these distances:
78 14 0.15
79 54 0.59
80 23 0.25
81 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.26
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
GATATTGTCACTTAGCA
Found at i:41272555 original size:79 final size:81
Alignment explanation
Indices: 41272446--41272628 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
41272436 TACTCGTTCA
* *
41272446 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
41272509 ATTTAGTAAC-TCGCACC
65 ATATAGTAACTTAGCA-C
**
41272526 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
41272589 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
41272605 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
41272629 CATCATTCGA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 59 0.66
80 28 0.31
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Done.