Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 13 of 153
Found at i:4327339 original size:40 final size:40
Alignment explanation
Indices: 4327265--4327345 Score: 137
Period size: 40 Copynumber: 2.0 Consensus size: 40
4327255 AAATTTAAAC
4327265 AGGGCCTAGTAACTAAAGTTTTGAATCCCAGTTTACACCAG
1 AGGGCCTAGTAACTAAAG-TTTGAATCCCAGTTTACACCAG
4327306 AGGGCCTAGTAACTACAAG-TTGAATCCCAGTTTACACCAG
1 AGGGCCTAGTAACTA-AAGTTTGAATCCCAGTTTACACCAG
4327346 TAAAAAAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
40 21 0.54
41 15 0.38
42 3 0.08
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (40 bp):
AGGGCCTAGTAACTAAAGTTTGAATCCCAGTTTACACCAG
Found at i:4332971 original size:13 final size:14
Alignment explanation
Indices: 4332953--4332985 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
4332943 CTCATTACTT
*
4332953 TTATTTTTAA-TTA
1 TTATTTTTAACATA
4332966 TTATTTTTAACATA
1 TTATTTTTAACATA
4332980 TTATTT
1 TTATTT
4332986 CCTCTAGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTTAACATA
Found at i:4334180 original size:23 final size:21
Alignment explanation
Indices: 4334139--4334180 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
4334129 TAATATTAAA
*
4334139 ATAATAAAATTACATTTTACT
1 ATAATAAAATTACAATTTACT
4334160 ATAATAAAAATATACAATTTA
1 ATAAT-AAAAT-TACAATTTA
4334181 ATTTTTATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (21 bp):
ATAATAAAATTACAATTTACT
Found at i:4334182 original size:81 final size:81
Alignment explanation
Indices: 4334015--4334184 Score: 179
Period size: 81 Copynumber: 2.1 Consensus size: 81
4334005 GTAATAAATT
* * * * *
4334015 TTTAATTTATACTTTTTATAATTTATAAAATTTTAAATTAATAATGATAAAATTACACTTTAGTA
1 TTTAATTTATAATTTTTATAAATTATAAAATTATAAATTAATAATAATAAAATTACACTTTACTA
*
4334080 TTTAAAATAATCAAAA
66 TTAAAAATAATCAAAA
* *
4334096 ATTAATTTA-AATTTTTA-AAATTATAAAGATATATAATATTAA-AATAATAAAATTACATTTTA
1 TTTAATTTATAATTTTTATAAATTATAAA-AT-TATAA-ATTAATAATAATAAAATTACACTTTA
*
4334158 CTATAATAAAAAT-AT-ACAA
63 CTAT--TAAAAATAATCAAAA
4334177 TTTAATTT
1 TTTAATTT
4334185 TTATCAAAAA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
79 9 0.12
80 9 0.12
81 43 0.58
82 7 0.09
83 6 0.08
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (81 bp):
TTTAATTTATAATTTTTATAAATTATAAAATTATAAATTAATAATAATAAAATTACACTTTACTA
TTAAAAATAATCAAAA
Found at i:4336690 original size:11 final size:11
Alignment explanation
Indices: 4336674--4336713 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4336664 GGTTTTCTCT
4336674 CTATTTTGCTA
1 CTATTTTGCTA
* *
4336685 CCATTTTACTA
1 CTATTTTGCTA
*
4336696 CTATGTTGCTA
1 CTATTTTGCTA
4336707 CTATTTT
1 CTATTTT
4336714 ATTTTTATTG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.20, G:0.07, T:0.53
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:4336785 original size:30 final size:30
Alignment explanation
Indices: 4336751--4336812 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
4336741 ACTTATTTTA
*
4336751 TTGTTAATTTTGTTACTATTTTAAAGACAT
1 TTGTTAATTTTGCTACTATTTTAAAGACAT
* *
4336781 TTGTTAATTTTGCTATTATTTTAAAGTCAT
1 TTGTTAATTTTGCTACTATTTTAAAGACAT
4336811 TT
1 TT
4336813 ACTTGTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.06, G:0.10, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGCTACTATTTTAAAGACAT
Found at i:4348538 original size:6 final size:6
Alignment explanation
Indices: 4348527--4348551 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4348517 ATGTCCACAG
4348527 TTCCAT TTCCAT TTCCAT TTCCAT T
1 TTCCAT TTCCAT TTCCAT TTCCAT T
4348552 AAAGACCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCCAT
Found at i:4360439 original size:21 final size:19
Alignment explanation
Indices: 4360385--4360438 Score: 54
Period size: 21 Copynumber: 2.7 Consensus size: 19
4360375 CTTGTAATGT
*
4360385 TATTTTTTATTTTAAAATA
1 TATTTTTAATTTTAAAATA
* *
4360404 AATTTAATAAATTTTAAATATA
1 TATTT--TTAATTTTAAA-ATA
4360426 TATTTTTAATTTT
1 TATTTTTAATTTT
4360439 TTTCATGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
19 4 0.15
20 7 0.26
21 9 0.33
22 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTTAATTTTAAAATA
Found at i:4360916 original size:29 final size:30
Alignment explanation
Indices: 4360884--4360957 Score: 73
Period size: 29 Copynumber: 2.5 Consensus size: 30
4360874 TGTATAGTTT
*
4360884 AATCAAAATCAAAGTTTTATATATAT-A-TG
1 AATC-AAATCAAAGTTTCATATATATAATTG
*
4360913 AATCGCAATTCAAA-TTTCATATATATAATTG
1 AAT--CAAATCAAAGTTTCATATATATAATTG
*
4360944 CATCAAATCAAAGT
1 AATCAAATCAAAGT
4360958 AAATATTAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
29 22 0.61
30 9 0.25
31 5 0.14
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.35
Consensus pattern (30 bp):
AATCAAATCAAAGTTTCATATATATAATTG
Found at i:4367903 original size:5 final size:5
Alignment explanation
Indices: 4367895--4367924 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
4367885 TAATTTAATT
4367895 TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA
4367925 AGTTCAGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:4372777 original size:6 final size:6
Alignment explanation
Indices: 4372766--4372790 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4372756 TATACTCCAA
4372766 TAATAT TAATAT TAATAT TAATAT T
1 TAATAT TAATAT TAATAT TAATAT T
4372791 GTTTTTTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATAT
Found at i:4377272 original size:18 final size:19
Alignment explanation
Indices: 4377228--4377272 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
4377218 CTGATTTTTC
*
4377228 TTCCTTTTGTTTTTGGGGT
1 TTCCTTTTGTTTTTGGGGA
**
4377247 TTAATTTTGTTTTT-GGGA
1 TTCCTTTTGTTTTTGGGGA
4377265 TTCCTTTT
1 TTCCTTTT
4377273 TCTTTCCATT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.07, C:0.09, G:0.20, T:0.64
Consensus pattern (19 bp):
TTCCTTTTGTTTTTGGGGA
Found at i:4382551 original size:16 final size:15
Alignment explanation
Indices: 4382522--4382552 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
4382512 CCCTTTTCTT
4382522 TGAAAATAGAATGAA
1 TGAAAATAGAATGAA
4382537 TGAAAATATGAATGAA
1 TGAAAATA-GAATGAA
4382553 GGGAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.19, T:0.23
Consensus pattern (15 bp):
TGAAAATAGAATGAA
Found at i:4385354 original size:27 final size:27
Alignment explanation
Indices: 4385322--4385395 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
4385312 AATCACATTG
*
4385322 GCGGCACCAAAGGTGCCAAAGAGATTA
1 GCGGCACCAATGGTGCCAAAGAGATTA
* * *
4385349 GTGGCACCAATGGTGCCAAAGTGATTG
1 GCGGCACCAATGGTGCCAAAGAGATTA
4385376 GCGGCACCAATGGTGCCAAA
1 GCGGCACCAATGGTGCCAAA
4385396 TGACTAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (27 bp):
GCGGCACCAATGGTGCCAAAGAGATTA
Found at i:4385497 original size:19 final size:19
Alignment explanation
Indices: 4385470--4385539 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
4385460 TCAACTCATT
*
4385470 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
4385489 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
4385507 TTCTCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
4385526 TTTTAATTTAATAA
1 TTTTAATTTAATAA
4385540 ACTATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:4385520 original size:37 final size:37
Alignment explanation
Indices: 4385475--4385545 Score: 142
Period size: 37 Copynumber: 1.9 Consensus size: 37
4385465 TCATTTTTTT
4385475 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
4385512 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
4385546 AAGTATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:4385786 original size:18 final size:19
Alignment explanation
Indices: 4385749--4385787 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4385739 TCAACTCATT
* *
4385749 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACACTA
4385768 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACACTA
4385786 TT
1 TT
4385788 ACGTAATACT
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTTAATTTAATAACACTA
Found at i:4386052 original size:19 final size:19
Alignment explanation
Indices: 4386027--4386137 Score: 95
Period size: 19 Copynumber: 6.1 Consensus size: 19
4386017 TACTTAATAG
4386027 TTTATTAAATTAAAATAAA
1 TTTATTAAATTAAAATAAA
* * * *
4386046 ATTATTAAATGAGAAT-AG
1 TTTATTAAATTAAAATAAA
*
4386064 TTTATTAAATTAAAATAGA
1 TTTATTAAATTAAAATAAA
* * * *
4386083 CTTATTAAATGAGAAT-AG
1 TTTATTAAATTAAAATAAA
*
4386101 TTTATTAAATTAAAATAGA
1 TTTATTAAATTAAAATAAA
*
4386120 GTTATTAAA-TAAAA-AAA
1 TTTATTAAATTAAAATAAA
4386137 T
1 T
4386138 GAGTTAAAGG
Statistics
Matches: 68, Mismatches: 22, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
17 2 0.03
18 32 0.47
19 34 0.50
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (19 bp):
TTTATTAAATTAAAATAAA
Found at i:4386068 original size:37 final size:37
Alignment explanation
Indices: 4386022--4386129 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
4386012 AGTATTACTT
*
4386022 AATAGTTTATTAAATTAAAATAAAATTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAATTATTAAATGAG
*
4386059 AATAGTTTATTAAATTAAAATAGACTTATTAAATGAG
1 AATAGTTTATTAAATTAAAATAGAATTATTAAATGAG
*
4386096 AATAGTTTATTAAATTAAAATAGAGTTATTAAAT
1 AATAGTTTATTAAATTAAAATAGAATTATTAAAT
4386130 AAAAAAATGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (37 bp):
AATAGTTTATTAAATTAAAATAGAATTATTAAATGAG
Found at i:4386364 original size:29 final size:27
Alignment explanation
Indices: 4386331--4386396 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 27
4386321 TTTTTTGTGT
*
4386331 ATATTTTTGTAAATAATCAAAAAATAATA
1 ATATTTTTGTAAATAA-AAAAAAAT-ATA
*
4386360 ATATTTTGGTAAATAAAAAAAAATATA
1 ATATTTTTGTAAATAAAAAAAAATATA
4386387 ATATTTTTGT
1 ATATTTTTGT
4386397 TAATTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 12 0.35
28 7 0.21
29 15 0.44
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.41
Consensus pattern (27 bp):
ATATTTTTGTAAATAAAAAAAAATATA
Found at i:4386394 original size:28 final size:30
Alignment explanation
Indices: 4386331--4386395 Score: 93
Period size: 28 Copynumber: 2.3 Consensus size: 30
4386321 TTTTTTGTGT
*
4386331 ATATTTTT-GTAAATAATCAAAAAATAATA
1 ATATTTTTGGTAAATAATAAAAAAATAATA
4386360 ATA-TTTTGGTAAATAA-AAAAAAAT-ATA
1 ATATTTTTGGTAAATAATAAAAAAATAATA
4386387 ATATTTTTG
1 ATATTTTTG
4386396 TTAATTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 6 0.18
28 16 0.48
29 11 0.33
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (30 bp):
ATATTTTTGGTAAATAATAAAAAAATAATA
Found at i:4396657 original size:16 final size:16
Alignment explanation
Indices: 4396636--4396679 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
4396626 TGTCAAGTTG
4396636 TTTCAAGTTTAAATCT-
1 TTTCAAGTTTAAAT-TA
*
4396652 TTTCAAGTTTGAATTA
1 TTTCAAGTTTAAATTA
*
4396668 TTTTAAGTTTAA
1 TTTCAAGTTTAA
4396680 TCTCCGAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 1 0.04
16 23 0.96
ACGTcount: A:0.32, C:0.07, G:0.09, T:0.52
Consensus pattern (16 bp):
TTTCAAGTTTAAATTA
Found at i:4398100 original size:13 final size:12
Alignment explanation
Indices: 4398082--4398125 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
4398072 GATTTAAGAA
4398082 ATAAATATAATAT
1 ATAAATATAA-AT
4398095 ATAAATATAAAT
1 ATAAATATAAAT
4398107 ATTAAA-ATAAAT
1 A-TAAATATAAAT
*
4398119 TTAAATA
1 ATAAATA
4398126 AATTAACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 4 0.14
12 10 0.36
13 14 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
ATAAATATAAAT
Found at i:4398102 original size:6 final size:6
Alignment explanation
Indices: 4398082--4398125 Score: 54
Period size: 6 Copynumber: 7.2 Consensus size: 6
4398072 GATTTAAGAA
*
4398082 ATAAAT ATAATAT ATAAAT ATAAAT ATTAAA- ATAAAT TTAAAT A
1 ATAAAT ATAA-AT ATAAAT ATAAAT A-TAAAT ATAAAT ATAAAT A
4398126 AATTAACAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
5 4 0.12
6 19 0.58
7 10 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATAAAT
Found at i:4398413 original size:19 final size:21
Alignment explanation
Indices: 4398390--4398432 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
4398380 TTATATATGC
4398390 ATATATAAAAA-ATAGTAGATT
1 ATATA-AAAAATATAGTAGATT
4398411 ATATAAAAAATATAGTAGATT
1 ATATAAAAAATATAGTAGATT
4398432 A
1 A
4398433 ATATTAAACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (21 bp):
ATATAAAAAATATAGTAGATT
Found at i:4399989 original size:50 final size:50
Alignment explanation
Indices: 4399933--4400211 Score: 256
Period size: 50 Copynumber: 5.6 Consensus size: 50
4399923 TCGGGGAAAC
* * *
4399933 AAGATTCGCTGTCATAGCTTCAATCTATTCCACTGCACCGCCAGGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
* ** * * **
4399983 AAGATTCGCCGTTGT-GACTTCAATCTATTTAACTGCAATGTCAGGGAAAC
1 AAGATTCGCCGTCGTAG-CTTCAATCTATTCCACTGCAACGCCAGGGAAGT
* * * * * *
4400033 AAGATTCGTCGTCGTAGCTTTAATCTGTTCCACTACACCGCCAAGGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
* ** * *** *
4400083 AAGATTCGCCGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGGAA-C
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACG-CCAGGGAAGT
* * * * *
4400133 AAGATTCGCCGTCGTAGCCTCAATCTGTTCCACTACATCGCCAGAGAAGT
1 AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
*
4400183 AAGATTCGCCGTTGTAGCTTCAATCTATT
1 AAGATTCGCCGTCGTAGCTTCAATCTATT
4400212 TAACTGTAAT
Statistics
Matches: 172, Mismatches: 53, Indels: 8
0.74 0.23 0.03
Matches are distributed among these distances:
49 5 0.03
50 162 0.94
51 5 0.03
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (50 bp):
AAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCAACGCCAGGGAAGT
Found at i:4400083 original size:100 final size:99
Alignment explanation
Indices: 4399900--4400222 Score: 470
Period size: 100 Copynumber: 3.2 Consensus size: 99
4399890 GGATTGGTTT
* * * *
4399900 CTTCCATCTGTTTAACTGCAATGTCGGGGAAACAAGATTCGCTGTCATAGCTTCAATCTATTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGC-GTCGTAGCTTCAATCTGTTCCA
* *
4399965 CTGCACCGCCAGGGAAGTAAGATTCGCCGTTGT-G
65 CTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
* *
4399999 ACTTCAATCTATTTAACTGCAATGTCAGGGAAACAAGATTCGTCGTCGTAGCTTTAATCTGTTCC
1 -CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCG-CGTCGTAGCTTCAATCTGTTCC
4400064 ACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
64 ACTACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
* * *
4400100 CTTCAATCTATTTAACTGCAATGTTGGGGGAACAAGATTCGCCGTCGTAGCCTCAATCTGTTCCA
1 CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCG-CGTCGTAGCTTCAATCTGTTCCA
*
4400165 CTACATCGCC-AGAGAAGTAAGATTCGCCGTTGTAG
65 CTACACCGCCAAG-GAAGTAAGATTCGCCGTTGTAG
*
4400200 CTTCAATCTATTTAACTGTAATG
1 CTTCAATCTATTTAACTGCAATG
4400223 CCAAAGAGAT
Statistics
Matches: 204, Mismatches: 16, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
99 2 0.01
100 200 0.98
101 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (99 bp):
CTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCGCGTCGTAGCTTCAATCTGTTCCAC
TACACCGCCAAGGAAGTAAGATTCGCCGTTGTAG
Found at i:4402282 original size:21 final size:22
Alignment explanation
Indices: 4402246--4402294 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
4402236 CCTTAGCCTC
*
4402246 TTCATTTTTACTTTTTCCA-TTT
1 TTCATTATTACTTTTT-CATTTT
4402268 TTCATTATT-CTTTTTCATTTT
1 TTCATTATTACTTTTTCATTTT
4402289 TTCATT
1 TTCATT
4402295 TCATTCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 15 0.60
22 8 0.32
ACGTcount: A:0.14, C:0.16, G:0.00, T:0.69
Consensus pattern (22 bp):
TTCATTATTACTTTTTCATTTT
Found at i:4402288 original size:7 final size:7
Alignment explanation
Indices: 4402246--4402306 Score: 54
Period size: 7 Copynumber: 8.3 Consensus size: 7
4402236 CCTTAGCCTC
4402246 TTCATTT
1 TTCATTT
4402253 TT-ACTTT
1 TTCA-TTT
4402260 TTCCATTT
1 TT-CATTT
*
4402268 TTCATTA
1 TTCATTT
4402275 TTC-TTT
1 TTCATTT
4402281 TTCATTTT
1 TTCA-TTT
4402289 TTCATTT
1 TTCATTT
4402296 CATTCATTT
1 --TTCATTT
4402305 TT
1 TT
4402307 TTACGATTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
6 6 0.13
7 19 0.42
8 12 0.27
9 8 0.18
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (7 bp):
TTCATTT
Found at i:4402803 original size:18 final size:17
Alignment explanation
Indices: 4402780--4402831 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 17
4402770 CCTAGTAGAG
4402780 GTTTTTGTTTCTTTTTTT
1 GTTTTT-TTTCTTTTTTT
*
4402798 GTTTTTTGTTCTTCTTTT
1 GTTTTTT-TTCTTTTTTT
4402816 GTTCTTTTTTTCTTTT
1 G-T-TTTTTTTCTTTT
4402832 GGATTGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 16 0.55
19 7 0.24
20 5 0.17
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.81
Consensus pattern (17 bp):
GTTTTTTTTCTTTTTTT
Found at i:4402814 original size:21 final size:19
Alignment explanation
Indices: 4402781--4402825 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 19
4402771 CTAGTAGAGG
* *
4402781 TTTTTGTTTCTTTTTTTGT
1 TTTTTGTTTCTTTTGTTCT
4402800 TTTTTGTTCTTCTTTTGTTCT
1 TTTTTG-T-TTCTTTTGTTCT
4402821 TTTTT
1 TTTTT
4402826 TCTTTTGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 1 0.05
21 15 0.68
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (19 bp):
TTTTTGTTTCTTTTGTTCT
Found at i:4402921 original size:14 final size:14
Alignment explanation
Indices: 4402898--4402931 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4402888 ATCAATGTTA
* *
4402898 TTCCAGATAAAGTC
1 TTCCACATAAAATC
4402912 TTCCACATAAAATC
1 TTCCACATAAAATC
4402926 TTCCAC
1 TTCCAC
4402932 TTTCATTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (14 bp):
TTCCACATAAAATC
Found at i:4406912 original size:18 final size:19
Alignment explanation
Indices: 4406861--4406933 Score: 64
Period size: 18 Copynumber: 3.9 Consensus size: 19
4406851 ACACTAACGA
*
4406861 AATATACAAATTTAAATAT
1 AATATATAAATTTAAATAT
**
4406880 AAT-T-TAAGAAATAAATAT
1 AATATATAA-ATTTAAATAT
*
4406898 AATATATAAATTAAAATATT
1 AATATATAAATTTAAATA-T
4406918 AA-A-ATAAATTTAAATA
1 AATATATAAATTTAAATA
4406934 AATTAACAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
17 2 0.05
18 24 0.56
19 11 0.26
20 6 0.14
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
AATATATAAATTTAAATAT
Found at i:4406961 original size:29 final size:28
Alignment explanation
Indices: 4406903--4406981 Score: 86
Period size: 29 Copynumber: 2.8 Consensus size: 28
4406893 AATATAATAT
*
4406903 ATAAATTAAAATATTAAAATAAATTTAA
1 ATAAATTAAAATATTAAAATAAATTGAA
* * *
4406931 ATAAATTAACAATATTGAAATGAGTTGAA
1 ATAAATTAA-AATATTAAAATAAATTGAA
* *
4406960 ATAAGTTAAAGATGTTAAAATA
1 ATAAATTAAA-ATATTAAAATA
4406982 TTTGAAAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 10 0.24
29 31 0.76
ACGTcount: A:0.57, C:0.01, G:0.09, T:0.33
Consensus pattern (28 bp):
ATAAATTAAAATATTAAAATAAATTGAA
Found at i:4419170 original size:24 final size:24
Alignment explanation
Indices: 4419122--4419179 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
4419112 AACTCATTTT
4419122 ATTTAAT-TTTTTTATATATTGAC
1 ATTTAATATTTTTTATATATTGAC
* *
4419145 ATCTTAATATTTTTTA-ATGTTTAC
1 AT-TTAATATTTTTTATATATTGAC
4419169 ATTATAATATT
1 ATT-TAATATT
4419180 ATATATCACC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.10
24 20 0.67
25 7 0.23
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (24 bp):
ATTTAATATTTTTTATATATTGAC
Found at i:4423833 original size:3 final size:3
Alignment explanation
Indices: 4423827--4423886 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
4423817 AAAAAAAAAA
4423827 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
4423875 AAG AAG AAG AAG
1 AAG AAG AAG AAG
4423887 GGGCCTACAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4439102 original size:30 final size:30
Alignment explanation
Indices: 4439066--4439128 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
4439056 ACTTATTTTA
4439066 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
4439096 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
4439126 TTG
1 TTG
4439129 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:4441311 original size:38 final size:38
Alignment explanation
Indices: 4441269--4441345 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
4441259 CCTTAATTTG
4441269 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
1 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
4441307 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
1 TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
4441345 T
1 T
4441346 TCACTACCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (38 bp):
TATTATAGGCCCTCATAAAGCCCTTAATAAATCCAAAA
Found at i:4443144 original size:5 final size:6
Alignment explanation
Indices: 4443124--4443157 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
4443114 ATGAATAGAA
* *
4443124 AAAATG GAAATG AAAATA AAAATG AAAATG AAAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAA
4443158 CTTACAATCC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:4443146 original size:18 final size:18
Alignment explanation
Indices: 4443123--4443157 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4443113 AATGAATAGA
*
4443123 AAAAATGGAAATGAAAAT
1 AAAAATGAAAATGAAAAT
4443141 AAAAATGAAAATGAAAA
1 AAAAATGAAAATGAAAA
4443158 CTTACAATCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (18 bp):
AAAAATGAAAATGAAAAT
Found at i:4464020 original size:24 final size:24
Alignment explanation
Indices: 4463983--4464094 Score: 127
Period size: 24 Copynumber: 4.7 Consensus size: 24
4463973 TCGTTCTTTG
*
4463983 GTAAATGATGAATTGAC-GAATAAT
1 GTAAAGGATGAATTGACGGAA-AAT
*
4464007 GTAAAGGATAAATTGACGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
* * *
4464031 ATAAAGGAGGAACTGACGGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
**
4464055 GTAAAGGATGAATTGATAGAAAAT
1 GTAAAGGATGAATTGACGGAAAAT
* *
4464079 GTAAATGCTGAATTGA
1 GTAAAGGATGAATTGA
4464095 TGGCAATTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
24 71 0.96
25 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.25, T:0.23
Consensus pattern (24 bp):
GTAAAGGATGAATTGACGGAAAAT
Found at i:4464856 original size:9 final size:9
Alignment explanation
Indices: 4464836--4464893 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
4464826 TTTGGTTAAA
*
4464836 AATTAACTG
1 AATTAACCG
*
4464845 AATTACCCG
1 AATTAACCG
*
4464854 AATTAACTG
1 AATTAACCG
4464863 AATTAACCG
1 AATTAACCG
* *
4464872 AATTACCCA
1 AATTAACCG
4464881 AATTAACCG
1 AATTAACCG
4464890 AATT
1 AATT
4464894 GAATCACTAT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:4464859 original size:18 final size:18
Alignment explanation
Indices: 4464836--4464893 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
4464826 TTTGGTTAAA
*
4464836 AATTAACTGAATTACCCG
1 AATTAACTGAATTAACCG
4464854 AATTAACTGAATTAACCG
1 AATTAACTGAATTAACCG
* **
4464872 AATTACCCAAATTAACCG
1 AATTAACTGAATTAACCG
4464890 AATT
1 AATT
4464894 GAATCACTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (18 bp):
AATTAACTGAATTAACCG
Found at i:4464874 original size:27 final size:27
Alignment explanation
Indices: 4464836--4464893 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
4464826 TTTGGTTAAA
* * *
4464836 AATTAACTGAATTACCCGAATTAACTG
1 AATTAACCGAATTACCCAAATTAACCG
4464863 AATTAACCGAATTACCCAAATTAACCG
1 AATTAACCGAATTACCCAAATTAACCG
4464890 AATT
1 AATT
4464894 GAATCACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTACCCAAATTAACCG
Found at i:4468409 original size:22 final size:20
Alignment explanation
Indices: 4468367--4468407 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4468357 TGTTATAACT
4468367 TTTTTTTATTTACCAATATA
1 TTTTTTTATTTACCAATATA
*
4468387 TTTTTTTATTTACCAAAATA
1 TTTTTTTATTTACCAATATA
4468407 T
1 T
4468408 ATCAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTTATTTACCAATATA
Found at i:4468495 original size:27 final size:27
Alignment explanation
Indices: 4468465--4468535 Score: 92
Period size: 27 Copynumber: 2.6 Consensus size: 27
4468455 TGGTCACGCT
* *
4468465 AATGGCATTGGCGTCACCGATGGTGCC
1 AATGCCATTGGCGGCACCGATGGTGCC
4468492 AATGCCATTGGCGGCACCGATGGTGCC
1 AATGCCATTGGCGGCACCGATGGTGCC
4468519 ATATTG--ATTGGCGGCAC
1 A-A-TGCCATTGGCGGCAC
4468536 TATTTGTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 37 0.93
28 1 0.03
29 2 0.05
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (27 bp):
AATGCCATTGGCGGCACCGATGGTGCC
Found at i:4469700 original size:92 final size:92
Alignment explanation
Indices: 4469587--4469770 Score: 350
Period size: 92 Copynumber: 2.0 Consensus size: 92
4469577 TCATTGGGAT
4469587 GAAGAGGTCGATAGTGACGCTGATCCCGATGTGGACGATGTACCTGATGATATTGACGATGAAGA
1 GAAGAGGTCGATAGTGACGCTGATCCCGATGTGGACGATGTACCTGATGATATTGACGATGAAGA
*
4469652 TGTCAACAACGATGAATGCATTAACGC
66 TGTCAACAACGATGAAGGCATTAACGC
4469679 GAAGAGGTCGATAGTGACGCTGATCCCGATGTGGACGATGTACCTGATGATATTGACGATGAAGA
1 GAAGAGGTCGATAGTGACGCTGATCCCGATGTGGACGATGTACCTGATGATATTGACGATGAAGA
*
4469744 TGTCAACAACGATGAAGGTATTAACGC
66 TGTCAACAACGATGAAGGCATTAACGC
4469771 TTCTTCGGTC
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 90 1.00
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.23
Consensus pattern (92 bp):
GAAGAGGTCGATAGTGACGCTGATCCCGATGTGGACGATGTACCTGATGATATTGACGATGAAGA
TGTCAACAACGATGAAGGCATTAACGC
Found at i:4471821 original size:934 final size:934
Alignment explanation
Indices: 4470009--4471876 Score: 3718
Period size: 934 Copynumber: 2.0 Consensus size: 934
4469999 GATATCAGTG
*
4470009 AATTTTAAAGTCTTCGTGTCTAATCCGATAATATATGTTAAGGAGTGTTGAAAGGCAACGGAAGG
1 AATTATAAAGTCTTCGTGTCTAATCCGATAATATATGTTAAGGAGTGTTGAAAGGCAACGGAAGG
4470074 CTGCAATTGGCGGGTACGAGCTGCATTCATTAGAAGTTCTCAAATGTGGGAGATACGAAAATTTG
66 CTGCAATTGGCGGGTACGAGCTGCATTCATTAGAAGTTCTCAAATGTGGGAGATACGAAAATTTG
4470139 TTTGTCCTCATACATTCACATCAACACGTATGACAGAAGATCATAGAAAACTTGATTCGAAAACT
131 TTTGTCCTCATACATTCACATCAACACGTATGACAGAAGATCATAGAAAACTTGATTCGAAAACT
4470204 ATTTGTACGTGTATCATGCCAATGGTGAAGGACATGCCGACCATTAAAGTTTCGGTACTCATTGC
196 ATTTGTACGTGTATCATGCCAATGGTGAAGGACATGCCGACCATTAAAGTTTCGGTACTCATTGC
4470269 GGAAATGCAAGCACGATTCCAGTATCGAGTCTCATATCGGAAGGCATGGATAGCTAAACAGATGG
261 GGAAATGCAAGCACGATTCCAGTATCGAGTCTCATATCGGAAGGCATGGATAGCTAAACAGATGG
4470334 CGATGGAGCAACTGTATGGGGATTACGATTCGTCGTATAACGAGCTTCAAGGTTGGATAGCTGCT
326 CGATGGAGCAACTGTATGGGGATTACGATTCGTCGTATAACGAGCTTCAAGGTTGGATAGCTGCT
4470399 ATGATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGA
391 ATGATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGA
4470464 CCAGTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGG
456 CCAGTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGG
4470529 CATTTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAG
521 CATTTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAG
4470594 ATACTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGT
586 ATACTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGT
4470659 AGATAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGA
651 AGATAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGA
4470724 ACGATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGT
716 ACGATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGT
4470789 ATGCCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAA
781 ATGCCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAA
4470854 TGCAGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTT
846 TGCAGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTT
4470919 ACATTATTTCAGTGCATCATGTTT
911 ACATTATTTCAGTGCATCATGTTT
*
4470943 AATTATAAAGTCTTCGTGTCTACTCCGATAATATATGTTAAGGAGTGTTGAAAGGCAACGGAAGG
1 AATTATAAAGTCTTCGTGTCTAATCCGATAATATATGTTAAGGAGTGTTGAAAGGCAACGGAAGG
4471008 CTGCAATTGGCGGGTACGAGCTGCATTCATTAGAAGTTCTCAAATGTGGGAGATACGAAAATTTG
66 CTGCAATTGGCGGGTACGAGCTGCATTCATTAGAAGTTCTCAAATGTGGGAGATACGAAAATTTG
4471073 TTTGTCCTCATACATTCACATCAACACGTATGACAGAAGATCATAGAAAACTTGATTCGAAAACT
131 TTTGTCCTCATACATTCACATCAACACGTATGACAGAAGATCATAGAAAACTTGATTCGAAAACT
4471138 ATTTGTACGTGTATCATGCCAATGGTGAAGGACATGCCGACCATTAAAGTTTCGGTACTCATTGC
196 ATTTGTACGTGTATCATGCCAATGGTGAAGGACATGCCGACCATTAAAGTTTCGGTACTCATTGC
4471203 GGAAATGCAAGCACGATTCCAGTATCGAGTCTCATATCGGAAGGCATGGATAGCTAAACAGATGG
261 GGAAATGCAAGCACGATTCCAGTATCGAGTCTCATATCGGAAGGCATGGATAGCTAAACAGATGG
4471268 CGATGGAGCAACTGTATGGGGATTACGATTCGTCGTATAACGAGCTTCAAGGTTGGATAGCTGCT
326 CGATGGAGCAACTGTATGGGGATTACGATTCGTCGTATAACGAGCTTCAAGGTTGGATAGCTGCT
4471333 ATGATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGA
391 ATGATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGA
4471398 CCAGTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGG
456 CCAGTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGG
4471463 CATTTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAG
521 CATTTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAG
4471528 ATACTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGT
586 ATACTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGT
4471593 AGATAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGA
651 AGATAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGA
4471658 ACGATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGT
716 ACGATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGT
4471723 ATGCCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAA
781 ATGCCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAA
4471788 TGCAGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTT
846 TGCAGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTT
4471853 ACATTATTTCAGTGCATCATGTTT
911 ACATTATTTCAGTGCATCATGTTT
4471877 GAAATTTATT
Statistics
Matches: 932, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
934 932 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (934 bp):
AATTATAAAGTCTTCGTGTCTAATCCGATAATATATGTTAAGGAGTGTTGAAAGGCAACGGAAGG
CTGCAATTGGCGGGTACGAGCTGCATTCATTAGAAGTTCTCAAATGTGGGAGATACGAAAATTTG
TTTGTCCTCATACATTCACATCAACACGTATGACAGAAGATCATAGAAAACTTGATTCGAAAACT
ATTTGTACGTGTATCATGCCAATGGTGAAGGACATGCCGACCATTAAAGTTTCGGTACTCATTGC
GGAAATGCAAGCACGATTCCAGTATCGAGTCTCATATCGGAAGGCATGGATAGCTAAACAGATGG
CGATGGAGCAACTGTATGGGGATTACGATTCGTCGTATAACGAGCTTCAAGGTTGGATAGCTGCT
ATGATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGA
CCAGTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGG
CATTTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAG
ATACTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGT
AGATAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGA
ACGATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGT
ATGCCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAA
TGCAGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTT
ACATTATTTCAGTGCATCATGTTT
Found at i:4472799 original size:762 final size:762
Alignment explanation
Indices: 4471336--4472859 Score: 3048
Period size: 762 Copynumber: 2.0 Consensus size: 762
4471326 AGCTGCTATG
4471336 ATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGACCA
1 ATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGACCA
4471401 GTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGGCAT
66 GTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGGCAT
4471466 TTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAGATA
131 TTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAGATA
4471531 CTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGTAGA
196 CTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGTAGA
4471596 TAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGAACG
261 TAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGAACG
4471661 ATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGTATG
326 ATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGTATG
4471726 CCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAATGC
391 CCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAATGC
4471791 AGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTTACA
456 AGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTTACA
4471856 TTATTTCAGTGCATCATGTTTGAAATTTATTAATTTAGTGTGTTAAGGGGAAATAAAAGAAAATA
521 TTATTTCAGTGCATCATGTTTGAAATTTATTAATTTAGTGTGTTAAGGGGAAATAAAAGAAAATA
4471921 ATAAATAAGGAGGGATTAAAAGTTAATTAGCCACATATTTGTGCCGCATTTTTTTCCCCTCCATC
586 ATAAATAAGGAGGGATTAAAAGTTAATTAGCCACATATTTGTGCCGCATTTTTTTCCCCTCCATC
4471986 ACCCTTTTTTTCCCTCTATTATTTTGGTAAATAAAGAAAAAGTTTATAATATTTTAGTTTTTTTT
651 ACCCTTTTTTTCCCTCTATTATTTTGGTAAATAAAGAAAAAGTTTATAATATTTTAGTTTTTTTT
4472051 GTAATATTTTGCTAAAAAACCCGCAATAAACCCTTTCCCCTGCCCTT
716 GTAATATTTTGCTAAAAAACCCGCAATAAACCCTTTCCCCTGCCCTT
4472098 ATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGACCA
1 ATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGACCA
4472163 GTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGGCAT
66 GTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGGCAT
4472228 TTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAGATA
131 TTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAGATA
4472293 CTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGTAGA
196 CTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGTAGA
4472358 TAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGAACG
261 TAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGAACG
4472423 ATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGTATG
326 ATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGTATG
4472488 CCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAATGC
391 CCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAATGC
4472553 AGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTTACA
456 AGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTTACA
4472618 TTATTTCAGTGCATCATGTTTGAAATTTATTAATTTAGTGTGTTAAGGGGAAATAAAAGAAAATA
521 TTATTTCAGTGCATCATGTTTGAAATTTATTAATTTAGTGTGTTAAGGGGAAATAAAAGAAAATA
4472683 ATAAATAAGGAGGGATTAAAAGTTAATTAGCCACATATTTGTGCCGCATTTTTTTCCCCTCCATC
586 ATAAATAAGGAGGGATTAAAAGTTAATTAGCCACATATTTGTGCCGCATTTTTTTCCCCTCCATC
4472748 ACCCTTTTTTTCCCTCTATTATTTTGGTAAATAAAGAAAAAGTTTATAATATTTTAGTTTTTTTT
651 ACCCTTTTTTTCCCTCTATTATTTTGGTAAATAAAGAAAAAGTTTATAATATTTTAGTTTTTTTT
4472813 GTAATATTTTGCTAAAAAACCCGCAATAAACCCTTTCCCCTGCCCTT
716 GTAATATTTTGCTAAAAAACCCGCAATAAACCCTTTCCCCTGCCCTT
4472860 TGGTCGTATT
Statistics
Matches: 762, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
762 762 1.00
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.32
Consensus pattern (762 bp):
ATGGAGTACGTACCGGAGACTGTGATTGAGTTGCAGACAAGTTCATATTACGGCCCGGATGACCA
GTTACAGCTGGCAAAAAAGATTTTCCATCGGATGTTCTGGACGTTTGATCCATGTGTGTGGGCAT
TTCCCCACTGCAAGCCAGTTGTGCAGGTGGATGGGACCTGGCTGTATGGAAAATATACACAGATA
CTGCTTCTTGCAGTTGCTCAAGACGGTAACAGAAACGTGCTCCCGATAGCATTTGCTATCGTAGA
TAAAGAGAACATGGAGTCTTGGGAATTCTTCCTCACAAATCTGCGAAGGTATGTTATTAGGAACG
ATAACATTTGCATCATCTCCGATAGAGGGAAGGGTTTAATTGCAGCTATTAGGCGTTCCGGTATG
CCGTGGAGATCCGTTTACTGCATTCGTCACATTGCGTCTAACTTCCATAAAGATTATAAGAATGC
AGACTGGAAGAGACAATTCGTGGCAATGGGTAAATATCATAAACTTAGTCTTTTATAATTTTACA
TTATTTCAGTGCATCATGTTTGAAATTTATTAATTTAGTGTGTTAAGGGGAAATAAAAGAAAATA
ATAAATAAGGAGGGATTAAAAGTTAATTAGCCACATATTTGTGCCGCATTTTTTTCCCCTCCATC
ACCCTTTTTTTCCCTCTATTATTTTGGTAAATAAAGAAAAAGTTTATAATATTTTAGTTTTTTTT
GTAATATTTTGCTAAAAAACCCGCAATAAACCCTTTCCCCTGCCCTT
Found at i:4473507 original size:21 final size:21
Alignment explanation
Indices: 4473483--4473614 Score: 98
Period size: 21 Copynumber: 6.4 Consensus size: 21
4473473 CCTTCCTTCC
4473483 CTCTTCTTCTTCCTTTTTTTT
1 CTCTTCTTCTTCCTTTTTTTT
* *
4473504 CTCTTCTCCTTTCCTTTTCTTT
1 CTCTTCTTC-TTCCTTTTTTTT
* *
4473526 C-CTTCTTTCTTTCTTTTTTCT
1 CTCTTC-TTCTTCCTTTTTTTT
*
4473547 -TC-TCTT-TTCC-TTTTCTT
1 CTCTTCTTCTTCCTTTTTTTT
*
4473564 CTTCTTCTTTCTTTC-TTTTTTT
1 C-TCTTC-TTCTTCCTTTTTTTT
* *
4473586 CTCTTCTCCTTTCCTTTTCTTT
1 CTCTTCTTC-TTCCTTTTTTTT
4473608 C-CTTCTT
1 CTCTTCTT
4473615 TCTTTTTCTT
Statistics
Matches: 86, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
17 5 0.06
18 3 0.03
19 4 0.05
20 6 0.07
21 37 0.43
22 31 0.36
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (21 bp):
CTCTTCTTCTTCCTTTTTTTT
Found at i:4473510 original size:18 final size:18
Alignment explanation
Indices: 4473487--4473623 Score: 68
Period size: 18 Copynumber: 7.1 Consensus size: 18
4473477 CCTTCCCTCT
4473487 TCTTCTTCCTTTTTTTTC
1 TCTTCTTCCTTTTTTTTC
*
4473505 TCTTCTCCTTTCCTTTTCTTTCC
1 TC-T-T-C-TTCCTTTT-TTTTC
*
4473528 TTCTTTCTTTCTTTTTTCTTC
1 -TC-TTCTTCCTTTTTT-TTC
4473549 TCTT-TTCCTTTTCTTCTTC
1 TCTTCTTCCTTTT-TT-TTC
*
4473568 TTCTTTCTTTC-TTTTTTTC
1 -TC-TTCTTCCTTTTTTTTC
*
4473587 TCTTC-TCCTTTCCTTTTC
1 TCTTCTTCCTTT-TTTTTC
4473605 T-TTCCTT-CTTTCTTTTTC
1 TCTT-CTTCCTTT-TTTTTC
4473623 T
1 T
4473624 TTCCTCTCCT
Statistics
Matches: 96, Mismatches: 8, Indels: 30
0.72 0.06 0.22
Matches are distributed among these distances:
16 2 0.02
17 7 0.07
18 29 0.30
19 13 0.14
20 9 0.09
21 15 0.16
22 12 0.12
23 5 0.05
24 4 0.04
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (18 bp):
TCTTCTTCCTTTTTTTTC
Found at i:4473528 original size:32 final size:31
Alignment explanation
Indices: 4473459--4473539 Score: 76
Period size: 34 Copynumber: 2.5 Consensus size: 31
4473449 AATAAAATTA
4473459 CTTT-CTTTTTTTT-TCCTTCCTTCCCTCTT
1 CTTTCCTTTTTTTTCTCCTTCCTTCCCTCTT
* * *
4473488 CTTCTTCCTTTTTTTTCTCTTCTCCTTTCCTTTT
1 C-T-TTCCTTTTTTTTCTCCT-TCCTTCCCTCTT
4473522 CTTTCCTTCTTTCTTTCT
1 CTTTCCTT-TTT-TTTCT
4473540 TTTTTCTTCT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
29 1 0.02
30 1 0.02
31 2 0.05
32 15 0.36
33 7 0.17
34 16 0.38
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (31 bp):
CTTTCCTTTTTTTTCTCCTTCCTTCCCTCTT
Found at i:4473535 original size:4 final size:4
Alignment explanation
Indices: 4473519--4473656 Score: 101
Period size: 4 Copynumber: 34.0 Consensus size: 4
4473509 CTCCTTTCCT
*
4473519 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTC TTTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTT-C TTTC T-TTC
* * *
4473565 -TTC -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC TTTTC TTTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC
*
4473613 TTTC -TT- TTTC TTTCC TCTCC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC
4473657 CCTCTCCTTC
Statistics
Matches: 109, Mismatches: 10, Indels: 30
0.73 0.07 0.20
Matches are distributed among these distances:
3 16 0.15
4 71 0.65
5 15 0.14
6 7 0.06
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTC
Found at i:4473559 original size:44 final size:42
Alignment explanation
Indices: 4473485--4473656 Score: 195
Period size: 40 Copynumber: 4.3 Consensus size: 42
4473475 TTCCTTCCCT
*
4473485 CTTC-TTCTTCCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTT-CTTTTCTTTC
* *
4473527 CTTCTTTCTTTCTTTTTTCTTCTCTTTTCCTTT-TCTTC-TT-
1 CTTCTTTCTTTCTTTTTT-TTCTCTTCTCCTTTCTTTTCTTTC
4473567 CTTCTTTCTTTC-TTTTTTTCTCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTT-CTTTTCTTTC
*
4473609 CTTCTTTC--T-TTTTCTTTC-C-TCTCCTTTC-TTTCTTTC
1 CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCTTTTCTTTC
*
4473645 TTTCTTTCTTTC
1 CTTCTTTCTTTC
4473657 CCTCTCCTTC
Statistics
Matches: 113, Mismatches: 7, Indels: 23
0.79 0.05 0.16
Matches are distributed among these distances:
36 15 0.13
37 1 0.01
38 22 0.19
39 6 0.05
40 24 0.21
41 4 0.04
42 16 0.14
43 12 0.11
44 13 0.12
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (42 bp):
CTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCTTTTCTTTC
Found at i:4473595 original size:82 final size:78
Alignment explanation
Indices: 4473484--4473656 Score: 242
Period size: 82 Copynumber: 2.2 Consensus size: 78
4473474 CTTCCTTCCC
* * *
4473484 TCTTC-TTCTTCCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTCTTTTTTCTT
1 TCTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTT-TTCTTTCCT
*
4473548 CTCTTTTCCTTTTCTTCT
65 CTCCTTT-C-TTTC-T-T
4473566 TCTTCTTTCTTTC-TTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTTTCTTTCCTC
1 TCTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTTTCTTTCCTC
4473630 TCCTTTCTTTCTT
66 TCCTTTCTTTCTT
4473643 TCTTTCTTTCTTTC
1 TC-TTCTTTCTTTC
4473657 CCTCTCCTTC
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
77 3 0.04
78 12 0.14
79 4 0.05
80 1 0.01
81 13 0.15
82 46 0.54
83 6 0.07
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (78 bp):
TCTTCTTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTCTTTTTCTTTCCTC
TCCTTTCTTTCTT
Found at i:4473613 original size:48 final size:46
Alignment explanation
Indices: 4473512--4473626 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 46
4473502 TTCTCTTCTC
* * *
4473512 CTTTCCTT-TTCTTTCCTTCTTTCTTTCTTTTTTCTTCTCTTTTCCT
1 CTTTCCTTCTTC-TTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCT
4473558 -TTT-CTTCTTCTTCTTTCTTTCTTT-TTTTCTCTTCTCCTTTCCTTTT
1 CTTTCCTTCTTCTTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCC---T
4473604 CTTTCCTTCTTTCTT-TTTCTTTC
1 CTTTCCTTC-TTCTTCTTTCTTTC
4473627 CTCTCCTTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
43 16 0.27
44 16 0.27
45 6 0.10
46 1 0.02
47 3 0.05
48 12 0.20
49 5 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (46 bp):
CTTTCCTTCTTCTTCTTTCTTTCTTTCTTTTCTCTTCTCCTTTCCT
Found at i:4473835 original size:28 final size:28
Alignment explanation
Indices: 4473803--4473857 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
4473793 TTTTTACAAG
4473803 TTTTTTTATATATTTTGGTAAATAAAAT
1 TTTTTTTATATATTTTGGTAAATAAAAT
4473831 TTTTTTTATATATTTTGGTAAATAAAA
1 TTTTTTTATATATTTTGGTAAATAAAA
4473858 AAAGTTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.56
Consensus pattern (28 bp):
TTTTTTTATATATTTTGGTAAATAAAAT
Found at i:4474628 original size:14 final size:13
Alignment explanation
Indices: 4474602--4474652 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
4474592 ATTTATTTTA
4474602 AATATAATAATAT
1 AATATAATAATAT
4474615 AATATAATTAATAT
1 AATATAA-TAATAT
* *
4474629 AAT-TTACAATAT
1 AATATAATAATAT
*
4474641 AATAAAATAATA
1 AATATAATAATA
4474653 ACATACTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 8 0.26
13 14 0.45
14 9 0.29
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:4476981 original size:23 final size:23
Alignment explanation
Indices: 4476926--4476975 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
4476916 ACGTTCCAAC
*
4476926 TTTTTTTTTAAAATTATATTTAA
1 TTTTTATTTAAAATTATATTTAA
*
4476949 TTTTTATTTAAAATT-T-TTTAG
1 TTTTTATTTAAAATTATATTTAA
4476970 TTTTTA
1 TTTTTA
4476976 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 10 0.40
22 1 0.04
23 14 0.56
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (23 bp):
TTTTTATTTAAAATTATATTTAA
Found at i:4477151 original size:16 final size:16
Alignment explanation
Indices: 4477107--4477158 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
4477097 ATCAATAAGA
4477107 AAAACATTTTTAAAATT
1 AAAA-ATTTTTAAAATT
**
4477124 AAAAATGATTAAAATT
1 AAAAATTTTTAAAATT
*
4477140 ATAAATTTTTAAAAATT
1 AAAAATTTTT-AAAATT
4477157 AA
1 AA
4477159 TTAAATATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 17 0.61
17 11 0.39
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
AAAAATTTTTAAAATT
Found at i:4477299 original size:23 final size:21
Alignment explanation
Indices: 4477259--4477306 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4477249 AATTTGACAA
* *
4477259 AAAAATATAAATTTAATAACT
1 AAAAATAAAAATTTAATAAAT
4477280 AAAAATAAAAATATTAAATAAAT
1 AAAAATAAAAAT-TT-AATAAAT
4477303 AAAA
1 AAAA
4477307 CTATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 11 0.48
22 2 0.09
23 10 0.43
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (21 bp):
AAAAATAAAAATTTAATAAAT
Found at i:4477564 original size:13 final size:13
Alignment explanation
Indices: 4477543--4477591 Score: 62
Period size: 13 Copynumber: 3.8 Consensus size: 13
4477533 CTCCACATCT
* *
4477543 ATTTGATTAATTA
1 ATTTTATTAATTG
4477556 ATTTTATTAATTG
1 ATTTTATTAATTG
*
4477569 ATTTAATTAATTG
1 ATTTTATTAATTG
*
4477582 ATTCTATTAA
1 ATTTTATTAA
4477592 CTGTTTATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (13 bp):
ATTTTATTAATTG
Found at i:4492637 original size:24 final size:24
Alignment explanation
Indices: 4492605--4492658 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
4492595 TCTTTCTAGA
4492605 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
4492629 ATATTTAGTATTTATTAGCATAAT
1 ATATTTAGTATTTATTAGCATAAT
*
4492653 TTATTT
1 ATATTT
4492659 GACCTACTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
ATATTTAGTATTTATTAGCATAAT
Found at i:4494722 original size:24 final size:24
Alignment explanation
Indices: 4494695--4494741 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
4494685 GCTTATAATA
4494695 GGTAGCTCCAAAGAGCAATTAACG
1 GGTAGCTCCAAAGAGCAATTAACG
* *
4494719 GGTAGCTTCGAAGAGCAATTAAC
1 GGTAGCTCCAAAGAGCAATTAAC
4494742 AGGAAGTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (24 bp):
GGTAGCTCCAAAGAGCAATTAACG
Found at i:4494821 original size:26 final size:26
Alignment explanation
Indices: 4494786--4494851 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
4494776 AAGCGAGGAC
*
4494786 TAATGGGAAGCTCACAAAGAGCC-TT
1 TAATGGGAAGCTCACAAAGAGCCATA
*
4494811 TAATCGGGAAGCTCACGAAGAGCCATA
1 TAAT-GGGAAGCTCACAAAGAGCCATA
*
4494838 TAATGGGATGCTCA
1 TAATGGGAAGCTCA
4494852 TAAGAGTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.11
26 27 0.75
27 5 0.14
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (26 bp):
TAATGGGAAGCTCACAAAGAGCCATA
Found at i:4496142 original size:21 final size:21
Alignment explanation
Indices: 4496076--4496142 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
4496066 ATACACCAAT
* *
4496076 AGAAGCTCGTAAGAGCTAAAC
1 AGAAGCTCATAAGAGCTGAAC
* * * * *
4496097 AAAAACTCATAAGAGTTGTAT
1 AGAAGCTCATAAGAGCTGAAC
4496118 AGAAGCTCATAAGAGCTGAAC
1 AGAAGCTCATAAGAGCTGAAC
4496139 AGAA
1 AGAA
4496143 AGTAAAACAC
Statistics
Matches: 34, Mismatches: 12, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (21 bp):
AGAAGCTCATAAGAGCTGAAC
Found at i:4498056 original size:27 final size:26
Alignment explanation
Indices: 4498009--4498061 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
4497999 TTTTAAAAAA
* ** *
4498009 TAAATTTTAAAATTTTTTTAATTGTT
1 TAAATTTTAAAAATTAATTAAATGTT
4498035 TAAATTTTTAAAAATTAATTAAATGTT
1 TAAA-TTTTAAAAATTAATTAAATGTT
4498062 GATGTGTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (26 bp):
TAAATTTTAAAAATTAATTAAATGTT
Found at i:4507798 original size:22 final size:21
Alignment explanation
Indices: 4507747--4507799 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
4507737 TTTGCTTGTT
* * *
4507747 TTACTGTTTTTTATTGTTTTG
1 TTACTATTTTTTATTATATTG
4507768 TTA-TCATTTTATTATTATATTG
1 TTACT-ATTTT-TTATTATATTG
4507790 TTACTATTTT
1 TTACTATTTT
4507800 GTTGTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 1 0.04
21 7 0.27
22 17 0.65
23 1 0.04
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.68
Consensus pattern (21 bp):
TTACTATTTTTTATTATATTG
Found at i:4508846 original size:18 final size:17
Alignment explanation
Indices: 4508829--4508896 Score: 50
Period size: 18 Copynumber: 3.9 Consensus size: 17
4508819 TAATAATATA
4508829 TTAAAATTTAATTTTA-
1 TTAAAATTTAATTTTAT
* *
4508845 TAAATTAATTTAA-TGTAT
1 TTAA--AATTTAATTTTAT
*
4508863 TTAAAATTTTTAAGTTTAT
1 TTAAAA--TTTAATTTTAT
*
4508882 TTAAAATTAAATTTT
1 TTAAAATTTAATTTT
4508897 TAAATACTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
16 5 0.12
17 10 0.25
18 15 0.38
19 10 0.25
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTAAAATTTAATTTTAT
Found at i:4509081 original size:13 final size:12
Alignment explanation
Indices: 4509039--4509080 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
4509029 ATTGTGCATG
4509039 TTAATTTTAAAT
1 TTAATTTTAAAT
*
4509051 TAAATTTTAAAT
1 TTAATTTTAAAT
4509063 TTAATATTTAAAT
1 TTAAT-TTTAAAT
4509076 TTAAT
1 TTAAT
4509081 AATAACGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATTTTAAAT
Found at i:4520157 original size:21 final size:21
Alignment explanation
Indices: 4520124--4520165 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4520114 TCATAAATTT
* * *
4520124 TTTTACATCATATAATTAAAA
1 TTTTAAATAATATAATAAAAA
4520145 TTTTAAATAATATAATAAAAA
1 TTTTAAATAATATAATAAAAA
4520166 AAATTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTTAAATAATATAATAAAAA
Found at i:4548732 original size:25 final size:26
Alignment explanation
Indices: 4548704--4548761 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 26
4548694 CATCAAAATC
4548704 TATTTTCTTTA-GAAATATAA-ATTAA
1 TATTTTCTTTATGAAA-ATAATATTAA
*
4548729 TATTTTTTTTATGAAAATAATTATTAA
1 TATTTTCTTTATGAAAATAA-TATTAA
4548756 TATTTT
1 TATTTT
4548762 TAAGAAAATG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 14 0.48
26 4 0.14
27 11 0.38
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (26 bp):
TATTTTCTTTATGAAAATAATATTAA
Found at i:4548746 original size:27 final size:25
Alignment explanation
Indices: 4548704--4548762 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 25
4548694 CATCAAAATC
*
4548704 TATTTTCTTTAGAAAT-ATAAATTAA
1 TATTTTTTTTAGAAATAAT-AATTAA
*
4548729 TATTTTTTTTATGAAAATAATTATTAA
1 TATTTTTTTTA-G-AAATAATAATTAA
4548756 TATTTTT
1 TATTTTT
4548763 AAGAAAATGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 10 0.34
26 1 0.03
27 16 0.55
28 2 0.07
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (25 bp):
TATTTTTTTTAGAAATAATAATTAA
Found at i:4549633 original size:30 final size:30
Alignment explanation
Indices: 4549599--4549661 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
4549589 GCGGAAAATA
* *
4549599 GCCCATTCCGGTAAATAATT-AAAAAAACCG
1 GCCCATTCCGATAAAT-ATTGAAAAAAAACG
* *
4549629 GCCCATTTCGATAAATTTTGAAAAAAAACG
1 GCCCATTCCGATAAATATTGAAAAAAAACG
4549659 GCC
1 GCC
4549662 TTTTTTGGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.07
30 26 0.93
ACGTcount: A:0.41, C:0.22, G:0.14, T:0.22
Consensus pattern (30 bp):
GCCCATTCCGATAAATATTGAAAAAAAACG
Found at i:4563323 original size:27 final size:27
Alignment explanation
Indices: 4563266--4563324 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
4563256 TCGAAAAATT
** *
4563266 TATTGTAATTTATATTTTTAAGTTAAT
1 TATTGTAATTTATATTAATAAGTTAAA
*
4563293 TATTGTAATTTATGTTAAATAAG-TAAA
1 TATTGTAATTTATATT-AATAAGTTAAA
4563320 TATTG
1 TATTG
4563325 ATTTTGAGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 23 0.85
28 4 0.15
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (27 bp):
TATTGTAATTTATATTAATAAGTTAAA
Found at i:4563703 original size:44 final size:43
Alignment explanation
Indices: 4563503--4563871 Score: 161
Period size: 44 Copynumber: 8.4 Consensus size: 43
4563493 GATTCGCCAC
* * * * * *
4563503 CGTAACCTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTCCA
1 CGTAACCT-AGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* * * * *
4563547 C-TACCGCTTAAGGAGATAAGATCTGAAATCTTCAATCTATTTCA
1 CGTAAC-C-TAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* * *
4563591 CTGCCAA-CTAGGGGGAT-AGAAT-T-AC-TGGCTTCAATGTACTCCA
1 C-G-TAACCTAGGGAGATAAG-ATCTGACAT--CTTCAATCTACTCCA
* * * * *
4563634 CTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCA
1 C-GTAACCT-AGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* *
4563679 C-TAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCA
1 CGTAA--CCTAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
** *
4563723 CTGTCAACC-AGGGAGAT-AGAAT-T-ACGGCTTCAATGTACTCCA
1 C-GT-AACCTAGGGAGATAAG-ATCTGACATCTTCAATCTACTCCA
* * * * * *
4563765 CTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCA
1 C-GTAACC-TAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
* *
4563810 C-TAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCA
1 CGTAA--CCTAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
*
4563854 CTGCCAACC-AGGGAGATA
1 C-G-TAACCTAGGGAGATA
4563872 GAATTACGGC
Statistics
Matches: 239, Mismatches: 56, Indels: 60
0.67 0.16 0.17
Matches are distributed among these distances:
41 5 0.02
42 21 0.09
43 41 0.17
44 124 0.52
45 40 0.17
46 2 0.01
47 6 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (43 bp):
CGTAACCTAGGGAGATAAGATCTGACATCTTCAATCTACTCCA
Found at i:4563741 original size:132 final size:131
Alignment explanation
Indices: 4563499--4563903 Score: 702
Period size: 131 Copynumber: 3.1 Consensus size: 131
4563489 ATTGGATTCG
* * ** * *
4563499 CCACCGTAACCTCAGGGAGGTAAAATTTGCCATCTTCGATCTGCTCCACTACCGCTTAAGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
* * *
4563564 AAGATCTGAAATCTTCAATCTATTTCACTGCCAACTAGGGGGATAGAATTACTGGCTTCAATGTA
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTAC-GGCTTCAATGTA
4563629 CT
130 CT
4563631 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
*
4563696 AAGATCTGAAATCTTCAATCTATTCCACTGTCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
4563761 T
131 T
*
4563762 CCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
1 CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
4563827 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
66 AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
4563892 T
131 T
4563893 CCACTGTAACC
1 CCACTGTAACC
4563904 ACAGTCCACT
Statistics
Matches: 261, Mismatches: 12, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
131 154 0.59
132 107 0.41
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (131 bp):
CCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTGCTCCACTAATGCCTAGGGAGAT
AAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGATAGAATTACGGCTTCAATGTAC
T
Found at i:4563767 original size:42 final size:43
Alignment explanation
Indices: 4563558--4563904 Score: 162
Period size: 44 Copynumber: 8.0 Consensus size: 43
4563548 TACCGCTTAA
* * * * * *
4563558 GGAGATA-AGATCTGAAATCTTCAATCTATTTCACTGCCAACTAG
1 GGAGATAGA-ATCTGACAGCTTCAATCTACTCCACTG-TAACCAG
* * *
4563602 GGGGATAGAAT-T-ACTGGCTTCAATGTACTCCACTGTAACCTCAG
1 GGAGATAGAATCTGAC-AGCTTCAATCTACTCCACTGTAA-C-CAG
* * * * * *
4563646 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC--TAATGCCTAG
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAA--CC-AG
* * *
4563690 GGAGATA-AGATCTGAAATCTTCAATCTATTCCACTGTCAACCAG
1 GGAGATAGA-ATCTGACAGCTTCAATCTACTCCACTGT-AACCAG
* *
4563734 GGAGATAGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCACAG
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAA-C-CAG
* * * * * *
4563777 GGAGGTAAAATCTGCCATCTTCGATCTGCTCCAC--TAATGCCTAG
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAA--CC-AG
* * * *
4563821 GGAGATA-AGATCTGAAATCTTCAATCTATTCCACTGCCAACCAG
1 GGAGATAGA-ATCTGACAGCTTCAATCTACTCCACTG-TAACCAG
* *
4563865 GGAGATAGAAT-T-ACGGCTTCAATGTACTCCACTGTAACCA
1 GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAACCA
4563905 CAGTCCACTA
Statistics
Matches: 227, Mismatches: 52, Indels: 51
0.69 0.16 0.15
Matches are distributed among these distances:
41 7 0.03
42 39 0.17
43 41 0.18
44 99 0.44
45 35 0.15
46 2 0.01
47 4 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (43 bp):
GGAGATAGAATCTGACAGCTTCAATCTACTCCACTGTAACCAG
Found at i:4563982 original size:102 final size:102
Alignment explanation
Indices: 4563806--4564111 Score: 603
Period size: 102 Copynumber: 3.0 Consensus size: 102
4563796 TTCGATCTGC
4563806 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
4563871 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
66 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
4563908 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
*
4563973 AGAATTACGGCTTCAATATACTCCACTGTAACCACAG
66 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
4564010 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
1 TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
4564075 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
66 AGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
4564112 GGAGGTAAAA
Statistics
Matches: 202, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 202 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (102 bp):
TCCACTAATGCCTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGCCAACCAGGGAGAT
AGAATTACGGCTTCAATGTACTCCACTGTAACCACAG
Found at i:4565649 original size:23 final size:24
Alignment explanation
Indices: 4565623--4565670 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
4565613 CCTTAGCCTC
4565623 TCCATTTTTACTTTTTC-CATTTT
1 TCCATTTTTACTTTTTCACATTTT
*
4565646 TCCATTTTTATTTTTTCACATTTT
1 TCCATTTTTACTTTTTCACATTTT
4565670 T
1 T
4565671 TTTTGCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.15, C:0.19, G:0.00, T:0.67
Consensus pattern (24 bp):
TCCATTTTTACTTTTTCACATTTT
Found at i:4565661 original size:16 final size:15
Alignment explanation
Indices: 4565642--4565674 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4565632 ACTTTTTCCA
4565642 TTTTTC-CATTTTTAT
1 TTTTTCACATTTTT-T
4565657 TTTTTCACATTTTTT
1 TTTTTCACATTTTTT
4565672 TTT
1 TTT
4565675 GCAACTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCACATTTTTT
Found at i:4566153 original size:1 final size:1
Alignment explanation
Indices: 4566147--4566262 Score: 88
Period size: 1 Copynumber: 116.0 Consensus size: 1
4566137 CCGGTAGAGG
* * * * * * * * * * *
4566147 TTTTTTTGTTTCTTTTTATTTTTTGTTTTTTGTTCTCTTTTTTTCTTTTTTTCTCTTTTTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
4566212 TTTTTGTTTTTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4566263 AACTGAATCT
Statistics
Matches: 83, Mismatches: 32, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (1 bp):
T
Found at i:4566170 original size:18 final size:18
Alignment explanation
Indices: 4566147--4566261 Score: 110
Period size: 18 Copynumber: 6.4 Consensus size: 18
4566137 CCGGTAGAGG
*
4566147 TTTTTTTGTTTCTTTTT-
1 TTTTTTTGTTTTTTTTTC
*
4566164 ATTTTTTGTTTTTTGTTCTC
1 TTTTTTTGTTTTTT-TT-TC
* *
4566184 TTTTTTTCTTTTTTTCTC
1 TTTTTTTGTTTTTTTTTC
*
4566202 TTTTTTTATTTTTTTGTT-
1 TTTTTTTGTTTTTTT-TTC
* *
4566220 TTTTTTT-TGTTTTTTTG
1 TTTTTTTGTTTTTTTTTC
*
4566237 TTTTTTTGTTTTTTTTTG
1 TTTTTTTGTTTTTTTTTC
4566255 TTTTTTT
1 TTTTTTT
4566262 TAACTGAATC
Statistics
Matches: 83, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
16 2 0.02
17 25 0.30
18 41 0.49
19 3 0.04
20 12 0.14
ACGTcount: A:0.02, C:0.05, G:0.07, T:0.86
Consensus pattern (18 bp):
TTTTTTTGTTTTTTTTTC
Found at i:4566261 original size:45 final size:45
Alignment explanation
Indices: 4566146--4566261 Score: 144
Period size: 45 Copynumber: 2.6 Consensus size: 45
4566136 CCCGGTAGAG
* *
4566146 GTTTTTTTGTTTCTTTTTATTTTTTGTTTTTTGTTCTCTTTTTTT
1 GTTTTTTTGTTTTTTTTTTTTTTTTGTTTTTTGTTCTCTTTTTTT
* * * * *
4566191 CTTTTTTTCTCTTTTTTTATTTTTTTGTTTTTT-TTTTGTTTTTTT
1 GTTTTTTTGT-TTTTTTTTTTTTTTTGTTTTTTGTTCTCTTTTTTT
4566236 GTTTTTTTGTTTTTTTTTGTTTTTTT
1 GTTTTTTTGTTTTTTTTT-TTTTTTT
4566262 TAACTGAATC
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
44 7 0.12
45 33 0.56
46 19 0.32
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.85
Consensus pattern (45 bp):
GTTTTTTTGTTTTTTTTTTTTTTTTGTTTTTTGTTCTCTTTTTTT
Found at i:4570472 original size:3 final size:3
Alignment explanation
Indices: 4570464--4570522 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
4570454 ACATACATGC
* *
4570464 AAT AAT AAT -AT AGT AAT AATT AAA AAT AAAT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AA-T AAT AAT -AAT AAT AAT AAT AAT AAT
* *
4570509 CAT AAT AAA AAT AA
1 AAT AAT AAT AAT AA
4570523 ACTAAAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
2 3 0.07
3 35 0.80
4 6 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:4570499 original size:17 final size:17
Alignment explanation
Indices: 4570477--4570516 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4570467 AATAATATAG
4570477 TAATAATTAAAAATAA-A
1 TAATAA-TAAAAATAACA
*
4570494 TAATAATAATAATAACA
1 TAATAATAAAAATAACA
4570511 TAATAA
1 TAATAA
4570517 AAATAAACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATAATAAAAATAACA
Found at i:4570514 original size:31 final size:27
Alignment explanation
Indices: 4570464--4570523 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 27
4570454 ACATACATGC
*
4570464 AATAATAATATAGTAATAATTAAAAATA
1 AATAATAATATAATAATAA-TAAAAATA
4570492 AATAATAATAATAATAACATAATAAAAATA
1 AATAATAAT-ATAAT-A-ATAATAAAAATA
4570522 AA
1 AA
4570524 CTAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.32
29 4 0.14
30 11 0.39
31 4 0.14
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
AATAATAATATAATAATAATAAAAATA
Found at i:4570521 original size:17 final size:16
Alignment explanation
Indices: 4570488--4570522 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
4570478 AATAATTAAA
*
4570488 AATAAATAATAATAAT
1 AATAAATAATAAAAAT
4570504 AATAACATAATAAAAAT
1 AATAA-ATAATAAAAAT
4570521 AA
1 AA
4570523 ACTAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AATAAATAATAAAAAT
Found at i:4574157 original size:20 final size:20
Alignment explanation
Indices: 4574132--4574174 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
4574122 GTTACCCTCC
4574132 AAAAAACACTTAAAACGTGA
1 AAAAAACACTTAAAACGTGA
4574152 AAAAAACACTTAAAACGTGA
1 AAAAAACACTTAAAACGTGA
4574172 AAA
1 AAA
4574175 CATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAAACACTTAAAACGTGA
Found at i:4575933 original size:27 final size:27
Alignment explanation
Indices: 4575888--4575941 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
4575878 AACTTTAATT
*
4575888 GTGCCAATAAAAATGGCACCATTGGTG
1 GTGCCAATAAAAATAGCACCATTGGTG
* *
4575915 GTGCCAATGAGAATAGCACCATTGGTG
1 GTGCCAATAAAAATAGCACCATTGGTG
4575942 TCGCCATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (27 bp):
GTGCCAATAAAAATAGCACCATTGGTG
Found at i:4592626 original size:19 final size:20
Alignment explanation
Indices: 4592596--4592636 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
4592586 AAATTTTGAG
*
4592596 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
4592616 AAATT-TTATTTATCTTTTA
1 AAATTATTATTTATCTTTTA
4592635 AA
1 AA
4592637 GAAAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:4597722 original size:3 final size:3
Alignment explanation
Indices: 4597714--4597761 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
4597704 AACTAGCCCT
4597714 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4597762 GATATAAATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:4597913 original size:41 final size:42
Alignment explanation
Indices: 4597863--4597943 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
4597853 CTATTTTCTG
*
4597863 GACTAATATAA-AAACATAGTGAAACATCACATCTAATTTAT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
* * *
4597904 GACTCATATAACAAACATAATGAAACATCACTTTTAATTT
1 GACTAATATAACAAACATAATGAAACATCACATCTAATTT
4597944 GGCAAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
41 10 0.29
42 25 0.71
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (42 bp):
GACTAATATAACAAACATAATGAAACATCACATCTAATTTAT
Found at i:4599781 original size:37 final size:37
Alignment explanation
Indices: 4599720--4599865 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
4599710 TACGTATGAT
* *
4599720 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
4599755 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4599792 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
4599829 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
4599866 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:4599948 original size:52 final size:52
Alignment explanation
Indices: 4599872--4600143 Score: 403
Period size: 52 Copynumber: 5.3 Consensus size: 52
4599862 TAGCTAAAGC
* * *
4599872 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
4599925 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
4599977 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* *
4600029 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
* ** *
4600075 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
4600127 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
4600144 ATCAGAAGTA
Statistics
Matches: 200, Mismatches: 12, Indels: 14
0.88 0.05 0.06
Matches are distributed among these distances:
46 43 0.22
49 1 0.00
52 138 0.69
53 18 0.09
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
Found at i:4600003 original size:150 final size:150
Alignment explanation
Indices: 4599829--4600143 Score: 522
Period size: 150 Copynumber: 2.1 Consensus size: 150
4599819 TAAGTGTAGC
* * * *
4599829 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACT
*
4599894 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAGT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGT
* *
4599959 GTAGCCGAAGCTATCACTTAT
130 GTAGCCAAAGCTACCACTTAT
*
4599980 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
*
4600045 GATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
66 GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
*
4600110 TAGCTAAAGCTACCACTTAT
131 TAGCCAAAGCTACCACTTAT
4600130 CACTTTGTCACTTG
1 CACTTT-TCACTTG
4600144 ATCAGAAGTA
Statistics
Matches: 153, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
150 137 0.90
151 16 0.10
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (150 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTG
TAGCCAAAGCTACCACTTAT
Found at i:4600040 original size:98 final size:98
Alignment explanation
Indices: 4599829--4600149 Score: 447
Period size: 98 Copynumber: 3.3 Consensus size: 98
4599819 TAAGTGTAGC
* **
4599829 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC---T---TT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTT
* *
4599888 GTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
4599921 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTT
4599986 TCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
60 TCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* * *
4600025 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTT
** *
4600090 GTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
66 GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
4600123 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
4600150 AGTACTCAAA
Statistics
Matches: 206, Mismatches: 11, Indels: 18
0.88 0.05 0.08
Matches are distributed among these distances:
92 10 0.05
95 1 0.00
98 150 0.73
101 2 0.01
104 43 0.21
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTTCACTT
GTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:4602871 original size:19 final size:20
Alignment explanation
Indices: 4602837--4602883 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
4602827 ACTCTTAAAA
*
4602837 TTTTAGAAATTATTATTTATT
1 TTTTA-AAATTATTATTTATC
*
4602858 TTTTAAAATT-TTATTTCTC
1 TTTTAAAATTATTATTTATC
4602877 TTTTAAA
1 TTTTAAA
4602884 GTAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 14 0.58
20 5 0.21
21 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (20 bp):
TTTTAAAATTATTATTTATC
Found at i:4608686 original size:3 final size:3
Alignment explanation
Indices: 4608678--4608725 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
4608668 AACTAGCCCT
4608678 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4608725 T
1 T
4608726 ATAAATTAAC
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:4608866 original size:41 final size:42
Alignment explanation
Indices: 4608821--4608902 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
4608811 CCTATTTTCT
* *
4608821 TGACTAATATAA-AAACATAGTGAAAGATCACATCTAATTTA
1 TGACTAATATAACAAACATAATGAAACATCACATCTAATTTA
*
4608862 TGACTCATATAACAAACATAATGAAACATCACATCTAATTT
1 TGACTAATATAACAAACATAATGAAACATCACATCTAATTT
4608903 GGCAAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
41 11 0.30
42 26 0.70
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (42 bp):
TGACTAATATAACAAACATAATGAAACATCACATCTAATTTA
Found at i:4610129 original size:19 final size:20
Alignment explanation
Indices: 4610099--4610139 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
4610089 AAATTTTGAG
*
4610099 AAATTATTATTTATTTTTTA
1 AAATTATTATTTATCTTTTA
*
4610119 AAATT-TTATTTCTCTTTTA
1 AAATTATTATTTATCTTTTA
4610138 AA
1 AA
4610140 GTAAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTATTATTTATCTTTTA
Found at i:4610635 original size:16 final size:16
Alignment explanation
Indices: 4610614--4610645 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
4610604 TCTCCTCTTC
4610614 TTTTTTTGTTGCCCTT
1 TTTTTTTGTTGCCCTT
4610630 TTTTTTTGTTGCCCTT
1 TTTTTTTGTTGCCCTT
4610646 CCACCTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.19, G:0.12, T:0.69
Consensus pattern (16 bp):
TTTTTTTGTTGCCCTT
Found at i:4613200 original size:82 final size:82
Alignment explanation
Indices: 4613113--4613276 Score: 276
Period size: 82 Copynumber: 2.0 Consensus size: 82
4613103 TTAGTACATA
*
4613113 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAATA-TGTTTTTTCCAAG
1 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAA-ACTGTTTTTTCCAAA
4613177 GATTCAAAAGCATTTTCT
65 GATTCAAAAGCATTTTCT
* * *
4613195 AAACACATTAAATTATAAATAATGGTTAAAAATGTGACTTGACTTTAAAACTGTTTTTTTCAAAG
1 AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAAACTGTTTTTTCCAAAG
4613260 ATTCAAAAGCATTTTCT
66 ATTCAAAAGCATTTTCT
4613277 TACTTCTGAA
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
81 1 0.01
82 76 0.99
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (82 bp):
AAACACATTAAATTATAAATAATGCTTAAAAATGTCACTTGACTTTAAAACTGTTTTTTCCAAAG
ATTCAAAAGCATTTTCT
Found at i:4617228 original size:18 final size:18
Alignment explanation
Indices: 4617205--4617325 Score: 110
Period size: 18 Copynumber: 6.7 Consensus size: 18
4617195 AAAACAAAAA
4617205 TTTTGAAACACGAGAATT
1 TTTTGAAACACGAGAATT
*
4617223 TTTTGAAAACACGA-AAAT
1 TTTTG-AAACACGAGAATT
* *
4617241 TTTTGAAACAAGAAAATT
1 TTTTGAAACACGAGAATT
4617259 TTTTGAAA-AC-ATGAATTTT
1 TTTTGAAACACGA-GAA--TT
*
4617278 TTTTAAAACAC-A-AAGTT
1 TTTTGAAACACGAGAA-TT
4617295 TTTT-AAACACGAGAATT
1 TTTTGAAACACGAGAATT
4617312 TTTTGAAAACACGA
1 TTTTG-AAACACGA
4617326 AAACACGAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 19
0.77 0.06 0.17
Matches are distributed among these distances:
16 7 0.08
17 23 0.27
18 28 0.33
19 25 0.29
20 3 0.03
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (18 bp):
TTTTGAAACACGAGAATT
Found at i:4617346 original size:43 final size:41
Alignment explanation
Indices: 4617282--4617409 Score: 122
Period size: 43 Copynumber: 3.1 Consensus size: 41
4617272 AATTTTTTTT
*
4617282 AAAACAC-AAAGTTTTTTAAACACGAGAATTTTTTGAAAACAC
1 AAAACACGAAAG-TTTTGAAACACG-GAATTTTTTGAAAACAC
*
4617324 GAAAACACGAAAGTTTTGAAACAC-GAA-TTTTT-AAAA-AA
1 -AAAACACGAAAGTTTTGAAACACGGAATTTTTTGAAAACAC
* * *
4617362 AAAACAAGAAAATTTTGAAAGACGGGAATTTTTTTTGAAAACAC
1 AAAACACGAAAGTTTTGAAACAC-GGAA--TTTTTTGAAAACAC
4617406 AAAA
1 AAAA
4617410 TTTTTTTAGC
Statistics
Matches: 71, Mismatches: 6, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
37 20 0.28
38 1 0.01
39 7 0.10
40 5 0.07
41 3 0.04
42 5 0.07
43 21 0.30
44 9 0.13
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (41 bp):
AAAACACGAAAGTTTTGAAACACGGAATTTTTTGAAAACAC
Found at i:4617413 original size:18 final size:18
Alignment explanation
Indices: 4617392--4617482 Score: 64
Period size: 18 Copynumber: 5.1 Consensus size: 18
4617382 GACGGGAATT
4617392 TTTTTTGAAAACACAAAA
1 TTTTTTGAAAACACAAAA
* *
4617410 TTTTTT--TAGCACAAAA
1 TTTTTTGAAAACACAAAA
* *
4617426 -ATTTTG-AAACACTAGAA
1 TTTTTTGAAAACAC-AAAA
*
4617443 TTTTTCTGAAAACACTAAA
1 TTTTT-TGAAAACACAAAA
* *
4617462 TTTTTTTAAAATACGAAAA
1 TTTTTTGAAAACAC-AAAA
4617481 TT
1 TT
4617483 GTGATAAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
15 4 0.07
16 12 0.22
17 3 0.05
18 16 0.29
19 14 0.25
20 6 0.11
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.38
Consensus pattern (18 bp):
TTTTTTGAAAACACAAAA
Found at i:4617469 original size:52 final size:53
Alignment explanation
Indices: 4617370--4617469 Score: 148
Period size: 52 Copynumber: 1.9 Consensus size: 53
4617360 AAAAAACAAG
* * *
4617370 AAAATTTTGAAAGACGGGAATTTTTTTTGAAAACACAAAATTTTTTTAGCACA
1 AAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAATTTTTTTAGCACA
* *
4617423 AAAATTTTGAAACACTAGAA-TTTTTCTGAAAACACTAAATTTTTTTA
1 AAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAATTTTTTTA
4617470 AAATACGAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 25 0.60
53 17 0.40
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (53 bp):
AAAATTTTGAAACACGAGAATTTTTTCTGAAAACACAAAATTTTTTTAGCACA
Found at i:4618467 original size:23 final size:24
Alignment explanation
Indices: 4618441--4618496 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
4618431 TTCTTTTTCC
4618441 TTTTGGTTGCTG-TTTTTTTTCTT
1 TTTTGGTTGCTGTTTTTTTTTCTT
**
4618464 TTTTACTTGCTGTTTTTTTTTCTT
1 TTTTGGTTGCTGTTTTTTTTTCTT
4618488 TTTTGGTTG
1 TTTTGGTTG
4618497 TTGCCTTGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.02, C:0.09, G:0.16, T:0.73
Consensus pattern (24 bp):
TTTTGGTTGCTGTTTTTTTTTCTT
Found at i:4618763 original size:23 final size:23
Alignment explanation
Indices: 4618715--4618765 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4618705 GTGAGGGCCC
* **
4618715 TTTTGCTGCTGTTTTCTTGGTGT
1 TTTTGCTGCTATTTTCTTCATGT
*
4618738 TTTTGCTGCTATTTTCTTTCATTT
1 TTTTGCTGCTATTTTC-TTCATGT
4618762 TTTT
1 TTTT
4618766 TTTGCTTTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.04, C:0.14, G:0.16, T:0.67
Consensus pattern (23 bp):
TTTTGCTGCTATTTTCTTCATGT
Found at i:4619288 original size:23 final size:24
Alignment explanation
Indices: 4619256--4619300 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
4619246 TTAATTAAAC
*
4619256 TTTATAAATAATTAATATTTATTG
1 TTTATAAATAATTAAAATTTATTG
*
4619280 TTTA-AAATATTTAAAATTTAT
1 TTTATAAATAATTAAAATTTAT
4619301 ATTGCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTATAAATAATTAAAATTTATTG
Found at i:4620348 original size:31 final size:31
Alignment explanation
Indices: 4620311--4620370 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
4620301 TGGGTTGTCT
4620311 TTTAGTTTTAGTTTTATTGGATTGGGTAAAC
1 TTTAGTTTTAGTTTTATTGGATTGGGTAAAC
*
4620342 TTTAGTTTTAGTTTTATTGGGTTGGGTAA
1 TTTAGTTTTAGTTTTATTGGATTGGGTAA
4620371 TTGAGTTTGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.25, T:0.53
Consensus pattern (31 bp):
TTTAGTTTTAGTTTTATTGGATTGGGTAAAC
Found at i:4626028 original size:21 final size:21
Alignment explanation
Indices: 4625988--4626045 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
4625978 TTCCAAAAGG
*
4625988 CAAAACGGTAGAAATGTAGGGA
1 CAAAACGGTA-AAATATAGGGA
*
4626010 CAAAACGGTAAAATATAGGGG
1 CAAAACGGTAAAATATAGGGA
*
4626031 CAAAAAGGATAAAAT
1 CAAAACGG-TAAAAT
4626046 TCTATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.52, C:0.09, G:0.26, T:0.14
Consensus pattern (21 bp):
CAAAACGGTAAAATATAGGGA
Found at i:4630383 original size:33 final size:33
Alignment explanation
Indices: 4630336--4630399 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
4630326 GGGAGGAGGC
4630336 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
* * * *
4630369 GGTGGAGTCTGCATGGTTTTTGGAGGTGGAG
1 GGTGGAGGCAGCATGGTTTTTGAAGGCGGAG
4630400 GCGGCAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.16, C:0.09, G:0.47, T:0.28
Consensus pattern (33 bp):
GGTGGAGGCAGCATGGTTTTTGAAGGCGGAGCT
Found at i:4657752 original size:14 final size:14
Alignment explanation
Indices: 4657733--4657771 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4657723 ATTATGTGTT
4657733 TTATTTAATTTTAA
1 TTATTTAATTTTAA
**
4657747 TTATTTGTTTTTAA
1 TTATTTAATTTTAA
*
4657761 TTTTTTAATTT
1 TTATTTAATTT
4657772 ACAATAAGTA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (14 bp):
TTATTTAATTTTAA
Found at i:4659688 original size:224 final size:222
Alignment explanation
Indices: 4659288--4659735 Score: 806
Period size: 224 Copynumber: 2.0 Consensus size: 222
4659278 AAAATGTTAC
* * * *
4659288 AACATGATAACATAAGTGATTTAAACGTAGCATTTCAAATATAAGTGACTAAAATATAACCTGAG
1 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
4659353 GCAAACAAAAGTGATTATTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATTT
66 GCAAACAAAAGTGATTATTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATTT
* *
4659418 ACGGGAAATAACAAATTAAGTTTAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGCT
131 ACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGCT
*
4659483 AAATTCCTAACGACTACTAGGGCCCTA
196 AAATTCCTAACGACTACTAGGGCCATA
4659510 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
1 AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
*
4659575 GCAAACAAAAGTGATTATTTTAGTAGTTTATCCTTTTTTTTGAATTATATAATATTAATAACTAT
66 GCAAACAAAAGTGATTA-TTTAGTAGTTTA-CCCTTTTTTTGAATTATATAATATTAATAACTAT
4659640 TTACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAG
129 TTACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAG
4659705 CTAAATTCCTAACGACTACTAGGGCCATA
194 CTAAATTCCTAACGACTACTAGGGCCATA
4659734 AA
1 AA
4659736 TTGACGGTGC
Statistics
Matches: 216, Mismatches: 8, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
222 78 0.36
223 12 0.06
224 126 0.58
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.31
Consensus pattern (222 bp):
AACATGATAACATAAGAGACTAAAACGTAACATTTCAAATATAAGTGACTAAAATATAACCTGAG
GCAAACAAAAGTGATTATTTAGTAGTTTACCCTTTTTTTGAATTATATAATATTAATAACTATTT
ACGGAAAATAACAAATTAAGTTAAAAAAAATGTATAAATCGACCTTAAAGATAATATTGGAAGCT
AAATTCCTAACGACTACTAGGGCCATA
Found at i:4670709 original size:18 final size:18
Alignment explanation
Indices: 4670686--4670778 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
4670676 CCCAACTACT
*
4670686 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
4670704 GTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACC
*
4670722 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
4670740 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
4670758 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
4670776 GTA
1 GTA
4670779 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:4670731 original size:36 final size:36
Alignment explanation
Indices: 4670684--4670778 Score: 163
Period size: 36 Copynumber: 2.6 Consensus size: 36
4670674 ATCCCAACTA
*
4670684 CTGTATACGTGAACAGTACCGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACCGTATACGTGAATAGTG
*
4670720 CTGTATACGTGAATAGTACTGTATACGTGAATAGTG
1 CTGTATACGTGAATAGTACCGTATACGTGAATAGTG
*
4670756 CCGTATACGTGAATAGTACCGTA
1 CTGTATACGTGAATAGTACCGTA
4670779 AACGGTCGTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (36 bp):
CTGTATACGTGAATAGTACCGTATACGTGAATAGTG
Found at i:4673204 original size:14 final size:15
Alignment explanation
Indices: 4673181--4673210 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
4673171 TAAATTTAAT
4673181 TAAATCAATTAAAAA
1 TAAATCAATTAAAAA
4673196 TAAAT-AATTAAAAA
1 TAAATCAATTAAAAA
4673210 T
1 T
4673211 TTGAAAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAATCAATTAAAAA
Found at i:4675647 original size:5 final size:5
Alignment explanation
Indices: 4675618--4675701 Score: 90
Period size: 5 Copynumber: 17.4 Consensus size: 5
4675608 TCAGTTTATT
4675618 TAATA T-ATAA TAATA T-ATAA TAATA TAATA TAATA TAAT- TAATA TAATA
1 TAATA TAAT-A TAATA TAAT-A TAATA TAATA TAATA TAATA TAATA TAATA
*
4675667 TAATA TAATA T-ATAA TAAAA TAATA T-AT- TAATA TA
1 TAATA TAATA TAAT-A TAATA TAATA TAATA TAATA TA
4675702 TTTAAAACAT
Statistics
Matches: 68, Mismatches: 2, Indels: 18
0.77 0.02 0.20
Matches are distributed among these distances:
3 1 0.01
4 14 0.21
5 48 0.71
6 5 0.07
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:4675663 original size:29 final size:28
Alignment explanation
Indices: 4675622--4675701 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 28
4675612 TTTATTTAAT
4675622 ATATAATAATAT-ATAATAATATAATATA
1 ATATAATAATATAAT-ATAATATAATATA
4675650 ATATAATTAATATAATATAATATAATATATA
1 ATATAA-TAATATAATATAATAT-A-ATATA
*
4675681 ATAAAATAATAT-AT-TAATATA
1 ATATAATAATATAATATAATATA
4675702 TTTAAAACAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
27 1 0.02
28 12 0.26
29 15 0.32
30 9 0.19
31 10 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATATAATAATATAATATAATATAATATA
Done.