Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr3
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: 36364294
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2168405 characters in sequence are not A, C, G, or T
File 49 of 91
Found at i:17135579 original size:42 final size:41
Alignment explanation
Indices: 17135527--17135710 Score: 287
Period size: 41 Copynumber: 4.4 Consensus size: 41
17135517 TTGATCATTT
*
17135527 AAATATTAATATTTTATTGATAATTTAATCATTAATATTTTA
1 AAATATTAATATTTTATTGATAACTTAAT-ATTAATATTTTA
* *
17135569 AAATATTAATATTTTATTGATAATTTAATCATTAAAATTTTA
1 AAATATTAATATTTTATTGATAACTTAAT-ATTAATATTTTA
**
17135611 AAATATTAATATTTTATTTTTAACTTAATATTAATATTTTA
1 AAATATTAATATTTTATTGATAACTTAATATTAATATTTTA
**
17135652 AAATATTAATATTTTATTTTTAACTTAATATTAATATTTTA
1 AAATATTAATATTTTATTGATAACTTAATATTAATATTTTA
17135693 AAATATTAATATTTTATT
1 AAATATTAATATTTTATT
17135711 AGAAGTTGGA
Statistics
Matches: 137, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
41 70 0.51
42 67 0.49
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (41 bp):
AAATATTAATATTTTATTGATAACTTAATATTAATATTTTA
Found at i:17135640 original size:19 final size:19
Alignment explanation
Indices: 17135616--17135683 Score: 82
Period size: 19 Copynumber: 3.4 Consensus size: 19
17135606 TTTTAAAATA
17135616 TTAATATTTTATTTTTAAC
1 TTAATATTTTATTTTTAAC
* * *
17135635 TTAATATTAATATTTTAAAATA
1 TTAATATT-TTATTTT-TAA-C
17135657 TTAATATTTTATTTTTAAC
1 TTAATATTTTATTTTTAAC
17135676 TTAATATT
1 TTAATATT
17135684 AATATTTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
19 16 0.40
20 8 0.20
21 8 0.20
22 8 0.20
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (19 bp):
TTAATATTTTATTTTTAAC
Found at i:17136451 original size:23 final size:21
Alignment explanation
Indices: 17136403--17136453 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
17136393 ATAGTTTAAT
* *
17136403 TATTAATATTTTTATTTATAA
1 TATTAATATTATTATTTAAAA
17136424 T-TTAATATTATTATGATTAAAA
1 TATTAATATTATTAT--TTAAAA
17136446 TATTAATA
1 TATTAATA
17136454 ATTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.48
21 1 0.04
22 6 0.24
23 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TATTAATATTATTATTTAAAA
Found at i:17136573 original size:26 final size:26
Alignment explanation
Indices: 17136520--17136607 Score: 83
Period size: 26 Copynumber: 3.4 Consensus size: 26
17136510 AATAAAACAT
*
17136520 TAATATTTTAA-AATATTTTATATT-A
1 TAATATTTTAATAATA-TTAATATTAA
*
17136545 TAATATTTTAATCATATTAATATTAA
1 TAATATTTTAATAATATTAATATTAA
* * * *
17136571 TAATATTTAAATTATATATAA-AATAT
1 TAATATTTTAATAATAT-TAATATTAA
17136597 TAATATTTTAA
1 TAATATTTTAA
17136608 AATTTATAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
25 18 0.34
26 32 0.60
27 3 0.06
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (26 bp):
TAATATTTTAATAATATTAATATTAA
Found at i:17136602 original size:15 final size:15
Alignment explanation
Indices: 17136504--17136602 Score: 51
Period size: 15 Copynumber: 6.5 Consensus size: 15
17136494 ATTAGGGTAT
* *
17136504 TTAATAAATAAAACA
1 TTAATATATAAAATA
*
17136519 TTAATATTTTAAAATA
1 TTAATA-TATAAAATA
* * *
17136535 TTTTATATTATAATATT
1 -TTAATA-TATAAAATA
*
17136552 TTAATCATAT-TAATA
1 TTAAT-ATATAAAATA
**
17136567 TTAATAATATTTAA-A
1 TTAAT-ATATAAAATA
17136582 TT-ATATATAAAATA
1 TTAATATATAAAATA
17136596 TTAATAT
1 TTAATAT
17136603 TTTAAAATTT
Statistics
Matches: 64, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
13 6 0.09
14 5 0.08
15 24 0.38
16 16 0.25
17 13 0.20
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAATATATAAAATA
Found at i:17136614 original size:29 final size:29
Alignment explanation
Indices: 17136563--17136621 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
17136553 TAATCATATT
*
17136563 AATATTAATAATATTTAAATTATATATAA
1 AATATTAATAATATTTAAATTATAAATAA
17136592 AATATTAAT-AT-TTTAAAATTTATAAATAA
1 AATATTAATAATATTT-AAA-TTATAAATAA
17136621 A
1 A
17136622 TTTTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
27 3 0.11
28 5 0.19
29 19 0.70
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (29 bp):
AATATTAATAATATTTAAATTATAAATAA
Found at i:17139572 original size:4 final size:4
Alignment explanation
Indices: 17139563--17139588 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17139553 ATCATGAAAT
17139563 ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC AT
17139589 CTAACTAATT
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:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:17160344 original size:44 final size:44
Alignment explanation
Indices: 17160276--17160370 Score: 163
Period size: 44 Copynumber: 2.2 Consensus size: 44
17160266 AGGTTTGATA
* *
17160276 CTATAGTGAGATTTGGTTTCCGTTTGGTTATTCTTTAGAAGAAT
1 CTATAGTGAGAATTGGTTTCCGTTTGGTTATTCTATAGAAGAAT
*
17160320 CTATCGTGAGAATTGGTTTCCGTTTGGTTATTCTATAGAAGAAT
1 CTATAGTGAGAATTGGTTTCCGTTTGGTTATTCTATAGAAGAAT
17160364 CTATAGT
1 CTATAGT
17160371 AAGGGCAGGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (44 bp):
CTATAGTGAGAATTGGTTTCCGTTTGGTTATTCTATAGAAGAAT
Found at i:17179775 original size:14 final size:13
Alignment explanation
Indices: 17179753--17179810 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
17179743 CAATTATCTA
*
17179753 TATTTTTTAGTTAT
1 TATTATTTA-TTAT
17179767 TATTATTTAATTAT
1 TATTATTT-ATTAT
17179781 TATT-TTTATT-T
1 TATTATTTATTAT
*
17179792 TATTATATT-TTTT
1 TATTAT-TTATTAT
17179805 TATTAT
1 TATTAT
17179811 CATATTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
11 5 0.13
12 6 0.15
13 12 0.31
14 15 0.38
15 1 0.03
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (13 bp):
TATTATTTATTAT
Found at i:17179900 original size:6 final size:6
Alignment explanation
Indices: 17179875--17179918 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
17179865 TATATATATA
* *
17179875 TATTTAT TATTAT TATTTT TACTTT T-TTTT TATTTT TATTTT TA
1 TATTT-T TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TA
17179919 CATTTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
5 4 0.12
6 24 0.75
7 4 0.12
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.77
Consensus pattern (6 bp):
TATTTT
Found at i:17179907 original size:23 final size:23
Alignment explanation
Indices: 17179881--17179926 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
17179871 TATATATTTA
*
17179881 TTATTATTATTTTTACTTTTTTT
1 TTATTATTATTTTTACATTTTTT
*
17179904 TTATTTTTATTTTTACATTTTTT
1 TTATTATTATTTTTACATTTTTT
17179927 ATAGTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (23 bp):
TTATTATTATTTTTACATTTTTT
Found at i:17180095 original size:7 final size:7
Alignment explanation
Indices: 17180064--17180125 Score: 55
Period size: 7 Copynumber: 9.6 Consensus size: 7
17180054 TATGTTTGAA
17180064 TTATTA-
1 TTATTAT
*
17180070 TTATTTT
1 TTATTAT
*
17180077 TTATCAT
1 TTATTAT
17180084 TTATTA-
1 TTATTAT
17180090 -T-TTAT
1 TTATTAT
17180095 TTATTAT
1 TTATTAT
17180102 TTATTAT
1 TTATTAT
17180109 TTATT-T
1 TTATTAT
17180115 ATTATT-T
1 -TTATTAT
17180122 TTAT
1 TTAT
17180126 CGAGTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
4 3 0.06
5 1 0.02
6 11 0.23
7 32 0.68
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (7 bp):
TTATTAT
Found at i:17180098 original size:11 final size:11
Alignment explanation
Indices: 17180064--17180125 Score: 62
Period size: 11 Copynumber: 6.0 Consensus size: 11
17180054 TATGTTTGAA
17180064 TTATTA-TTAT
1 TTATTATTTAT
* *
17180074 TTTTTA-TCAT
1 TTATTATTTAT
17180084 TTATTATTTAT
1 TTATTATTTAT
17180095 TTATTATTTA-
1 TTATTATTTAT
17180105 TTATTTATTTA-
1 TTA-TTATTTAT
17180116 TTATT-TTTAT
1 TTATTATTTAT
17180126 CGAGTAATTT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
9 4 0.09
10 18 0.40
11 23 0.51
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTATTTAT
Found at i:17181020 original size:37 final size:37
Alignment explanation
Indices: 17180987--17181076 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 37
17180977 TCCAACCGGT
*
17180987 GGCTGCTGCTCCCTAACAGTCGACCTTTTCAACCGAC
1 GGCTGCTGCTCCCCAACAGTCGACCTTTTCAACCGAC
* * *
17181024 GGTTGCTGCTCCCCAACAGTCGACCTTTTCAATCAAC
1 GGCTGCTGCTCCCCAACAGTCGACCTTTTCAACCGAC
17181061 GG-TCGCTGCTCCCCAA
1 GGCT-GCTGCTCCCCAA
17181077 TCGGTTGTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
36 1 0.02
37 47 0.98
ACGTcount: A:0.19, C:0.38, G:0.19, T:0.24
Consensus pattern (37 bp):
GGCTGCTGCTCCCCAACAGTCGACCTTTTCAACCGAC
Found at i:17181872 original size:37 final size:37
Alignment explanation
Indices: 17181831--17182162 Score: 434
Period size: 37 Copynumber: 8.9 Consensus size: 37
17181821 ACTAAATTTT
* * *
17181831 TTTTAAAATAAATTCCTCAAAACTGAGGCCACGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
*
17181868 TTTTAAAATGAACTCCTCAAAACTGAGGCAATGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
* * * *
17181905 CTTTAAAATGAACTCCTCAAAATTGAGGCACCGAAAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
17181942 -TTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
* *
17181978 TTTAAAAATGAACTCCTCAAAACTGAGGCAATGAGAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
* * *
17182015 TTTTAAAAATGAACTCCTCAAAGCTGAGGCACCAAGAC
1 TTTT-AAAATGAACTCCTCAAAACTGAGGCAACGAGAC
*
17182053 TTTAAAAATGAACTCCTCAAAACTGAGGCAACGAGAAC
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAG-AC
* * *
17182091 TTTTAAAAGTGAGCTCCTCAAAGCTGAGGCAACGTA-CC
1 TTTTAAAA-TGAACTCCTCAAAACTGAGGCAACG-AGAC
* * *
17182129 TTTAAAAATGAATTCCTCAAAATTGAGGCAACGA
1 TTTTAAAATGAACTCCTCAAAACTGAGGCAACGA
17182163 AACCTTTTTT
Statistics
Matches: 258, Mismatches: 32, Indels: 11
0.86 0.11 0.04
Matches are distributed among these distances:
36 34 0.13
37 151 0.59
38 49 0.19
39 23 0.09
40 1 0.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (37 bp):
TTTTAAAATGAACTCCTCAAAACTGAGGCAACGAGAC
Found at i:17182053 original size:75 final size:75
Alignment explanation
Indices: 17181835--17182162 Score: 434
Period size: 75 Copynumber: 4.4 Consensus size: 75
17181825 AATTTTTTTT
* * * *
17181835 AAAATAAATTCCTCAAAACTGAGGCCACGAGACTTTTAAAATGAACTCCTCAAAACTGAGGCAAT
1 AAAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAACTCCTCAAAACTGAGGCAAC
*
17181900 GAGACCTTT-
66 AAGACCTTTA
* * *
17181909 AAAATGAACTCCTCAAAATTGAGGCACCGAAAC-TTTAAAATGAACTCCTCAAAACTGAGGCAAC
1 AAAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAACTCCTCAAAACTGAGGCAAC
*
17181973 GAGA-CTTTA
66 AAGACCTTTA
* * *
17181982 AAAATGAACTCCTCAAAACTGAGGCAATGAGACTTTTAAAAATGAACTCCTCAAAGCTGAGGCAC
1 AAAATGAACTCCTCAAAACTGAGGCAACGAGACTTTT-AAAATGAACTCCTCAAAACTGAGGCAA
17182047 CAAGA-CTTTA
65 CAAGACCTTTA
* *
17182057 AAAATGAACTCCTCAAAACTGAGGCAACGAGAACTTTTAAAAGTGAGCTCCTCAAAGCTGAGGCA
1 AAAATGAACTCCTCAAAACTGAGGCAACGAG-ACTTTTAAAA-TGAACTCCTCAAAACTGAGGCA
17182122 AC--GTACCTTTA
64 ACAAG-ACCTTTA
* *
17182133 AAAATGAATTCCTCAAAATTGAGGCAACGA
1 AAAATGAACTCCTCAAAACTGAGGCAACGA
17182163 AACCTTTTTT
Statistics
Matches: 228, Mismatches: 19, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
72 4 0.02
73 63 0.28
74 31 0.14
75 69 0.30
76 61 0.27
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.21
Consensus pattern (75 bp):
AAAATGAACTCCTCAAAACTGAGGCAACGAGACTTTTAAAATGAACTCCTCAAAACTGAGGCAAC
AAGACCTTTA
Found at i:17198158 original size:37 final size:36
Alignment explanation
Indices: 17198096--17198228 Score: 130
Period size: 37 Copynumber: 3.7 Consensus size: 36
17198086 CAACGATCAG
* * * *
17198096 CTTTCCAACCGGTGGCTGCTTCTCCCTAACAGTCGGC
1 CTTTTCAACCGGCGGTTGCTGCTCCC-AACAGTCGGC
17198133 CTTTTCAACCGGCGGTTGCTGCTCCCCAACAGTCGGC
1 CTTTTCAACCGGCGGTTGCTGCT-CCCAACAGTCGGC
* * * *
17198170 CTTTTCAATCGACGGTCGCTGCTCCC--CAATCGG-
1 CTTTTCAACCGGCGGTTGCTGCTCCCAACAGTCGGC
*
17198203 -TTGTTCAACCGGTGGTTGCTGCTCCC
1 CTT-TTCAACCGGCGGTTGCTGCTCCC
17198229 CAATCGGTCA
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
32 2 0.02
33 19 0.23
34 6 0.07
36 3 0.04
37 49 0.60
38 3 0.04
ACGTcount: A:0.13, C:0.36, G:0.23, T:0.28
Consensus pattern (36 bp):
CTTTTCAACCGGCGGTTGCTGCTCCCAACAGTCGGC
Found at i:17198224 original size:33 final size:32
Alignment explanation
Indices: 17198134--17198236 Score: 116
Period size: 33 Copynumber: 3.0 Consensus size: 32
17198124 ACAGTCGGCC
17198134 TTTTCAACCGGCGGTTGCTGCTCCCCAACAGTCGG
1 TTTTCAACCGGCGGTTGCTGCTCCCC-A-A-TCGG
* * *
17198169 CCTTTTCAATCGACGGTCGCTGCTCCCCAATCGG
1 --TTTTCAACCGGCGGTTGCTGCTCCCCAATCGG
*
17198203 TTGTTCAACCGGTGGTTGCTGCTCCCCAATCGG
1 TT-TTCAACCGGCGGTTGCTGCTCCCCAATCGG
17198236 T
1 T
17198237 CAACTCTCTC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.03
33 27 0.47
34 4 0.07
35 1 0.02
36 1 0.02
37 23 0.40
ACGTcount: A:0.14, C:0.34, G:0.24, T:0.28
Consensus pattern (32 bp):
TTTTCAACCGGCGGTTGCTGCTCCCCAATCGG
Found at i:17198780 original size:13 final size:12
Alignment explanation
Indices: 17198762--17198822 Score: 68
Period size: 13 Copynumber: 4.8 Consensus size: 12
17198752 CTCTCCCTTC
17198762 TTTTTTATTTCTT
1 TTTTTTATTT-TT
17198775 TTTTTTATTTTT
1 TTTTTTATTTTT
17198787 TATTTTTATTATTT
1 T-TTTTTATT-TTT
* *
17198801 TTATTATATATTT
1 TT-TTTTATTTTT
17198814 TTTTTTATT
1 TTTTTTATT
17198823 CATTTTTGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
12 8 0.20
13 24 0.59
14 9 0.22
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTATTTTT
Found at i:17198802 original size:26 final size:26
Alignment explanation
Indices: 17198762--17198829 Score: 77
Period size: 26 Copynumber: 2.6 Consensus size: 26
17198752 CTCTCCCTTC
* *
17198762 TTTTTTATT-TCTTTT-TTTTATTTTT
1 TTTTTTATTAT-TTTTATTATATATTT
17198787 TATTTTTATTATTTTTATTATATATTT
1 T-TTTTTATTATTTTTATTATATATTT
17198814 TTTTTTATTCATTTTT
1 TTTTTTATT-ATTTTT
17198830 GTGTTTATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
25 1 0.03
26 20 0.54
27 16 0.43
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTTATTATTTTTATTATATATTT
Found at i:17198828 original size:13 final size:12
Alignment explanation
Indices: 17198762--17198829 Score: 64
Period size: 13 Copynumber: 5.2 Consensus size: 12
17198752 CTCTCCCTTC
*
17198762 TTTTTTATTTCTT
1 TTTTTTA-TTATT
*
17198775 TTTTTTATTTTT
1 TTTTTTATTATT
17198787 TATTTTTATTATT
1 T-TTTTTATTATT
*
17198800 TTTATTATATATTT
1 TTTTTTAT-TA-TT
17198814 TTTTTTATTCATT
1 TTTTTTATT-ATT
17198827 TTT
1 TTT
17198830 GTGTTTATAA
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
12 11 0.23
13 26 0.55
14 10 0.21
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (12 bp):
TTTTTTATTATT
Found at i:17200007 original size:36 final size:35
Alignment explanation
Indices: 17199926--17200095 Score: 166
Period size: 36 Copynumber: 4.7 Consensus size: 35
17199916 TCAATTTAGC
*
17199926 TCATGTGCACTCCCACACCGCACATGG-CAAAT-A
1 TCATGTGCACTCCCACACCGCACATGGCCATATCA
*
17199959 TCATGTGAACTCCCACACCGCACATGGCCTATATCA
1 TCATGTGCACTCCCACACCGCACATGGCC-ATATCA
* *
17199995 TCATGTGCACTCCCACACCACACGTGG-CATATGTCA
1 TCATGTGCACTCCCACACCGCACATGGCCATA--TCA
* * *** *
17200031 TCAGCGTGTGCATTCCCACACCACACACCACCATCACCA
1 TCA---TGTGCACTCCCACACCGCACATGGCCAT-ATCA
17200070 TCATGTGCACTCCCACACCGCACATG
1 TCATGTGCACTCCCACACCGCACATG
17200096 CACGGTTATA
Statistics
Matches: 112, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
33 26 0.23
34 4 0.04
35 4 0.04
36 50 0.45
39 24 0.21
40 3 0.03
41 1 0.01
ACGTcount: A:0.27, C:0.39, G:0.14, T:0.19
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCGCACATGGCCATATCA
Found at i:17218036 original size:19 final size:20
Alignment explanation
Indices: 17218009--17218054 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
17217999 AGGAGACAAG
*
17218009 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
17218028 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
17218047 ATAATATT
1 ATAATATT
17218055 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:17218622 original size:2 final size:2
Alignment explanation
Indices: 17218615--17218641 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17218605 AAGAAATAGA
17218615 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17218642 ATTGACCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17218889 original size:34 final size:34
Alignment explanation
Indices: 17218851--17218941 Score: 137
Period size: 34 Copynumber: 2.7 Consensus size: 34
17218841 ATTTAAGGGT
** *
17218851 TGATTTTGGAGGCTGAAAAGTGCCATTTTTTTGC
1 TGATTTTGGAGGCCAAAAAGTGCCATTTTTCTGC
* *
17218885 TGATTTTAGAGGCCAAAAAGTGTCATTTTTCTGC
1 TGATTTTGGAGGCCAAAAAGTGCCATTTTTCTGC
17218919 TGATTTTGGAGGCCAAAAAGTGC
1 TGATTTTGGAGGCCAAAAAGTGC
17218942 AGATTTTTGC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (34 bp):
TGATTTTGGAGGCCAAAAAGTGCCATTTTTCTGC
Found at i:17219309 original size:26 final size:26
Alignment explanation
Indices: 17219280--17219359 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
17219270 AAAAGAAAAT
*
17219280 AACAAGATAGAAAATGGGCATGGCTC
1 AACAAGATAGAAAATGGGCATGGCCC
*
17219306 AACAAGATAGAAAATTGGACATGGCCC
1 AACAAGATAGAAAA-TGGGCATGGCCC
* *
17219333 AATAA-A-GGAAGAATGGGCATGGCCC
1 AACAAGATAGAA-AATGGGCATGGCCC
17219358 AA
1 AA
17219360 TTAAAAAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
25 16 0.34
26 17 0.36
27 14 0.30
ACGTcount: A:0.44, C:0.16, G:0.26, T:0.14
Consensus pattern (26 bp):
AACAAGATAGAAAATGGGCATGGCCC
Found at i:17219372 original size:25 final size:24
Alignment explanation
Indices: 17219325--17219374 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
17219315 GAAAATTGGA
17219325 CATGGCCCAATAAAGGAAGAATGGG
1 CATGGCCCAATAAA-GAAGAATGGG
17219350 CATGGCCCAATTAAA-AAGAAATGGG
1 CATGGCCCAA-TAAAGAAG-AATGGG
17219375 AGAAGCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 16 0.70
26 4 0.17
ACGTcount: A:0.42, C:0.16, G:0.28, T:0.14
Consensus pattern (24 bp):
CATGGCCCAATAAAGAAGAATGGG
Found at i:17222139 original size:29 final size:30
Alignment explanation
Indices: 17222098--17222157 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
17222088 ACATGGCGTG
*
17222098 TAACAATATTTTTTTGAACATGGCATGTAA
1 TAACAACATTTTTTTGAACATGGCATGTAA
* *
17222128 TAACAACA-TTTTTTGAATATGGTATGTAA
1 TAACAACATTTTTTTGAACATGGCATGTAA
17222157 T
1 T
17222158 TTGGTTTCTA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (30 bp):
TAACAACATTTTTTTGAACATGGCATGTAA
Found at i:17224951 original size:27 final size:27
Alignment explanation
Indices: 17224911--17224968 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
17224901 GTTTTATTTT
17224911 ATTT-TTTAAAATATTAATAATTTATA
1 ATTTATTTAAAATATTAATAATTTATA
* *
17224937 GTTTATTTAAGATATTAATAATTTATA
1 ATTTATTTAAAATATTAATAATTTATA
17224964 ATTTA
1 ATTTA
17224969 AACATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (27 bp):
ATTTATTTAAAATATTAATAATTTATA
Found at i:17225032 original size:15 final size:15
Alignment explanation
Indices: 17225004--17225038 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
17224994 ATTCTTTATT
17225004 TTTAAAACATTAAAA
1 TTTAAAACATTAAAA
17225019 TATTAAAA-ATTAAAA
1 T-TTAAAACATTAAAA
17225034 TTTAA
1 TTTAA
17225039 TTTAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 9 0.47
16 6 0.32
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TTTAAAACATTAAAA
Found at i:17225143 original size:19 final size:18
Alignment explanation
Indices: 17225109--17225145 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17225099 TTATTTTAAA
*
17225109 TTCTTTTTTGTTTTTCTT
1 TTCTTTTTTGTCTTTCTT
17225127 TTCTTTTATTGTCTTTCTT
1 TTCTTTT-TTGTCTTTCTT
17225146 GTTCGTTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.03, C:0.14, G:0.05, T:0.78
Consensus pattern (18 bp):
TTCTTTTTTGTCTTTCTT
Found at i:17227547 original size:3 final size:3
Alignment explanation
Indices: 17227541--17227570 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17227531 ATAATAATAA
17227541 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17227571 ATAGTCATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:17227650 original size:3 final size:3
Alignment explanation
Indices: 17227642--17227669 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17227632 TATGTTCCAA
17227642 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17227670 TATTATTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:17229806 original size:73 final size:73
Alignment explanation
Indices: 17229714--17229854 Score: 219
Period size: 73 Copynumber: 1.9 Consensus size: 73
17229704 CGCTACAGTG
* * ** *
17229714 AAATTCAGAGCATGGGTTAAGGCTGCCTACTTGAGAGTTTCTCACTACAACGAAAATGAATCTTG
1 AAATTCAAAGCATGGGTTAAGGCTACCTACCCGAGAGTTTCTCACTACAACGAAAATGAATCTCG
17229779 CTGCAACA
66 CTGCAACA
* *
17229787 AAATTCAAAGCATGGGTTAAGGCTACCTACCCGAGAGTTTCTCGCTGCAACGAAAATGAATCTCG
1 AAATTCAAAGCATGGGTTAAGGCTACCTACCCGAGAGTTTCTCACTACAACGAAAATGAATCTCG
17229852 CTG
66 CTG
17229855 TAGTGAGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 61 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (73 bp):
AAATTCAAAGCATGGGTTAAGGCTACCTACCCGAGAGTTTCTCACTACAACGAAAATGAATCTCG
CTGCAACA
Found at i:17230004 original size:2 final size:2
Alignment explanation
Indices: 17229997--17230049 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
17229987 ACTTTTTAAC
17229997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17230039 AT AT AT AT AT A
1 AT AT AT AT AT A
17230050 CATACATCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17230176 original size:43 final size:40
Alignment explanation
Indices: 17230082--17230191 Score: 118
Period size: 38 Copynumber: 2.7 Consensus size: 40
17230072 CTCGTTACAC
*
17230082 TCAGCTCATGTGCACTCCCTACACGCACAATGCAATATCA
1 TCAGCTCATGTGCACTCCCTACACGCACAAAGCAATATCA
* * *
17230122 ACA--TCATGTGCACTCCTTACTCGCACAAAGCTAAGTTATCA
1 TCAGCTCATGTGCACTCCCTACACGCACAAAGC-AA--TATCA
*
17230163 TCAGCTCATGTGCACT-TCTACACCGCACA
1 TCAGCTCATGTGCACTCCCTACA-CGCACA
17230192 TAGTTGGATC
Statistics
Matches: 56, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
38 25 0.45
39 2 0.04
40 2 0.04
41 7 0.12
42 3 0.05
43 17 0.30
ACGTcount: A:0.29, C:0.34, G:0.13, T:0.25
Consensus pattern (40 bp):
TCAGCTCATGTGCACTCCCTACACGCACAAAGCAATATCA
Found at i:17230973 original size:23 final size:20
Alignment explanation
Indices: 17230948--17230989 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17230938 GATGGGAGGA
*
17230948 AAAAGAAGAAGAAGCTGCTGG
1 AAAA-AAGAGGAAGCTGCTGG
*
17230969 AAAAATGAGGAAGCTGCTGG
1 AAAAAAGAGGAAGCTGCTGG
17230989 A
1 A
17230990 GATTAGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.45, C:0.10, G:0.33, T:0.12
Consensus pattern (20 bp):
AAAAAAGAGGAAGCTGCTGG
Found at i:17234051 original size:10 final size:10
Alignment explanation
Indices: 17234024--17234056 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
17234014 ATTTTATTTA
17234024 TTTATTTAT-T
1 TTTATTT-TCT
17234034 TTTATTTTCT
1 TTTATTTTCT
17234044 TTTATTTTCT
1 TTTATTTTCT
17234054 TTT
1 TTT
17234057 TTTCAAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 1 0.05
10 21 0.95
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTATTTTCT
Found at i:17241780 original size:28 final size:29
Alignment explanation
Indices: 17241747--17241813 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
17241737 AAAGCTAATA
17241747 AAGACAAACAT-ACTTTCTTATCTAAATT
1 AAGACAAACATGACTTTCTTATCTAAATT
** *
17241775 AAGACAAACATGTTTTTCTTGTCTAAATT
1 AAGACAAACATGACTTTCTTATCTAAATT
*
17241804 AAAACAAACA
1 AAGACAAACA
17241814 CAAACACATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.32
29 23 0.68
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (29 bp):
AAGACAAACATGACTTTCTTATCTAAATT
Found at i:17245837 original size:20 final size:20
Alignment explanation
Indices: 17245809--17245855 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
17245799 TTATAATTAA
*
17245809 TTTATTTTTAAGTTAGTTAT
1 TTTAATTTTAAGTTAGTTAT
* * *
17245829 TTTAATTTTATGTTATTTCT
1 TTTAATTTTAAGTTAGTTAT
17245849 TTTAATT
1 TTTAATT
17245856 GTTTAATATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (20 bp):
TTTAATTTTAAGTTAGTTAT
Found at i:17248451 original size:43 final size:43
Alignment explanation
Indices: 17248404--17248513 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 43
17248394 TTCCCAGCTC
* ** *
17248404 ATGCGCACTCTCTACTCGCACATGGCTAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGGCTT
* *
17248447 ATGCGCACTCCCTACTCGCACATAACTGGGTCATCATCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGGCTT
*
17248490 ATGCGCACTCCCTACTTGCACATA
1 ATGCGCACTCCCTACTCGCACATA
17248514 GTCGAGTCAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 60 1.00
ACGTcount: A:0.21, C:0.35, G:0.19, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACTAGGTCATCACCGGCTT
Found at i:17257289 original size:12 final size:11
Alignment explanation
Indices: 17257262--17257297 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 11
17257252 GAAATCATGC
17257262 CAAGAAA-AAA
1 CAAGAAAGAAA
17257272 CAAGAAAGAAA
1 CAAGAAAGAAA
17257283 GCAAGAAAGAAA
1 -CAAGAAAGAAA
17257295 CAA
1 CAA
17257298 ATCCACAGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.29
11 6 0.25
12 11 0.46
ACGTcount: A:0.72, C:0.11, G:0.17, T:0.00
Consensus pattern (11 bp):
CAAGAAAGAAA
Found at i:17261653 original size:2 final size:2
Alignment explanation
Indices: 17261648--17261684 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17261638 TCAAAGCAAT
17261648 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17261685 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17262622 original size:2 final size:2
Alignment explanation
Indices: 17262615--17262654 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
17262605 NNNNNNNNNN
17262615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17262655 TATTGTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17263383 original size:15 final size:17
Alignment explanation
Indices: 17263352--17263389 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
17263342 TAAATCTTCA
17263352 TAATTAATAATTATTAT
1 TAATTAATAATTATTAT
17263369 TAATTAA-AA-TATTAT
1 TAATTAATAATTATTAT
*
17263384 TTATTA
1 TAATTA
17263390 TTTTTATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 2 0.10
17 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTAATAATTATTAT
Found at i:17265606 original size:47 final size:47
Alignment explanation
Indices: 17265555--17265701 Score: 231
Period size: 47 Copynumber: 3.1 Consensus size: 47
17265545 AGGTTCAAAA
*
17265555 TTTGTGACACGCCATGGAAGGAATCTGTGACACGGTAGGGTTTAGAG
1 TTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTTAGAG
* * *
17265602 TTTGTGATACACCATGGAAGGAATCTATGACACGGTAAGGTTTAGAG
1 TTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTTAGAG
* *
17265649 TTTGTGACACGTCATGGAGGGAATCTATGACACGGTAGGGTTTAGAG
1 TTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTTAGAG
*
17265696 TGTGTG
1 TTTGTG
17265702 GCACAGCATG
Statistics
Matches: 90, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 90 1.00
ACGTcount: A:0.27, C:0.13, G:0.33, T:0.28
Consensus pattern (47 bp):
TTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTTAGAG
Found at i:17265738 original size:94 final size:94
Alignment explanation
Indices: 17265533--17265743 Score: 244
Period size: 94 Copynumber: 2.2 Consensus size: 94
17265523 GTGACACAGT
* *
17265533 TGTGACACGACAAGGTTCAAAATTTGTGACACGCCATGGAAGGAATCTGTGACACGGTAGGGTTT
1 TGTGACACGACAAGGTTTAAAATTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTT
* *
17265598 AGAGTTTGTGATACACCATGGAAGGAATC
66 AGAGTGTGTGACACACCATGGAAGGAATC
* ** * * * *
17265627 TATGACACGGTAAGGTTTAGAGTTTGTGACACGTCATGGAGGGAATCTATGACACGGTAGGGTTT
1 TGTGACACGACAAGGTTTAAAATTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTT
* * ***
17265692 AGAGTGTGTGGCACAGCATGGCTTGAA-C
66 AGAGTGTGTGACACACCATGGAAGGAATC
* *
17265720 ATGTGACACGACATGGTTTGAAAT
1 -TGTGACACGACAAGGTTTAAAAT
17265744 AGGAAGTGGG
Statistics
Matches: 93, Mismatches: 23, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
93 1 0.01
94 92 0.99
ACGTcount: A:0.29, C:0.15, G:0.30, T:0.26
Consensus pattern (94 bp):
TGTGACACGACAAGGTTTAAAATTTGTGACACGCCATGGAAGGAATCTATGACACGGTAGGGTTT
AGAGTGTGTGACACACCATGGAAGGAATC
Found at i:17266377 original size:31 final size:31
Alignment explanation
Indices: 17266334--17266705 Score: 415
Period size: 31 Copynumber: 12.6 Consensus size: 31
17266324 GTGTCAGCGT
* *
17266334 TGGCATGTAACAACATTTGACTTGCTATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* *
17266365 TGGCGTGTAACAACATTTTACTTGATATCCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
**
17266396 TGGCGTGTAACAACATTTGACTTGATACACA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* * * *
17266427 TAGCGTATAACAACATTTTACGTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
17266458 TGGCGTGTAACAACACTTT-ACTTGATATGCA
1 TGGCGTGTAACAACA-TTTGACTTGATATGCA
*
17266489 TGGCATGTAACAAC-----A--T--TATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* * *
17266511 TGGCCTATAACAACATTTAACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
* *
17266542 TGGCGTGTAACAACATTTTACGTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
17266573 TGGCGTGTAACAACACTTT-ACTTGATATGCA
1 TGGCGTGTAACAACA-TTTGACTTGATATGCA
17266604 TGGCGTGTAACAAC-----A--T--TATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
17266626 TGGCGTGTAACAACATTTAACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
17266657 TGGCGTGTAACAACATTTTACTTGATATGCA
1 TGGCGTGTAACAACATTTGACTTGATATGCA
*
17266688 TGACGTGTAACAACATTT
1 TGGCGTGTAACAACATTT
17266706 ATTTCTTTCT
Statistics
Matches: 295, Mismatches: 26, Indels: 40
0.82 0.07 0.11
Matches are distributed among these distances:
22 38 0.13
24 2 0.01
26 2 0.01
27 2 0.01
29 2 0.01
31 243 0.82
32 6 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (31 bp):
TGGCGTGTAACAACATTTGACTTGATATGCA
Found at i:17266511 original size:22 final size:22
Alignment explanation
Indices: 17266483--17266527 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
17266473 CTTTACTTGA
*
17266483 TATGCATGGCATGTAACAACAT
1 TATGCATGGCATATAACAACAT
*
17266505 TATGCATGGCCTATAACAACAT
1 TATGCATGGCATATAACAACAT
17266527 T
1 T
17266528 TAACTTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.29
Consensus pattern (22 bp):
TATGCATGGCATATAACAACAT
Found at i:17266573 original size:84 final size:84
Alignment explanation
Indices: 17266432--17266587 Score: 267
Period size: 84 Copynumber: 1.9 Consensus size: 84
17266422 ACACATAGCG
* *
17266432 TATAACAACATTTTACGTGATATGCATGGCGTGTAACAACACTTTACTTGATATGCATGGCATGT
1 TATAACAACATTTAACGTGATATGCATGGCGTGTAACAACACTTTACGTGATATGCATGGCATGT
17266497 AACAACATTATGCATGGCC
66 AACAACATTATGCATGGCC
* * *
17266516 TATAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACGTGATATGCATGGCGTGT
1 TATAACAACATTTAACGTGATATGCATGGCGTGTAACAACACTTTACGTGATATGCATGGCATGT
17266581 AACAACA
66 AACAACA
17266588 CTTTACTTGA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 67 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (84 bp):
TATAACAACATTTAACGTGATATGCATGGCGTGTAACAACACTTTACGTGATATGCATGGCATGT
AACAACATTATGCATGGCC
Found at i:17266596 original size:115 final size:115
Alignment explanation
Indices: 17266394--17266706 Score: 529
Period size: 115 Copynumber: 2.7 Consensus size: 115
17266384 ACTTGATATC
* ** * *
17266394 CATGGCGTGTAACAACATTTGACTTGATACACATAGCGTATAACAACATTTTACGTGATATGCAT
1 CATGGCGTGTAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACGTGATATGCAT
17266459 GGCGTGTAACAACACTTTACTTGATATGCATGGCATGTAACAACATTATG
66 GGCGTGTAACAACACTTTACTTGATATGCATGGCATGTAACAACATTATG
* *
17266509 CATGGCCTATAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACGTGATATGCAT
1 CATGGCGTGTAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACGTGATATGCAT
*
17266574 GGCGTGTAACAACACTTTACTTGATATGCATGGCGTGTAACAACATTATG
66 GGCGTGTAACAACACTTTACTTGATATGCATGGCATGTAACAACATTATG
*
17266624 CATGGCGTGTAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACTTGATATGCAT
1 CATGGCGTGTAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACGTGATATGCAT
*
17266689 GACGTGTAACAACA-TTTA
66 GGCGTGTAACAACACTTTA
17266707 TTTCTTTCTT
Statistics
Matches: 186, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
114 4 0.02
115 182 0.98
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (115 bp):
CATGGCGTGTAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACGTGATATGCAT
GGCGTGTAACAACACTTTACTTGATATGCATGGCATGTAACAACATTATG
Found at i:17266624 original size:84 final size:84
Alignment explanation
Indices: 17266536--17266704 Score: 302
Period size: 84 Copynumber: 2.0 Consensus size: 84
17266526 TTTAACTTGA
*
17266536 TATGCATGGCGTGTAACAACATTTTACGTGATATGCATGGCGTGTAACAACACTTTACTTGATAT
1 TATGCATGGCGTGTAACAACATTTAACGTGATATGCATGGCGTGTAACAACACTTTACTTGATAT
*
17266601 GCATGGCGTGTAACAACAT
66 GCATGACGTGTAACAACAT
* *
17266620 TATGCATGGCGTGTAACAACATTTAACTTGATATGCATGGCGTGTAACAACATTTTACTTGATAT
1 TATGCATGGCGTGTAACAACATTTAACGTGATATGCATGGCGTGTAACAACACTTTACTTGATAT
17266685 GCATGACGTGTAACAACAT
66 GCATGACGTGTAACAACAT
17266704 T
1 T
17266705 TATTTCTTTC
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (84 bp):
TATGCATGGCGTGTAACAACATTTAACGTGATATGCATGGCGTGTAACAACACTTTACTTGATAT
GCATGACGTGTAACAACAT
Found at i:17266626 original size:22 final size:22
Alignment explanation
Indices: 17266598--17266642 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
17266588 CTTTACTTGA
17266598 TATGCATGGCGTGTAACAACAT
1 TATGCATGGCGTGTAACAACAT
17266620 TATGCATGGCGTGTAACAACAT
1 TATGCATGGCGTGTAACAACAT
17266642 T
1 T
17266643 TAACTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (22 bp):
TATGCATGGCGTGTAACAACAT
Found at i:17268395 original size:145 final size:145
Alignment explanation
Indices: 17268132--17268477 Score: 442
Period size: 145 Copynumber: 2.4 Consensus size: 145
17268122 GCAGTGAACG
* * * *
17268132 GTCGGTAAGGAT-GGTTCTAAAGGTTTTTGTTTAACAATTTCATATGTGATTATCAAATAACATA
1 GTCGGTAA-GATCGGTTCTAACGGTTTGTGTTAAACAATTCCATATGTGATTATCAAATAACATA
* * * *
17268196 TCTGTGTTTGCAGTTGGACCATGCGACGACAACTCCACAACCACCGAGAGGTCCTCCTCAAACGC
65 TCTATGTTTGCAATTGGACCATACGACAACAACTCCACAACCACCGAGAGGTCCTCCTCAAACGC
17268261 ACCATGCTAACGAGCC
130 ACCATGCTAACGAGCC
* *
17268277 GTCGGTAAGATCGGTTCTAACGGTTTGTGTTAAACAATTCCATATGTGATTATCGAATAATATAT
1 GTCGGTAAGATCGGTTCTAACGGTTTGTGTTAAACAATTCCATATGTGATTATCAAATAACATAT
* * * * * *
17268342 CTATGTTTGCAATTGGACCATACGACAATAGCTCTACAACCATCGAGAGGTCCTCCTCAGATGCA
66 CTATGTTTGCAATTGGACCATACGACAACAACTCCACAACCACCGAGAGGTCCTCCTCAAACGCA
** *
17268407 TTATGCTAACGAGCT
131 CCATGCTAACGAGCC
* * * * * * *
17268422 GTCGGTAAAATCGGTTCTAACTGTTTGTGTTCAACATTTCCACATATGTTTATCAA
1 GTCGGTAAGATCGGTTCTAACGGTTTGTGTTAAACAATTCCATATGTGATTATCAA
17268478 GTACCACAGT
Statistics
Matches: 173, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
144 3 0.02
145 170 0.98
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (145 bp):
GTCGGTAAGATCGGTTCTAACGGTTTGTGTTAAACAATTCCATATGTGATTATCAAATAACATAT
CTATGTTTGCAATTGGACCATACGACAACAACTCCACAACCACCGAGAGGTCCTCCTCAAACGCA
CCATGCTAACGAGCC
Found at i:17270698 original size:31 final size:31
Alignment explanation
Indices: 17270673--17270980 Score: 262
Period size: 31 Copynumber: 9.9 Consensus size: 31
17270663 CATGTCATGT
* *
17270673 CATAAATCTGCTTGCACTCAACATGTCACGC
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
** * * * *
17270704 CATAAATCTGC-AACAAGTCAACCTGTCACAC
1 CATAAATCTGCTTGC-ACTCAGCGTGTCACGC
* *
17270735 CATATATCTGC-TACAACAT-AGCGTGTCACGC
1 CATAAATCTGCTTGC-AC-TCAGCGTGTCACGC
* *
17270766 CATAAATATGCTTGCACTCAGCGTGTCACCC
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
* ** * * *
17270797 CATGAATCTGCTACCACTTAGAGTGTCATGC
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
* * *
17270828 CATAAATCTACTTGCACTTAGTGTGTCACGC
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
* * *
17270859 CATAAATCTACTTGCACTCAGCATGTCACGT
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
* * * *
17270890 CAAAAATCTGCTGGCACTCAGAGTGTCACAC
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
* * *
17270921 CATAAATTTGCTTGCACTCAGCATGTCAAGC
1 CATAAATCTGCTTGCACTCAGCGTGTCACGC
* **
17270952 CATAAATTTGCTACCACTCAGCGTGTCAC
1 CATAAATCTGCTTGCACTCAGCGTGTCAC
17270981 CGGAAGATGA
Statistics
Matches: 222, Mismatches: 51, Indels: 8
0.79 0.18 0.03
Matches are distributed among these distances:
30 2 0.01
31 217 0.98
32 3 0.01
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (31 bp):
CATAAATCTGCTTGCACTCAGCGTGTCACGC
Found at i:17275249 original size:23 final size:23
Alignment explanation
Indices: 17275206--17275335 Score: 113
Period size: 23 Copynumber: 5.7 Consensus size: 23
17275196 TCAGTCATGT
* * *
17275206 TGTTACACGTCATTTTTAAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* *
17275229 TGTTACACGCCATG-CCCAAAAA
1 TGTTACACGCCATGTTCAAAAAA
* *
17275251 T-TCTACACG-CAAGTTCAAAAAT
1 TGT-TACACGCCATGTTCAAAAAA
* **
17275273 TGTTACACGCCATGTTCACAGCA
1 TGTTACACGCCATGTTCAAAAAA
*
17275296 TGTTACACGCCATGTTAAATAAAAA
1 TGTTACACGCCATGTT-CA-AAAAA
17275321 TGTTACACGCCATGT
1 TGTTACACGCCATGT
17275336 GCTAACACAT
Statistics
Matches: 83, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.05
22 24 0.29
23 37 0.45
24 1 0.01
25 17 0.20
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.28
Consensus pattern (23 bp):
TGTTACACGCCATGTTCAAAAAA
Found at i:17275257 original size:22 final size:21
Alignment explanation
Indices: 17275224--17275286 Score: 56
Period size: 22 Copynumber: 2.9 Consensus size: 21
17275214 GTCATTTTTA
17275224 AAAAATGTTACACGCCATGCCC
1 AAAAAT-TTACACGCCATGCCC
* **
17275246 AAAAATTCTACACG-CAAGTTC
1 AAAAATT-TACACGCCATGCCC
17275267 AAAAATTGTTACACGCCATG
1 AAAAA-T-TTACACGCCATG
17275287 TTCACAGCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
21 10 0.30
22 19 0.58
23 4 0.12
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (21 bp):
AAAAATTTACACGCCATGCCC
Found at i:17275311 original size:12 final size:12
Alignment explanation
Indices: 17275273--17275312 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
17275263 GTTCAAAAAT
17275273 TGTTACACGCCA
1 TGTTACACGCCA
17275285 TGTT-CACAG-CA
1 TGTTACAC-GCCA
17275296 TGTTACACGCCA
1 TGTTACACGCCA
17275308 TGTTA
1 TGTTA
17275313 AATAAAAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.40
12 15 0.60
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (12 bp):
TGTTACACGCCA
Found at i:17280383 original size:4 final size:4
Alignment explanation
Indices: 17280374--17280549 Score: 109
Period size: 4 Copynumber: 44.0 Consensus size: 4
17280364 GCTTATGTAC
* * * * * * * * *
17280374 ATAT ATAT ATAT GTGT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * *
17280422 ATGT ATGT ATGT ATAT ATGT ATAT ATGT ATAT GTAT ATAT GTAT GTAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * * *
17280470 GTAT GTAT GTAT GTAT GTAT ATAT ATAT ATGT ATGT ATGT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* *
17280518 ATAT ATGT ATGT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
17280550 GTATNNNNNT
Statistics
Matches: 154, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 154 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (4 bp):
ATAT
Found at i:17280398 original size:8 final size:8
Alignment explanation
Indices: 17280387--17280531 Score: 181
Period size: 8 Copynumber: 18.6 Consensus size: 8
17280377 TATATATATG
17280387 TGTATGTA
1 TGTATGTA
17280395 TGTATGTA
1 TGTATGTA
17280403 TGTATGTA
1 TGTATGTA
*
17280411 TATATGTA
1 TGTATGTA
17280419 TGTATGTA
1 TGTATGTA
17280427 TGTATGTA
1 TGTATGTA
*
17280435 TATATGTA
1 TGTATGTA
*
17280443 TATATGTA
1 TGTATGTA
17280451 --TATGTA
1 TGTATGTA
*
17280457 TATATGTA
1 TGTATGTA
17280465 TGTATGTA
1 TGTATGTA
17280473 TGTATGTA
1 TGTATGTA
17280481 TGTATGTA
1 TGTATGTA
*
17280489 --TATATA
1 TGTATGTA
*
17280495 TATATGTA
1 TGTATGTA
17280503 TGTATGTA
1 TGTATGTA
* *
17280511 TATATATA
1 TGTATGTA
*
17280519 TATATGTA
1 TGTATGTA
17280527 TGTAT
1 TGTAT
17280532 ATATATATAT
Statistics
Matches: 122, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
6 11 0.09
8 111 0.91
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (8 bp):
TGTATGTA
Found at i:17280404 original size:12 final size:12
Alignment explanation
Indices: 17280387--17280531 Score: 181
Period size: 12 Copynumber: 12.4 Consensus size: 12
17280377 TATATATATG
17280387 TGTATGTATGTA
1 TGTATGTATGTA
17280399 TGTATGTATGTA
1 TGTATGTATGTA
*
17280411 TATATGTATGTA
1 TGTATGTATGTA
17280423 TGTATGTATGTA
1 TGTATGTATGTA
* *
17280435 TATATGTATATA
1 TGTATGTATGTA
17280447 TGTA--TATGTA
1 TGTATGTATGTA
*
17280457 TATATGTATGTA
1 TGTATGTATGTA
17280469 TGTATGTATGTA
1 TGTATGTATGTA
17280481 TGTATGTA--TA
1 TGTATGTATGTA
* *
17280491 TATATATATGTA
1 TGTATGTATGTA
*
17280503 TGTATGTATATA
1 TGTATGTATGTA
* *
17280515 TATATATATGTA
1 TGTATGTATGTA
17280527 TGTAT
1 TGTAT
17280532 ATATATATAT
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
10 16 0.14
12 96 0.86
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (12 bp):
TGTATGTATGTA
Found at i:17280534 original size:12 final size:12
Alignment explanation
Indices: 17280389--17280547 Score: 178
Period size: 12 Copynumber: 13.2 Consensus size: 12
17280379 TATATATGTG
*
17280389 TATGTATGTATG
1 TATGTATGTATA
17280401 TATGTATGTATA
1 TATGTATGTATA
*
17280413 TATGTATGTATG
1 TATGTATGTATA
17280425 TATGTATGTATA
1 TATGTATGTATA
17280437 TATGTA--TATA
1 TATGTATGTATA
* *
17280447 TGTATATGTATA
1 TATGTATGTATA
*
17280459 TATGTATGTATG
1 TATGTATGTATA
*
17280471 TATGTATGTATG
1 TATGTATGTATA
*
17280483 TATGTATATATATA
1 TATG--TATGTATA
*
17280497 TATGTATGTATG
1 TATGTATGTATA
* *
17280509 TATATATATATA
1 TATGTATGTATA
17280521 TATGTATGTATA
1 TATGTATGTATA
* *
17280533 TATATATATATA
1 TATGTATGTATA
17280545 TAT
1 TAT
17280548 ATGTATNNNN
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
10 8 0.06
12 106 0.85
14 10 0.08
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (12 bp):
TATGTATGTATA
Found at i:17290429 original size:29 final size:28
Alignment explanation
Indices: 17290381--17290444 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
17290371 GTCTATGGGC
* *
17290381 AATTTTTCAGTTTTTGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGCAAAAATGT
*
17290409 AATTTTTCACTTTATAGGGGCAAAAGTGT
1 AATTTTTCACTTT-TAGGGGCAAAAATGT
*
17290438 AAGTTTT
1 AATTTTT
17290445 AAAAATTTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (28 bp):
AATTTTTCACTTTTAGGGGCAAAAATGT
Found at i:17290433 original size:28 final size:29
Alignment explanation
Indices: 17290381--17290444 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
17290371 GTCTATGGGC
* *
17290381 AATTTTTCAGTTTTTGGGGCAAAAA-TGT
1 AATTTTTCACTTTTAGGGGCAAAAAGTGT
17290409 AATTTTTCACTTTATAGGGGC-AAAAGTGT
1 AATTTTTCACTTT-TAGGGGCAAAAAGTGT
*
17290438 AAGTTTT
1 AATTTTT
17290445 AAAAATTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 16 0.52
29 15 0.48
ACGTcount: A:0.30, C:0.08, G:0.20, T:0.42
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGCAAAAAGTGT
Found at i:17292882 original size:32 final size:32
Alignment explanation
Indices: 17292822--17292882 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 32
17292812 ATATTTAATC
* * *
17292822 ACTAGAAGTGGATGAATTATTATGCCCACTGG
1 ACTAGAAGTGAATGAATAATTATACCCACTGG
* *
17292854 ACTAGAAGTGAATGGATAATTTTACCCAC
1 ACTAGAAGTGAATGAATAATTATACCCAC
17292883 CAAATTAGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 24 1.00
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.28
Consensus pattern (32 bp):
ACTAGAAGTGAATGAATAATTATACCCACTGG
Found at i:17292946 original size:27 final size:27
Alignment explanation
Indices: 17292916--17292968 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
17292906 TTATTTATCA
*
17292916 GAAGTAGATAGATATGTTTACCCACTG
1 GAAGTAGATAAATATGTTTACCCACTG
* *
17292943 GAAGTAGATAAATATTTTTACTCACT
1 GAAGTAGATAAATATGTTTACCCACT
17292969 AAAAGTGGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (27 bp):
GAAGTAGATAAATATGTTTACCCACTG
Found at i:17292974 original size:27 final size:27
Alignment explanation
Indices: 17292917--17293010 Score: 75
Period size: 27 Copynumber: 3.5 Consensus size: 27
17292907 TATTTATCAG
* * **
17292917 AAGTAGATAGATATGTTTACCCACTGG
1 AAGTAGATAAATATTTTTACCCACTAA
*
17292944 AAGTAGATAAATATTTTTACTCACTAA
1 AAGTAGATAAATATTTTTACCCACTAA
* * * *
17292971 AAGTGGATGAAA-ACTTTTACGCACCAA
1 AAGTAGAT-AAATATTTTTACCCACTAA
17292998 AAGT-GAATAAATA
1 AAGTAG-ATAAATA
17293011 GTGAAGAGAT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
26 4 0.07
27 48 0.87
28 3 0.05
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (27 bp):
AAGTAGATAAATATTTTTACCCACTAA
Found at i:17293782 original size:17 final size:17
Alignment explanation
Indices: 17293760--17293795 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
17293750 TGAATCCCTA
*
17293760 CATTTTTTAGACTTATT
1 CATTTTTTAAACTTATT
17293777 CATTTTTTAAACTTATT
1 CATTTTTTAAACTTATT
17293794 CA
1 CA
17293796 AGATGATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.14, G:0.03, T:0.56
Consensus pattern (17 bp):
CATTTTTTAAACTTATT
Found at i:17296317 original size:19 final size:19
Alignment explanation
Indices: 17296293--17296341 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
17296283 GCTATAAATA
*
17296293 TCTTCTCCTTCCAGCAGCT
1 TCTTCTTCTTCCAGCAGCT
*
17296312 TCTTCTTATTCCAGCAGCT
1 TCTTCTTCTTCCAGCAGCT
17296331 TCTTCTTCTTC
1 TCTTCTTCTTC
17296342 TTCTCCTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.10, C:0.37, G:0.08, T:0.45
Consensus pattern (19 bp):
TCTTCTTCTTCCAGCAGCT
Found at i:17297240 original size:38 final size:40
Alignment explanation
Indices: 17297197--17297302 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 40
17297187 ATAGTGCCTG
* * **
17297197 TGTGCAAGATGTGGGGGGATGTACATGATGGCA-TTGAT-
1 TGTGCACGATGTGGGGGGATGTACATGATGACACCGGATA
* *
17297235 TGTGCACGATGTGGGGGGATGCACATGATGACACCGGTTA
1 TGTGCACGATGTGGGGGGATGTACATGATGACACCGGATA
*
17297275 TGTGCACGATGTGGAGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
17297303 GTTGGGTGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
38 30 0.52
39 2 0.03
40 26 0.45
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACATGATGACACCGGATA
Found at i:17299110 original size:38 final size:38
Alignment explanation
Indices: 17299068--17299145 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
17299058 ACAGGATGTA
17299068 GGAGTGTGAATGATGATATTGCTTGTGCGCGATGTGGG
1 GGAGTGTGAATGATGATATTGCTTGTGCGCGATGTGGG
17299106 GGAGTGTGAATGATGATATTGCTTGTGCGCGATGTGGG
1 GGAGTGTGAATGATGATATTGCTTGTGCGCGATGTGGG
17299144 GG
1 GG
17299146 TGCACACGAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.18, C:0.08, G:0.44, T:0.31
Consensus pattern (38 bp):
GGAGTGTGAATGATGATATTGCTTGTGCGCGATGTGGG
Found at i:17303547 original size:2 final size:2
Alignment explanation
Indices: 17303540--17303588 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17303530 CGTCTATAGC
17303540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17303582 AT AT AT A
1 AT AT AT A
17303589 CATGTACACC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17304101 original size:19 final size:19
Alignment explanation
Indices: 17304077--17304116 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
17304067 CGTTAAAACC
17304077 TATATTTACCAATAAGCCA
1 TATATTTACCAATAAGCCA
17304096 TATATTTACCAATAAGCCA
1 TATATTTACCAATAAGCCA
17304115 TA
1 TA
17304117 ACAACCTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.42, C:0.20, G:0.05, T:0.33
Consensus pattern (19 bp):
TATATTTACCAATAAGCCA
Found at i:17312852 original size:19 final size:20
Alignment explanation
Indices: 17312828--17312873 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
17312818 TATTTTAAGA
17312828 TATGTTTTGCATG-TTTATT
1 TATGTTTTGCATGTTTTATT
17312847 TATGTTTTGCATGTTTTATT
1 TATGTTTTGCATGTTTTATT
*
17312867 TGTGTTT
1 TATGTTT
17312874 CAAAAATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.13, C:0.04, G:0.17, T:0.65
Consensus pattern (20 bp):
TATGTTTTGCATGTTTTATT
Found at i:17314151 original size:27 final size:30
Alignment explanation
Indices: 17314121--17314184 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 30
17314111 CAATTTTCAA
17314121 TTATAATTTA-CTTATTTTTAA-TT-ATTT
1 TTATAATTTAGCTTATTTTTAAGTTAATTT
*
17314148 TTATAA-TTAGTTTATTTTTAAGTTAATTT
1 TTATAATTTAGCTTATTTTTAAGTTAATTT
17314177 TT-TAATTT
1 TTATAATTT
17314185 TATGTTATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
26 3 0.09
27 16 0.50
28 5 0.16
29 8 0.25
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (30 bp):
TTATAATTTAGCTTATTTTTAAGTTAATTT
Found at i:17314185 original size:19 final size:19
Alignment explanation
Indices: 17314158--17314203 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
17314148 TTATAATTAG
*
17314158 TTTATTTTTAAGTTAATTT
1 TTTAATTTTAAGTTAATTT
* *
17314177 TTTAATTTTATGTTATTTT
1 TTTAATTTTAAGTTAATTT
17314196 TTTAATTT
1 TTTAATTT
17314204 GGTTATTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.72
Consensus pattern (19 bp):
TTTAATTTTAAGTTAATTT
Found at i:17315924 original size:80 final size:80
Alignment explanation
Indices: 17315796--17316032 Score: 348
Period size: 80 Copynumber: 3.0 Consensus size: 80
17315786 TTATCATACT
* * * * *
17315796 TTAGCCCATCGTGCATATGATTATCGTCAACACATACTTCTCATGGCATACATTTCATAACCCCA
1 TTAGCCCATAGTGTATATGACTATC-TCAACACATACATCTCATGGCATACATTTCATAACCTCA
17315861 TAAATCACTTACATGC
65 TAAATCACTTACATGC
* * * **
17315877 TTAGCCCATAGTGTATATGACTATCTCAACACGTACATCACATGGCATATATTTTGTAACCTCAT
1 TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCAT
*
17315942 AAATCACTTACATGG
66 AAATCACTTACATGC
* *
17315957 TTAGCCCATAGTGTATATGACTATTTCAACACAAACATCTCATGGCATACATTTCATAACCTCAT
1 TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCAT
17316022 AAATCACTTAC
66 AAATCACTTAC
17316033 TACTCAACCC
Statistics
Matches: 138, Mismatches: 18, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
80 116 0.84
81 22 0.16
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (80 bp):
TTAGCCCATAGTGTATATGACTATCTCAACACATACATCTCATGGCATACATTTCATAACCTCAT
AAATCACTTACATGC
Found at i:17318990 original size:16 final size:16
Alignment explanation
Indices: 17318954--17319010 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
17318944 AGTTCTTTGT
*
17318954 TTTTAGTTTTAGTTTAA
1 TTTTAGTTTT-CTTTAA
*
17318971 TTTTAGTTTTCTTTAG
1 TTTTAGTTTTCTTTAA
*
17318987 TTTTCAG-TATCTTTAA
1 TTTT-AGTTTTCTTTAA
17319003 TTTTAGTT
1 TTTTAGTT
17319011 GTTTGAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
15 2 0.06
16 20 0.59
17 12 0.35
ACGTcount: A:0.19, C:0.05, G:0.11, T:0.65
Consensus pattern (16 bp):
TTTTAGTTTTCTTTAA
Found at i:17320688 original size:33 final size:33
Alignment explanation
Indices: 17320646--17320719 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
17320636 AAAGGCATTC
17320646 TCGCTGCAACGAAGCTGCAGCGAGAATGAATTT
1 TCGCTGCAACGAAGCTGCAGCGAGAATGAATTT
* *
17320679 TCGCTGCAACGAAGCTGTAGTGAGAATGAATTT
1 TCGCTGCAACGAAGCTGCAGCGAGAATGAATTT
*
17320712 TCACTGCA
1 TCGCTGCA
17320720 GTGAAATTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (33 bp):
TCGCTGCAACGAAGCTGCAGCGAGAATGAATTT
Found at i:17321047 original size:2 final size:2
Alignment explanation
Indices: 17321040--17321080 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
17321030 ATTCCATAAG
17321040 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17321081 NAAGCACTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17321165 original size:22 final size:22
Alignment explanation
Indices: 17321137--17321179 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
17321127 AGTTAGAAGA
*
17321137 ATTCTTGTTACAACGAAAATCC
1 ATTCTTGCTACAACGAAAATCC
* *
17321159 ATTCTTGCTGCAATGAAAATC
1 ATTCTTGCTACAACGAAAATC
17321180 AATTTGGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (22 bp):
ATTCTTGCTACAACGAAAATCC
Found at i:17321340 original size:36 final size:35
Alignment explanation
Indices: 17321293--17321420 Score: 159
Period size: 36 Copynumber: 3.6 Consensus size: 35
17321283 GCTCACCAAC
17321293 TCATGTGCACTCCCACACCATACATAGCTGAA-ATCA
1 TCATGTGCACTCCCACACCA-ACATAGCT-AATATCA
* *
17321329 TCATGTGCACTCCCACACCGCACATAGCTAATATCG
1 TCATGTGCACTCCCACACC-AACATAGCTAATATCA
* *
17321365 TCATGTGCACTCCCACACCGAACATGGCAAATATCA
1 TCATGTGCACTCCCACACC-AACATAGCTAATATCA
* *
17321401 TTATGTACACTCCCACACCA
1 TCATGTGCACTCCCACACCA
17321421 CATCATCACC
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
35 3 0.04
36 79 0.96
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (35 bp):
TCATGTGCACTCCCACACCAACATAGCTAATATCA
Found at i:17324960 original size:38 final size:40
Alignment explanation
Indices: 17324909--17325012 Score: 140
Period size: 38 Copynumber: 2.6 Consensus size: 40
17324899 ATAGTGCCCG
*
17324909 TGTGCACGATGTGGGGGAATGTACACGATGGCA-CTGAT-
1 TGTGCACGATGTGGGGGAATGTACACGATGGCACCGGATA
* * *
17324947 TGTGCACGATGTGGGGGAATGCACATGATGGCACCGGCTA
1 TGTGCACGATGTGGGGGAATGTACACGATGGCACCGGATA
*
17324987 TGTGCACGATGTGGGGGGGATGTACA
1 TGTGCACGATGT-GGGGGAATGTACA
17325013 TGAGCCGGGT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
38 31 0.54
39 3 0.05
40 12 0.21
41 11 0.19
ACGTcount: A:0.22, C:0.16, G:0.39, T:0.22
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGAATGTACACGATGGCACCGGATA
Found at i:17329423 original size:54 final size:56
Alignment explanation
Indices: 17329293--17329441 Score: 221
Period size: 54 Copynumber: 2.7 Consensus size: 56
17329283 GCATTATCTA
* **
17329293 TGCACAATGTGGGGGGATGCACATGAGTTGGGTGAGACACGATGACTCCGGCTATG
1 TGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGATGCGATGACTCCGGCTATG
* * * *
17329349 TACACAATGTGGGGGAATGCACATGAGCTGGGTGAGATGGGGT-A-TCCGGCTATG
1 TGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGATGCGATGACTCCGGCTATG
17329403 TGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGATG
1 TGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGATG
17329442 TGGTGGTATA
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
54 47 0.56
55 1 0.01
56 36 0.43
ACGTcount: A:0.23, C:0.15, G:0.40, T:0.21
Consensus pattern (56 bp):
TGCACAATGTGGGGGGATGCACATGAGCTGGGTGAGATGCGATGACTCCGGCTATG
Found at i:17333774 original size:17 final size:17
Alignment explanation
Indices: 17333752--17333786 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17333742 TTTTCCAATC
*
17333752 GTAGAGTCTCCAATGGT
1 GTAGAGTCTCCAACGGT
17333769 GTAGAGTCTCCAACGGT
1 GTAGAGTCTCCAACGGT
17333786 G
1 G
17333787 ATCCACAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.20, G:0.31, T:0.26
Consensus pattern (17 bp):
GTAGAGTCTCCAACGGT
Found at i:17338753 original size:26 final size:27
Alignment explanation
Indices: 17338710--17338760 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
17338700 TTTTAATGTC
*
17338710 ATATTTTATTTTTATTTTTATATAACT
1 ATATTTTATTTTTATTTTAATATAACT
17338737 ATATTTT-TTATTT-TTTTAATATAA
1 ATATTTTATT-TTTATTTTAATATAA
17338761 TTTTTATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (27 bp):
ATATTTTATTTTTATTTTAATATAACT
Found at i:17338764 original size:20 final size:23
Alignment explanation
Indices: 17338717--17338776 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
17338707 GTCATATTTT
17338717 ATTTTTATTTTTATATAACTATA
1 ATTTTTATTTTTATATAACTATA
*
17338740 TTTTTTATTTTT-T-TAA-TATA
1 ATTTTTATTTTTATATAACTATA
*
17338760 ATTTTTATATTATATAT
1 ATTTTTAT-TTTTATAT
17338777 TTTATTTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 11 0.35
21 6 0.19
22 2 0.06
23 12 0.39
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTTTTATTTTTATATAACTATA
Found at i:17338765 original size:14 final size:15
Alignment explanation
Indices: 17338745--17338786 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
17338735 CTATATTTTT
17338745 TATTTTTTTAATATA
1 TATTTTTTTAATATA
* *
17338760 -ATTTTTATATTATA
1 TATTTTTTTAATATA
17338774 TATTTTATTTAAT
1 TATTTT-TTTAAT
17338787 TTTTTTCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
14 12 0.57
15 5 0.24
16 4 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTTTAATATA
Found at i:17339033 original size:13 final size:13
Alignment explanation
Indices: 17339015--17339067 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
17339005 TTATAATTTA
17339015 ATTATATTATAAT
1 ATTATATTATAAT
17339028 ATTATATTATAAT
1 ATTATATTATAAT
*
17339041 AATT-TATTATAAA
1 -ATTATATTATAAT
*
17339054 ATAAATATTATAAT
1 AT-TATATTATAAT
17339068 TTAATTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 2 0.06
13 21 0.62
14 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTATATTATAAT
Found at i:17344487 original size:47 final size:47
Alignment explanation
Indices: 17344405--17344543 Score: 161
Period size: 47 Copynumber: 3.0 Consensus size: 47
17344395 AATAAATTGA
* ** * *
17344405 AATGAACAAATAATAAGTCAAAGTCAAGATGTTTTCCTAAGTCAAAT
1 AATGAACAAATAATAAATCAAAGGAAAAATATTTTCCTAAGTCAAAT
** * * *
17344452 AATGAACAAATAATAAATTGAAGGAAAAATATTTTCCTATGACTAAT
1 AATGAACAAATAATAAATCAAAGGAAAAATATTTTCCTAAGTCAAAT
* * *
17344499 AATGAACAAATAATAAATCAAAGTAAGAATATTTTGCTAAGTCAA
1 AATGAACAAATAATAAATCAAAGGAAAAATATTTTCCTAAGTCAA
17344544 GTGCCAACAA
Statistics
Matches: 74, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
47 74 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.28
Consensus pattern (47 bp):
AATGAACAAATAATAAATCAAAGGAAAAATATTTTCCTAAGTCAAAT
Found at i:17344612 original size:38 final size:37
Alignment explanation
Indices: 17344552--17344624 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
17344542 AAGTGCCAAC
* *
17344552 AAAAATAATGAATCGAGATAAAATATTTTCCTAAGAA
1 AAAAATAAGGAATCAAGATAAAATATTTTCCTAAGAA
*
17344589 AAAAATTAAGGAATCAAGGTAAAATATTTTCCTAAG
1 AAAAA-TAAGGAATCAAGATAAAATATTTTCCTAAG
17344625 CTAAATGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 5 0.16
38 27 0.84
ACGTcount: A:0.52, C:0.08, G:0.12, T:0.27
Consensus pattern (37 bp):
AAAAATAAGGAATCAAGATAAAATATTTTCCTAAGAA
Found at i:17349387 original size:19 final size:20
Alignment explanation
Indices: 17349353--17349390 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
17349343 GAAGAAGACC
17349353 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
17349373 AGCTGCTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
17349391 GTATTTATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:17352926 original size:27 final size:29
Alignment explanation
Indices: 17352891--17352948 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 29
17352881 GACAAGTGTT
*
17352891 CTGGTGGTGA-AAAATTACAATTTTGCCC
1 CTGGTGGTGACAAAATTACAATTTTACCC
*
17352919 CTGG-GGTGACAAAATTACTATTTTACCC
1 CTGGTGGTGACAAAATTACAATTTTACCC
17352947 CT
1 CT
17352949 ATACTTCGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (29 bp):
CTGGTGGTGACAAAATTACAATTTTACCC
Found at i:17357257 original size:46 final size:47
Alignment explanation
Indices: 17357160--17357275 Score: 198
Period size: 46 Copynumber: 2.5 Consensus size: 47
17357150 AATAAATTGA
* *
17357160 AATGAACAAATAGTAAATCAAAGTAAAGATATTTTCCTAAGTCAAAT
1 AATGAACAAATAATAAATCAAAGTAAAGAAATTTTCCTAAGTCAAAT
*
17357207 AATGAACAAATAATAAATCTAAGTAAA-AAATTTTCCTAAGTCAAAT
1 AATGAACAAATAATAAATCAAAGTAAAGAAATTTTCCTAAGTCAAAT
17357253 AATGAACAAATAATAAATCAAAG
1 AATGAACAAATAATAAATCAAAG
17357276 CATGAACATT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
46 40 0.62
47 25 0.38
ACGTcount: A:0.55, C:0.10, G:0.09, T:0.26
Consensus pattern (47 bp):
AATGAACAAATAATAAATCAAAGTAAAGAAATTTTCCTAAGTCAAAT
Found at i:17357595 original size:32 final size:33
Alignment explanation
Indices: 17357517--17357597 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
17357507 GAAATGAGCT
*
17357517 TTTTACGAGATCAAGCGAAACCCTCACAATACA
1 TTTTACGAGATCAAGCGAAACCCACACAATACA
* * *
17357550 TTTTA-TAGGATCAAGTGAAACCCACACATTAC-
1 TTTTACGA-GATCAAGCGAAACCCACACAATACA
*
17357582 TTTTACGAAATCAAGC
1 TTTTACGAGATCAAGC
17357598 ATAACCCTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
32 12 0.31
33 27 0.69
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.26
Consensus pattern (33 bp):
TTTTACGAGATCAAGCGAAACCCACACAATACA
Found at i:17361338 original size:37 final size:34
Alignment explanation
Indices: 17361288--17361375 Score: 88
Period size: 37 Copynumber: 2.4 Consensus size: 34
17361278 TTACAAAGTA
17361288 CAAAACAATAAATTGCTC-TCAACACTTGTACCATGAG
1 CAAAA-AATAAATTGCTCAT-AACACTTG--CCATGAG
**
17361325 CAAAAAATTAAATTGCTCATGGCACTTGCCATGAG
1 CAAAAAA-TAAATTGCTCATAACACTTGCCATGAG
*
17361360 CAACAAACTAAATTGC
1 CAA-AAAATAAATTGC
17361376 ACATGGTGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
35 18 0.40
36 5 0.11
37 21 0.47
38 1 0.02
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (34 bp):
CAAAAAATAAATTGCTCATAACACTTGCCATGAG
Found at i:17371828 original size:59 final size:60
Alignment explanation
Indices: 17371765--17371914 Score: 196
Period size: 59 Copynumber: 2.5 Consensus size: 60
17371755 TCTTATCTAA
* *
17371765 TCGTGGGAACTCCCCATGCCACCAAATATAAATCGAAACTTCAAGTCCCC-TTTACGTAC
1 TCGTGGGAACTCCCCAAGCCACCAAATATAAATCGAAACTTCAAGTCCCCATTTACCTAC
* * * *
17371824 TCGTGAGAATTCCCCAAGCCACCAAATATTAATCGAGACTTCAAGTCCCCATTTACCTAC
1 TCGTGGGAACTCCCCAAGCCACCAAATATAAATCGAAACTTCAAGTCCCCATTTACCTAC
* * *
17371884 TCATGGAAACACCCCACA-CCACCAAATATAA
1 TCGTGGGAACTCCCCA-AGCCACCAAATATAA
17371915 GTTGAGGCTT
Statistics
Matches: 77, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 45 0.58
60 31 0.40
61 1 0.01
ACGTcount: A:0.34, C:0.33, G:0.11, T:0.22
Consensus pattern (60 bp):
TCGTGGGAACTCCCCAAGCCACCAAATATAAATCGAAACTTCAAGTCCCCATTTACCTAC
Found at i:17374372 original size:19 final size:20
Alignment explanation
Indices: 17374348--17374385 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
17374338 TATTTTACCA
*
17374348 TAGTTAGTTTACT-CTTGTT
1 TAGTTAGTTAACTGCTTGTT
17374367 TAGTTAGTTAACTGCTTGT
1 TAGTTAGTTAACTGCTTGT
17374386 ATATAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (20 bp):
TAGTTAGTTAACTGCTTGTT
Found at i:17377763 original size:70 final size:70
Alignment explanation
Indices: 17377679--17377859 Score: 176
Period size: 70 Copynumber: 2.6 Consensus size: 70
17377669 TTATTTTTTG
* *
17377679 AATATTAATAATTGAAATTTTAAATATTAATATTTTATTTTTAAAATATT-AATAATTGA-TTAT
1 AATATTAATAATTGAAATTTTAAATATTAATATTTTATTTAT-AAATATTAAAT-ATTGACAT-T
17377742 TTATTTAA
63 TTATTTAA
* * * * *
17377750 AATATTAAT-ATTGATCA-TTTAAATATTGACATTTTATTTATAATTTTTAAATATTGACATTTT
1 AATATTAATAATTGA-AATTTTAAATATTAATATTTTATTTATAAATATTAAATATTGACATTTT
*
17377813 ATTTAT
65 ATTTAA
* *
17377819 AAT-TTAATCATT-AATATTGTAAAATATTAATATTTTATTTA
1 AATATTAATAATTGAA-ATT-TTAAATATTAATATTTTATTTA
17377860 ATTTAAATAT
Statistics
Matches: 91, Mismatches: 12, Indels: 15
0.77 0.10 0.13
Matches are distributed among these distances:
68 7 0.08
69 25 0.27
70 49 0.54
71 10 0.11
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.52
Consensus pattern (70 bp):
AATATTAATAATTGAAATTTTAAATATTAATATTTTATTTATAAATATTAAATATTGACATTTTA
TTTAA
Found at i:17377769 original size:22 final size:22
Alignment explanation
Indices: 17377679--17377776 Score: 83
Period size: 22 Copynumber: 4.3 Consensus size: 22
17377669 TTATTTTTTG
* *
17377679 AATATTAATAATTGAAATTTTA
1 AATATTAATAATTGATATTTAA
* * *
17377701 AATATTAATATTTTATTTTTAA
1 AATATTAATAATTGATATTTAA
17377723 AATATTAATAATTGATTATTTATTTAA
1 AATATTAATAATTG---A--TATTTAA
17377750 AATATTAAT-ATTGATCATTT-A
1 AATATTAATAATTGAT-ATTTAA
17377771 AATATT
1 AATATT
17377777 GACATTTTAT
Statistics
Matches: 62, Mismatches: 8, Indels: 13
0.75 0.10 0.16
Matches are distributed among these distances:
21 8 0.13
22 33 0.53
23 1 0.02
25 1 0.02
26 4 0.06
27 15 0.24
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
AATATTAATAATTGATATTTAA
Found at i:17377785 original size:15 final size:15
Alignment explanation
Indices: 17377756--17377813 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
17377746 TTAAAATATT
17377756 AATATTGATCA-TTTA
1 AATATTGA-CATTTTA
17377771 AATATTGACATTTTA
1 AATATTGACATTTTA
**
17377786 TTTA-T-A-ATTTTTA
1 AATATTGACA-TTTTA
17377799 AATATTGACATTTTA
1 AATATTGACATTTTA
17377814 TTTATAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
12 1 0.03
13 8 0.24
14 4 0.12
15 20 0.59
16 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (15 bp):
AATATTGACATTTTA
Found at i:17377802 original size:28 final size:28
Alignment explanation
Indices: 17377767--17377823 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
17377757 ATATTGATCA
17377767 TTTAAATATTGACATTTTATTTATAATT
1 TTTAAATATTGACATTTTATTTATAATT
17377795 TTTAAATATTGACATTTTATTTATAATT
1 TTTAAATATTGACATTTTATTTATAATT
17377823 T
1 T
17377824 AATCATTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (28 bp):
TTTAAATATTGACATTTTATTTATAATT
Found at i:17378003 original size:133 final size:131
Alignment explanation
Indices: 17377789--17378080 Score: 321
Period size: 133 Copynumber: 2.2 Consensus size: 131
17377779 CATTTTATTT
* * *
17377789 ATAATT-TTTA-AATATTGACATTTTATTTATAATTTAATCATTAATATTGTAAAATATTAATAT
1 ATAATTATTTATAATATTAATATTTTATTTATAATTTAA-CATTAATATTATAAAATATTAATAT
*
17377852 TTTATTTAATTTAAATATTATTATGATCAATTA-TTTTATTTTATTTTA-TTTTTAGATATTAAT
65 TTTATTTAATTT-AA-A-TATTATGATCAATTATTTTTATTTTATTTTATTTTTTAAATATTAAT
17377915 AATAG
127 AATAG
* *
17377920 ATAATTATTTATAATATTAATATTTTATTTATAATTTAA-A-T-GT-TTATAAAATATTCATATT
1 ATAATTATTTATAATATTAATATTTTATTTATAATTTAACATTAATATTATAAAATATTAATATT
* *
17377981 TTATTTATAATTTAAATGATATTATGATTATTTATTTTTATTTTATTTTATTTTTTAAATATTAA
66 TTA-TT-TAATTT-AA--ATATTATGATCAATTATTTTTATTTTATTTTATTTTTTAAATATTAA
* **
17378046 TATTTT
126 TAATAG
* *
17378052 ATAGTTTATTTATAATATTAATAATTTAT
1 ATA-ATTATTTATAATATTAATATTTTAT
17378081 CATTTAAATA
Statistics
Matches: 139, Mismatches: 14, Indels: 14
0.83 0.08 0.08
Matches are distributed among these distances:
128 19 0.14
129 3 0.02
130 23 0.17
131 23 0.17
132 23 0.17
133 48 0.35
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.57
Consensus pattern (131 bp):
ATAATTATTTATAATATTAATATTTTATTTATAATTTAACATTAATATTATAAAATATTAATATT
TTATTTAATTTAAATATTATGATCAATTATTTTTATTTTATTTTATTTTTTAAATATTAATAATA
G
Found at i:17378015 original size:159 final size:152
Alignment explanation
Indices: 17377852--17378416 Score: 439
Period size: 159 Copynumber: 3.7 Consensus size: 152
17377842 ATATTAATAT
* *
17377852 TTTATTTAATTTAAATATTATTATGATCAATTATTTTATTTTATTTTATTTTTAGATATTAATAA
1 TTTATTTAATTT--ATATTATTATGTTTAA-TATTTTATTTTATTTTATTTTTA-ATATTAATAA
* * *
17377917 TAGATAATTATTTATAATATTAATATTTTATTTATAATTTAA-ATGTTTATAAAATATTCATATT
62 TAG-T-ATCATTTA-AATATTAATATTTTATTTATAATTTAACAT-TTTATAAAATACTAATATT
*
17377981 TTATTTATAATTTAAATGATATTATGATTA
123 TTATTTATAATTTAAATGTTATTATGATTA
* * * *
17378011 TTTATTTTTATTT-TATT-TTATTTTTTAAATATTAATATTTTATAGTTTATTTATAATATTAAT
1 TTTA-TTTAATTTATATTATTA-TGTTT-AATATT-TTATTTTAT--TTTATTTTTAATATTAAT
* * * *
17378074 AAT-TTATCATTTAAATATTCATATTTTATTTATAATTTAATCACTAATCTT-TTAAATACTAAG
60 AATAGTATCATTTAAATATTAATATTTTATTTATAATTTAA-CA-T--T-TTATAAAATACTAAT
*
17378137 ATTTTATTTGTAATTTAAATGTTATTATGATTA
120 ATTTTATTTATAATTTAAATGTTATTATGATTA
* * * * * ** *
17378170 TTTATTCTTATTT-TATT-TTATTGTTTAA-ATGTGA--ATAATTTATTTAAAATATTAATGATA
1 TTTATT-TAATTTATATTATTA-TGTTTAATATTTTATTTTATTTTATTTTTAATATTAATAATA
* * *
17378230 G-ATCATTCAAATATTAATATTTTATTAATAATTTAATCATTTCATAAAATACTAATATTTTATT
64 GTATCATTTAAATATTAATATTTTATTTATAATTTAA-CATTTTATAAAATACTAATATTTTATT
*
17378294 TATAATTTAAATGTTATTCTGATTA
128 TATAATTTAAATGTTATTATGATTA
* * * * *
17378319 TTTATTTATATTT-TA-T-TT-T-TTAAATAGTAATAATTTATAATTTA--TTTAA-ATTATTAA
1 TTTATTTA-ATTTATATTATTATGTTTAATA-T-TTTATTT-TATTTTATTTTTAATATTAATAA
* *
17378376 TAAGCAATAATTTAAATATTAATATTTTATTTATAATTTAA
62 T-AG-TATCATTTAAATATTAATATTTTATTTATAATTTAA
17378417 ATATTATTAA
Statistics
Matches: 337, Mismatches: 45, Indels: 56
0.77 0.10 0.13
Matches are distributed among these distances:
145 4 0.01
146 2 0.01
147 1 0.00
148 14 0.04
149 59 0.18
151 40 0.12
152 54 0.16
154 2 0.01
155 26 0.08
156 11 0.03
157 14 0.04
158 15 0.04
159 77 0.23
160 18 0.05
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (152 bp):
TTTATTTAATTTATATTATTATGTTTAATATTTTATTTTATTTTATTTTTAATATTAATAATAGT
ATCATTTAAATATTAATATTTTATTTATAATTTAACATTTTATAAAATACTAATATTTTATTTAT
AATTTAAATGTTATTATGATTA
Found at i:17378025 original size:170 final size:158
Alignment explanation
Indices: 17377978--17378416 Score: 464
Period size: 159 Copynumber: 2.9 Consensus size: 158
17377968 AAATATTCAT
* *
17377978 ATTTTATTTATAATTTAAATGATATTATGATTATTTATTTTTATTTTATTTTATTTTTTAAATAT
1 ATTTTATTTATAATTTAAATGATATTATGATTATTTATTCTTATTTTATTTAATTTTTTAAATAT
* * *
17378043 TAATATTTTATAGTTTATTTATAATATTAATAATTTATCATTTAAATATTCATATTTTATTTATA
66 CAATATTTTATAGTTTATTTATAATATTAATAATTAATCATTTAAATATTAATATTTTATTTATA
*
17378108 ATTTAATCACTAATCTTTTAAATACTAAG
131 ATTTAA-CACTAATCTTTAAAATACTAAG
* * * * *
17378137 ATTTTATTTGTAATTTAAATGTTATTATGATTATTTATTCTTATTTTATTTTATTGTTTAAATGT
1 ATTTTATTTATAATTTAAATGATATTATGATTATTTATTCTTATTTTATTTAATTTTTTAAATAT
* * * * *
17378202 -GA-A---TA-A-TTTATTTAAAATATTAATGA-TAGATCATTCAAATATTAATATTTTATTAAT
66 CAATATTTTATAGTTTATTTATAATATTAATAATTA-ATCATTTAAATATTAATATTTTATTTAT
* * *
17378259 AATTTAATCA-T-TTC-ATAAAATACTAAT
130 AATTTAA-CACTAATCTTTAAAATACTAAG
* * *
17378286 ATTTTATTTATAATTTAAATGTTATTCTGATTATTTA-T-TTA---TATTTTATTTTTTAAATAG
1 ATTTTATTTATAATTTAAATGATATTATGATTATTTATTCTTATTTTATTTAATTTTTTAAATA-
* * ** *
17378346 T-AATAATTTATAATTTATTTA-AATTATTAATAAGCAATAATTTAAATATTAATATTTTATTTA
65 TCAATATTTTATAGTTTATTTATAA-TATTAATAATTAATCATTTAAATATTAATATTTTATTTA
17378409 TAATTTAA
129 TAATTTAA
17378417 ATATTATTAA
Statistics
Matches: 244, Mismatches: 26, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
144 16 0.07
145 2 0.01
146 1 0.00
147 3 0.01
148 1 0.00
149 47 0.19
150 5 0.02
151 50 0.20
152 54 0.22
153 1 0.00
154 2 0.01
157 1 0.00
158 1 0.00
159 60 0.25
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (158 bp):
ATTTTATTTATAATTTAAATGATATTATGATTATTTATTCTTATTTTATTTAATTTTTTAAATAT
CAATATTTTATAGTTTATTTATAATATTAATAATTAATCATTTAAATATTAATATTTTATTTATA
ATTTAACACTAATCTTTAAAATACTAAG
Found at i:17378049 original size:22 final size:22
Alignment explanation
Indices: 17378024--17378104 Score: 81
Period size: 22 Copynumber: 3.5 Consensus size: 22
17378014 ATTTTTATTT
17378024 TATTTTATTTTTTAAATATTAA
1 TATTTTATTTTTTAAATATTAA
17378046 TATTTTATAGTTTATTTATAATATTAA
1 TA-TTT-TA-TTT-TTTA-AATATTAA
* ** *
17378073 TAATTTATCATTTAAATATTCA
1 TATTTTATTTTTTAAATATTAA
17378095 TATTTTATTT
1 TATTTTATTT
17378105 ATAATTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
22 16 0.34
23 7 0.15
24 3 0.06
25 5 0.11
26 6 0.13
27 10 0.21
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (22 bp):
TATTTTATTTTTTAAATATTAA
Found at i:17378049 original size:27 final size:26
Alignment explanation
Indices: 17378019--17378086 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
17378009 TATTTATTTT
*
17378019 TATTTTAT-TTTATTTTTTAAATATTAA
1 TATTTTATATTTA-TTTAT-AATATTAA
17378046 TATTTTATAGTTTATTTATAATATTAA
1 TATTTTATA-TTTATTTATAATATTAA
*
17378073 TAATTTATCATTTA
1 TATTTTAT-ATTTA
17378087 AATATTCATA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 27 0.75
28 5 0.14
29 4 0.11
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (26 bp):
TATTTTATATTTATTTATAATATTAA
Found at i:17378128 original size:41 final size:41
Alignment explanation
Indices: 17378056--17378154 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
17378046 TATTTTATAG
* * * * *
17378056 TTTATTTATAATATTAATAATTTATCATTTAAATATTCATAT
1 TTTATTTATAAT-TTAATAACTAATCATTTAAATACTAAGAT
* *
17378098 TTTATTTATAATTTAATCACTAATCTTTTAAATACTAAGAT
1 TTTATTTATAATTTAATAACTAATCATTTAAATACTAAGAT
*
17378139 TTTATTTGTAATTTAA
1 TTTATTTATAATTTAA
17378155 ATGTTATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 37 0.76
42 12 0.24
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.54
Consensus pattern (41 bp):
TTTATTTATAATTTAATAACTAATCATTTAAATACTAAGAT
Found at i:17378501 original size:108 final size:111
Alignment explanation
Indices: 17378276--17378530 Score: 347
Period size: 113 Copynumber: 2.3 Consensus size: 111
17378266 TCATTTCATA
* * **
17378276 AAATACTAATATTTTATTTATAATTTAAATGTTATTCTGATTATTTATTTATATTTTATTTTTTA
1 AAATATTAATATTTTATTTATAATTTAAATATTATTAAGATTATTTATTTATATTTTATTTTTTA
* *
17378341 AATAGTAATAATTTATAATTTATTTAAATTATTAATAAGCAATAATTT
66 AATAG-AAT-ATTTATAATTTATTTAAAATATTAATAAGCAATAACTT
*
17378389 AAATATTAATATTTTATTTATAATTTAAATATTATTAAGATTATTTATTTTTATTTTATTTTTTC
1 AAATATTAATATTTTATTTATAATTTAAATATTATTAAGATTATTTATTTATATTTTATTTTTT-
*** *
17378454 AAA-AG-AT-TTT-TAATTTATTTAAAATATTAATAATTGATTACTT
65 AAATAGAATATTTATAATTTATTTAAAATATTAATAAGCAATAACTT
*
17378497 AAATATTAATATTTTATTTATAATTTAATTATTA
1 AAATATTAATATTTTATTTATAATTTAAATATTA
17378531 ATATTTTCAT
Statistics
Matches: 129, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
108 60 0.47
109 3 0.02
111 2 0.02
113 61 0.47
114 3 0.02
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (111 bp):
AAATATTAATATTTTATTTATAATTTAAATATTATTAAGATTATTTATTTATATTTTATTTTTTA
AATAGAATATTTATAATTTATTTAAAATATTAATAAGCAATAACTT
Found at i:17390237 original size:2 final size:2
Alignment explanation
Indices: 17390230--17390254 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17390220 TTTTATGATG
17390230 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
17390255 TTGAGGATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17391638 original size:20 final size:20
Alignment explanation
Indices: 17391610--17391653 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
17391600 GAGTGCTTTC
*
17391610 TTTGAATTATAGTGCTGCTA
1 TTTGAATTATAATGCTGCTA
*
17391630 TTTGGATTATAATGCTGCTA
1 TTTGAATTATAATGCTGCTA
17391650 TTTG
1 TTTG
17391654 CTGTTGTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.48
Consensus pattern (20 bp):
TTTGAATTATAATGCTGCTA
Found at i:17393205 original size:2 final size:2
Alignment explanation
Indices: 17393200--17393231 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17393190 AAAAATAAGA
*
17393200 AT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17393232 TGGCTTGCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:17395652 original size:2 final size:2
Alignment explanation
Indices: 17395645--17395745 Score: 122
Period size: 2 Copynumber: 51.5 Consensus size: 2
17395635 CTGTTAAATA
17395645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
17395687 AT AT AT AT AT AT -T AT AT GT AT -T GAT A- AGT A- AT AT -T NAT
1 AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A-T AT AT AT AT -AT
*
17395725 AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT A
17395746 GGCATAAATA
Statistics
Matches: 87, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
1 5 0.06
2 79 0.91
3 3 0.03
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17396261 original size:15 final size:15
Alignment explanation
Indices: 17396241--17396309 Score: 129
Period size: 15 Copynumber: 4.6 Consensus size: 15
17396231 TTTACAATGC
*
17396241 AATGTGATTACAGGT
1 AATGTGATTACAAGT
17396256 AATGTGATTACAAGT
1 AATGTGATTACAAGT
17396271 AATGTGATTACAAGT
1 AATGTGATTACAAGT
17396286 AATGTGATTACAAGT
1 AATGTGATTACAAGT
17396301 AATGTGATT
1 AATGTGATT
17396310 GTAAGGAGAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
15 53 1.00
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.35
Consensus pattern (15 bp):
AATGTGATTACAAGT
Found at i:17396276 original size:30 final size:30
Alignment explanation
Indices: 17396232--17396309 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
17396222 TGCTGTTACT
* *
17396232 TTACAATGCAATGTGATTACAGGTAATGTGA
1 TTACAA-GTAATGTGATTACAAGTAATGTGA
17396263 TTACAAGTAATGTGATTACAAGTAATGTGA
1 TTACAAGTAATGTGATTACAAGTAATGTGA
17396293 TTACAAGTAATGTGATT
1 TTACAAGTAATGTGATT
17396310 GTAAGGAGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 39 0.87
31 6 0.13
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.35
Consensus pattern (30 bp):
TTACAAGTAATGTGATTACAAGTAATGTGA
Found at i:17396565 original size:33 final size:33
Alignment explanation
Indices: 17396528--17396614 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
17396518 TTTTGATGTC
**
17396528 ATATATTTTATTTTTATTTTTTATTATAATATT
1 ATATATTTTATTTTTATTTTTTAAAATAATATT
* *
17396561 ATATACTTTATTTTTATTTTTTAAAATAATTTT
1 ATATATTTTATTTTTATTTTTTAAAATAATATT
* *
17396594 TTATATTATATATTTTATTTT
1 ATATATTTTAT-TTTTATTTT
17396615 AATTTCTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 37 0.80
34 9 0.20
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (33 bp):
ATATATTTTATTTTTATTTTTTAAAATAATATT
Found at i:17396660 original size:15 final size:14
Alignment explanation
Indices: 17396640--17396721 Score: 60
Period size: 15 Copynumber: 5.6 Consensus size: 14
17396630 TATTATATAA
17396640 ATTTTAATTTTTTAT
1 ATTTTAATTTTTT-T
*
17396655 ATTTTATTTTATTTT
1 ATTTTAATTT-TTTT
* *
17396670 AATTTCTAATTCTTAT
1 -ATTT-TAATTTTTTT
* *
17396686 ATTAT-A-TATTTT
1 ATTTTAATTTTTTT
17396698 ATTTTAATATTTTTT
1 ATTTTAAT-TTTTTT
17396713 ATTTTAATT
1 ATTTTAATT
17396722 ATAATATTAT
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
12 8 0.15
13 2 0.04
14 2 0.04
15 26 0.50
16 10 0.19
17 4 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (14 bp):
ATTTTAATTTTTTT
Found at i:17396672 original size:55 final size:53
Alignment explanation
Indices: 17396587--17396718 Score: 167
Period size: 55 Copynumber: 2.4 Consensus size: 53
17396577 TTTTTTAAAA
*
17396587 TAATTTTTTATATTATATATTTTATTTTAATTTCTTATACCTATATTATATAAATTT
1 TAATTTTTTATATT-T-TATTTTATTTTAATTTCTAATACCTATATTATAT--ATTT
* *
17396644 TAATTTTTTATATTTTATTTTATTTTAATTTCTAATTCTTATATTATATATTT
1 TAATTTTTTATATTTTATTTTATTTTAATTTCTAATACCTATATTATATATTT
* *
17396697 T-ATTTTAATATTTTTTATTTTA
1 TAATTTT-TTATATTTTATTTTA
17396719 ATTATAATAT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
52 5 0.07
53 18 0.26
55 31 0.45
56 1 0.01
57 14 0.20
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (53 bp):
TAATTTTTTATATTTTATTTTATTTTAATTTCTAATACCTATATTATATATTT
Found at i:17399156 original size:38 final size:38
Alignment explanation
Indices: 17399105--17399180 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
17399095 TGATAGATTT
*
17399105 GTATCGTTATGGATATGTTCATCCCT-ATGAGTGTCATG
1 GTATCATTATGGATATGTTCAT-CCTGATGAGTGTCATG
*
17399143 GTATCATTGTGGATATGTTCATCCTGATGAGTGTCATG
1 GTATCATTATGGATATGTTCATCCTGATGAGTGTCATG
17399181 AGAAGGAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.21, C:0.14, G:0.25, T:0.39
Consensus pattern (38 bp):
GTATCATTATGGATATGTTCATCCTGATGAGTGTCATG
Found at i:17400558 original size:7 final size:7
Alignment explanation
Indices: 17400543--17400581 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
17400533 TTGTGCCATC
*
17400543 AACCTTA
1 AACCCTA
17400550 AACCCTA
1 AACCCTA
17400557 AACCCTA
1 AACCCTA
*
17400564 AACCCTG
1 AACCCTA
17400571 AACCCTGA
1 AACCCT-A
17400579 AAC
1 AAC
17400582 TAAGAAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
7 25 0.89
8 3 0.11
ACGTcount: A:0.41, C:0.38, G:0.05, T:0.15
Consensus pattern (7 bp):
AACCCTA
Done.