Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 77 of 144
Found at i:17134533 original size:18 final size:20
Alignment explanation
Indices: 17134507--17134544 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
17134497 ATAAAAATAT
*
17134507 TTTTTAATA-TTTTA-TTAA
1 TTTTAAATAGTTTTACTTAA
17134525 TTTTAAATAGTTTTACTTAA
1 TTTTAAATAGTTTTACTTAA
17134545 AGGATGACAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 5 0.29
20 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTAAATAGTTTTACTTAA
Found at i:17139807 original size:26 final size:25
Alignment explanation
Indices: 17139748--17139808 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
17139738 AATTATAAAT
* *
17139748 ATATAATATGATATATATAAATTTAA
1 ATATAATAT-AAATACATAAATTTAA
* *
17139774 AAAT-ATATAAATACATACAATTTTA
1 ATATAATATAAATACATA-AATTTAA
17139799 ATATAATATA
1 ATATAATATA
17139809 TATAAAAGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
24 7 0.25
25 13 0.46
26 8 0.29
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATAATATAAATACATAAATTTAA
Found at i:17139966 original size:44 final size:44
Alignment explanation
Indices: 17139918--17140003 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 44
17139908 AATAAATTAA
* * *
17139918 AATTTGAGATAATTATACATTTAAAAATATTTATAGTTTAATAT
1 AATTTGAGATAATTACACATTTAAAAATAATTATAATTTAATAT
*
17139962 AATTTGTGATAATTACACATTTAAAAATAATTATAATTTAAT
1 AATTTGAGATAATTACACATTTAAAAATAATTATAATTTAAT
17140004 TTATAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (44 bp):
AATTTGAGATAATTACACATTTAAAAATAATTATAATTTAATAT
Found at i:17145802 original size:21 final size:21
Alignment explanation
Indices: 17145770--17145812 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
17145760 TTAAAAGAAA
*
17145770 TAAAAAAGAAAGGATTCAATT
1 TAAAAAAGAAAGGATTAAATT
*
17145791 TAAAAATA-AAAGGGTTAAATT
1 TAAAAA-AGAAAGGATTAAATT
17145812 T
1 T
17145813 TAACAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (21 bp):
TAAAAAAGAAAGGATTAAATT
Found at i:17147790 original size:17 final size:17
Alignment explanation
Indices: 17147756--17147790 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17147746 CTCCCCAATA
**
17147756 TATTTCTTTCATCTAGG
1 TATTTCTTTCATAGAGG
17147773 TATTTCTTTCATAGAGG
1 TATTTCTTTCATAGAGG
17147790 T
1 T
17147791 TTCATTTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.14, G:0.14, T:0.51
Consensus pattern (17 bp):
TATTTCTTTCATAGAGG
Found at i:17148800 original size:16 final size:15
Alignment explanation
Indices: 17148779--17148819 Score: 50
Period size: 16 Copynumber: 2.8 Consensus size: 15
17148769 AGAAGGTTTA
17148779 AAAAATTTGAGATTTT
1 AAAAATTTGAGA-TTT
*
17148795 AAAAATTTCAG-TTT
1 AAAAATTTGAGATTT
17148809 -AAAATTTGAGA
1 AAAAATTTGAGA
17148820 AGAAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 9 0.41
14 3 0.14
16 10 0.45
ACGTcount: A:0.46, C:0.02, G:0.12, T:0.39
Consensus pattern (15 bp):
AAAAATTTGAGATTT
Found at i:17149938 original size:48 final size:48
Alignment explanation
Indices: 17149873--17149979 Score: 151
Period size: 48 Copynumber: 2.2 Consensus size: 48
17149863 TTAGGTGAGA
* * * *
17149873 GTTTAGATAAGGGCAATCCTATCAAAAGTAGCTCAGATATAAGAGAGG
1 GTTTAGATAAGAGCAATCCTATCAAAAGCAGCCCAAATATAAGAGAGG
* * *
17149921 GTTTAAATAAGAGCAATCCTGTCAATAGCAGCCCAAATATAAGAGAGG
1 GTTTAGATAAGAGCAATCCTATCAAAAGCAGCCCAAATATAAGAGAGG
17149969 GTTTAGATAAG
1 GTTTAGATAAG
17149980 GGTGTGAATA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (48 bp):
GTTTAGATAAGAGCAATCCTATCAAAAGCAGCCCAAATATAAGAGAGG
Found at i:17150084 original size:27 final size:28
Alignment explanation
Indices: 17150031--17150104 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 28
17150021 ATGTAGTGGT
17150031 GAAGCT-TTTCAAAAGGGAG---GGGAG
1 GAAGCTGTTTCAAAAGGGAGATAGGGAG
17150055 GAAGCTGTTTC-AAAGGGAGATAGGGAG
1 GAAGCTGTTTCAAAAGGGAGATAGGGAG
* * *
17150082 GAAGTTG-TTCTAGAGGGAGATAG
1 GAAGCTGTTTCAAAAGGGAGATAG
17150105 TGATAGTGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 14 0.33
25 4 0.09
26 3 0.07
27 22 0.51
ACGTcount: A:0.32, C:0.07, G:0.41, T:0.20
Consensus pattern (28 bp):
GAAGCTGTTTCAAAAGGGAGATAGGGAG
Found at i:17155377 original size:24 final size:24
Alignment explanation
Indices: 17155329--17155385 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
17155319 GAACTGGGCT
* *
17155329 TTTCTTTTAGGTATTTCGGGTTTG
1 TTTCTTTTGGGTATTTAGGGTTTG
*
17155353 TTTCCTTTTGGGTTTTTAGGG-TTG
1 TTT-CTTTTGGGTATTTAGGGTTTG
17155377 TTTCTTTTG
1 TTTCTTTTG
17155386 ACCTGTTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.21
24 9 0.31
25 14 0.48
ACGTcount: A:0.05, C:0.09, G:0.25, T:0.61
Consensus pattern (24 bp):
TTTCTTTTGGGTATTTAGGGTTTG
Found at i:17155661 original size:53 final size:53
Alignment explanation
Indices: 17155601--17155702 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 53
17155591 TGAAAAAAAT
* * * * * *
17155601 TTATTAAAAACTAAAATTGACTTTTGAATTTGTTAAGTAATTGAAAATTTAGA
1 TTATTAAAAACTAAAATTGACTCTAGAATTTATAAAGGAAATGAAAATTTAGA
17155654 TTATTAAAAACTAAAATTGACTCTAGAATTTATAAAGGAAATGAAAATT
1 TTATTAAAAACTAAAATTGACTCTAGAATTTATAAAGGAAATGAAAATT
17155703 AAAATTGAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 43 1.00
ACGTcount: A:0.47, C:0.05, G:0.11, T:0.37
Consensus pattern (53 bp):
TTATTAAAAACTAAAATTGACTCTAGAATTTATAAAGGAAATGAAAATTTAGA
Found at i:17155707 original size:37 final size:37
Alignment explanation
Indices: 17155660--17155745 Score: 100
Period size: 37 Copynumber: 2.3 Consensus size: 37
17155650 TAGATTATTA
* *
17155660 AAAACTAAAATTGACTCTAGAATTTATAAAGGAAATG
1 AAAATTAAAATTGAATCTAGAATTTATAAAGGAAATG
* * * *
17155697 AAAATTAAAATTGAATTTTGAATTTATAAAGTAACTG
1 AAAATTAAAATTGAATCTAGAATTTATAAAGGAAATG
* *
17155734 AGAATTTAAATT
1 AAAATTAAAATT
17155746 AAAGCAATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.34
Consensus pattern (37 bp):
AAAATTAAAATTGAATCTAGAATTTATAAAGGAAATG
Found at i:17160525 original size:46 final size:45
Alignment explanation
Indices: 17160469--17160717 Score: 187
Period size: 46 Copynumber: 5.7 Consensus size: 45
17160459 TAATGTCTTC
* **
17160469 AATCTACCCCTCTTGACTTAGGAATAAAAGATTGGATGGTGGCTTT
1 AATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGCTTT
* * * *
17160515 AATCTGCCCCTCTTGACTTAGGGGCAAAAGATTGAATGATGGTTTT
1 AATCTGCCCCTCTTGA-TTAGGGGTAAAAGATTGGATGGTGGCTTT
* * * *
17160561 AATTTGCCCTTACTGGATTAGGGGTAAAAGATTGGA--G-GGCTTC
1 AATCTGCCCCT-CTTGATTAGGGGTAAAAGATTGGATGGTGGCTTT
* * * * * *
17160604 AATTTGCCCCTCTAGATTAGGGGTAGAAGACT-G-T-ATGGCTTC
1 AATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGCTTT
* * * *
17160646 AATCTGCCCCTACTAGATTAAGGG-AAAAGATTGGA---TGACTTC
1 AATCTGCCCCT-CTTGATTAGGGGTAAAAGATTGGATGGTGGCTTT
17160688 AATCTGCCCCT-TTAGATTAGGGGTAAAAGA
1 AATCTGCCCCTCTT-GATTAGGGGTAAAAGA
17160718 CTTGATGACT
Statistics
Matches: 168, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
40 1 0.01
41 9 0.05
42 63 0.38
43 26 0.15
46 65 0.39
47 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (45 bp):
AATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGATGGTGGCTTT
Found at i:17160644 original size:42 final size:43
Alignment explanation
Indices: 17160565--17160817 Score: 242
Period size: 42 Copynumber: 6.0 Consensus size: 43
17160555 GGTTTTAATT
* * * * * *
17160565 TGCCCTTACTGGATTAGGGGTAAAAGATTGGAGGGCTTCAATT
1 TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAATC
* * *
17160608 TGCCCCT-CTAGATTAGGGGTAGAAGACTGTATGGCTTCAATC
1 TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAATC
* *
17160650 TGCCCCTACTAGATTAAGGG-AAAAGATTGGATGACTTCAATC
1 TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAATC
* *
17160692 TGCCCCT-TTAGATTAGGGGTAAAAGACTTGATGACTTCAATC
1 TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAATC
* * * * * ** *
17160734 TGACCCTATTGGGTCAAAGGTAAAAGATTGGATGACTTCAATC
1 TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAATC
* * * * * *
17160777 TACCTCTACTGGATTAGGGGTAAATGATTGGATGGCTTCAA
1 TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAA
17160818 AAAGATTGAA
Statistics
Matches: 173, Mismatches: 34, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
41 10 0.06
42 87 0.50
43 76 0.44
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (43 bp):
TGCCCCTACTAGATTAGGGGTAAAAGACTGGATGACTTCAATC
Found at i:17160688 original size:84 final size:83
Alignment explanation
Indices: 17160515--17160817 Score: 275
Period size: 84 Copynumber: 3.5 Consensus size: 83
17160505 TGGTGGCTTT
* * * * * * *
17160515 AATCTGCCCCTCTTGACTTAGGGGCAAAAGATTGAATGATGGTTTTAATTTGCCCTTACTGGATT
1 AATCTGCCCCTCTAGA-TTAGGGG-TAAAGACTG--T-ATGGCTTCAATCTGCCCCTACTGGATT
* * *
17160580 AGGGGTAAAAGATTGGAGGGCTTC
61 AAGGG-AAAAGATTGGATGACTTC
* *
17160604 AATTTGCCCCTCTAGATTAGGGGTAGAAGACTGTATGGCTTCAATCTGCCCCTACTAGATTAAGG
1 AATCTGCCCCTCTAGATTAGGGGTA-AAGACTGTATGGCTTCAATCTGCCCCTACTGGATTAAGG
17160669 GAAAAGATTGGATGACTTC
65 GAAAAGATTGGATGACTTC
* * * * * *
17160688 AATCTGCCCCTTTAGATTAGGGGTAAAAGACT-TGATGACTTCAATCTGACCCTATTGGGTCAAA
1 AATCTGCCCCTCTAGATTAGGGGT-AAAGACTGT-ATGGCTTCAATCTGCCCCTACTGGAT-TAA
*
17160752 GGTAAAAGATTGGATGACTTC
63 GGGAAAAGATTGGATGACTTC
* * * * *
17160773 AATCTACCTCTACTGGATTAGGGGTAAATGATTGGATGGCTTCAA
1 AATCTGCCCCT-CTAGATTAGGGGTAAA-GACTGTATGGCTTCAA
17160818 AAAGATTGAA
Statistics
Matches: 179, Mismatches: 28, Indels: 17
0.80 0.12 0.08
Matches are distributed among these distances:
83 1 0.01
84 65 0.36
85 61 0.34
86 24 0.13
87 1 0.01
88 13 0.07
89 14 0.08
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (83 bp):
AATCTGCCCCTCTAGATTAGGGGTAAAGACTGTATGGCTTCAATCTGCCCCTACTGGATTAAGGG
AAAAGATTGGATGACTTC
Found at i:17160838 original size:62 final size:62
Alignment explanation
Indices: 17160755--17160879 Score: 153
Period size: 62 Copynumber: 2.0 Consensus size: 62
17160745 GGTCAAAGGT
* * * * * *
17160755 AAAAGATTGGATGACTTCAATCTACCTCTACTGGATTAGGGGTAAATGATTGGATGGCTTCA
1 AAAAGATTGAATGACTTCAATCTACCCCTACTAGATTAGAGGTAAAAGATTGAATGGCTTCA
* * *
17160817 AAAAGATTGAAT-AGCTTCAATCTTCCCCTTCTAGATTAGATGTAAAAGATTGAATGGCTTCA
1 AAAAGATTGAATGA-CTTCAATCTACCCCTACTAGATTAGAGGTAAAAGATTGAATGGCTTCA
17160879 A
1 A
17160880 TCTACCTCTA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
61 1 0.02
62 52 0.98
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (62 bp):
AAAAGATTGAATGACTTCAATCTACCCCTACTAGATTAGAGGTAAAAGATTGAATGGCTTCA
Found at i:17160963 original size:45 final size:43
Alignment explanation
Indices: 17160817--17161090 Score: 245
Period size: 43 Copynumber: 6.3 Consensus size: 43
17160807 GATGGCTTCA
* * **
17160817 AAAAGATTGA-ATAGCTTCAATCTTCCCCTTCTAGATTAGATGT
1 AAAAGATTGAGATGGCTTCAATCTACCCC-TCTAGATTAGGGGT
*
17160860 AAAAGATTGA-ATGGCTTCAATCTACCTCTACTAGATTAGGGGT
1 AAAAGATTGAGATGGCTTCAATCTACCCCT-CTAGATTAGGGGT
* * *
17160903 AAAAGACT-AGATGGCTTCAATCTGCCCCTCTTGATTAGGGGT
1 AAAAGATTGAGATGGCTTCAATCTACCCCTCTAGATTAGGGGT
*
17160945 AAAAGATTGAATGATGGCTTCAATCTACCCCTACTAAATTAGGGGT
1 AAAAGATTG-A-GATGGCTTCAATCTACCCCT-CTAGATTAGGGGT
* * * * ** * * *
17160991 AAAAGACTG-GATGACTTTAGTCTGTCCCTCTTGACTAGAGGT
1 AAAAGATTGAGATGGCTTCAATCTACCCCTCTAGATTAGGGGT
* * *
17161033 AAAAGATTGGACGGTAGCTTCAATCTACCCCTCTTA-ACTAGGGGT
1 AAAAGATT-GA-GATGGCTTCAATCTACCCCTC-TAGATTAGGGGT
17161078 AAAAGATTG-GATG
1 AAAAGATTGAGATG
17161091 AGGTGATGTA
Statistics
Matches: 186, Mismatches: 35, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
42 39 0.21
43 76 0.41
44 2 0.01
45 49 0.26
46 20 0.11
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (43 bp):
AAAAGATTGAGATGGCTTCAATCTACCCCTCTAGATTAGGGGT
Found at i:17160979 original size:88 final size:85
Alignment explanation
Indices: 17160830--17161083 Score: 296
Period size: 88 Copynumber: 2.9 Consensus size: 85
17160820 AGATTGAATA
* * * *
17160830 GCTTCAATCTTCCCCTTCTAGATTAGATGTAAAAGATTGA-ATGGCTTCAATCTACCTCTACTAG
1 GCTTCAATCTGCCCC-TCTTGATTAGAGGTAAAAGATTGAGATGGCTTCAATCTACCCCTACTA-
17160894 ATTAGGGGTAAAAGACTAGATG
64 ATTAGGGGTAAAAGACTAGATG
*
17160916 GCTTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGAATGATGGCTTCAATCTACCCCTACTA
1 GCTTCAATCTGCCCCTCTTGATTAGAGGTAAAAGATTG-A-GATGGCTTCAATCTACCCCTACT-
*
17160981 AATTAGGGGTAAAAGACTGGATG
63 AATTAGGGGTAAAAGACTAGATG
* * * * * * *
17161004 ACTTTAGTCTGTCCCTCTTGACTAGAGGTAAAAGATTGGACGGTAGCTTCAATCTACCCCT-CTT
1 GCTTCAATCTGCCCCTCTTGATTAGAGGTAAAAGATT-GA-GATGGCTTCAATCTACCCCTAC-T
*
17161068 AACTAGGGGTAAAAGA
63 AATTAGGGGTAAAAGA
17161084 TTGGATGAGG
Statistics
Matches: 146, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
85 20 0.14
86 15 0.10
87 16 0.11
88 93 0.64
89 2 0.01
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (85 bp):
GCTTCAATCTGCCCCTCTTGATTAGAGGTAAAAGATTGAGATGGCTTCAATCTACCCCTACTAAT
TAGGGGTAAAAGACTAGATG
Found at i:17161975 original size:6 final size:6
Alignment explanation
Indices: 17161966--17162000 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
17161956 CAACCTCTCT
*
17161966 TTTTTC TTTTTC TTTTTC TTTTT- TTTTTT TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
17162001 CTCTTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (6 bp):
TTTTTC
Found at i:17161985 original size:19 final size:17
Alignment explanation
Indices: 17161963--17162011 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 17
17161953 CCTCAACCTC
17161963 TCTTTTTTCTTTTTCTTTT
1 TCTTTTTT-TTTTT-TTTT
17161982 TCTTTTTTTTTTTTTTT
1 TCTTTTTTTTTTTTTTT
17161999 TCCTCTTTTTTTT
1 T-CT-TTTTTTTT
17162012 GGGTGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.18
18 7 0.25
19 16 0.57
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (17 bp):
TCTTTTTTTTTTTTTTT
Found at i:17167013 original size:33 final size:32
Alignment explanation
Indices: 17166976--17167082 Score: 108
Period size: 33 Copynumber: 3.2 Consensus size: 32
17166966 GCGATTGCAT
*
17166976 AAATAATAAATGATAAATAAATATATAAAATAA
1 AAATAATAAATGATAAA-AAATAAATAAAATAA
* **
17167009 AAATAAAAAATGGATTGAAAATAACATAAAAT-A
1 AAATAATAAAT-GATAAAAAATAA-ATAAAATAA
* *
17167042 AAATATTAAATGAATAAAAAAGAAATAAAATAA
1 AAATAATAAATG-ATAAAAAATAAATAAAATAA
*
17167075 AAAAAATA
1 AAATAATA
17167083 GGATTCAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
32 8 0.14
33 40 0.68
34 11 0.19
ACGTcount: A:0.71, C:0.01, G:0.06, T:0.22
Consensus pattern (32 bp):
AAATAATAAATGATAAAAAATAAATAAAATAA
Found at i:17168049 original size:18 final size:19
Alignment explanation
Indices: 17168014--17168051 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17168004 CGTTTTAGGG
*
17168014 TTTCTTTTTTTTACTTCTT
1 TTTCTTTTTTTCACTTCTT
17168033 TTTCTTTTTTTCA-TTCTT
1 TTTCTTTTTTTCACTTCTT
17168051 T
1 T
17168052 GCAGATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTTTTTCACTTCTT
Found at i:17168246 original size:18 final size:18
Alignment explanation
Indices: 17168211--17168245 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17168201 GCTTCGAAAT
17168211 GAAAAATACAAAATAAAA
1 GAAAAATACAAAATAAAA
*
17168229 GAAAAATA-AATATAAAA
1 GAAAAATACAAAATAAAA
17168246 ATATATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (18 bp):
GAAAAATACAAAATAAAA
Found at i:17176062 original size:28 final size:28
Alignment explanation
Indices: 17176021--17176085 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
17176011 AAATTTTGAT
*
17176021 TTTTTTAAATATTTATCGG-ATTAGATCGC
1 TTTTTT-AATATTTAT-GGAATTAGATCGA
* *
17176050 TTTTTTAATATTTGTGGAATTAGATCTA
1 TTTTTTAATATTTATGGAATTAGATCGA
17176078 TTTTTTAA
1 TTTTTTAA
17176086 AACACACTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.54
Consensus pattern (28 bp):
TTTTTTAATATTTATGGAATTAGATCGA
Found at i:17182170 original size:13 final size:13
Alignment explanation
Indices: 17182148--17182185 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
17182138 TTGTTTACGT
17182148 TAGTTCATGTATC
1 TAGTTCATGTATC
* *
17182161 TAGTTTATGTTTC
1 TAGTTCATGTATC
17182174 TAGTTCATGTAT
1 TAGTTCATGTAT
17182186 TGTACTAGAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (13 bp):
TAGTTCATGTATC
Found at i:17186873 original size:45 final size:44
Alignment explanation
Indices: 17186755--17187304 Score: 583
Period size: 45 Copynumber: 12.4 Consensus size: 44
17186745 TTTCTGGATC
* * * * *
17186755 AGGGGTAAAAGACTGGA--TGGCTTCAATCTACTCCTCTGGATT
1 AGGGGTAAAAGATTGGACGTGGCTTCAATCTGCCCCTCTTGACT
* * *
17186797 AAGGGTAAAAGACTGGA--TGGCTTCAATCTGCCCCTTTTGACT
1 AGGGGTAAAAGATTGGACGTGGCTTCAATCTGCCCCTCTTGACT
* * *
17186839 AAGGGTAAAAGATTGGACGTTAGCTTCAATCTGCCCTTCTTGACT
1 AGGGGTAAAAGATTGGACG-TGGCTTCAATCTGCCCCTCTTGACT
* *
17186884 AGGGGTAAAAGATTGAAAAGTGGCTTCAATCTGCCCCTCTTGACT
1 AGGGGTAAAAGATTG-GACGTGGCTTCAATCTGCCCCTCTTGACT
* * * **
17186929 AGGAGTAAAGGATTGGTCGGTGGCTTCAATCTATCCCTCTTGACT
1 AGGGGTAAAAGATTGGAC-GTGGCTTCAATCTGCCCCTCTTGACT
* *
17186974 AGGGGTAAAAGATTGGATGGTGGCTTCAATCT-ACCCTACTTGACT
1 AGGGGTAAAAGATTGGA-CGTGGCTTCAATCTGCCCCT-CTTGACT
* * * * *
17187019 AGAGGTAAAAGATTGGAAGGTGGCTTCAGTCTGCCCCTCTGGATT
1 AGGGGTAAAAGATTGG-ACGTGGCTTCAATCTGCCCCTCTTGACT
* * * *
17187064 AGGGGGAAAAGATTGGATGGTGACTTCAATCTGCCCTTCTTGACT
1 AGGGGTAAAAGATTGGA-CGTGGCTTCAATCTGCCCCTCTTGACT
** * *
17187109 AAAGGTAAAAGATTGGAC-T-GCTTCAATCTGCCCCTCTAGATT
1 AGGGGTAAAAGATTGGACGTGGCTTCAATCTGCCCCTCTTGACT
* * * *
17187151 AGGGGTAAAAGATTGGACAGTGACTTCAATCTACTCCTTTTGACT
1 AGGGGTAAAAGATTGGAC-GTGGCTTCAATCTGCCCCTCTTGACT
* * *
17187196 AGGGGTAAAAGATTGGACAGTGGTTTCAATTTGCCCCTCTTGATT
1 AGGGGTAAAAGATTGGAC-GTGGCTTCAATCTGCCCCTCTTGACT
* *
17187241 AGGGGTAAAAGATTGGAATGTGGTTTCAATCTGCCCCTCTTGACT
1 AGGGGTAAAAGATTGG-ACGTGGCTTCAATCTGCCCCTCTTGACT
17187286 AGGGGTAAAAGATTGGACG
1 AGGGGTAAAAGATTGGACG
17187305 AGATGATGTA
Statistics
Matches: 428, Mismatches: 66, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
42 87 0.20
43 1 0.00
44 8 0.02
45 324 0.76
46 8 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (44 bp):
AGGGGTAAAAGATTGGACGTGGCTTCAATCTGCCCCTCTTGACT
Found at i:17188220 original size:22 final size:23
Alignment explanation
Indices: 17188192--17188234 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
17188182 AATGAAAGAA
*
17188192 CTAAAAAAAA-TGGCAAACATTG
1 CTAAAAAAAATTGCCAAACATTG
17188214 CTAAAAAAAATTGCCAAACAT
1 CTAAAAAAAATTGCCAAACAT
17188235 AAGATGAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.56, C:0.16, G:0.09, T:0.19
Consensus pattern (23 bp):
CTAAAAAAAATTGCCAAACATTG
Found at i:17195331 original size:16 final size:15
Alignment explanation
Indices: 17195285--17195332 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
17195275 ATTTTAATTT
17195285 ATTTATTTTATTTTTGG
1 ATTTA-TTT-TTTTTGG
17195302 -TTTATTTTTTTTGG
1 ATTTATTTTTTTTGG
*
17195316 ATTTGTTTTGTTTTGG
1 ATTTATTTT-TTTTGG
17195332 A
1 A
17195333 CCGAGCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.25
15 10 0.36
16 11 0.39
ACGTcount: A:0.12, C:0.00, G:0.17, T:0.71
Consensus pattern (15 bp):
ATTTATTTTTTTTGG
Found at i:17197474 original size:97 final size:95
Alignment explanation
Indices: 17197222--17197563 Score: 343
Period size: 94 Copynumber: 3.6 Consensus size: 95
17197212 CTATTGCTAC
* * * *
17197222 TTTTTTTTTGTTTTTCGGTAATTGGTGGCTGCTGCAATTGGTTCTATTCAATTGCTGGCTCTTCA
1 TTTTTTTTTTTTTTTTGGCAATTGGTGGCTGCTGCAATTGATTCTATTCAATTGCTGGCTCTTCA
* * * *
17197287 CATCTTTGTAAATTCTCCCTGTTGCTATTA-
66 CGTCTTTG-CAATTCTTCCTGCTGCTATTAT
** * * ** *
17197317 -TTTTTTTGGTTTTTTGACAATTGGTGGCTGTTGCAATTTCTTCTATTCAATTGCTAGCTCTTCA
1 TTTTTTTTTTTTTTTTGGCAATTGGTGGCTGCTGCAATTGATTCTATTCAATTGCTGGCTCTTCA
* * *
17197381 TGTCTTTGCAACTACTTCCTACTGCTATTAT
66 CGTCTTTGCAA-TTCTTCCTGCTGCTATTAT
* * * *
17197412 TTTTTGTTTTTTTTTTTGGCAATTGGTGGTTGCTGCCATTGATTCTATTTAATTGTTGGCTCTTC
1 TTTTT-TTTTTTTTTTTGGCAATTGGTGGCTGCTGCAATTGATTCTATTCAATTGCTGGCTCTTC
*
17197477 ACGTCTTTGCAATTGTT-CT-CTGCT-TCTAT
65 ACGTCTTTGCAATTCTTCCTGCTGCTAT-TAT
* * ** * * *
17197506 TATTTTTTATTTTTTCAGCAACTGGTGGCTACTGCAATTGGTTCTATTCAATTGCTGG
1 TTTTTTTTTTTTTTTTGGCAATTGGTGGCTGCTGCAATTGATTCTATTCAATTGCTGG
17197564 TTGCTGCTGC
Statistics
Matches: 202, Mismatches: 40, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
93 46 0.23
94 88 0.44
95 2 0.01
96 7 0.03
97 59 0.29
ACGTcount: A:0.15, C:0.17, G:0.17, T:0.50
Consensus pattern (95 bp):
TTTTTTTTTTTTTTTTGGCAATTGGTGGCTGCTGCAATTGATTCTATTCAATTGCTGGCTCTTCA
CGTCTTTGCAATTCTTCCTGCTGCTATTAT
Found at i:17198983 original size:27 final size:26
Alignment explanation
Indices: 17198944--17199011 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 26
17198934 TCGCAGAATG
*
17198944 TAGCTCATTCGAGTCCAAAACAAAATT
1 TAGCTCATACGAG-CCAAAACAAAATT
* * * *
17198971 TAGCTCATACGAGCCTAGACAGAGTT
1 TAGCTCATACGAGCCAAAACAAAATT
*
17198997 TAGCTCTTACGAGCC
1 TAGCTCATACGAGCC
17199012 CAGACAGAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
26 23 0.66
27 12 0.34
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (26 bp):
TAGCTCATACGAGCCAAAACAAAATT
Found at i:17199007 original size:26 final size:26
Alignment explanation
Indices: 17198969--17199045 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
17198959 CAAAACAAAA
* *
17198969 TTTAGCTCATACGAGCCTAGACAGAG
1 TTTAGCTCTTACGAGCCCAGACAGAG
17198995 TTTAGCTCTTACGAGCCCAGACAGAG
1 TTTAGCTCTTACGAGCCCAGACAGAG
* *
17199021 TTTAACTCTTACGAGCCCATACAGA
1 TTTAGCTCTTACGAGCCCAGACAGA
17199046 ATAATGCTCT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (26 bp):
TTTAGCTCTTACGAGCCCAGACAGAG
Found at i:17199055 original size:26 final size:26
Alignment explanation
Indices: 17198972--17199063 Score: 89
Period size: 26 Copynumber: 3.5 Consensus size: 26
17198962 AACAAAATTT
* * * *
17198972 AGCTCATACGAGCCTAGACAGAGTTT
1 AGCTCTTACGAGCCCAGACAGAGATA
*
17198998 AGCTCTTACGAGCCCAGACAGAGTTTA
1 AGCTCTTACGAGCCCAGACAGAG-ATA
*
17199025 A-CTCTTACGAGCCCATACAGA-ATA
1 AGCTCTTACGAGCCCAGACAGAGATA
*
17199049 ATGCTCTTTCGAGCC
1 A-GCTCTTACGAGCC
17199064 AAAATCATAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
24 3 0.05
26 51 0.89
27 3 0.05
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (26 bp):
AGCTCTTACGAGCCCAGACAGAGATA
Found at i:17199083 original size:27 final size:28
Alignment explanation
Indices: 17199042--17199116 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
17199032 CGAGCCCATA
*
17199042 CAGAATAATGC-TCTTTCGAGCCAAAAT
1 CAGAATAACGCTTCTTTCGAGCCAAAAT
*
17199069 CATAATAACG-TTCTTTCGAGCCAAAAT
1 CAGAATAACGCTTCTTTCGAGCCAAAAT
*
17199096 CAGAATAATGCTT-TTTCGAGC
1 CAGAATAACGCTTCTTTCGAGC
17199117 TAGAAACAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 40 0.95
28 2 0.05
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (28 bp):
CAGAATAACGCTTCTTTCGAGCCAAAAT
Found at i:17204118 original size:50 final size:47
Alignment explanation
Indices: 17203989--17204118 Score: 131
Period size: 50 Copynumber: 2.6 Consensus size: 47
17203979 TGTAAGTATA
*
17203989 TTGTTTTG-GTAATTCTCTCCAAAAGAAAACACTCATATATAATACGCAT
1 TTGTTTTGTGTAA-TCTCT-C-AAAGAAAACACTCATATATAATACACAT
* *
17204038 TTGTTTTGTATAAAT-TCTCATAAAAAAACACTCAAATATATAATACACAT
1 TTGTTTTGTGT-AATCTCTCA-AAGAAAACACTC--ATATATAATACACAT
17204088 TTGTTTTGTGT-ATCTCTCAAATGAATAACAC
1 TTGTTTTGTGTAATCTCTCAAA-GAA-AACAC
17204119 AATTAAATTC
Statistics
Matches: 68, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
47 1 0.01
48 16 0.24
49 18 0.26
50 31 0.46
51 2 0.03
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.37
Consensus pattern (47 bp):
TTGTTTTGTGTAATCTCTCAAAGAAAACACTCATATATAATACACAT
Found at i:17204861 original size:20 final size:20
Alignment explanation
Indices: 17204833--17204954 Score: 110
Period size: 20 Copynumber: 6.2 Consensus size: 20
17204823 CAATAAAAAT
17204833 AACAGTAAAAACAACACCAA
1 AACAGTAAAAACAACACCAA
*
17204853 AATAGTAAAAA-ATAGCACCAA
1 AACAGTAAAAACA-A-CACCAA
*
17204874 AACAGTAAAAA-AATA--AA
1 AACAGTAAAAACAACACCAA
* * *
17204891 AACAATAAAAGCAATACCAA
1 AACAGTAAAAACAACACCAA
*
17204911 AACAGTAAAAAC-GCAACCAA
1 AACAGTAAAAACAAC-ACCAA
* *
17204931 AACAGTAAAAAAAAAACCAA
1 AACAGTAAAAACAACACCAA
17204951 AACA
1 AACA
17204955 ATAATATAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
17 11 0.13
18 4 0.05
19 2 0.02
20 49 0.59
21 17 0.20
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.08
Consensus pattern (20 bp):
AACAGTAAAAACAACACCAA
Found at i:17204911 original size:58 final size:57
Alignment explanation
Indices: 17204833--17204943 Score: 152
Period size: 57 Copynumber: 1.9 Consensus size: 57
17204823 CAATAAAAAT
* *
17204833 AACAGTAAAAACAACACCAAAATAGTAAAAAATAGC-ACCAAAACAGTAAAAAAATAAA
1 AACAATAAAAACAACACCAAAACAGT-AAAAA-AGCAACCAAAACAGTAAAAAAATAAA
* * *
17204891 AACAATAAAAGCAATACCAAAACAGTAAAAACGCAACCAAAACAGTAAAAAAA
1 AACAATAAAAACAACACCAAAACAGTAAAAAAGCAACCAAAACAGTAAAAAAA
17204944 AAACCAAAAC
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
56 2 0.04
57 23 0.49
58 22 0.47
ACGTcount: A:0.67, C:0.17, G:0.07, T:0.09
Consensus pattern (57 bp):
AACAATAAAAACAACACCAAAACAGTAAAAAAGCAACCAAAACAGTAAAAAAATAAA
Found at i:17204941 original size:9 final size:9
Alignment explanation
Indices: 17204872--17204922 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
17204862 AAATAGCACC
*
17204872 AAAACAGTA
1 AAAACAATA
17204881 AAAA-AATA
1 AAAACAATA
17204889 AAAACAATA
1 AAAACAATA
*
17204898 AAAGCAATA
1 AAAACAATA
*
17204907 CCAAAACAGTA
1 --AAAACAATA
17204918 AAAAC
1 AAAAC
17204923 GCAACCAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 7 0.20
9 21 0.60
11 7 0.20
ACGTcount: A:0.71, C:0.14, G:0.06, T:0.10
Consensus pattern (9 bp):
AAAACAATA
Found at i:17204944 original size:58 final size:59
Alignment explanation
Indices: 17204833--17204958 Score: 150
Period size: 58 Copynumber: 2.1 Consensus size: 59
17204823 CAATAAAAAT
* * *
17204833 AACAGTAAAAACAACACCAAAATAGTAAAAAATAGCACCAAAACAGTAAAAAAATA-AA
1 AACAATAAAAACAACACCAAAACAGTAAAAAATAGCACCAAAACAGTAAAAAAAAACAA
* * *
17204891 AACAATAAAAGCAATACCAAAACAGT-AAAAA-CGCAACCAAAACAGTAAAAAAAAAACCAA
1 AACAATAAAAACAACACCAAAACAGTAAAAAATAGC-ACCAAAACAGT-AAAAAAAAA-CAA
17204951 AACAATAA
1 AACAATAA
17204959 TATAATTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
56 2 0.03
57 16 0.28
58 30 0.52
60 10 0.17
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.09
Consensus pattern (59 bp):
AACAATAAAAACAACACCAAAACAGTAAAAAATAGCACCAAAACAGTAAAAAAAAACAA
Found at i:17206056 original size:93 final size:93
Alignment explanation
Indices: 17205878--17206063 Score: 239
Period size: 93 Copynumber: 2.0 Consensus size: 93
17205868 GCAACAACAA
* *
17205878 CCAACAATTGAATAGAACCAATTGCAGCAGCCACCAATTATCGAAACAACAAAAAATAATAGCAA
1 CCAACAATTGAATAGAACCAATTGCAGCAACCACCAATTACCGAAACAACAAAAAATAATAGCAA
* * * *
17205943 CGGGGAGCATTTGCAGAGACGTGAAGAG
66 CAGGAAGCAGTTGCACAGACGTGAAGAG
* * * *
17205971 CCAACAATTGAATAGAACCAATTGTAGCAACCACCAGTTGCCGAAA-AACAAAAAAATACTAGCA
1 CCAACAATTGAATAGAACCAATTGCAGCAACCACCAATTACCGAAACAAC-AAAAAATAATAGCA
* * *
17206035 GCAGGAAGCGGTTGTACAGACGTGAAGAG
65 ACAGGAAGCAGTTGCACAGACGTGAAGAG
17206064 AAAATTTTAA
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
92 3 0.04
93 76 0.96
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (93 bp):
CCAACAATTGAATAGAACCAATTGCAGCAACCACCAATTACCGAAACAACAAAAAATAATAGCAA
CAGGAAGCAGTTGCACAGACGTGAAGAG
Found at i:17206389 original size:61 final size:58
Alignment explanation
Indices: 17206260--17206430 Score: 168
Period size: 59 Copynumber: 2.9 Consensus size: 58
17206250 TTAATATAAT
* * * * *
17206260 ATTTGGTATCTGAATTTGACATTTTTTCCTAATTTGGTACTTAAA-TGTTTTTGATCCA
1 ATTTGATACCTGAACTTGACATTTTTTCCTAATTTGGTAC-TAAACTTTTTTTGACCCA
** *
17206318 ATTT-ACTACCTGAACTTGACACTTTTTTTTTAATTTGATATCTAAACTTTTTTTGGACCCA
1 ATTTGA-TACCTGAACTTGACA-TTTTTTCCTAATTTGGTA-CTAAACTTTTTTT-GACCCA
* * *
17206379 ATTTGATACCTAAACTTGGCA-TTTTTCCTAATTTGGTACCTAAGCTTTTTTT
1 ATTTGATACCTGAACTTGACATTTTTTCCTAATTTGGTA-CTAAACTTTTTTT
17206431 TAGATTCAAT
Statistics
Matches: 92, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
58 17 0.18
59 45 0.49
60 7 0.08
61 22 0.24
62 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.49
Consensus pattern (58 bp):
ATTTGATACCTGAACTTGACATTTTTTCCTAATTTGGTACTAAACTTTTTTTGACCCA
Found at i:17206714 original size:31 final size:30
Alignment explanation
Indices: 17206653--17206787 Score: 147
Period size: 31 Copynumber: 4.6 Consensus size: 30
17206643 GGACTCCAGA
* *
17206653 AAGTTTAAGTACCAACTTAAAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAAAAAAATGTC
*
17206683 AAGTTTAAGTATCAAATTAAGAAAAAATGTC
1 AAGTTTAAGTACCAAATTAA-AAAAAATGTC
*
17206714 AAGTTTAAGTATCAAATTAGACAAAAAA--T-
1 AAGTTTAAGTACCAAATTA-A-AAAAAATGTC
17206743 -A-TTT-AGATACCAAATTAAAAAAAATGTC
1 AAGTTTAAG-TACCAAATTAAAAAAAATGTC
*
17206771 AAGTTAAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
17206788 ATTATATTAA
Statistics
Matches: 90, Mismatches: 6, Indels: 18
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.07
26 3 0.03
27 13 0.14
28 1 0.01
29 1 0.01
30 29 0.32
31 30 0.33
32 7 0.08
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAAAAAAAATGTC
Found at i:17208551 original size:18 final size:16
Alignment explanation
Indices: 17208515--17208557 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
17208505 GTATTAAATT
17208515 TATAATATTTTATAATA
1 TATAAT-TTTTATAATA
*
17208532 TATTATTTTTATATATTA
1 TATAATTTTTATA-A-TA
17208550 TATAATTT
1 TATAATTT
17208558 AAAATACATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 7 0.32
17 6 0.27
18 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATAATTTTTATAATA
Found at i:17208627 original size:22 final size:23
Alignment explanation
Indices: 17208608--17208656 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
17208598 TATTTTAATG
17208608 TAAATAT-TAAAAAATATTAAGA
1 TAAATATATAAAAAATATTAAGA
* *
17208630 TAATTATATAAAAAA-ATTTA-A
1 TAAATATATAAAAAATATTAAGA
17208651 TAAATA
1 TAAATA
17208657 AAAAAATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
21 6 0.26
22 10 0.43
23 7 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAATATATAAAAAATATTAAGA
Found at i:17208668 original size:15 final size:15
Alignment explanation
Indices: 17208637--17208692 Score: 51
Period size: 17 Copynumber: 3.5 Consensus size: 15
17208627 AGATAATTAT
17208637 ATAAAAAAATTTAATAA
1 ATAAAAAAA-TT-ATAA
17208654 ATAAAAAAATTATAAA
1 ATAAAAAAATTAT-AA
* *
17208670 ATATTAAATATTA-AA
1 ATA-AAAAAATTATAA
17208685 ATAAAAAA
1 ATAAAAAA
17208693 TAGAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.09
15 7 0.21
16 7 0.21
17 16 0.48
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
ATAAAAAAATTATAA
Found at i:17210434 original size:11 final size:11
Alignment explanation
Indices: 17210418--17210492 Score: 51
Period size: 11 Copynumber: 6.5 Consensus size: 11
17210408 TTTTACGAGT
17210418 TTATTTTTTAA
1 TTATTTTTTAA
17210429 TTATTTTTTAAA
1 TTATTTTTT-AA
* * *
17210441 TAATATTATAA
1 TTATTTTTTAA
* *
17210452 TTAGTTGTTAA
1 TTATTTTTTAA
*
17210463 TTAGTGTTTTAA
1 TTA-TTTTTTAA
*
17210475 TTCATTATTTAAA
1 TT-ATT-TTTTAA
17210488 TTATT
1 TTATT
17210493 GAACATAATT
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
11 20 0.43
12 19 0.40
13 8 0.17
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.60
Consensus pattern (11 bp):
TTATTTTTTAA
Found at i:17211915 original size:15 final size:16
Alignment explanation
Indices: 17211895--17211927 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17211885 TATACATATA
17211895 TTTTTA-TAATTAAAT
1 TTTTTATTAATTAAAT
*
17211910 TTTTTATTATTTAAAT
1 TTTTTATTAATTAAAT
17211926 TT
1 TT
17211928 AATTCAAGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTATTAATTAAAT
Found at i:17216759 original size:20 final size:20
Alignment explanation
Indices: 17216710--17216760 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
17216700 AAAAATATTA
*
17216710 ATACTTTTTGAAAAGGTATCG
1 ATACTTTTT-TAAAGGTATCG
17216731 ATACTTTTTTAAAGGTATCG
1 ATACTTTTTTAAAGGTATCG
17216751 ATACTTTTTT
1 ATACTTTTTT
17216761 TCATTGTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (20 bp):
ATACTTTTTTAAAGGTATCG
Found at i:17217270 original size:20 final size:19
Alignment explanation
Indices: 17217226--17217289 Score: 58
Period size: 20 Copynumber: 3.3 Consensus size: 19
17217216 AGTAAAAAAG
*
17217226 AATTTTTATAATTTTTTAA
1 AATTTTTATAATTTTTCAA
*
17217245 ACATTTTTATAACTTTTTCAT
1 A-ATTTTTATAA-TTTTTCAA
* *
17217266 AATTTCTCTAATCTTTT-AA
1 AATTTTTATAAT-TTTTCAA
17217285 AATTT
1 AATTT
17217290 AAGAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 8 0.22
20 22 0.59
21 7 0.19
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTATAATTTTTCAA
Found at i:17225397 original size:18 final size:18
Alignment explanation
Indices: 17225382--17225422 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
17225372 TCAAATGCGA
*
17225382 TCACAGAATCAGATGCAG
1 TCACACAATCAGATGCAG
*
17225400 TCATACAATCAGATGCAG
1 TCACACAATCAGATGCAG
*
17225418 CCACA
1 TCACA
17225423 AGTTCAAATG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.27, G:0.17, T:0.17
Consensus pattern (18 bp):
TCACACAATCAGATGCAG
Found at i:17231550 original size:3 final size:3
Alignment explanation
Indices: 17231542--17231591 Score: 52
Period size: 3 Copynumber: 16.7 Consensus size: 3
17231532 GTATTGCGGT
17231542 AGA AGA AGA AGCA AG- AGA AGA AGA GAGA A-A AGA A-A AGA AGGA AGA
1 AGA AGA AGA AG-A AGA AGA AGA AGA -AGA AGA AGA AGA AGA A-GA AGA
17231587 AGA AG
1 AGA AG
17231592 GAATTGCCCC
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
2 6 0.15
3 26 0.63
4 9 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:17242000 original size:12 final size:12
Alignment explanation
Indices: 17241983--17242009 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
17241973 CTTAGAGGAG
17241983 TTTACTTATATT
1 TTTACTTATATT
17241995 TTTACTTATATT
1 TTTACTTATATT
17242007 TTT
1 TTT
17242010 GAGACGATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.70
Consensus pattern (12 bp):
TTTACTTATATT
Found at i:17242962 original size:38 final size:40
Alignment explanation
Indices: 17242915--17242995 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
17242905 ATTAAAAATT
*
17242915 TAAATTATTAAAAA-T-AAATTGACTCTTGAAT-TATAAAG
1 TAAACTATTAAAAATTAAAATTGACT-TTGAATATATAAAG
*
17242953 TAAACTATTAAAAATTAAAATTGAGTTTGAATATATAAAG
1 TAAACTATTAAAAATTAAAATTGACTTTGAATATATAAAG
17242993 TAA
1 TAA
17242996 CTGAGAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 13 0.34
39 7 0.18
40 18 0.47
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.36
Consensus pattern (40 bp):
TAAACTATTAAAAATTAAAATTGACTTTGAATATATAAAG
Found at i:17242971 original size:53 final size:53
Alignment explanation
Indices: 17242864--17242974 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 53
17242854 ATTGAAAAAC
* * *
17242864 AATTATTAAAAACTAAAATTGACTTTTGAATTTGTTAAGTAATTAAAAATTTA
1 AATTATTAAAAACTAAAATTGACTCTTGAATTTGTAAACTAATTAAAAATTTA
*
17242917 AATTATTAAAAA-T-AAATTGACTCTTGAATTATAAAGTAAACT-ATTAAAAATTAA
1 AATTATTAAAAACTAAAATTGACTCTTGAATT-T---GTAAACTAATTAAAAATTTA
17242971 AATT
1 AATT
17242975 GAGTTTGAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 7
0.82 0.07 0.11
Matches are distributed among these distances:
51 16 0.32
52 2 0.04
53 12 0.24
54 15 0.30
55 5 0.10
ACGTcount: A:0.50, C:0.05, G:0.06, T:0.39
Consensus pattern (53 bp):
AATTATTAAAAACTAAAATTGACTCTTGAATTTGTAAACTAATTAAAAATTTA
Found at i:17243049 original size:6 final size:7
Alignment explanation
Indices: 17243037--17243063 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
17243027 TTTTTTTTAC
17243037 TTAAAAA
1 TTAAAAA
17243044 TTAAAAA
1 TTAAAAA
17243051 TTAAAAA
1 TTAAAAA
17243058 TTAAAA
1 TTAAAA
17243064 CAGTATAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:17246599 original size:42 final size:42
Alignment explanation
Indices: 17246495--17246634 Score: 174
Period size: 43 Copynumber: 3.3 Consensus size: 42
17246485 TTATGCGAAA
* * ** * *
17246495 AAGCGCCGCTAAAGAGCATGTTCTTTAGTGGCACTTTTACAAC
1 AAGCGCCGCTAAAG-CCATGTTCTTTAGCGGTGCTTTCACCAC
*
17246538 AAGCGCCGCTAAAAGCCATGTTCTTTAGCGGTGCTTTCCCCA-
1 AAGCGCCGCT-AAAGCCATGTTCTTTAGCGGTGCTTTCACCAC
*
17246580 AAGCGCCGCTAAAGTCCATGTTCTTTAGCGGTGCTTTCTCCAC
1 AAGCGCCGCTAAAG-CCATGTTCTTTAGCGGTGCTTTCACCAC
17246623 AAGCGCCGCTAA
1 AAGCGCCGCTAA
17246635 TATAACAGAT
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
41 4 0.05
42 36 0.42
43 42 0.49
44 4 0.05
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (42 bp):
AAGCGCCGCTAAAGCCATGTTCTTTAGCGGTGCTTTCACCAC
Found at i:17247059 original size:66 final size:66
Alignment explanation
Indices: 17246948--17247101 Score: 227
Period size: 66 Copynumber: 2.3 Consensus size: 66
17246938 GCTTGCCTCG
* * * * *
17246948 CTGCTGCCTCCACTTTAAGTTGTAGGTGGAGTTCTTCATATTTTTTTTGAGACTCTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTAAGACTCTGCTTCTCTC
17247013 A
66 A
* * *
17247014 CTGCAGCCTCCTCTTTAAGTTTTAGATGGAGTTCATCATATTTTTTTTAAGCCTTTGCTTCTCTC
1 CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTAAGACTCTGCTTCTCTC
*
17247079 G
66 A
17247080 CTGCAGCCTCCTCTTTAAGTTG
1 CTGCAGCCTCCTCTTTAAGTTG
17247102 AGCAATTTGC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 78 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.44
Consensus pattern (66 bp):
CTGCAGCCTCCTCTTTAAGTTGTAGATGGAGTTCATCATATTTTTTTTAAGACTCTGCTTCTCTC
A
Found at i:17253041 original size:69 final size:68
Alignment explanation
Indices: 17252939--17253131 Score: 247
Period size: 69 Copynumber: 2.8 Consensus size: 68
17252929 TAAACTAAAT
*
17252939 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAATTAA-AT
1 AATTAAATATTTGGATTG-TTTTAATAATTAAATATT-AATTAAATAT-ATTAAATAATTAACAT
17253003 ATTTTG
63 ATTTTG
*
17253009 AATTAAATATTTGGATTGTTTTAATAATTAAATATTTAATTAAATGTATTTAAATAA-TAACATA
1 AATTAAATATTTGGATTGTTTTAATAATTAAATA-TTAATTAAATATA-TTAAATAATTAACATA
*
17253073 TTTTT
64 TTTTG
17253078 AATTAAATATTTCGG-TTGTTTT--TAA-TAAATAATTAATTAAATAT-TTAAATAATT
1 AATTAAATATTT-GGATTGTTTTAATAATTAAAT-ATTAATTAAATATATTAAATAATT
17253132 GGATTGTTTT
Statistics
Matches: 113, Mismatches: 4, Indels: 17
0.84 0.03 0.13
Matches are distributed among these distances:
64 8 0.07
65 1 0.01
66 16 0.14
67 4 0.04
68 4 0.04
69 59 0.52
70 21 0.19
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (68 bp):
AATTAAATATTTGGATTGTTTTAATAATTAAATATTAATTAAATATATTAAATAATTAACATATT
TTG
Found at i:17253162 original size:112 final size:117
Alignment explanation
Indices: 17253010--17253296 Score: 390
Period size: 112 Copynumber: 2.5 Consensus size: 117
17253000 AATATTTTGA
* *
17253010 ATTAAATATTTGGATTG-TTTTAATAATTAAATATTTAATTAAATGTATTTAAATAA-TAACATA
1 ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAA-ATA
*
17253073 TTTTTAATTAAATATTTCGGTTGTTTTTAATAAATAA-T-TAATTAAA-T-AT
65 TTTTGAATTAAATATTTCGGTTGTTTTTAATAAATAACTATAATTAAACTAAT
* * *
17253122 -TTAAATAATTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAGTAATTAAATAT
1 ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAATAT
* * *
17253186 TTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAACTAAAT
66 TTTGAATTAAATATTTCGGTTGTTTTTAATAAATAACT-ATAATTAAACT-AAT
* *
17253240 AATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATA
1 -ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATA
17253297 CTAAATTAAA
Statistics
Matches: 151, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
111 15 0.10
112 72 0.48
113 4 0.03
115 7 0.05
116 1 0.01
118 2 0.01
120 50 0.33
ACGTcount: A:0.44, C:0.01, G:0.07, T:0.48
Consensus pattern (117 bp):
ATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAATAT
TTTGAATTAAATATTTCGGTTGTTTTTAATAAATAACTATAATTAAACTAAT
Found at i:17253165 original size:181 final size:187
Alignment explanation
Indices: 17252856--17253248 Score: 514
Period size: 181 Copynumber: 2.1 Consensus size: 187
17252846 TTATTTTTAA
* * *
17252856 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAA
1 TAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTCGGTTGTTTTTAATAAATAA
* *
17252921 CTAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATA
66 CT-ATAATTAAACT-AAT-ATTAAATAATTGAATTGTTTTTAATAATTAAATATTAAATTAAATA
17252986 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTG-TTTTAATAATTAAATATT
128 TAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTTAATAATTAAATATT
* * *
17253045 TAATTAAATGTATTTAAATAA-TAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATA
1 TAATTAAATATAATTAAATAATTAA-ATATTTTGAATTAAATATTTCGGTTGTTTTTAATAAATA
* * *
17253109 A-T-TAATTAAA-T-AT-TTAAATAATTGGATTGTTTTTAATTATTAAATATTTAATTAAATATA
65 ACTATAATTAAACTAATATTAAATAATTGAATTGTTTTTAATAATTAAATATTAAATTAAATATA
* * * * * *
17253169 ATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAAT
130 ATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTTAATAATTAAATATT
17253227 T-ATTAAACTAAATAATTAAATA
1 TAATTAAA-T--ATAATTAAATA
17253249 TTTGAATTGT
Statistics
Matches: 180, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
181 85 0.47
182 17 0.09
183 2 0.01
184 9 0.05
185 1 0.01
186 7 0.04
188 4 0.02
189 55 0.31
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.47
Consensus pattern (187 bp):
TAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTCGGTTGTTTTTAATAAATAA
CTATAATTAAACTAATATTAAATAATTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAA
TTAAATAATTAAATATTTTGAATTAAATATTTGGATTGTTTTTAATAATTAAATATT
Found at i:17253289 original size:22 final size:22
Alignment explanation
Indices: 17253264--17253318 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
17253254 ATTGTTTTTA
*
17253264 ATAATTAAATATTAAATTAAAT
1 ATAATTAAATACTAAATTAAAT
17253286 ATAATTAAATACTAAATTAAAT
1 ATAATTAAATACTAAATTAAAT
17253308 ATAATTAAATA
1 ATAATTAAATA
17253319 ATTATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAATTAAATACTAAATTAAAT
Found at i:17253293 original size:10 final size:10
Alignment explanation
Indices: 17253264--17253318 Score: 74
Period size: 10 Copynumber: 5.1 Consensus size: 10
17253254 ATTGTTTTTA
17253264 ATAATTAAAT
1 ATAATTAAAT
17253274 ATTAAATTAAAT
1 A-T-AATTAAAT
17253286 ATAATTAAAT
1 ATAATTAAAT
17253296 ACTAAATTAAAT
1 A-T-AATTAAAT
17253308 ATAATTAAAT
1 ATAATTAAAT
17253318 A
1 A
17253319 ATTATATATT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
10 19 0.46
11 4 0.10
12 18 0.44
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (10 bp):
ATAATTAAAT
Found at i:17253304 original size:323 final size:320
Alignment explanation
Indices: 17252963--17253696 Score: 1089
Period size: 323 Copynumber: 2.3 Consensus size: 320
17252953 ATTGTTTTTA
* *
17252963 ATAATTAAATATTAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTGT
1 ATAATTAAATAATAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTTT
17253028 TTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGG
66 TTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGG
17253093 TTGTTTTTAATAAATAATTAATTAAATATTTAAATAATTGGATTGTTTTTAATTATTAAAT-ATT
131 TTGTTTTTAATAAATAATTAATTAAATATTTAAATAATTGGATTGTTTTTAATTATTAAATCATT
* * * *
17253157 TAATTAAATATAATTAAGTAATTAAATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAA
196 TAATTAAATATAATTAACTAATAAAATATTTTGAATTAAATATTTGGGTTATTTTTAAT--AT--
17253222 CTAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAAT
257 CTAATTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAAT
* *
17253286 ATAATTAAATACTAAATTAAATATAATTAAATAATTATATATTTTGAATTAAATATTTGGATTTT
1 ATAATTAAATAATAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTTT
17253351 TTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGG
66 TTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGG
* *
17253416 TTGTTTTTAATAAATAATTAATTAAATATTTAAATATTTGGATTGTTTTTAATTATTAAATCCTT
131 TTGTTTTTAATAAATAATTAATTAAATATTTAAATAATTGGATTGTTTTTAATTATTAAATCATT
* * *
17253481 TAATTAAATATAATTAACTAATAAAATATTTTTAATTAAATATTTGGGTTATTTTTAATATTTAT
196 TAATTAAATATAATTAACTAATAAAATATTTTGAATTAAATATTTGGGTTATTTTTAATATCTAA
* ** ** * * * *
17253546 TTATTTATTTATTTATTTAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTATAT
261 TTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAAT
* * ** * * * * * *
17253606 ATAACTAAATAATAAAATATTTAATTATTAAATATTTAATTATATAT-AACTAAATATTTGGGTT
1 ATAATTAAATAATAAATTAAAT-ATAATTAAATAATTAAATAT-TTTGAATTAAATATTTGGATT
17253670 ATTTTTAATAATTAAATA--TAATTAAAT
64 -TTTTTAATAATTAAATATTTAATTAAAT
17253697 AATTAACTAA
Statistics
Matches: 374, Mismatches: 33, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
320 79 0.21
321 31 0.08
322 21 0.06
323 187 0.50
324 56 0.15
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (320 bp):
ATAATTAAATAATAAATTAAATATAATTAAATAATTAAATATTTTGAATTAAATATTTGGATTTT
TTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGG
TTGTTTTTAATAAATAATTAATTAAATATTTAAATAATTGGATTGTTTTTAATTATTAAATCATT
TAATTAAATATAATTAACTAATAAAATATTTTGAATTAAATATTTGGGTTATTTTTAATATCTAA
TTATTAAACTAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAAT
Found at i:17253339 original size:120 final size:119
Alignment explanation
Indices: 17253115--17253340 Score: 260
Period size: 120 Copynumber: 1.9 Consensus size: 119
17253105 AATAATTAAT
* * * * * *
17253115 TAAATATTTAAATAATTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAGTAATT
1 TAAATAATTAAATAATTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAACT
* * * * * * *
17253180 AAATATTTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAAC
66 AAATAATATGAATTAAATAATT-GATTATTTTGAATAAATAACTAATTATTAAAC
*
17253235 TAAATAATTAAATATTTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAAT-ACT
1 TAAATAATTAAATAATTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAACT
17253299 AAATTAAATAT-AATTAAATAATT-ATATATTTTGAATTAAATA
66 AAA-T-AATATGAATTAAATAATTGAT-TATTTTGAA-TAAATA
17253341 TTTGGATTTT
Statistics
Matches: 88, Mismatches: 14, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
118 1 0.01
119 12 0.14
120 72 0.82
121 3 0.03
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.46
Consensus pattern (119 bp):
TAAATAATTAAATAATTGAATTGTTTTTAATAATTAAATATTAAATTAAATATAATTAAATAACT
AAATAATATGAATTAAATAATTGATTATTTTGAATAAATAACTAATTATTAAAC
Found at i:17253369 original size:211 final size:205
Alignment explanation
Indices: 17253122--17253497 Score: 533
Period size: 211 Copynumber: 1.8 Consensus size: 205
17253112 AATTAAATAT
* *
17253122 TTAAATAATTGGATTGTTTTTAATTATTAAATATTTAATTAAATATAATTAAGTAATTAA-ATAT
1 TTAAATAATTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAA-TAACATAT
* * *
17253186 TTTGAATTAAGTATTTGGGTTGTTTTTAATAAATAACTAATTATTAAACTAAATAATTAAATATT
65 TTTGAATTAAATATTTCGGTTGTTTTTAATAAATAA-T--TAATTAAA-T--AT--TTAAATATT
17253251 TGAATTGTTTTTAATAATTAAAT-ATTAAATTAAATATAATTAAATACTAAATTAAATATAATTA
122 TGAATTGTTTTTAATAATTAAATCATTAAATTAAATATAATTAAATACTAAATTAAATATAATTA
17253315 AATAATTATATATTTTGAA
187 AATAATTATATATTTTGAA
* * *
17253334 TTAAATATTTGGATT-TTTTTAATAATTAAATATTTAATTAAATGTATTTAAATAATAACATATT
1 TTAAATAATTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATAACATATT
* *
17253398 TTTAATTAAATATTTCGGTTGTTTTTAATAAATAATTAATTAAATATTTAAATATTTGGATTGTT
66 TTGAATTAAATATTTCGGTTGTTTTTAATAAATAATTAATTAAATATTTAAATATTTGAATTGTT
* * *
17253463 TTTAATTATTAAATCCTTTAATTAAATATAATTAA
131 TTTAATAATTAAATCATTAAATTAAATATAATTAA
17253498 CTAATAAAAT
Statistics
Matches: 149, Mismatches: 13, Indels: 12
0.86 0.07 0.07
Matches are distributed among these distances:
203 30 0.20
204 18 0.12
205 2 0.01
207 1 0.01
208 7 0.05
210 4 0.03
211 73 0.49
212 14 0.09
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (205 bp):
TTAAATAATTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATAACATATT
TTGAATTAAATATTTCGGTTGTTTTTAATAAATAATTAATTAAATATTTAAATATTTGAATTGTT
TTTAATAATTAAATCATTAAATTAAATATAATTAAATACTAAATTAAATATAATTAAATAATTAT
ATATTTTGAA
Found at i:17253446 original size:117 final size:115
Alignment explanation
Indices: 17253308--17253642 Score: 410
Period size: 113 Copynumber: 2.9 Consensus size: 115
17253298 TAAATTAAAT
* *
17253308 ATAATTAAATAATTATATATTTTGAATTAAATATTTGGATT-TTTTTAATAATTAAATATTTAAT
1 ATAATTAATTAATTATATA-TTT--ATTAAATATTTGGATTGTTTTTAATTATTAAATATTTAAT
* * * *
17253372 TAAATGTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTA
63 TAAATATAATTAAATAATAAAATATTTTTAATTAAATATTTCGGTTATTTTTA
* * *
17253425 ATAAATAATTAATTA-A-ATAT-TTAAATATTTGGATTGTTTTTAATTATTAAATCCTTTAATTA
1 ATAATTAATTAATTATATATTTATTAAATATTTGGATTGTTTTTAATTATTAAAT-ATTTAATTA
* *
17253487 AATATAATTAACTAATAAAATATTTTTAATTAAATATTTGGGTTATTTTTA
65 AATATAATTAAATAATAAAATATTTTTAATTAAATATTTCGGTTATTTTTA
* * * * *
17253538 ATATTTATTTATTTATTTATTTATTTAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTA
1 ATAATTAATTAATTATATATTTA-TTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTA
* *
17253603 TATATAACTAAATAATAAAATATTTAATT-ATTAAATATTT
65 AATATAATTAAATAATAAAATATTT--TTAATTAAATATTT
17253643 AATTATATAT
Statistics
Matches: 188, Mismatches: 22, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
111 15 0.08
112 15 0.08
113 64 0.34
114 2 0.01
115 4 0.02
116 31 0.16
117 55 0.29
118 2 0.01
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (115 bp):
ATAATTAATTAATTATATATTTATTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAA
ATATAATTAAATAATAAAATATTTTTAATTAAATATTTCGGTTATTTTTA
Found at i:17253548 original size:4 final size:4
Alignment explanation
Indices: 17253539--17253564 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17253529 TTATTTTTAA
17253539 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
17253565 AATATTTGAA
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:17253597 original size:46 final size:46
Alignment explanation
Indices: 17253511--17253750 Score: 145
Period size: 46 Copynumber: 5.1 Consensus size: 46
17253501 ATAAAATATT
** ** *
17253511 TTTAATTAAATATTTGGGTTATTTTTAATATTTATTTATTTATTTA
1 TTTAATTAAATATTTGAATTATTTTTAATATTTAAATATTTAATTA
* *
17253557 TTTATTTAAATATTTGAATTGTTTTTAAT-TATTAAATATTTAATTA
1 TTTAATTAAATATTTGAATTATTTTTAATAT-TTAAATATTTAATTA
* * * *
17253603 TATATAACTAAATA-AT-AA-AATATTTAAT-TATTAAATATTTAATTA
1 T-T-TAATTAAATATTTGAATTATTTTTAATAT-TTAAATATTTAATTA
* ** * *
17253648 TATATAACTAAATATTTGGGTTATTTTTAATAATTAAATATAATTAAATAA
1 T-T-TAATTAAATATTTGAATTATTTTTAATATTTAAATAT--TT-AATTA
* *
17253699 TTAACTAATTAAATATTTGAA-T-TTTTTAATAATTAAAT-TATTAAATA
1 TT---TAATTAAATATTTGAATTATTTTTAATATTTAAATAT-TTAATTA
17253746 TTTAA
1 TTTAA
17253751 ATATTTAATT
Statistics
Matches: 156, Mismatches: 26, Indels: 26
0.75 0.12 0.12
Matches are distributed among these distances:
44 3 0.02
45 39 0.25
46 41 0.26
47 7 0.04
48 27 0.17
49 1 0.01
50 19 0.12
51 6 0.04
52 13 0.08
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (46 bp):
TTTAATTAAATATTTGAATTATTTTTAATATTTAAATATTTAATTA
Found at i:17253600 original size:15 final size:15
Alignment explanation
Indices: 17253580--17253648 Score: 77
Period size: 15 Copynumber: 4.6 Consensus size: 15
17253570 TTGAATTGTT
17253580 TTTAATTATTAAATA
1 TTTAATTATTAAATA
*
17253595 TTTAATTA-TATATAA
1 TTTAATTATTAAAT-A
* * * *
17253610 CTAAATAATAAAATA
1 TTTAATTATTAAATA
17253625 TTTAATTATTAAATA
1 TTTAATTATTAAATA
17253640 TTTAATTAT
1 TTTAATTAT
17253649 ATATAACTAA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
14 4 0.10
15 35 0.83
16 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (15 bp):
TTTAATTATTAAATA
Found at i:17253664 original size:117 final size:115
Alignment explanation
Indices: 17253264--17253664 Score: 368
Period size: 113 Copynumber: 3.5 Consensus size: 115
17253254 ATTGTTTTTA
* * ** * * * * * *
17253264 ATAATTAAATATTAAATTAAATATAATTAAATA-CTAAATTAAATATAATTAAATAATTATATAT
1 ATAATTAAATAATAAAATATTTTTAATTAAATATTTCAATTATATATAA-TAAATATTTATTTAT
* * *
17253328 T-TTGAATTAAATATTTGGATT-TTTTTAATAATTAAATATTTAATTAAAT
65 TATTTATTTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAAT
* * * ** * * * *
17253377 GTATTTAAATAATAACATATTTTTAATTAAATATTTCGGTTGTTTTTAATAAATA---ATTAATT
1 ATAATTAAATAATAAAATATTTTTAATTAAATATTTCAATTATATATAATAAATATTTATTTATT
** *
17253439 AAATATTTAAATATTTGGATTGTTTTTAATTATTAAATCCTTTAATTAAAT
66 ATTTATTTAAATATTTGGATTGTTTTTAATTATTAAAT-ATTTAATTAAAT
* *** * * **
17253490 ATAATTAACTAATAAAATATTTTTAATTAAATATTTGGGTTATTTTTAATATTTATTTATTTATT
1 ATAATTAAATAATAAAATATTTTTAATTAAATATTTCAATTATATATAATAAATATTTATTTA-T
* *
17253555 TATTTATTTAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTATAT
65 TATTTATTTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAAT
*
17253606 ATAACTAAATAATAAAATATTTAATT-ATTAAATATTT-AATTATATATAACTAAATATTT
1 ATAATTAAATAATAAAATATTT--TTAATTAAATATTTCAATTATATATAA-TAAATATTT
17253665 GGGTTATTTT
Statistics
Matches: 231, Mismatches: 46, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
110 5 0.02
111 16 0.07
112 15 0.06
113 89 0.39
114 7 0.03
116 42 0.18
117 55 0.24
118 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (115 bp):
ATAATTAAATAATAAAATATTTTTAATTAAATATTTCAATTATATATAATAAATATTTATTTATT
ATTTATTTAAATATTTGGATTGTTTTTAATTATTAAATATTTAATTAAAT
Found at i:17253675 original size:93 final size:91
Alignment explanation
Indices: 17253563--17253761 Score: 215
Period size: 93 Copynumber: 2.2 Consensus size: 91
17253553 TTTATTTATT
* *
17253563 TAAATATTTGAATTGTTTTTAATTATTAAATATTTAATTATATATAACTAAATAATAAAATATTT
1 TAAATATTTGAATTATTTTTAATAATTAAATA--TAATTA-A-ATAACTAAATAATAAAATATTT
*
17253628 -AATTATTAAAT-ATTTAATTATATATAAC
62 GAATTATTAAATAATTAAATTATATATAAC
** * * *
17253656 TAAATATTTGGGTTATTTTTAATAATTAAATATAATTAAATAATTAACTAATTAAATATTTGAAT
1 TAAATATTTGAATTATTTTTAATAATTAAATATAATTAAATAACTAAATAATAAAATATTTGAAT
* * * **
17253721 TTTTTAATAATTAAATTATTAAATATT
66 TATTAAATAATTAAATTA-TATATAAC
17253748 TAAATATTT-AATTA
1 TAAATATTTGAATTA
17253762 GTAATAATTA
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
89 19 0.22
90 10 0.11
91 17 0.19
92 14 0.16
93 28 0.32
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.49
Consensus pattern (91 bp):
TAAATATTTGAATTATTTTTAATAATTAAATATAATTAAATAACTAAATAATAAAATATTTGAAT
TATTAAATAATTAAATTATATATAAC
Found at i:17253698 original size:8 final size:8
Alignment explanation
Indices: 17253676--17253758 Score: 67
Period size: 8 Copynumber: 10.1 Consensus size: 8
17253666 GGTTATTTTT
17253676 AATAATTAA
1 AATAATT-A
17253685 ATATAATTA
1 A-ATAATTA
17253694 AATAATTA
1 AATAATTA
*
17253702 ACTAATTA
1 AATAATTA
* *
17253710 AATATTTG
1 AATAATTA
** *
17253718 AATTTTTT
1 AATAATTA
17253726 AATAATTA
1 AATAATTA
*
17253734 AATTATTA
1 AATAATTA
*
17253742 AATATTTA
1 AATAATTA
*
17253750 AATATTTA
1 AATAATTA
17253758 A
1 A
17253759 TTAGTAATAA
Statistics
Matches: 61, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
8 52 0.85
9 3 0.05
10 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (8 bp):
AATAATTA
Found at i:17256690 original size:41 final size:41
Alignment explanation
Indices: 17256645--17256726 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
17256635 ATAATTTATT
*
17256645 ATTTGACTTTTAGCGGCGCTTTTACATAATCGCCGCTAATG
1 ATTTGACTTTTAGCGGCGCTTTTACATAAGCGCCGCTAATG
*
17256686 ATTTGACTTTTAGCGGCGCTTTTTCATAAGCGCCGCTAATG
1 ATTTGACTTTTAGCGGCGCTTTTACATAAGCGCCGCTAATG
17256727 CTCTTTTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.37
Consensus pattern (41 bp):
ATTTGACTTTTAGCGGCGCTTTTACATAAGCGCCGCTAATG
Found at i:17262853 original size:15 final size:16
Alignment explanation
Indices: 17262835--17262872 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
17262825 ACCAAGTGCT
17262835 AAAAATTAAATA-TTA
1 AAAAATTAAATACTTA
*
17262850 AAAATTTAAATACTTA
1 AAAAATTAAATACTTA
*
17262866 TAAAATT
1 AAAAATT
17262873 TGTTTGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATTAAATACTTA
Found at i:17272005 original size:23 final size:23
Alignment explanation
Indices: 17271979--17272066 Score: 133
Period size: 23 Copynumber: 3.9 Consensus size: 23
17271969 CTTAATAACC
17271979 AATTGTAATAACTATATAATTTA
1 AATTGTAATAACTATATAATTTA
17272002 AATTGTAATAACTATATAATTTA
1 AATTGTAATAACTATATAATTTA
**
17272025 AATTGTAATAACTATATAAAAT-
1 AATTGTAATAACTATATAATTTA
* *
17272047 CATAGTAATAACTATATAAT
1 AATTGTAATAACTATATAAT
17272067 AAGCATAGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
22 17 0.28
23 43 0.72
ACGTcount: A:0.50, C:0.06, G:0.05, T:0.40
Consensus pattern (23 bp):
AATTGTAATAACTATATAATTTA
Found at i:17274841 original size:18 final size:19
Alignment explanation
Indices: 17274815--17274899 Score: 50
Period size: 18 Copynumber: 4.3 Consensus size: 19
17274805 TAATAATTTA
*
17274815 AATATAAAT-TTTATAAAT
1 AATAAAAATATTTATAAAT
*
17274833 AATAAAAATATATA-AAAT
1 AATAAAAATATTTATAAAT
*
17274851 TATAAATGTAATAAATTTTATAAAT
1 AATAAA---AAT--A-TTTATAAAT
17274876 AATAAAGAATATTTA-AAAT
1 AATAAA-AATATTTATAAAT
*
17274895 TATAA
1 AATAA
17274900 TTTGAATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
18 17 0.33
19 11 0.21
20 4 0.08
21 4 0.08
23 4 0.08
24 3 0.06
25 9 0.17
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAAAAATATTTATAAAT
Found at i:17274857 original size:16 final size:17
Alignment explanation
Indices: 17274826--17274881 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
17274816 ATATAAATTT
* *
17274826 TATAAATAATAAAAATA
1 TATAAATATTATAAATA
*
17274843 TATAAA-ATTATAAATG
1 TATAAATATTATAAATA
*
17274859 TAATAAATTTTATAAATA
1 T-ATAAATATTATAAATA
17274877 -ATAAA
1 TATAAA
17274882 GAATATTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 13 0.41
17 11 0.34
18 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TATAAATATTATAAATA
Found at i:17275448 original size:18 final size:18
Alignment explanation
Indices: 17275393--17275450 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
17275383 TTTTTATTTC
17275393 ATATTG-TTTTAATTTTT
1 ATATTGTTTTTAATTTTT
***
17275410 -TATT-TTTAATTAATAAAT
1 ATATTGTTT--TTAATTTTT
17275428 ATATTGTTTTTAATTTTT
1 ATATTGTTTTTAATTTTT
17275446 ATATT
1 ATATT
17275451 TTAATTCATC
Statistics
Matches: 30, Mismatches: 6, Indels: 9
0.67 0.13 0.20
Matches are distributed among these distances:
16 6 0.20
18 17 0.57
19 4 0.13
20 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
ATATTGTTTTTAATTTTT
Found at i:17275948 original size:17 final size:16
Alignment explanation
Indices: 17275911--17275955 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
17275901 TTATTTTATG
*
17275911 AATAAAAAAT-TATTA
1 AATAAAAAATAAATTA
*
17275926 ATTAAAAAATAAATTAA
1 AATAAAAAATAAATT-A
17275943 AATAAAAAATAAA
1 AATAAAAAATAAA
17275956 ATATTTATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 9 0.36
16 3 0.12
17 13 0.52
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AATAAAAAATAAATTA
Found at i:17275972 original size:22 final size:20
Alignment explanation
Indices: 17275915--17275974 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
17275905 TTTATGAATA
17275915 AAAAATTATTAATTAAAAA-
1 AAAAATTATTAATTAAAAAT
* * *
17275934 ATAAATTA-AAATAAAAAAT
1 AAAAATTATTAATTAAAAAT
17275953 AAAATATTTATTAATTAAAAAT
1 AAAA-A-TTATTAATTAAAAAT
17275975 TACAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
18 8 0.26
19 10 0.32
20 1 0.03
21 3 0.10
22 9 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTATTAATTAAAAAT
Found at i:17277411 original size:30 final size:30
Alignment explanation
Indices: 17277350--17277408 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
17277340 TAGATAGGGG
*
17277350 GTGAGATGGGAGTAAAAGTTTTGAAGGAAA
1 GTGAGATGGGAGTAAAAGTTTTGAAGAAAA
*
17277380 GTGAGA-GGGAGTAAAAGTTTTGGAGAAAA
1 GTGAGATGGGAGTAAAAGTTTTGAAGAAAA
17277409 AGTAAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.37, T:0.22
Consensus pattern (30 bp):
GTGAGATGGGAGTAAAAGTTTTGAAGAAAA
Found at i:17289275 original size:51 final size:51
Alignment explanation
Indices: 17289212--17289390 Score: 272
Period size: 51 Copynumber: 3.5 Consensus size: 51
17289202 GAATCTATAA
* *
17289212 ACTCACGATGACACTTAGTCATCGGACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* *
17289263 ACTCACAATGACACTTAGTCATCGGACCTTTAATCCATACA-GATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* * *
17289313 AATCACGAT-ACACTTAGTCATCGAACCTTTAATCCATAAAGAATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
*
17289363 ACTCACGATAACACTTAGTCATCGGACC
1 ACTCACGATGACACTTAGTCATCGGACC
17289391 CTTTCGTCTA
Statistics
Matches: 115, Mismatches: 11, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
49 29 0.25
50 31 0.27
51 55 0.48
ACGTcount: A:0.34, C:0.26, G:0.11, T:0.29
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
Found at i:17292945 original size:7 final size:7
Alignment explanation
Indices: 17292933--17292965 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
17292923 AGGAAAGAAA
17292933 GATGAGG
1 GATGAGG
17292940 GATGAGG
1 GATGAGG
17292947 GATGAGG
1 GATGAGG
17292954 GATGAGG
1 GATGAGG
17292961 GATGA
1 GATGA
17292966 TTAGGAATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.55, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:17293388 original size:23 final size:22
Alignment explanation
Indices: 17293357--17293400 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17293347 AAAGAAATAA
*
17293357 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
17293379 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
17293401 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:17298407 original size:51 final size:51
Alignment explanation
Indices: 17298344--17298571 Score: 359
Period size: 51 Copynumber: 4.5 Consensus size: 51
17298334 GAATCTATAA
*
17298344 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATACAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* * * *
17298395 ACTCACGATGACACTAAGTCATTGGACCATTAATCCATAAAGGATTCATTC
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
17298446 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATACAA-GATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATA-AAGGATTCATTT
* *
17298497 ACTCATGATGACACTTAGTCATCGGACCTTTAACCCATAAAGGATTCATTT
1 ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
* *
17298548 ACTCACAATGACACTTAATCATCG
1 ACTCACGATGACACTTAGTCATCG
17298572 AACCGTTTCG
Statistics
Matches: 161, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 2 0.01
51 157 0.98
52 2 0.01
ACGTcount: A:0.32, C:0.25, G:0.13, T:0.30
Consensus pattern (51 bp):
ACTCACGATGACACTTAGTCATCGGACCTTTAATCCATAAAGGATTCATTT
Found at i:17300002 original size:14 final size:13
Alignment explanation
Indices: 17299978--17300023 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
17299968 TAACACCATA
*
17299978 AACCCTAACCCTT
1 AACCCTAACCCCT
17299991 AACCCTTAACCCCT
1 AACCC-TAACCCCT
17300005 AACCTCT-ACCCCT
1 AACC-CTAACCCCT
17300018 AACCCT
1 AACCCT
17300024 TGACCATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.07
13 15 0.50
14 12 0.40
15 1 0.03
ACGTcount: A:0.28, C:0.50, G:0.00, T:0.22
Consensus pattern (13 bp):
AACCCTAACCCCT
Found at i:17300022 original size:7 final size:7
Alignment explanation
Indices: 17299980--17300022 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
17299970 ACACCATAAA
17299980 CCCTAAC
1 CCCTAAC
*
17299987 CCTTAAC
1 CCCTAAC
*
17299994 CCTTAAC
1 CCCTAAC
17300001 CCCTAAC
1 CCCTAAC
*
17300008 CTCT-AC
1 CCCTAAC
17300014 CCCTAAC
1 CCCTAAC
17300021 CC
1 CC
17300023 TTGACCATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:17300328 original size:14 final size:13
Alignment explanation
Indices: 17300304--17300349 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
17300294 TAACACCATA
*
17300304 AACCCTAACCCTT
1 AACCCTAACCCCT
17300317 AACCCTTAACCCCT
1 AACCC-TAACCCCT
17300331 AACCTCT-ACCCCT
1 AACC-CTAACCCCT
17300344 AACCCT
1 AACCCT
17300350 TGACCATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 2 0.07
13 15 0.50
14 12 0.40
15 1 0.03
ACGTcount: A:0.28, C:0.50, G:0.00, T:0.22
Consensus pattern (13 bp):
AACCCTAACCCCT
Found at i:17300348 original size:7 final size:7
Alignment explanation
Indices: 17300306--17300348 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
17300296 ACACCATAAA
17300306 CCCTAAC
1 CCCTAAC
*
17300313 CCTTAAC
1 CCCTAAC
*
17300320 CCTTAAC
1 CCCTAAC
17300327 CCCTAAC
1 CCCTAAC
*
17300334 CTCT-AC
1 CCCTAAC
17300340 CCCTAAC
1 CCCTAAC
17300347 CC
1 CC
17300349 TTGACCATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
6 5 0.16
7 26 0.84
ACGTcount: A:0.26, C:0.53, G:0.00, T:0.21
Consensus pattern (7 bp):
CCCTAAC
Found at i:17300554 original size:326 final size:327
Alignment explanation
Indices: 17299947--17300603 Score: 1307
Period size: 326 Copynumber: 2.0 Consensus size: 327
17299937 GTGACAATGG
17299947 ATTTCGTTAGTGAGTTATCTTTAACACCATAAACCCTAACCCTTAACCCTTAACCCCTAACCTCT
1 ATTTCGTTAGTGAGTTATCTTTAACACCATAAACCCTAACCCTTAACCCTTAACCCCTAACCTCT
17300012 ACCCCTAACCCTTGACCATGAACCCTAAACCTATCTTCTAACCCTCACCCTGAACTCATGATTTG
66 ACCCCTAACCCTTGACCATGAACCCTAAACCTATCTTCTAACCCTCACCCTGAACTCATGATTTG
17300077 CAAAAGTAAATATTAATCAGCACAGAGCAATTACAAACCAACTACTATTGGTGATATGATAGCCA
131 CAAAAGTAAATATTAATCAGCACAGAGCAATTACAAACCAACTACTATTGGTGATATGATAGCCA
17300142 ATGCACTAGGCTTTATCATATCCCTCAAAGATGCCGATAACAACATAGTGACCGTAACCTGCTTT
196 ATGCACTAGGCTTTATCATATCCCTCAAAGATGCCGATAACAACATAGTGACCGTAACCTGCTTT
17300207 CTCCTGGAAAATGAGAAATAACAGTATGAATAGGATTAATTTATAACAAAATTCCAATAACTCTT
261 CTCCTGGAAAATGAGAAATAACAGTATGAATAGGATTAATTTATAACAAAATTCCAATAACTCTT
17300272 TA
326 TA
17300274 ATTTCGTTAGTGA-TTATCTTTAACACCATAAACCCTAACCCTTAACCCTTAACCCCTAACCTCT
1 ATTTCGTTAGTGAGTTATCTTTAACACCATAAACCCTAACCCTTAACCCTTAACCCCTAACCTCT
17300338 ACCCCTAACCCTTGACCATGAACCCTAAACCTATCTTCTAACCCTCACCCTGAACTCATGATTTG
66 ACCCCTAACCCTTGACCATGAACCCTAAACCTATCTTCTAACCCTCACCCTGAACTCATGATTTG
17300403 CAAAAGTAAATATTAATCAGCACAGAGCAATTACAAACCAACTACTATTGGTGATATGATAGCCA
131 CAAAAGTAAATATTAATCAGCACAGAGCAATTACAAACCAACTACTATTGGTGATATGATAGCCA
17300468 ATGCACTAGGCTTTATCATATCCCTCAAAGATGCCGATAACAACATAGTGACCGTAACCTGCTTT
196 ATGCACTAGGCTTTATCATATCCCTCAAAGATGCCGATAACAACATAGTGACCGTAACCTGCTTT
17300533 CTCCTGGAAAATGAGAAATAACAGTATGAATAGGATTAATTTATAACAAAATTCCAATAACTCTT
261 CTCCTGGAAAATGAGAAATAACAGTATGAATAGGATTAATTTATAACAAAATTCCAATAACTCTT
17300598 TA
326 TA
17300600 ATTT
1 ATTT
17300604 GTTTGTGTTG
Statistics
Matches: 330, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
326 317 0.96
327 13 0.04
ACGTcount: A:0.35, C:0.26, G:0.11, T:0.28
Consensus pattern (327 bp):
ATTTCGTTAGTGAGTTATCTTTAACACCATAAACCCTAACCCTTAACCCTTAACCCCTAACCTCT
ACCCCTAACCCTTGACCATGAACCCTAAACCTATCTTCTAACCCTCACCCTGAACTCATGATTTG
CAAAAGTAAATATTAATCAGCACAGAGCAATTACAAACCAACTACTATTGGTGATATGATAGCCA
ATGCACTAGGCTTTATCATATCCCTCAAAGATGCCGATAACAACATAGTGACCGTAACCTGCTTT
CTCCTGGAAAATGAGAAATAACAGTATGAATAGGATTAATTTATAACAAAATTCCAATAACTCTT
TA
Found at i:17302262 original size:24 final size:24
Alignment explanation
Indices: 17302228--17302285 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
17302218 GTTGACGAAA
*
17302228 AACCAAGAAAATTGAAATAAAAAG
1 AACCAAAAAAATTGAAATAAAAAG
17302252 AACCAAAAAAATTGAAATAAAAAG
1 AACCAAAAAAATTGAAATAAAAAG
17302276 AACCAAAAAA
1 AACCAAAAAA
17302286 TCTTCGCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.71, C:0.10, G:0.09, T:0.10
Consensus pattern (24 bp):
AACCAAAAAAATTGAAATAAAAAG
Found at i:17302985 original size:14 final size:14
Alignment explanation
Indices: 17302966--17302999 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
17302956 CGATAACATT
17302966 TATAGGGGAAATAA
1 TATAGGGGAAATAA
*
17302980 TATAGGGGAGATAA
1 TATAGGGGAAATAA
17302994 TATAGG
1 TATAGG
17303000 AAACGGTAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.32, T:0.24
Consensus pattern (14 bp):
TATAGGGGAAATAA
Found at i:17304580 original size:20 final size:18
Alignment explanation
Indices: 17304542--17304582 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
17304532 TTAAAACCCC
*
17304542 AAACCAAAATTGACACTA
1 AAACCAAAATTGAAACTA
17304560 AAACCACAAATTGAAACCTA
1 AAACCA-AAATTGAAA-CTA
17304580 AAA
1 AAA
17304583 TAAAATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 6 0.30
19 8 0.40
20 6 0.30
ACGTcount: A:0.59, C:0.22, G:0.05, T:0.15
Consensus pattern (18 bp):
AAACCAAAATTGAAACTA
Found at i:17307034 original size:13 final size:12
Alignment explanation
Indices: 17306964--17307045 Score: 60
Period size: 13 Copynumber: 6.6 Consensus size: 12
17306954 TTCATATACA
*
17306964 TATATATATTAGT
1 TATA-ATATTAAT
*
17306977 TAATAATAATAA-
1 T-ATAATATTAAT
*
17306989 TATAATACTAAT
1 TATAATATTAAT
*
17307001 TA-AATAATAATT
1 TATAATATTAA-T
*
17307013 TATATTATTATAT
1 TATAATATTA-AT
17307026 TATAATATTAAT
1 TATAATATTAAT
17307038 TAATAATA
1 T-ATAATA
17307046 AATTAAAGAA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
11 16 0.29
12 9 0.16
13 27 0.48
14 4 0.07
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:17314117 original size:13 final size:12
Alignment explanation
Indices: 17314047--17314128 Score: 51
Period size: 13 Copynumber: 6.6 Consensus size: 12
17314037 TTCATATACA
*
17314047 TATATATATTAGT
1 TATA-ATATTAAT
*
17314060 TAATAATAATAA-
1 T-ATAATATTAAT
*
17314072 TATAATACTAAT
1 TATAATATTAAT
* *
17314084 TA-AATAATAGTT
1 TATAATATTA-AT
*
17314096 TATATTATTATAT
1 TATAATATTA-AT
17314109 TATAATATTAAT
1 TATAATATTAAT
17314121 TAATAATA
1 T-ATAATA
17314129 AATTAAAGAA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
11 15 0.28
12 9 0.17
13 27 0.50
14 3 0.06
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.46
Consensus pattern (12 bp):
TATAATATTAAT
Found at i:17316228 original size:56 final size:56
Alignment explanation
Indices: 17316058--17316234 Score: 169
Period size: 56 Copynumber: 3.1 Consensus size: 56
17316048 ATGTGCTAGT
* * * * * *
17316058 CCGTGTGTGTATACTGACTTGGAACACACGGGCTAGACACATGGGCATGTGTCGGA
1 CCGTGTGTGTATACTGTCTTGGAACACTCGGGCTGGACACACGGGCGTGTGTCAGA
* * * * **
17316114 CCGTGTGTGCATACTGTTTTGGAAATAGCATACAGG--GGACACACGGGCGTGTCCCAGA
1 CCGTGTGTGTATACTGTCTTGG-AACA-C-T-CGGGCTGGACACACGGGCGTGTGTCAGA
* *
17316172 CCGTGTGTGTATGCCGTCTTGGAACACTCGGGCTGGACACACGGGCGTGTGTCAGA
1 CCGTGTGTGTATACTGTCTTGGAACACTCGGGCTGGACACACGGGCGTGTGTCAGA
*
17316228 CTGTGTG
1 CCGTGTG
17316235 CATATATTGT
Statistics
Matches: 94, Mismatches: 21, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
54 3 0.03
55 1 0.01
56 46 0.49
57 6 0.06
58 35 0.37
60 3 0.03
ACGTcount: A:0.20, C:0.23, G:0.33, T:0.24
Consensus pattern (56 bp):
CCGTGTGTGTATACTGTCTTGGAACACTCGGGCTGGACACACGGGCGTGTGTCAGA
Found at i:17317482 original size:42 final size:42
Alignment explanation
Indices: 17317416--17317548 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 42
17317406 TCCAGTTACA
* ** * *
17317416 AATAATCCTATGCTCTTGTTGAGACATAGGTCTTTCATTTAT
1 AATAATCTTATGCTCTACTCGAGACATAAGTCTTTCATTTAT
*
17317458 AATAATCTTATGCTCTACTCGAGACATAAAT-TTTCCATTTAT
1 AATAATCTTATGCTCTACTCGAGACATAAGTCTTT-CATTTAT
* * *
17317500 AAACAATCTTATGCTCTACCCGAGACATAAGTCTTCCATTTAAT
1 -AATAATCTTATGCTCTACTCGAGACATAAGTCTTTCATTT-AT
17317544 AATAA
1 AATAA
17317549 CTAAGTCTTC
Statistics
Matches: 76, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.04
42 32 0.42
43 37 0.49
44 4 0.05
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.38
Consensus pattern (42 bp):
AATAATCTTATGCTCTACTCGAGACATAAGTCTTTCATTTAT
Found at i:17322764 original size:13 final size:13
Alignment explanation
Indices: 17322717--17322765 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
17322707 TAATGAAACC
17322717 AAAATCCAAAATT
1 AAAATCCAAAATT
17322730 -AAATCCGAAAA--
1 AAAATCC-AAAATT
*
17322741 AATAGTCCAAAATT
1 AA-AATCCAAAATT
17322755 AAAATCCAAAA
1 AAAATCCAAAA
17322766 CATGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 11 0.38
13 16 0.55
14 2 0.07
ACGTcount: A:0.61, C:0.16, G:0.04, T:0.18
Consensus pattern (13 bp):
AAAATCCAAAATT
Found at i:17326840 original size:13 final size:13
Alignment explanation
Indices: 17326822--17326847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17326812 AATACATTTA
17326822 TCATATCAAAACC
1 TCATATCAAAACC
17326835 TCATATCAAAACC
1 TCATATCAAAACC
17326848 AGAAGAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (13 bp):
TCATATCAAAACC
Found at i:17329076 original size:6 final size:6
Alignment explanation
Indices: 17329057--17329125 Score: 65
Period size: 6 Copynumber: 12.2 Consensus size: 6
17329047 CCATTTATGT
* * * *
17329057 TTTAAT TTTGAA TTTAAA -TTAAT TTTTAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
17329102 TTT-AT TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
17329126 CAAATTATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.08
5 8 0.16
6 39 0.76
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:17329080 original size:17 final size:17
Alignment explanation
Indices: 17329067--17329131 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
17329057 TTTAATTTTG
* *
17329067 AATTTAAATTAATTTTT
1 AATTTAAATTAAATTTA
*
17329084 AATTT-ATTTAAATTTA
1 AATTTAAATTAAATTTA
**
17329100 AATTTATTTTAAATTTA
1 AATTTAAATTAAATTTA
*
17329117 AATTTAAATCAAATT
1 AATTTAAATTAAATT
17329132 ATGAAAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 13 0.32
17 27 0.68
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:17329102 original size:27 final size:28
Alignment explanation
Indices: 17329057--17329125 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 28
17329047 CCATTTATGT
* *
17329057 TTTAATTTTGAATTTAAATTAATTTTTAA
1 TTTAA-TTTAAATTTAAATTAATTTTAAA
*
17329086 TTT-ATTTAAATTTAAATTTATTTTAAA
1 TTTAATTTAAATTTAAATTAATTTTAAA
17329113 TTTAAATTTAAAT
1 TTT-AATTTAAAT
17329126 CAAATTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 23 0.66
28 1 0.03
29 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTAATTTAAATTTAAATTAATTTTAAA
Found at i:17329103 original size:16 final size:17
Alignment explanation
Indices: 17329056--17329122 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
17329046 CCCATTTATG
* *
17329056 TTTTAATTTTGAATTTA
1 TTTTAAATTTAAATTTA
** * *
17329073 AATTAATTTTTAATTTA
1 TTTTAAATTTAAATTTA
17329090 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
17329106 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
17329123 AATCAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.30
17 30 0.70
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:17329121 original size:33 final size:33
Alignment explanation
Indices: 17329057--17329122 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
17329047 CCATTTATGT
* * * *
17329057 TTTAATTTTGAATTTAAATTAATTTTTAATTTA
1 TTTAAATTTAAATTTAAATTAAATTTAAATTTA
**
17329090 TTTAAATTTAAATTTATTTTAAATTTAAATTTA
1 TTTAAATTTAAATTTAAATTAAATTTAAATTTA
17329123 AATCAAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (33 bp):
TTTAAATTTAAATTTAAATTAAATTTAAATTTA
Found at i:17329133 original size:27 final size:28
Alignment explanation
Indices: 17329057--17329151 Score: 72
Period size: 27 Copynumber: 3.4 Consensus size: 28
17329047 CCATTTATGT
* * * *
17329057 TTTAATTTTGAATTTAAATTAATTTTTAA
1 TTTAAATTTAAATTCAAATT-ATTTTAAA
*
17329086 TTT--ATTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTAAATTCAAA-TTATTTTAAA
**
17329113 TTTAAATTTAAA-TCAAATTA-TGAAAA
1 TTTAAATTTAAATTCAAATTATTTTAAA
17329139 TATTAAATTTAAA
1 T-TTAAATTTAAA
17329152 CATTAAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.09
27 35 0.62
28 6 0.11
29 10 0.18
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTAAATTTAAATTCAAATTATTTTAAA
Found at i:17331152 original size:59 final size:59
Alignment explanation
Indices: 17331086--17331279 Score: 241
Period size: 59 Copynumber: 3.3 Consensus size: 59
17331076 CCTGGACTGT
*
17331086 CCAAAAATTACCATTTTACCCTCGAACTTTTAAAAATTCTATTTTTGACATCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTTAAAAATTCTATTTTTGACCTCGATTTCA
** * * *
17331145 CCAAAAATTACCATTTTATCCC-CGAACTTTCCAAAATTCCATTTTCGACCTCGATTTTA
1 CCAAAAATTACCATTTTA-CCCTCGAACTTTTAAAAATTCTATTTTTGACCTCGATTTCA
* * *
17331204 CCAAAAATTACTATTTTACCCTCGAA--TTTACCAAAATTCTCTTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTTA--AAAATTCTATTTTTGACCTCGATTTCA
* *
17331263 TCGAAAATTACCATTTT
1 CCAAAAATTACCATTTT
17331280 GCCCCCGCGA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
57 2 0.02
58 3 0.03
59 106 0.93
60 3 0.03
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCGAACTTTTAAAAATTCTATTTTTGACCTCGATTTCA
Found at i:17331179 original size:30 final size:29
Alignment explanation
Indices: 17331086--17331284 Score: 112
Period size: 30 Copynumber: 6.8 Consensus size: 29
17331076 CCTGGACTGT
17331086 CCAAAAATTACCATTTTACCCTCGAACTTT-
1 CCAAAAATTACCATTTTACCC-CGAA-TTTA
* * **
17331116 -TAAAAATT-CTATTTTTGACATCG-ATTTCA
1 CCAAAAATTACCA-TTTT-ACCCCGAATTT-A
17331145 CCAAAAATTACCATTTTATCCCCGAACTTT-
1 CCAAAAATTACCATTTTA-CCCCGAA-TTTA
* *
17331175 CC-AAAATT-CCATTTTCGACCTCGATTTTA
1 CCAAAAATTACCATTTT--ACCCCGAATTTA
*
17331204 CCAAAAATTACTATTTTACCCTCGAATTTA
1 CCAAAAATTACCATTTTACCC-CGAATTTA
*
17331234 CC-AAAATT-CTCTTTTTGACCCCG-ATTTCA
1 CCAAAAATTAC-CATTTT-ACCCCGAATTT-A
* * *
17331263 TCGAAAATTACCATTTTGCCCC
1 CCAAAAATTACCATTTTACCCC
17331285 CGCGAGTCCA
Statistics
Matches: 131, Mismatches: 18, Indels: 41
0.69 0.09 0.22
Matches are distributed among these distances:
27 3 0.02
28 18 0.14
29 48 0.37
30 49 0.37
31 10 0.08
32 3 0.02
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.37
Consensus pattern (29 bp):
CCAAAAATTACCATTTTACCCCGAATTTA
Found at i:17331307 original size:118 final size:116
Alignment explanation
Indices: 17331086--17331299 Score: 279
Period size: 118 Copynumber: 1.8 Consensus size: 116
17331076 CCTGGACTGT
*
17331086 CCAAAAATTACCATTTTACCCTCGAACTTTTAAAAATTCTATTTTTGACATCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCTCGAAC-TTTAAAAATTCTATTTTTGACACCGATTTCACCAAAA
* **
17331151 ATTACCATTTTATCCCCGAACTTTCCAAAATTCCATTTTCGACCTCGATTTTA
65 ATTACCATTTTACCCCCG-ACAGTCCAAAATTCCATTTTCGACCTCGATTTTA
* * * * *
17331204 CCAAAAATTACTATTTTACCCTCGAA-TTTACCAAAATTCTCTTTTTGACCCCGATTTCATCGAA
1 CCAAAAATTACCATTTTACCCTCGAACTTTA--AAAATTCTATTTTTGACACCGATTTCACCAAA
*
17331268 AATTACCATTTTGCCCCCG-CGAGTCCAAAATT
64 AATTACCATTTTACCCCCGAC-AGTCCAAAATT
17331300 ATCATTTTAC
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
116 5 0.06
117 9 0.11
118 69 0.83
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (116 bp):
CCAAAAATTACCATTTTACCCTCGAACTTTAAAAATTCTATTTTTGACACCGATTTCACCAAAAA
TTACCATTTTACCCCCGACAGTCCAAAATTCCATTTTCGACCTCGATTTTA
Found at i:17343779 original size:76 final size:76
Alignment explanation
Indices: 17343550--17343848 Score: 508
Period size: 76 Copynumber: 3.9 Consensus size: 76
17343540 GAGCACCAAC
* *
17343550 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
17343615 GTAAGAGCAAG
66 GTAAGAGCAAG
*
17343626 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTG
1 ATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAG-CTGGATAACAAGTCTTTATCTCTGAAATTG
17343691 AAGTAAGAGCAAG
64 AAGTAAGAGCAAG
* *
17343704 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
17343769 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
17343780 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGACATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
17343845 GTAA
66 GTAA
17343849 AGACTGGATA
Statistics
Matches: 212, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
76 110 0.52
77 57 0.27
78 45 0.21
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:17343892 original size:191 final size:191
Alignment explanation
Indices: 17343644--17344039 Score: 774
Period size: 191 Copynumber: 2.1 Consensus size: 191
17343634 CCTATCCTCT
17343644 TGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCAT
1 TGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCAT
17343709 TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAG
66 TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAG
*
17343774 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTC
131 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTGTATCTC
*
17343835 TGACATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCAT
1 TGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCAT
17343900 TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAG
66 TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAG
17343965 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTGTATCTC
131 AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTGTATCTC
17344026 TGAAATTGAAGTAA
1 TGAAATTGAAGTAA
17344040 GAGTAAGATC
Statistics
Matches: 202, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
191 202 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (191 bp):
TGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCAT
TTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAG
AGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTGTATCTC
Found at i:17343953 original size:76 final size:76
Alignment explanation
Indices: 17343839--17344256 Score: 701
Period size: 76 Copynumber: 5.5 Consensus size: 76
17343829 TATCTCTGAC
17343839 ATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
1 ATTGAAGTAAAG-CTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
17343904 TATCCTCTTGAA
65 TATCCTCTTGAA
*
17343916 ATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
17343981 ATCCTCTTGAA
66 ATCCTCTTGAA
* * * * * *
17343992 ATTGAAGTAGAGTTGGATAACAAGTCTGTATCTCTGAAATTGAAGTAAGAGTAAGATCTTTTCCT
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
17344057 ATCCTCTTGAA
66 ATCCTCTTGAA
17344068 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAGCAAGATCATTTC
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTA--TCTCTGAAATTGAAGTAAGAGCAAGATCATTTC
17344133 CTATCCTCTTGAA
64 CTATCCTCTTGAA
* *
17344146 ATTGAAGTAAAGCTGGATATCAAGACTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCCT
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
17344211 ATCCTCTTGAA
66 ATCCTCTTGAA
* * *
17344222 ATTGAAGTAGAGCCGGATATCAAGACTTTATCTCT
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCT
17344257 CTGAAGCTAT
Statistics
Matches: 323, Mismatches: 16, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
76 238 0.74
77 12 0.04
78 73 0.23
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (76 bp):
ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
ATCCTCTTGAA
Found at i:17344057 original size:267 final size:269
Alignment explanation
Indices: 17343563--17344117 Score: 947
Period size: 267 Copynumber: 2.1 Consensus size: 269
17343553 ATTTCCTATC
* *
17343563 CTCT-TGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGA
1 CTCTCTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGA
*
17343627 TCATTTTCCTATCCTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGA
66 TCATTTTCCTATCCTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTGTATCTCTGAAATTGA
*
17343692 AGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATC
131 AGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTGTATC
* *
17343757 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAAC
196 TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAAC
17343822 AAGTCTTTA
261 AAGTCTTTA
* *
17343831 -TCTCTGACATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
1 CTCTCTGAAATTGAAGTAAAG-CTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
17343895 ATCA-TTTCCTATCCTCTTGAAATTGAAGTAAAG-CTGGATATCAAGTCTGTATCTCTGAAATTG
65 ATCATTTTCCTATCCTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTGTATCTCTGAAATTG
* *
17343958 AAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTGTAT
130 AAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTGTAT
* * *
17344023 CTCTGAAATTGAAGTAAGAGTAAGATCTTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAT
195 CTCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAA
17344088 CAAGTCTTTA
260 CAAGTCTTTA
17344098 TCTCTCTGAAATTGAAGTAA
1 -CTCTCTGAAATTGAAGTAA
17344118 GAGCAAGATC
Statistics
Matches: 269, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
267 164 0.61
268 43 0.16
269 62 0.23
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Consensus pattern (269 bp):
CTCTCTGAAATTGAAGTAAAGCTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGA
TCATTTTCCTATCCTCTTGAAATTGAAGTAAAGACTGGATATCAAGTCTGTATCTCTGAAATTGA
AGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGTCTGTATC
TCTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAAC
AAGTCTTTA
Found at i:17344154 original size:230 final size:229
Alignment explanation
Indices: 17343839--17344256 Score: 739
Period size: 230 Copynumber: 1.8 Consensus size: 229
17343829 TATCTCTGAC
17343839 ATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
1 ATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
*
17343904 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAAGTAAGAGCA
66 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGACTGTATCTCTGAAATTGAAGTAAGAGCA
* ** *
17343969 AGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTGTATCTCTGAAATTG
131 AGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCCGGATAACAAGACTGTATCTCTGAAATTG
17344034 AAGTAAGAGTAAGATCTTTTCCTATCCTCTTGAA
196 AAGTAAGAGTAAGATCTTTTCCTATCCTCTTGAA
17344068 ATTGAAGTAAAG-CTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAGCAAGATCATTT
1 ATTGAAGTAAAGACTGGATATCAAGTCTTTA--TCTCTGAAATTGAAGTAAGAGCAAGATCATTT
*
17344132 CCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGACTTTATCTCTGAAATTGAAGTAAGAG
64 CCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGACTGTATCTCTGAAATTGAAGTAAGAG
* *
17344197 CAAGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCCGGATATCAAGACTTTATCTCT
129 CAAGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCCGGATAACAAGACTGTATCTCT
17344257 CTGAAGCTAT
Statistics
Matches: 179, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
228 18 0.10
229 12 0.07
230 149 0.83
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (229 bp):
ATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGACTGTATCTCTGAAATTGAAGTAAGAGCA
AGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCCGGATAACAAGACTGTATCTCTGAAATTG
AAGTAAGAGTAAGATCTTTTCCTATCCTCTTGAA
Found at i:17344280 original size:154 final size:154
Alignment explanation
Indices: 17343839--17344261 Score: 715
Period size: 154 Copynumber: 2.8 Consensus size: 154
17343829 TATCTCTGAC
17343839 ATTGAAGTAAAGACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
1 ATTGAAGTAAAG-CTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
*
17343904 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTA--TCTCTGAAATTGAAGTAAGAG
65 TATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAG
17343967 CAAGATCATTTCCTATCCTCTTGAA
130 CAAGATCATTTCCTATCCTCTTGAA
* * * * * *
17343992 ATTGAAGTAGAGTTGGATAACAAGTCTGTATCTCTGAAATTGAAGTAAGAGTAAGATCTTTTCCT
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
17344057 ATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAGC
66 ATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAGC
17344122 AAGATCATTTCCTATCCTCTTGAA
131 AAGATCATTTCCTATCCTCTTGAA
* *
17344146 ATTGAAGTAAAGCTGGATATCAAGACTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATCTCCT
1 ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
* * *
17344211 ATCCTCTTGAAATTGAAGTAGAGCCGGATATCAAGACTTTATCTCTCTGAA
66 ATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAA
17344262 GCTATAGTAG
Statistics
Matches: 250, Mismatches: 18, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
152 88 0.35
153 11 0.04
154 151 0.60
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (154 bp):
ATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCCT
ATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTCTGAAATTGAAGTAAGAGC
AAGATCATTTCCTATCCTCTTGAA
Found at i:17344553 original size:6 final size:6
Alignment explanation
Indices: 17344534--17344602 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
17344524 ACTTTTATGT
* * *
17344534 TTTAAT TTTGAA TTTAAA -TTAATT TTTAAA -TT-A- TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA
*
17344579 TTT-AT TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
17344603 CAAATTATCA
Statistics
Matches: 50, Mismatches: 7, Indels: 12
0.72 0.10 0.17
Matches are distributed among these distances:
4 3 0.06
5 11 0.22
6 32 0.64
7 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:17344574 original size:17 final size:19
Alignment explanation
Indices: 17344554--17344592 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
17344544 AATTTAAATT
17344554 AATTTTTAAA-TTA-TTTA
1 AATTTTTAAATTTATTTTA
17344571 AA--TTTAAATTTATTTTA
1 AATTTTTAAATTTATTTTA
17344588 AATTT
1 AATTT
17344593 AAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 6
0.75 0.00 0.25
Matches are distributed among these distances:
15 6 0.33
16 3 0.17
17 8 0.44
19 1 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
AATTTTTAAATTTATTTTA
Found at i:17344576 original size:27 final size:26
Alignment explanation
Indices: 17344544--17344628 Score: 79
Period size: 27 Copynumber: 3.3 Consensus size: 26
17344534 TTTAATTTTG
17344544 AATTTAAATTAATTTTTAAATTATTTA
1 AATTTAAATTAATTTTTAAA-TATTTA
*
17344571 AATTTAAATTTA-TTTT-AA-ATTTA
1 AATTTAAATTAATTTTTAAATATTTA
* * *
17344594 AATTTAAATCAAATTATCAAA-ATATTA
1 AATTTAAAT-TAATTTTTAAATAT-TTA
17344621 AATTTAAA
1 AATTTAAA
17344629 CATTAAAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
23 14 0.29
24 1 0.02
25 4 0.08
26 8 0.16
27 22 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AATTTAAATTAATTTTTAAATATTTA
Found at i:17344593 original size:17 final size:16
Alignment explanation
Indices: 17344558--17344599 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
17344548 TAAATTAATT
17344558 TTTAAA-TTATTTAAA
1 TTTAAATTTATTTAAA
17344573 TTTAAATTTATTTTAAA
1 TTTAAATTTA-TTTAAA
17344590 TTTAAATTTA
1 TTTAAATTTA
17344600 AATCAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.24
16 3 0.12
17 16 0.64
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTAAATTTATTTAAA
Found at i:17344607 original size:17 final size:17
Alignment explanation
Indices: 17344570--17344608 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
17344560 TAAATTATTT
** *
17344570 AAATTTAAATTTATTTT
1 AAATTTAAATTTAAATC
17344587 AAATTTAAATTTAAATC
1 AAATTTAAATTTAAATC
17344604 AAATT
1 AAATT
17344609 ATCAAAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
AAATTTAAATTTAAATC
Found at i:17346622 original size:59 final size:59
Alignment explanation
Indices: 17346558--17346935 Score: 469
Period size: 59 Copynumber: 6.4 Consensus size: 59
17346548 CGTAAACTAT
** * *
17346558 CCAAAAATTACCATTTTACCCTCGAACTTTCTGAAA-TCATATTTTTAACCACGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTAACCTCGATTTCA
*
17346617 CCAAAAATTACCATTTTACCC-CTAAACTTTCCAAAAATTCCA-TTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTC-GAACTTTCC-AAAATTCCATTTTTAACCTCGATTTCA
* * * *
17346676 CCAAAAAATTACCATTTTACCCTCAAACTTTCAAAAATTCCA-TTTTAACCCCAATTTCA
1 CC-AAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
17346735 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCTATTTTTGATCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
17346794 CCAAAAATTACCATTTTATCCC-CAAACTTTCCAAAATTCCATTTTCAACCTCAATTTCA
1 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * * * * *
17346853 CCAAAAATTACTATTTTACCCTTGAATTTTCCAAAATTCCCTTTTTGACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
17346912 CTAAAAATTACCATTTTGCCCTCG
1 CCAAAAATTACCATTTTACCCTCG
17346936 CGAGTCTAAA
Statistics
Matches: 277, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
58 40 0.14
59 200 0.72
60 34 0.12
61 3 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:17346662 original size:29 final size:29
Alignment explanation
Indices: 17346617--17346888 Score: 156
Period size: 29 Copynumber: 9.2 Consensus size: 29
17346607 CACGATTTCA
17346617 CCAAAAATTACCATTTTACCCCTAAACTTT
1 CCAAAAATTACCATTTTA-CCCTAAACTTT
* **
17346647 CCAAAAATT-CCATTTTAACCTCGA-TTT
1 CCAAAAATTACCATTTTACCCTAAACTTT
17346674 CACCAAAAAATTACCATTTTACCCTCAAACTTT
1 --CC-AAAAATTACCATTTTACCCT-AAACTTT
*
17346707 -CAAAAATT-CCATTTTAACCC-CAA-TTT
1 CCAAAAATTACCATTTT-ACCCTAAACTTT
*
17346733 CACCAAAAATTACCATTTTACCCTCGAACTTT
1 --CCAAAAATTACCATTTTACCCT-AAACTTT
* * **
17346765 CC-AAAATT-CTATTTTTGA-TCTCGA-TTT
1 CCAAAAATTACCA-TTTT-ACCCTAAACTTT
*
17346792 CACCAAAAATTACCATTTTATCCCCAAACTTT
1 --CCAAAAATTACCATTTTA-CCCTAAACTTT
* *
17346824 CC-AAAATT-CCATTTTCAACCTCAA-TTT
1 CCAAAAATTACCATTTT-ACCCTAAACTTT
* * *
17346851 CACCAAAAATTACTATTTTACCCTTGAATTTT
1 --CCAAAAATTACCATTTTACCC-TAAACTTT
17346883 CCAAAA
1 CCAAAA
17346889 TTCCCTTTTT
Statistics
Matches: 189, Mismatches: 23, Indels: 60
0.69 0.08 0.22
Matches are distributed among these distances:
26 3 0.02
27 11 0.06
28 25 0.13
29 57 0.30
30 54 0.29
31 26 0.14
32 10 0.05
33 3 0.02
ACGTcount: A:0.36, C:0.28, G:0.02, T:0.35
Consensus pattern (29 bp):
CCAAAAATTACCATTTTACCCTAAACTTT
Found at i:17346854 original size:177 final size:177
Alignment explanation
Indices: 17346558--17346935 Score: 548
Period size: 177 Copynumber: 2.1 Consensus size: 177
17346548 CGTAAACTAT
**
17346558 CCAAAAATTACCATTTTACCCTCGAACTTTCTGAAATCATATTTTTAACCACGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATCATATTTTTAACCACGATTTCACCAAAA
*
17346623 ATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTAACCTCGATTTCACCAAAAAATTAC
66 ATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTAACCTCAATTTCACC-AAAAATTAC
17346688 CATTTTACCCTCAAACTTTCAAAAATT-CCATTTTAACCCCAATTTCA
130 CATTTTACCCTCAAACTTTCAAAAATTCCCATTTTAACCCCAATTTCA
* * *
17346735 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-TATTTTTGATCTCGATTTCACCAAA
1 CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAA-TCATATTTTTAACCACGATTTCACCAAA
17346799 AATTACCATTTTATCCCC-AAACTTTCC-AAAATTCCATTTTCAACCTCAATTTCACCAAAAATT
65 AATTACCATTTTA-CCCCTAAACTTTCCAAAAATTCCATTTT-AACCTCAATTTCACCAAAAATT
* ** * * * * *
17346862 ACTATTTTACCCTTGAATTTTCCAAAATTCCCTTTTTGACCCCGATTTCA
128 ACCATTTTACCCTCAAACTTTCAAAAATTCCCATTTTAACCCCAATTTCA
* *
17346912 CTAAAAATTACCATTTTGCCCTCG
1 CCAAAAATTACCATTTTACCCTCG
17346936 CGAGTCTAAA
Statistics
Matches: 181, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
176 44 0.24
177 131 0.72
178 6 0.03
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (177 bp):
CCAAAAATTACCATTTTACCCTCGAACTTTCCAAAATCATATTTTTAACCACGATTTCACCAAAA
ATTACCATTTTACCCCTAAACTTTCCAAAAATTCCATTTTAACCTCAATTTCACCAAAAATTACC
ATTTTACCCTCAAACTTTCAAAAATTCCCATTTTAACCCCAATTTCA
Done.