Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 94 of 240
Found at i:29541092 original size:21 final size:19
Alignment explanation
Indices: 29541068--29541113 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
29541058 AAATTTTATT
29541068 AAAAATCATAAAAATATAGAA
1 AAAAAT-ATAAAAAT-TAGAA
* *
29541089 AAAAATTTAAAAATTATAA
1 AAAAATATAAAAATTAGAA
29541108 AAAAAT
1 AAAAAT
29541114 TAATATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 7 0.30
21 6 0.26
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
AAAAATATAAAAATTAGAA
Found at i:29541100 original size:19 final size:19
Alignment explanation
Indices: 29541076--29541114 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
29541066 TTAAAAATCA
29541076 TAAAAATATAGAAAAAAATT
1 TAAAAAT-TAGAAAAAAATT
*
29541096 TAAAAATTATAAAAAAATT
1 TAAAAATTAGAAAAAAATT
29541115 AATATAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (19 bp):
TAAAAATTAGAAAAAAATT
Found at i:29545465 original size:26 final size:27
Alignment explanation
Indices: 29545415--29545466 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
29545405 TTTTTCTAAT
* *
29545415 TTTTTATCTTTTATAATAAAATTTTAG
1 TTTTTATATTTTATAAGAAAATTTTAG
*
29545442 TTTTTATATTTT-TAAGAAATTTTTA
1 TTTTTATATTTTATAAGAAAATTTTA
29545467 AATTTCTAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.62
Consensus pattern (27 bp):
TTTTTATATTTTATAAGAAAATTTTAG
Found at i:29545514 original size:18 final size:18
Alignment explanation
Indices: 29545491--29545526 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29545481 TTCTATATGT
29545491 TTTTATAAATTTTGAATA
1 TTTTATAAATTTTGAATA
* *
29545509 TTTTATATATTTTTAATA
1 TTTTATAAATTTTGAATA
29545527 ATATTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (18 bp):
TTTTATAAATTTTGAATA
Found at i:29545533 original size:30 final size:29
Alignment explanation
Indices: 29545465--29545540 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
29545455 AAGAAATTTT
* *
29545465 TAAATTTCTAGAATTTTTCTATATGTTTTTA
1 TAAATTT-T-GAATTTTTATATATGTTTTAA
29545496 TAAATTTTGAATATTTTATATAT-TTTTAA
1 TAAATTTTGAAT-TTTTATATATGTTTTAA
*
29545525 TAATATTTTTAATTTT
1 TAA-ATTTTGAATTTT
29545541 AAATGATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
29 15 0.38
30 18 0.45
31 7 0.17
ACGTcount: A:0.33, C:0.03, G:0.04, T:0.61
Consensus pattern (29 bp):
TAAATTTTGAATTTTTATATATGTTTTAA
Found at i:29545973 original size:29 final size:30
Alignment explanation
Indices: 29545897--29545962 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
29545887 TTAATTTTTA
29545897 TTATTAAAATAA-AAATATAATATTGAATAAT
1 TTATTAAAATAATAAAT-T-ATATTGAATAAT
29545928 TTATTAAAATAATAAATTATATT-AATAAT
1 TTATTAAAATAATAAATTATATTGAATAAT
29545957 TTATTA
1 TTATTA
29545963 TATTATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 12 0.35
30 5 0.15
31 13 0.38
32 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
TTATTAAAATAATAAATTATATTGAATAAT
Found at i:29562200 original size:109 final size:110
Alignment explanation
Indices: 29561988--29562300 Score: 481
Period size: 109 Copynumber: 2.9 Consensus size: 110
29561978 TAAATTCAAG
* * * * *
29561988 AGGATATTTTGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGTACG-TTCCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
29562050 GAATTTCCAAACACAAAACATTGCCTTATTTTAAATTTTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAATATTTTTAAA
29562095 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
29562160 GAATTTCTAAACGCAAAACATTGCCTCATTTTAAA-ATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTTATTTTAAATATTTTTAAA
*
29562204 AGGATGTTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* *
29562269 GAATTTCCCAAACGCTAAATATTGCCTTATTT
66 GAATTT-CCAAACGCAAAACATTGCCTTATTT
29562301 AGAAAAACAT
Statistics
Matches: 188, Mismatches: 14, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
107 25 0.13
109 105 0.56
110 58 0.31
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (110 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTTATTTTAAATATTTTTAAA
Found at i:29564543 original size:40 final size:40
Alignment explanation
Indices: 29564489--29564576 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
29564479 GGTTTCTTCT
*
29564489 ATCTTCTCCACTACTGCTTAGGGAGATAAGACTTGAT-TCG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGT-G
29564529 ATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTG
29564569 ATCTGCTC
1 ATCTGCTC
29564577 TACTGTAATC
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (40 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGACTTGATGTG
Found at i:29564697 original size:131 final size:130
Alignment explanation
Indices: 29564548--29565082 Score: 364
Period size: 131 Copynumber: 4.1 Consensus size: 130
29564538 ACTACTGCTT
* * *
29564548 AGGGAGATAAGA-CTTGATGTGATCTGCTCTACTGTAA-TCTCAGGGAGATAAGATCTCTGGT-T
1 AGGGAGATAAGATCCTGATGTAATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTCT-GTCT
*
29564610 TCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAATTCTTTGGTCTACTCCACTGTAA
64 TCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTG-AATTC-TTGATCTACTCCACTGTAA
29564675 CCTC
127 CCTC
** * * ** * *
29564679 AGGGAGATAAGA-CCTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATC-CTTTATTT
1 AGGGAGATAAGATCCTGATGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTCTGT-CTT
* * ** * * * * * *
29564742 TAATCCGCTCCACTACAACTTCAGGGAGATAGGA--T-AGTGTCTTCGATCTGCTCCGCTGTAAT
65 CAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTT-GATCTACTCCACTGTAAC
29564804 CTC
128 CTC
* * * * *
29564807 AGGGAGATAAGATCTCTGGCT-TCAATCTGTTCCACTGTAACCTCGGGGAGATAAGATCTGAAAT
1 AGGGAGATAAGATC-CT-GATGT-AATCTGCTCCACTGTAACTTCAGGGAGATAAGATCT---CT
* * * * * *
29564871 -TCTTCAGTCTGCTCCATTGTAACCTCAGAGAGATAAGACCTG-ATGC--GATCTACTCTACTGT
60 GTCTTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTGATCTACTCCACTGT
*
29564932 AACTTC
125 AACCTC
* * * * * **
29564938 AGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGAT-AGTGTCT
1 AGGGAGATAAGATCC-TGA-TGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTCTGTCT
* * * * * * **
29565002 TCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CTGGCTTCAATCTGTTCCACTGTAA
64 TCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAT-TCTT-GATCTACTCCACTGTAA
29565065 CCTC
127 CCTC
29565069 AGGGAGATAAGATC
1 AGGGAGATAAGATC
29565083 TGAAATTCTT
Statistics
Matches: 311, Mismatches: 69, Indels: 48
0.73 0.16 0.11
Matches are distributed among these distances:
127 6 0.02
128 67 0.22
129 3 0.01
130 5 0.02
131 196 0.63
132 2 0.01
133 27 0.09
134 2 0.01
135 3 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (130 bp):
AGGGAGATAAGATCCTGATGTAATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTCTGTCTTC
AATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAATTCTTGATCTACTCCACTGTAACCTC
Found at i:29564807 original size:218 final size:218
Alignment explanation
Indices: 29564568--29565259 Score: 1240
Period size: 218 Copynumber: 3.2 Consensus size: 218
29564558 GACTTGATGT
** * *
29564568 GATCTGCTCTACTGTAATCTCAGGGAGATAAGATCTCTGGTTTCAATCTGCTCCACTGTAACCTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
* *
29564633 AGGGAGATAAGATCTGAAATTCTTTGGTCTACTCCACTGTAACCTCAGGGAGATAAGACCTGATG
66 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATG
* **
29564698 CGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTACAACTT
131 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
29564763 CAGGGAGATAGGATAGTGTCTTC
196 CAGGGAGATAGGATAGTGTCTTC
29564786 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
* * * *
29564851 GGGGAGATAAGATCTGAAATTCTTCAGTCTGCTCCATTGTAACCTCAGAGAGATAAGACCTGATG
66 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATG
29564916 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
131 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
29564981 CAGGGAGATAGGATAGTGTCTTC
196 CAGGGAGATAGGATAGTGTCTTC
29565004 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
* *
29565069 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACTTTAGAGAGATAAGACCTGATG
66 AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATG
*
29565134 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTTTAATCCGCTCCACTGTAACTT
131 CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
29565199 CAGGGAGATAGGATAGTGTCTTC
196 CAGGGAGATAGGATAGTGTCTTC
29565222 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
1 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT
29565260 AACATTCACT
Statistics
Matches: 454, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
218 454 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (218 bp):
GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTC
AGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGTAACCTCAGAGAGATAAGACCTGATG
CGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTT
CAGGGAGATAGGATAGTGTCTTC
Found at i:29565225 original size:87 final size:87
Alignment explanation
Indices: 29564508--29565257 Score: 421
Period size: 87 Copynumber: 8.7 Consensus size: 87
29564498 ACTACTGCTT
* * * * * *
29564508 AGGGAGATAAGA-CTTG-ATTCGATCTGCTCCACTACT-GCTT-AGGGAGATAAGA-C-TTGATG
1 AGGGAGATAAGATCCTGTCTTCGATCTGCTCCACT-GTAACTTCAGGGAGATAAGATCTTTTATT
* *
29564567 T-GATCTGCTCTACTGTAA-TCTC
65 TCAATCTGCTCCACTGTAACT-TC
* * *
29564589 AGGGAGATAAGATCTCTGGT-TTCAATCTGCTCCACTGTAACCTCAGGGAGATAAGATCTGAAAT
1 AGGGAGATAAGATC-CT-GTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCT---TT
* ** * *
29564653 TCTTT-GGTCTACTCCACTGTAACCTC
61 TATTTCAATCTGCTCCACTGTAACTTC
* * * * ** *
29564679 AGGGAGATAAGA-CCTG-ATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTT
1 AGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
* * **
29564742 TAATCCGCTCCACTACAACTTC
66 CAATCTGCTCCACTGTAACTTC
* ** * * ***
29564764 AGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCTCTGGCT
1 AGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCTTTTATT
* *
29564828 TCAATCTGTTCCACTGTAACCTC
65 TCAATCTGCTCCACTGTAACTTC
* * * * *
29564851 GGGGAGATAAGAT-CTGAAATTCTTC-AGTCTGCTCCATTGTAACCTCAGAGAGATAAGA-C-CT
1 AGGGAGATAAGATCCTG----TCTTCGA-TCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTT
* * * * *
29564912 GA-TGCGATCTACTCTACTGTAACTTC
61 TATTTCAATCTGCTCCACTGTAACTTC
* * * ** * * ** * *
29564938 AGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAACTTCAGGGAGATAGGATAGTGT-CT
1 AGGGAGATAAGATCCTGT-CTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATT
* *
29565002 TCGATCTGCTCCGCTGTAA-TCTC
65 TCAATCTGCTCCACTGTAACT-TC
* * * * ***
29565025 AGGGAGATAAGATCTCTGGCTTCAATCTGTTCCACTGTAACCTCAGGGAGATAAGATCTGAAATT
1 AGGGAGATAAGATC-CTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTA-T
** * *
29565090 CTTCGGTCTACTCCACTGTAACTTT
64 -TTCAATCTGCTCCACTGTAACTTC
* * * * * *
29565115 AGAGAGATAAGA-CCTG-ATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCTTTTATTT
1 AGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
* *
29565178 TAATCCGCTCCACTGTAACTTC
66 CAATCTGCTCCACTGTAACTTC
* ** *
29565200 AGGGAGATAGGATAGTGTCTTCGATCTGCTCCGCTGTAA-TCTCAGGGAGATAAGATCT
1 AGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACT-TCAGGGAGATAAGATCT
29565258 CTAACATTCA
Statistics
Matches: 501, Mismatches: 130, Indels: 70
0.71 0.19 0.10
Matches are distributed among these distances:
81 12 0.02
82 1 0.00
83 2 0.00
84 24 0.05
85 93 0.19
86 12 0.02
87 249 0.50
88 12 0.02
89 4 0.01
90 91 0.18
91 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (87 bp):
AGGGAGATAAGATCCTGTCTTCGATCTGCTCCACTGTAACTTCAGGGAGATAAGATCTTTTATTT
CAATCTGCTCCACTGTAACTTC
Found at i:29577063 original size:109 final size:110
Alignment explanation
Indices: 29576843--29577157 Score: 433
Period size: 109 Copynumber: 2.9 Consensus size: 110
29576833 TAAATTCAAG
* * * * *
29576843 AGGATATTTTGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGTACG-TTCCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
29576905 GAATTTCCAAACACAAAACATTGCCTTC-TTTTAAAAAAAATTTTAAA
66 GAATTTCCAAACGCAAAACATTGCC-TCATTTT--AAAAAATTTTAAA
29576952 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
*
29577017 GAATTTCCAAACGCAAAACATTGCCTCATTTT-AAAATTTTTAAA
66 GAATTTCCAAACGCAAAACATTGCCTCATTTTAAAAAATTTTAAA
* * *
29577061 AGGATGTTTAACTATTTGGTTGAACGAGAAAAATCGAAACCCAACACATTAGGGCACGTTTTCTC
1 AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
* * * *
29577126 AAATTTCCCAAACGCTAAATATTGCCTTATTT
66 GAATTT-CCAAACGCAAAACATTGCCTCATTT
29577158 AGAAAAACAT
Statistics
Matches: 187, Mismatches: 14, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
109 103 0.55
110 22 0.12
111 29 0.16
112 33 0.18
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (110 bp):
AGGATATTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTTCTC
GAATTTCCAAACGCAAAACATTGCCTCATTTTAAAAAATTTTAAA
Found at i:29593618 original size:5 final size:5
Alignment explanation
Indices: 29593605--29593635 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
29593595 TACAGTATCC
*
29593605 CTCAT CTCAA CTCAA CTCAA CTCAA CTCAA C
1 CTCAA CTCAA CTCAA CTCAA CTCAA CTCAA C
29593636 AGTCCAGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (5 bp):
CTCAA
Found at i:29598605 original size:45 final size:45
Alignment explanation
Indices: 29598551--29598643 Score: 177
Period size: 45 Copynumber: 2.1 Consensus size: 45
29598541 TAACATGAAC
*
29598551 GTGTTTTCATTCACTCTCATTACCCATAATTTATAACACATTGTT
1 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
29598596 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
1 GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
29598641 GTG
1 GTG
29598644 AATTAACCCA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.26, C:0.23, G:0.09, T:0.43
Consensus pattern (45 bp):
GTGTTTTCATTCACTCTCACTACCCATAATTTATAACACATTGTT
Found at i:29601846 original size:123 final size:125
Alignment explanation
Indices: 29601627--29601903 Score: 506
Period size: 123 Copynumber: 2.2 Consensus size: 125
29601617 TTCCGAGTTA
29601627 ACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
1 ACGTTTCTGAG-CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAA
*
29601691 ATCGTGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAAT-ATTTT-TTTTG
65 ATCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
*
29601750 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGATAAGAAATTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
29601815 TCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
66 TCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
29601875 ACGTTTCTGAGCAAATAGTATAAAATCGC
1 ACGTTTCTGAGCAAATAGTATAAAATCGC
29601904 GCCCTCGTGG
Statistics
Matches: 149, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
123 109 0.73
124 6 0.04
125 34 0.23
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (125 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
TCGTGCCCTCGTGGACACGATTTCGCTACAGTTGGTCATGTAAGAAATAATTTTCTTTTG
Found at i:29608695 original size:73 final size:73
Alignment explanation
Indices: 29608565--29608700 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 73
29608555 CTTTGACTTT
* *
29608565 GGTCACACGGCCAAGCCACACACCCGTGTGCTAGACTGTGTGAGCATACTGACTTGCATTAATAA
1 GGTCACACGGCCAAGCCACACACCCGTGTGCTAGACCGTGTGAGCATACTGACTTGCACTAATAA
29608630 GATGCAGG
66 GATGCAGG
* ** * * **
29608638 GGTCACATGGCCAAGCCACATGCTCGTGTGCTATG-CCGTGTGAGCATTCTGTTTTGCACTAAT
1 GGTCACACGGCCAAGCCACACACCCGTGTGCTA-GACCGTGTGAGCATACTGACTTGCACTAAT
29608701 TAAAAGATAC
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
73 52 0.98
74 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.25
Consensus pattern (73 bp):
GGTCACACGGCCAAGCCACACACCCGTGTGCTAGACCGTGTGAGCATACTGACTTGCACTAATAA
GATGCAGG
Found at i:29609718 original size:15 final size:15
Alignment explanation
Indices: 29609693--29609727 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29609683 TACTTTATTT
*
29609693 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
29609707 TAATTAATATTAAGA
1 TAATTAATATTAAGA
29609722 TAATTA
1 TAATTA
29609728 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:29612593 original size:69 final size:69
Alignment explanation
Indices: 29612482--29612622 Score: 237
Period size: 69 Copynumber: 2.0 Consensus size: 69
29612472 CTCGAAACAT
*
29612482 TTAGGAATGTCGAGATCAACATTCCGCTGTTGGACGCCATCAAGAAAATACCACAGTATGCTAAA
1 TTAGGAATGTCGAGATCAACATTCCACTGTTGGACGCCATCAAGAAAATACCACAGTATGCTAAA
29612547 TTTC
66 TTTC
* * * *
29612551 TTAGGAATGTCGAGATTAACATTCCACTGTTGGACGCCATCAAGCAAATACCGCGGTATGCTAAA
1 TTAGGAATGTCGAGATCAACATTCCACTGTTGGACGCCATCAAGAAAATACCACAGTATGCTAAA
29612616 TTTC
66 TTTC
29612620 TTA
1 TTA
29612623 AAGAGCTTTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 67 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (69 bp):
TTAGGAATGTCGAGATCAACATTCCACTGTTGGACGCCATCAAGAAAATACCACAGTATGCTAAA
TTTC
Found at i:29613759 original size:4 final size:4
Alignment explanation
Indices: 29613744--29613810 Score: 52
Period size: 4 Copynumber: 16.5 Consensus size: 4
29613734 AATTTTTATT
*
29613744 TTTA TTTA --TA TTTA TTTA TTTA TTTTC TTTA CTTTA TTTA -TTA CTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA -TTTA
29613792 TTTTA TTT- TATTA TTTA TT
1 -TTTA TTTA T-TTA TTTA TT
29613811 ACTTATTCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
2 2 0.04
3 4 0.08
4 31 0.60
5 15 0.29
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:29613765 original size:18 final size:18
Alignment explanation
Indices: 29613744--29613785 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
29613734 AATTTTTATT
29613744 TTTATTTATATTTA-TTTA
1 TTTATTT-TATTTACTTTA
*
29613762 TTTATTTTCTTTACTTTA
1 TTTATTTTATTTACTTTA
29613780 TTTATT
1 TTTATT
29613786 ACTTTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTTATTTACTTTA
Found at i:29613801 original size:18 final size:16
Alignment explanation
Indices: 29613738--29613810 Score: 69
Period size: 17 Copynumber: 4.4 Consensus size: 16
29613728 CAACCCAATT
29613738 TTTATTTTTATTTA-TA
1 TTTA-TTTTATTTATTA
*
29613754 TTTA-TTTATTTATTTTC
1 TTTATTTTATTTA--TTA
*
29613771 TTTACTTTATTTATTA
1 TTTATTTTATTTATTA
29613787 CTTTATTTTATTTTATTA
1 -TTTATTTTA-TTTATTA
29613805 TTTATT
1 TTTATT
29613811 ACTTATTCGG
Statistics
Matches: 48, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 8 0.17
16 6 0.12
17 19 0.40
18 15 0.31
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTATTTTATTTATTA
Found at i:29613801 original size:22 final size:22
Alignment explanation
Indices: 29613738--29613810 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
29613728 CAACCCAATT
29613738 TTTATTTTTATTTATATTTATTTA
1 TTTA-TTTTATTT-TATTTATTTA
*
29613762 TTTATTTT-CTTTACTTTATTTA
1 TTTATTTTATTTTA-TTTATTTA
*
29613784 -TTACTTTATTTTATTT-TATTA
1 TTTATTTTATTTTATTTAT-TTA
29613805 TTTATT
1 TTTATT
29613811 ACTTATTCGG
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
20 1 0.02
21 14 0.34
22 18 0.44
23 4 0.10
24 4 0.10
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTATTTTATTTTATTTATTTA
Found at i:29615293 original size:25 final size:25
Alignment explanation
Indices: 29615265--29615379 Score: 85
Period size: 25 Copynumber: 4.6 Consensus size: 25
29615255 GTATAACAAA
*
29615265 AAGCTCTTGCGAGCCAATTATCGAG
1 AAGCTCTTGAGAGCCAATTATCGAG
* * * *
29615290 AAGCT-TAT-ACGAG-CTATAAACGGG
1 AAGCTCT-TGA-GAGCCAATTATCGAG
** *
29615314 AAGCTCAAGAGAGCC-ATTAATCGGG
1 AAGCTCTTGAGAGCCAATT-ATCGAG
*
29615339 AAGCTCTTGAGAGCCAAATATCGAG
1 AAGCTCTTGAGAGCCAATTATCGAG
*
29615364 AAGCTCGTGAGAGCCA
1 AAGCTCTTGAGAGCCA
29615380 TATAACAGAA
Statistics
Matches: 69, Mismatches: 14, Indels: 14
0.71 0.14 0.14
Matches are distributed among these distances:
24 18 0.26
25 49 0.71
26 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (25 bp):
AAGCTCTTGAGAGCCAATTATCGAG
Found at i:29622481 original size:25 final size:24
Alignment explanation
Indices: 29622453--29622546 Score: 84
Period size: 25 Copynumber: 3.8 Consensus size: 24
29622443 AGCTCTTGCA
29622453 AGCCAATTATCGGGAAGCTCATACG
1 AGCCAATTATCGGGAAGCTCATA-G
*
29622478 AGCC-ATAAAT-GGGAAGCTCAATAG
1 AGCCAAT-TATCGGGAAGCTC-ATAG
* * *
29622502 AGCCATTTATCAGGAAGCTTATGAG
1 AGCCAATTATCGGGAAGCTCAT-AG
* *
29622527 ATCCAAATATCGGGAAGCTC
1 AGCCAATTATCGGGAAGCTC
29622547 GTGAAAGCCA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
24 20 0.37
25 34 0.63
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.21
Consensus pattern (24 bp):
AGCCAATTATCGGGAAGCTCATAG
Found at i:29622914 original size:59 final size:61
Alignment explanation
Indices: 29622822--29622938 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 61
29622812 CCTCGACAAG
29622822 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTT-TTTT-CTCGATCCAATTCCGTA
1 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCCGTA
29622881 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCC
1 TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCC
29622939 ATATTAGGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
59 38 0.68
60 4 0.07
61 14 0.25
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.42
Consensus pattern (61 bp):
TATACATAGATTTGTAAGCTACTAGTCCGATACTTTTTCTTTTCCTCGATCCAATTCCGTA
Found at i:29626834 original size:24 final size:24
Alignment explanation
Indices: 29626806--29626866 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
29626796 GGGATTATAA
*
29626806 GAAGATGAAAGGTG-GAGAGTTAAG
1 GAAGATGAAAGGTGAAAG-GTTAAG
*
29626830 GAAGATGAAATGTGAAAGGTTAAG
1 GAAGATGAAAGGTGAAAGGTTAAG
*
29626854 AAAGATGAAAGGT
1 GAAGATGAAAGGT
29626867 TGAACATCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (24 bp):
GAAGATGAAAGGTGAAAGGTTAAG
Found at i:29627598 original size:29 final size:29
Alignment explanation
Indices: 29627556--29627613 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
29627546 ATTGGATACT
29627556 CAATAGCAATTCTTTATAATATCATTGTG
1 CAATAGCAATTCTTTATAATATCATTGTG
29627585 CAATAGCAATTCTTTATAATATCATTGTG
1 CAATAGCAATTCTTTATAATATCATTGTG
29627614 TAACAATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.41
Consensus pattern (29 bp):
CAATAGCAATTCTTTATAATATCATTGTG
Found at i:29632931 original size:24 final size:24
Alignment explanation
Indices: 29632899--29632951 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
29632889 ATAAATCATC
**
29632899 AATA-TAATTAAAATTATTATATT
1 AATATTAATTAAAACAATTATATT
29632922 AATATTAATTAAAACAATTATATT
1 AATATTAATTAAAACAATTATATT
29632946 AATATT
1 AATATT
29632952 TAAAAAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (24 bp):
AATATTAATTAAAACAATTATATT
Found at i:29632956 original size:21 final size:22
Alignment explanation
Indices: 29632899--29632960 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
29632889 ATAAATCATC
* *
29632899 AATATAATTAAAATTATTATATT
1 AATATTATTAAAA-AATTATATT
29632922 AATATTAATTAAAACAATTATATT
1 AATATT-ATTAAAA-AATTATATT
29632946 AATA-T-TTAAAAAATT
1 AATATTATTAAAAAATT
29632961 CCTTCCCCCA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
23 6 0.17
24 19 0.54
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATTATTAAAAAATTATATT
Found at i:29636111 original size:25 final size:25
Alignment explanation
Indices: 29636083--29636159 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
29636073 TGAATTTTTT
*
29636083 TTAATATTAATA-TAATTATTTTTCA
1 TTAATATTAATATTAA-TATTTTTAA
*
29636108 TTAATATTAATATTGATATTTTTAA
1 TTAATATTAATATTAATATTTTTAA
*
29636133 TTATATATTAATTATTTATAATTTTTA
1 TTA-ATATTAA-TATTAAT-ATTTTTA
29636160 TATAATTTTC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
25 23 0.51
26 9 0.20
27 6 0.13
28 7 0.16
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (25 bp):
TTAATATTAATATTAATATTTTTAA
Found at i:29666414 original size:19 final size:20
Alignment explanation
Indices: 29666377--29666417 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
29666367 TGGGTAGGAC
29666377 TGTTTTCACAAAATCTGCAT
1 TGTTTTCACAAAATCTGCAT
* *
29666397 TGTTTT-ACTAAATGTGCAT
1 TGTTTTCACAAAATCTGCAT
29666416 TG
1 TG
29666418 ACGTGATCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
TGTTTTCACAAAATCTGCAT
Found at i:29668311 original size:26 final size:26
Alignment explanation
Indices: 29668278--29668337 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
29668268 TTTACAACAG
* *
29668278 TAAAATTTTGACAATTTTATTCCTGA
1 TAAAATTTTGACAATTTTACTCCTAA
**
29668304 TAAAATTTTGATGATTTTACTCCTAA
1 TAAAATTTTGACAATTTTACTCCTAA
29668330 TAAAATTT
1 TAAAATTT
29668338 CGAGAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (26 bp):
TAAAATTTTGACAATTTTACTCCTAA
Found at i:29679585 original size:3 final size:3
Alignment explanation
Indices: 29679568--29679635 Score: 66
Period size: 3 Copynumber: 23.0 Consensus size: 3
29679558 AGGTTAGATC
* * * * *
29679568 AAT AAA AAT -AT AAT AAT AGT AGT AGT AAT AAT AAT AAT AAT AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
29679615 AAC AAT AAT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
29679636 GAAGCTCAAG
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
2 2 0.04
3 52 0.96
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:29679632 original size:21 final size:21
Alignment explanation
Indices: 29679577--29679633 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
29679567 CAATAAAAAT
* *
29679577 ATAATAATAGTAGTAGTAATA
1 ATAATAATAGTAATAGTAACA
* *
29679598 ATAATAATAATAATATTAACA
1 ATAATAATAGTAATAGTAACA
29679619 ATAATAATAGTAATA
1 ATAATAATAGTAATA
29679634 ATGAAGCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
ATAATAATAGTAATAGTAACA
Found at i:29680540 original size:4 final size:4
Alignment explanation
Indices: 29680531--29680560 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
29680521 TTTTCCTTCG
29680531 AAAT AAAT -AAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
29680561 CCGAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:29681321 original size:51 final size:51
Alignment explanation
Indices: 29681251--29681365 Score: 124
Period size: 51 Copynumber: 2.3 Consensus size: 51
29681241 GGGAGATGTG
* * ** * * *
29681251 ATTCGTTGCCTTTAACTTTAATCTGTTCCATTAG-AACGCTAGGGAAATAAT
1 ATTCGCTGCCTTCAACTTTAATCCATTCCACT-GCAACGCCAGGGAAATAAA
* *
29681302 ATTTGCTGCCTTCAGCTTTAATCCATTCCACTGCAACGCCAGGGAAATAAA
1 ATTCGCTGCCTTCAACTTTAATCCATTCCACTGCAACGCCAGGGAAATAAA
*
29681353 ATTCGCTGTCTTC
1 ATTCGCTGCCTTC
29681366 GATCTGCTCT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 1 0.02
51 51 0.98
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (51 bp):
ATTCGCTGCCTTCAACTTTAATCCATTCCACTGCAACGCCAGGGAAATAAA
Found at i:29681552 original size:44 final size:44
Alignment explanation
Indices: 29681501--29682100 Score: 186
Period size: 44 Copynumber: 13.6 Consensus size: 44
29681491 CATTTTTTTT
*
29681501 ATCTACTCCACTACTGCTTAGGGAGACAAGATTTACATTCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACATTCTTCA
* * * * * * * *
29681545 ACCTACTCCACTGCTGCTCAGGGAGATGAGA-TTA-GTAGCCTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACAT-TCTTCA
* * * ** *
29681588 ATCTGCTTCC-CTACTACCTT-GGGAAGATAAGATTCACCGTCTTCG
1 ATCTAC-TCCACTACT-GCTTAGGG-AGATAAGATTTACATTCTTCA
* * * *
29681633 ATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTACATTCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACATTCTTCA
* ** * * * * *
29681677 ACCTACTCCACTGTTGCTCAGGGAGATGAGA-TTA-ATAGCCTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACAT-TCTTCA
* * * * ** *
29681720 ATCTGCTTGC-CTACTACATT-GGGAAGATAAGATTCACCGTCTTCG
1 ATCTAC-TCCACTACTGC-TTAGGG-AGATAAGATTTACATTCTTCA
* * ** *
29681765 ATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACATTCTTCA
* * * * * * *
29681809 ACCTACTCCACTGCTGCTCAGGGAGATAGGA-TTA-GTGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACAT-TCTTCA
** ** * * ** *
29681852 ATCTGTTTCC-CTACTATTTTGGGAAGATAAGATTCACCGTCTTCG
1 ATCT-ACTCCACTACTGCTTAGGG-AGATAAGATTTACATTCTTCA
* * * * * *
29681897 ATCTGCTCCGCTGCTGCTTAGGGAAACAAGATCTACATTCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACATTCTTCA
* * * * ** * *
29681941 ACCTACTCCACTGCTGCTCAGGGAGATAGGA-TT-GGTGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACAT-TCTTCA
* * * * **
29681984 ATCTGCTTCC-TTACTACTTTGGGAAGATAAGACTCAACA-TCTTCA
1 ATCTAC-TCCACTACTGCTTAGGG-AGATAAGA-TTTACATTCTTCA
* * * * * * *
29682029 ATCTACTCCGCTACTGCTTAGAGAGACAGGATCTACAATATTCA
1 ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACATTCTTCA
* * * *
29682073 ACCTACTCAACTGCTGCTCAGGGAGATA
1 ATCTACTCCACTACTGCTTAGGGAGATA
29682101 GGACTTGTTA
Statistics
Matches: 381, Mismatches: 145, Indels: 60
0.65 0.25 0.10
Matches are distributed among these distances:
42 5 0.01
43 74 0.19
44 229 0.60
45 73 0.19
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.29
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGATAAGATTTACATTCTTCA
Found at i:29681695 original size:132 final size:132
Alignment explanation
Indices: 29681343--29682103 Score: 1015
Period size: 132 Copynumber: 5.8 Consensus size: 132
29681333 TGCAACGCCA
* * * ** * * * * *
29681343 GGGAA-ATAAAATTCGCTGTCTTCGATCTGCTCTACTACTGCTCAAGGAGACATGATCTGCAATC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
* * *
29681407 TTCAACCTACTCCACTACTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCCTACTAGC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
29681472 TT
131 TT
* * * ** * * *
29681474 GGGAAGATAAGATTCGCCATTTTTTTTATCTACTCCACTACTGCTTAGGGAGACAAGATTTACAT
1 GGGAAGATAAGATTCACC--GTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACAT
* *
29681539 TCTTCAACCTACTCCACTGCTGCTCAGGGAGAT-GAGATTAGTAGCCTAAATCTGCTTCCCTACT
64 TCTTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAGTGGCTTAAATCTGCTTCCCTACT
29681603 ACCTT
128 ACCTT
*
29681608 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATTTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
* * * * * *
29681673 TTAAACCTACTCCACTGTTGCTCAGGGAGAT-GAGATTAATAGCCTAAATCTGCTTGCCTACTAC
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAG-GATTAGTGGCTTAAATCTGCTTCCCTACTAC
*
29681737 ATT
130 CTT
*
29681740 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACCAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
* **
29681805 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGTTTCCCTACTATT
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
29681870 TT
131 TT
* *
29681872 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTGCTGCTTAGGGAAACAAGATCTACATTC
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
* * *
29681937 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTGGTGGCTTAAATCTGCTTCCTTACTACT
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
29682002 TT
131 TT
* * * * * * * * *
29682004 GGGAAGATAAGACTCAACATCTTCAATCTACTCCGCTACTGCTTAGAGAGACAGGATCTACAATA
1 GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
*
29682069 TTCAACCTACTCAACTGCTGCTCAGGGAGATAGGA
66 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGA
29682104 CTTGTTATCT
Statistics
Matches: 564, Mismatches: 61, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
131 5 0.01
132 445 0.79
133 2 0.00
134 112 0.20
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
GGGAAGATAAGATTCACCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTACATTC
TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGATTAGTGGCTTAAATCTGCTTCCCTACTACC
TT
Found at i:29682699 original size:12 final size:12
Alignment explanation
Indices: 29682682--29682706 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29682672 TGACAACAAA
29682682 ATCTGAAGGGAT
1 ATCTGAAGGGAT
29682694 ATCTGAAGGGAT
1 ATCTGAAGGGAT
29682706 A
1 A
29682707 GTCTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (12 bp):
ATCTGAAGGGAT
Found at i:29690336 original size:11 final size:12
Alignment explanation
Indices: 29690305--29690339 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
29690295 CCGGTCAGCC
*
29690305 TATATTACTTTT
1 TATATTAATTTT
29690317 TATATTAATTTT
1 TATATTAATTTT
29690329 TATA-TAATTTT
1 TATATTAATTTT
29690340 AAAATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:29690493 original size:30 final size:30
Alignment explanation
Indices: 29690459--29690521 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
29690449 ACTTAACAAG
*
29690459 CAAATATCTCTAACATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
* *
29690489 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATATCTCTAAAATAATAACAAAATTAA
29690519 CAA
1 CAA
29690522 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (30 bp):
CAAATATCTCTAAAATAATAACAAAATTAA
Found at i:29701130 original size:17 final size:17
Alignment explanation
Indices: 29701108--29701141 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29701098 AATAAAGGAA
29701108 GTAATCTTAGAAGATTT
1 GTAATCTTAGAAGATTT
*
29701125 GTAATCTTAGAGGATTT
1 GTAATCTTAGAAGATTT
29701142 TATTCTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.41
Consensus pattern (17 bp):
GTAATCTTAGAAGATTT
Found at i:29703359 original size:38 final size:38
Alignment explanation
Indices: 29703260--29703375 Score: 196
Period size: 39 Copynumber: 3.0 Consensus size: 38
29703250 TAATTACCCA
*
29703260 ACCCAGTTACCAACCCAATAAAACTAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
*
29703298 ACCCAATTACCCAACCCAATAAAACTAAAATTAAAGTCT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGTCT
*
29703337 ACCCAATTACCAACCCAATAAAAATAAAACTAAAGTCT
1 ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
29703375 A
1 A
29703376 ACTCTTAAGT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 36 0.49
39 37 0.51
ACGTcount: A:0.50, C:0.28, G:0.03, T:0.19
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGTCT
Found at i:29703531 original size:17 final size:17
Alignment explanation
Indices: 29703511--29703573 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
29703501 TAATTTCAAG
29703511 AATTATGTAATGTTTTT
1 AATTATGTAATGTTTTT
* ***
29703528 AATTATGTAGTGATTCAA
1 AATTATGTAATG-TTTTT
*
29703546 AGACTTATGTAATATTTTT
1 A-A-TTATGTAATGTTTTT
29703565 AATTATGTA
1 AATTATGTA
29703574 GTGATTCAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
17 18 0.53
18 4 0.12
19 4 0.12
20 8 0.24
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (17 bp):
AATTATGTAATGTTTTT
Found at i:29703554 original size:37 final size:37
Alignment explanation
Indices: 29703508--29703582 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
29703498 TGTTAATTTC
*
29703508 AAGAATTATGTAATGTTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
*
29703545 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
29703582 A
1 A
29703583 TTCGGGTAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.04, G:0.15, T:0.45
Consensus pattern (37 bp):
AAGAATTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:29704487 original size:19 final size:20
Alignment explanation
Indices: 29704463--29704503 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
29704453 TATATTTGGA
*
29704463 AATTATAAATT-TAACTAAT
1 AATTATAAATTATAAATAAT
29704482 AATTATAAATTATAAATAAT
1 AATTATAAATTATAAATAAT
29704502 AA
1 AA
29704504 GATTTTTCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATAAATTATAAATAAT
Found at i:29710679 original size:96 final size:96
Alignment explanation
Indices: 29710505--29710695 Score: 222
Period size: 96 Copynumber: 2.0 Consensus size: 96
29710495 TTATACTTAG
* * * * *
29710505 CATGGAGATATTCTGGTTTGGCGAACACTTTCACTACGCAAAATTTCAAGCACATTGAATTCTCT
1 CATGGAAATACTCTAGTTTGGCGAACACTTTCACTACGCAAAATTTCAAGCACATCGAATCCTCT
* * *
29710570 ATTATGGCGGAACCATAGCGAATTCATATAA
66 ATTATAGCAGAACCATAGCGAATACATATAA
* * * * * *
29710601 CATGGAAATACTCTAGTTTGGCGGACACTTTCACTACTCGTAACTTT-GAGCACCTCGAATCCTC
1 CATGGAAATACTCTAGTTTGGCGAACACTTTCACTACGC-AAAATTTCAAGCACATCGAATCCTC
* *
29710665 TATTCTAGCAGAACCATAGCGGATACATATA
65 TATTATAGCAGAACCATAGCGAATACATATA
29710696 TCAATTATAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
96 73 0.94
97 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (96 bp):
CATGGAAATACTCTAGTTTGGCGAACACTTTCACTACGCAAAATTTCAAGCACATCGAATCCTCT
ATTATAGCAGAACCATAGCGAATACATATAA
Found at i:29710877 original size:23 final size:23
Alignment explanation
Indices: 29710851--29710895 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
29710841 TAAATTATGC
*
29710851 CACAAAGGTATT-TCGGAATACGT
1 CACAAAGGCATTCT-GGAATACGT
29710874 CACAAAGGCATTCTGGAATACG
1 CACAAAGGCATTCTGGAATACG
29710896 ACAAAAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (23 bp):
CACAAAGGCATTCTGGAATACGT
Found at i:29715834 original size:104 final size:106
Alignment explanation
Indices: 29715652--29715861 Score: 379
Period size: 104 Copynumber: 2.0 Consensus size: 106
29715642 GATAATATTG
* *
29715652 AAAAATTCAATACAAGTATGTTGACTAAAATTACTAGAAACCCTTTCCCTAAGGTTAAAAGGAAA
1 AAAAATTCAATACAAGTATATTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
29715717 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
66 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
*
29715758 AAAAATTCAATACATGTATATTGACT-AAA-TACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
1 AAAAATTCAATACAAGTATATTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
29715821 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
66 ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
29715862 GCATAATACT
Statistics
Matches: 101, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
104 74 0.73
105 3 0.03
106 24 0.24
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (106 bp):
AAAAATTCAATACAAGTATATTGACTAAAATTACTAGAAACCCTTCCCCTAAGGTTAAAAGGAAA
ACAATAATGCTTGATTTGATACTTAGTGATTTATGTGACAT
Found at i:29717879 original size:25 final size:25
Alignment explanation
Indices: 29717827--29717884 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
29717817 TCACCACTAT
*
29717827 GGCTTTCCAAATAATATGCCACATA
1 GGCTTTCCAAATAATATGCCACAAA
* *
29717852 GGCTTTTCAAATAACT-TGCTACAAA
1 GGCTTTCCAAATAA-TATGCCACAAA
29717877 GGCTTTCC
1 GGCTTTCC
29717885 TCCTATAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 27 0.96
26 1 0.04
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.31
Consensus pattern (25 bp):
GGCTTTCCAAATAATATGCCACAAA
Found at i:29718840 original size:118 final size:117
Alignment explanation
Indices: 29718618--29718844 Score: 339
Period size: 118 Copynumber: 1.9 Consensus size: 117
29718608 CCTATTACAG
* * * *
29718618 ATAGTTTACTAATGTTTCCACTATATGTGACCCCCATGCAAGGTCTTCCTCCATATCCTACTGTT
1 ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCTACATAACCTACTGTT
*
29718683 ATTACATATTTTAACATTCTTACTCTTCAACAATTGTAACATACAGAGATAT
66 ATTACATATTTTAACATTCTTACTCTTCAACAATCGTAACATACAGAGATAT
* * *
29718735 ATAGTTTACTAATGTTTTAATTATATGTGACCCCCATACAAGGTCTTCC-ACTTACACCTTACTG
1 ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCTACATA-ACC-TACTG
* *
29718799 TTTTTACATCTTTTAACATTCTTACTCTTCAACAATCGTAACATAC
64 TTATTACATATTTTAACATTCTTACTCTTCAACAATCGTAACATAC
29718845 TGACCTATAA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
116 3 0.03
117 47 0.48
118 48 0.49
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (117 bp):
ATAGTTTACTAATGTTTCAACTATATGTGACCCCCATACAAGGTCTTCCTACATAACCTACTGTT
ATTACATATTTTAACATTCTTACTCTTCAACAATCGTAACATACAGAGATAT
Found at i:29722031 original size:27 final size:27
Alignment explanation
Indices: 29721980--29722031 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
29721970 GGTGTTAATC
*
29721980 AAAAGTTATATCTTTTGGTTATTGATT
1 AAAAGTTATATCTTTTGATTATTGATT
* *
29722007 AAAAGTTATATCTTTTTATTTTTGA
1 AAAAGTTATATCTTTTGATTATTGA
29722032 CAAAGAATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.04, G:0.12, T:0.54
Consensus pattern (27 bp):
AAAAGTTATATCTTTTGATTATTGATT
Found at i:29722762 original size:15 final size:15
Alignment explanation
Indices: 29722742--29722775 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
29722732 GTGATGGATG
29722742 AGATGAGTGATGT-CA
1 AGATGAGTG-TGTGCA
29722757 AGATGAGTGTGTGCA
1 AGATGAGTGTGTGCA
29722772 AGAT
1 AGAT
29722776 AAAGCAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.32, C:0.06, G:0.35, T:0.26
Consensus pattern (15 bp):
AGATGAGTGTGTGCA
Found at i:29729934 original size:39 final size:39
Alignment explanation
Indices: 29729891--29729990 Score: 101
Period size: 39 Copynumber: 2.6 Consensus size: 39
29729881 CATGTTTTTG
* *
29729891 AGTATTGTGATATATACTTGAATGTTAAGTGATTATATA
1 AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
* * * * *
29729930 AGTATTGTTATATATGCTTAAATTTTATGTGAATATATG
1 AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
* * * *
29729969 TGTAATGTGATACATGCTTAAA
1 AGTATTGTGATATATACTTAAA
29729991 AGTGAATATG
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.35, C:0.04, G:0.17, T:0.44
Consensus pattern (39 bp):
AGTATTGTGATATATACTTAAATGTTAAGTGAATATATA
Found at i:29731627 original size:32 final size:30
Alignment explanation
Indices: 29731571--29731633 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 30
29731561 TGTGTCAAGC
29731571 GCCGTGGACCATACGGGTTAGCCCAATTAG
1 GCCGTGGACCATACGGGTTAGCCCAATTAG
*
29731601 GCCGTGTGAGCCATA-GAGGTTGGCCCAATTAG
1 GCCGTG-GA-CCATACG-GGTTAGCCCAATTAG
29731633 G
1 G
29731634 TCATGTGGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 6 0.21
31 3 0.10
32 20 0.69
ACGTcount: A:0.22, C:0.24, G:0.33, T:0.21
Consensus pattern (30 bp):
GCCGTGGACCATACGGGTTAGCCCAATTAG
Found at i:29736999 original size:21 final size:21
Alignment explanation
Indices: 29736975--29737017 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29736965 TTCTGTTTAG
*
29736975 TCTTTCGAGCTTCTT-TTCAGC
1 TCTTACGAGCTT-TTGTTCAGC
*
29736996 TCTTACGATCTTTTGTTCAGC
1 TCTTACGAGCTTTTGTTCAGC
29737017 T
1 T
29737018 TTCAAGCTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.12, C:0.26, G:0.14, T:0.49
Consensus pattern (21 bp):
TCTTACGAGCTTTTGTTCAGC
Found at i:29741274 original size:70 final size:67
Alignment explanation
Indices: 29741155--29741287 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 67
29741145 TAAACAAATA
* ** *
29741155 TAATGGTTTTGCCTTTTAACTTAATGAGTAAACATTTATCAAAATGACGTAGCTTTGCCTTTTAA
1 TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAAAGACGTAGCTTTGCCTTTTAA
29741220 TT
66 TT
* *
29741222 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAAAGACGTAGTTTTGTCTTT
1 TAATGGTTTTGACTTTTAAC-TTA-AAAA-GTAAACATTTATCAAAAAGACGTAGCTTTGCCTTT
29741287 T
63 T
29741288 CTTATTCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 19 0.33
68 3 0.05
69 2 0.04
70 33 0.58
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (67 bp):
TAATGGTTTTGACTTTTAACTTAAAAAGTAAACATTTATCAAAAAGACGTAGCTTTGCCTTTTAA
TT
Found at i:29742186 original size:20 final size:20
Alignment explanation
Indices: 29742161--29742210 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
29742151 TTTTAGGGAT
*
29742161 GCCTATGTGGCATCTTGTCA
1 GCCTATGTGGCATCCTGTCA
* *
29742181 GCCTATATGACATCCTGTCA
1 GCCTATGTGGCATCCTGTCA
*
29742201 GCCTTTGTGG
1 GCCTATGTGG
29742211 TGTACTCTGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (20 bp):
GCCTATGTGGCATCCTGTCA
Found at i:29748281 original size:14 final size:14
Alignment explanation
Indices: 29748262--29748290 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29748252 AAAAATCAAG
29748262 CACCAATCCACCTC
1 CACCAATCCACCTC
29748276 CACCAATCCACCTC
1 CACCAATCCACCTC
29748290 C
1 C
29748291 GGTCCTTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.59, G:0.00, T:0.14
Consensus pattern (14 bp):
CACCAATCCACCTC
Found at i:29750678 original size:61 final size:61
Alignment explanation
Indices: 29750612--29751058 Score: 341
Period size: 61 Copynumber: 7.4 Consensus size: 61
29750602 TTTAAATTAT
* *
29750612 ATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
* * ** * * * * *
29750673 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCAA-ATT-A-T
1 ATTTTA-TAGTATCATATATTATAATTTTAGTAAATTCATATAAGAA-TATTT-AATATTAAGA
* *
29750732 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
* * ** * * * * *
29750793 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTA-ATAATAATTATTTCAA-ATT-A-T
1 ATTTTA-TAGTATCATATATTATAATTTTAGTAAATTCATATAAGAA-TATTT-AATATTAAGA
* * *
29750852 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTGATTGTTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
* * ** * * * * *
29750913 ATTTTATTA-AATCATATATTTTAATTAAAATATATTTA-ATAATAATTATGTTAA-ATT-A-T
1 ATTTTA-TAGTATCATATATTATAATTTTAGTAAATTCATATAAGAA-TAT-TTAATATTAAGA
* * *
29750972 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAAAATATTGATTATTAAGA
1 ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
* *
29751033 ATTTTATTA-AATCATATATTTTAATT
1 ATTTTA-TAGTATCATATATTATAATT
29751059 AAAATATATT
Statistics
Matches: 291, Mismatches: 70, Indels: 50
0.71 0.17 0.12
Matches are distributed among these distances:
58 10 0.03
59 103 0.35
60 42 0.14
61 123 0.42
62 13 0.04
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (61 bp):
ATTTTATAGTATCATATATTATAATTTTAGTAAATTCATATAAGAATATTTAATATTAAGA
Found at i:29750735 original size:120 final size:120
Alignment explanation
Indices: 29750578--29751081 Score: 920
Period size: 120 Copynumber: 4.2 Consensus size: 120
29750568 TATATTTAGA
* * *
29750578 AAAATTATATTTAATAATAATTATTTTAAATTATATTTTATAGTATTATATATTATGATTTTAGT
1 AAAA-TATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
* *
29750643 AAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
29750699 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
29750764 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
29750819 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
1 AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
*
29750884 AATTCATATAAGAATATTGATTGTTAAGAATTTTATTAAATCATATATTTTAATT
66 AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
29750939 AAAATATATTTAATAATAATTATGTT-AAATTATATTTTATAGTATCATATATTATAATTTTAGT
1 AAAATATATTTAATAATAATTAT-TTCAAATTATATTTTATAGTATCATATATTATAATTTTAGT
*
29751003 AAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
65 AAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
29751059 AAAATATATTTAATAATAATTAT
1 AAAATATATTTAATAATAATTAT
29751082 GTTAAAATAT
Statistics
Matches: 374, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
120 368 0.98
121 6 0.02
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.49
Consensus pattern (120 bp):
AAAATATATTTAATAATAATTATTTCAAATTATATTTTATAGTATCATATATTATAATTTTAGTA
AATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATCATATATTTTAATT
Found at i:29751321 original size:16 final size:16
Alignment explanation
Indices: 29751300--29751332 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29751290 TTGATTTGCT
29751300 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
29751316 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
29751332 A
1 A
29751333 ATACAGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.21, C:0.36, G:0.06, T:0.36
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:29751728 original size:13 final size:14
Alignment explanation
Indices: 29751702--29751733 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
29751692 TCAAATTTAG
29751702 TAAA-ATAACATTT
1 TAAATATAACATTT
29751715 TAAATATAAC-TTT
1 TAAATATAACATTT
29751728 TAAATA
1 TAAATA
29751734 GTAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAATATAACATTT
Found at i:29752925 original size:14 final size:14
Alignment explanation
Indices: 29752904--29752939 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
29752894 AATTATAACA
29752904 AAAATATAAA-AAT
1 AAAATATAAACAAT
29752917 AATAATATAAACAAT
1 AA-AATATAAACAAT
29752932 AAAATATA
1 AAAATATA
29752940 TTTTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 14 0.67
15 5 0.24
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (14 bp):
AAAATATAAACAAT
Found at i:29754709 original size:23 final size:24
Alignment explanation
Indices: 29754669--29754717 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 24
29754659 ATTTTACAAA
*
29754669 AAAATTATAATAAAATTTTTATAT
1 AAAATTATAATAAAATTTATATAT
*
29754693 AAAATTA-ATTAAAATTTATATAT
1 AAAATTATAATAAAATTTATATAT
29754716 AA
1 AA
29754718 TAAAATTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTATAATAAAATTTATATAT
Found at i:29754814 original size:13 final size:12
Alignment explanation
Indices: 29754769--29754806 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
29754759 CCATTTCAAT
29754769 TAAAATTTTATA
1 TAAAATTTTATA
*
29754781 T-AATTTTTATA
1 TAAAATTTTATA
29754792 TAAAATTTTA-A
1 TAAAATTTTATA
29754803 TAAA
1 TAAA
29754807 TATATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 15 0.65
12 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TAAAATTTTATA
Found at i:29762235 original size:31 final size:31
Alignment explanation
Indices: 29762199--29762280 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
29762189 CTTAACCTAA
* ** *
29762199 TGACTTAAATAAAAACTTTTGAATAGTTTAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
*
29762230 TGACTTAAATGGAAACTTTCAAATAGTTCAG
1 TGACTTAAATGAAAACTTTCAAATAGTTCAG
**
29762261 TGACCAAAATGAAAACTTTC
1 TGACTTAAATGAAAACTTTC
29762281 CCATAATTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAGTTCAG
Found at i:29762294 original size:31 final size:31
Alignment explanation
Indices: 29762205--29762295 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 31
29762195 CTAATGACTT
* ** * **
29762205 AAATAAAAACTTTTGAATAGTTTAGTGACTT
1 AAATGAAAACTTTCAAATAATTTAGTGACCA
* * *
29762236 AAATGGAAACTTTCAAATAGTTCAGTGACCA
1 AAATGAAAACTTTCAAATAATTTAGTGACCA
**
29762267 AAATGAAAACTTTCCCATAATTTAGTGAC
1 AAATGAAAACTTTCAAATAATTTAGTGAC
29762296 TAATAATGCA
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (31 bp):
AAATGAAAACTTTCAAATAATTTAGTGACCA
Found at i:29762865 original size:15 final size:15
Alignment explanation
Indices: 29762827--29762864 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
29762817 GATTTCGTAT
* *
29762827 TTAAATTTTCAATAC
1 TTAACTTTTCAACAC
29762842 TTAACTTTTCAACAC
1 TTAACTTTTCAACAC
29762857 TT-ACTTTT
1 TTAACTTTT
29762865 TTAGTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAACTTTTCAACAC
Found at i:29763341 original size:113 final size:112
Alignment explanation
Indices: 29763188--29763485 Score: 336
Period size: 113 Copynumber: 2.6 Consensus size: 112
29763178 AGAATTAGTG
* * *
29763188 GCGTTTTAT-AGAAAGCGCCGCAAAAAACCTAAGT-CGAACGACGTCGTTTACCGAGCTTTTGGG
1 GCGTTTT-TGAGAAAGCGCCGCAAAAAACCTAA-TCCCAACGACGCCGTTT-CTGAGCTTTTGGG
29763251 GATTTAGCGGCATTTTTAATAA-AGCGCCGCTAATG-TTCAGGGCTTTAGCC
63 GATTTAGCGGCATTTTTAATAACA-CGCCGCTAATGCTT-AGGGCTTTAGCC
* ** *
29763301 GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGATGCCGTTTTCTGAGCTTTCAAGTG
1 GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCG-TTTCTGAGCTTT-TGGGG
* * * **
29763366 A-TTAGTGGCGTTTTTAATAACATGCCGCTAATGCTTAGGGCTTTAGTG
64 ATTTAGCGGCATTTTTAATAACACGCCGCTAATGCTTAGGGCTTTAGCC
* * * *
29763414 GCGTTTTTGAAAAAGCGCCGCAAGAAAACCTAAGCACAACGACACCGTTTCTGAGCTTTTCGGGG
1 GCGTTTTTGAGAAAGCGCCGCAA-AAAACCTAATCCCAACGACGCCGTTTCTGAGCTTTT-GGGG
29763479 ATTTAGC
64 ATTTAGC
29763486 AAGAAGCGCT
Statistics
Matches: 155, Mismatches: 21, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
112 2 0.01
113 121 0.78
114 32 0.21
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (112 bp):
GCGTTTTTGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCGTTTCTGAGCTTTTGGGGAT
TTAGCGGCATTTTTAATAACACGCCGCTAATGCTTAGGGCTTTAGCC
Found at i:29764000 original size:21 final size:21
Alignment explanation
Indices: 29763976--29764073 Score: 72
Period size: 21 Copynumber: 4.5 Consensus size: 21
29763966 CAGGTATGGA
*
29763976 TTTAGGGTTTGGGATTTAAGG
1 TTTAGGGTTTGGGATTTAGGG
* * * *
29763997 TTTAGGGGTTAGG-TGTTATGC
1 TTTAGGGTTTGGGAT-TTAGGG
*
29764018 TTTAGGGGTTAGGAGGATTTAGGG
1 TTTA-GGGTT-TG-GGATTTAGGG
* *
29764042 GTTAGGGGTTAGGGATTTAGGG
1 TTTA-GGGTTTGGGATTTAGGG
29764064 TTTAGGGTTT
1 TTTAGGGTTT
29764074 CAACGGTAAG
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
20 1 0.02
21 24 0.41
22 17 0.29
23 1 0.02
24 15 0.25
25 1 0.02
ACGTcount: A:0.17, C:0.01, G:0.42, T:0.40
Consensus pattern (21 bp):
TTTAGGGTTTGGGATTTAGGG
Found at i:29764071 original size:7 final size:7
Alignment explanation
Indices: 29763976--29764073 Score: 65
Period size: 7 Copynumber: 13.4 Consensus size: 7
29763966 CAGGTATGGA
29763976 TTTAGGG
1 TTTAGGG
29763983 TTT-GGG
1 TTTAGGG
*
29763989 ATTTAAGG
1 -TTTAGGG
29763997 TTTAGGG
1 TTTAGGG
*
29764004 GTTA-GG
1 TTTAGGG
* *
29764010 TGTTATGC
1 T-TTAGGG
29764018 TTTAGGG
1 TTTAGGG
*
29764025 GTTAGGAGG
1 TTTA-G-GG
29764034 ATTTAGGG
1 -TTTAGGG
*
29764042 GTTAGGG
1 TTTAGGG
*
29764049 GTTAGGG
1 TTTAGGG
29764056 ATTTAGGG
1 -TTTAGGG
29764064 TTTAGGG
1 TTTAGGG
29764071 TTT
1 TTT
29764074 CAACGGTAAG
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
6 5 0.07
7 48 0.67
8 13 0.18
9 3 0.04
10 3 0.04
ACGTcount: A:0.17, C:0.01, G:0.42, T:0.40
Consensus pattern (7 bp):
TTTAGGG
Found at i:29764397 original size:38 final size:39
Alignment explanation
Indices: 29764346--29764431 Score: 120
Period size: 38 Copynumber: 2.2 Consensus size: 39
29764336 ATAAAATTTT
* * * *
29764346 TTAGGGGTTATGCTTTAGGGGTTAGGGA-GATTTAGGGG
1 TTAGGGTTTATGCTTTAAGGGTTAAGAAGGATTTAGGGG
29764384 TTAGGGTTTATGCTTTAAGGGTTAAGAAGGATTTAGGGG
1 TTAGGGTTTATGCTTTAAGGGTTAAGAAGGATTTAGGGG
29764423 TTATGGGTT
1 TTA-GGGTT
29764432 AGGGATTTGG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
38 24 0.57
39 13 0.31
40 5 0.12
ACGTcount: A:0.21, C:0.02, G:0.40, T:0.37
Consensus pattern (39 bp):
TTAGGGTTTATGCTTTAAGGGTTAAGAAGGATTTAGGGG
Found at i:29766668 original size:31 final size:31
Alignment explanation
Indices: 29766630--29766709 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
29766620 TTGGATTTTA
*
29766630 ATTGGTTTTTGCAGCTAAGATGATACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGATACCTTCT
* *
29766661 ATTGGTTTTTACTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGATACCTTCT
* *
29766692 ATTGATTTCTGCTGCTAA
1 ATTGGTTTTTGCTGCTAA
29766710 ATGGCTAAGA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGATACCTTCT
Found at i:29769398 original size:21 final size:21
Alignment explanation
Indices: 29769372--29769442 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
29769362 CTACAACTTA
*
29769372 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
* *
29769393 AAGCAGCGGCTGCAGTGAGGG
1 AAGCAGAGGCTGCAGCGAGGG
*
29769414 AAGCAGAGGCTGCAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGGG
29769435 AAGCAGAG
1 AAGCAGAG
29769443 CAGAACAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.31, C:0.18, G:0.46, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGGG
Found at i:29769823 original size:42 final size:42
Alignment explanation
Indices: 29769759--29769877 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
29769749 GTTTTTGTAT
* *
29769759 AAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGTGCTTAGAA-
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-AAC
* *
29769801 AAAACCGCCGCTAAAGACCATGTTCTTTAGAGGCGCTTAAAC
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAC
** *
29769843 AAAAACGCCGCTAAAGAATATGGTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
29769878 TTTTTGTTTG
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 2 0.03
42 66 0.97
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAAAC
Found at i:29774494 original size:12 final size:12
Alignment explanation
Indices: 29774477--29774502 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29774467 TCCAACTGAG
29774477 TTTTTGTTTGCT
1 TTTTTGTTTGCT
29774489 TTTTTGTTTGCT
1 TTTTTGTTTGCT
29774501 TT
1 TT
29774503 ATTAATTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.15, T:0.77
Consensus pattern (12 bp):
TTTTTGTTTGCT
Found at i:29776045 original size:18 final size:19
Alignment explanation
Indices: 29776003--29776053 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 19
29775993 ACAAATACAC
29776003 ATAAATT-AAATG-AAATG
1 ATAAATTGAAATGAAAATG
*
29776020 A-AATTTGAAATGAAAAT-
1 ATAAATTGAAATGAAAATG
29776037 ATAAATTGAAATGAAAA
1 ATAAATTGAAATGAAAA
29776054 AAAAAATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
16 4 0.14
17 7 0.24
18 18 0.62
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (19 bp):
ATAAATTGAAATGAAAATG
Found at i:29776064 original size:19 final size:19
Alignment explanation
Indices: 29776020--29776064 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
29776010 AAATGAAATG
* *
29776020 AAATTTGAAATGAAAATAT
1 AAATTTGAAATGAAAAAAA
29776039 AAA-TTGAAATGAAAAAAA
1 AAATTTGAAATGAAAAAAA
29776057 AAATTTGA
1 AAATTTGA
29776065 CAAGACATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 16 0.70
19 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.11, T:0.27
Consensus pattern (19 bp):
AAATTTGAAATGAAAAAAA
Found at i:29776269 original size:25 final size:24
Alignment explanation
Indices: 29776235--29776288 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
29776225 TTAAATGAGA
* * *
29776235 AAAAATTTGAATTTAAATGAAATTT
1 AAAATTTTGAAATAAAATGAAA-TT
29776260 AAAATTTTGAAATAAAATGAAATT
1 AAAATTTTGAAATAAAATGAAATT
29776284 AAAAT
1 AAAAT
29776289 ATAAATTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (24 bp):
AAAATTTTGAAATAAAATGAAATT
Found at i:29776292 original size:18 final size:18
Alignment explanation
Indices: 29776271--29776322 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
29776261 AAATTTTGAA
*
29776271 ATAAAATGAAATTAAAAT
1 ATAAAATGAAATGAAAAT
*
29776289 ATAAATTGAAATGAAAA-
1 ATAAAATGAAATGAAAAT
*
29776306 A-AAACTGAATATGAAAA
1 ATAAAATGAA-ATGAAAA
29776323 AAGAATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
16 7 0.23
17 8 0.27
18 15 0.50
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.23
Consensus pattern (18 bp):
ATAAAATGAAATGAAAAT
Found at i:29776343 original size:5 final size:5
Alignment explanation
Indices: 29776333--29776429 Score: 50
Period size: 5 Copynumber: 17.6 Consensus size: 5
29776323 AAGAATAAAT
* *
29776333 TGAAA TGAAA TGAAA TGTGAAA TGAATA TGAAA TAAAA TGTAATT TGAAA
1 TGAAA TGAAA TGAAA --TGAAA TGAA-A TGAAA TGAAA TG-AA-A TGAAA
* * * **
29776383 TGAATC TAAAA CGAAA TGAAA GTTGAAA TGAAA AAAAA TTGAAA TGA
1 TGAA-A TGAAA TGAAA TGAAA --TGAAA TGAAA TGAAA -TGAAA TGA
29776430 GACAAAAAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
5 42 0.61
6 15 0.22
7 12 0.17
ACGTcount: A:0.56, C:0.02, G:0.18, T:0.25
Consensus pattern (5 bp):
TGAAA
Found at i:29776366 original size:28 final size:28
Alignment explanation
Indices: 29776333--29776534 Score: 104
Period size: 28 Copynumber: 7.5 Consensus size: 28
29776323 AAGAATAAAT
29776333 TGAAATGAAATGAAATGTGAAATGAATA
1 TGAAATGAAATGAAATGTGAAATGAATA
* * * *
29776361 TGAAATAAAATGTAATTTGAAATGAATC
1 TGAAATGAAATGAAATGTGAAATGAATA
* *
29776389 TAAAACGAAATGAAA-GTTGAAATGAA-A
1 TGAAATGAAATGAAATG-TGAAATGAATA
** * **** *
29776416 AAAAATTGAAATGAGACAAAAAATTAATA
1 TGAAA-TGAAATGAAATGTGAAATGAATA
*
29776445 AG-AA--AAAT-AAAT-TGAAAT-AATA
1 TGAAATGAAATGAAATGTGAAATGAATA
** * *
29776467 AAAAAT-AAATTTAAATG-GAAA--AAAA
1 TGAAATGAAA-TGAAATGTGAAATGAATA
* *
29776492 TTAAATGAAATGAAATGTGAAATGAAAA
1 TGAAATGAAATGAAATGTGAAATGAATA
29776520 TGAAATGAAATGAAA
1 TGAAATGAAATGAAA
29776535 AAAAAATGAT
Statistics
Matches: 133, Mismatches: 28, Indels: 26
0.71 0.15 0.14
Matches are distributed among these distances:
22 5 0.04
23 6 0.05
24 5 0.04
25 18 0.14
26 15 0.11
27 4 0.03
28 78 0.59
29 2 0.02
ACGTcount: A:0.60, C:0.01, G:0.15, T:0.23
Consensus pattern (28 bp):
TGAAATGAAATGAAATGTGAAATGAATA
Found at i:29776383 original size:17 final size:16
Alignment explanation
Indices: 29776267--29776383 Score: 68
Period size: 17 Copynumber: 7.4 Consensus size: 16
29776257 TTTAAAATTT
29776267 TGAAATAAAATGAA-A
1 TGAAATAAAATGAATA
*
29776282 TTAAAATATAAATTGAA-A
1 -TGAAATA-AAA-TGAATA
*
29776300 TGAAAAAAAACTGAATA
1 TGAAATAAAA-TGAATA
* *
29776317 TGAAAAAAGAATAAAT-
1 TGAAATAA-AATGAATA
*
29776333 TGAAATGAAATGAA-A
1 TGAAATAAAATGAATA
*
29776348 TG---TGAAATGAATA
1 TGAAATAAAATGAATA
*
29776361 TGAAATAAAATGTAATT
1 TGAAATAAAATG-AATA
29776378 TGAAAT
1 TGAAAT
29776384 GAATCTAAAA
Statistics
Matches: 81, Mismatches: 10, Indels: 19
0.74 0.09 0.17
Matches are distributed among these distances:
12 9 0.11
13 3 0.04
15 7 0.09
16 25 0.31
17 30 0.37
18 7 0.09
ACGTcount: A:0.60, C:0.01, G:0.14, T:0.26
Consensus pattern (16 bp):
TGAAATAAAATGAATA
Found at i:29776436 original size:16 final size:16
Alignment explanation
Indices: 29776405--29776539 Score: 96
Period size: 16 Copynumber: 8.0 Consensus size: 16
29776395 GAAATGAAAG
29776405 TTGAAATGAAAAAAAA
1 TTGAAATGAAAAAAAA
29776421 TTGAAATGAGACAAAAAA
1 TTGAAATGA-A-AAAAAA
*
29776439 TT-AATAAGAAAAATAAA
1 TTGAA-ATGAAAAA-AAA
*
29776456 TTGAAATAATAAAAAATAAA
1 TTG--A-AATGAAAAA-AAA
* *
29776476 TTTAAATGGAAAAAAA
1 TTGAAATGAAAAAAAA
**
29776492 TT-AAATGAAATGAAA
1 TTGAAATGAAAAAAAA
*
29776507 TGTGAAATGAAAATGAAA
1 T-TGAAATGAAAA-AAAA
29776525 -TGAAATGAAAAAAAA
1 TTGAAATGAAAAAAAA
29776540 ATGATAAGAC
Statistics
Matches: 97, Mismatches: 11, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
15 14 0.14
16 29 0.30
17 24 0.25
18 16 0.16
20 13 0.13
21 1 0.01
ACGTcount: A:0.65, C:0.01, G:0.13, T:0.21
Consensus pattern (16 bp):
TTGAAATGAAAAAAAA
Found at i:29776502 original size:5 final size:5
Alignment explanation
Indices: 29776489--29776534 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
29776479 AAATGGAAAA
*
29776489 AAATT AAATG AAATG AAATGTG AAATG AAAATG AAATG AAATG AAA
1 AAATG AAATG AAATG AAA--TG AAATG -AAATG AAATG AAATG AAA
29776535 AAAAAATGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 27 0.73
6 5 0.14
7 5 0.14
ACGTcount: A:0.61, C:0.00, G:0.17, T:0.22
Consensus pattern (5 bp):
AAATG
Found at i:29776502 original size:20 final size:20
Alignment explanation
Indices: 29776447--29776503 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
29776437 AATTAATAAG
*
29776447 AAAAATAAATTGAAAT-AATA
1 AAAAATAAATTGAAATGGA-A
*
29776467 AAAAATAAATTTAAATGGAA
1 AAAAATAAATTGAAATGGAA
29776487 AAAAATTAAA-TGAAATG
1 AAAAA-TAAATTGAAATG
29776504 AAATGTGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.25
Consensus pattern (20 bp):
AAAAATAAATTGAAATGGAA
Found at i:29776514 original size:12 final size:12
Alignment explanation
Indices: 29776497--29776531 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
29776487 AAAAATTAAA
29776497 TGAAATGAAATG
1 TGAAATGAAATG
*
29776509 TGAAATGAAA-A
1 TGAAATGAAATG
29776520 TGAAATGAAATG
1 TGAAATGAAATG
29776532 AAAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:29777120 original size:18 final size:17
Alignment explanation
Indices: 29777099--29777133 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29777089 TTATTATTAA
*
29777099 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
29777117 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29777134 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29777199 original size:157 final size:157
Alignment explanation
Indices: 29776986--29777302 Score: 571
Period size: 157 Copynumber: 2.0 Consensus size: 157
29776976 TAGAATACCC
*
29776986 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
* * *
29777051 TTATCAATAATAAATATTTTAATCATATTTAAAAATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
29777116 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
29777143 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
*
29777208 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
29777273 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
29777300 TTA
1 TTA
29777303 ATATTCTTAT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
157 153 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTATTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAAAATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:29777273 original size:16 final size:16
Alignment explanation
Indices: 29777236--29777277 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
29777226 TTAATCATAT
*
29777236 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
29777252 TT-AAATATATTATAA
1 TTAAAATATATTATAA
29777267 TTAAAATATAT
1 TTAAAATATAT
29777278 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:29777284 original size:14 final size:15
Alignment explanation
Indices: 29777245--29777286 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29777235 TTTAAACATA
*
29777245 ATTATTATTAAATAT
1 ATTATAATTAAATAT
29777260 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
29777274 A-TATAATTTAATA
1 ATTATAATTAAATA
29777287 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:29777374 original size:120 final size:121
Alignment explanation
Indices: 29777234--29777531 Score: 496
Period size: 120 Copynumber: 2.5 Consensus size: 121
29777224 ATTTAATCAT
*
29777234 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
29777299 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
*
29777356 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTCATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
29777419 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
29777475 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
29777532 TAAAATAATT
Statistics
Matches: 168, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 156 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:29777404 original size:14 final size:15
Alignment explanation
Indices: 29777355--29777406 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
29777345 GTAAAATATA
29777355 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
29777370 TATTAAATATATTAT
1 AATTAAATATATTAT
29777385 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
29777398 AATTTAATA
1 AATTAAATA
29777407 AAATTCTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:29777618 original size:24 final size:25
Alignment explanation
Indices: 29777572--29777619 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
29777562 TATGAATTTG
29777572 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
29777598 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
29777620 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:29777623 original size:92 final size:92
Alignment explanation
Indices: 29777527--29777755 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
29777517 TGATTTAATA
* * *
29777527 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
29777589 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
29777619 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
29777684 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
29777709 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
29777756 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:29780859 original size:33 final size:33
Alignment explanation
Indices: 29780820--29780895 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
29780810 ATTATAAAGC
*
29780820 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
29780853 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
29780886 ATGTATAATT
1 ATGTATAATT
29780896 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:29780993 original size:37 final size:37
Alignment explanation
Indices: 29780938--29781019 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
29780928 GTATAAATAT
* *
29780938 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
*
29780975 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
29781012 ATTGATTA
1 ATTGATTA
29781020 ATAAATATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.40
Consensus pattern (37 bp):
ATTGATTAGTTCAATAAAGCATGTTCAAAGTTTGAAC
Found at i:29784209 original size:5 final size:5
Alignment explanation
Indices: 29784169--29784194 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
29784159 GCAAATCGGC
29784169 AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA A
29784195 TCGGATGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:29784816 original size:17 final size:16
Alignment explanation
Indices: 29784773--29784823 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
29784763 TCAAATTTAA
* *
29784773 TTTAATTTAATTTCAT
1 TTTAATTTCACTTCAT
*
29784789 TTTCATTTCACTTCAT
1 TTTAATTTCACTTCAT
29784805 TTTAATTTTCACTTCAT
1 TTTAA-TTTCACTTCAT
29784822 TT
1 TT
29784824 AAAATTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.24, C:0.16, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTTCACTTCAT
Found at i:29784851 original size:20 final size:19
Alignment explanation
Indices: 29784828--29784922 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 19
29784818 TCATTTAAAA
29784828 TTTTTTC-CATTTAAATTTAT
1 TTTTTTCTCATTT-AATTT-T
29784848 TTTTTTCTCATTTAA--TT
1 TTTTTTCTCATTTAATTTT
29784865 TTTTTT-TCATATTAA--TT
1 TTTTTTCTCAT-TTAATTTT
*
29784882 TTTTGTCTCATTTCAATTTAT
1 TTTTTTCTCATTT-AATTT-T
*
29784903 TTATTTTTTCATTTCAATTT
1 TT-TTTTCTCATTT-AATTT
29784923 ATATTTTATT
Statistics
Matches: 64, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
16 4 0.06
17 20 0.31
18 7 0.11
20 10 0.16
21 8 0.12
22 15 0.23
ACGTcount: A:0.21, C:0.11, G:0.01, T:0.67
Consensus pattern (19 bp):
TTTTTTCTCATTTAATTTT
Found at i:29784867 original size:16 final size:16
Alignment explanation
Indices: 29784842--29784900 Score: 75
Period size: 16 Copynumber: 3.6 Consensus size: 16
29784832 TTCCATTTAA
29784842 ATTT-ATTTTTTTCTC
1 ATTTAATTTTTTTCTC
*
29784857 ATTTAATTTTTTTTTC
1 ATTTAATTTTTTTCTC
29784873 ATATTAATTTTTTGTCTC
1 AT-TTAATTTTTT-TCTC
29784891 ATTTCAATTT
1 ATTT-AATTT
29784901 ATTTATTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
15 4 0.11
16 12 0.32
17 12 0.32
18 10 0.26
ACGTcount: A:0.20, C:0.10, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTTAATTTTTTTCTC
Found at i:29784867 original size:17 final size:17
Alignment explanation
Indices: 29784847--29784900 Score: 74
Period size: 17 Copynumber: 3.1 Consensus size: 17
29784837 TTTAAATTTA
29784847 TTTTTTTCTCATTTAAT
1 TTTTTTTCTCATTTAAT
29784864 TTTTTTT-TCATATTAAT
1 TTTTTTTCTCAT-TTAAT
*
29784881 TTTTTGTCTCATTTCAAT
1 TTTTTTTCTCATTT-AAT
29784899 TT
1 TT
29784901 ATTTATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 4 0.12
17 20 0.61
18 9 0.27
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTTTTCTCATTTAAT
Found at i:29784895 original size:23 final size:22
Alignment explanation
Indices: 29784869--29784935 Score: 64
Period size: 22 Copynumber: 2.9 Consensus size: 22
29784859 TTAATTTTTT
29784869 TTTCATATTAATTT-TTTGTCTCA
1 TTTCA-ATTAATTTATTT-TCTCA
* *
29784892 TTTCAATTTATTTATTTTTTCA
1 TTTCAATTAATTTATTTTCTCA
29784914 TTTCAATTTATATTTTATTTTC
1 TTTCAA-TTA-A-TTTATTTTC
29784936 ATTCCAACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 17 0.47
23 10 0.28
24 1 0.03
25 8 0.22
ACGTcount: A:0.22, C:0.10, G:0.01, T:0.66
Consensus pattern (22 bp):
TTTCAATTAATTTATTTTCTCA
Found at i:29784936 original size:40 final size:39
Alignment explanation
Indices: 29784827--29784936 Score: 97
Period size: 40 Copynumber: 2.8 Consensus size: 39
29784817 TTCATTTAAA
*
29784827 ATTTTTTCCATTTAAATTTATTTTT-TTCTC-ATTTAATTT
1 ATTTTTT-CATTT-AATTTATTTTTATTTTCAATTTAATTT
29784866 -TTTTTTCATATTAATTT-TTTGTCTCA-TTTCAATTT-ATTT
1 ATTTTTTCAT-TTAATTTATTT-T-T-ATTTTCAATTTAATTT
29784905 ATTTTTTCATTTCAATTTATATTTTATTTTCA
1 ATTTTTTCATTT-AATTTAT-TTTTATTTTCA
29784937 TTCCAACTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 21
0.73 0.01 0.26
Matches are distributed among these distances:
36 3 0.05
37 9 0.15
38 9 0.15
39 10 0.17
40 24 0.41
41 2 0.03
42 2 0.03
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (39 bp):
ATTTTTTCATTTAATTTATTTTTATTTTCAATTTAATTT
Found at i:29784938 original size:23 final size:22
Alignment explanation
Indices: 29784879--29784951 Score: 78
Period size: 23 Copynumber: 3.2 Consensus size: 22
29784869 TTTCATATTA
29784879 ATTTTTTGTCTCATTTCAATTTAT
1 ATTTTTT-T-TCATTTCAATTTAT
29784903 -TTATTTTTTCATTTCAATTTAT
1 ATT-TTTTTTCATTTCAATTTAT
*
29784925 ATTTTATTTTCATTCCAACTTT-T
1 ATTTT-TTTTCATTTCAA-TTTAT
29784948 ATTT
1 ATTT
29784952 CATAGATCCT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
22 16 0.36
23 21 0.48
24 7 0.16
ACGTcount: A:0.22, C:0.12, G:0.01, T:0.64
Consensus pattern (22 bp):
ATTTTTTTTCATTTCAATTTAT
Found at i:29787226 original size:89 final size:87
Alignment explanation
Indices: 29787130--29787483 Score: 321
Period size: 89 Copynumber: 4.0 Consensus size: 87
29787120 TATTTGATAA
* ** *
29787130 AAAATATATAATTCGAAA-AATTAATAATACGCAAC-AAATTAAATTTATAGATACAAGAAAATA
1 AAAATATAAAATTC-AAACAACAAATAATACG-AACTAAATTAAATTTACAGATACAA-AAAATA
29787193 CAAACATTCTAGAATAATAATACACG
63 CAAACATTCTA-AATAATAATACACG
* **
29787219 AAAATATAAAATTCAAACAACAAACAATAC-AGACTAAATTAAATTTACAGACCCAACAAAATAC
1 AAAATATAAAATTCAAACAACAAATAATACGA-ACTAAATTAAATTTACAGATACAA-AAAATAC
*
29787283 AAACAGATGGGTC-AAAT--TAATACACA
64 AAAC--AT---TCTAAATAATAATACACG
* * * *
29787309 AAAATTTAAAATTCAAATTAA-AAATAATACGGACTAAATTAAATTTACATATACAAAAAATACA
1 AAAATATAAAATTCAAA-CAACAAATAATACGAACTAAATTAAATTTACAGATACAAAAAATACA
* *
29787373 AACATTTTAAGA-AATTATTACACG
65 AACATTCTAA-ATAA-TAATACACG
* * * *
29787397 AAAATATAAAATTGAAACCACAAATAATACTG-ACTAAATTAAATTTACAAATATAAAAAAATAC
1 AAAATATAAAATTCAAACAACAAATAATAC-GAACTAAATTAAATTTACAGATA-CAAAAAATAC
*
29787461 AAACATTCTAAAGAAATAATACA
64 AAACATTCTAAA-TAATAATACA
29787484 AAAATTTTGA
Statistics
Matches: 218, Mismatches: 27, Indels: 40
0.76 0.09 0.14
Matches are distributed among these distances:
84 1 0.00
85 2 0.01
86 1 0.00
87 4 0.02
88 57 0.26
89 88 0.40
90 55 0.25
91 4 0.02
92 3 0.01
93 1 0.00
94 2 0.01
ACGTcount: A:0.57, C:0.13, G:0.05, T:0.25
Consensus pattern (87 bp):
AAAATATAAAATTCAAACAACAAATAATACGAACTAAATTAAATTTACAGATACAAAAAATACAA
ACATTCTAAATAATAATACACG
Found at i:29804107 original size:44 final size:44
Alignment explanation
Indices: 29803938--29804375 Score: 203
Period size: 44 Copynumber: 10.0 Consensus size: 44
29803928 CAAATCAGTA
* **
29803938 AAGATAGCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
* * *
29803982 AAGAT-GACAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
1 AAGATAG-CAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTG
* * * * * * *
29804026 AAGCCACTA--AG-CCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTG
1 AAG--A-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
* **
29804070 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCA
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
* * * *
29804114 AAGACAGCAAATCTTATCTTTCC-AAG-A-TAGTGGGAAGCAGATTT
1 AAGATAGCAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTG
* * * * *
29804158 AAGCCACTA--AG-CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTG
1 AAG--A-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
**
29804202 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCA
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
** * * * * *
29804246 AAGACGGCAAATCTTAACTTTCC-AAG-A-TAGTGGGAAACAGATTT
1 AAGATAGCAGATCTTATC-TCCCTAAGCAGTAGT-GG-AGCAGATTG
* * * * * *
29804290 AAGCCACTA--AG-TATTGTCTCCCTGAGCAGCAGTGGAGTAGGTTG
1 AAG--A-TAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
*
29804334 AAGATAGCAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGAT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
29804376 CAAAGACGGC
Statistics
Matches: 283, Mismatches: 73, Indels: 76
0.66 0.17 0.18
Matches are distributed among these distances:
41 6 0.02
42 15 0.05
43 25 0.09
44 203 0.72
45 21 0.07
46 11 0.04
47 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (44 bp):
AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTG
Found at i:29804178 original size:132 final size:132
Alignment explanation
Indices: 29803938--29804470 Score: 895
Period size: 132 Copynumber: 4.0 Consensus size: 132
29803928 CAAATCAGTA
* * *
29803938 AAGATAGCAGATCTTACCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATGACAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
*
29804003 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
29804068 TG
131 TG
* *
29804070 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATCAAAGACAGCAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
*
29804135 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
29804200 TG
131 TG
*
29804202 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTAACTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* ** * *
29804267 CCAAGATAGTGGGAAACAGATTTAAGCCACTAAGTATTGTCTCCCTGAGCAGCAGTGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
29804332 TG
131 TG
*
29804334 AAGATAGCAGATCTCATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
1 AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
* ** * *
29804399 CCAAGATAGTGGGAAGCAGGTTTAAGCCACCGAGCCTTATCTCCCTAAGCAGTAGCGGAGTAGGT
66 CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
29804464 TG
131 TG
29804466 AAGAT
1 AAGAT
29804471 TACAAATCCT
Statistics
Matches: 375, Mismatches: 26, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
132 375 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (132 bp):
AAGATAGCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCAAATCTTATCTTT
CCAAGATAGTGGGAAGCAGATTTAAGCCACTAAGCCTTATCTCCCTGAGCAGCAGCGGAGTAGGT
TG
Found at i:29805179 original size:13 final size:13
Alignment explanation
Indices: 29805156--29805197 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
29805146 AAGCAAAAAA
29805156 TTGTATTTTCTTTT
1 TTGT-TTTTCTTTT
29805170 ATT-TTTTTCTTTT
1 -TTGTTTTTCTTTT
*
29805183 TTGTTTTACTTTT
1 TTGTTTTTCTTTT
29805196 TT
1 TT
29805198 CGGCCTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 2 0.08
13 20 0.80
14 1 0.04
15 2 0.08
ACGTcount: A:0.07, C:0.07, G:0.05, T:0.81
Consensus pattern (13 bp):
TTGTTTTTCTTTT
Found at i:29805189 original size:20 final size:20
Alignment explanation
Indices: 29805161--29805198 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29805151 AAAAATTGTA
*
29805161 TTTTCTTTTATTTTTTTCTT
1 TTTTCTTTTACTTTTTTCTT
*
29805181 TTTTGTTTTACTTTTTTC
1 TTTTCTTTTACTTTTTTC
29805199 GGCCTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTCTTTTACTTTTTTCTT
Found at i:29806280 original size:22 final size:22
Alignment explanation
Indices: 29806250--29806295 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
29806240 ACACCAAAAC
*
29806250 AGGCTTTTAGCCGCGCTTTTTT
1 AGGCCTTTAGCCGCGCTTTTTT
*
29806272 AGGCCTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCCGCGCTTTTTT
29806294 AG
1 AG
29806296 CGCCGCAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.11, C:0.22, G:0.26, T:0.41
Consensus pattern (22 bp):
AGGCCTTTAGCCGCGCTTTTTT
Found at i:29806589 original size:86 final size:86
Alignment explanation
Indices: 29806558--29806788 Score: 302
Period size: 87 Copynumber: 2.7 Consensus size: 86
29806548 TTTTTTTCTC
**
29806558 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACCTAAT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACAGAAT
*
29806623 CTTTAGCGGCGCTTTCCCCTA
66 CTTTAGCGGCACTTTCCCCTA
* * * **
29806644 AAACGCCGCAATAGACCCTGATCTATAGCGGCTCTTCGACCACAAAACGCCACTAAAGAACCTAA
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAC-AAACGCCGCTAAAGAACAGAA
* * *
29806709 TCTTTAGCTGCGCTTTCCCCAA
65 TCTTTAGCGGCACTTTCCCCTA
* * **
29806731 AAACGCCGCTAA-AGACCATGATCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGA
1 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGA
29806789 CCCTTATTTT
Statistics
Matches: 131, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
86 55 0.42
87 74 0.56
88 2 0.02
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (86 bp):
AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACAGAAT
CTTTAGCGGCACTTTCCCCTA
Found at i:29806755 original size:130 final size:129
Alignment explanation
Indices: 29806578--29806829 Score: 323
Period size: 130 Copynumber: 1.9 Consensus size: 129
29806568 ATAGACCCTG
* *
29806578 ATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCT
1 ATCTATAGCGGCGCTTTCACCAAAAACGCCGCTAAAGAACCTAATCTTTAGCGGCGCTTTCCCC-
29806643 A-AAACGCCGC-AATAGACCCTGATCTATAGCGGCT-CTTCGACCACAAAACGCCACTAAAGAAC
65 ACAAACGCCGCTAA-AGACCCTGATCTATAGCGG-TGCTTCGACCA-AAAACGCCACTAAAGAAC
29806705 CTA
127 CTA
* * * * **
29806708 ATCTTTAGCTGCGCTTTCCCCAAAAACGCCGCTAAAG-ACCATGATCTTTAGCGGCGCTTTTTCC
1 ATCTATAGCGGCGCTTTCACCAAAAACGCCGCTAAAGAACC-TAATCTTTAGCGGCGCTTTCCCC
* * * *
29806772 ACAAACGCCGCTAAAGACCCTTATTTTTAGCGGTGCTTTGACCAAAAACGCCACTAAA
65 ACAAACGCCGCTAAAGACCCTGATCTATAGCGGTGCTTCGACCAAAAACGCCACTAAA
29806830 TTTGACAGAT
Statistics
Matches: 106, Mismatches: 12, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
129 19 0.18
130 85 0.80
131 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (129 bp):
ATCTATAGCGGCGCTTTCACCAAAAACGCCGCTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCA
CAAACGCCGCTAAAGACCCTGATCTATAGCGGTGCTTCGACCAAAAACGCCACTAAAGAACCTA
Found at i:29806821 original size:43 final size:43
Alignment explanation
Indices: 29806558--29806829 Score: 287
Period size: 43 Copynumber: 6.3 Consensus size: 43
29806548 TTTTTTTCTC
* *
29806558 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCAC
1 AAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTGACCAA
* * ** *
29806601 AAACGCCGCTAAAGAACCTAATCTTTAGCGGCGCTTTCCCCTA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
* * *
29806644 AAACGCCGC-AATAGACCCTGATCTATAGCGGCTCTTCGACCACA
1 AAACGCCGCTAA-AGACCCTGATCTTTAGCGGCGCTTTGACCA-A
* * * * **
29806688 AAACGCCACTAAAGAACCTAATCTTTAGCTGCGCTTTCCCCAA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
* ** *
29806731 AAACGCCGCTAAAGACCATGATCTTTAGCGGCGCTTTTTCCAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
* * *
29806774 AAACGCCGCTAAAGACCCTTATTTTTAGCGGTGCTTTGACCAA
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
*
29806817 AAACGCCACTAAA
1 AAACGCCGCTAAA
29806830 TTTGACAGAT
Statistics
Matches: 185, Mismatches: 40, Indels: 8
0.79 0.17 0.03
Matches are distributed among these distances:
42 2 0.01
43 148 0.80
44 33 0.18
45 2 0.01
ACGTcount: A:0.30, C:0.31, G:0.17, T:0.22
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCTTTGACCAA
Found at i:29806822 original size:86 final size:86
Alignment explanation
Indices: 29806558--29806823 Score: 372
Period size: 86 Copynumber: 3.1 Consensus size: 86
29806548 TTTTTTTCTC
29806558 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACCTAAT
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACCTAAT
*
29806623 CTTTAGCGGCGCTTTCCCCTA
66 CTTTAGCGGCGCTTTCCCCAA
* * *
29806644 AAACGCCGCAATAGACCCTGATCTATAGCGGCTCTTCGACCACAAAACGCCACTAAAGAACCTAA
1 AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCAC-AAACGCCGCTAAAGAACCTAA
*
29806709 TCTTTAGCTGCGCTTTCCCCAA
65 TCTTTAGCGGCGCTTTCCCCAA
* * ** * *
29806731 AAACGCCGCTAA-AGACCATGATCTTTAGCGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTA
1 AAACGCCGC-AATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACCTAA
* * **
29806795 TTTTTAGCGGTGCTTTGACCAA
65 TCTTTAGCGGCGCTTTCCCCAA
29806817 AAACGCC
1 AAACGCC
29806824 ACTAAATTTG
Statistics
Matches: 159, Mismatches: 19, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
86 83 0.52
87 74 0.47
88 2 0.01
ACGTcount: A:0.29, C:0.32, G:0.17, T:0.22
Consensus pattern (86 bp):
AAACGCCGCAATAGACCCTGATCTATAGCGGCGCTTTGACCACAAACGCCGCTAAAGAACCTAAT
CTTTAGCGGCGCTTTCCCCAA
Found at i:29807236 original size:21 final size:21
Alignment explanation
Indices: 29807135--29807233 Score: 108
Period size: 21 Copynumber: 4.7 Consensus size: 21
29807125 GACGCTACTT
29807135 TGCTTCCCTCGCTGCAGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
** *
29807156 TGCTTCCCTCGCTTTAGCCTA
1 TGCTTCCCTCGCTGCAGCCTC
*
29807177 TGCTTCCCTCGCTGCAGCCTG
1 TGCTTCCCTCGCTGCAGCCTC
* * * *
29807198 TACTTCTCTAGCTGCCGCCTC
1 TGCTTCCCTCGCTGCAGCCTC
* *
29807219 TGCTTCTCTTGCTGC
1 TGCTTCCCTCGCTGC
29807234 CGCATCTACT
Statistics
Matches: 65, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.06, C:0.41, G:0.18, T:0.34
Consensus pattern (21 bp):
TGCTTCCCTCGCTGCAGCCTC
Found at i:29807376 original size:65 final size:65
Alignment explanation
Indices: 29807254--29807383 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 65
29807244 TTAAGCTACT
* * * * *
29807254 GCTGGAGTTCTTCGTACTTTCGTTGATCCTCAGCTTCTCTCGCTGCTGCATCTGCTTTCAGTTGT
1 GCTGGAGTTCTTCATACTTTC-TTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
29807319 A
65 A
* *
29807320 GCTGGAGTTCTTCATATCTTT-TTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTTGT
1 GCTGGAGTTCTTCATA-CTTTCTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGT
29807384 GTAATTTGCT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
65 37 0.66
66 15 0.27
67 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.42
Consensus pattern (65 bp):
GCTGGAGTTCTTCATACTTTCTTGAACCTCAGCTTCTCTCGATGCTGCATCCGCTTTAAGTTGTA
Found at i:29812807 original size:9 final size:9
Alignment explanation
Indices: 29812790--29812920 Score: 70
Period size: 9 Copynumber: 15.9 Consensus size: 9
29812780 TAAGTATAAT
*
29812790 TAAGCTATG
1 TAAGTTATG
29812799 TAAGTTATG
1 TAAGTTATG
29812808 T-A-TTATG
1 TAAGTTATG
29812815 TAAGTTAT-
1 TAAGTTATG
*
29812823 TTA-TTATG
1 TAAGTTATG
* **
29812831 AAAACTATG
1 TAAGTTATG
*
29812840 TAAGTTGTG
1 TAAGTTATG
29812849 T-A-TTATG
1 TAAGTTATG
*
29812856 -AA--AAT-
1 TAAGTTATG
* *
29812861 TATGCTATG
1 TAAGTTATG
*
29812870 TAAGTTATA
1 TAAGTTATG
* *
29812879 TAAGTCATA
1 TAAGTTATG
29812888 TAAGTTATG
1 TAAGTTATG
29812897 T-A-TTATG
1 TAAGTTATG
29812904 TAAGTTATG
1 TAAGTTATG
29812913 TAAGTTAT
1 TAAGTTAT
29812921 TTATTATGCA
Statistics
Matches: 92, Mismatches: 19, Indels: 22
0.69 0.14 0.17
Matches are distributed among these distances:
6 3 0.03
7 21 0.23
8 10 0.11
9 58 0.63
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:29812816 original size:16 final size:16
Alignment explanation
Indices: 29812795--29812914 Score: 78
Period size: 16 Copynumber: 7.9 Consensus size: 16
29812785 ATAATTAAGC
29812795 TATGTAAGTTATGTAT
1 TATGTAAGTTATGTAT
*
29812811 TATGTAAGTTATTTAT
1 TATGTAAGTTATGTAT
*
29812827 TATG-AA---A---AC
1 TATGTAAGTTATGTAT
*
29812836 TATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAT
* * *
29812852 TATGAAAATTATG--C
1 TATGTAAGTTATGTAT
*
29812866 TATGTAAGTTATATAAGT
1 TATGTAAGTTATGT-A-T
* *
29812884 CATATAAGTTATGTAT
1 TATGTAAGTTATGTAT
29812900 TATGTAAGTTATGTA
1 TATGTAAGTTATGTA
29812915 AGTTATTTAT
Statistics
Matches: 76, Mismatches: 17, Indels: 22
0.66 0.15 0.19
Matches are distributed among these distances:
9 5 0.07
10 2 0.03
12 1 0.01
14 10 0.13
15 2 0.03
16 44 0.58
17 1 0.01
18 11 0.14
ACGTcount: A:0.36, C:0.03, G:0.17, T:0.45
Consensus pattern (16 bp):
TATGTAAGTTATGTAT
Done.