Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr4
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: 92286807
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3302597 characters in sequence are not A, C, G, or T
File 124 of 271
Found at i:41775706 original size:23 final size:22
Alignment explanation
Indices: 41775664--41775705 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
41775654 TAATTATAAT
* *
41775664 TAAAGAAAAAAGACTAAAAATG
1 TAAAAAAAAAAAACTAAAAATG
41775686 TAAAAAAAAAAAACTAAAAA
1 TAAAAAAAAAAAACTAAAAA
41775706 AGTTAATTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (22 bp):
TAAAAAAAAAAAACTAAAAATG
Found at i:41780533 original size:46 final size:46
Alignment explanation
Indices: 41780485--41781481 Score: 1773
Period size: 46 Copynumber: 21.7 Consensus size: 46
41780475 CCATAGTGTC
* * * * *
41780485 TTTCAACTATGGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTATT
** * * * *
41780531 TTTCAACCATGGTCTTATTCATTTCATGTCACGATGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
*** *** * *
41780577 TTTCAACCATGGTCTTATTTATTTCCCGTCATGTTGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
* * *
41780623 TTTCAACCATGGTCTTCCACGTTTCATATCAGG-TGCCATGGTATC
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780668 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780714 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780760 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780806 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780852 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780898 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780944 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41780990 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781036 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781082 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781128 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781174 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781220 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781266 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781312 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781358 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781404 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
1 TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
41781450 TTTCAACCATGGTCTTACACATTTCATATCAG
1 TTTCAACCATGGTCTTACACATTTCATATCAG
41781482 AGAGCACACT
Statistics
Matches: 928, Mismatches: 21, Indels: 4
0.97 0.02 0.00
Matches are distributed among these distances:
45 47 0.05
46 881 0.95
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.39
Consensus pattern (46 bp):
TTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATT
Found at i:41788622 original size:39 final size:39
Alignment explanation
Indices: 41788510--41788624 Score: 185
Period size: 39 Copynumber: 2.9 Consensus size: 39
41788500 TGTGTGAGAT
* *
41788510 TTATATTCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTG
* *
41788549 TTATATCCGGGCTAAGTCCCAAAGGTATTCGTGTTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTG
*
41788588 TTATATCCGGGCTAAGTCCCGAAGGCATTTGTGTTGG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGG
41788625 AAATGTGTGA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 69 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.32
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGTTGGTG
Found at i:41793769 original size:23 final size:24
Alignment explanation
Indices: 41793743--41793795 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
41793733 CCACCAAATA
*
41793743 AAATATTACTCTTTTAAAAT-TTT
1 AAATATAACTCTTTTAAAATATTT
* *
41793766 AAATATAATTTTTTTAAAATATTT
1 AAATATAACTCTTTTAAAATATTT
*
41793790 GAATAT
1 AAATAT
41793796 CTTTAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (24 bp):
AAATATAACTCTTTTAAAATATTT
Found at i:41793834 original size:7 final size:7
Alignment explanation
Indices: 41793822--41793854 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
41793812 AAAAATATAT
41793822 AATTTAA
1 AATTTAA
41793829 AATTTAA
1 AATTTAA
41793836 AATTTAA
1 AATTTAA
41793843 AATTTAA
1 AATTTAA
41793850 AATTT
1 AATTT
41793855 TTAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
AATTTAA
Found at i:41793846 original size:21 final size:21
Alignment explanation
Indices: 41793813--41793887 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
41793803 AATAATTTTA
*
41793813 AAAATATATAATTTAAAATTT
1 AAAATATAAAATTTAAAATTT
*
41793834 AAAATTTAAAATTTAAAATTTTT
1 AAAATATAAAATTTAAAA--TTT
*
41793857 AAAATAT-ACATTTAAAATATT
1 AAAATATAAAATTTAAAAT-TT
41793878 ATAAA-ATAAA
1 A-AAATATAAA
41793888 TAATAAATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
20 1 0.02
21 21 0.48
22 13 0.30
23 9 0.20
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATATAAAATTTAAAATTT
Found at i:41794033 original size:11 final size:11
Alignment explanation
Indices: 41794017--41794041 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41794007 AAATATTGTA
41794017 AAACAAATAAT
1 AAACAAATAAT
41794028 AAACAAATAAT
1 AAACAAATAAT
41794039 AAA
1 AAA
41794042 AAACAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (11 bp):
AAACAAATAAT
Found at i:41794284 original size:12 final size:12
Alignment explanation
Indices: 41794267--41794299 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
41794257 CGACCCACCC
41794267 ATATTAATTTTT
1 ATATTAATTTTT
41794279 ATATT-ATTTTT
1 ATATTAATTTTT
41794290 ATA-TAATTTT
1 ATATTAATTTT
41794300 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:41794540 original size:22 final size:22
Alignment explanation
Indices: 41794515--41794557 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
41794505 TATCCAAATA
41794515 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
41794537 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
41794558 AATAGGAAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:41794561 original size:11 final size:11
Alignment explanation
Indices: 41794522--41794562 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
41794512 ATAATAACAA
41794522 CAAAATAGTAG
1 CAAAATAGTAG
* *
41794533 CAACATAATAG
1 CAAAATAGTAG
*
41794544 TAAAATAGTAG
1 CAAAATAGTAG
41794555 CAAAATAG
1 CAAAATAG
41794563 GAAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:41799277 original size:48 final size:48
Alignment explanation
Indices: 41799194--41799491 Score: 328
Period size: 48 Copynumber: 6.2 Consensus size: 48
41799184 TACATTGGCT
* * * *
41799194 CTCATATATCGATGCCGATGCCATGTTCCAAACATGGTCTTACACTAT
1 CTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
* * * *
41799242 CCCACATGTCGAGGCC-ATTGCCATATCCCAGACATGGTCTTACACTAG
1 CTCACATATCGAGGCCGA-TGCCATGTCCCAAACATGGTCTTACACTAG
* * * * *
41799290 CTCTCATATAGATGCCGATGCCACGTTCCAAACATGGTCTTACACTAG
1 CTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
* * * *
41799338 CTCACATATCGAAGCCGACGCCATGTCCCAAACATGGTCTTACATTGG
1 CTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
* * *
41799386 CTCACATATCAAGGCCGATGCCATGTCCCAGACATGGTCTTATACTAG
1 CTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
* * * * * * * *
41799434 CTCTCATATAGATGCTGATTCCATATTCCAAACATGGTCTTACACTGG
1 CTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
41799482 CTCACATATC
1 CTCACATATC
41799492 CCTAGAATCA
Statistics
Matches: 203, Mismatches: 45, Indels: 4
0.81 0.18 0.02
Matches are distributed among these distances:
47 1 0.00
48 201 0.99
49 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (48 bp):
CTCACATATCGAGGCCGATGCCATGTCCCAAACATGGTCTTACACTAG
Found at i:41799333 original size:96 final size:96
Alignment explanation
Indices: 41799177--41799490 Score: 364
Period size: 96 Copynumber: 3.2 Consensus size: 96
41799167 TATCACAGAT
* * *
41799177 ATGGTCTTACATTGGCTCTCATATATCGATGCCGATGCCATGTTCCAAACATGGTCTTACACTAT
1 ATGGTCTTACACTGGCTCACATATA--GATGCCGATGCCATGTTCCAAACATGGTCTTACACTAG
* * * *
41799242 CCCACATGTCGAGGCCATTGCCATATCCCAGAC
64 CTCACATATCGAAGCCATTGCCATATCCCAAAC
* * *
41799275 ATGGTCTTACACTAGCTCTCATATAGATGCCGATGCCACGTTCCAAACATGGTCTTACACTAGCT
1 ATGGTCTTACACTGGCTCACATATAGATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCT
* *
41799340 CACATATCGAAGCCGA-CGCCATGTCCCAAAC
66 CACATATCGAAGCC-ATTGCCATATCCCAAAC
* * * * *
41799371 ATGGTCTTACATTGGCTCACATATCA-AGGCCGATGCCATGTCCCAGACATGGTCTTATACTAGC
1 ATGGTCTTACACTGGCTCACATAT-AGATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGC
* * * * *
41799435 TCTCATATAGATGCTGATT-CCATATTCCAAAC
65 TCACATATCGAAGC-CATTGCCATATCCCAAAC
41799467 ATGGTCTTACACTGGCTCACATAT
1 ATGGTCTTACACTGGCTCACATAT
41799491 CCCTAGAATC
Statistics
Matches: 186, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
96 161 0.87
97 2 0.01
98 23 0.12
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (96 bp):
ATGGTCTTACACTGGCTCACATATAGATGCCGATGCCATGTTCCAAACATGGTCTTACACTAGCT
CACATATCGAAGCCATTGCCATATCCCAAAC
Found at i:41799401 original size:144 final size:144
Alignment explanation
Indices: 41799194--41799491 Score: 427
Period size: 144 Copynumber: 2.1 Consensus size: 144
41799184 TACATTGGCT
* * * * * * *
41799194 CTCATATATCGATGCCGATGCCATGTTCCAAACATGGTCTTACACTATCCCACATGTCGAGGCC-
1 CTCACATATCGAAGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCCCACATATCAAGGCCG
*
41799258 ATTGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATAGATGCCGATGCCACGTTCCAAAC
66 A-TGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATAGATGCCGATGCCACATTCCAAAC
41799323 ATGGTCTTACACTAG
130 ATGGTCTTACACTAG
* * *
41799338 CTCACATATCGAAGCCGACGCCATGTCCCAAACATGGTCTTACATTGGCTCACATATCAAGGCCG
1 CTCACATATCGAAGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCCCACATATCAAGGCCG
* * * * *
41799403 ATGCCATGTCCCAGACATGGTCTTATACTAGCTCTCATATAGATGCTGATTCCATATTCCAAACA
66 ATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATAGATGCCGATGCCACATTCCAAACA
*
41799468 TGGTCTTACACTGG
131 TGGTCTTACACTAG
41799482 CTCACATATC
1 CTCACATATC
41799492 CCTAGAATCA
Statistics
Matches: 136, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
144 135 0.99
145 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (144 bp):
CTCACATATCGAAGCCGACGCCATGTCCCAAACATGGTCTTACACTAGCCCACATATCAAGGCCG
ATGCCATATCCCAGACATGGTCTTACACTAGCTCTCATATAGATGCCGATGCCACATTCCAAACA
TGGTCTTACACTAG
Found at i:41801847 original size:24 final size:26
Alignment explanation
Indices: 41801795--41801847 Score: 65
Period size: 24 Copynumber: 2.1 Consensus size: 26
41801785 ATAAATATTT
*
41801795 TTTAACAAAAATACAAAAAATCAAGA
1 TTTAACAAAAATACAAAAAATCAAAA
* *
41801821 TTTAA-AAAAAT-CAAAAATTGAAAA
1 TTTAACAAAAATACAAAAAATCAAAA
41801845 TTT
1 TTT
41801848 GCAATAAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 13 0.54
25 6 0.25
26 5 0.21
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (26 bp):
TTTAACAAAAATACAAAAAATCAAAA
Found at i:41810938 original size:21 final size:21
Alignment explanation
Indices: 41810914--41810982 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 21
41810904 AATAAATAAT
41810914 AAATACTATATAATTTAATTA
1 AAATACTATATAATTTAATTA
*
41810935 AAATTAGTATGACTAATTATAA--A
1 AAA-TACTAT-A-TAATT-TAATTA
* *
41810958 AAATACTATGTAATTTAGTTA
1 AAATACTATATAATTTAATTA
41810979 AAAT
1 AAAT
41810983 TCATTTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
19 2 0.05
20 5 0.13
21 8 0.21
22 10 0.26
23 5 0.13
24 5 0.13
25 3 0.08
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (21 bp):
AAATACTATATAATTTAATTA
Found at i:41810996 original size:44 final size:44
Alignment explanation
Indices: 41810898--41811034 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 44
41810888 TCTTTGACTA
41810898 AGTATTAATAA--ATAATAAATACTATATAATTTAATTAAAATT
1 AGTATTAATAATTATAATAAATACTATATAATTTAATTAAAATT
* * * * *
41810940 AGTATGACTAATTATAAAAAATACTATGTAATTTAGTTAAAATT
1 AGTATTAATAATTATAATAAATACTATATAATTTAATTAAAATT
* ** *
41810984 CA-TTTTAATAATTTATAATGGATACTATCTAATTTAATTAAATATTT
1 -AGTATTAATAA-TTATAATAAATACTATATAATTTAATTAAA-A-TT
41811031 AGTA
1 AGTA
41811035 GACAAAAATA
Statistics
Matches: 74, Mismatches: 14, Indels: 9
0.76 0.14 0.09
Matches are distributed among these distances:
42 9 0.12
44 34 0.46
45 26 0.35
46 2 0.03
47 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (44 bp):
AGTATTAATAATTATAATAAATACTATATAATTTAATTAAAATT
Found at i:41819035 original size:18 final size:19
Alignment explanation
Indices: 41819001--41819039 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
41818991 CTTTAAACCC
41819001 AAACACTAAACCCTAACAA
1 AAACACTAAACCCTAACAA
*
41819020 AAACCCTAAA-CCTAACAA
1 AAACACTAAACCCTAACAA
41819038 AA
1 AA
41819040 TTAAAAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.10
Consensus pattern (19 bp):
AAACACTAAACCCTAACAA
Found at i:41819305 original size:30 final size:30
Alignment explanation
Indices: 41819252--41819311 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
41819242 AATTAAAGAA
** *
41819252 ATTAAAAGATAAAATTAGTATTTCCTTTCT
1 ATTAAAAGATAAAATTAACATTTCATTTCT
*
41819282 ATTAAAAGATAAATTTAACATTTCATTTCT
1 ATTAAAAGATAAAATTAACATTTCATTTCT
41819312 TCTTCATGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (30 bp):
ATTAAAAGATAAAATTAACATTTCATTTCT
Found at i:41820646 original size:39 final size:39
Alignment explanation
Indices: 41820587--41820666 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
41820577 CAACTCGTAG
* *
41820587 AATCTCACTATCTCGAAGACTCTTTTGGTAGATTTTGTA
1 AATCACACTATCCCGAAGACTCTTTTGGTAGATTTTGTA
41820626 AATCACACTATCCCGAAGACTCTTTTGGTAGATTTTGTA
1 AATCACACTATCCCGAAGACTCTTTTGGTAGATTTTGTA
41820665 AA
1 AA
41820667 CATTTGGCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (39 bp):
AATCACACTATCCCGAAGACTCTTTTGGTAGATTTTGTA
Found at i:41834225 original size:291 final size:291
Alignment explanation
Indices: 41833690--41834254 Score: 1058
Period size: 291 Copynumber: 1.9 Consensus size: 291
41833680 TTCATCATCC
* * *
41833690 CAAACAATTTTTGTTTCTAAGGTACTCTCCCTTCACAAAATTTTGTGTCTTTACCATCTATTATT
1 CAAACAATTTTTGTTGCTAAGGTACTCTCCCTCCACAAAATTTCGTGTCTTTACCATCTATTATT
* *
41833755 ATTTTGATTTTAAATGTCAATCGACATAAAACTATAAGTATATAGTTAGATATGATAATATAGTT
66 ATTTTGATTTTAAATGTCAATCGACATAAAACTATAAGTATATAATTAGATATAATAATATAGTT
41833820 TCATAAAAAATAAGAATAATACATCACGAATGGATGAAAGCCATAAGATGAACACTAATGAAAAA
131 TCATAAAAAATAAGAATAATACATCACGAATGGATGAAAGCCATAAGATGAACACTAATGAAAAA
41833885 ATTCTCAAAGATCCATAGTAAACAATAACGAGGATATAAAAAAGATAGTTAATCAATTAAGAGAA
196 ATTCTCAAAGATCCATAGTAAACAATAACGAGGATATAAAAAAGATAGTTAATCAATTAAGAGAA
41833950 TATATACCAAAATTCTCAAGTACCTTAGCAA
261 TATATACCAAAATTCTCAAGTACCTTAGCAA
*
41833981 CAAACAGTTTTTGTTGCTAAGGTACTCTCCCTCCACAAAATTTCGTGTCTTTACCATCTATTATT
1 CAAACAATTTTTGTTGCTAAGGTACTCTCCCTCCACAAAATTTCGTGTCTTTACCATCTATTATT
41834046 ATTTTGATTTTAAATGTCAATCGACATAAAACTATAAGTATATAATTAGATATAATAATATAGTT
66 ATTTTGATTTTAAATGTCAATCGACATAAAACTATAAGTATATAATTAGATATAATAATATAGTT
41834111 TCATAAAAAATAAGAATAATACATCACGAATGGATGAAAGCCATAAGATGAACACTAATGAAAAA
131 TCATAAAAAATAAGAATAATACATCACGAATGGATGAAAGCCATAAGATGAACACTAATGAAAAA
* *
41834176 ATTCTCAAAGATCCATAGTAAACAATAATGAGGATATAAAAATGATAGTTAATCAATTAAGAGAA
196 ATTCTCAAAGATCCATAGTAAACAATAACGAGGATATAAAAAAGATAGTTAATCAATTAAGAGAA
41834241 TATATACCAAAATT
261 TATATACCAAAATT
41834255 TTCAGATTAT
Statistics
Matches: 266, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
291 266 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.31
Consensus pattern (291 bp):
CAAACAATTTTTGTTGCTAAGGTACTCTCCCTCCACAAAATTTCGTGTCTTTACCATCTATTATT
ATTTTGATTTTAAATGTCAATCGACATAAAACTATAAGTATATAATTAGATATAATAATATAGTT
TCATAAAAAATAAGAATAATACATCACGAATGGATGAAAGCCATAAGATGAACACTAATGAAAAA
ATTCTCAAAGATCCATAGTAAACAATAACGAGGATATAAAAAAGATAGTTAATCAATTAAGAGAA
TATATACCAAAATTCTCAAGTACCTTAGCAA
Found at i:41837022 original size:75 final size:74
Alignment explanation
Indices: 41836883--41837080 Score: 191
Period size: 75 Copynumber: 2.8 Consensus size: 74
41836873 GTAGTTGGTA
* * *
41836883 AAATATTGAAAATAGAAGAGTAAAGTAAAATATAAATAAAATTAAGGGAGAAATTTGTAGATAAA
1 AAATATTGAAAACAAAAGAGCAAAGTAAAATATAAATAAAATTAAGGGAGAAATTTGTAGATAAA
41836948 TAATAATAAT
66 -AATAATAAT
* * * *
41836958 AAATATTGAAAACAAAATAGCAAATTAAAATGTAAATAAAATTAAGGGAGCAA-TT-T---T---
1 AAATATTGAAAACAAAAGAGCAAAGTAAAATATAAATAAAATTAAGGGAGAAATTTGTAGATAAA
41837015 AAT-ATAA-
66 AATAATAAT
* * ** * *
41837022 AAATATTGAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACGGAGCAATTTGT
1 AAATATTGAAAACAAAAGAGC-AAAGTAAAATATAAATAAAATTAAGGGAGAAATTTGT
41837081 GAATAAATAT
Statistics
Matches: 109, Mismatches: 11, Indels: 14
0.81 0.08 0.10
Matches are distributed among these distances:
64 20 0.18
65 33 0.30
66 5 0.05
67 1 0.01
70 1 0.01
73 1 0.01
74 2 0.02
75 46 0.42
ACGTcount: A:0.57, C:0.03, G:0.13, T:0.27
Consensus pattern (74 bp):
AAATATTGAAAACAAAAGAGCAAAGTAAAATATAAATAAAATTAAGGGAGAAATTTGTAGATAAA
AATAATAAT
Found at i:41837026 original size:64 final size:67
Alignment explanation
Indices: 41836948--41837078 Score: 205
Period size: 65 Copynumber: 2.0 Consensus size: 67
41836938 TGTAGATAAA
* *
41836948 TAATAATAATAAATATTGAAAACAAAATAGC-AAATTAAAATGTAAATAAAATTAAGGGAGCAAT
1 TAATAATAATAAATATTGAAAACAAAATAGCGAAATTAAAATATAAATAAAATTAACGGAGCAAT
41837012 TT
66 TT
* *
41837014 TAAT-ATAA-AAATATTGAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACGGAGCAAT
1 TAATAATAATAAATATTGAAAACAAAATAGCGAAATTAAAATATAAATAAAATTAACGGAGCAAT
41837077 TT
66 TT
41837079 GTGAATAAAT
Statistics
Matches: 60, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 20 0.33
65 36 0.60
66 4 0.07
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (67 bp):
TAATAATAATAAATATTGAAAACAAAATAGCGAAATTAAAATATAAATAAAATTAACGGAGCAAT
TT
Found at i:41837078 original size:30 final size:30
Alignment explanation
Indices: 41836976--41837078 Score: 80
Period size: 34 Copynumber: 3.3 Consensus size: 30
41836966 AAAACAAAAT
* * *
41836976 AGCAAATTAAAATGTAAATAAAATTAAGGG
1 AGCAATTTAAAATATAAATAAAATTAAAGG
* * * **
41837006 AGCAATTTTAATATAAAAATATTGAAAATAAAAT
1 AGCAA-TTTAAAATATAAATA---AAATTAAAGG
*
41837040 AGCGAATTTAAAATATAAATAAAATTAACGG
1 AGC-AATTTAAAATATAAATAAAATTAAAGG
41837071 AGCAATTT
1 AGCAATTT
41837079 GTGAATAAAT
Statistics
Matches: 54, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
30 10 0.19
31 20 0.37
34 22 0.41
35 2 0.04
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (30 bp):
AGCAATTTAAAATATAAATAAAATTAAAGG
Found at i:41837129 original size:154 final size:154
Alignment explanation
Indices: 41836940--41837267 Score: 568
Period size: 154 Copynumber: 2.1 Consensus size: 154
41836930 GAGAAATTTG
* *
41836940 TAGATAAATAATAATAATAAATATTGAAAACAAAATAGCAAATTAAAATGTAAATAAAATTAAGG
1 TAGAT-AATAATAATAATAAATATTGAAAACAAAATAGAAAATTAAAATGTAAATAAAATTAAAG
*
41837005 GAGCAATTTTAATATAAAAATATTGAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACG
65 GAGCAATTTTAATATAAAAATATTAAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACG
41837070 GAGCAATTTGTGAATAAATATACAAA
130 GAGCAATTTGTGAATAAATATAC-AA
* *
41837096 TA-ATAATAATAATAATAAATATTGAAAATAAAATAGAAAATTAAAATGTAAATAAAATTAAATG
1 TAGATAATAATAATAATAAATATTGAAAACAAAATAGAAAATTAAAATGTAAATAAAATTAAAGG
* *
41837160 AGTAATTTTAATATAAAAATATTAAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAAGGG
66 AGCAATTTTAATATAAAAATATTAAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACGG
41837225 AGCAATTTGTGAATAAATATACAA
131 AGCAATTTGTGAATAAATATACAA
41837249 TAGATAATAATAATAATAA
1 TAGATAATAATAATAATAA
41837268 TAATAATAAT
Statistics
Matches: 164, Mismatches: 7, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
153 4 0.02
154 156 0.95
155 2 0.01
156 2 0.01
ACGTcount: A:0.59, C:0.03, G:0.09, T:0.29
Consensus pattern (154 bp):
TAGATAATAATAATAATAAATATTGAAAACAAAATAGAAAATTAAAATGTAAATAAAATTAAAGG
AGCAATTTTAATATAAAAATATTAAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACGG
AGCAATTTGTGAATAAATATACAA
Found at i:41837190 original size:89 final size:89
Alignment explanation
Indices: 41837014--41837180 Score: 223
Period size: 89 Copynumber: 1.9 Consensus size: 89
41837004 GGAGCAATTT
* * *
41837014 TAAT-ATAAAAATATTGAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAACGGAGCAATT
1 TAATAATAAAAATATTGAAAATAAAATAGCAAAATTAAAATATAAATAAAATTAAAGGAGCAATT
* *
41837078 TGTGAATAAATATACAAATAATAA
66 TGTAAATAAAAATACAAATAATAA
* * *
41837102 TAATAATAATAAATATTGAAAATAAAATAG-AAAATTAAAATGTAAATAAAATTAAATGAGTAAT
1 TAATAATAA-AAATATTGAAAATAAAATAGCAAAATTAAAATATAAATAAAATTAAAGGAGCAAT
41837166 TT-TAATATAAAAATA
65 TTGTAA-ATAAAAATA
41837181 TTAAAAATAA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 6 0.09
89 42 0.62
90 20 0.29
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (89 bp):
TAATAATAAAAATATTGAAAATAAAATAGCAAAATTAAAATATAAATAAAATTAAAGGAGCAATT
TGTAAATAAAAATACAAATAATAA
Found at i:41837232 original size:65 final size:66
Alignment explanation
Indices: 41837102--41837232 Score: 176
Period size: 65 Copynumber: 2.0 Consensus size: 66
41837092 CAAATAATAA
* * * *
41837102 TAATAATAATAAATATTGAAAATAAAATAGAAAATTAAAATGTAAATAAAATTAAATGAGTAATT
1 TAATAATAATAAATATTAAAAATAAAATAGAAAATTAAAATATAAATAAAATTAAAGGAGCAATT
41837167 T
66 T
* * *
41837168 TAAT-ATAA-AAATATTAAAAATAAAATAGCGAATTTAAAATATAAATAAAATTAAGGGAGCAAT
1 TAATAATAATAAATATTAAAAATAAAATAG-AAAATTAAAATATAAATAAAATTAAAGGAGCAAT
41837231 TT
65 TT
41837233 GTGAATAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
64 19 0.33
65 34 0.60
66 4 0.07
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (66 bp):
TAATAATAATAAATATTAAAAATAAAATAGAAAATTAAAATATAAATAAAATTAAAGGAGCAATT
T
Found at i:41837260 original size:3 final size:3
Alignment explanation
Indices: 41837247--41837288 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
41837237 ATAAATATAC
41837247 AAT AGAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41837289 ATATTGAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41837373 original size:17 final size:17
Alignment explanation
Indices: 41837353--41837406 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
41837343 ACAAATACAA
41837353 ATATAAATAAAATAAAT
1 ATATAAATAAAATAAAT
*
41837370 ATATAAGTAAAATAAA-
1 ATATAAATAAAATAAAT
* *
41837386 GTAGAAATAAAA-AAAT
1 ATATAAATAAAATAAAT
41837402 A-ATAA
1 ATATAA
41837407 TAATCTAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 6 0.20
16 9 0.30
17 15 0.50
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (17 bp):
ATATAAATAAAATAAAT
Found at i:41840963 original size:40 final size:40
Alignment explanation
Indices: 41840856--41841038 Score: 129
Period size: 40 Copynumber: 4.6 Consensus size: 40
41840846 GTTATGAAAT
* * * **
41840856 TAGCAGGCTTCGTGCCAATGAATCTATCAACCTTAGT-GC
1 TAGCAGGCTTTGTGCCAGTGAATTTATCAGGCTTAGTGGC
** * * * * *
41840895 TTAGCAAACTTTGTGTC-GATGTAGTTATCGGGCTTTGTGGC
1 -TAGCAGGCTTTGTGCCAG-TGAATTTATCAGGCTTAGTGGC
* * *
41840936 TAGTAGGCCTTGTGCCAGTGAATTTATCAAGCTTAGT-GC
1 TAGCAGGCTTTGTGCCAGTGAATTTATCAGGCTTAGTGGC
* * * * *
41840975 TTAGCAGGCTTTATGCCAGTGTAGTTATCAGGCTTGGTGCC
1 -TAGCAGGCTTTGTGCCAGTGAATTTATCAGGCTTAGTGGC
*
41841016 TAGCAGGCTTTGTGCCGGTGAAT
1 TAGCAGGCTTTGTGCCAGTGAAT
41841039 CAAGTTTTTT
Statistics
Matches: 104, Mismatches: 34, Indels: 10
0.70 0.23 0.07
Matches are distributed among these distances:
39 2 0.02
40 98 0.94
41 4 0.04
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.33
Consensus pattern (40 bp):
TAGCAGGCTTTGTGCCAGTGAATTTATCAGGCTTAGTGGC
Found at i:41841000 original size:80 final size:80
Alignment explanation
Indices: 41840856--41841039 Score: 219
Period size: 80 Copynumber: 2.3 Consensus size: 80
41840846 GTTATGAAAT
* * *
41840856 TAGCAGG-CTTCGTGCCAATGAATCTATCAACCTTAGTGCTTAGCAAACTTTGTGTCGATGTAGT
1 TAGCAGGCCTT-GTGCCAGTGAATCTATCAACCTTAGTGCTTAGCAAACTTTATGCCGATGTAGT
* * *
41840920 TATCGGGCTTTGTGGC
65 TATCAGGCTTGGTGCC
* * * **
41840936 TAGTAGGCCTTGTGCCAGTGAATTTATCAAGCTTAGTGCTTAGCAGGCTTTATGCC-AGTGTAGT
1 TAGCAGGCCTTGTGCCAGTGAATCTATCAACCTTAGTGCTTAGCAAACTTTATGCCGA-TGTAGT
41841000 TATCAGGCTTGGTGCC
65 TATCAGGCTTGGTGCC
* *
41841016 TAGCAGGCTTTGTGCCGGTGAATC
1 TAGCAGGCCTTGTGCCAGTGAATC
41841040 AAGTTTTTTA
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 1 0.01
80 83 0.95
81 3 0.03
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (80 bp):
TAGCAGGCCTTGTGCCAGTGAATCTATCAACCTTAGTGCTTAGCAAACTTTATGCCGATGTAGTT
ATCAGGCTTGGTGCC
Found at i:41842417 original size:21 final size:21
Alignment explanation
Indices: 41842383--41842422 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
41842373 TGAGAATATG
*
41842383 GGCGTGTGGATTAGCCACATA
1 GGCGTGTGGATTAGACACATA
41842404 GGCGTGT-GAGTTAGACACA
1 GGCGTGTGGA-TTAGACACA
41842423 CGTCCATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.25, C:0.17, G:0.35, T:0.23
Consensus pattern (21 bp):
GGCGTGTGGATTAGACACATA
Found at i:41849201 original size:39 final size:39
Alignment explanation
Indices: 41848956--41849185 Score: 424
Period size: 39 Copynumber: 5.9 Consensus size: 39
41848946 ATATATATAT
41848956 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
1 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
41848995 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
1 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
*
41849034 GAGAATTATATCCGGACTTCATGTCCGCAGGCTCTATGC
1 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
*
41849073 GAGAATTATATCCGGACTTCATGTCCGCAGGCTCTATGC
1 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
41849112 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
1 GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
* *
41849151 GAGAATTATATCCGGACTTTAGGTCCGCAGGCTAT
1 GAGAATTATATCCGGACTTCATGTCCGCAGGCTAT
41849186 GTGCTGGACA
Statistics
Matches: 187, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 187 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.28
Consensus pattern (39 bp):
GAGAATTATATCCGGACTTCATGTCCGCAGGCTATATGC
Found at i:41855354 original size:39 final size:39
Alignment explanation
Indices: 41855311--41855390 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
41855301 TGTGAATATA
*
41855311 TATATATGAGAATTATATCCGGACTTCATGTCCGCAGGC
1 TATATACGAGAATTATATCCGGACTTCATGTCCGCAGGC
*
41855350 TATATGCGAGAATTATATCCGGACTTCATGTCCGCAGGC
1 TATATACGAGAATTATATCCGGACTTCATGTCCGCAGGC
41855389 TA
1 TA
41855391 CGTGCTGGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (39 bp):
TATATACGAGAATTATATCCGGACTTCATGTCCGCAGGC
Found at i:41863442 original size:39 final size:39
Alignment explanation
Indices: 41863399--41863478 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
41863389 TGTGAATATA
*
41863399 TATATGCGAGAATTATATCCGGACTTCATGTCCACAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCACAGGC
* *
41863438 TATATGCGAGAATTATATCCGGACTTTAGGTCCGCAGGC
1 TATATGCGAGAATTATATCCGGACTTCAGGTCCACAGGC
41863477 TA
1 TA
41863479 CGTGCTGGAC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (39 bp):
TATATGCGAGAATTATATCCGGACTTCAGGTCCACAGGC
Found at i:41866344 original size:31 final size:31
Alignment explanation
Indices: 41866309--41866371 Score: 110
Period size: 31 Copynumber: 2.0 Consensus size: 31
41866299 CAAATTGACT
41866309 ATTGAACTATTTA-AAAGTTTTTATTTAAGTC
1 ATTGAACTA-TTAGAAAGTTTTTATTTAAGTC
41866340 ATTGAACTATTAGAAAGTTTTTATTTAAGTC
1 ATTGAACTATTAGAAAGTTTTTATTTAAGTC
41866371 A
1 A
41866372 CTCATTTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 3 0.10
31 28 0.90
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTGAACTATTAGAAAGTTTTTATTTAAGTC
Found at i:41870435 original size:25 final size:27
Alignment explanation
Indices: 41870403--41870457 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
41870393 TTTTTTTTTA
*
41870403 TTTAAAA-AAACTACCATATTT-TTCTT
1 TTTAAAATACACTACCAT-TTTCTTCTT
*
41870429 TTTAAAATACCCTACCATTTTCTTCTT
1 TTTAAAATACACTACCATTTTCTTCTT
41870456 TT
1 TT
41870458 CTTTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.40
27 15 0.60
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTAAAATACACTACCATTTTCTTCTT
Found at i:41873696 original size:3 final size:3
Alignment explanation
Indices: 41873688--41873717 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
41873678 CATTACTGAG
41873688 GAA GAA GAA GAA GAA GAA GAA GAA G-A GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
41873718 TTTTGGTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41883020 original size:25 final size:25
Alignment explanation
Indices: 41882986--41883036 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
41882976 ATTTTCACTA
41882986 TACCAGACCACCCAATAGACTTATG
1 TACCAGACCACCCAATAGACTTATG
*
41883011 TACCAGACCACCTAATAGACTTATG
1 TACCAGACCACCCAATAGACTTATG
41883036 T
1 T
41883037 TCAATTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.12, T:0.24
Consensus pattern (25 bp):
TACCAGACCACCCAATAGACTTATG
Found at i:41888936 original size:17 final size:17
Alignment explanation
Indices: 41888914--41888953 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
41888904 CCTTTCTTAT
*
41888914 AAAAATAATATAATATA
1 AAAAATAATAAAATATA
* *
41888931 AAAAATTATAAAATTTA
1 AAAAATAATAAAATATA
41888948 AAAAAT
1 AAAAAT
41888954 GAATTAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (17 bp):
AAAAATAATAAAATATA
Found at i:41891229 original size:11 final size:10
Alignment explanation
Indices: 41891211--41891240 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
41891201 AAAAAAAATA
41891211 TTTTATTATT
1 TTTTATTATT
41891221 TTATTATTATT
1 TT-TTATTATT
41891232 TTTTATTAT
1 TTTTATTAT
41891241 AAAAGGAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTATTATT
Found at i:41891235 original size:13 final size:14
Alignment explanation
Indices: 41891209--41891240 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
41891199 AAAAAAAAAA
41891209 TATT-TTATTATTT
1 TATTATTATTATTT
41891222 TATTATTATT-TTT
1 TATTATTATTATTT
41891235 TATTAT
1 TATTAT
41891241 AAAAGGAGGT
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:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:41895947 original size:34 final size:34
Alignment explanation
Indices: 41895904--41896007 Score: 190
Period size: 34 Copynumber: 3.1 Consensus size: 34
41895894 CGGTCAAGCC
41895904 ACACGCCCGTGTGCTAGGCCGTATGAACATACTA
1 ACACGCCCGTGTGCTAGGCCGTATGAACATACTA
* *
41895938 ACACGCCCGTGCGCTAGGACGTATGAACATACTA
1 ACACGCCCGTGTGCTAGGCCGTATGAACATACTA
41895972 ACACGCCCGTGTGCTAGGCCGTATGAACATACTA
1 ACACGCCCGTGTGCTAGGCCGTATGAACATACTA
41896006 AC
1 AC
41896008 TTCTAAAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 66 1.00
ACGTcount: A:0.28, C:0.30, G:0.23, T:0.19
Consensus pattern (34 bp):
ACACGCCCGTGTGCTAGGCCGTATGAACATACTA
Found at i:41897017 original size:42 final size:41
Alignment explanation
Indices: 41896967--41897079 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 41
41896957 GCTAAATAGG
* *
41896967 AACCCATAAGGGTTGAACGGAAGCTCATAAAATCTGAACAGA
1 AACCCATAAGGGTTAAACAGAAGCTCATAAAAT-TGAACAGA
* * * * *
41897009 AACTCATAAGAGTTAAACAGAAGCTCAATACAGTTGAACGGA
1 AACCCATAAGGGTTAAACAGAAGCTC-ATAAAATTGAACAGA
* * *
41897051 AACCCATTAGGGTTAAACTGAAACTCATA
1 AACCCATAAGGGTTAAACAGAAGCTCATA
41897080 TGAGTTAAAC
Statistics
Matches: 58, Mismatches: 12, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
41 3 0.05
42 50 0.86
43 5 0.09
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (41 bp):
AACCCATAAGGGTTAAACAGAAGCTCATAAAATTGAACAGA
Found at i:41897090 original size:21 final size:22
Alignment explanation
Indices: 41897007--41897093 Score: 83
Period size: 21 Copynumber: 4.1 Consensus size: 22
41896997 AATCTGAACA
*
41897007 GAAACTCATA-AGAGTTAAACA
1 GAAACTCATATAGAGTTAAACT
* * * *
41897028 GAAGCTCA-ATACAGTTGAACG
1 GAAACTCATATAGAGTTAAACT
* *
41897049 GAAACCCAT-TAGGGTTAAACT
1 GAAACTCATATAGAGTTAAACT
41897070 GAAACTCATAT-GAGTTAAACT
1 GAAACTCATATAGAGTTAAACT
41897091 GAA
1 GAA
41897094 GCTCGTGAGA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.02
21 49 0.96
22 1 0.02
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (22 bp):
GAAACTCATATAGAGTTAAACT
Found at i:41898242 original size:21 final size:21
Alignment explanation
Indices: 41898208--41898247 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41898198 AATTTAGTTC
*
41898208 TTTTCTATCAAAACGTTAAAA
1 TTTTCTAACAAAACGTTAAAA
* *
41898229 TTTTCTAACGAAACTTTAA
1 TTTTCTAACAAAACGTTAA
41898248 TACTACCTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTCTAACAAAACGTTAAAA
Found at i:41914194 original size:5 final size:5
Alignment explanation
Indices: 41914185--41914233 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
41914175 TTAAGAATGT
* * *
41914185 TATTA AATTA TATTA TATTA TATTA TATTA TATTT TATTA AATTA TATT
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATT
41914234 TAATAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:41916380 original size:19 final size:21
Alignment explanation
Indices: 41916358--41916402 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
41916348 AAATTTCACA
*
41916358 TTTAAT-TATTGTT-ATAATT
1 TTTAATATATTATTAATAATT
*
41916377 TTT-ATATATTATTAATGATT
1 TTTAATATATTATTAATAATT
41916397 TTTAAT
1 TTTAAT
41916403 GTTTAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.10
19 9 0.43
20 8 0.38
21 2 0.10
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTAATATATTATTAATAATT
Found at i:41926931 original size:13 final size:13
Alignment explanation
Indices: 41926900--41926941 Score: 50
Period size: 12 Copynumber: 3.2 Consensus size: 13
41926890 AATAAAGGAT
* *
41926900 TAAGTAAAGAATA
1 TAAGTAAATAAAA
41926913 -AAGTAAATAAAA
1 TAAGTAAATAAAA
41926925 TAAGTAAATAATAA
1 TAAGTAAATAA-AA
41926939 TAA
1 TAA
41926942 AAATAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.40
13 10 0.40
14 5 0.20
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.24
Consensus pattern (13 bp):
TAAGTAAATAAAA
Found at i:41926945 original size:25 final size:27
Alignment explanation
Indices: 41926877--41926947 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 27
41926867 ATCAAATTAG
*
41926877 AATAATAAGTTAAAATAAAGGATTAAGTA
1 AATAATAA-TAAAAATAAA-GATTAAGTA
* *
41926906 AAGAATAA-AGTAAATAAA-A-TAAGTA
1 AATAATAATA-AAAATAAAGATTAAGTA
41926931 AATAATAATAAAAATAA
1 AATAATAATAAAAATAA
41926948 GAAAAAGGGG
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
25 19 0.54
26 2 0.06
28 7 0.20
29 7 0.20
ACGTcount: A:0.66, C:0.00, G:0.10, T:0.24
Consensus pattern (27 bp):
AATAATAATAAAAATAAAGATTAAGTA
Found at i:41928461 original size:43 final size:43
Alignment explanation
Indices: 41928393--41928547 Score: 240
Period size: 43 Copynumber: 3.6 Consensus size: 43
41928383 CCGGCATTAC
* *
41928393 GCCTGCTAGGCACGAAGGCCTGAATACACATCA-CTAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATC-GGCACGAA
* *
41928436 GCCTGCTAGGCACGAAGGTCCGAATACGCATCATCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
*
41928479 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCGCGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
*
41928522 GCCTGCTAGGCACAAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
41928548 TAATACCAGC
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
43 102 0.99
44 1 0.01
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.13
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCATCGGCACGAA
Found at i:41928588 original size:38 final size:38
Alignment explanation
Indices: 41928540--41928639 Score: 137
Period size: 38 Copynumber: 2.6 Consensus size: 38
41928530 GGCACAAAGG
* * * *
41928540 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
41928578 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
* **
41928616 CCCAGATATTTTACCAGCACGAAG
1 CCCGGATATAATACCAGCACGAAG
41928640 GAACACCAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:41928742 original size:43 final size:43
Alignment explanation
Indices: 41928681--41928813 Score: 198
Period size: 43 Copynumber: 3.1 Consensus size: 43
41928671 CCGGCATTAC
*
41928681 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
41928724 GCCTGCTAGGCATGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* * * *
41928767 GCCTGTTAGGCACGAAGGCTCGAATATA-AT-ACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
41928808 GCCTGC
1 GCCTGC
41928814 GGGATTTAAC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
41 15 0.18
42 2 0.02
43 65 0.79
ACGTcount: A:0.30, C:0.31, G:0.26, T:0.14
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:41928880 original size:38 final size:38
Alignment explanation
Indices: 41928790--41928882 Score: 143
Period size: 38 Copynumber: 2.4 Consensus size: 38
41928780 GAAGGCTCGA
* * *
41928790 ATATAATACCAGCACGAAGCCTGCGGGATTTAACCCGG
1 ATATAATTCCAGCATGAAGCCTGCGAGATTTAACCCGG
41928828 ATAT-ATTACCAGCATGAAGCCTGCGAGATTTAACCCGG
1 ATATAATT-CCAGCATGAAGCCTGCGAGATTTAACCCGG
41928866 ATATAATTCCAGCATGA
1 ATATAATTCCAGCATGA
41928883 CAATTCCAGC
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
37 2 0.04
38 45 0.90
39 3 0.06
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (38 bp):
ATATAATTCCAGCATGAAGCCTGCGAGATTTAACCCGG
Found at i:41928943 original size:40 final size:40
Alignment explanation
Indices: 41928882--41929044 Score: 197
Period size: 40 Copynumber: 4.1 Consensus size: 40
41928872 TTCCAGCATG
*
41928882 ACAATTCCAGCATATAGCCTGCTGGTCTTTAAGCCCGGAT
1 ACAATTCCAGCATATAGCCTGCTGGTCTTTAAGCCCGAAT
* * *
41928922 ACAATTCCAGCACGA-AACCTGC-GGATCTTTAAGCCTGAAT
1 ACAATTCCAGCA-TATAGCCTGCTGG-TCTTTAAGCCCGAAT
* *
41928962 ATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGAAT
1 ACAATTCCAGCATATAGCCTGCTGGTCTTTAAGCCCGAAT
* * *
41929002 ATAATTCCAGCATATAGCCTG-TGGGTCTTTAGGCCCGGAT
1 ACAATTCCAGCATATAGCCTGCT-GGTCTTTAAGCCCGAAT
41929042 ACA
1 ACA
41929045 CATCAAATAT
Statistics
Matches: 106, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
39 3 0.03
40 100 0.94
41 3 0.03
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (40 bp):
ACAATTCCAGCATATAGCCTGCTGGTCTTTAAGCCCGAAT
Found at i:41935655 original size:13 final size:13
Alignment explanation
Indices: 41935637--41935671 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
41935627 AGCACATGGG
41935637 CGTGTGGCTAACC
1 CGTGTGGCTAACC
*
41935650 CGTGTGGCTAGCC
1 CGTGTGGCTAACC
41935663 CGTGTGGCT
1 CGTGTGGCT
41935672 CACACTGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.09, C:0.29, G:0.37, T:0.26
Consensus pattern (13 bp):
CGTGTGGCTAACC
Found at i:41951004 original size:63 final size:62
Alignment explanation
Indices: 41950900--41951027 Score: 211
Period size: 63 Copynumber: 2.0 Consensus size: 62
41950890 AAAGTTGTTT
* * *
41950900 TAGGGCAGCTCTTACTTGGGTAACCAGACAAATTAGGTAATTAAGTTTGTTTCATTGTTCTTG
1 TAGGCCAGCTCTTAATTGGGTAACCACACAAATTAGGTAATTAAGTTTG-TTCATTGTTCTTG
*
41950963 TAGGCCAGCTCTTAATTGGGTAACCACACAAATTAGGTAATTAAGTTTGTTCATTGTTTTTG
1 TAGGCCAGCTCTTAATTGGGTAACCACACAAATTAGGTAATTAAGTTTGTTCATTGTTCTTG
41951025 TAG
1 TAG
41951028 TCTCCCACAT
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
62 15 0.25
63 46 0.75
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (62 bp):
TAGGCCAGCTCTTAATTGGGTAACCACACAAATTAGGTAATTAAGTTTGTTCATTGTTCTTG
Found at i:41972024 original size:47 final size:47
Alignment explanation
Indices: 41971970--41972099 Score: 188
Period size: 47 Copynumber: 2.8 Consensus size: 47
41971960 ACAATCGATA
*
41971970 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTTATCCCGG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCGG
* * * *
41972017 AGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCCTCTCTG
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCGG
* * *
41972064 AATACCTATACCATGGCCCCTAGCTAAATCAAGGTA
1 AGTACCTATACCATGGCCCATAGCCAAATCAAGGTA
41972100 TTATTCGCAC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 75 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (47 bp):
AGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCATCCCGG
Found at i:41974809 original size:487 final size:487
Alignment explanation
Indices: 41973896--41974873 Score: 1776
Period size: 487 Copynumber: 2.0 Consensus size: 487
41973886 GGGAATGCAT
* * * *
41973896 CTACTCAGGGCAGTTATAATCTAAGACAAGGAAATTATACTCAAGAACAGTAGAATTATAGTCAG
1 CTACTCAGGGCAATTATAATCTAACACAAGGAAATTATACTCAACAACAGTAGAATTACAGTCAG
* *
41973961 CATCTTCAAAGGTATCAACAATAAGGTTAGACACAATCTCATCAAAATCAGATGCAATCACAACA
66 CATCTTCAAAGGTATCAACAACAAGGTTAGACACAATCTCATCAAAATCAGATGCAACCACAACA
*
41974026 TTTTTTAATGATGATACAGAATATCCAAGGATAGTGACAACAATAGTATACACAAACTTCTATTT
131 TTTTTCAATGATGATACAGAATATCCAAGGATAGTGACAACAATAGTATACACAAACTTCTATTT
*
41974091 CTAACCCATTGATTGCTCTTGAGGCGTTAATACGAGAGCATATTACTTGCACAAAAGCTATTGTT
196 CTAACCCATTGATTGCTCTTGAGGCGTTAATACGAGAGCATATTACTTGCACAAAAGCTATTATT
* *
41974156 TAAGAAAATTCATCTTCCATTCGAGCATTGGAGGCAGAATTGGGACAACTTGCTTCATATCTGAA
261 TAAGAAAATCCATCTTCCATTCGAGCATTGGAGGCAGAATTAGGACAACTTGCTTCATATCTGAA
*
41974221 TATTAGACCACAAGGTGTAACACCTCACATCCGTACCCTATGCTGGGACGGAATACAAGGCATTA
326 TACTAGACCACAAGGTGTAACACCTCACATCCGTACCCTATGCTGGGACGGAATACAAGGCATTA
*
41974286 CTTAACTTGAACACATACACTCACACGGTTCCCAGTCACCATAATTAGGACAAATTTAAAACTTT
391 CTTAACTTGAACACATACACTCACACGGCTCCCAGTCACCATAATTAGGACAAATTTAAAACTTT
41974351 TCCGATCTTTATCAAAACTCCATAATAAATGC
456 TCCGATCTTTATCAAAACTCCATAATAAATGC
*
41974383 CTACTCAGGGCAATTATAATCTAACACAAGGAAATTATACTCAACAACAGTAGAATTACAGTTAG
1 CTACTCAGGGCAATTATAATCTAACACAAGGAAATTATACTCAACAACAGTAGAATTACAGTCAG
41974448 CATCTTCAAAGGTATCAACAACAAGGTTAGACACAATCTCATCAAAATCAGATGCAACCACAACA
66 CATCTTCAAAGGTATCAACAACAAGGTTAGACACAATCTCATCAAAATCAGATGCAACCACAACA
*
41974513 TTTTTCAATGATGATATAGAATATCCAAGGATAGTGACAACAATAGTATACACAAACTTCTATTT
131 TTTTTCAATGATGATACAGAATATCCAAGGATAGTGACAACAATAGTATACACAAACTTCTATTT
*
41974578 CTGACCCATTGATTGCTCTTGAGGCGTTAATACGAGAGCATATTACTTGCACAAAAGCTATTATT
196 CTAACCCATTGATTGCTCTTGAGGCGTTAATACGAGAGCATATTACTTGCACAAAAGCTATTATT
*
41974643 TAAGAAAATCCATCTTCCATTCGAGCATTGGAGGCTGAATTAGGACAACTTGCTTCATATCTGAA
261 TAAGAAAATCCATCTTCCATTCGAGCATTGGAGGCAGAATTAGGACAACTTGCTTCATATCTGAA
* *
41974708 TACTAGACCACAATGTGTAACACCTCACATCCGTGCCCTATGCTGGGACGGAATACAAGGCATTA
326 TACTAGACCACAAGGTGTAACACCTCACATCCGTACCCTATGCTGGGACGGAATACAAGGCATTA
41974773 CTTAACTTGAACACATACACTCACACGGCTCCCAGTCACCATAATTAGGACAAATTTAAAACTTT
391 CTTAACTTGAACACATACACTCACACGGCTCCCAGTCACCATAATTAGGACAAATTTAAAACTTT
**
41974838 TCCGATCTTTATCAAAACTTTATAATAAATGC
456 TCCGATCTTTATCAAAACTCCATAATAAATGC
41974870 CTAC
1 CTAC
41974874 GAGGATTTAA
Statistics
Matches: 471, Mismatches: 20, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
487 471 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (487 bp):
CTACTCAGGGCAATTATAATCTAACACAAGGAAATTATACTCAACAACAGTAGAATTACAGTCAG
CATCTTCAAAGGTATCAACAACAAGGTTAGACACAATCTCATCAAAATCAGATGCAACCACAACA
TTTTTCAATGATGATACAGAATATCCAAGGATAGTGACAACAATAGTATACACAAACTTCTATTT
CTAACCCATTGATTGCTCTTGAGGCGTTAATACGAGAGCATATTACTTGCACAAAAGCTATTATT
TAAGAAAATCCATCTTCCATTCGAGCATTGGAGGCAGAATTAGGACAACTTGCTTCATATCTGAA
TACTAGACCACAAGGTGTAACACCTCACATCCGTACCCTATGCTGGGACGGAATACAAGGCATTA
CTTAACTTGAACACATACACTCACACGGCTCCCAGTCACCATAATTAGGACAAATTTAAAACTTT
TCCGATCTTTATCAAAACTCCATAATAAATGC
Found at i:41976202 original size:46 final size:44
Alignment explanation
Indices: 41976116--41976235 Score: 150
Period size: 46 Copynumber: 2.6 Consensus size: 44
41976106 GTAGGATGCT
* ** *
41976116 GATGCCATGACCTAGACATGGTCTTACACTGGTTCATCTCGTTATC
1 GATG-CATGTCCTAGACAT-GTCTTACACTGGTTCATCTCGAGACC
*
41976162 GATGCATGTCCTAGACATGTCTTACACTGGCTTACATCTCGAGGCC
1 GATGCATGTCCTAGACATGTCTTACACTGG-TT-CATCTCGAGACC
*
41976208 GATGCATGTGCTAGACATGTCTTACACT
1 GATGCATGTCCTAGACATGTCTTACACT
41976236 AGCTCTTGTC
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 12 0.18
45 15 0.23
46 39 0.59
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (44 bp):
GATGCATGTCCTAGACATGTCTTACACTGGTTCATCTCGAGACC
Found at i:41976255 original size:46 final size:47
Alignment explanation
Indices: 41976161--41976334 Score: 158
Period size: 46 Copynumber: 3.7 Consensus size: 47
41976151 ATCTCGTTAT
*
41976161 CGATGCATGTCCTAGACATGTCTTACACTGGCT-TACATCTCGAGGC
1 CGATGCATGTCCTAGACATGTCTTACACTGGCTCTACATCTCAAGGC
* * ** *
41976207 CGATGCATGTGCTAGACATGTCTTACACTAGCTCT-TGTCTCAATGC
1 CGATGCATGTCCTAGACATGTCTTACACTGGCTCTACATCTCAAGGC
* * * **
41976253 CGATGCCATATCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTGGC
1 CGATG-CATGTCCTAGACAT-GTCTTACACTGGCTCTACAT-CTCAAGGC
* * * *
41976301 TGATGCATGTCCCAGAGATGTCTTACACTAGCTC
1 CGATGCATGTCCTAGACATGTCTTACACTGGCTC
41976335 ACAATAACCC
Statistics
Matches: 104, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
46 57 0.55
47 24 0.23
48 22 0.21
49 1 0.01
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (47 bp):
CGATGCATGTCCTAGACATGTCTTACACTGGCTCTACATCTCAAGGC
Found at i:41976284 original size:94 final size:92
Alignment explanation
Indices: 41976161--41976334 Score: 226
Period size: 94 Copynumber: 1.9 Consensus size: 92
41976151 ATCTCGTTAT
* * * * *
41976161 CGATGCATGTCCTAGACATGTCTTACACTGGCT-TACAT-CTCGAGGCCGATGCATGTGCTAGAC
1 CGATGCATATCCCAGACATGTCTTACACTGGCTCT-CATAAT-GAGGCCGATGCATGTCCCAGAC
41976224 ATGTCTTACACTAGCTCTTGTCTCAATGC
64 ATGTCTTACACTAGCTCTTGTCTCAATGC
* * *
41976253 CGATGCCATATCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGCTGATGCATGTCCCAGAG
1 CGATG-CATATCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGAC
41976318 ATGTCTTACACTAGCTC
64 ATGTCTTACACTAGCTC
41976335 ACAATAACCC
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
92 5 0.07
93 12 0.17
94 51 0.73
95 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (92 bp):
CGATGCATATCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGACAT
GTCTTACACTAGCTCTTGTCTCAATGC
Found at i:41980957 original size:328 final size:328
Alignment explanation
Indices: 41980360--41981017 Score: 1226
Period size: 328 Copynumber: 2.0 Consensus size: 328
41980350 TCTTCGTGAC
41980360 GTAGTGAATTACCATTGGAACGAGTCGAATTTATTCAAGGTATGCAATAACAACATCATTCGTTG
1 GTAGTGAATTACCATTGGAACGAGTCGAATTTATTCAAGGTATGCAATAACAACATCATTCGTTG
*
41980425 TTGTGTTTTAGAAGAAGAGATGCTTTCAATCCTGAAGCACTATCGTGATGCTCCTTATGGAGGCC
66 TTGTGTTTTAGAAGAAGAGATGCTTTCAATCCTGAAGCACTATCATGATGCTCCTTATGGAGGCC
* *
41980490 ATTTCGGTGGTATGAGAACTGCTGCTAAGGTTCTATAATCAGGATTCTACTGGCCATCATTGTTC
131 ATTTCGGTGGTATGAGAACTACTGCGAAGGTTCTATAATCAGGATTCTACTGGCCATCATTGTTC
41980555 AAAGATTCTCATAATTTTATGAATCAATGCAATAAATGTCAGCACAACGGTTCTATTTCCCGACA
196 AAAGATTCTCATAATTTTATGAATCAATGCAATAAATGTCAGCACAACGGTTCTATTTCCCGACA
*
41980620 TAATGAAATGTTACAACTGCCAATTATGGAAGTTGAATTGTTTGATGTTTGGGGACTGGATTTTA
261 TAATGAAATGTTACAACTGCCAATTATGGAAGTTGAATTGTTTGATGTTTGGGGAATGGATTTTA
41980685 TGG
326 TGG
*
41980688 GTAGTGAATTACCATTGGAACGAGTCGAATTTATTCAAGGTATGCAATAACAACATCATTTGTTG
1 GTAGTGAATTACCATTGGAACGAGTCGAATTTATTCAAGGTATGCAATAACAACATCATTCGTTG
* * *
41980753 TTGTGTTTTGGAAGAAGAGATGCTTTCAATCTTGAAGCACTGTCATGATGCTCCTTATGGAGGCC
66 TTGTGTTTTAGAAGAAGAGATGCTTTCAATCCTGAAGCACTATCATGATGCTCCTTATGGAGGCC
41980818 ATTTCGGTGGTATGAGAACTACTGCGAAGGTTCTATAATCAGGATTCTACTGGCCATCATTGTTC
131 ATTTCGGTGGTATGAGAACTACTGCGAAGGTTCTATAATCAGGATTCTACTGGCCATCATTGTTC
*
41980883 AAAGATTCTCATAATTTTGTGAATCAATGCAATAAATGTCAGCACAACGGTTCTATTTCCCGACA
196 AAAGATTCTCATAATTTTATGAATCAATGCAATAAATGTCAGCACAACGGTTCTATTTCCCGACA
*
41980948 TAATGAAATGTTGCAACTGCCAATTATGGAAGTTGAATTGTTTGATGTTTGGGGAATGGATTTTA
261 TAATGAAATGTTACAACTGCCAATTATGGAAGTTGAATTGTTTGATGTTTGGGGAATGGATTTTA
41981013 TGG
326 TGG
41981016 GT
1 GT
41981018 CCGTTTCCAA
Statistics
Matches: 320, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
328 320 1.00
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.34
Consensus pattern (328 bp):
GTAGTGAATTACCATTGGAACGAGTCGAATTTATTCAAGGTATGCAATAACAACATCATTCGTTG
TTGTGTTTTAGAAGAAGAGATGCTTTCAATCCTGAAGCACTATCATGATGCTCCTTATGGAGGCC
ATTTCGGTGGTATGAGAACTACTGCGAAGGTTCTATAATCAGGATTCTACTGGCCATCATTGTTC
AAAGATTCTCATAATTTTATGAATCAATGCAATAAATGTCAGCACAACGGTTCTATTTCCCGACA
TAATGAAATGTTACAACTGCCAATTATGGAAGTTGAATTGTTTGATGTTTGGGGAATGGATTTTA
TGG
Found at i:41989424 original size:6 final size:6
Alignment explanation
Indices: 41989410--41989453 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
41989400 TATCAACTAC
*
41989410 ATCTTT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
1 ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT ATCTAT AT
41989454 ACATACACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (6 bp):
ATCTAT
Found at i:41990293 original size:24 final size:25
Alignment explanation
Indices: 41990264--41990321 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 25
41990254 ATTCCATATC
41990264 ACATTC-ACCTCAATTAACTACTAA
1 ACATTCTACCTCAATTAACTACTAA
41990288 ACATTCCTTGACCTCAATTAACTACTAA
1 ACATT-C-T-ACCTCAATTAACTACTAA
41990316 ACATTC
1 ACATTC
41990322 CTTGATTAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 5 0.17
25 1 0.03
27 1 0.03
28 23 0.77
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (25 bp):
ACATTCTACCTCAATTAACTACTAA
Found at i:41990310 original size:28 final size:28
Alignment explanation
Indices: 41990270--41990326 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
41990260 TATCACATTC
41990270 ACCTCAATTAACTACTAAACATTCCTTG
1 ACCTCAATTAACTACTAAACATTCCTTG
41990298 ACCTCAATTAACTACTAAACATTCCTTG
1 ACCTCAATTAACTACTAAACATTCCTTG
41990326 A
1 A
41990327 TTAATTCCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.32
Consensus pattern (28 bp):
ACCTCAATTAACTACTAAACATTCCTTG
Found at i:41992891 original size:21 final size:21
Alignment explanation
Indices: 41992867--41992907 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
41992857 ATCTTTTCTA
*
41992867 AAGTTAAAAGTCAAAACTATT
1 AAGTTAAAAGGCAAAACTATT
41992888 AAGTTAAAAGGCAAAACTAT
1 AAGTTAAAAGGCAAAACTAT
41992908 GTCGTTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.24
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATT
Found at i:42000383 original size:7 final size:7
Alignment explanation
Indices: 42000371--42000411 Score: 73
Period size: 7 Copynumber: 5.9 Consensus size: 7
42000361 AATTAATTAG
42000371 AATTTTA
1 AATTTTA
42000378 AATTTTA
1 AATTTTA
42000385 AATTTTA
1 AATTTTA
42000392 AATTTTA
1 AATTTTA
*
42000399 AATTTTG
1 AATTTTA
42000406 AATTTT
1 AATTTT
42000412 TAATAAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (7 bp):
AATTTTA
Found at i:42005575 original size:48 final size:48
Alignment explanation
Indices: 42005521--42005616 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
42005511 CAATCTTAAT
42005521 TTAAAAAAAAATCGATAAAACATGCAACAATTATAATAATAGTTTACG
1 TTAAAAAAAAATCGATAAAACATGCAACAATTATAATAATAGTTTACG
42005569 TTAAAAAAAAATCGATAAAACATGCAACAATTATAATAATAGTTTACG
1 TTAAAAAAAAATCGATAAAACATGCAACAATTATAATAATAGTTTACG
42005617 ATAAGTAGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.54, C:0.10, G:0.08, T:0.27
Consensus pattern (48 bp):
TTAAAAAAAAATCGATAAAACATGCAACAATTATAATAATAGTTTACG
Found at i:42008541 original size:34 final size:34
Alignment explanation
Indices: 42008474--42008543 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
42008464 AAGTTGTCAT
* *
42008474 CAAGCTAACTAAACAAGTCATTCAGCTATCTAAA
1 CAAGCTAACTAAACAAGTCATTCAACTACCTAAA
*
42008508 CAAGCTAACTAAACAAGTCATTCAATTACCTAAA
1 CAAGCTAACTAAACAAGTCATTCAACTACCTAAA
42008542 CA
1 CA
42008544 CATCAAGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (34 bp):
CAAGCTAACTAAACAAGTCATTCAACTACCTAAA
Found at i:42018253 original size:48 final size:48
Alignment explanation
Indices: 42018197--42018295 Score: 171
Period size: 48 Copynumber: 2.1 Consensus size: 48
42018187 TACTTTTACA
*
42018197 AGTACGTCCTCTATAATACCCTTAGGATATTTAACAGATCAATCAGCT
1 AGTACGTCCTCTATAATACCCCTAGGATATTTAACAGATCAATCAGCT
* *
42018245 AGTACGTCCTTTATAATACCCCTAGGATATTTAACAGATCAATTAGCT
1 AGTACGTCCTCTATAATACCCCTAGGATATTTAACAGATCAATCAGCT
42018293 AGT
1 AGT
42018296 TGAATACTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (48 bp):
AGTACGTCCTCTATAATACCCCTAGGATATTTAACAGATCAATCAGCT
Found at i:42029477 original size:96 final size:96
Alignment explanation
Indices: 42029312--42029707 Score: 314
Period size: 96 Copynumber: 4.1 Consensus size: 96
42029302 ATTGAATGGT
* * *
42029312 AACATGGCATCAGCCTCGATATGTGTCAGTGTAAGACCAAGTCTGGGACATGCCATCGGCACCGA
1 AACATGGCATCAACCTCGATATGTGTCAGTGTAAGACCAAGTCTAGGACATGACATCGGCACCGA
** * *
42029377 TTTATGAGAGTTAGTGTGAGACCATGTTTGG
66 TTTATGAGAGCCAGTGTAAGAACATGTTTGG
* * * * * *
42029408 GACATGGCATCAACCTCGATATGTGTCAGTGTAAGACTATGTCTAGGACATGACATCGGTACTGG
1 AACATGGCATCAACCTCGATATGTGTCAGTGTAAGACCAAGTCTAGGACATGACATCGGCACCGA
42029473 TTTATGAGAGCCAGTGTAAGAACATGTTTGG
66 TTTATGAGAGCCAGTGTAAGAACATGTTTGG
*** * * * * * * * * *
42029504 AACATGGCATTGGCATTGTTATGTGAGCCAGTGTAAGACCATGTCTGGGATATGGCATCAGC-CT
1 AACATGGCATCAACCTCGATATGT--GTCAGTGTAAGACCAAGTCTAGGACATGACATCGGCAC-
* * *
42029568 C-A-ATAT-ACGAGCTAGTGTAAGACCATGTTTGG
63 CGATTTATGA-GAGCCAGTGTAAGAACATGTTTGG
* **** * * * * * *
42029600 AACTTGGCATCGGTATTGTTATATGTGTCATTGTAAGACCATGTCTGGGCCATGGCATCGGCACC
1 AACATGGCATCAACCTCG--ATATGTGTCAGTGTAAGACCAAGTCTAGGACATGACATCGGCACC
* * * *
42029665 GATGTATGAGAGCTAGTGTAAGACCATGTTCGG
64 GATTTATGAGAGCCAGTGTAAGAACATGTTTGG
*
42029698 GACATGGCAT
1 AACATGGCAT
42029708 TGGCATTTTA
Statistics
Matches: 245, Mismatches: 45, Indels: 18
0.80 0.15 0.06
Matches are distributed among these distances:
95 1 0.00
96 172 0.70
97 3 0.01
98 68 0.28
99 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (96 bp):
AACATGGCATCAACCTCGATATGTGTCAGTGTAAGACCAAGTCTAGGACATGACATCGGCACCGA
TTTATGAGAGCCAGTGTAAGAACATGTTTGG
Found at i:42029490 original size:50 final size:48
Alignment explanation
Indices: 42029434--42029549 Score: 119
Period size: 50 Copynumber: 2.4 Consensus size: 48
42029424 CGATATGTGT
*
42029434 CAGTGTAAGACTATGTCTAGG-ACATGACATCGGTACTGGTTTATGAGAGC
1 CAGTGTAAGAC-ATGTCTAGGAACATGACATCGGCA-TGG-TTATGAGAGC
* * * * *
42029484 CAGTGTAAGAACATGT-TTGGAACATGGCATTGGCATTGTTATGTGAGC
1 CAGTGTAAG-ACATGTCTAGGAACATGACATCGGCATGGTTATGAGAGC
42029532 CAGTGTAAGACCATGTCT
1 CAGTGTAAGA-CATGTCT
42029550 GGGATATGGC
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
47 1 0.02
48 23 0.41
49 6 0.11
50 24 0.43
51 2 0.04
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (48 bp):
CAGTGTAAGACATGTCTAGGAACATGACATCGGCATGGTTATGAGAGC
Found at i:42029537 original size:48 final size:48
Alignment explanation
Indices: 42029338--42029714 Score: 240
Period size: 48 Copynumber: 7.8 Consensus size: 48
42029328 CGATATGTGT
* * * ** *
42029338 CAGTGTAAGACCAAGTCTGGGACATGCCATCGGCACCGATTTATGAGAGT
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTG--TTATGAGAGC
* * ** * * * * *
42029388 TAGTGTGAGACCATGTTTGGGACATGGCATCAACCTCGATAT--GTGT
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTATGAGAGC
* * * * * *
42029434 CAGTGTAAGACTATGTCTAGGACATGACATCGGTACTGGTTTATGAGAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCA-TTG-TTATGAGAGC
* * * *
42029484 CAGTGTAAGAACATGTTTGGAACATGGCATTGGCATTGTTATGTGAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTATGAGAGC
* * * * ***
42029532 CAGTGTAAGACCATGTCTGGGATATGGCATCAGCCTCAATAT-ACGAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTATGA-GAGC
* * * * * *
42029580 TAGTGTAAGACCATGTTTGGAACTTGGCATCGGTATTGTTAT-ATGTGT
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTATGA-GAGC
* * * **
42029628 CATTGTAAGACCATGTCTGGGCCATGGCATCGGCACCGATGTATGAGAGC
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTG-T-TATGAGAGC
* * *
42029678 TAGTGTAAGACCATGTTCGGGACATGGCATTGGCATT
1 CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATT
42029715 TTACCTTTTT
Statistics
Matches: 240, Mismatches: 79, Indels: 16
0.72 0.24 0.05
Matches are distributed among these distances:
46 28 0.12
47 2 0.01
48 114 0.47
49 3 0.01
50 92 0.38
51 1 0.00
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (48 bp):
CAGTGTAAGACCATGTTTGGGACATGGCATCGGCATTGTTATGAGAGC
Found at i:42034629 original size:29 final size:27
Alignment explanation
Indices: 42034597--42034679 Score: 87
Period size: 29 Copynumber: 2.9 Consensus size: 27
42034587 CATAAACGCT
42034597 TTCCTTTATGAAGGTTTTCCACAAAGGC
1 TTCCTTT-TGAAGGTTTTCCACAAAGGC
* **
42034625 ATTCCTTTTGGAGGTTCACCACAAAGGC
1 -TTCCTTTTGAAGGTTTTCCACAAAGGC
42034653 TTACC-TTTGTAGAGGTTTTCCACAAAG
1 TT-CCTTTTG-A-AGGTTTTCCACAAAG
42034680 ACTTTCCGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
27 6 0.13
28 19 0.42
29 20 0.44
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (27 bp):
TTCCTTTTGAAGGTTTTCCACAAAGGC
Found at i:42034639 original size:28 final size:28
Alignment explanation
Indices: 42034597--42034679 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
42034587 CATAAACGCT
*
42034597 TTCCTTTATGAAGGTTTTCCACAAAGGC
1 TTCCTTTATGGAGGTTTTCCACAAAGGC
**
42034625 ATTCCTTT-TGGAGGTTCACCACAAAGGC
1 -TTCCTTTATGGAGGTTTTCCACAAAGGC
* *
42034653 TTACCTTTGTAGAGGTTTTCCACAAAG
1 TT-CCTTTATGGAGGTTTTCCACAAAG
42034680 ACTTTCCGTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.04
28 22 0.48
29 22 0.48
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (28 bp):
TTCCTTTATGGAGGTTTTCCACAAAGGC
Found at i:42034696 original size:57 final size:57
Alignment explanation
Indices: 42034578--42034948 Score: 285
Period size: 57 Copynumber: 6.5 Consensus size: 57
42034568 TTCCTTTTTT
* * * * *
42034578 AGAGGTT-GCCATAAACGCTTTCCTTT--ATGAAGGTTTTCCACAAAGGCATTCCTTTT
1 AGAGGTTCGCCACAAAGGCTTTCCTTTGCA-G-AGGTTTTCCACAAAGACTTTCCTTTC
* * * * *
42034634 GGAGGTTCACCACAAAGGCTTACCTTTGTAGAGGTTTTCCACAAAGACTTTCCGTTC
1 AGAGGTTCGCCACAAAGGCTTTCCTTTGCAGAGGTTTTCCACAAAGACTTTCCTTTC
* * * * * *
42034691 AGAGGTTCGCCATAACA-GTTTTCCTTTGCAAAGGTTTGCCATAAA-ATTTTTCCTTTC
1 AGAGGTTCGCCACAA-AGGCTTTCCTTTGCAGAGGTTTTCCACAAAGA-CTTTCCTTTC
* * * * * *
42034748 AGAGGTTTGCCACAAATGCTTTTCGTTATG--GAGGTTTTCCATAAAGGCTTACCTTTC
1 AGAGGTTCGCCACAAAGGC-TTTCCTT-TGCAGAGGTTTTCCACAAAGACTTTCCTTTC
* * *
42034805 AGAGGTTTGCCACAAAGGCTATCCTTTGCAGAGG-TTTCCACAAAGGCTTTCCTTTC
1 AGAGGTTCGCCACAAAGGCTTTCCTTTGCAGAGGTTTTCCACAAAGACTTTCCTTTC
* * * * * **
42034861 AAAGGATT-TCCACAAAGGTTTTCTTTTGCAGAGGTTTGT-CATAAAGACTTTCCTTAA
1 AGAGG-TTCGCCACAAAGGCTTTCCTTTGCAGAGGTTT-TCCACAAAGACTTTCCTTTC
* * *
42034918 AAAGGTTTGCCATAAAGGCTTTCCTTTGCAG
1 AGAGGTTCGCCACAAAGGCTTTCCTTTGCAG
42034949 TTATGATCTT
Statistics
Matches: 253, Mismatches: 47, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
55 2 0.01
56 61 0.24
57 178 0.70
58 9 0.04
59 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (57 bp):
AGAGGTTCGCCACAAAGGCTTTCCTTTGCAGAGGTTTTCCACAAAGACTTTCCTTTC
Found at i:42034713 original size:28 final size:28
Alignment explanation
Indices: 42034682--42034944 Score: 156
Period size: 28 Copynumber: 9.3 Consensus size: 28
42034672 CCACAAAGAC
* * *
42034682 TTTCCGTTCAGAGGTTCGCCATAACAGT
1 TTTCCTTTCAGAGGTTTGCCATAAAAGT
* *
42034710 TTTCCTTTGCAAAGGTTTGCCATAAAATT
1 TTTCCTTT-CAGAGGTTTGCCATAAAAGT
* *
42034739 TTTCCTTTCAGAGGTTTGCCACAAATGCT
1 TTTCCTTTCAGAGGTTTGCCATAAAAG-T
* * * * *
42034768 TTTCGTTAT-GGAGGTTTTCCATAAAGGC
1 TTTCCTT-TCAGAGGTTTGCCATAAAAGT
* * * *
42034796 TTACCTTTCAGAGGTTTGCCACAAAGGC
1 TTTCCTTTCAGAGGTTTGCCATAAAAGT
* * * *
42034824 TATCCTTTGCAGAGGTTT-CCACAAAGGC
1 TTTCCTTT-CAGAGGTTTGCCATAAAAGT
* * *
42034852 TTTCCTTTCAAAGGATTT-CCACAAAGGT
1 TTTCCTTTCAGAGG-TTTGCCATAAAAGT
* * *
42034880 TTTCTTTTGCAGAGGTTTGTCAT-AAAGAC
1 TTTCCTTT-CAGAGGTTTGCCATAAAAG-T
** * * *
42034909 TTTCCTTAAAAAGGTTTGCCATAAAGGC
1 TTTCCTTTCAGAGGTTTGCCATAAAAGT
42034937 TTTCCTTT
1 TTTCCTTT
42034945 GCAGTTATGA
Statistics
Matches: 187, Mismatches: 38, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
27 6 0.03
28 110 0.59
29 70 0.37
30 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (28 bp):
TTTCCTTTCAGAGGTTTGCCATAAAAGT
Found at i:42034904 original size:113 final size:114
Alignment explanation
Indices: 42034712--42034948 Score: 268
Period size: 113 Copynumber: 2.1 Consensus size: 114
42034702 ATAACAGTTT
* * ** *
42034712 TCCTTTGCAAAGGTTTGCCATAAAATTTTTCCTTTCAGAGGTTTGCCACAAATGCTTTTCGTTAT
1 TCCTTTGCAGAGGTTTGCCACAAAAGCTTTCCTTTCAAAGGTTTGCCACAAATGCTTTTCGTTAT
* ** *
42034777 GGAGGTTTTCCATAAAGGCTTACCTTTCAGAGGTTTGCCACAAAGGCTA
66 GGAGGTTTTCCATAAAGACTTACCTTAAAAAGGTTTGCCACAAAGGCTA
* * *
42034826 TCCTTTGCAGAGGTTT-CCACAAAGGCTTTCCTTTCAAAGGATTT-CCACAAA-GGTTTTC-TTT
1 TCCTTTGCAGAGGTTTGCCACAAAAGCTTTCCTTTCAAAGG-TTTGCCACAAATGCTTTTCGTTA
* * *
42034887 TGCAGAGGTTTGT-CATAAAGACTTTCCTTAAAAAGGTTTGCCATAAAGGCTT
65 TG--GAGGTTT-TCCATAAAGACTTACCTTAAAAAGGTTTGCCACAAAGGCTA
42034939 TCCTTTGCAG
1 TCCTTTGCAG
42034949 TTATGATCTT
Statistics
Matches: 104, Mismatches: 15, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
111 4 0.04
112 6 0.06
113 75 0.72
114 19 0.18
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (114 bp):
TCCTTTGCAGAGGTTTGCCACAAAAGCTTTCCTTTCAAAGGTTTGCCACAAATGCTTTTCGTTAT
GGAGGTTTTCCATAAAGACTTACCTTAAAAAGGTTTGCCACAAAGGCTA
Found at i:42034915 original size:85 final size:84
Alignment explanation
Indices: 42034578--42034944 Score: 253
Period size: 85 Copynumber: 4.3 Consensus size: 84
42034568 TTCCTTTTTT
* * * **
42034578 AGAGGTTGCCATAAACGCTTTCCTTTATGAAGGTTTTCCACAAAGGCATTCCTTTTG--GAGGTT
1 AGAGGTTTCCACAAAGGCTTTCCTTTA--AAGGTTTTCCACAAAGGTTTTCC-TTTGCAGAGGTT
** * * *
42034641 CACCACAAAGGCTTACCTTTGT
63 TGCCACAAAGACTTTCCTTTGC
* * * ** * *
42034663 AGAGGTTTTCCACAAAGACTTTCCGTTCAGAGGTTCGCCATAACA-GTTTTCCTTTGCAAAGGTT
1 AGAGG-TTTCCACAAAGGCTTTCC-TTTAAAGGTTTTCCACAA-AGGTTTTCCTTTGCAGAGGTT
* *
42034727 TGCCATAAA-ATTTTTCCTTT-C
63 TGCCACAAAGA-CTTTCCTTTGC
* * ** * * *
42034748 AGAGGTTTGCCACAAATGCTTTTCGTTATGGAGGTTTTCCATAAAGGCTTACCTTT-CAGAGGTT
1 AGAGGTTT-CCACAAAGGC-TTTCCTT-TAAAGGTTTTCCACAAAGGTTTTCCTTTGCAGAGGTT
* *
42034812 TGCCACAAAGGCTATCCTTTGC
63 TGCCACAAAGACTTTCCTTTGC
* *
42034834 AGAGGTTTCCACAAAGGCTTTCCTTTCAAAGGATTTCCACAAAGGTTTTCTTTTGCAGAGGTTTG
1 AGAGGTTTCCACAAAGGCTTTCCTTT-AAAGGTTTTCCACAAAGGTTTTCCTTTGCAGAGGTTTG
* * **
42034899 TCATAAAGACTTTCC-TTAA
65 CCACAAAGACTTTCCTTTGC
* *
42034918 AAAGGTTTGCCATAAAGGCTTTCCTTT
1 AGAGGTTT-CCACAAAGGCTTTCCTTT
42034945 GCAGTTATGA
Statistics
Matches: 217, Mismatches: 50, Indels: 30
0.73 0.17 0.10
Matches are distributed among these distances:
83 1 0.00
84 42 0.19
85 105 0.48
86 66 0.30
87 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (84 bp):
AGAGGTTTCCACAAAGGCTTTCCTTTAAAGGTTTTCCACAAAGGTTTTCCTTTGCAGAGGTTTGC
CACAAAGACTTTCCTTTGC
Found at i:42037733 original size:28 final size:28
Alignment explanation
Indices: 42037671--42037973 Score: 272
Period size: 28 Copynumber: 10.8 Consensus size: 28
42037661 ATTCCAGAGA
* *
42037671 TTGCCAC-AAGGCTATCTTTTTCAGAGG-
1 TTGCCACAAAGGCTTTCCTTTT-AGAGGT
* *
42037698 TTACCACAAATGCTTTCCTTTTAGAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGT
* * *
42037726 TTTCCACAAAGGCTTTCATTTAAGAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGT
* * *
42037754 TTGCCACAAAGGCCTTCCTTTACAAAGGT
1 TTGCCACAAAGGCTTTCCTTT-TAGAGGT
*
42037783 TTGCCACAAAGGTTTTCCTTTTAGAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGT
* *
42037811 TCGCCATAAAGGCTTT-CTTTTACAGAGGT
1 TTGCCACAAAGGCTTTCCTTTT--AGAGGT
42037840 TTGCCACAAAGGCTTTCCTTTTAGAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGT
** * * * *
42037868 TCACCATAAAGG-TTTTCATTTACGGAGTT
1 TTGCCACAAAGGCTTTCCTTTTA--GAGGT
* * *
42037897 TTTCCACAGAGGCTTTCCTTTTAAAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGT
* * ** *
42037925 TTGCCATAAAGGTTTTCCTTCCAGAGGC
1 TTGCCACAAAGGCTTTCCTTTTAGAGGT
*
42037953 TCGCCACAAAGGCTTTCCTTT
1 TTGCCACAAAGGCTTTCCTTT
42037974 CTCTAGGGCG
Statistics
Matches: 219, Mismatches: 48, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
27 24 0.11
28 126 0.58
29 56 0.26
30 13 0.06
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (28 bp):
TTGCCACAAAGGCTTTCCTTTTAGAGGT
Found at i:42037802 original size:85 final size:84
Alignment explanation
Indices: 42037671--42037973 Score: 317
Period size: 85 Copynumber: 3.6 Consensus size: 84
42037661 ATTCCAGAGA
* * * *
42037671 TTGCCAC-AAGGCTATCTTTTTCAGAGGTT-ACCACAAATGCTTTCCTTTTAGAGGTTTTCCACA
1 TTGCCACAAAGGCTTTC-CTTTCAGAGGTTCGCCACAAAGGCTTTCCTTTTAGAGGTTTTCCACA
*
42037734 AAGGCTTTCATTTAAGAGGT
65 AAGGCTTTCTTTTAAGAGGT
* * * * ** *
42037754 TTGCCACAAAGGCCTTCCTTTACAAAGGTTTGCCACAAAGGTTTTCCTTTTAGAGGTTCGCCATA
1 TTGCCACAAAGGCTTTCCTTT-CAGAGGTTCGCCACAAAGGCTTTCCTTTTAGAGGTTTTCCACA
42037819 AAGGCTTTCTTTTACAGAGGT
65 AAGGCTTTCTTTTA-AGAGGT
* * * * * *
42037840 TTGCCACAAAGGCTTTCCTTTTAGAGGTTCACCATAAAGG-TTTTCATTTACGGAGTTTTTCCAC
1 TTGCCACAAAGGCTTTCCTTTCAGAGGTTCGCCACAAAGGCTTTCCTTTTA--GAGGTTTTCCAC
*
42037904 AGAGGCTTTCCTTTTAA-AGGT
64 AAAGGCTTT-CTTTTAAGAGGT
* * * *
42037925 TTGCCATAAAGGTTTTCCTTCCAGAGGCTCGCCACAAAGGCTTTCCTTT
1 TTGCCACAAAGGCTTTCCTTTCAGAGGTTCGCCACAAAGGCTTTCCTTT
42037974 CTCTAGGGCG
Statistics
Matches: 179, Mismatches: 33, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
83 10 0.06
84 22 0.12
85 92 0.51
86 49 0.27
87 6 0.03
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (84 bp):
TTGCCACAAAGGCTTTCCTTTCAGAGGTTCGCCACAAAGGCTTTCCTTTTAGAGGTTTTCCACAA
AGGCTTTCTTTTAAGAGGT
Found at i:42037809 original size:57 final size:57
Alignment explanation
Indices: 42037671--42037973 Score: 317
Period size: 57 Copynumber: 5.4 Consensus size: 57
42037661 ATTCCAGAGA
* * * * * *
42037671 TTGCCAC-AAGGCTATCTTTTTCAGAGG-TTACCACAAATGCTTTCCTTT-TAGAGGT
1 TTGCCACAAAGGCTTTCCTTTT-AGAGGTTTGCCATAAAGGCTTTCCTTTACAGAGGT
* * * * * *
42037726 TTTCCACAAAGGCTTTCATTTAAGAGGTTTGCCACAAAGGCCTTCCTTTACAAAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCATAAAGGCTTTCCTTTACAGAGGT
* * *
42037783 TTGCCACAAAGGTTTTCCTTTTAGAGGTTCGCCATAAAGGCTTTCTTTTACAGAGGT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCATAAAGGCTTTCCTTTACAGAGGT
** * * * *
42037840 TTGCCACAAAGGCTTTCCTTTTAGAGGTTCACCATAAAGGTTTTCATTTACGGAGTT
1 TTGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCATAAAGGCTTTCCTTTACAGAGGT
* * * * * *
42037897 TTTCCACAGAGGCTTTCCTTTTAAAGGTTTGCCATAAAGGTTTTCC-TTCCAGAGGC
1 TTGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCATAAAGGCTTTCCTTTACAGAGGT
*
42037953 TCGCCACAAAGGCTTTCCTTT
1 TTGCCACAAAGGCTTTCCTTT
42037974 CTCTAGGGCG
Statistics
Matches: 208, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
55 11 0.05
56 53 0.25
57 144 0.69
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.35
Consensus pattern (57 bp):
TTGCCACAAAGGCTTTCCTTTTAGAGGTTTGCCATAAAGGCTTTCCTTTACAGAGGT
Found at i:42038759 original size:22 final size:22
Alignment explanation
Indices: 42038743--42038792 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
42038733 ACACCACTGA
42038743 ACCACCATACCACCACCCTAAC
1 ACCACCATACCACCACCCTAAC
* * **
42038765 ACCACTATATCACCACCCTTGC
1 ACCACCATACCACCACCCTAAC
42038787 ACCACC
1 ACCACC
42038793 TTGAAATACC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.32, C:0.52, G:0.02, T:0.14
Consensus pattern (22 bp):
ACCACCATACCACCACCCTAAC
Found at i:42038895 original size:35 final size:37
Alignment explanation
Indices: 42038819--42038896 Score: 94
Period size: 35 Copynumber: 2.2 Consensus size: 37
42038809 TTCCATAACT
*
42038819 TATT-TTCTCTTTTCTTTTCTTCATTTTGAGAATAAA
1 TATTATTCTCTTTTCTTTTCTTCATTTTCAGAATAAA
* *
42038855 -A-TATTCTCTTTTCTTTTTTTCTTTTTCA-AA-AAA
1 TATTATTCTCTTTTCTTTTCTTCATTTTCAGAATAAA
42038888 TATTATTCT
1 TATTATTCT
42038897 TACTACTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
33 3 0.08
34 4 0.11
35 29 0.81
ACGTcount: A:0.23, C:0.14, G:0.03, T:0.60
Consensus pattern (37 bp):
TATTATTCTCTTTTCTTTTCTTCATTTTCAGAATAAA
Found at i:42043982 original size:27 final size:27
Alignment explanation
Indices: 42043951--42044128 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42043941 TAAATTGTAC
42043951 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
42043978 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42044004 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
42044032 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
42044060 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
42044087 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
42044114 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
42044129 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:42044065 original size:82 final size:81
Alignment explanation
Indices: 42043952--42044107 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42043942 AAATTGTACA
* *
42043952 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
42044016 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
42044033 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
42044098 TGCGAGTTGA
65 TGCGAATTGA
42044108 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:42044119 original size:82 final size:81
Alignment explanation
Indices: 42043948--42044128 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
42043938 GATTAAATTG
* *
42043948 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
42044013 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
42044029 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
42044093 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
42044111 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
42044129 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:42064330 original size:21 final size:20
Alignment explanation
Indices: 42064304--42064375 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 20
42064294 AAATTATATA
42064304 GTCTGAACTCACTGAGTTGTG
1 GTCTGAACTCA-TGAGTTGTG
**
42064325 GTCTGAGTTCATGTTA-TATGTG
1 GTCTGAACTCATG--AGT-TGTG
42064347 AGATCTGAACTCATTGAGTTGTG
1 -G-TCTGAACTCA-TGAGTTGTG
42064370 GTCTGA
1 GTCTGA
42064376 GTTCATGATA
Statistics
Matches: 40, Mismatches: 4, Indels: 14
0.69 0.07 0.24
Matches are distributed among these distances:
20 2 0.05
21 15 0.38
22 6 0.15
23 6 0.15
24 9 0.22
25 2 0.05
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.38
Consensus pattern (20 bp):
GTCTGAACTCATGAGTTGTG
Found at i:42064353 original size:24 final size:23
Alignment explanation
Indices: 42064321--42064392 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 23
42064311 CTCACTGAGT
42064321 TGTG-GTCTGAGTTCATGTTATA
1 TGTGAGTCTGAGTTCATGTTATA
** *
42064343 TGTGAGATCTGAACTCAT-TGAGT-
1 TGTGAG-TCTGAGTTCATGTTA-TA
*
42064366 TGTG-GTCTGAGTTCATGATATA
1 TGTGAGTCTGAGTTCATGTTATA
42064388 TGTGA
1 TGTGA
42064393 CACATGTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 11
0.67 0.13 0.20
Matches are distributed among these distances:
21 10 0.27
22 10 0.27
23 7 0.19
24 10 0.27
ACGTcount: A:0.22, C:0.10, G:0.28, T:0.40
Consensus pattern (23 bp):
TGTGAGTCTGAGTTCATGTTATA
Found at i:42064357 original size:45 final size:45
Alignment explanation
Indices: 42064305--42064392 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
42064295 AATTATATAG
*
42064305 TCTGAACTCACTGAGTTGTGGTCTGAGTTCATGTTATATGTGAGA
1 TCTGAACTCACTGAGTTGTGGTCTGAGTTCATGATATATGTGAGA
*
42064350 TCTGAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGA
1 TCTGAACTCACTGAGTTGTGGTCTGAGTTCATGATATATGTGA
42064393 CACATGTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.23, C:0.12, G:0.26, T:0.39
Consensus pattern (45 bp):
TCTGAACTCACTGAGTTGTGGTCTGAGTTCATGATATATGTGAGA
Found at i:42072347 original size:58 final size:58
Alignment explanation
Indices: 42072277--42072393 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
42072267 AAAAGTCCTT
* *
42072277 AGTCAAATATTATTGTGGGTTTGGACAATGATAATGTATTGAAACTAATGTGTAGTTG
1 AGTCAAATATTATTGTGGGTGTGGACAATGATAATGCATTGAAACTAATGTGTAGTTG
42072335 AGTCAAATATTATTGTGGGTGTGGACAATGATAATGCATTGAAACTAATGTGTAGTTG
1 AGTCAAATATTATTGTGGGTGTGGACAATGATAATGCATTGAAACTAATGTGTAGTTG
42072393 A
1 A
42072394 TTGATGATAA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (58 bp):
AGTCAAATATTATTGTGGGTGTGGACAATGATAATGCATTGAAACTAATGTGTAGTTG
Found at i:42072884 original size:43 final size:44
Alignment explanation
Indices: 42072808--42072896 Score: 171
Period size: 43 Copynumber: 2.0 Consensus size: 44
42072798 CTTTTTTTTT
42072808 TATTGTAGCCTACTAAAAAAATCAAGAAATATGATATTGAAATA
1 TATTGTAGCCTACTAAAAAAATCAAGAAATATGATATTGAAATA
42072852 TATTGTAGCCTACT-AAAAAATCAAGAAATATGATATTGAAATA
1 TATTGTAGCCTACTAAAAAAATCAAGAAATATGATATTGAAATA
42072895 TA
1 TA
42072897 CAAGTGTCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 31 0.69
44 14 0.31
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.30
Consensus pattern (44 bp):
TATTGTAGCCTACTAAAAAAATCAAGAAATATGATATTGAAATA
Found at i:42086826 original size:13 final size:13
Alignment explanation
Indices: 42086808--42086834 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42086798 GACTCCATGG
42086808 TTCAAATATAAAA
1 TTCAAATATAAAA
42086821 TTCAAATATAAAA
1 TTCAAATATAAAA
42086834 T
1 T
42086835 CTGGAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.33
Consensus pattern (13 bp):
TTCAAATATAAAA
Found at i:42087394 original size:82 final size:82
Alignment explanation
Indices: 42087257--42087420 Score: 310
Period size: 82 Copynumber: 2.0 Consensus size: 82
42087247 TTAGCTTTCA
*
42087257 AGCACAGAATTGTTATCGTAAAGGGAAAGTAGGCTGGGCTGGAACGTCTAACGACACAATTCCGT
1 AGCACAGAATTGTTATCGTAAAGGGAAAGTAGGCTGGGCTGGAACGTCTAACGACACAATTCCGC
42087322 ATTTCTTTCAGGATGAT
66 ATTTCTTTCAGGATGAT
*
42087339 AGCACAGAATTGTTATCGTAAAGGGAAAGTAGGCTGGGCTGGAACGTCTAACGACACAATTCTGC
1 AGCACAGAATTGTTATCGTAAAGGGAAAGTAGGCTGGGCTGGAACGTCTAACGACACAATTCCGC
42087404 ATTTCTTTCAGGATGAT
66 ATTTCTTTCAGGATGAT
42087421 TTTCCCACAT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 80 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (82 bp):
AGCACAGAATTGTTATCGTAAAGGGAAAGTAGGCTGGGCTGGAACGTCTAACGACACAATTCCGC
ATTTCTTTCAGGATGAT
Found at i:42092377 original size:43 final size:43
Alignment explanation
Indices: 42092329--42092413 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
42092319 AATGCATAAC
42092329 CTTAAATTTTACCTAGCCATGTCAATTTTTGTCCATACCAAAT
1 CTTAAATTTTACCTAGCCATGTCAATTTTTGTCCATACCAAAT
*
42092372 CTTAAATTTTACCTAGCCATGTCCATTTTTGTCCATACCAAA
1 CTTAAATTTTACCTAGCCATGTCAATTTTTGTCCATACCAAA
42092414 ATATAATGCT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (43 bp):
CTTAAATTTTACCTAGCCATGTCAATTTTTGTCCATACCAAAT
Found at i:42096762 original size:58 final size:58
Alignment explanation
Indices: 42096693--42096809 Score: 216
Period size: 58 Copynumber: 2.0 Consensus size: 58
42096683 TTATCATCAA
* *
42096693 TCAACTACACATTAGTTTCAATGCATTATCATTGTCCACACCCACAATAATATTTGAC
1 TCAACTACACATTAGTTTCAATACATTATCATTGTCCAAACCCACAATAATATTTGAC
42096751 TCAACTACACATTAGTTTCAATACATTATCATTGTCCAAACCCACAATAATATTTGAC
1 TCAACTACACATTAGTTTCAATACATTATCATTGTCCAAACCCACAATAATATTTGAC
42096809 T
1 T
42096810 AAGGACTTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.36, C:0.25, G:0.06, T:0.33
Consensus pattern (58 bp):
TCAACTACACATTAGTTTCAATACATTATCATTGTCCAAACCCACAATAATATTTGAC
Found at i:42101831 original size:40 final size:40
Alignment explanation
Indices: 42101737--42101957 Score: 220
Period size: 40 Copynumber: 5.5 Consensus size: 40
42101727 TATTCGAATG
*
42101737 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACT
* * *
42101778 ATAACCGGACTAAGAT-CCGAAGGCATTCGTG-TGAGTTG-CT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCT-AG-TGACT
* *
42101818 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* *
42101858 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
* * * * * *
42101898 ACATGCGGGCTAAGACCCGAAGGC-CTTGTGCAAGT-AGTT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGA-CT
*
42101937 ATATCC-GGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
42101958 ATTACTTGAG
Statistics
Matches: 148, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
38 14 0.09
39 13 0.09
40 91 0.61
41 29 0.20
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:42107779 original size:24 final size:24
Alignment explanation
Indices: 42107752--42107799 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
42107742 GGGTAGATGG
*
42107752 CAGGCTTTCCCAAAGGCCAACCTA
1 CAGGCTTTCCCAAAGACCAACCTA
42107776 CAGGCTTTCCCAAAGACCAACCTA
1 CAGGCTTTCCCAAAGACCAACCTA
42107800 TAAGGTGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.17
Consensus pattern (24 bp):
CAGGCTTTCCCAAAGACCAACCTA
Found at i:42110957 original size:26 final size:26
Alignment explanation
Indices: 42110928--42110979 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
42110918 AATGGTAATT
*
42110928 AAATGTT-GAATTTATATGTTGTTATG
1 AAATGTTAGAATTTATAT-ATGTTATG
42110954 AAATGTTAGAATTTATATATGTTATG
1 AAATGTTAGAATTTATATATGTTATG
42110980 GCCAAATATG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (26 bp):
AAATGTTAGAATTTATATATGTTATG
Found at i:42119108 original size:15 final size:15
Alignment explanation
Indices: 42119072--42119121 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
42119062 CGATATCCTT
42119072 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
42119086 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
*
42119102 TTT-CATCACAT-CA
1 TTTGCATCTCATGCA
42119115 TTTGCAT
1 TTTGCAT
42119122 TCAAAGTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 11 0.34
16 6 0.19
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:42124909 original size:32 final size:32
Alignment explanation
Indices: 42124868--42124932 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
42124858 AAAGAGGCAA
42124868 TAGAGAATATAACCCTAAAGAAGGGGAAAGAG
1 TAGAGAATATAACCCTAAAGAAGGGGAAAGAG
* *
42124900 TAGAGAATATAACCCTAGAGGAGGGGAAAGAG
1 TAGAGAATATAACCCTAAAGAAGGGGAAAGAG
42124932 T
1 T
42124933 TAAAAATTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.09, G:0.31, T:0.14
Consensus pattern (32 bp):
TAGAGAATATAACCCTAAAGAAGGGGAAAGAG
Found at i:42129453 original size:205 final size:205
Alignment explanation
Indices: 42129098--42129679 Score: 850
Period size: 206 Copynumber: 2.8 Consensus size: 205
42129088 ACAAGCCACA
* *
42129098 ACATAGCAGATCTGGCATTCAGATGTTTATACTGAAGCAGATCCAAAATGATTTGGGCATCCTTG
1 ACATAGCAGATCTGGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTT-GGCATCCTTG
* * * * *
42129163 TGCTTACAAGGAACAAATCAAAGACATAGCTGATTTGACTTTCATGTGTTTACAATGAAGCAAAT
65 TGCTTACAAGGAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGAGGAAGCAAAT
* * *
42129228 CTAAGATGA-TTGGTCATCTCTGTATTGTCAGAGAGCAAATCGAAGTTTGGCATCTCCACTTCAA
130 CTAAGATGATTTGG-CATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCAA
42129292 CGGGGAGCAGAT
194 CGGGGAGCAGAT
*
42129304 ACATAGCAGATCTGGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGGTTTGGCATCCTTGT
1 ACATAGCAGATCTGGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
*
42129369 GCTTACAAGGAGCAAATCAAAGACGTAGCTGATTTGGCTTTCACGTGTTTACGAGGAAGCAAATC
66 GCTTACAAGGAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGAGGAAGCAAATC
*
42129434 TAAGATGATTTGGCATCTCTGTATTTTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCAACG
131 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCAACG
42129499 GGGAGCAGAT
196 GGGAGCAGAT
* * * * *
42129509 ACATAGCAGATAT--CATCTTCAGATAATCT-CACTGAAGCAAGATCCAAGATGATTTGGCATTC
1 ACATAGCAGATCTGGC-T-TTCAGAT-GTTTATACTGAAGC-AGATCCAAGATGATTTGGCATCC
* * * * *
42129571 TTGTGCTTACAAGGAGCAAATCGAAGACATAGCTGATTTGGTTTTCGCGTGCTTACGCTGG-AGC
62 TTGTGCTTACAAGGAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACG-AGGAAGC
*
42129635 AAATCTAAGATGATTTGGCGTCTCTGTATTGTCAGAGAACAAATC
126 AAATCTAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATC
42129680 CAAGAAGCAG
Statistics
Matches: 343, Mismatches: 27, Indels: 12
0.90 0.07 0.03
Matches are distributed among these distances:
203 1 0.00
204 1 0.00
205 163 0.48
206 176 0.51
207 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (205 bp):
ACATAGCAGATCTGGCTTTCAGATGTTTATACTGAAGCAGATCCAAGATGATTTGGCATCCTTGT
GCTTACAAGGAGCAAATCAAAGACATAGCTGATTTGGCTTTCACGTGTTTACGAGGAAGCAAATC
TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCAACG
GGGAGCAGAT
Found at i:42131334 original size:25 final size:23
Alignment explanation
Indices: 42131298--42131355 Score: 57
Period size: 25 Copynumber: 2.5 Consensus size: 23
42131288 TTTACCTTAC
42131298 TTTTA-TATTATACATTATAAGATTA
1 TTTTATTA-TATACATTAT--GATTA
* *
42131323 TTTTATTATATATATTATTATTA
1 TTTTATTATATACATTATGATTA
42131346 -TTTATTATAT
1 TTTTATTATAT
42131356 CTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
22 10 0.33
23 4 0.13
25 14 0.47
26 2 0.07
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTATTATATACATTATGATTA
Found at i:42131336 original size:20 final size:22
Alignment explanation
Indices: 42131313--42131355 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
42131303 TATTATACAT
42131313 TATAAGATTA-T-TTTATTATA
1 TATAAGATTATTATTTATTATA
**
42131333 TATATTATTATTATTTATTATA
1 TATAAGATTATTATTTATTATA
42131355 T
1 T
42131356 CTTATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 1 0.05
22 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TATAAGATTATTATTTATTATA
Found at i:42131360 original size:20 final size:17
Alignment explanation
Indices: 42131319--42131488 Score: 55
Period size: 19 Copynumber: 9.3 Consensus size: 17
42131309 ACATTATAAG
42131319 ATTATTTTATTATATAT
1 ATTATTTTATTATATAT
42131336 ATTATTATTATTTATTATAT
1 ATTATT-TTA-TTA-TATAT
* *
42131356 CTTATTTT-TTCACAAATTATT
1 ATTATTTTATT---ATA-TA-T
42131377 ATTATTTTACATTAT-TATT
1 ATTATTTT--ATTATATA-T
* *
42131396 TTTATATTATTATTATAT
1 ATTATTTTATTA-TATAT
* *
42131414 CTTACTTGTATTATATAT
1 ATTA-TTTTATTATATAT
42131432 -TTATTAATTATTTATATAT
1 ATTATT--TTA-TTATATAT
* *
42131451 ATTGTTCTTA-CATATAT
1 ATTATT-TTATTATATAT
*
42131468 ATTTTTGTTATT-T-TAT
1 ATTATT-TTATTATATAT
42131484 ATTAT
1 ATTAT
42131489 ATATTTCTTA
Statistics
Matches: 117, Mismatches: 17, Indels: 39
0.68 0.10 0.23
Matches are distributed among these distances:
16 9 0.08
17 30 0.26
18 15 0.13
19 35 0.30
20 17 0.15
21 9 0.08
24 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (17 bp):
ATTATTTTATTATATAT
Found at i:42131404 original size:14 final size:14
Alignment explanation
Indices: 42131373--42131409 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
42131363 TTTCACAAAT
42131373 TATTATTA-TTTTA
1 TATTATTATTTTTA
*
42131386 CATTATTATTTTTA
1 TATTATTATTTTTA
42131400 TATTATTATT
1 TATTATTATT
42131410 ATATCTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.33
14 14 0.67
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTATTATTTTTA
Found at i:42131490 original size:38 final size:38
Alignment explanation
Indices: 42131425--42131498 Score: 91
Period size: 38 Copynumber: 1.9 Consensus size: 38
42131415 TTACTTGTAT
42131425 TATATATTTATTAATTATTTATATATAT-TGTTCTTACA
1 TATATATTTATTAATTATTTATATATATAT-TTCTTACA
*
42131463 TATATATTT-TT-GTTATTTTATATTATATATTTCTTA
1 TATATATTTATTAATTA-TTTATA-TATATATTTCTTA
42131499 TTTCCTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
36 3 0.09
37 8 0.25
38 20 0.62
39 1 0.03
ACGTcount: A:0.31, C:0.04, G:0.03, T:0.62
Consensus pattern (38 bp):
TATATATTTATTAATTATTTATATATATATTTCTTACA
Found at i:42131987 original size:13 final size:12
Alignment explanation
Indices: 42131934--42131990 Score: 51
Period size: 13 Copynumber: 4.4 Consensus size: 12
42131924 AGTCATTTCA
42131934 TTTATATATATAT
1 TTTATATAT-TAT
** *
42131947 TGCATATATCAT
1 TTTATATATTAT
42131959 GTGTTATATATTAT
1 -T-TTATATATTAT
42131973 TTTATATATTTAT
1 TTTATATA-TTAT
42131986 TTTAT
1 TTTAT
42131991 GAACATGTAC
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
12 9 0.26
13 18 0.51
14 8 0.23
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.60
Consensus pattern (12 bp):
TTTATATATTAT
Found at i:42138619 original size:40 final size:40
Alignment explanation
Indices: 42138575--42138836 Score: 337
Period size: 39 Copynumber: 6.7 Consensus size: 40
42138565 GCTCCTCGTT
* *
42138575 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGT-ATCTCGCA
* * *
42138615 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42138655 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42138694 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
42138733 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
* *
42138772 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCA-CTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGA-ATTAGT-ATC-TCGCA
42138813 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42138837 CATCATTCAA
Statistics
Matches: 205, Mismatches: 9, Indels: 17
0.89 0.04 0.07
Matches are distributed among these distances:
38 2 0.01
39 128 0.62
40 64 0.31
41 11 0.05
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTATCTCGCA
Found at i:42146813 original size:29 final size:28
Alignment explanation
Indices: 42146774--42146846 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 28
42146764 CTTAATAATC
42146774 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTG-C-TGTACATTTA
*
42146804 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCTGTAC-ATTTA
42146833 AACCCGCACACTTA
1 AACCCGCACACTTA
42146847 TTTAAACTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 5 0.13
28 1 0.03
29 30 0.77
30 3 0.08
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCTGTACATTTA
Found at i:42146851 original size:18 final size:18
Alignment explanation
Indices: 42146828--42146864 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
42146818 GTGCTGTACA
*
42146828 ATTTAAACCCGCACACTT
1 ATTTAAACCCACACACTT
*
42146846 ATTTAAACTCACACACTT
1 ATTTAAACCCACACACTT
42146864 A
1 A
42146865 GTGCCATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.30
Consensus pattern (18 bp):
ATTTAAACCCACACACTT
Found at i:42147034 original size:29 final size:28
Alignment explanation
Indices: 42146995--42147070 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 28
42146985 CTTAATAATC
42146995 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTG-C-TGTACATTTA
*
42147025 AACTCGCACACTTAGTGCTGTACAATTTA
1 AACCCGCACACTTAGTGCTGTAC-ATTTA
42147054 AACCCGCACACTTAGTG
1 AACCCGCACACTTAGTG
42147071 TCAATCTCAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.79
30 3 0.07
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (28 bp):
AACCCGCACACTTAGTGCTGTACATTTA
Found at i:42147051 original size:221 final size:221
Alignment explanation
Indices: 42146668--42147067 Score: 773
Period size: 221 Copynumber: 1.8 Consensus size: 221
42146658 AACTCAAGGT
* *
42146668 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATATAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATATAAATAATTTATA
42146733 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
42146798 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTATTTAAACTCACACACT
131 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTATTTAAACTCACACACT
42146863 TAGTGCCATGCATTTCAAGTTCGCAC
196 TAGTGCCATGCATTTCAAGTTCGCAC
*
42146889 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATATAAATAATTTATA
42146954 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
42147019 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTA
131 ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTA
42147068 GTGTCAATCT
Statistics
Matches: 176, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
221 176 1.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.30
Consensus pattern (221 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATATAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCGCACACTTAGTGCTGTACAATTTAAACCCGCACACTTATTTAAACTCACACACT
TAGTGCCATGCATTTCAAGTTCGCAC
Found at i:42155101 original size:145 final size:145
Alignment explanation
Indices: 42154904--42155177 Score: 521
Period size: 145 Copynumber: 1.9 Consensus size: 145
42154894 AACTCAAGGT
**
42154904 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCAACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
*
42154969 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCCCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
42155034 ATTTCAAGTTCGCAC
131 ATTTCAAGTTCGCAC
42155049 ACTTACCTTTTCCGCTGTCCAAAATCAACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCAACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
42155114 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATG
42155178 TACTTTAAAC
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
145 126 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (145 bp):
ACTTACCTTTTCCGCTGTCCAAAATCAACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ATTTCAAGTTCGCAC
Found at i:42155194 original size:29 final size:30
Alignment explanation
Indices: 42155155--42155233 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
42155145 CTTAATAATC
42155155 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
42155185 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
42155214 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
42155234 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:42157501 original size:18 final size:17
Alignment explanation
Indices: 42157468--42157501 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42157458 GTAATCTTCA
*
42157468 TGGGCCCACGAGCCCAT
1 TGGGCCCACCAGCCCAT
42157485 TGGGCCCACACAGCCCA
1 TGGGCCCAC-CAGCCCA
42157502 ACGAGACCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.21, C:0.44, G:0.26, T:0.09
Consensus pattern (17 bp):
TGGGCCCACCAGCCCAT
Found at i:42164680 original size:39 final size:40
Alignment explanation
Indices: 42164625--42164700 Score: 127
Period size: 39 Copynumber: 1.9 Consensus size: 40
42164615 AGTGCTGTCC
*
42164625 GGGCCTTAGCCCTAAACAGAAAGAGGGTGGGCCTAAGTCT
1 GGGCCTTAGCCCTAAACAGAAACAGGGTGGGCCTAAGTCT
*
42164665 GGGCCTT-GCCCTAAACAGAAACAGTGTGGGCCTAAG
1 GGGCCTTAGCCCTAAACAGAAACAGGGTGGGCCTAAG
42164701 CCCAATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 27 0.79
40 7 0.21
ACGTcount: A:0.28, C:0.24, G:0.32, T:0.17
Consensus pattern (40 bp):
GGGCCTTAGCCCTAAACAGAAACAGGGTGGGCCTAAGTCT
Found at i:42164861 original size:27 final size:27
Alignment explanation
Indices: 42164837--42164892 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
42164827 AGAAAAGCTG
42164837 CCAATAACAGTAAATGTGGCAAAGCCA
1 CCAATAACAGTAAATGTGGCAAAGCCA
* ** *
42164864 CCAGTAACAGTAGTTGTGGCAGAG-CA
1 CCAATAACAGTAAATGTGGCAAAGCCA
42164890 CCA
1 CCA
42164893 GTATAGTACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CCAATAACAGTAAATGTGGCAAAGCCA
Found at i:42168823 original size:17 final size:18
Alignment explanation
Indices: 42168801--42168834 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42168791 TCCTAGGCTA
42168801 TGTGGGC-CACACGGGCG
1 TGTGGGCTCACACGGGCG
*
42168818 TGTGGGCTCACATGGGC
1 TGTGGGCTCACACGGGC
42168835 CCCGTATTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.12, C:0.26, G:0.44, T:0.18
Consensus pattern (18 bp):
TGTGGGCTCACACGGGCG
Found at i:42170094 original size:47 final size:47
Alignment explanation
Indices: 42170036--42170157 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
42170026 GCATTGGCAC
*
42170036 TAAGACAAGGATACCCTGTAAGACCATGTTTGGAACATGGAATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
*
42170083 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
* *
42170130 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
42170158 CCAAGGCATG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGAATTTGG
Done.