Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 132 of 202
Found at i:40843199 original size:23 final size:25
Alignment explanation
Indices: 40843154--40843202 Score: 66
Period size: 23 Copynumber: 2.0 Consensus size: 25
40843144 ATTTGAATTG
*
40843154 TGAACATGAGAAATGATGAATTGAA
1 TGAACATGAGAAATGAAGAATTGAA
*
40843179 TGAA-ATG-GAAATGAAGCATTGAA
1 TGAACATGAGAAATGAAGAATTGAA
40843202 T
1 T
40843203 TGTTAAGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 3 0.14
25 4 0.18
ACGTcount: A:0.47, C:0.04, G:0.24, T:0.24
Consensus pattern (25 bp):
TGAACATGAGAAATGAAGAATTGAA
Found at i:40844288 original size:20 final size:21
Alignment explanation
Indices: 40844254--40844293 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
40844244 ATCAAGGATC
*
40844254 CCAATAGCTAGAAAC-TCCCT
1 CCAATAGCTACAAACGTCCCT
*
40844274 CCAATAGCTCCAAACGTCCC
1 CCAATAGCTACAAACGTCCC
40844294 AAAATCAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (21 bp):
CCAATAGCTACAAACGTCCCT
Found at i:40848812 original size:18 final size:18
Alignment explanation
Indices: 40848789--40848846 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
40848779 ATTTAAGCCA
40848789 ATTTAAAATTTAAAAATT
1 ATTTAAAATTTAAAAATT
40848807 ATTTAAAATTATAAAAAAGTT
1 ATTTAAAATT-T-AAAAA-TT
**
40848828 ATAAAAAATTT-AAAATT
1 ATTTAAAATTTAAAAATT
40848845 AT
1 AT
40848847 AAATTTTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
17 4 0.11
18 14 0.40
19 1 0.03
20 6 0.17
21 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTTAAAATTTAAAAATT
Found at i:40848829 original size:11 final size:10
Alignment explanation
Indices: 40848800--40848842 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
40848790 TTTAAAATTT
*
40848800 AAAAATTATT
1 AAAAATTATA
*
40848810 TAAAATTATA
1 AAAAATTATA
40848820 AAAAAGTTATA
1 AAAAA-TTATA
40848831 AAAAATT-TA
1 AAAAATTATA
40848840 AAA
1 AAA
40848843 TTATAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
9 5 0.17
10 14 0.48
11 10 0.34
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (10 bp):
AAAAATTATA
Found at i:40848974 original size:11 final size:11
Alignment explanation
Indices: 40848952--40848995 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
40848942 TATTTTATAA
40848952 TTTTA-AAA-T
1 TTTTAGAAATT
*
40848961 TTTTATAAATT
1 TTTTAGAAATT
*
40848972 TTTTAGAATTT
1 TTTTAGAAATT
40848983 TTTTAGAAATT
1 TTTTAGAAATT
40848994 TT
1 TT
40848996 ATGACTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 22 0.73
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (11 bp):
TTTTAGAAATT
Found at i:40878968 original size:12 final size:12
Alignment explanation
Indices: 40878950--40878986 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
40878940 CCCATATTAA
40878950 AATTTTTTATAT
1 AATTTTTTATAT
*
40878962 TATTTTTTATAT
1 AATTTTTTATAT
*
40878974 AATTTTTAATAT
1 AATTTTTTATAT
40878986 A
1 A
40878987 TATACTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
AATTTTTTATAT
Found at i:40879033 original size:25 final size:22
Alignment explanation
Indices: 40879005--40879059 Score: 56
Period size: 25 Copynumber: 2.3 Consensus size: 22
40878995 ATCAAAAATA
*
40879005 CTAAAAATATTAAAATAAATATTTT
1 CTAAAAAT-TGAAAAT-AAT-TTTT
40879030 CTAACAAATTGAAAATAATTTTT
1 CTAA-AAATTGAAAATAATTTTT
*
40879053 TTAAAAA
1 CTAAAAA
40879060 ATATGTATAC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 3 0.11
23 7 0.26
24 3 0.11
25 10 0.37
26 4 0.15
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (22 bp):
CTAAAAATTGAAAATAATTTTT
Found at i:40881524 original size:3 final size:3
Alignment explanation
Indices: 40881516--40881547 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
40881506 ACCTTAGTCA
40881516 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
40881548 CATACCCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40896908 original size:90 final size:90
Alignment explanation
Indices: 40896784--40897247 Score: 750
Period size: 90 Copynumber: 5.1 Consensus size: 90
40896774 TCGACAGCAA
** * *
40896784 AGCAGATCGAAGATACCAACCTAGTCTCCCTGAGCAGCAGTGAAGTAGGTTGAAAGACATTACAG
1 AGCAGATCGAAGACCCCAGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
40896849 ATCTTATCTCCCTAAGCAGTAGTGG
66 ATCTTATCTCCCTAAGCAGTAGTGG
* * *
40896874 AGCAAATCGAAGACCCCAGTCTAGTCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
1 AGCAGATCGAAGACCCCAGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
40896939 ATCTTATCTCCCTAAGCAGTAGTGG
66 ATCTTATCTCCCTAAGCAGTAGTGG
* * *
40896964 AGCAAATCGAAGACCCCAGTCTAGTCTCCTTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
1 AGCAGATCGAAGACCCCAGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
40897029 ATCTTATCTCCCTAAGCAGTAGTGG
66 ATCTTATCTCCCTAAGCAGTAGTGG
**
40897054 AGCAGATCGAAGACCCTGGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
1 AGCAGATCGAAGACCCCAGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
*
40897119 ATCTTATCTCCCTAAGTAGTAGTGG
66 ATCTTATCTCCCTAAGCAGTAGTGG
* *
40897144 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGTAGCAGTGGAGTAGGTTAAGAAA-ACATTAC
1 AGCAGATCGAAGACCCCAGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTT--GAAAGACATTAC
* *
40897208 AGATCTTATCTCCCTAAGCAGTAATAG
64 AGATCTTATCTCCCTAAGCAGTAGTGG
40897235 AGCAGATCGAAGA
1 AGCAGATCGAAGA
40897248 AGGCGGATTT
Statistics
Matches: 352, Mismatches: 20, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
90 304 0.86
91 44 0.12
92 4 0.01
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (90 bp):
AGCAGATCGAAGACCCCAGCCTAGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAGACATTACAG
ATCTTATCTCCCTAAGCAGTAGTGG
Found at i:40896910 original size:43 final size:43
Alignment explanation
Indices: 40896784--40897188 Score: 206
Period size: 43 Copynumber: 9.0 Consensus size: 43
40896774 TCGACAGCAA
** ** *
40896784 AGCAGATCGAAGATACCAACCTAGTCTCCCTGAGCAGCAGTGA
1 AGCAGATCGAAGACCCCAGTCTAGTCTCCCTGAGCAGCAGTGG
* * * ** * *
40896827 AGTAGGTTGAAAGACATTACAGATCTTA-TCTCCCTAAGCAGTAGTGG
1 AGCAGATCG-AAGAC--CCCAG-TC-TAGTCTCCCTGAGCAGCAGTGG
* *
40896874 AGCAAATCGAAGACCCCAGTCTAGTCTCCTTGAGCAGCAGTGG
1 AGCAGATCGAAGACCCCAGTCTAGTCTCCCTGAGCAGCAGTGG
* * * ** * *
40896917 AGTAGGTTGAAAGACATTACAGATCTTA-TCTCCCTAAGCAGTAGTGG
1 AGCAGATCG-AAGAC--CCCAG-TC-TAGTCTCCCTGAGCAGCAGTGG
* *
40896964 AGCAAATCGAAGACCCCAGTCTAGTCTCCTTGAGCAGCAGTGG
1 AGCAGATCGAAGACCCCAGTCTAGTCTCCCTGAGCAGCAGTGG
* * * ** * *
40897007 AGTAGGTTGAAAGACATTACAGATCTTA-TCTCCCTAAGCAGTAGTGG
1 AGCAGATCG-AAGAC--CCCAG-TC-TAGTCTCCCTGAGCAGCAGTGG
** *
40897054 AGCAGATCGAAGACCCTGGCCTAGTCTCCCTGAGCAGCAGTGG
1 AGCAGATCGAAGACCCCAGTCTAGTCTCCCTGAGCAGCAGTGG
* * * ** * * *
40897097 AGTAGGTTGAAAGACATTACAGATCTTA-TCTCCCTAAGTAGTAGTGG
1 AGCAGATCG-AAGAC--CCCAG-TC-TAGTCTCCCTGAGCAGCAGTGG
* * *
40897144 AGCAGATCGAAGACCCCAGCCTTGTCTCCCTGAGTAGCAGTGG
1 AGCAGATCGAAGACCCCAGTCTAGTCTCCCTGAGCAGCAGTGG
40897187 AG
1 AG
40897189 TAGGTTAAGA
Statistics
Matches: 261, Mismatches: 77, Indels: 48
0.68 0.20 0.12
Matches are distributed among these distances:
42 7 0.03
43 96 0.37
44 29 0.11
46 29 0.11
47 92 0.35
48 8 0.03
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.22
Consensus pattern (43 bp):
AGCAGATCGAAGACCCCAGTCTAGTCTCCCTGAGCAGCAGTGG
Found at i:40906578 original size:43 final size:43
Alignment explanation
Indices: 40906508--40906664 Score: 137
Period size: 43 Copynumber: 3.7 Consensus size: 43
40906498 AGCTCGTACA
* *
40906508 ATGCCAAC-GTCCCAAACGTGGTCTTACATGTAATCAAATAACG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAAT-ACG
* *** *
40906551 ATGCC-ACTGTCCCAGACATGGTTTTACACAAAATCATATACG
1 ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATACG
* *
40906593 ATGACAA-TGTCTC-GAACATGGTCTTACATGTAAATCTCAAAT-CG
1 ATGCCAACTGTCCCAG-ACATGGTCTTACATGT-AA--TCAAATACG
*
40906637 ATGCCAACT-TCCCAGACGTGGTCTTACA
1 ATGCCAACTGTCCCAGACATGGTCTTACA
40906665 CGATATCACA
Statistics
Matches: 89, Mismatches: 17, Indels: 15
0.74 0.14 0.12
Matches are distributed among these distances:
41 1 0.01
42 26 0.29
43 32 0.36
44 23 0.26
45 7 0.08
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAACTGTCCCAGACATGGTCTTACATGTAATCAAATACG
Found at i:40917056 original size:37 final size:37
Alignment explanation
Indices: 40916997--40917079 Score: 114
Period size: 37 Copynumber: 2.2 Consensus size: 37
40916987 GTCAAACTGA
40916997 AACAAGCCAAACTCTCATAAGAGCTAATCCAACCGAT
1 AACAAGCCAAACTCTCATAAGAGCTAATCCAACCGAT
* * *
40917034 AACATGCCAAATTCTCCA-AAGAGCTAATCCAACTGAT
1 AACAAGCCAAACTCT-CATAAGAGCTAATCCAACCGAT
*
40917071 AACACGCCA
1 AACAAGCCA
40917080 GATGCTCTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
37 39 0.95
38 2 0.05
ACGTcount: A:0.42, C:0.30, G:0.11, T:0.17
Consensus pattern (37 bp):
AACAAGCCAAACTCTCATAAGAGCTAATCCAACCGAT
Found at i:40930115 original size:39 final size:39
Alignment explanation
Indices: 40930051--40930140 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
40930041 CACCAGTTTT
* * *
40930051 ACCACCACCACCTCCTGTGCCTAGAAGTGCATCATTACC
1 ACCACCACCACCTCCTATGCATAGAACTGCATCATTACC
* *
40930090 ACCCCCACCACCTCCTATTCATAGAACTGCATCATTACC
1 ACCACCACCACCTCCTATGCATAGAACTGCATCATTACC
40930129 ACCACCACCACC
1 ACCACCACCACC
40930141 ACCACCTATG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.28, C:0.46, G:0.08, T:0.19
Consensus pattern (39 bp):
ACCACCACCACCTCCTATGCATAGAACTGCATCATTACC
Found at i:40933317 original size:22 final size:21
Alignment explanation
Indices: 40933287--40933332 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
40933277 GTCTTTTACC
*
40933287 ACCCTTAAAGGGCTT-TCATAAT
1 ACCCATAAAGGG-TTATCAT-AT
40933309 ACCCATAAAGGGTTATCATAT
1 ACCCATAAAGGGTTATCATAT
40933330 ACC
1 ACC
40933333 GGTGTGCACC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.28
Consensus pattern (21 bp):
ACCCATAAAGGGTTATCATAT
Found at i:40937770 original size:15 final size:15
Alignment explanation
Indices: 40937750--40937781 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
40937740 TAGAATATAT
*
40937750 AAGAAAAATTTGGAA
1 AAGAAAAATATGGAA
40937765 AAGAAAAATATGGAA
1 AAGAAAAATATGGAA
40937780 AA
1 AA
40937782 AATTGAACTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.19, T:0.16
Consensus pattern (15 bp):
AAGAAAAATATGGAA
Found at i:40939002 original size:6 final size:6
Alignment explanation
Indices: 40938991--40939022 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
40938981 TATCGTAACC
40938991 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
1 TTTCCT TTTCCT TTTCCT TTTCCT TTTCCT TT
40939023 ACATTGTTGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCCT
Found at i:40953058 original size:20 final size:20
Alignment explanation
Indices: 40952994--40953058 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 20
40952984 TACCAAAGTA
* * *
40952994 CAAACAGGGCCACAAATGTG
1 CAAACAGGGGCACGAATGGG
* * *
40953014 CAAATAGGGGTATCGAA--GA
1 CAAACAGGGGCA-CGAATGGG
40953033 CAAACAGGGGCACGAATGGG
1 CAAACAGGGGCACGAATGGG
40953053 CAAACA
1 CAAACA
40953059 AGGGTATTGA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
18 4 0.12
19 10 0.30
20 16 0.48
21 3 0.09
ACGTcount: A:0.42, C:0.20, G:0.29, T:0.09
Consensus pattern (20 bp):
CAAACAGGGGCACGAATGGG
Found at i:40953076 original size:20 final size:20
Alignment explanation
Indices: 40953032--40953098 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 20
40953022 GGTATCGAAG
* * *
40953032 ACAAACAGGGGCACGAATGG
1 ACAAACAAGGGCATGAATGT
* *
40953052 GCAAACAAGGGTATTGAA-GT
1 ACAAACAAGGGCA-TGAATGT
* *
40953072 ACAAATAGGGGCATGAATGT
1 ACAAACAAGGGCATGAATGT
40953092 ACAAACA
1 ACAAACA
40953099 TTCAATAATT
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
19 4 0.11
20 28 0.80
21 3 0.09
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.13
Consensus pattern (20 bp):
ACAAACAAGGGCATGAATGT
Found at i:40953097 original size:40 final size:40
Alignment explanation
Indices: 40952989--40953098 Score: 132
Period size: 39 Copynumber: 2.8 Consensus size: 40
40952979 AGGGGTACCA
* * * *
40952989 AAGTACAAACAGGGCCACAAATGTGCAAATAGGGGTATCG
1 AAGTACAAACAGGGGCACGAATGTGCAAACAAGGGTATCG
* *
40953029 AAG-ACAAACAGGGGCACGAATGGGCAAACAAGGGTATTG
1 AAGTACAAACAGGGGCACGAATGTGCAAACAAGGGTATCG
* * *
40953068 AAGTACAAATAGGGGCATGAATGTACAAACA
1 AAGTACAAACAGGGGCACGAATGTGCAAACA
40953099 TTCAATAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
39 33 0.56
40 26 0.44
ACGTcount: A:0.43, C:0.15, G:0.28, T:0.14
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACGAATGTGCAAACAAGGGTATCG
Found at i:40957173 original size:22 final size:22
Alignment explanation
Indices: 40957145--40957192 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
40957135 CCGAGTACAA
40957145 ATACATCACTTTCTATAGTTTT
1 ATACATCACTTTCTATAGTTTT
40957167 ATACATCACTTTCTATAGTTTT
1 ATACATCACTTTCTATAGTTTT
40957189 ATAC
1 ATAC
40957193 TTGATTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.04, T:0.48
Consensus pattern (22 bp):
ATACATCACTTTCTATAGTTTT
Found at i:40964080 original size:27 final size:27
Alignment explanation
Indices: 40964026--40964080 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
40964016 AATATAATAT
*
40964026 AATTATAAAAAAATTAAATTGTACTTA
1 AATTATAAAAAAATTAAATTGTAATTA
* *
40964053 AATTATTAAAATATTTAAATT-TAATTA
1 AATTA-TAAAAAAATTAAATTGTAATTA
40964080 A
1 A
40964081 TTTTATAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.46
28 13 0.54
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (27 bp):
AATTATAAAAAAATTAAATTGTAATTA
Found at i:40965574 original size:13 final size:13
Alignment explanation
Indices: 40965558--40965587 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40965548 TTTTTACATT
*
40965558 TTAATTTTCTTAG
1 TTAATTTACTTAG
40965571 TTAATTTACTTAG
1 TTAATTTACTTAG
40965584 TTAA
1 TTAA
40965588 AATCTAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:40971754 original size:16 final size:15
Alignment explanation
Indices: 40971724--40971757 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
40971714 ATAACTAATA
*
40971724 TATAATTATATTTAT
1 TATAATTATAATTAT
40971739 TATAATGTATAATTAT
1 TATAAT-TATAATTAT
40971755 TAT
1 TAT
40971758 CAACTTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATAATTATAATTAT
Found at i:40976476 original size:13 final size:13
Alignment explanation
Indices: 40976460--40976489 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
40976450 TTTTTACCTT
*
40976460 TTAATTTTCTTAG
1 TTAATTTACTTAG
40976473 TTAATTTACTTAG
1 TTAATTTACTTAG
40976486 TTAA
1 TTAA
40976490 AATCTTGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.57
Consensus pattern (13 bp):
TTAATTTACTTAG
Found at i:40979581 original size:41 final size:41
Alignment explanation
Indices: 40979519--40979638 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
40979509 ATCTGACCTT
* * * *
40979519 TCGGGGCTTTAGTGACGTTTTTGAAAAAGCGCCGCTAAGGC
1 TCGGAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAAGGC
** *
40979560 TCGGAGCTTTAGCGGCGTTTTTGAGAAAGCTTCGCTAATGC
1 TCGGAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAAGGC
* * * * *
40979601 TCGGAACTTTAACAGTGTTTTTGAGAAAGCGCCACTAA
1 TCGGAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAA
40979639 AACATTTTAT
Statistics
Matches: 65, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 65 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (41 bp):
TCGGAGCTTTAGCGGCGTTTTTGAGAAAGCGCCGCTAAGGC
Found at i:40979762 original size:25 final size:26
Alignment explanation
Indices: 40979720--40979770 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
40979710 AATGGATAAA
* * *
40979720 TTTGAAATAATGACACATAGAAAAAT
1 TTTGAAATAATAAAACATAAAAAAAT
40979746 TTTGAAATAA-AAAACATAAAAAAAT
1 TTTGAAATAATAAAACATAAAAAAAT
40979771 ATTCGTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.61, C:0.06, G:0.08, T:0.25
Consensus pattern (26 bp):
TTTGAAATAATAAAACATAAAAAAAT
Found at i:40980050 original size:14 final size:15
Alignment explanation
Indices: 40980022--40980054 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
40980012 AAAGTTTATA
40980022 GATTATGGAATTAGG
1 GATTATGGAATTAGG
40980037 GATTATGG-ATTAGG
1 GATTATGGAATTAGG
40980051 GATT
1 GATT
40980055 CTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:40980219 original size:81 final size:83
Alignment explanation
Indices: 40980131--40980292 Score: 249
Period size: 81 Copynumber: 2.0 Consensus size: 83
40980121 AGATTCAGTG
40980131 TCAGGTTAGGCTTTAGGGTTTAGATTAATTAGTGTGTTTT-AA-TT-TATATTAAATAAGATTTA
1 TCAGGTTAGGCTTTAGGGTTTAGATTAATTAGTGT-TTTTAAATTTATATATTAAATAAGATTTA
*
40980193 GGGGTTAGGGGTTAGGGAT
65 GGGGTTAGGAGTTAGGGAT
* * *
40980212 TCAGGTTAGGGTTTAGGGTTTAGGTTAATTAGTGTTTTTAAATTTATATATTAAATAAGGTTTAG
1 TCAGGTTAGGCTTTAGGGTTTAGATTAATTAGTGTTTTTAAATTTATATATTAAATAAGATTTAG
*
40980277 GGGTTAGTAGTTAGGG
66 GGGTTAGGAGTTAGGG
40980293 GTTAGGGATT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
80 4 0.05
81 35 0.48
82 2 0.03
83 32 0.44
ACGTcount: A:0.27, C:0.02, G:0.28, T:0.43
Consensus pattern (83 bp):
TCAGGTTAGGCTTTAGGGTTTAGATTAATTAGTGTTTTTAAATTTATATATTAAATAAGATTTAG
GGGTTAGGAGTTAGGGAT
Found at i:40980220 original size:20 final size:19
Alignment explanation
Indices: 40980195--40980238 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
40980185 AAGATTTAGG
40980195 GGTTAGGGGTTAGGGATTCA
1 GGTTAGGGGTTAGGG-TTCA
* *
40980215 GGTTAGGGTTTAGGGTTTA
1 GGTTAGGGGTTAGGGTTCA
40980234 GGTTA
1 GGTTA
40980239 ATTAGTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.18, C:0.02, G:0.43, T:0.36
Consensus pattern (19 bp):
GGTTAGGGGTTAGGGTTCA
Found at i:40980296 original size:7 final size:7
Alignment explanation
Indices: 40980273--40980324 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
40980263 TAAATAAGGT
40980273 TTAGGGG
1 TTAGGGG
**
40980280 TTAGTAG
1 TTAGGGG
40980287 TTAGGGG
1 TTAGGGG
*
40980294 TTAGGGA
1 TTAGGGG
*
40980301 TTTGGGG
1 TTAGGGG
*
40980308 TTATGGG
1 TTAGGGG
*
40980315 TTAGAGG
1 TTAGGGG
40980322 TTA
1 TTA
40980325 AGAGTTAGTG
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.37
Consensus pattern (7 bp):
TTAGGGG
Found at i:40980449 original size:7 final size:7
Alignment explanation
Indices: 40980437--40980486 Score: 55
Period size: 7 Copynumber: 7.1 Consensus size: 7
40980427 ATTGTAAAAG
40980437 AGGGGTT
1 AGGGGTT
40980444 AGGGGTT
1 AGGGGTT
*
40980451 AGAGGTT
1 AGGGGTT
* **
40980458 AAGAATT
1 AGGGGTT
*
40980465 AGGGATT
1 AGGGGTT
40980472 AGGGGTT
1 AGGGGTT
40980479 AGGGGTT
1 AGGGGTT
40980486 A
1 A
40980487 TGGATAGGTA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.46, T:0.28
Consensus pattern (7 bp):
AGGGGTT
Found at i:40985003 original size:43 final size:43
Alignment explanation
Indices: 40984894--40985081 Score: 247
Period size: 43 Copynumber: 4.4 Consensus size: 43
40984884 TAATTTTTTT
* * *
40984894 TAAAGGTTATGTT-TTTAGCGGCGTTT-TTACGAGAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGAC-AAAAGCGCCGC
* * **
40984936 TAAAGGT-TTGTTCTTTTGCGGCGTTTGTGACAAAAGCGTGGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
40984978 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
* * *
40985021 TGAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGTGCTGC
1 TAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
*
40985064 TAAAGGTCATGATCTTTA
1 TAAAGGTCATGTTCTTTA
40985082 CCGAAGTTTT
Statistics
Matches: 128, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
41 4 0.03
42 34 0.27
43 90 0.70
ACGTcount: A:0.22, C:0.16, G:0.28, T:0.33
Consensus pattern (43 bp):
TAAAGGTCATGTTCTTTAGCGGCGTTTGTGACAAAAGCGCCGC
Found at i:40987996 original size:17 final size:17
Alignment explanation
Indices: 40987974--40988007 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40987964 CACTAACACT
* *
40987974 AAAATGTAATGACAATG
1 AAAATGCAATGAAAATG
40987991 AAAATGCAATGAAAATG
1 AAAATGCAATGAAAATG
40988008 TATACTTATC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.18, T:0.21
Consensus pattern (17 bp):
AAAATGCAATGAAAATG
Found at i:41014670 original size:5 final size:5
Alignment explanation
Indices: 41014660--41014686 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
41014650 AAAATGTACA
41014660 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
41014687 TGTTCGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:41023895 original size:49 final size:49
Alignment explanation
Indices: 41023827--41023927 Score: 148
Period size: 49 Copynumber: 2.1 Consensus size: 49
41023817 TCTTATAAGG
* *
41023827 AACATATGGAAAGCATTAAACATGTTATATTCTTTCCAAAAATAATTAT
1 AACATATGGAAAGCATTAAAAATGTTATATTCTTTCCAAAAAGAATTAT
* * * *
41023876 AACATATTGACAGTATTAAAAATGTTATATTCTTTTCAAAAAGAATTAT
1 AACATATGGAAAGCATTAAAAATGTTATATTCTTTCCAAAAAGAATTAT
41023925 AAC
1 AAC
41023928 TACCATGTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.36
Consensus pattern (49 bp):
AACATATGGAAAGCATTAAAAATGTTATATTCTTTCCAAAAAGAATTAT
Found at i:41031324 original size:187 final size:186
Alignment explanation
Indices: 41031009--41031378 Score: 553
Period size: 187 Copynumber: 2.0 Consensus size: 186
41030999 TCTCTCAATT
* * *
41031009 GGAATAACCAAATCTTGTCACTTGCGAAAGATAAATAAACTGAATACTTCGATATTATAAAAGAA
1 GGAATAACCAAATCTTATCACTTACGAAAGAGAAATAAACTGAATACTTCGATATTATAAAAGAA
* *
41031074 CTATTAGATCGAAATCAATTCCAAAAGGAAAGAAGCATTTCTGGAAAACAAAGGAAAACTTAATC
66 CTATTAGATCAAAATCAATTCCAAAAGGAAAGAAGAATTTCTGGAAAACAAAGGAAAACTTAATC
41031139 TAAATACTACTCAAAAACTTCGAGGGGGTTTTGGATGCGTCTAAGAAAACTTAGATC
131 TAAATACTACTCAAAAACTTCG-GGGGGTTTTGGATGCGTCTAAGAAAACTTAGATC
* * * * *
41031196 GGAATAATCAAATCTTATGACTTACGAAAGAGAAATAAATTGAATACTTTGATATTATAAAATAA
1 GGAATAACCAAATCTTATCACTTACGAAAGAGAAATAAACTGAATACTTCGATATTATAAAAGAA
* * * *
41031261 CTCTTGGATCAAAATCGATTCCAAGAGGAAAGAA-AATTTTCTGGAAAACAAAGGAAAACTTAAT
66 CTATTAGATCAAAATCAATTCCAAAAGGAAAGAAGAA-TTTCTGGAAAACAAAGGAAAACTTAAT
** * *
41031325 CTAAATACTACTCATCAACTTCGGGGGGTTTTGGATGTGTCTAAGAAGACTTAG
130 CTAAATACTACTCAAAAACTTCGGGGGGTTTTGGATGCGTCTAAGAAAACTTAG
41031379 TTACATTAAA
Statistics
Matches: 164, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
186 30 0.18
187 134 0.82
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (186 bp):
GGAATAACCAAATCTTATCACTTACGAAAGAGAAATAAACTGAATACTTCGATATTATAAAAGAA
CTATTAGATCAAAATCAATTCCAAAAGGAAAGAAGAATTTCTGGAAAACAAAGGAAAACTTAATC
TAAATACTACTCAAAAACTTCGGGGGGTTTTGGATGCGTCTAAGAAAACTTAGATC
Found at i:41034207 original size:29 final size:29
Alignment explanation
Indices: 41034137--41034209 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 29
41034127 TTCACCACTT
* * *
41034137 AGGCGTCCTTTTAATAGAGTTGGCCACAA
1 AGGCATCCTTTTAATAGAGATAGCCACAA
* *
41034166 A-GCATTCGTTTAACTA-AGATAGCCACAA
1 AGGCATCCTTTTAA-TAGAGATAGCCACAA
41034194 AGGCATCCTTTTAATA
1 AGGCATCCTTTTAATA
41034210 AAGGTAACCA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
28 22 0.63
29 13 0.37
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (29 bp):
AGGCATCCTTTTAATAGAGATAGCCACAA
Found at i:41054016 original size:13 final size:13
Alignment explanation
Indices: 41053995--41054024 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
41053985 CTACATGGGT
*
41053995 CACATGGCTGAGA
1 CACAAGGCTGAGA
41054008 CACAAGGCTGAGA
1 CACAAGGCTGAGA
41054021 CACA
1 CACA
41054025 TGCCTGTGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.27, G:0.27, T:0.10
Consensus pattern (13 bp):
CACAAGGCTGAGA
Found at i:41057049 original size:27 final size:26
Alignment explanation
Indices: 41057019--41057193 Score: 104
Period size: 27 Copynumber: 6.5 Consensus size: 26
41057009 GTACGTTGTC
*
41057019 AAGGCATTCCATTTAGAATTTGCCACG
1 AAGGCATTCC-TTTAGAATTTGCCACA
* * * * *
41057046 AAGGCTTTCCCTTCAGAGTCTACCACA
1 AAGGCATT-CCTTTAGAATTTGCCACA
* * *
41057073 AAGGCATTCCTTTCGTATATTGCTACA
1 AAGGCATTCCTTTAGAAT-TTGCCACA
* *
41057100 AAGGCATTCCTTTCA-TATATTGCCAAA
1 AAGGCATTCCTTT-AGAAT-TTGCCACA
* **
41057127 AAGGCATT-GTTTCCATATATTGCCACA
1 AAGGCATTCCTTTAGA-AT-TTGCCACA
* *
41057154 AAGGCATTCCTTCCATATATTT-CCACA
1 AAGGCATTCCTT-TAGA-ATTTGCCACA
41057181 AAGGCATTCCTTT
1 AAGGCATTCCTTT
41057194 CATAACGTGT
Statistics
Matches: 115, Mismatches: 26, Indels: 15
0.74 0.17 0.10
Matches are distributed among these distances:
26 9 0.08
27 96 0.83
28 6 0.05
29 4 0.03
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.33
Consensus pattern (26 bp):
AAGGCATTCCTTTAGAATTTGCCACA
Found at i:41057197 original size:27 final size:27
Alignment explanation
Indices: 41057068--41057197 Score: 190
Period size: 27 Copynumber: 4.8 Consensus size: 27
41057058 TCAGAGTCTA
*
41057068 CCACAAAGGCATTCCTTTCGTATATTG
1 CCACAAAGGCATTCCTTTCATATATTG
*
41057095 CTACAAAGGCATTCCTTTCATATATTG
1 CCACAAAGGCATTCCTTTCATATATTG
* *
41057122 CCAAAAAGGCATT-GTTTCCATATATTG
1 CCACAAAGGCATTCCTTT-CATATATTG
* *
41057149 CCACAAAGGCATTCCTTCCATATATTT
1 CCACAAAGGCATTCCTTTCATATATTG
41057176 CCACAAAGGCATTCCTTTCATA
1 CCACAAAGGCATTCCTTTCATA
41057198 ACGTGTTTAT
Statistics
Matches: 91, Mismatches: 10, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
26 3 0.03
27 86 0.95
28 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (27 bp):
CCACAAAGGCATTCCTTTCATATATTG
Found at i:41061915 original size:27 final size:27
Alignment explanation
Indices: 41061885--41062121 Score: 178
Period size: 27 Copynumber: 8.8 Consensus size: 27
41061875 TACAGTCCGT
* *
41061885 CAAAAAAGAATTCCTTTAATATATTTC
1 CAAAAAAGCATTCCTTTCATATATTTC
*
41061912 CAAAAAGGCATTCCTTTCATATATTTC
1 CAAAAAAGCATTCCTTTCATATATTTC
* *
41061939 CACAAAAGTC-TTCC-TTCTATATATTGC
1 CAAAAAAG-CATTCCTTTC-ATATATTTC
* * * *
41061966 CATAAAAGAATTCCTTTCATGTATTTT
1 CAAAAAAGCATTCCTTTCATATATTTC
* * *
41061993 CATAAAGGCATTCCTTCCATATATTGT-
1 CAAAAAAGCATTCCTTTCATATATT-TC
* * *
41062020 CACAAAGGCATTCCTTTCATATA-TTG
1 CAAAAAAGCATTCCTTTCATATATTTC
* * *
41062046 CAACAAAGGCTTTCCTTTCATATATTGC
1 CAA-AAAAGCATTCCTTTCATATATTTC
* * *
41062074 CATAAAGGCATTCC-TTCTATATATTGC
1 CAAAAAAGCATTCCTTTC-ATATATTTC
* * *
41062101 CACATAGGCATTCCTTTCATA
1 CAAAAAAGCATTCCTTTCATA
41062122 GCGTGTTCAC
Statistics
Matches: 175, Mismatches: 25, Indels: 20
0.80 0.11 0.09
Matches are distributed among these distances:
25 1 0.01
26 9 0.05
27 154 0.88
28 11 0.06
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.37
Consensus pattern (27 bp):
CAAAAAAGCATTCCTTTCATATATTTC
Found at i:41061946 original size:54 final size:54
Alignment explanation
Indices: 41061888--41062121 Score: 233
Period size: 54 Copynumber: 4.3 Consensus size: 54
41061878 AGTCCGTCAA
* * * *
41061888 AAAAGAATTCCTTTAATATATTTCCAAAAAGGCATTCCTTTCATATATTTCCAC
1 AAAAGCATTCCTTTCATATATTGCCAAAAAGGCATTCCTTTCATATATTGCCAC
* * ** *
41061942 AAAAGTC-TTCC-TTCTATATATTGCCATAAAA-GAATTCCTTTCATGTATTTTCAT
1 AAAAG-CATTCCTTTC-ATATATTGCCA-AAAAGGCATTCCTTTCATATATTGCCAC
* * * * *
41061996 AAAGGCATTCCTTCCATATATTGTCACAAAGGCATTCCTTTCATATATTGCAAC
1 AAAAGCATTCCTTTCATATATTGCCAAAAAGGCATTCCTTTCATATATTGCCAC
* * *
41062050 AAAGGCTTTCCTTTCATATATTGCCATAAAGGCATTCC-TTCTATATATTGCCAC
1 AAAAGCATTCCTTTCATATATTGCCAAAAAGGCATTCCTTTC-ATATATTGCCAC
* *
41062104 ATAGGCATTCCTTTCATA
1 AAAAGCATTCCTTTCATA
41062122 GCGTGTTCAC
Statistics
Matches: 149, Mismatches: 24, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
53 9 0.06
54 134 0.90
55 6 0.04
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (54 bp):
AAAAGCATTCCTTTCATATATTGCCAAAAAGGCATTCCTTTCATATATTGCCAC
Found at i:41061974 original size:81 final size:82
Alignment explanation
Indices: 41061888--41062121 Score: 273
Period size: 81 Copynumber: 2.9 Consensus size: 82
41061878 AGTCCGTCAA
* * *
41061888 AAAAGAATTCCTTTAATATATTTCCAAAAAGGCATTCCTTTCATATATTTCCACAAAAGTC-TTC
1 AAAAGAATTCCTTTCATATATTTCCATAAAGGCATTCCTTTCATATATTTCCACAAAAGGCATTC
* *
41061952 C-TTCTATATATTGCCAT
66 CTTTC-ATATATTGCAAC
* * *
41061969 AAAAGAATTCCTTTCATGTATTTTCATAAAGGCATTCCTTCCATATATTGT-CAC-AAAGGCATT
1 AAAAGAATTCCTTTCATATATTTCCATAAAGGCATTCCTTTCATATATT-TCCACAAAAGGCATT
41062032 CCTTTCATATATTGCAAC
65 CCTTTCATATATTGCAAC
* ** * * *
41062050 AAAGGCTTTCCTTTCATATATTGCCATAAAGGCATTCC-TTCTATATATTGCCAC-ATAGGCATT
1 AAAAGAATTCCTTTCATATATTTCCATAAAGGCATTCCTTTC-ATATATTTCCACAAAAGGCATT
41062113 CCTTTCATA
65 CCTTTCATA
41062122 GCGTGTTCAC
Statistics
Matches: 131, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
80 7 0.05
81 120 0.92
82 4 0.03
ACGTcount: A:0.32, C:0.22, G:0.09, T:0.38
Consensus pattern (82 bp):
AAAAGAATTCCTTTCATATATTTCCATAAAGGCATTCCTTTCATATATTTCCACAAAAGGCATTC
CTTTCATATATTGCAAC
Found at i:41064921 original size:22 final size:22
Alignment explanation
Indices: 41064893--41064938 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
41064883 TAACTATTTG
41064893 TTCAGGTTCATTT-GAGTCTAGA
1 TTCAGGTTCATTTGGA-TCTAGA
41064915 TTCAGGTTCATTTGGATCTAGA
1 TTCAGGTTCATTTGGATCTAGA
41064937 TT
1 TT
41064939 ACATTATGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (22 bp):
TTCAGGTTCATTTGGATCTAGA
Found at i:41074638 original size:18 final size:17
Alignment explanation
Indices: 41074535--41074640 Score: 63
Period size: 17 Copynumber: 5.9 Consensus size: 17
41074525 TTAGAAGTTG
* *
41074535 ATTTTTATTTATTTTTA
1 ATTTTTAATAATTTTTA
41074552 TATTTTTATATAAGTTTTGATA
1 -ATTTTTA-ATAA-TTTT--TA
* *
41074574 ATCTTTTAAT-TTTTTTG
1 AT-TTTTAATAATTTTTA
* *
41074591 ATTTTT-TTACATATTTA
1 ATTTTTAATA-ATTTTTA
41074608 ATTTTTAATAATTTTTA
1 ATTTTTAATAATTTTTA
*
41074625 ATTTATTTATAATTTT
1 ATTT-TTAATAATTTT
41074641 GTACTCATCG
Statistics
Matches: 68, Mismatches: 11, Indels: 18
0.70 0.11 0.19
Matches are distributed among these distances:
15 1 0.01
16 4 0.06
17 23 0.34
18 19 0.28
19 6 0.09
20 4 0.06
21 4 0.06
22 7 0.10
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTAATAATTTTTA
Found at i:41075145 original size:22 final size:21
Alignment explanation
Indices: 41075101--41075176 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 21
41075091 CTCTCTAAGA
*
41075101 TTCTCTCTAATATT-CTCTTAAT
1 TTCTCTC-AAT-TTCCTCTCAAT
41075123 TTCCTCTCAATTTCCTCTCAAT
1 TT-CTCTCAATTTCCTCTCAAT
*
41075145 TTGCTCTCAATTTCCTTTCAAAT
1 TT-CTCTCAATTTCCTCTC-AAT
41075168 TTCTCTCAA
1 TTCTCTCAA
41075177 ATCCCTATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
21 2 0.04
22 36 0.75
23 10 0.21
ACGTcount: A:0.21, C:0.29, G:0.01, T:0.49
Consensus pattern (21 bp):
TTCTCTCAATTTCCTCTCAAT
Found at i:41075178 original size:11 final size:11
Alignment explanation
Indices: 41075115--41075176 Score: 81
Period size: 11 Copynumber: 5.6 Consensus size: 11
41075105 CTCTAATATT
*
41075115 CTCTTAATTTC
1 CTCTCAATTTC
41075126 CTCTCAATTTC
1 CTCTCAATTTC
*
41075137 CTCTCAATTTG
1 CTCTCAATTTC
41075148 CTCTCAATTTC
1 CTCTCAATTTC
*
41075159 CTTTCAAATTT-
1 CTCTC-AATTTC
41075170 CTCTCAA
1 CTCTCAA
41075177 ATCCCTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
10 2 0.04
11 38 0.84
12 5 0.11
ACGTcount: A:0.21, C:0.31, G:0.02, T:0.47
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:41076249 original size:44 final size:44
Alignment explanation
Indices: 41076200--41076289 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
41076190 GCTAAAAATT
41076200 TATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTGGATTACC
1 TATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTGGATTACC
41076244 TATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTGGATTACC
1 TATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTGGATTACC
41076288 TA
1 TA
41076290 GCTCTCTTGA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (44 bp):
TATTTAATTAGGTGGAACCATCCGGCAAGTTATGCTGGATTACC
Found at i:41076399 original size:7 final size:7
Alignment explanation
Indices: 41076387--41076412 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
41076377 TAGTTGATTG
41076387 GTATTTA
1 GTATTTA
41076394 GTATTTA
1 GTATTTA
41076401 GTATTTA
1 GTATTTA
41076408 GTATT
1 GTATT
41076413 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:41079442 original size:83 final size:82
Alignment explanation
Indices: 41079351--41079518 Score: 291
Period size: 83 Copynumber: 2.0 Consensus size: 82
41079341 TTCAGTACTT
*
41079351 CTGCTGACAAAGCATCATACTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAA
1 CTGCTGACAAAGCATCATACTTAAAGCGTTTTTGACACTGTTTACTCAGAAACGTCTACTCGAAA
41079416 TTATTTTTTCAGGAGATA
66 TTA-TTTTTCAGGAGATA
* *
41079434 CTGCTGACAAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTACTCAGAAACGTCTACTCGAAA
1 CTGCTGACAAAGCATCATACTTAAAGCGTTTTTGACACTGTTTACTCAGAAACGTCTACTCGAAA
*
41079499 TTATTTTTCAGGAGCTA
66 TTATTTTTCAGGAGATA
41079516 CTG
1 CTG
41079519 TAGCAAAAGC
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 16 0.20
83 65 0.80
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (82 bp):
CTGCTGACAAAGCATCATACTTAAAGCGTTTTTGACACTGTTTACTCAGAAACGTCTACTCGAAA
TTATTTTTCAGGAGATA
Found at i:41079770 original size:51 final size:51
Alignment explanation
Indices: 41079706--41079825 Score: 213
Period size: 51 Copynumber: 2.4 Consensus size: 51
41079696 TCAAGTAACC
* *
41079706 CTAAACCCCAAACCCTAATTTATTTAAGTTTTTACTTAAAAACTCTAAACT
1 CTAAACACTAAACCCTAATTTATTTAAGTTTTTACTTAAAAACTCTAAACT
*
41079757 CTAAACACTAAACCCTAATTTATTTAATTTTTTACTTAAAAACTCTAAACT
1 CTAAACACTAAACCCTAATTTATTTAAGTTTTTACTTAAAAACTCTAAACT
41079808 CTAAACACTAAACCCTAA
1 CTAAACACTAAACCCTAA
41079826 ACTAATTTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 66 1.00
ACGTcount: A:0.42, C:0.23, G:0.01, T:0.34
Consensus pattern (51 bp):
CTAAACACTAAACCCTAATTTATTTAAGTTTTTACTTAAAAACTCTAAACT
Found at i:41079890 original size:46 final size:45
Alignment explanation
Indices: 41079818--41079986 Score: 139
Period size: 46 Copynumber: 3.6 Consensus size: 45
41079808 CTAAACACTA
*
41079818 AACCCTAAA--CTAATTTATTATAAATTTGTAATTAATTTACTCAAGT
1 AACCCTAAACCCTAATTTATT-T-AATTTTTAATTAA-TTACTCAAGT
** * * **
41079864 AACCCTAAACCCTAATTTATTTAATTTTTCCTTAA-AAATC-TTT
1 AACCCTAAACCCTAATTTATTTAATTTTTAATTAATTACTCAAGT
*
41079907 AACTCTAAACCCTAATTTAATTTTTAATTTTTTTAATTAAATTACTCAAGT
1 AACCCTAAACCCTAATTT-A--TTTAA--TTTTTAATT-AATTACTCAAGT
* *
41079958 AACCCTAAACCCTAATTTAATTGATTTTT
1 AACCCTAAACCCTAATTTATTTAATTTTT
41079987 TCTTAAAAAA
Statistics
Matches: 96, Mismatches: 17, Indels: 20
0.72 0.13 0.15
Matches are distributed among these distances:
43 18 0.19
44 4 0.04
46 29 0.30
47 1 0.01
48 20 0.21
49 2 0.02
50 4 0.04
51 18 0.19
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (45 bp):
AACCCTAAACCCTAATTTATTTAATTTTTAATTAATTACTCAAGT
Found at i:41079957 original size:94 final size:100
Alignment explanation
Indices: 41079764--41079995 Score: 287
Period size: 94 Copynumber: 2.3 Consensus size: 100
41079754 ACTCTAAACA
41079764 CTAAACCCTAATTTATTTAATTTTTTACTTAAAAACTCTAAACTCTAAACACTAAACCCTAAACT
1 CTAAACCCTAATTTATTTAA-TTTTTACTTAAAAACTCT--A-TCTAAACACTAAACCCTAAACT
*
41079829 AATTTATTATAAATTTGTAATTAATTTACTCAAGTAACC
62 AATTTATTATAAATTTGTAATTAAATTACTCAAGTAACC
* * **
41079868 CTAAACCCTAATTTATTTAATTTTTCCTTAAAAA-TCT-T-T-AACTCTAAACCCTAATTTAATT
1 CTAAACCCTAATTTATTTAATTTTTACTTAAAAACTCTATCTAAACACTAAACCCTAAACTAATT
** *
41079929 T-TTA-ATTTTTTTAATTAAATTACTCAAGTAACC
66 TATTATAAATTTGTAATTAAATTACTCAAGTAACC
* * *
41079962 CTAAACCCTAATTTAATTGATTTTTTCTTAAAAA
1 CTAAACCCTAATTTATTTAATTTTTACTTAAAAA
41079996 ATAATAAACA
Statistics
Matches: 117, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
94 56 0.48
95 3 0.03
96 20 0.17
97 1 0.01
98 1 0.01
102 3 0.03
103 13 0.11
104 20 0.17
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (100 bp):
CTAAACCCTAATTTATTTAATTTTTACTTAAAAACTCTATCTAAACACTAAACCCTAAACTAATT
TATTATAAATTTGTAATTAAATTACTCAAGTAACC
Found at i:41079977 original size:51 final size:52
Alignment explanation
Indices: 41079846--41079979 Score: 155
Period size: 51 Copynumber: 2.8 Consensus size: 52
41079836 TATAAATTTG
*
41079846 TAATTAATTTACTCAAGTAACCCTAAACCCTAATTT-A--TTTAATTTTTCCT
1 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTTTTAATTTTT-CT
* *
41079896 TAA--AAA-T-CT---TTAACTCTAAACCCTAATTTAATTTTTAATTTTT-T
1 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTTTTAATTTTTCT
41079940 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATT
1 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATT
41079980 GATTTTTTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 19
0.74 0.05 0.20
Matches are distributed among these distances:
43 18 0.26
44 5 0.07
46 15 0.22
47 2 0.03
48 4 0.06
50 3 0.04
51 22 0.32
ACGTcount: A:0.37, C:0.18, G:0.01, T:0.43
Consensus pattern (52 bp):
TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTTTTAATTTTTCT
Found at i:41080016 original size:94 final size:94
Alignment explanation
Indices: 41079846--41080016 Score: 229
Period size: 94 Copynumber: 1.8 Consensus size: 94
41079836 TATAAATTTG
* * ** *
41079846 TAATTAATTTACTCAAGTAACCCTAAACCCTAATTTATTTAATTTTTCCTTAAAAATCTTTAACT
1 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTAATTTTTCCTTAAAAATAATAAACT
* *
41079911 CTAAACCCTAATTTAATTTTTAATTTTTT
66 CGAAACACTAATTTAATTTTTAATTTTTT
* *
41079940 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTGATTTTTTCTTAAAAAATAATAAAC
1 TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTAATTTTTCCTT-AAAAATAATAAAC
41080005 AT-GAAA-ACTAAT
65 -TCGAAACACTAAT
41080017 CCAATTTTGA
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
94 52 0.79
95 13 0.20
96 1 0.02
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.42
Consensus pattern (94 bp):
TAATTAAATTACTCAAGTAACCCTAAACCCTAATTTAATTAATTTTTCCTTAAAAATAATAAACT
CGAAACACTAATTTAATTTTTAATTTTTT
Found at i:41083838 original size:17 final size:17
Alignment explanation
Indices: 41083816--41083875 Score: 111
Period size: 17 Copynumber: 3.5 Consensus size: 17
41083806 ATAGATAATC
41083816 GGAAGCTCGACCGGTTT
1 GGAAGCTCGACCGGTTT
41083833 GGAAGCTCGACCGGTTT
1 GGAAGCTCGACCGGTTT
*
41083850 GGAAGCTCGACTGGTTT
1 GGAAGCTCGACCGGTTT
41083867 GGAAGCTCG
1 GGAAGCTCG
41083876 TCGGTGATCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.18, C:0.22, G:0.37, T:0.23
Consensus pattern (17 bp):
GGAAGCTCGACCGGTTT
Found at i:41092982 original size:18 final size:18
Alignment explanation
Indices: 41092959--41092993 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41092949 TAGAAAATAC
41092959 TTTTAT-ATTAATATTTAT
1 TTTTATAATTAA-ATTTAT
41092977 TTTTATAATTAAATTTA
1 TTTTATAATTAAATTTA
41092994 ATATAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTATAATTAAATTTAT
Found at i:41094222 original size:13 final size:13
Alignment explanation
Indices: 41094204--41094240 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
41094194 TTTAAATCAA
41094204 ACTTTTCAAAACT
1 ACTTTTCAAAACT
*
41094217 ACTTTTCAAAAGT
1 ACTTTTCAAAACT
*
41094230 ACTTTCCAAAA
1 ACTTTTCAAAA
41094241 ACAATATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.35
Consensus pattern (13 bp):
ACTTTTCAAAACT
Found at i:41094395 original size:7 final size:7
Alignment explanation
Indices: 41094385--41094409 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41094375 AATCGAAAAA
41094385 AATTTCG
1 AATTTCG
41094392 AATTTCG
1 AATTTCG
41094399 AATTTCG
1 AATTTCG
41094406 AATT
1 AATT
41094410 ATTCGAATCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (7 bp):
AATTTCG
Found at i:41094454 original size:18 final size:18
Alignment explanation
Indices: 41094420--41094454 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41094410 ATTCGAATCG
* *
41094420 AGTTAATCGAGTTAATTA
1 AGTTAATCGAATCAATTA
41094438 AGTTAATCGAATCAATT
1 AGTTAATCGAATCAATT
41094455 CGAATTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (18 bp):
AGTTAATCGAATCAATTA
Found at i:41094514 original size:9 final size:9
Alignment explanation
Indices: 41094500--41094546 Score: 94
Period size: 9 Copynumber: 5.2 Consensus size: 9
41094490 TGAATTTTCG
41094500 AATTCGAAT
1 AATTCGAAT
41094509 AATTCGAAT
1 AATTCGAAT
41094518 AATTCGAAT
1 AATTCGAAT
41094527 AATTCGAAT
1 AATTCGAAT
41094536 AATTCGAAT
1 AATTCGAAT
41094545 AA
1 AA
41094547 AAACTATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:41094594 original size:27 final size:27
Alignment explanation
Indices: 41094556--41094608 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
41094546 AAAACTATAT
*
41094556 TTTTTTATTTTTAAAATACACCACATA
1 TTTTTTATTTTTAAAAAACACCACATA
*
41094583 TTTTTTATTTTTAAAAAACACTACAT
1 TTTTTTATTTTTAAAAAACACCACAT
41094609 TTAAAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTTTATTTTTAAAAAACACCACATA
Found at i:41096008 original size:19 final size:19
Alignment explanation
Indices: 41095984--41096022 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
41095974 ATATTTGTAT
41095984 GTAACTTTCTTGAATTAAA
1 GTAACTTTCTTGAATTAAA
41096003 GTAACTTTCTTGAATTAAA
1 GTAACTTTCTTGAATTAAA
41096022 G
1 G
41096023 CATGTAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (19 bp):
GTAACTTTCTTGAATTAAA
Found at i:41096903 original size:19 final size:19
Alignment explanation
Indices: 41096856--41096893 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41096846 TTTTTGTATT
* *
41096856 AATTTTGTTGTTTATTTGG
1 AATTATGTTGCTTATTTGG
41096875 AATTATGTTGCTTATTTGG
1 AATTATGTTGCTTATTTGG
41096894 GTTGATGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.03, G:0.21, T:0.58
Consensus pattern (19 bp):
AATTATGTTGCTTATTTGG
Found at i:41097263 original size:22 final size:23
Alignment explanation
Indices: 41097238--41097282 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
41097228 TCCTTAGATA
41097238 TTAATT-TTTTAAGTAATAATTT
1 TTAATTGTTTTAAGTAATAATTT
**
41097260 TTAATTGTTTTATTTAATAATTT
1 TTAATTGTTTTAAGTAATAATTT
41097283 CATATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (23 bp):
TTAATTGTTTTAAGTAATAATTT
Found at i:41102472 original size:4 final size:4
Alignment explanation
Indices: 41102463--41102491 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
41102453 TGCATTGAGC
41102463 ACAA ACAA ACAA ACAA ACAA ACAA A-AA AC
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA AC
41102492 CATCTTGGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:41103338 original size:13 final size:13
Alignment explanation
Indices: 41103297--41103340 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
41103287 AGTCAAATAA
41103297 AAATAATTAAGA-
1 AAATAATTAAGAT
* *
41103309 AAGTAATTAAAAT
1 AAATAATTAAGAT
*
41103322 AAATAACTAAGAT
1 AAATAATTAAGAT
41103335 AAATAA
1 AAATAA
41103341 AATAGAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (13 bp):
AAATAATTAAGAT
Found at i:41106557 original size:67 final size:68
Alignment explanation
Indices: 41106467--41106602 Score: 204
Period size: 67 Copynumber: 2.0 Consensus size: 68
41106457 ACAACATGCC
* *
41106467 AACAACAATTTAAGCACTCCAATACCTCATCCT-ACCTTAAATCAATACTTTTTTACTATAAGCT
1 AACAACAATTTAAGCACTCCAATACCTCAT-CTAACCTTAAATCAATAATTTATTACTATAAGCT
41106531 AATT
65 AATT
* * *
41106535 AACATCAATTTAA-CACTCCAATACTTCATGTAACCTTAAATCAATAATTTATTACTATAAGCTA
1 AACAACAATTTAAGCACTCCAATACCTCATCTAACCTTAAATCAATAATTTATTACTATAAGCTA
41106599 ATT
66 ATT
41106602 A
1 A
41106603 CCTATTGTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
66 1 0.02
67 49 0.79
68 12 0.19
ACGTcount: A:0.40, C:0.22, G:0.03, T:0.35
Consensus pattern (68 bp):
AACAACAATTTAAGCACTCCAATACCTCATCTAACCTTAAATCAATAATTTATTACTATAAGCTA
ATT
Found at i:41120372 original size:24 final size:25
Alignment explanation
Indices: 41120345--41120392 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41120335 TAAAAAATAT
*
41120345 AATAAA-ATGAAAAATTAATTAAAC
1 AATAAACATGAAAAATAAATTAAAC
*
41120369 AATAAACATTAAAAATAAATTAAA
1 AATAAACATGAAAAATAAATTAAA
41120393 AAATCTAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (25 bp):
AATAAACATGAAAAATAAATTAAAC
Found at i:41120583 original size:14 final size:16
Alignment explanation
Indices: 41120553--41120584 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
41120543 AAATTTGAAA
41120553 TTTTATTGTTATGTCT
1 TTTTATTGTTATGTCT
41120569 TTTTATT-TT-TGTCT
1 TTTTATTGTTATGTCT
41120583 TT
1 TT
41120585 CGTATTTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 2 0.12
16 7 0.44
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.75
Consensus pattern (16 bp):
TTTTATTGTTATGTCT
Found at i:41125650 original size:50 final size:50
Alignment explanation
Indices: 41125533--41125766 Score: 206
Period size: 50 Copynumber: 4.6 Consensus size: 50
41125523 ACATTCAAAA
* * * *
41125533 CCATGTCCCAGACATGGTCTTACATGGGA-TGTTTCTTGTAC--TGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGAGACT-TCTCATAT-CGGTGCCAATG
* * * *
41125582 CCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGTGCCTATG
1 CCATGTCCCAGACATGGTCTTACATGAGACTTCTCATATCGGTGCCAATG
* * * * * *
41125632 CCATGTCCTAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGAGACTTCTCATATCGGTGCCAATG
* * *
41125682 CCATGTCCCAAACATGGTCTTACA-AAGGACTTCTCATAATCTCAATGATGCCAATG
1 CCATGTCCCAGACATGGTCTTACATGA-GACTTCTCAT-A--TC---GGTGCCAATG
41125738 CCATGTCCCAGACATGGTCTTACATGAGA
1 CCATGTCCCAGACATGGTCTTACATGAGA
41125767 TCTCTTTACC
Statistics
Matches: 147, Mismatches: 27, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
48 1 0.01
49 31 0.21
50 79 0.54
53 1 0.01
56 34 0.23
57 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (50 bp):
CCATGTCCCAGACATGGTCTTACATGAGACTTCTCATATCGGTGCCAATG
Found at i:41125716 original size:100 final size:102
Alignment explanation
Indices: 41125533--41125761 Score: 250
Period size: 100 Copynumber: 2.2 Consensus size: 102
41125523 ACATTCAAAA
* ** * * * * *
41125533 CCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTACTGCCAATGCCATATCCCAGATATG
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTACTGCCAATGCCATATCCCAAACATG
* * * *
41125598 GTCTTACATGAGAGTTCTCAT-A-TC-GGTGCCTATG
66 GTCTTACAAGAGACTTCTCATAACTCAGATGCCAATG
* * *
41125632 CCATGTCCTAGACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAATGCCATGTCCCAAACAT
1 CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTA-CTGCCAATGCCATATCCCAAACAT
41125697 GGTCTTACAA-AGGACTTCTCATAATCTCAATGATGCCAATG
65 GGTCTTACAAGA-GACTTCTCATAA-CTC-A-GATGCCAATG
41125738 CCATGTCCCAGACATGGTCTTACA
1 CCATGTCCCAGACATGGTCTTACA
41125762 TGAGATCTCT
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
99 34 0.32
100 38 0.36
101 1 0.01
103 2 0.02
106 31 0.29
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (102 bp):
CCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTACTGCCAATGCCATATCCCAAACATG
GTCTTACAAGAGACTTCTCATAACTCAGATGCCAATG
Found at i:41127807 original size:25 final size:25
Alignment explanation
Indices: 41127779--41127827 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
41127769 AGTTGCCTGA
* *
41127779 AAAGCCTATGTGGTGTATTATTTGG
1 AAAGCCTACGTGGCGTATTATTTGG
41127804 AAAGCCTACGTGGCGTATTATTTG
1 AAAGCCTACGTGGCGTATTATTTG
41127828 AAAAACCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (25 bp):
AAAGCCTACGTGGCGTATTATTTGG
Found at i:41127842 original size:25 final size:25
Alignment explanation
Indices: 41127776--41127835 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
41127766 GTGAGTTGCC
* * *
41127776 TGAAAAGCCTATGTGGTGTATTATT
1 TGAAAAACCTACGTGGCGTATTATT
* *
41127801 TGGAAAGCCTACGTGGCGTATTATT
1 TGAAAAACCTACGTGGCGTATTATT
41127826 TGAAAAACCT
1 TGAAAAACCT
41127836 TAGTGGCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (25 bp):
TGAAAAACCTACGTGGCGTATTATT
Found at i:41135142 original size:15 final size:16
Alignment explanation
Indices: 41135122--41135155 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41135112 TTCCCAAACC
*
41135122 TATTCGTT-TGTGAAT
1 TATTCGTTAAGTGAAT
41135137 TATTCGTTAAGTGAAT
1 TATTCGTTAAGTGAAT
41135153 TAT
1 TAT
41135156 GCTTGGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.26, C:0.06, G:0.18, T:0.50
Consensus pattern (16 bp):
TATTCGTTAAGTGAAT
Found at i:41136500 original size:45 final size:45
Alignment explanation
Indices: 41136350--41136524 Score: 199
Period size: 45 Copynumber: 3.9 Consensus size: 45
41136340 ATGCTTTCAT
* * *
41136350 ATGATGCCATAACATCTTTTAGCTATGGTCTTACTCATTTTAATC
1 ATGACGCCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
** * * * **
41136395 ATGACGCTGTATCCTCCTTCAATTATGGTCTTACTCA-TTTTATC
1 ATGACGCCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
***
41136439 ATGACATGATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
1 ATGACGCCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
* * *
41136484 GTGACGCCATAGCATCTTTTAGCTATGGTCTTACTCATTTT
1 ATGACGCCATAACATCTTTCAGCTATGGTCTTACTCATTTT
41136525 ACGTGTATAG
Statistics
Matches: 104, Mismatches: 25, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
44 34 0.33
45 70 0.67
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (45 bp):
ATGACGCCATAACATCTTTCAGCTATGGTCTTACTCATTTTTATC
Found at i:41136511 original size:89 final size:89
Alignment explanation
Indices: 41136358--41136525 Score: 237
Period size: 89 Copynumber: 1.9 Consensus size: 89
41136348 ATATGATGCC
* ** * * *
41136358 ATAACATCTTTTAGCTATGGTCTTACTCATTTTAATCATGACGCTGTATCCTCCTTCAATTATGG
1 ATAACATCTTTCAGCTATGGTCTTACTCATTTTAATCATGACGCCATAGCATCCTTCAACTATGG
41136423 TCTTACTCATTTTATCATGACATG
66 TCTTACTCATTTTATCATGACATG
* * * * *
41136447 ATAACATCTTTCAGCTATGGTCTTACTCATTTTTATCGTGACGCCATAGCATCTTTTAGCTATGG
1 ATAACATCTTTCAGCTATGGTCTTACTCATTTTAATCATGACGCCATAGCATCCTTCAACTATGG
41136512 TCTTACTCATTTTA
66 TCTTACTCATTTTA
41136526 CGTGTATAGC
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
89 68 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.43
Consensus pattern (89 bp):
ATAACATCTTTCAGCTATGGTCTTACTCATTTTAATCATGACGCCATAGCATCCTTCAACTATGG
TCTTACTCATTTTATCATGACATG
Found at i:41139384 original size:13 final size:13
Alignment explanation
Indices: 41139366--41139394 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
41139356 CATTGAGTAT
41139366 CAATGTCAATGGA
1 CAATGTCAATGGA
41139379 CAATGTCAATGGA
1 CAATGTCAATGGA
41139392 CAA
1 CAA
41139395 AAATTAATGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.21
Consensus pattern (13 bp):
CAATGTCAATGGA
Found at i:41142053 original size:20 final size:20
Alignment explanation
Indices: 41142028--41142079 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
41142018 TATGAACCAC
41142028 TCCATTTACTTACTTATCAT
1 TCCATTTACTTACTTATCAT
* *
41142048 TCCATTAACTTACTTTTCAT
1 TCCATTTACTTACTTATCAT
*
41142068 TTCATTTACTTA
1 TCCATTTACTTA
41142080 GCATAAGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (20 bp):
TCCATTTACTTACTTATCAT
Found at i:41143836 original size:421 final size:420
Alignment explanation
Indices: 41143053--41144311 Score: 2305
Period size: 415 Copynumber: 3.0 Consensus size: 420
41143043 GCTATTTGGT
*
41143053 AAATTTTCTCTTCTCCTCGATTTTCCACTCGTTCTCAATCTAAATTAATAATTTCATTCAATTCA
1 AAATTTTCTCTTCTCCTCGATTTTCCACTCATTCTCAATCTAAATTAATAATTTCATTCAATTCA
* * *
41143118 TTAATTTAGATAGTAAATCCAATTCGTTTTATGCAATTTAGTCATTTTTTATA-TTTTATAAAAT
66 TTAATTTAGATAGTAAATCTAATTCATTTTATGCAATTTAGTCATTTTCTATATTTTTATAAAAT
**
41143182 TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCTATGTCCCAATGACTAAGTACAGGGGCTA
131 TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCTATGTCCCAATGACTAAGTACAATGGCTA
41143247 GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
196 GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
41143312 ACATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
261 ACATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
41143377 AAGAAAGACATAAGTAGAAAAATGTTTTTGCTGTTCTTTTTTATTTATTACCTAATTATTTACTT
326 AAGAAAGACATAAGTAGAAAAATGTTTTTGCTGTTC-TTTTTATTTATTACCTAATTATTTACTT
*
41143442 TAATATTATTAAAAATATACCATATCATTAA
390 TAATATCATTAAAAATATACCATATCATTAA
41143473 AAATTTTCTCTTCTCCTCGATTTTCCACTCATTCTCAATCTAAATTAATAATTTCATTCAATTCA
1 AAATTTTCTCTTCTCCTCGATTTTCCACTCATTCTCAATCTAAATTAATAATTTCATTCAATTCA
*
41143538 TTAATTTAGATAGTAAATCTAATTCATTTTATGCAATTTAGTCATTTTCTATATTTTTATAAAAC
66 TTAATTTAGATAGTAAATCTAATTCATTTTATGCAATTTAGTCATTTTCTATATTTTTATAAAAT
41143603 TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCTATGTCCCAATGACTAAGTACAATGGCTA
131 TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCTATGTCCCAATGACTAAGTACAATGGCTA
41143668 GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
196 GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
*
41143733 ATATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
261 ACATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
*
41143798 AAGAAAGACATAAGTAGAAAAATGTTTTTGCTGTTCTTTTTACTTATTACCTAATTATTTACTTT
326 AAGAAAGACATAAGTAGAAAAATGTTTTTGCTGTTCTTTTTATTTATTACCTAATTATTTACTTT
41143863 AATATCATT---AA-A-ACCATATCATTAA
391 AATATCATTAAAAATATACCATATCATTAA
*
41143888 AAATTTTCTCTTCTCCTCGATTTTCCACTCATTCTCAATCTAAATTAATAATTTCATTTAATTCA
1 AAATTTTCTCTTCTCCTCGATTTTCCACTCATTCTCAATCTAAATTAATAATTTCATTCAATTCA
*
41143953 TTAATTTAGATAGTAAATCTAATTTATTTTATGCAATTTAGTCATTTTCTATATTTTTATAAAAT
66 TTAATTTAGATAGTAAATCTAATTCATTTTATGCAATTTAGTCATTTTCTATATTTTTATAAAAT
*
41144018 TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCAATGTCCCAATGACTAAGTACAATGGCTA
131 TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCTATGTCCCAATGACTAAGTACAATGGCTA
41144083 GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
196 GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
41144148 ACATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
261 ACATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
* *
41144213 AAGAAAGACATAAGCAAAAAAATGTTTTTGCTGTTCTTTTTATTTATTACCTAATTATTTACTTT
326 AAGAAAGACATAAGTAGAAAAATGTTTTTGCTGTTCTTTTTATTTATTACCTAATTATTTACTTT
* *
41144278 AATATCATTAAAAATATATCATATAAATTAA
391 AATATCATTAAAAATATACCATAT-CATTAA
41144309 AAA
1 AAA
41144312 AAATTAGGCA
Statistics
Matches: 812, Mismatches: 20, Indels: 13
0.96 0.02 0.02
Matches are distributed among these distances:
415 404 0.50
416 1 0.00
417 2 0.00
418 2 0.00
419 1 0.00
420 156 0.19
421 246 0.30
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (420 bp):
AAATTTTCTCTTCTCCTCGATTTTCCACTCATTCTCAATCTAAATTAATAATTTCATTCAATTCA
TTAATTTAGATAGTAAATCTAATTCATTTTATGCAATTTAGTCATTTTCTATATTTTTATAAAAT
TACCCTCAACTTTTCATTTTTATTCAATTTAGTCCCTATGTCCCAATGACTAAGTACAATGGCTA
GCTGGACCTAGTTGCAACAATCTCAAAAACATAAAAATTACAAGAAATGGATAAGACTATCACCT
ACATGCAACACTTGAATGTTGGTCGAATGTCTCTTGCTCCAAAAATGGAGTTCTCACGGTTGAAG
AAGAAAGACATAAGTAGAAAAATGTTTTTGCTGTTCTTTTTATTTATTACCTAATTATTTACTTT
AATATCATTAAAAATATACCATATCATTAA
Found at i:41147478 original size:7 final size:7
Alignment explanation
Indices: 41147466--41147518 Score: 106
Period size: 7 Copynumber: 7.6 Consensus size: 7
41147456 AATTAATTAA
41147466 TTTTATT
1 TTTTATT
41147473 TTTTATT
1 TTTTATT
41147480 TTTTATT
1 TTTTATT
41147487 TTTTATT
1 TTTTATT
41147494 TTTTATT
1 TTTTATT
41147501 TTTTATT
1 TTTTATT
41147508 TTTTATT
1 TTTTATT
41147515 TTTT
1 TTTT
41147519 TCATAAATTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:41156434 original size:2 final size:2
Alignment explanation
Indices: 41156427--41156468 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
41156417 GCTTGTGAAA
41156427 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
41156469 CATATGTACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41158451 original size:56 final size:56
Alignment explanation
Indices: 41158341--41158452 Score: 129
Period size: 57 Copynumber: 2.0 Consensus size: 56
41158331 TTGGGTCCCA
* * *
41158341 ATTTTTTTTTTTTTGAGACACTGATGGCTAGCACCAACTTTATTAAATTAAAAAAT
1 ATTTTTTTTGTTTTGAGACACTGATGGCTAGCACCAACCTTATCAAATTAAAAAAT
* * *
41158397 ATTTTTTTTGGTTTTGGGATACTGATGG-T-GACACCAACCTTATCAGATTTAAAAAA
1 ATTTTTTTT-GTTTTGAGACACTGATGGCTAG-CACCAACCTTATCA-AATTAAAAAA
41158453 AATGGTTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.02
56 22 0.47
57 24 0.51
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.41
Consensus pattern (56 bp):
ATTTTTTTTGTTTTGAGACACTGATGGCTAGCACCAACCTTATCAAATTAAAAAAT
Found at i:41163245 original size:20 final size:20
Alignment explanation
Indices: 41163220--41163261 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
41163210 CTGATAACTA
*
41163220 CCGTTCACCATCGATCACTG
1 CCGTTCACCATCAATCACTG
*
41163240 CCGTTCACCGTCAATCACTG
1 CCGTTCACCATCAATCACTG
41163260 CC
1 CC
41163262 AATCACCTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.43, G:0.14, T:0.24
Consensus pattern (20 bp):
CCGTTCACCATCAATCACTG
Found at i:41165190 original size:89 final size:89
Alignment explanation
Indices: 41165110--41165422 Score: 452
Period size: 89 Copynumber: 3.5 Consensus size: 89
41165100 TCGAAAAATT
* * *
41165110 AATAATACGCAAC-AAATTAAATTTACAGATACAAGAAAATACAAACATTCTAGAATATTAATAC
1 AATAATACG-AACTAAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAAAATTAATAC
41165174 ATGAAAATATAAAATTCAAACAACA
65 ATGAAAATATAAAATTCAAACAACA
* ** * *
41165199 AATAATACGAGCTAAATTAAATTTACAGACCCAAAAAAATACGACCATTCTAAAAAATTAATACA
1 AATAATACGAACTAAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAAAATTAATACA
*
41165264 CGAAAATATAAAATTCAAACAACA
66 TGAAAATATAAAATTCAAACAACA
*
41165288 AATAATACGGACTAAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAAAATTAATACA
1 AATAATACGAACTAAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAAAATTAATAC-
*
41165353 AT-AAAATATAAAATTCGAACAACA
65 ATGAAAATATAAAATTCAAACAACA
**
41165377 AATAATAC-AGACTAAATTTGATTTACAGATACAAAAATAATACAAA
1 AATAATACGA-ACTAAATTAAATTTACAGATACAAAAA-AATACAAA
41165423 AATTTTGAAT
Statistics
Matches: 200, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
88 2 0.01
89 189 0.94
90 9 0.05
ACGTcount: A:0.58, C:0.14, G:0.05, T:0.23
Consensus pattern (89 bp):
AATAATACGAACTAAATTAAATTTACAGATACAAAAAAATACAAACATTCTAAAAAATTAATACA
TGAAAATATAAAATTCAAACAACA
Found at i:41165385 original size:33 final size:32
Alignment explanation
Indices: 41165316--41165385 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
41165306 AAATTTACAG
* *
41165316 ATACAAAAAAATACAAACATTCTAAAAAATTA
1 ATACAAAAAAATACAAACATTCGAAAAAAATA
* *
41165348 ATACAATAAAATATAAA-ATTCGAACAACAAATA
1 ATACAAAAAAATACAAACATTCGAA-AA-AAATA
41165381 ATACA
1 ATACA
41165386 GACTAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.19
32 17 0.53
33 9 0.28
ACGTcount: A:0.64, C:0.13, G:0.01, T:0.21
Consensus pattern (32 bp):
ATACAAAAAAATACAAACATTCGAAAAAAATA
Found at i:41165992 original size:53 final size:54
Alignment explanation
Indices: 41165914--41166028 Score: 160
Period size: 53 Copynumber: 2.1 Consensus size: 54
41165904 ATCAGTGGCC
* * * * **
41165914 CAAAAAAGAATTCGAGACCCGAAAAAGGTGGTGTCGGCCATCACTGTCTTAAAA
1 CAAAAAAAAATTCGAGACCCAAAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
*
41165968 CAAAAAAAAATT-GGGACCCAAAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
1 CAAAAAAAAATTCGAGACCCAAAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
41166021 CAAAAAAA
1 CAAAAAAA
41166029 TTCTCGAAAC
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
53 43 0.80
54 11 0.20
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.16
Consensus pattern (54 bp):
CAAAAAAAAATTCGAGACCCAAAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
Found at i:41166046 original size:53 final size:53
Alignment explanation
Indices: 41165914--41166046 Score: 144
Period size: 53 Copynumber: 2.5 Consensus size: 53
41165904 ATCAGTGGCC
* * * **
41165914 CAAAAAAGAATTCGAGACCCGAAAAAGGTGGTGTCGGCCATCACTGTCTTAAAA
1 CAAAAAAAAATTCGAGACCCG-AAAAGATGGTGTCGGCCATCAATGTCCCAAAA
* *
41165968 CAAAAAAAAATT-GGGACCCAAAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
1 CAAAAAAAAATTCGAGACCC-GAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
* *
41166021 C-AAAAAAATTCTCGAAACCCGAAAAG
1 CAAAAAAAAAT-TCGAGACCCGAAAAG
41166047 TGTGTTGGTG
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
52 8 0.12
53 41 0.63
54 16 0.25
ACGTcount: A:0.44, C:0.21, G:0.19, T:0.16
Consensus pattern (53 bp):
CAAAAAAAAATTCGAGACCCGAAAAGATGGTGTCGGCCATCAATGTCCCAAAA
Found at i:41166589 original size:27 final size:27
Alignment explanation
Indices: 41166526--41166594 Score: 77
Period size: 27 Copynumber: 2.6 Consensus size: 27
41166516 GTGGAGGGGA
* *
41166526 TGCCATAGGCGGCACCAGTTGTGCCAG
1 TGCCATAGGCGGCACCAGTGGTGCCAC
* * *
41166553 TGGCAGAGGCGGCACC-GATGGTGCCCC
1 TGCCATAGGCGGCACCAG-TGGTGCCAC
41166580 TGCCATAGGCGGCAC
1 TGCCATAGGCGGCAC
41166595 TGCCCCTATA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
26 1 0.03
27 33 0.97
ACGTcount: A:0.17, C:0.32, G:0.36, T:0.14
Consensus pattern (27 bp):
TGCCATAGGCGGCACCAGTGGTGCCAC
Found at i:41166666 original size:4 final size:4
Alignment explanation
Indices: 41166657--41166798 Score: 70
Period size: 4 Copynumber: 35.2 Consensus size: 4
41166647 GGGAAAGGAG
* * *
41166657 AAGA AAGA AAGA AAG- AA-A AATA AAGAA AAGGA AAGGA GATGA GAGGA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA -AAGA
*
41166704 AAGA AAG- AA-A AAGA AGGA AAGAA AAGGA AAG- AAG- AAGA AA-A AAGA
1 AAGA AAGA AAGA AAGA AAGA AAG-A AA-GA AAGA AAGA AAGA AAGA AAGA
*
41166749 AAG- AA-A AAGA AGGA AAGAA AATGA AATGA GAAGA AA-A AAGA AAGA
1 AAGA AAGA AAGA AAGA AAG-A AA-GA AA-GA -AAGA AAGA AAGA AAGA
41166794 AAGA A
1 AAGA A
41166799 GAAGAAGAGG
Statistics
Matches: 113, Mismatches: 8, Indels: 34
0.73 0.05 0.22
Matches are distributed among these distances:
3 24 0.21
4 51 0.45
5 32 0.28
6 6 0.05
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (4 bp):
AAGA
Found at i:41166746 original size:31 final size:31
Alignment explanation
Indices: 41166651--41166831 Score: 108
Period size: 31 Copynumber: 5.7 Consensus size: 31
41166641 AGGAGAGGGA
*
41166651 AAGGAGAAGAAAGAAAGAAAGAAAA-ATAAAGAA-
1 AAGGA-AAG-AAGAAGGAAAGAAAAGA-AAA-AAG
41166684 AAGGAAAGGAGATGAGAGGAAAG-AAAG-AAAAAG
1 AAGGAAA-GA-A-GA-AGGAAAGAAAAGAAAAAAG
41166717 AAGGAAAGAA-AAGGAAAGAAGAAGAAAAAAG
1 AAGGAAAGAAGAAGGAAAGAA-AAGAAAAAAG
* **
41166748 AAAGAAA-AAGAAGGAAAGAAAATGAAATGAG
1 AAGGAAAGAAGAAGGAAAGAAAA-GAAAAAAG
* * * **
41166779 AA-GAAAAAAGAAAGAAAGAAGAAGAAGAGGG
1 AAGGAAAGAAGAAGGAAAGAA-AAGAAAAAAG
* *
41166810 AAGGAAGGAA-AAAGAAAGAAAA
1 AAGGAAAGAAGAAGGAAAGAAAA
41166832 AAAGGTGATT
Statistics
Matches: 124, Mismatches: 10, Indels: 31
0.75 0.06 0.19
Matches are distributed among these distances:
28 7 0.06
29 2 0.02
30 13 0.10
31 60 0.48
32 14 0.11
33 17 0.14
34 5 0.04
35 6 0.05
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (31 bp):
AAGGAAAGAAGAAGGAAAGAAAAGAAAAAAG
Found at i:41166832 original size:10 final size:10
Alignment explanation
Indices: 41166664--41166832 Score: 71
Period size: 10 Copynumber: 16.3 Consensus size: 10
41166654 GAGAAGAAAG
41166664 AAAGAAAGAA
1 AAAGAAAGAA
*
41166674 AAATAAAGAA
1 AAAGAAAGAA
* *
41166684 AAGGAAAGGA
1 AAAGAAAGAA
* * * *
41166694 GATGAGAG-G
1 AAAGAAAGAA
41166703 AAAGAAAGAA
1 AAAGAAAGAA
*
41166713 AAAGAAGGAA
1 AAAGAAAGAA
*
41166723 AGAA-AAGGAA
1 A-AAGAAAGAA
41166733 AGAAG-AAGAAA
1 A-AAGAAAG-AA
41166744 AAAGAAAGAA
1 AAAGAAAGAA
*
41166754 AAAGAAGGAA
1 AAAGAAAGAA
*
41166764 AGAA-AATG-A
1 A-AAGAAAGAA
*
41166773 AATGAGAAGAAA
1 AAAGA-AAG-AA
41166785 AAAGAAAGAA
1 AAAGAAAGAA
41166795 AGAAG-AAGAA
1 A-AAGAAAGAA
*
41166805 GAGGGAAGGAAGGAA
1 -A---AA-GAAAGAA
41166820 AAAGAAAGAA
1 AAAGAAAGAA
41166830 AAA
1 AAA
41166833 AAGGTGATTT
Statistics
Matches: 122, Mismatches: 21, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
8 1 0.01
9 8 0.07
10 80 0.66
11 19 0.16
12 5 0.04
13 3 0.02
14 2 0.02
15 4 0.03
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.02
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:41167397 original size:16 final size:15
Alignment explanation
Indices: 41167371--41167400 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41167361 GTACTGAAAT
41167371 AATATAAAATAATAA
1 AATATAAAATAATAA
41167386 AATATGAAAATAATA
1 AATAT-AAAATAATA
41167401 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:41167534 original size:155 final size:155
Alignment explanation
Indices: 41167162--41167590 Score: 552
Period size: 155 Copynumber: 2.7 Consensus size: 155
41167152 AAAAATGGTA
* *
41167162 TATTTAAAAAACACACTAAATTAATAAATTTCAAATATAATGTACTGAAATAATTTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATA
* *
41167227 AAATTAGAAAATATGATA-TTTT-TT-AAAGTAATAAAATGCGGAGAAAAAAATACGAACAAAGG
66 AAATTAGAAAATATGATATTTTTATTGAAAGTAATAAAATTCGG-GAAAATAATACGAACAAAGG
* *
41167289 GCCGAAGTAAGAGTTTTTTACTAAATT
130 GACGAAGTAAGAGGTTTTTAC-AAATT
* * *
41167316 T-TTTAAAAATTCAGA-TATAATTAATACAAATATTTCAAACAAAATGTACTGAAATAATATAAA
1 TATTTAAAAA-ACACACTA-AATTAAT---AA-ATTTCAAACATAATGTACTGAAATAATATAAA
41167379 ATAATAAAA-TATGAAAATAAT-ATATTTTTATTGAAAGTAATAAAATTCGGGAAAATAATACGA
60 ATAATAAAATTA-GAAAAT-ATGATATTTTTATTGAAAGTAATAAAATTCGGGAAAATAATACGA
** * *
41167442 GTAAAGGGTAGGAA-TAAGGGGGTTTTTA-AAATT
123 ACAAAGGG-ACGAAGTAA-GAGGTTTTTACAAATT
*
41167475 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATGTAAAATAATA
1 TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATA
*
41167540 AAATTAGAAAATATGATATTTTTATTGAAAGTAATAAAATTCGAGAAAATA
66 AAATTAGAAAATATGATATTTTTATTGAAAGTAATAAAATTCGGGAAAATA
41167591 GTACAAATAA
Statistics
Matches: 240, Mismatches: 18, Indels: 33
0.82 0.06 0.11
Matches are distributed among these distances:
153 10 0.04
154 13 0.05
155 80 0.33
156 4 0.02
157 4 0.02
158 47 0.20
159 22 0.09
160 33 0.14
161 27 0.11
ACGTcount: A:0.52, C:0.06, G:0.11, T:0.31
Consensus pattern (155 bp):
TATTTAAAAAACACACTAAATTAATAAATTTCAAACATAATGTACTGAAATAATATAAAATAATA
AAATTAGAAAATATGATATTTTTATTGAAAGTAATAAAATTCGGGAAAATAATACGAACAAAGGG
ACGAAGTAAGAGGTTTTTACAAATT
Found at i:41171505 original size:10 final size:10
Alignment explanation
Indices: 41171477--41171512 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
41171467 AAATATCTTT
41171477 TTTTTCTCTTC
1 TTTTTCTC-TC
*
41171488 TCTTTCTCTC
1 TTTTTCTCTC
41171498 TTTTTCTCTC
1 TTTTTCTCTC
41171508 TTTTT
1 TTTTT
41171513 TCCGGTAGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTTCTCTC
Found at i:41171512 original size:11 final size:11
Alignment explanation
Indices: 41171472--41171514 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
41171462 TAAAAAAATA
*
41171472 TCTTTTTTTTC
1 TCTTTTTTCTC
41171483 TCTTCTCTTTCTC
1 TCTT-T-TTTCTC
41171496 TC-TTTTTCTC
1 TCTTTTTTCTC
41171506 TCTTTTTTC
1 TCTTTTTTC
41171515 CGGTAGCACC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 8 0.29
11 11 0.39
12 2 0.07
13 7 0.25
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:41171540 original size:3 final size:3
Alignment explanation
Indices: 41171534--41171558 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41171524 CTCCTCTTTC
41171534 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
41171559 ATTTTTCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:41171815 original size:14 final size:14
Alignment explanation
Indices: 41171780--41171816 Score: 53
Period size: 11 Copynumber: 2.9 Consensus size: 14
41171770 TAATTTTTTA
41171780 TTTTGGGATTAATT
1 TTTTGGGATTAATT
41171794 TTTT---ATTAATT
1 TTTTGGGATTAATT
41171805 TTTTGGGATTAA
1 TTTTGGGATTAA
41171817 ATGAGTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
11 11 0.55
14 9 0.45
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.59
Consensus pattern (14 bp):
TTTTGGGATTAATT
Found at i:41172041 original size:20 final size:18
Alignment explanation
Indices: 41172008--41172046 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
41171998 ATTTAATCCA
*
41172008 TTGAATCTAGATAAGGTT
1 TTGAATCTAGATAAAGTT
41172026 TTGACATCTCAGATAAAGTT
1 TTGA-ATCT-AGATAAAGTT
41172046 T
1 T
41172047 AAAATAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 4 0.22
20 10 0.56
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (18 bp):
TTGAATCTAGATAAAGTT
Found at i:41173687 original size:11 final size:11
Alignment explanation
Indices: 41173671--41173728 Score: 59
Period size: 11 Copynumber: 5.4 Consensus size: 11
41173661 TATTTTTTAA
41173671 TTTTAAAATAT
1 TTTTAAAATAT
41173682 TTTTAAAATACT
1 TTTTAAAATA-T
* *
41173694 TTTT---TTAA
1 TTTTAAAATAT
41173702 TTTTAAAATAT
1 TTTTAAAATAT
41173713 TTTTAAAATACT
1 TTTTAAAATA-T
41173725 TTTT
1 TTTT
41173729 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
8 4 0.11
9 2 0.05
11 22 0.58
12 10 0.26
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:41173701 original size:31 final size:31
Alignment explanation
Indices: 41173663--41173730 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
41173653 AATATATTTA
41173663 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
41173694 TTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAATTTTAAAATATTTTTAAAATACT
41173725 TTTTTT
1 TTTTTT
41173731 TTATTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:41173738 original size:41 final size:41
Alignment explanation
Indices: 41173693--41173771 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
41173683 TTTAAAATAC
41173693 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
41173734 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
1 TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTT
41173772 AATTTTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (41 bp):
TTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTTTTA
Found at i:41173797 original size:21 final size:21
Alignment explanation
Indices: 41173751--41173808 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
41173741 AATTTTAAAA
* **
41173751 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTGG
41173771 TAATTTTTAAAATAAATTTTGG
1 T-ATTTTTAAAATAAATTTTGG
41173793 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
41173809 AGGCAGGGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.03
21 19 0.59
22 12 0.38
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.53
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTGG
Found at i:41175717 original size:34 final size:34
Alignment explanation
Indices: 41175679--41175747 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
41175669 AATTATAAAG
41175679 ATATATTTGATCATGGTATTTTAATTACTGTCTA
1 ATATATTTGATCATGGTATTTTAATTACTGTCTA
*
41175713 ATATATTTGATCATGGTATTTTGATTACTGTCTA
1 ATATATTTGATCATGGTATTTTAATTACTGTCTA
41175747 A
1 A
41175748 AGTTTGTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.13, T:0.49
Consensus pattern (34 bp):
ATATATTTGATCATGGTATTTTAATTACTGTCTA
Found at i:41177761 original size:23 final size:21
Alignment explanation
Indices: 41177735--41177775 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
41177725 AATTAAATTA
41177735 TATATATTATGATTTTAGTAT
1 TATATATTATGATTTTAGTAT
41177756 TATATATTATGATTTTAGTA
1 TATATATTATGATTTTAGTA
41177776 AATTCATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (21 bp):
TATATATTATGATTTTAGTAT
Found at i:41177941 original size:120 final size:120
Alignment explanation
Indices: 41177750--41178099 Score: 664
Period size: 120 Copynumber: 2.9 Consensus size: 120
41177740 ATTATGATTT
*
41177750 TAGTATTATATATTATGATTTTAGTAAATTCATATAAAAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
41177815 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
* *
41177870 TATTATTATATATTATGATTTTAGTAAATTTATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
41177935 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
41177990 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
41178055 ATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAA
41178100 ATATGATTAA
Statistics
Matches: 224, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 224 1.00
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
Found at i:41178337 original size:16 final size:16
Alignment explanation
Indices: 41178318--41178381 Score: 119
Period size: 16 Copynumber: 4.0 Consensus size: 16
41178308 ACTATTACGC
41178318 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
*
41178334 CTCTATTCCATTACAC
1 CTCTATTCCATTACAG
41178350 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
41178366 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
41178382 TGAACCAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.25, C:0.33, G:0.05, T:0.38
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:41178353 original size:32 final size:32
Alignment explanation
Indices: 41178311--41178380 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
41178301 TTGAATTACT
*
41178311 ATTACGCCTCTATTCCATTACAGCTCTATTCC
1 ATTACACCTCTATTCCATTACAGCTCTATTCC
41178343 ATTACACCTCTATTCCATTACAGCTCTATTCC
1 ATTACACCTCTATTCCATTACAGCTCTATTCC
41178375 ATTACA
1 ATTACA
41178381 GTGAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.33, G:0.04, T:0.37
Consensus pattern (32 bp):
ATTACACCTCTATTCCATTACAGCTCTATTCC
Found at i:41184617 original size:17 final size:17
Alignment explanation
Indices: 41184597--41184629 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41184587 TTTTTTAGGG
41184597 TTTTTCAAATTTTTATT
1 TTTTTCAAATTTTTATT
41184614 TTTTTCAAATTTTTAT
1 TTTTTCAAATTTTTAT
41184630 GATATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTCAAATTTTTATT
Found at i:41185546 original size:16 final size:16
Alignment explanation
Indices: 41185525--41185558 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
41185515 TGATTAGCAA
41185525 AATCGAAGAATTCCCT
1 AATCGAAGAATTCCCT
41185541 AATCGAAGAATTCCCT
1 AATCGAAGAATTCCCT
41185557 AA
1 AA
41185559 CTCTTACTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.24, G:0.12, T:0.24
Consensus pattern (16 bp):
AATCGAAGAATTCCCT
Found at i:41185812 original size:56 final size:55
Alignment explanation
Indices: 41185726--41185833 Score: 198
Period size: 56 Copynumber: 1.9 Consensus size: 55
41185716 GTATCCATTG
*
41185726 GATGATAAATCATCACTTTTAATTTGAATAGTGCTTATGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATT-AATTTGTAA
41185782 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTG
41185834 CAATCTATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
55 6 0.12
56 45 0.88
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTGTAA
Found at i:41187503 original size:477 final size:477
Alignment explanation
Indices: 41186609--41187566 Score: 1745
Period size: 477 Copynumber: 2.0 Consensus size: 477
41186599 CCACAACTTT
41186609 ATATCTAACAAGAGATCTCTTAGCCATTCCGCTTCCTTGCCAGTAGCTGCTAAGGCTATAAATTC
1 ATATCTAACAAGAGATCTCTTAGCCATTCCGCTTCCTTGCCAGTAGCTGCTAAGGCTATAAATTC
* * *
41186674 AGCCTCCATAGTTGAATGTGATATGCATGTTTGTTTCTTGGAGGCCCAACTAATGACTCTACCTC
66 AGCCTCCATAGTTGAATGTGATATGCAAGTTTGGTTCTTGGAGGCCCAACTAATGACTCCACCTC
41186739 CAATTGTAAAAATTCATCCCGATGTGAACTTATTGTCACTTAGACTTGTAATCCAACTTGCATCC
131 CAATTGTAAAAATTCATCCCGATGTGAACTTATTGTCACTTAGACTTGTAATCCAACTTGCATCC
*
41186804 GAGTAACCTTCTAGTACTGCGGGATAATCACTATAGAATAATCCAAAATTATTTATTTTCTTAAG
196 GAGTAACCTTCTAGTACTCCGGGATAATCACTATAGAATAATCCAAAATTATTTATTTTCTTAAG
*
41186869 ATAGCCAAAAATTCTACAAATGCCTTTCCAATGATCGGTACAAGGACAATTTGTAAATCTCGCTA
261 ATAGCCAAAAATTCTACAAATGCCTTTCCAATGATCGGTACAAGGACAATTTGTAAATCTCGCCA
* * *
41186934 ATTTGCACACAACAAATGTGATATTAGGTCTAGTACAATGCATTGCATACATTAGACTTCCGATT
326 ATTTGCACACAACAAATGCGATATCAGGTCTAGTACAATGCATTGAATACATTAGACTTCCGATT
** *
41186999 ATGCTGGCGTACTCAAGTTGCGATATAGCCCTGCCATTATTCTCACTTAACTTGAAGTTCGAATC
391 ACACTGGCGTACTCAAGTTGCGATATAGCCATGCCATTATTCTCACTTAACTTGAAGTTCGAATC
* *
41187064 GTATGGAGTGTTCGAATCCTTG
456 GTATGGAATGTTCAAATCCTTG
*
41187086 ATATCTAACAAGAGATCTCTTAGCCATTTCGCTTCCTTGCCAGTAGCTGCTAAGGCTATAAATTC
1 ATATCTAACAAGAGATCTCTTAGCCATTCCGCTTCCTTGCCAGTAGCTGCTAAGGCTATAAATTC
41187151 AGCCTCCATAGTTGAATGTGATATGCAAGTTTGGTTCTTGGAGGCCCAACTAATGACTCCACCTC
66 AGCCTCCATAGTTGAATGTGATATGCAAGTTTGGTTCTTGGAGGCCCAACTAATGACTCCACCTC
41187216 CAATTGTAAAAATTCATCCCGATGTGAACTTATTGTCACTTAGACTTGTAATCCAACTTGCATCC
131 CAATTGTAAAAATTCATCCCGATGTGAACTTATTGTCACTTAGACTTGTAATCCAACTTGCATCC
41187281 GAGTAACCTTCTAGTACTCCGGGATAATCACTATAGAATAATCCAAAATTATTTATTTTCTTAAG
196 GAGTAACCTTCTAGTACTCCGGGATAATCACTATAGAATAATCCAAAATTATTTATTTTCTTAAG
* *
41187346 TTAGCCAAAAATTCTACAAATGCCTTTCCAATTATCGGTACAAGGACAATTTGTAAATCTCGCCA
261 ATAGCCAAAAATTCTACAAATGCCTTTCCAATGATCGGTACAAGGACAATTTGTAAATCTCGCCA
*
41187411 ATTTGCACACAACAAATGCGATATCAGGTCTAGTACAATGCATTGAATACATTAGACTTCTGATT
326 ATTTGCACACAACAAATGCGATATCAGGTCTAGTACAATGCATTGAATACATTAGACTTCCGATT
*
41187476 GCACTGGCGTACTCAAGTTGCGATATAGCCATGCCATTATTCTCACTTAACTTGAAGTTCGAATC
391 ACACTGGCGTACTCAAGTTGCGATATAGCCATGCCATTATTCTCACTTAACTTGAAGTTCGAATC
*
41187541 GTATGTAATGTTCAAATCCTTG
456 GTATGGAATGTTCAAATCCTTG
41187563 ATAT
1 ATAT
41187567 TCAAGTGTTT
Statistics
Matches: 462, Mismatches: 19, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
477 462 1.00
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.32
Consensus pattern (477 bp):
ATATCTAACAAGAGATCTCTTAGCCATTCCGCTTCCTTGCCAGTAGCTGCTAAGGCTATAAATTC
AGCCTCCATAGTTGAATGTGATATGCAAGTTTGGTTCTTGGAGGCCCAACTAATGACTCCACCTC
CAATTGTAAAAATTCATCCCGATGTGAACTTATTGTCACTTAGACTTGTAATCCAACTTGCATCC
GAGTAACCTTCTAGTACTCCGGGATAATCACTATAGAATAATCCAAAATTATTTATTTTCTTAAG
ATAGCCAAAAATTCTACAAATGCCTTTCCAATGATCGGTACAAGGACAATTTGTAAATCTCGCCA
ATTTGCACACAACAAATGCGATATCAGGTCTAGTACAATGCATTGAATACATTAGACTTCCGATT
ACACTGGCGTACTCAAGTTGCGATATAGCCATGCCATTATTCTCACTTAACTTGAAGTTCGAATC
GTATGGAATGTTCAAATCCTTG
Found at i:41192550 original size:120 final size:121
Alignment explanation
Indices: 41192333--41192572 Score: 464
Period size: 120 Copynumber: 2.0 Consensus size: 121
41192323 TATGATATCC
41192333 TTGATTCCTTTGAGTTAAATCTGTTCACTCAATACAATCCTATTTTATCTCATTATCACCATTGT
1 TTGATTCCTTTGAGTTAAATCTGTTCACTCAATACAATCCTATTTTATCTCATTATCACCATTGT
41192398 GTCTTCTTAATGATTAATATAATCACTATCAACAAATGATTGTGATAAATTACTCG
66 GTCTTCTTAATGATTAATATAATCACTATCAACAAATGATTGTGATAAATTACTCG
41192454 TTGATTCCTTTGAGTTAAAT-TGTTCACTCAATACAATCCTATTTTATCTCATTATCACCATTGT
1 TTGATTCCTTTGAGTTAAATCTGTTCACTCAATACAATCCTATTTTATCTCATTATCACCATTGT
*
41192518 GTCTTCTTAATGATTAATATAATCACTGTCAACAAATGATTGTGATAAATTACTC
66 GTCTTCTTAATGATTAATATAATCACTATCAACAAATGATTGTGATAAATTACTC
41192573 TGTTCAAGAA
Statistics
Matches: 118, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
120 98 0.83
121 20 0.17
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (121 bp):
TTGATTCCTTTGAGTTAAATCTGTTCACTCAATACAATCCTATTTTATCTCATTATCACCATTGT
GTCTTCTTAATGATTAATATAATCACTATCAACAAATGATTGTGATAAATTACTCG
Found at i:41199299 original size:68 final size:68
Alignment explanation
Indices: 41199189--41199367 Score: 261
Period size: 68 Copynumber: 2.6 Consensus size: 68
41199179 GTTACACTAA
* * *
41199189 CTATGGTCTTAGACATTATAAAC-CTATGTTTAATGTCTTGGCGAACTCCATATGTTGCCATAAC
1 CTATGGTCTTAAACATTATGAACTC-ATGTTTAATGTCCTGGCGAACTCCATATGTTGCCATAAC
41199253 CTAG
65 CTAG
* *
41199257 CTATGGTCTTACACATTATGAACTCATGTTTAATGTCCTGGCGAACTCCATATGTTGCCATAGCC
1 CTATGGTCTTAAACATTATGAACTCATGTTTAATGTCCTGGCGAACTCCATATGTTGCCATAACC
*
41199322 TGG
66 TAG
** *
41199325 CTATGGTCTTAAACATTATGGGCTCATGTTTAAGGTCCTGGCG
1 CTATGGTCTTAAACATTATGAACTCATGTTTAATGTCCTGGCG
41199368 GACTTTTGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
68 100 0.99
69 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.35
Consensus pattern (68 bp):
CTATGGTCTTAAACATTATGAACTCATGTTTAATGTCCTGGCGAACTCCATATGTTGCCATAACC
TAG
Found at i:41210149 original size:14 final size:14
Alignment explanation
Indices: 41210130--41210160 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41210120 CAAACATTAG
41210130 GTTCCATCAGGTTT
1 GTTCCATCAGGTTT
41210144 GTTCCATCAGGTTT
1 GTTCCATCAGGTTT
41210158 GTT
1 GTT
41210161 ACAACCTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (14 bp):
GTTCCATCAGGTTT
Found at i:41211934 original size:20 final size:20
Alignment explanation
Indices: 41211901--41211938 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
41211891 TAACATGTCA
41211901 AAAATAAATAAAAATTTATG
1 AAAATAAATAAAAATTTATG
* *
41211921 AAAATTAATTAAAATTTA
1 AAAATAAATAAAAATTTA
41211939 ATAGGTTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATAAATAAAAATTTATG
Found at i:41213276 original size:68 final size:69
Alignment explanation
Indices: 41213199--41213334 Score: 166
Period size: 68 Copynumber: 2.0 Consensus size: 69
41213189 TTTAATAATT
* ** * *
41213199 TTAAAATTAAATTAAATTTAATACTTATCTTAATAG-TTTTTTATTAACTTAATATGAAAGTGAT
1 TTAAAATTAAATTAAATCTAATACTTATCTTAATAGATGCTATATTAACTTAATATGAAAGTAAT
41213263 TTTC
66 TTTC
* * * * * *
41213267 TTAATATTAAATTTAATCTAATATTTATCTTGATAGATGCTATATTAATTTAATATTAAAGTAAT
1 TTAAAATTAAATTAAATCTAATACTTATCTTAATAGATGCTATATTAACTTAATATGAAAGTAAT
41213332 TTT
66 TTT
41213335 GTTTAATCAT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
68 31 0.55
69 25 0.45
ACGTcount: A:0.40, C:0.05, G:0.06, T:0.49
Consensus pattern (69 bp):
TTAAAATTAAATTAAATCTAATACTTATCTTAATAGATGCTATATTAACTTAATATGAAAGTAAT
TTTC
Found at i:41217306 original size:51 final size:51
Alignment explanation
Indices: 41217220--41217329 Score: 166
Period size: 51 Copynumber: 2.2 Consensus size: 51
41217210 TAGACTCCTT
41217220 CAACCTTACGGTGATTGTCCTTGATGTTACAACTTTTGTAGCATATTGTCG
1 CAACCTTACGGTGATTGTCCTTGATGTTACAACTTTTGTAGCATATTGTCG
* * * ** *
41217271 CAACTTTATGGTGATTTTCCTTGATGTTATGACTTTTGTAGCATATTTTCG
1 CAACCTTACGGTGATTGTCCTTGATGTTACAACTTTTGTAGCATATTGTCG
41217322 CAACCTTA
1 CAACCTTA
41217330 ACACTTGATG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.22, C:0.18, G:0.17, T:0.43
Consensus pattern (51 bp):
CAACCTTACGGTGATTGTCCTTGATGTTACAACTTTTGTAGCATATTGTCG
Found at i:41218446 original size:38 final size:39
Alignment explanation
Indices: 41218395--41218474 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
41218385 TGGTACAACA
41218395 AAGCTAACAATGT-CCCCTTTTTTATATAAGAAAAAATT
1 AAGCTAACAATGTCCCCCTTTTTTATATAAGAAAAAATT
41218433 AAGCTAACAATGTCCCCCTTTTTTATATAAGAAAAAATT
1 AAGCTAACAATGTCCCCCTTTTTTATATAAGAAAAAATT
41218472 AAG
1 AAG
41218475 AGAGACTTAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 13 0.32
39 28 0.68
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (39 bp):
AAGCTAACAATGTCCCCCTTTTTTATATAAGAAAAAATT
Found at i:41229183 original size:16 final size:17
Alignment explanation
Indices: 41229156--41229190 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
41229146 AGAGAGTTGA
41229156 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
41229173 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
41229189 GA
1 GA
41229191 TTGATGAGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Done.