Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011306.1 Kokia drynarioides strain JFW-HI SEQ_126286, whole genome shotgun sequence
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: 547520
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 344 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3025 original size:18 final size:18
Alignment explanation
Indices: 3002--3044 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
2992 GAATAAATTT
3002 TTAATTAAATAATTTT-AA
1 TTAATTAAA-AATTTTAAA
*
3020 TTAATTAAAATTTTTAAA
1 TTAATTAAAAATTTTAAA
3038 TTAATTA
1 TTAATTA
3045 CACCTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:8742 original size:96 final size:96
Alignment explanation
Indices: 8568--8759 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
8558 TTTTTGGGAA
* *
8568 AAGGATATTCGATTATCTCGATTTAAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
8633 GAATCGAAGAT-AAAGAAACATTACCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* * * * * * *
8664 AAGGGTATTCGATTTTTTTGATTTGAAGAAAATTTTCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* *
8728 -GAAACTCGAA-ATAAAAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAGAACATTACCTCGATT
8760 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 2 0.02
96 70 0.86
97 9 0.11
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:9101 original size:58 final size:58
Alignment explanation
Indices: 8995--9159 Score: 145
Period size: 58 Copynumber: 2.8 Consensus size: 58
8985 AATACTCAGG
* *
8995 GGGTAAAATGGTAATTTTCAAAAAATTTGAGGTTAAAAATGGAATTTTTAGACATTCAA
1 GGGTAAAAGGGTAATTTT-AAAAAATTTGAGGTCAAAAATGGAATTTTTAGACATTCAA
* * * * * **
9054 GGGTAAAAGGGTAATTTT-AAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACATTCGG
1 GGGTAAAAGGGTAATTTTAAAAAATTT-GAGGTCAAAAATGGAATTTTTAGACATTCAA
* * ** * * *
9112 GGGCAAAA-TGTAATTTTTTAAAGTTTCGGGGTTAAAAATGGAATTTTT
1 GGGTAAAAGGGTAATTTTAAAAAATTT-GAGGTCAAAAATGGAATTTTT
9160 GGAAGTTTTG
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
57 14 0.16
58 56 0.64
59 17 0.20
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (58 bp):
GGGTAAAAGGGTAATTTTAAAAAATTTGAGGTCAAAAATGGAATTTTTAGACATTCAA
Found at i:9139 original size:29 final size:29
Alignment explanation
Indices: 9107--9218 Score: 100
Period size: 30 Copynumber: 3.8 Consensus size: 29
9097 TTTTTGGACA
* *
9107 TTCGGGGGCAAAATGTAATTTTTTAAAGT
1 TTCGGGGTCAAAATGTAATTTTTAAAAGT
* * **
9136 TTCGGGGTTAAAAATGGAATTTTTGGAAGT
1 TTCGGGG-TCAAAATGTAATTTTTAAAAGT
*
9166 TTTGGGGTCAAAAATAG-AATTTTTAAAAGT
1 TTCGGGGTC-AAAAT-GTAATTTTTAAAAGT
* * *
9196 TTCAGGGTCGAAATATAATTTTT
1 TTCGGGGTCAAAATGTAATTTTT
9219 GGATAGTTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
29 19 0.29
30 46 0.70
31 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (29 bp):
TTCGGGGTCAAAATGTAATTTTTAAAAGT
Found at i:9157 original size:30 final size:30
Alignment explanation
Indices: 9068--9204 Score: 109
Period size: 30 Copynumber: 4.6 Consensus size: 30
9058 AAAAGGGTAA
* * * *
9068 TTTTAAGAGTTTCGAGGTCGAAAATGGAGT
1 TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
* * * *
9098 TTTTGGACA--TTCGGGGGC-AAAATGTAAT
1 TTTT-AAAAGTTTCGGGGTCAAAAATGGAAT
* *
9126 TTTTTAAAGTTTCGGGGTTAAAAATGGAAT
1 TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
** * *
9156 TTTTGGAAGTTTTGGGGTCAAAAATAGAAT
1 TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
*
9186 TTTTAAAAGTTTCAGGGTC
1 TTTTAAAAGTTTCGGGGTC
9205 GAAATATAAT
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 2 0.02
28 12 0.14
29 14 0.17
30 53 0.64
31 2 0.02
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
Found at i:9160 original size:58 final size:58
Alignment explanation
Indices: 9023--9162 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
9013 CAAAAAATTT
* *
9023 GAGGTTAAAAATGGAATTTTTAGACATTCAAGGGTAAAAGGGTAATTTTAAGAGTTTC
1 GAGGTTAAAAATGGAATTTTTGGACATTCAAGGGCAAAAGGGTAATTTTAAGAGTTTC
** * ** *
9081 GAGGTCGAAAATGGAGTTTTTGGACATTCGGGGGCAAAA-TGTAATTTTTTAA-AGTTTC
1 GAGGTTAAAAATGGAATTTTTGGACATTCAAGGGCAAAAGGGTAA--TTTTAAGAGTTTC
*
9139 GGGGTTAAAAATGGAATTTTTGGA
1 GAGGTTAAAAATGGAATTTTTGGA
9163 AGTTTTGGGG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.06
58 58 0.85
59 6 0.09
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.34
Consensus pattern (58 bp):
GAGGTTAAAAATGGAATTTTTGGACATTCAAGGGCAAAAGGGTAATTTTAAGAGTTTC
Found at i:9231 original size:29 final size:29
Alignment explanation
Indices: 9140--9231 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
9130 TAAAGTTTCG
* * *
9140 GGGTTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTCAAAAATAGAATTTTTGGAAG-TTTA
**
9170 GGGTCAAAAATAGAATTTTTAAAAGTTTCA
1 GGGTCAAAAATAGAATTTTTGGAAGTTT-A
* *
9200 GGGTC-GAAATATAATTTTTGGATAGTTTA
1 GGGTCAAAAATAGAATTTTTGGA-AGTTTA
9229 GGG
1 GGG
9232 ACCTCCAGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 20 0.39
30 31 0.61
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTCAAAAATAGAATTTTTGGAAGTTTA
Found at i:9913 original size:77 final size:77
Alignment explanation
Indices: 9814--9962 Score: 217
Period size: 77 Copynumber: 1.9 Consensus size: 77
9804 TCGCTAGTCT
* * *
9814 GTAGCCACGCGTCGTTACGCGTCTCCGCCATAGCACTGTCCGATCGTCCACACGCCCCCATATCC
1 GTAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCAACACGCCCCCATATCC
9879 AGTCACCAATCC
66 AGTCACCAATCC
* ** * *
9891 GTAGCCACGCGCCGTTGCGCGTCTTTGCCATAGCACCGTCCGATCGTCAACACGCTCCCATCTCC
1 GTAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCAACACGCCCCCATATCC
*
9956 GGTCACC
66 AGTCACC
9963 GATAAGTTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.17, C:0.42, G:0.20, T:0.20
Consensus pattern (77 bp):
GTAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCAACACGCCCCCATATCC
AGTCACCAATCC
Found at i:11017 original size:16 final size:16
Alignment explanation
Indices: 10996--11048 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
10986 GTTTTTGGAC
* *
10996 TTTTAATTTAATTAAG
1 TTTTAATTAAATTAAA
* *
11012 TTTTAAATCAATTTAAA
1 TTTT-AATTAAATTAAA
11029 TTTTAATTAAATTTAAA
1 TTTTAATTAAA-TTAAA
11046 TTT
1 TTT
11049 AAAGAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAATTAAATTAAA
Found at i:11032 original size:17 final size:17
Alignment explanation
Indices: 11007--11077 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
10997 TTTAATTTAA
* *
11007 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
11024 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
11041 TTAAA-TTTAAAGAAAAT
1 TTAAATTTTAAA-TAAAT
*
11058 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
11076 TT
1 TT
11078 GAATCAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.11
17 28 0.64
18 8 0.18
19 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:11036 original size:6 final size:6
Alignment explanation
Indices: 11021--11068 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
11011 GTTTTAAATC
* **
11021 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GAA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
11067 AA
1 AA
11069 AATAAATTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:12933 original size:18 final size:18
Alignment explanation
Indices: 12910--12952 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
12900 GAATAAATTT
12910 TTAATTAAATAATTTT-AA
1 TTAATTAAA-AATTTTAAA
*
12928 TTAATTAAAATTTTTAAA
1 TTAATTAAAAATTTTAAA
12946 TTAATTA
1 TTAATTA
12953 CACCTTTAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:18650 original size:96 final size:96
Alignment explanation
Indices: 18476--18667 Score: 221
Period size: 96 Copynumber: 2.0 Consensus size: 96
18466 TTTTTGGGAA
* *
18476 AAGGATATTCGATTATCTCGATTTAAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
18541 GAATCGAAGAT-AAAGAAACATTACCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* * * * * * *
18572 AAGGGTATTCGATTTTTTTGATTTGAAGAAAATTTTCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATA-TTTC
* *
18636 -GAAACTCGAA-ATAAAAGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAAGAACATTACCTCGATT
18668 TTAAAGTTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
95 2 0.02
96 70 0.86
97 9 0.11
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTAAAGAAAAGTTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:19009 original size:58 final size:58
Alignment explanation
Indices: 18903--19067 Score: 145
Period size: 58 Copynumber: 2.8 Consensus size: 58
18893 AATACTCAGG
* *
18903 GGGTAAAATGGTAATTTTCAAAAAATTTGAGGTTAAAAATGGAATTTTTAGACATTCAA
1 GGGTAAAAGGGTAATTTT-AAAAAATTTGAGGTCAAAAATGGAATTTTTAGACATTCAA
* * * * * **
18962 GGGTAAAAGGGTAATTTT-AAGAGTTTCGAGGTCGAAAATGGAGTTTTTGGACATTCGG
1 GGGTAAAAGGGTAATTTTAAAAAATTT-GAGGTCAAAAATGGAATTTTTAGACATTCAA
* * ** * * *
19020 GGGCAAAA-TGTAATTTTTTAAAGTTTCGGGGTTAAAAATGGAATTTTT
1 GGGTAAAAGGGTAATTTTAAAAAATTT-GAGGTCAAAAATGGAATTTTT
19068 GGAAGTTTTG
Statistics
Matches: 87, Mismatches: 17, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
57 14 0.16
58 56 0.64
59 17 0.20
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (58 bp):
GGGTAAAAGGGTAATTTTAAAAAATTTGAGGTCAAAAATGGAATTTTTAGACATTCAA
Found at i:19047 original size:29 final size:29
Alignment explanation
Indices: 19015--19126 Score: 100
Period size: 30 Copynumber: 3.8 Consensus size: 29
19005 TTTTTGGACA
* *
19015 TTCGGGGGCAAAATGTAATTTTTTAAAGT
1 TTCGGGGTCAAAATGTAATTTTTAAAAGT
* * **
19044 TTCGGGGTTAAAAATGGAATTTTTGGAAGT
1 TTCGGGG-TCAAAATGTAATTTTTAAAAGT
*
19074 TTTGGGGTCAAAAATAG-AATTTTTAAAAGT
1 TTCGGGGTC-AAAAT-GTAATTTTTAAAAGT
* * *
19104 TTCAGGGTCGAAATATAATTTTT
1 TTCGGGGTCAAAATGTAATTTTT
19127 GGATAGTTTA
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
29 19 0.29
30 46 0.70
31 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (29 bp):
TTCGGGGTCAAAATGTAATTTTTAAAAGT
Found at i:19065 original size:30 final size:30
Alignment explanation
Indices: 18976--19112 Score: 109
Period size: 30 Copynumber: 4.6 Consensus size: 30
18966 AAAAGGGTAA
* * * *
18976 TTTTAAGAGTTTCGAGGTCGAAAATGGAGT
1 TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
* * * *
19006 TTTTGGACA--TTCGGGGGC-AAAATGTAAT
1 TTTT-AAAAGTTTCGGGGTCAAAAATGGAAT
* *
19034 TTTTTAAAGTTTCGGGGTTAAAAATGGAAT
1 TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
** * *
19064 TTTTGGAAGTTTTGGGGTCAAAAATAGAAT
1 TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
*
19094 TTTTAAAAGTTTCAGGGTC
1 TTTTAAAAGTTTCGGGGTC
19113 GAAATATAAT
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
27 2 0.02
28 12 0.14
29 14 0.17
30 53 0.64
31 2 0.02
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTTAAAAGTTTCGGGGTCAAAAATGGAAT
Found at i:19068 original size:58 final size:58
Alignment explanation
Indices: 18931--19070 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
18921 CAAAAAATTT
* *
18931 GAGGTTAAAAATGGAATTTTTAGACATTCAAGGGTAAAAGGGTAATTTTAAGAGTTTC
1 GAGGTTAAAAATGGAATTTTTGGACATTCAAGGGCAAAAGGGTAATTTTAAGAGTTTC
** * ** *
18989 GAGGTCGAAAATGGAGTTTTTGGACATTCGGGGGCAAAA-TGTAATTTTTTAA-AGTTTC
1 GAGGTTAAAAATGGAATTTTTGGACATTCAAGGGCAAAAGGGTAA--TTTTAAGAGTTTC
*
19047 GGGGTTAAAAATGGAATTTTTGGA
1 GAGGTTAAAAATGGAATTTTTGGA
19071 AGTTTTGGGG
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
57 4 0.06
58 58 0.85
59 6 0.09
ACGTcount: A:0.34, C:0.06, G:0.27, T:0.34
Consensus pattern (58 bp):
GAGGTTAAAAATGGAATTTTTGGACATTCAAGGGCAAAAGGGTAATTTTAAGAGTTTC
Found at i:19139 original size:29 final size:29
Alignment explanation
Indices: 19048--19139 Score: 87
Period size: 30 Copynumber: 3.1 Consensus size: 29
19038 TAAAGTTTCG
* * *
19048 GGGTTAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTCAAAAATAGAATTTTTGGAAG-TTTA
**
19078 GGGTCAAAAATAGAATTTTTAAAAGTTTCA
1 GGGTCAAAAATAGAATTTTTGGAAGTTT-A
* *
19108 GGGTC-GAAATATAATTTTTGGATAGTTTA
1 GGGTCAAAAATAGAATTTTTGGA-AGTTTA
19137 GGG
1 GGG
19140 ACCTCCAGGG
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
29 20 0.39
30 31 0.61
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (29 bp):
GGGTCAAAAATAGAATTTTTGGAAGTTTA
Found at i:19821 original size:77 final size:77
Alignment explanation
Indices: 19722--19870 Score: 217
Period size: 77 Copynumber: 1.9 Consensus size: 77
19712 TCGCTAGTCT
* * *
19722 GTAGCCACGCGTCGTTACGCGTCTCCGCCATAGCACTGTCCGATCGTCCACACGCCCCCATATCC
1 GTAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCAACACGCCCCCATATCC
19787 AGTCACCAATCC
66 AGTCACCAATCC
* ** * *
19799 GTAGCCACGCGCCGTTGCGCGTCTTTGCCATAGCACCGTCCGATCGTCAACACGCTCCCATCTCC
1 GTAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCAACACGCCCCCATATCC
*
19864 GGTCACC
66 AGTCACC
19871 GATAAGTTCA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 63 1.00
ACGTcount: A:0.17, C:0.42, G:0.20, T:0.20
Consensus pattern (77 bp):
GTAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCAACACGCCCCCATATCC
AGTCACCAATCC
Found at i:20925 original size:16 final size:16
Alignment explanation
Indices: 20904--20956 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
20894 GTTTTTGGAC
* *
20904 TTTTAATTTAATTAAG
1 TTTTAATTAAATTAAA
* *
20920 TTTTAAATCAATTTAAA
1 TTTT-AATTAAATTAAA
20937 TTTTAATTAAATTTAAA
1 TTTTAATTAAA-TTAAA
20954 TTT
1 TTT
20957 AAAGAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (16 bp):
TTTTAATTAAATTAAA
Found at i:20940 original size:17 final size:17
Alignment explanation
Indices: 20915--20985 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
20905 TTTAATTTAA
* *
20915 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
20932 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
20949 TTAAA-TTTAAAGAAAAT
1 TTAAATTTTAAA-TAAAT
*
20966 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
20984 TT
1 TT
20986 GAATCAATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
16 5 0.11
17 28 0.64
18 8 0.18
19 3 0.07
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:20944 original size:6 final size:6
Alignment explanation
Indices: 20929--20976 Score: 55
Period size: 6 Copynumber: 8.3 Consensus size: 6
20919 GTTTTAAATC
* **
20929 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GAA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
20975 AA
1 AA
20977 AATAAATTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 27 0.79
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:21730 original size:206 final size:206
Alignment explanation
Indices: 21410--21882 Score: 599
Period size: 206 Copynumber: 2.3 Consensus size: 206
21400 TTTTAATCCA
* * * * * * * * * * *
21410 CTTCTCTGTGTTTCATCAGGAAGACGAATTTGGTTCACTCCTCAGTATTTTGACAA-TAAGCTCA
1 CTTCTCTGTATCTCAGCAGGAAGACGAATTTAGTCCACTTCTCAGTA-TCTCATAAGGAAGCTAA
* *
21474 CCA-TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
65 TCATTTTATTACTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC
* * * **
21538 ACATCGAGCGTGGGTTTGTTTTGGTCTTCTTCTCAATATTTCATCAGGAAGATGACTGTATTGCT
130 ACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCATCACT
21603 TACTTCAATCTG
195 TACTTCAATCTG
* *
21615 CTTCTCTGTATCTCAGCAGGAAGACGAATTTAGTCCACTTCTCGGTATCTCATCAGGAAGCTAAT
1 CTTCTCTGTATCTCAGCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATAAGGAAGCTAAT
* * * * *
21680 CATTTTATTGCTTCGCCCTACTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCG
66 CATTTTATTACTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
* * * * *
21745 CATTGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCGGGAAGGTGATTGCATCACTT
131 CATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCATCACTT
**
21810 GTTTCAATCTG
196 ACTTCAATCTG
* * **
21821 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTTACTTCTCAGTATCTCATAAGGAAGCT
1 CTTCTCTGTATCTCAGCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATAAGGAAGCT
21883 GGGTTCGAAG
Statistics
Matches: 228, Mismatches: 38, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
204 4 0.02
205 48 0.21
206 176 0.77
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (206 bp):
CTTCTCTGTATCTCAGCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATAAGGAAGCTAAT
CATTTTATTACTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
CATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACTGCATCACTT
ACTTCAATCTG
Found at i:21946 original size:152 final size:154
Alignment explanation
Indices: 21698--21995 Score: 384
Period size: 152 Copynumber: 1.9 Consensus size: 154
21688 TGCTTCGCCC
* * * **
21698 TACTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCGCATTGAGCGTGGGTTTGA
1 TACTTCTCAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTTGTTCGCATCGAGC----GCCTGA
* * * * * * * *
21763 TTTGGTCTTCTTCTCAGTATCTCATCGGGAAGGTGATTGCATCACTTGTTTCAATCTGCTTCTCT
62 GTTGGTATTCTTCTCAGTATCTCATCAGGAAGATAACTGCATCACTTATTTCAATCCGCTTCTCT
*
21828 GTATCTCATCAGGAAGACGAATTTGGTT
127 GTATCTCACCAGGAAGACGAATTTGGTT
21856 TACTTCTCAGTATCTCATAAGGAAGCT-GGGTTCGAAGATTTGTTCGCATCGAGC-CCTGAGTTG
1 TACTTCTCAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTTGTTCGCATCGAGCGCCTGAGTTG
* * *
21919 GTATTCTTCTCTGTATCTCATCAGGAAGATAACTGCCTTACTTATTTCAATCCGCTTCTCTGTAT
66 GTATTCTTCTCAGTATCTCATCAGGAAGATAACTGCATCACTTATTTCAATCCGCTTCTCTGTAT
*
21984 CTTACCAGGAAG
131 CTCACCAGGAAG
21996 CTGGGATTCA
Statistics
Matches: 122, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
152 71 0.58
157 26 0.21
158 25 0.20
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.37
Consensus pattern (154 bp):
TACTTCTCAGTATCTCATAAGGAAGCTGGGGTTCGAAGATTTGTTCGCATCGAGCGCCTGAGTTG
GTATTCTTCTCAGTATCTCATCAGGAAGATAACTGCATCACTTATTTCAATCCGCTTCTCTGTAT
CTCACCAGGAAGACGAATTTGGTT
Found at i:22061 original size:116 final size:114
Alignment explanation
Indices: 21858--22128 Score: 357
Period size: 116 Copynumber: 2.4 Consensus size: 114
21848 ATTTGGTTTA
** * *
21858 CTTCTCAGTATCTCATAAGGAAGCTGGGTTCGAAGATTTGTTCGCATCGAGCCCTGAGTTGGTAT
1 CTTCTCAGTATCTCACCAGGAAGCTGGGTTCGAAGATTTGATCACATCGAGCCCTGAGTTGGTAT
* **
21923 TCTTCTCTGTATCTCATCAGGAAGATAACTGCCTTACTTATTTCAATCC-G
66 ACTTCTCTGTATCTCATCAGGAAGATAACCACCTTA-TTATTTCAA-CCTG
* *
21973 CTTCTCTGTATCTTACCAGGAAGCTGGGATTC-AAGGATTTGATCACATCGAGCCCTGAGTTGGT
1 CTTCTCAGTATCTCACCAGGAAGCTGGG-TTCGAA-GATTTGATCACATCGAGCCCTGAGTTGGT
* ** *
22037 ATACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTATTTCGACCTG
64 ATACTTCTCTGTATCTCATCAGGAAGATAACCACCTTATTATTTCAACCTG
*
22088 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTG
1 CTTCTCAGTATCTCACCAGGAAGCT-GGGTTCGAAGATTTG
22129 CTCGCTTTGA
Statistics
Matches: 135, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
114 2 0.01
115 66 0.49
116 67 0.50
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (114 bp):
CTTCTCAGTATCTCACCAGGAAGCTGGGTTCGAAGATTTGATCACATCGAGCCCTGAGTTGGTAT
ACTTCTCTGTATCTCATCAGGAAGATAACCACCTTATTATTTCAACCTG
Found at i:23238 original size:46 final size:46
Alignment explanation
Indices: 23186--23278 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
23176 AAAACTAGAT
* *
23186 CTCCCTCATAGAATTTCCTAGGACGAACCTTTTTGTCGTAAGCTCG
1 CTCCCTCATAGAATTCCCTAGGACAAACCTTTTTGTCGTAAGCTCG
23232 CTCCCTCATAGAATTCCCTAGGACAAACCTTTTTGTCGTAAGCTCG
1 CTCCCTCATAGAATTCCCTAGGACAAACCTTTTTGTCGTAAGCTCG
23278 C
1 C
23279 ATCATTCTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (46 bp):
CTCCCTCATAGAATTCCCTAGGACAAACCTTTTTGTCGTAAGCTCG
Found at i:28056 original size:10 final size:9
Alignment explanation
Indices: 28032--28058 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
28022 TCACTATGCC
28032 TTAAAAACT
1 TTAAAAACT
28041 TTAAAAACT
1 TTAAAAACT
28050 TTAAAAACT
1 TTAAAAACT
28059 CCTTCGCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
TTAAAAACT
Found at i:34172 original size:29 final size:29
Alignment explanation
Indices: 34140--34230 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 29
34130 TTTTTTGACA
* *
34140 TTCGGGGGCAAAATATAATTTTTAGAAGT
1 TTCGGGGTCAAAATATAATTTTTGGAAGT
*
34169 TTCGGGGTCAAAA-ATGGAGTTTTTGGAAGT
1 TTCGGGGTCAAAATAT--AATTTTTGGAAGT
* * *
34199 TTTGAGGTCGAAATATAATTTTTGGACAGT
1 TTCGGGGTCAAAATATAATTTTTGGA-AGT
34229 TT
1 TT
34231 AGGGACCTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
28 2 0.04
29 21 0.41
30 26 0.51
31 2 0.04
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.37
Consensus pattern (29 bp):
TTCGGGGTCAAAATATAATTTTTGGAAGT
Found at i:34935 original size:77 final size:77
Alignment explanation
Indices: 34807--34960 Score: 245
Period size: 77 Copynumber: 2.0 Consensus size: 77
34797 GCCCGCCGCG
* *
34807 AGTCCGCAGCCACGTGCCGTTACGCGTCTCCGCCATAGCACCGTCCGATCGTCCACGCACCCCCA
1 AGTCCGCAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCAATCGTCCACGCACCCCCA
34872 TCTCCGATCACC
66 TCTCCGATCACC
* * * **
34884 AGTCCGTAGCCACGCGCCGTTGCGCGTCTCCGCCATAGCACTGTCCAATCGTCCACGCGTCCCCA
1 AGTCCGCAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCAATCGTCCACGCACCCCCA
34949 TCTCCGATCACC
66 TCTCCGATCACC
34961 GGTAAGTTCA
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.16, C:0.45, G:0.20, T:0.18
Consensus pattern (77 bp):
AGTCCGCAGCCACGCGCCGTTACGCGTCTCCGCCATAGCACCGTCCAATCGTCCACGCACCCCCA
TCTCCGATCACC
Found at i:35238 original size:21 final size:18
Alignment explanation
Indices: 35184--35241 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 18
35174 ATTTTTTTAT
35184 TTAATATTATTTATTATTA
1 TTAATATTA-TTATTATTA
35203 TTAATAAATTCATTATTACCGTTA
1 TTAAT--ATT-ATTATTA---TTA
35227 TTAATATTATTATTA
1 TTAATATTATTATTA
35242 ATAATATTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
19 5 0.15
21 16 0.48
22 4 0.12
24 8 0.24
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (18 bp):
TTAATATTATTATTATTA
Found at i:36014 original size:17 final size:17
Alignment explanation
Indices: 35989--36074 Score: 58
Period size: 17 Copynumber: 5.4 Consensus size: 17
35979 TTTAATTTAA
* *
35989 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATAAAT
*
36006 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
**
36023 TTAAA----GCA-AA-T
1 TTAAATTTTAAATAAAT
*
36034 TTAAATTTAAAATAAAT
1 TTAAATTTTAAATAAAT
*
36051 TTAAATTTAAAAATAAAT
1 TTAAATTT-TAAATAAAT
36069 TTAAAT
1 TTAAAT
36075 AAATCTAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
11 6 0.11
12 2 0.04
15 1 0.02
16 2 0.04
17 28 0.52
18 15 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:36017 original size:28 final size:28
Alignment explanation
Indices: 35984--36055 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
35974 GGACTTTTAA
* *
35984 TTTAATTAAGTTTTAAATC-AATTTAAAT
1 TTTAATTAA-ATTTAAAGCAAATTTAAAT
36012 TTTAATTAAATTTAAAGCAAATTTAAAT
1 TTTAATTAAATTTAAAGCAAATTTAAAT
* *
36040 TTAAAATAAATTTAAA
1 TTTAATTAAATTTAAA
36056 TTTAAAAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 7 0.18
28 32 0.82
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTAATTAAATTTAAAGCAAATTTAAAT
Found at i:36018 original size:6 final size:6
Alignment explanation
Indices: 36003--36074 Score: 69
Period size: 6 Copynumber: 12.5 Consensus size: 6
35993 GTTTTAAATC
* ** *
36003 AATTTA AATTTT AA-TTA AATTTA AA-GCA AATTTA AATTTA AA-ATA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
**
36048 AATTTA AATTTA AAAATA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AAT
36075 AAATCTAATA
Statistics
Matches: 51, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
5 11 0.22
6 40 0.78
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:36065 original size:18 final size:17
Alignment explanation
Indices: 36017--36074 Score: 89
Period size: 17 Copynumber: 3.4 Consensus size: 17
36007 TAAATTTTAA
**
36017 TTAAATTTAAAGCAAAT
1 TTAAATTTAAAATAAAT
36034 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
36051 TTAAATTTAAAAATAAAT
1 TTAAATTT-AAAATAAAT
36069 TTAAAT
1 TTAAAT
36075 AAATCTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:36870 original size:30 final size:30
Alignment explanation
Indices: 36836--36895 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
36826 TAAGATTATC
36836 AAATTTCATTCAAATCAGAACCAATCACAA
1 AAATTTCATTCAAATCAGAACCAATCACAA
36866 AAATTTCATTCAAATCAGAACCAATCACAA
1 AAATTTCATTCAAATCAGAACCAATCACAA
36896 TTAGGGGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.50, C:0.23, G:0.03, T:0.23
Consensus pattern (30 bp):
AAATTTCATTCAAATCAGAACCAATCACAA
Found at i:37277 original size:42 final size:42
Alignment explanation
Indices: 37218--37301 Score: 116
Period size: 42 Copynumber: 2.0 Consensus size: 42
37208 CCAAATATTT
*
37218 TTAAACTCTAATATAATTTCATTAT-TAAAAAACACTCATAAA
1 TTAAACTCAAATATAATTT-ATTATCTAAAAAACACTCATAAA
* * *
37260 TTAAACTCAAATATAATTTTTTTTCTAAATAACACTCATAAA
1 TTAAACTCAAATATAATTTATTATCTAAAAAACACTCATAAA
37302 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 3 0.08
42 34 0.92
ACGTcount: A:0.48, C:0.14, G:0.00, T:0.38
Consensus pattern (42 bp):
TTAAACTCAAATATAATTTATTATCTAAAAAACACTCATAAA
Found at i:37506 original size:25 final size:25
Alignment explanation
Indices: 37478--37578 Score: 141
Period size: 25 Copynumber: 4.0 Consensus size: 25
37468 TTCTTCTTGT
*
37478 TTGTTGAGGCTGCT-TTCGCACTGAA
1 TTGTTGTGGCTGCTCTT-GCACTGAA
*
37503 TTGTTGTGGTTGCTCTTGCACTGAA
1 TTGTTGTGGCTGCTCTTGCACTGAA
* *
37528 TTGTTGTGGCTGCTCTCGCACTAAA
1 TTGTTGTGGCTGCTCTTGCACTGAA
*
37553 TTGTTGTGGTTGCTCTTGCACTGAA
1 TTGTTGTGGCTGCTCTTGCACTGAA
37578 T
1 T
37579 CTGCAAGCAG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
25 65 0.97
26 2 0.03
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.41
Consensus pattern (25 bp):
TTGTTGTGGCTGCTCTTGCACTGAA
Found at i:37555 original size:50 final size:50
Alignment explanation
Indices: 37478--37578 Score: 175
Period size: 50 Copynumber: 2.0 Consensus size: 50
37468 TTCTTCTTGT
* *
37478 TTGTTGAGGCTGCTTTCGCACTGAATTGTTGTGGTTGCTCTTGCACTGAA
1 TTGTTGAGGCTGCTCTCGCACTAAATTGTTGTGGTTGCTCTTGCACTGAA
*
37528 TTGTTGTGGCTGCTCTCGCACTAAATTGTTGTGGTTGCTCTTGCACTGAA
1 TTGTTGAGGCTGCTCTCGCACTAAATTGTTGTGGTTGCTCTTGCACTGAA
37578 T
1 T
37579 CTGCAAGCAG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.14, C:0.19, G:0.27, T:0.41
Consensus pattern (50 bp):
TTGTTGAGGCTGCTCTCGCACTAAATTGTTGTGGTTGCTCTTGCACTGAA
Found at i:43368 original size:22 final size:23
Alignment explanation
Indices: 43342--43398 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 23
43332 TTAAGTATTC
43342 TAATATGTTTTTATAAAATTTTA
1 TAATATGTTTTTATAAAATTTTA
* *
43365 -AATAAG-TTTTAT-TAATTTTA
1 TAATATGTTTTTATAAAATTTTA
*
43385 TAAT-TTTTTTTATA
1 TAATATGTTTTTATA
43399 TTTTATAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
20 7 0.26
21 15 0.56
22 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TAATATGTTTTTATAAAATTTTA
Found at i:43401 original size:19 final size:18
Alignment explanation
Indices: 43366--43452 Score: 76
Period size: 19 Copynumber: 5.0 Consensus size: 18
43356 AAAATTTTAA
43366 ATAAGTTTTATTAATTTT
1 ATAAGTTTTATTAATTTT
* *
43384 ATAATTTTTTTTATATTTT
1 ATAAGTTTTATTA-ATTTT
*
43403 ATAAGTTTATATCAATTTT
1 ATAAGTTT-TATTAATTTT
* *
43422 ATTA-TTTTA--AAATTT
1 ATAAGTTTTATTAATTTT
43437 ATAA-TTTTA-TAATTTT
1 ATAAGTTTTATTAATTTT
43453 TATGGAAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
15 13 0.23
16 5 0.09
17 2 0.04
18 14 0.25
19 20 0.35
20 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (18 bp):
ATAAGTTTTATTAATTTT
Found at i:43455 original size:9 final size:8
Alignment explanation
Indices: 43366--43452 Score: 69
Period size: 8 Copynumber: 11.0 Consensus size: 8
43356 AAAATTTTAA
43366 ATAAGTTTT
1 ATAA-TTTT
43375 ATTAATTTT
1 A-TAATTTT
43384 ATAA-TTT
1 ATAATTTT
43391 -T--TTTT
1 ATAATTTT
43396 AT-ATTTT
1 ATAATTTT
43403 ATAAGTTTAT
1 ATAA-TTT-T
43413 ATCAATTTT
1 AT-AATTTT
*
43422 ATTATTTT
1 ATAATTTT
*
43430 A-AAATTT
1 ATAATTTT
43437 ATAATTTT
1 ATAATTTT
43445 ATAATTTT
1 ATAATTTT
43453 TATGGAAAAA
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
5 3 0.05
6 2 0.03
7 14 0.22
8 23 0.35
9 12 0.18
10 9 0.14
11 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.02, T:0.62
Consensus pattern (8 bp):
ATAATTTT
Found at i:49171 original size:20 final size:20
Alignment explanation
Indices: 49146--49183 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
49136 TTTCAAAGTT
49146 GAGAGAGA-CTAATTTGTTAA
1 GAGAGAGATC-AATTTGTTAA
49166 GAGAGAGATCAATTTGTT
1 GAGAGAGATCAATTTGTT
49184 TATTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (20 bp):
GAGAGAGATCAATTTGTTAA
Found at i:49957 original size:14 final size:15
Alignment explanation
Indices: 49920--49954 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49910 TCCCAAATAA
* *
49920 ATAAAATTTAAATTC
1 ATAAAATTAAAAATC
49935 ATAAAATTAAAAATC
1 ATAAAATTAAAAATC
49950 ATAAA
1 ATAAA
49955 TTACAACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
ATAAAATTAAAAATC
Found at i:50869 original size:25 final size:24
Alignment explanation
Indices: 50820--50875 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
50810 AGTTATTTCA
* *
50820 AAAAAAATTATTATAAATCCGATT
1 AAAAAAATTATAATAAATCCAATT
*
50844 AAAAAAATTAATAATAAATTCAATT
1 AAAAAAATT-ATAATAAATCCAATT
*
50869 AGAAAAA
1 AAAAAAA
50876 CATAATATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (24 bp):
AAAAAAATTATAATAAATCCAATT
Found at i:52790 original size:182 final size:182
Alignment explanation
Indices: 52512--52893 Score: 674
Period size: 182 Copynumber: 2.1 Consensus size: 182
52502 AAAGCAGCTC
*
52512 CCGCCGTGTCCACTCGTGTCTGTCTTGGGACACTCGTGTCTGATTTTATATTTATTTGTATTTGT
1 CCGCCGTGTCCACTCATGTCTGTCTTGGGACACTCGTGTCTGATTTTATATTTATTTGTATTTGT
* *
52577 GAAGATTGACGTCAGCCATGGCTGTGTCGGTCTCAAGGGGCTTCCCCGTTTTATTGTTTTCATAA
66 GAAGATTGACGTCAGCCATGGATGTGTCGGTCCCAAGGGGCTTCCCCGTTTTATTGTTTTCATAA
* * *
52642 CCCCACAGTTTGGTTCATCTCTTCCTCTGTTTTTGGTCGCAAAAAGTTGGTT
131 CCCCACAGTGTGGTTCATCTCTTCCTCTGGTTTTGGTCCCAAAAAGTTGGTT
*
52694 TCGCCGTGTCCACTCATGTCTGTCTTGGGACACTCGTGTCTGATTTTATATTTATTTGTATTTGT
1 CCGCCGTGTCCACTCATGTCTGTCTTGGGACACTCGTGTCTGATTTTATATTTATTTGTATTTGT
* *
52759 GAAGATTGACGTCAGCCATGGATGTGTCGGTCCCAAGGGGTTTCCCCGTTTTATTGTTTTCATAG
66 GAAGATTGACGTCAGCCATGGATGTGTCGGTCCCAAGGGGCTTCCCCGTTTTATTGTTTTCATAA
*
52824 CCCCACAGTGTGGTTCATCTCTTCCTCTGGTTTTGGTCCCAAAAAGTTTGTT
131 CCCCACAGTGTGGTTCATCTCTTCCTCTGGTTTTGGTCCCAAAAAGTTGGTT
52876 CCGCCGTGTCCACTCATG
1 CCGCCGTGTCCACTCATG
52894 CCTTCACTCT
Statistics
Matches: 189, Mismatches: 11, Indels: 0
0.94 0.05 0.00
Matches are distributed among these distances:
182 189 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.39
Consensus pattern (182 bp):
CCGCCGTGTCCACTCATGTCTGTCTTGGGACACTCGTGTCTGATTTTATATTTATTTGTATTTGT
GAAGATTGACGTCAGCCATGGATGTGTCGGTCCCAAGGGGCTTCCCCGTTTTATTGTTTTCATAA
CCCCACAGTGTGGTTCATCTCTTCCTCTGGTTTTGGTCCCAAAAAGTTGGTT
Found at i:75686 original size:5 final size:5
Alignment explanation
Indices: 75676--75709 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
75666 TGTAGAAGAA
*
75676 GAGGG GAGGG GAGGG GAGGG GAGGG GAGAG GAGG
1 GAGGG GAGGG GAGGG GAGGG GAGGG GAGGG GAGG
75710 ATGACAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (5 bp):
GAGGG
Found at i:76415 original size:29 final size:30
Alignment explanation
Indices: 76372--76429 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 30
76362 AATAACATTT
*
76372 TTTTATAACGTAAGTGACTAAAATGTAACA
1 TTTTATAACATAAGTGACTAAAATGTAACA
*
76402 TTTTA-AACATAAGTGACTGAAATGTAAC
1 TTTTATAACATAAGTGACTAAAATGTAAC
76430 TTGAGGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (30 bp):
TTTTATAACATAAGTGACTAAAATGTAACA
Found at i:76631 original size:24 final size:24
Alignment explanation
Indices: 76603--76650 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
76593 ACTATTTTGA
76603 TACTTAAAATTTTACTTTGTTTAT
1 TACTTAAAATTTTACTTTGTTTAT
76627 TACTTAAAATTTTACTTTGTTTAT
1 TACTTAAAATTTTACTTTGTTTAT
76651 CAACATGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.58
Consensus pattern (24 bp):
TACTTAAAATTTTACTTTGTTTAT
Found at i:77349 original size:41 final size:41
Alignment explanation
Indices: 77301--77380 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 41
77291 TCTTATTGTA
*
77301 TTTTTAATTTGTTTGTTATTTTACGAATTGTTTTAATATCG
1 TTTTTAATTTGTTTGTTATTTTAAGAATTGTTTTAATATCG
* * *
77342 TTTTTAATTTGTTTGTTTTTTTAATATTTGTTTTAATAT
1 TTTTTAATTTGTTTGTTATTTTAAGAATTGTTTTAATAT
77381 TTTTAACTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.21, C:0.03, G:0.10, T:0.66
Consensus pattern (41 bp):
TTTTTAATTTGTTTGTTATTTTAAGAATTGTTTTAATATCG
Found at i:83391 original size:30 final size:31
Alignment explanation
Indices: 83350--83409 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
83340 TTTATGTATA
*
83350 TAATAAAAAAAAAAGTGGTCATTTTTATAAT
1 TAATAAAAAAAAAACTGGTCATTTTTATAAT
** *
83381 TAAT-AAAAAAATTCTGGTTATTTTTATAA
1 TAATAAAAAAAAAACTGGTCATTTTTATAA
83410 AAAGTTGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.40
Consensus pattern (31 bp):
TAATAAAAAAAAAACTGGTCATTTTTATAAT
Found at i:83911 original size:3 final size:3
Alignment explanation
Indices: 83903--83927 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
83893 ATCCAACTGA
83903 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
83928 CATTCTAGCA
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:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:84187 original size:7 final size:8
Alignment explanation
Indices: 84154--84184 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
84144 TGATCTAAAG
84154 GAAAAAAA
1 GAAAAAAA
84162 GAAAAAAA
1 GAAAAAAA
84170 GAAAAAAA
1 GAAAAAAA
84178 GAAAAAA
1 GAAAAAA
84185 GAAGCTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:87654 original size:30 final size:30
Alignment explanation
Indices: 87581--87656 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
87571 TTTGGTCCAA
*
87581 TTTGGTACTCAAACTTGACATTTTTCCTAG
1 TTTGGTACTTAAACTTGACATTTTTCCTAG
* *
87611 TTTGGTACCTAAACTTGACACTTTTT-TTAAG
1 TTTGGTACTTAAACTTGACA-TTTTTCCT-AG
87642 -TTGGTACTTAAACTT
1 TTTGGTACTTAAACTT
87657 TTTGGGTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 33 0.82
31 7 0.17
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (30 bp):
TTTGGTACTTAAACTTGACATTTTTCCTAG
Found at i:87694 original size:89 final size:87
Alignment explanation
Indices: 87520--87706 Score: 216
Period size: 89 Copynumber: 2.1 Consensus size: 87
87510 CTTAATATAA
* * * *
87520 AATTTGGTACATGAACCTGACACTTTTCTTAATTTGGTACCTAAACTTTTTTTTGGTCCAATTTG
1 AATTTGGTACATAAACCTGACACTTTTCTTAAGTTGGTACCTAAAC-TTTTTTGGGTCAAATTTG
*
87585 GTACTCAAACTTGACATTTTTCCT
65 GTACTCAAACTTAACATTTTT-CT
* * * * *
87609 AGTTTGGTACCTAAACTTGACACTTTTTTTAAGTTGGTACTTAAAC-TTTTTGGGTCAAATTTGG
1 AATTTGGTACATAAACCTGACACTTTTCTTAAGTTGGTACCTAAACTTTTTTGGGTCAAATTTGG
*
87673 TAC-CTAAACTTAACTCTTTTTTCT
66 TACTC-AAACTTAA--CATTTTTCT
87697 AATTTGGTAC
1 AATTTGGTAC
87707 TTAATTTTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
86 1 0.01
87 26 0.31
88 11 0.13
89 45 0.54
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.44
Consensus pattern (87 bp):
AATTTGGTACATAAACCTGACACTTTTCTTAAGTTGGTACCTAAACTTTTTTGGGTCAAATTTGG
TACTCAAACTTAACATTTTTCT
Found at i:88019 original size:59 final size:60
Alignment explanation
Indices: 87877--88049 Score: 204
Period size: 60 Copynumber: 2.9 Consensus size: 60
87867 ATTGAATTAA
* * * * *
87877 AAAAAAAAGCTTAGGCACCAAATTAGAAAAAAATGCCAAGTTTAGGTATCAAATTGGGTT
1 AAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAATTGAGTT
* * * * * *
87937 CAAAGAAAGTTTAGGTATCAAATTAGGAAAAAGTATCAAGTTCAGGTATCAAATTGAG-T
1 AAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAATTGAGTT
* * * *
87996 AAAAAAAAGTTTAAGTACCAAATTAAAAAAAAATGTCAAGTTCAAGTACCAAAT
1 AAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAAT
88050 GTTATAGTAA
Statistics
Matches: 92, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
59 45 0.49
60 47 0.51
ACGTcount: A:0.49, C:0.10, G:0.16, T:0.24
Consensus pattern (60 bp):
AAAAAAAAGTTTAGGTACCAAATTAGAAAAAAATGTCAAGTTCAGGTATCAAATTGAGTT
Found at i:98219 original size:23 final size:23
Alignment explanation
Indices: 98144--98210 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
98134 GGAAACAGTA
* *
98144 GGCACACAAAGTGCTGAATAGAG
1 GGCACACATAGTGCTGAACAGAG
98167 GGCACACATAGTGCTGAACAGAG
1 GGCACACATAGTGCTGAACAGAG
98190 GGCACACATAGTGCTGAACAG
1 GGCACACATAGTGCTGAACAG
98211 TAGACACACT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.36, C:0.21, G:0.30, T:0.13
Consensus pattern (23 bp):
GGCACACATAGTGCTGAACAGAG
Found at i:98316 original size:24 final size:26
Alignment explanation
Indices: 98278--98325 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
98268 TCTACATGGG
98278 CATAATCTCTCATAT-TCATCATTTCT
1 CATAATCTCTCATATATCA-CATTTCT
98304 CATAAT-T-TCATATATCACATTT
1 CATAATCTCTCATATATCACATTT
98326 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 11 0.52
25 4 0.19
26 6 0.29
ACGTcount: A:0.31, C:0.23, G:0.00, T:0.46
Consensus pattern (26 bp):
CATAATCTCTCATATATCACATTTCT
Found at i:101326 original size:30 final size:31
Alignment explanation
Indices: 101202--101331 Score: 117
Period size: 31 Copynumber: 4.3 Consensus size: 31
101192 AAATTGTTTT
*
101202 TTTGA-CCCTCAAATTTTCCAAAAAATTTGAA
1 TTTGACCCCT-AAATTTTCCAAAAAATTTCAA
* * *
101233 TTCGACCACTAAATTTTCCAAAAAATTCCAA
1 TTTGACCCCTAAATTTTCCAAAAAATTTCAA
* * * *
101264 TTTGACCTCTAAACTTT-C-TAGAATTTCCAA
1 TTTGACCCCTAAATTTTCCAAAAAATTT-CAA
*
101294 TTTGACCCCTAAAATTTT-C-AAAAATTTAAA
1 TTTGACCCCT-AAATTTTCCAAAAAATTTCAA
101324 TTTGACCC
1 TTTGACCC
101332 GATTTTAAAT
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
29 5 0.06
30 23 0.28
31 50 0.62
32 3 0.04
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.35
Consensus pattern (31 bp):
TTTGACCCCTAAATTTTCCAAAAAATTTCAA
Found at i:113107 original size:50 final size:50
Alignment explanation
Indices: 112980--113113 Score: 178
Period size: 50 Copynumber: 2.7 Consensus size: 50
112970 ATATTTTACC
* * * * *
112980 CCTAAAGCTATAAAGGTGCAGATTGAAACCATAAAGGCAAATCTCATACA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAAAGGCAAATCTCATACA
* * * *
113030 CCTAAAGCTGTAGAGGGGCAGAATGAAGCCGCAATGGCAAATCTCATTCA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAAAGGCAAATCTCATACA
*
113080 CCTAAAGCTGTAGAGGGGCAGATTGAAGTCACAA
1 CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAA
113114 GGACGAATCT
Statistics
Matches: 72, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 72 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (50 bp):
CCTAAAGCTGTAGAGGGGCAGATTGAAGCCACAAAGGCAAATCTCATACA
Found at i:113207 original size:40 final size:40
Alignment explanation
Indices: 113161--113335 Score: 212
Period size: 40 Copynumber: 4.4 Consensus size: 40
113151 AGTTACAACC
*
113161 TCCAATCTCTTACCCTAACCA-GAGGGCAGATTGAAGACCA
1 TCCAATCTCTTACCCTAACCATG-GGGCAGATTGAAGACAA
* * * *
113201 TTCAATCTTTTACCTTAATCA-GAGGGCAGATTGAAGACAA
1 TCCAATCTCTTACCCTAACCATG-GGGCAGATTGAAGACAA
* *
113241 TCTAATCTCTTACCCCAACCATGGGGCAGATTGAAGACAA
1 TCCAATCTCTTACCCTAACCATGGGGCAGATTGAAGACAA
** *
113281 TCCAATCTCTTACCCCGACCATGGGGCAGGTTGAA-ACAA
1 TCCAATCTCTTACCCTAACCATGGGGCAGATTGAAGACAA
*
113320 TCCAATCTTTTACCCT
1 TCCAATCTCTTACCCT
113336 TAAAGTTACA
Statistics
Matches: 118, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 18 0.15
40 99 0.84
41 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (40 bp):
TCCAATCTCTTACCCTAACCATGGGGCAGATTGAAGACAA
Found at i:113362 original size:27 final size:26
Alignment explanation
Indices: 113330--113382 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
113320 TCCAATCTTT
*
113330 TACCCTTAAAGTTACA-AAGGGGCAGA
1 TACCCCTAAAGTTACAGAA-GGGCAGA
113356 TACCCCTAAAGTTACAGAAGGGCAGA
1 TACCCCTAAAGTTACAGAAGGGCAGA
113382 T
1 T
113383 TGAAGCTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 23 0.92
27 2 0.08
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.19
Consensus pattern (26 bp):
TACCCCTAAAGTTACAGAAGGGCAGA
Found at i:115021 original size:31 final size:31
Alignment explanation
Indices: 114922--115062 Score: 137
Period size: 31 Copynumber: 4.6 Consensus size: 31
114912 TATTTTTTGA
* *
114922 CCCTCAAATTTTCC-AAATATTCTAATTCGAC
1 CCCT-AAATTTTCCAAAAAATTCCAATTCGAC
*
114953 CCCTAAATTTTCCAAAAAATAT-GAATTCGAC
1 CCCTAAATTTTCCAAAAAAT-TCCAATTCGAC
**
114984 CCCTAAATTTTCCAAAAAATTCCAATTTAAC
1 CCCTAAATTTTCCAAAAAATTCCAATTCGAC
* * * * *
115015 CTCTAAACTTT-CTAAAACTTCCAATTTGAC
1 CCCTAAATTTTCCAAAAAATTCCAATTCGAC
115045 CCCTAAAATTTT-CAAAAA
1 CCCT-AAATTTTCCAAAAA
115063 TTTAAATTTG
Statistics
Matches: 93, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
30 29 0.31
31 63 0.68
32 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.03, T:0.33
Consensus pattern (31 bp):
CCCTAAATTTTCCAAAAAATTCCAATTCGAC
Found at i:115071 original size:30 final size:31
Alignment explanation
Indices: 114917--115076 Score: 134
Period size: 31 Copynumber: 5.3 Consensus size: 31
114907 AAAATTATTT
*
114917 TTTGA-CCCTCAAATTTTCC-AAATA-TTCTAA
1 TTTGACCCCT-AAATTTTCCAAAAAATTTC-AA
* * *
114947 TTCGACCCCTAAATTTTCCAAAAAATATGAA
1 TTTGACCCCTAAATTTTCCAAAAAATTTCAA
* *
114978 TTCGACCCCTAAATTTTCCAAAAAATTCCAA
1 TTTGACCCCTAAATTTTCCAAAAAATTTCAA
* * * * * *
115009 TTTAACCTCTAAACTTT-CTAAAACTTCCAA
1 TTTGACCCCTAAATTTTCCAAAAAATTTCAA
*
115039 TTTGACCCCTAAAATTTT-C-AAAAATTTAAA
1 TTTGACCCCT-AAATTTTCCAAAAAATTTCAA
115069 TTTGACCC
1 TTTGACCC
115077 AATTTTAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
30 48 0.45
31 58 0.54
32 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.04, T:0.34
Consensus pattern (31 bp):
TTTGACCCCTAAATTTTCCAAAAAATTTCAA
Found at i:115771 original size:18 final size:18
Alignment explanation
Indices: 115748--115783 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
115738 TCCATTTTCA
115748 TTTTCTAAAATCTAAATC
1 TTTTCTAAAATCTAAATC
115766 TTTTCTAAAATCTAAATC
1 TTTTCTAAAATCTAAATC
115784 GAAACTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTCTAAAATCTAAATC
Found at i:128197 original size:15 final size:15
Alignment explanation
Indices: 128177--128221 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
128167 TTCCTCCTTC
128177 TCAACAGGCTCATCT
1 TCAACAGGCTCATCT
*
128192 TCAACA---TCAAC-
1 TCAACAGGCTCATCT
128203 TCAACAGGCTCATCT
1 TCAACAGGCTCATCT
128218 TCAA
1 TCAA
128222 AATCAATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
11 6 0.25
12 4 0.17
14 4 0.17
15 10 0.42
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.24
Consensus pattern (15 bp):
TCAACAGGCTCATCT
Found at i:128208 original size:26 final size:26
Alignment explanation
Indices: 128176--128227 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
128166 TTTCCTCCTT
*
128176 CTCAACAGGCTCATCTTCAACATCAA
1 CTCAACAGGCTCATCTTCAAAATCAA
128202 CTCAACAGGCTCATCTTCAAAATCAA
1 CTCAACAGGCTCATCTTCAAAATCAA
128228 TCATTCGGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.23
Consensus pattern (26 bp):
CTCAACAGGCTCATCTTCAAAATCAA
Found at i:134470 original size:13 final size:13
Alignment explanation
Indices: 134438--134479 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
134428 ATAGCAAACA
134438 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
134451 TTCTTTTC-TCTT
1 TTTTTTTCTTCTT
*
134463 TTATTTTTTTTCTT
1 TT-TTTTTCTTCTT
134477 TTT
1 TTT
134480 CTCATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 12 0.50
14 6 0.25
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:136393 original size:23 final size:23
Alignment explanation
Indices: 136367--136411 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
136357 TGCAAGATAG
*
136367 AATGTAGTAGACACATACGGTCT
1 AATGTAGTAGACACATAAGGTCT
*
136390 AATGTAGTAGTCACATAAGGTC
1 AATGTAGTAGACACATAAGGTC
136412 CTTCATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (23 bp):
AATGTAGTAGACACATAAGGTCT
Found at i:137283 original size:20 final size:21
Alignment explanation
Indices: 137258--137296 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
137248 ACAAGGAATT
137258 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
137278 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
137297 TAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:144657 original size:13 final size:13
Alignment explanation
Indices: 144625--144666 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
144615 ATAGCAAACA
144625 TTTTTTTCTTCTT
1 TTTTTTTCTTCTT
*
144638 TTCTTTTC-TCTT
1 TTTTTTTCTTCTT
*
144650 TTATTTTTTTTCTT
1 TT-TTTTTCTTCTT
144664 TTT
1 TTT
144667 CTCATTTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 6 0.25
13 12 0.50
14 6 0.25
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTTTCTTCTT
Found at i:146580 original size:23 final size:23
Alignment explanation
Indices: 146554--146598 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
146544 TGCAAGATAG
*
146554 AATGTAGTAGACACATACGGTCT
1 AATGTAGTAGACACATAAGGTCT
*
146577 AATGTAGTAGTCACATAAGGTC
1 AATGTAGTAGACACATAAGGTC
146599 CTTCATCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (23 bp):
AATGTAGTAGACACATAAGGTCT
Found at i:147470 original size:20 final size:21
Alignment explanation
Indices: 147445--147483 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
147435 ACAAGGAATT
147445 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
147465 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
147484 TAACAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:155637 original size:32 final size:27
Alignment explanation
Indices: 155549--155626 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
155539 TCATCCAAAC
* * * *
155549 TTTTGCCAGAGAGGCATTCGTCTCATA
1 TTTTGCCACAAAGGCATTCCTTTCATA
155576 TTTTGCCACAAAGGCATTCCTTTCATA
1 TTTTGCCACAAAGGCATTCCTTTCATA
* *
155603 TTTTTCCATAAAGGCATTCCTTTC
1 TTTTGCCACAAAGGCATTCCTTTC
155627 CTGATATATT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (27 bp):
TTTTGCCACAAAGGCATTCCTTTCATA
Found at i:155794 original size:27 final size:27
Alignment explanation
Indices: 155735--155795 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 27
155725 ATAGATGCAC
* * *
155735 TCCTCTCATATTTTTCCACTAAGGCAT
1 TCCTTTCATATTTTACCACAAAGGCAT
155762 TCCTTTCATATTTTACCACAAAGGCAT
1 TCCTTTCATATTTTACCACAAAGGCAT
*
155789 TTCTTTC
1 TCCTTTC
155796 TTGCCATGTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.43
Consensus pattern (27 bp):
TCCTTTCATATTTTACCACAAAGGCAT
Found at i:155816 original size:169 final size:169
Alignment explanation
Indices: 155494--155819 Score: 481
Period size: 169 Copynumber: 1.9 Consensus size: 169
155484 ACTTTCAAAG
155494 TTTGCCACTAAAGCTATTTCTTCAAAGTGCACCACAAAAAACATTTCATCCAAACTTTTGCCAGA
1 TTTGCCACTAAAGCTATTTCTTCAAAGTGCACCACAAAAAACATTTCATCCAAACTTTTGCCAGA
* * * *
155559 GAGGCATTCGTCTCATATTTTGCCACAAAGGCATTCCTTTCATATTTTTCCATAAAGGCATTCCT
66 GAGGCACTCCTCTCATATTTTGCCACAAAGGCATTCCTTTCATATTTTACCACAAAGGCATTCCT
* **
155624 TTCCTGATATATTTATGATATGAATTTTCCTAAGCTCAC
131 TTCCTGACATATTTACAATATGAATTTTCCTAAGCTCAC
* * * * *
155663 TTTGCCACTAAAGCTATTTCTTCAGAGTGCACCACAAAAAACATTTCATCCAGACTTTTTCTATA
1 TTTGCCACTAAAGCTATTTCTTCAAAGTGCACCACAAAAAACATTTCATCCAAACTTTTGCCAGA
* * * *
155728 GATGCACTCCTCTCATATTTTTCCACTAAGGCATTCCTTTCATATTTTACCACAAAGGCATTTCT
66 GAGGCACTCCTCTCATATTTTGCCACAAAGGCATTCCTTTCATATTTTACCACAAAGGCATTCCT
* * *
155793 TTCTTGCCATGTTTACAATATGAATTT
131 TTCCTGACATATTTACAATATGAATTT
155820 GACTAAGATC
Statistics
Matches: 138, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
169 138 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (169 bp):
TTTGCCACTAAAGCTATTTCTTCAAAGTGCACCACAAAAAACATTTCATCCAAACTTTTGCCAGA
GAGGCACTCCTCTCATATTTTGCCACAAAGGCATTCCTTTCATATTTTACCACAAAGGCATTCCT
TTCCTGACATATTTACAATATGAATTTTCCTAAGCTCAC
Found at i:161695 original size:18 final size:19
Alignment explanation
Indices: 161672--161708 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
161662 CTATACATAC
161672 ATCTAATAATTA-ATGTGT
1 ATCTAATAATTACATGTGT
*
161690 ATCTAATACTTACATGTGT
1 ATCTAATAATTACATGTGT
161709 CTGAAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.43
Consensus pattern (19 bp):
ATCTAATAATTACATGTGT
Found at i:164375 original size:18 final size:16
Alignment explanation
Indices: 164317--164376 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 16
164307 TAATTAATTT
164317 TAAAAAATTTTAAAAA
1 TAAAAAATTTTAAAAA
164333 TAAAAGGATATTTTAAAAA
1 TAAAA--A-ATTTTAAAAA
*
164352 T-TAAAATTATTAAAAAA
1 TAAAAAATT-TT-AAAAA
164369 TAAAAAAT
1 TAAAAAAT
164377 AAATATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 3 0.08
16 8 0.22
17 6 0.17
18 8 0.22
19 11 0.31
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (16 bp):
TAAAAAATTTTAAAAA
Found at i:167911 original size:30 final size:29
Alignment explanation
Indices: 167858--167918 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
167848 TATTAACATA
* *
167858 TTCATACCCTGTATTATTCACATTTGCAT
1 TTCATACCCTGTAATAATCACATTTGCAT
167887 TTCATACCCTGTAATAGATCACATTTGCAT
1 TTCATACCCTGTAATA-ATCACATTTGCAT
167917 TT
1 TT
167919 TCATGCCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (29 bp):
TTCATACCCTGTAATAATCACATTTGCAT
Found at i:194999 original size:10 final size:10
Alignment explanation
Indices: 194984--195014 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
194974 ATGCTCTGTA
194984 TATTGAAGTG
1 TATTGAAGTG
*
194994 TATTGAAGTA
1 TATTGAAGTG
195004 TATTGAAGTG
1 TATTGAAGTG
195014 T
1 T
195015 GTAAATGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (10 bp):
TATTGAAGTG
Found at i:202297 original size:10 final size:10
Alignment explanation
Indices: 202282--202312 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
202272 ATGCTTTGTA
202282 TATTGAAGTG
1 TATTGAAGTG
*
202292 TATTGAAGTA
1 TATTGAAGTG
202302 TATTGAAGTG
1 TATTGAAGTG
202312 T
1 T
202313 GTAAATGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (10 bp):
TATTGAAGTG
Found at i:204442 original size:20 final size:20
Alignment explanation
Indices: 204401--204440 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
204391 TTCTAAATTT
* *
204401 ATTTTATTTTCAACATTCAA
1 ATTTTAATTTCAACAATCAA
204421 ATTTTAATTTCAA-AATCAA
1 ATTTTAATTTCAACAATCAA
204440 A
1 A
204441 ATCAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTTTAATTTCAACAATCAA
Found at i:212810 original size:44 final size:44
Alignment explanation
Indices: 212747--212834 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
212737 TGTCTCAATC
212747 TGGAAGAAAATAGAACAGATATCAGCTATTTGAAAGATTTGATG
1 TGGAAGAAAATAGAACAGATATCAGCTATTTGAAAGATTTGATG
212791 TGGAAGAAAATAGAACAGATATCAGCTATTTGAAAGATTTGATG
1 TGGAAGAAAATAGAACAGATATCAGCTATTTGAAAGATTTGATG
212835 GACTATGTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (44 bp):
TGGAAGAAAATAGAACAGATATCAGCTATTTGAAAGATTTGATG
Found at i:213043 original size:64 final size:63
Alignment explanation
Indices: 212939--213057 Score: 193
Period size: 64 Copynumber: 1.9 Consensus size: 63
212929 GACATTTAAC
** *
212939 ATAACACTCTTAAGCTCATTAATTGGTACACTGTGTGCAAATATCTTATAATCGTTAAGAATT
1 ATAACACTCTTAAGCTCATTAATTGGTACACCATGCGCAAATATCTTATAATCGTTAAGAATT
*
213002 ATAACACTCATTAAGCTCATTAATTGGTACACCATGCGCAAATATCTTCTAATCGT
1 ATAACACTC-TTAAGCTCATTAATTGGTACACCATGCGCAAATATCTTATAATCGT
213058 GAAGGAAATT
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
63 9 0.18
64 42 0.82
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (63 bp):
ATAACACTCTTAAGCTCATTAATTGGTACACCATGCGCAAATATCTTATAATCGTTAAGAATT
Found at i:214813 original size:17 final size:16
Alignment explanation
Indices: 214788--214819 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
214778 TATAACTTCC
214788 TTTTTTTCGTATTTTA
1 TTTTTTTCGTATTTTA
214804 TTTTTCTTCGTATTTT
1 TTTTT-TTCGTATTTT
214820 TCCAATTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTTTTTCGTATTTTA
Found at i:217437 original size:30 final size:34
Alignment explanation
Indices: 217402--217468 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 34
217392 AATAGCATAT
*
217402 ATTTTTTTA-ATTTTTAAAA-GATTAAA-T-CAA
1 ATTTTTTAACATTTTTAAAAGGATTAAAGTACAA
217432 A-TTTTTAACATTTTTAAAAGGATTAAAGTACAA
1 ATTTTTTAACATTTTTAAAAGGATTAAAGTACAA
217465 ATTT
1 ATTT
217469 ATCATTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
29 6 0.19
30 11 0.35
31 7 0.23
32 1 0.03
33 4 0.13
34 2 0.06
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.46
Consensus pattern (34 bp):
ATTTTTTAACATTTTTAAAAGGATTAAAGTACAA
Found at i:220728 original size:16 final size:17
Alignment explanation
Indices: 220697--220731 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
220687 CATATAAAAT
*
220697 AATCTATATTATAATAA
1 AATCTATATTAGAATAA
220714 AATCTA-ATTAGAATAA
1 AATCTATATTAGAATAA
220730 AA
1 AA
220732 ATCCTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (17 bp):
AATCTATATTAGAATAA
Found at i:221347 original size:22 final size:23
Alignment explanation
Indices: 221302--221347 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
221292 TTTAATACTT
* *
221302 TAAAAATTATAATTTTACTATCG
1 TAAAAATTACAATTTTAATATCG
*
221325 TAAAAATTACAA-TTTAATTTCG
1 TAAAAATTACAATTTTAATATCG
221347 T
1 T
221348 TCCCCTAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAAAATTACAATTTTAATATCG
Found at i:221656 original size:25 final size:25
Alignment explanation
Indices: 221628--221703 Score: 77
Period size: 26 Copynumber: 3.1 Consensus size: 25
221618 TAATCACTTC
221628 TTTAATAATTAATAGTATTTTAAAT
1 TTTAATAATTAATAGTATTTTAAAT
**
221653 TTT-ATAATTTTAATAGTATTTTATTT
1 TTTAATAA--TTAATAGTATTTTAAAT
* *
221679 TTTAAAAACTAATA-T-TTTTAAAT
1 TTTAATAATTAATAGTATTTTAAAT
221702 TT
1 TT
221704 AAAAGTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 8 0.19
24 5 0.12
25 8 0.19
26 18 0.43
27 3 0.07
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (25 bp):
TTTAATAATTAATAGTATTTTAAAT
Found at i:223547 original size:22 final size:24
Alignment explanation
Indices: 223495--223587 Score: 111
Period size: 24 Copynumber: 4.0 Consensus size: 24
223485 ATGTAAAACC
* *
223495 GTGCCACAAGACAGAG-GAAAAGC
1 GTGCCACAAGACAGAGAAAAAAGT
* *
223518 ATGCCACAAGACAAAGAAAAAA-T
1 GTGCCACAAGACAGAGAAAAAAGT
*
223541 GTG-CACAAGATAGAGAAAAAAGT
1 GTGCCACAAGACAGAGAAAAAAGT
*
223564 GTGCCACAAGACAGAGGAAAAAGT
1 GTGCCACAAGACAGAGAAAAAAGT
223588 ACCACAAAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
22 16 0.28
23 20 0.34
24 22 0.38
ACGTcount: A:0.51, C:0.16, G:0.25, T:0.09
Consensus pattern (24 bp):
GTGCCACAAGACAGAGAAAAAAGT
Found at i:223561 original size:24 final size:24
Alignment explanation
Indices: 223495--223585 Score: 91
Period size: 23 Copynumber: 3.9 Consensus size: 24
223485 ATGTAAAACC
**
223495 GTGCCACAAGACAGAGGAAAAGCA-
1 GTGCCACAAGACAGA-GAAAAAAAT
*
223519 -TGCCACAAGACAAAG-AAAAAAT
1 GTGCCACAAGACAGAGAAAAAAAT
* *
223541 GTG-CACAAGATAGAGAAAAAAGT
1 GTGCCACAAGACAGAGAAAAAAAT
*
223564 GTGCCACAAGACAGAGGAAAAA
1 GTGCCACAAGACAGAGAAAAAA
223586 GTACCACAAA
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
21 4 0.07
22 11 0.20
23 24 0.44
24 16 0.29
ACGTcount: A:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (24 bp):
GTGCCACAAGACAGAGAAAAAAAT
Found at i:225791 original size:25 final size:25
Alignment explanation
Indices: 225757--225809 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
225747 TCTGGTGAAG
225757 CCATTTTAAATGGCACAATCCGTTT
1 CCATTTTAAATGGCACAATCCGTTT
*
225782 CCATTTTAAATGGCACCATCCGTTT
1 CCATTTTAAATGGCACAATCCGTTT
225807 CCA
1 CCA
225810 AGGTATGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.26, C:0.28, G:0.11, T:0.34
Consensus pattern (25 bp):
CCATTTTAAATGGCACAATCCGTTT
Found at i:229169 original size:51 final size:50
Alignment explanation
Indices: 229094--229259 Score: 219
Period size: 51 Copynumber: 3.2 Consensus size: 50
229084 TTAGATCTTG
*
229094 TTTATCTAAATTATTTTGTTCAGATATGATGTTTTTATAAAAAATAAATA
1 TTTATTTAAATTATTTTGTTCAGATATGATGTTTTTATAAAAAATAAATA
*
229144 TTTATTTAAATTACTTTTGTTCAGATCT-AGTGTTTTATATAAAAAAATAAATA
1 TTTATTTAAATTA-TTTTGTTCAGATATGA-TGTTTT-TAT-AAAAAATAAATA
* * *
229197 TTTATTTAAATTGTTTTTGTTCAGATATGGTG-TTTTATATAAATATAAATA
1 TTTATTTAAATT-ATTTTGTTCAGATATGATGTTTTTATA-AAAAATAAATA
229248 TTTATTTAAATT
1 TTTATTTAAATT
229260 GTTCAATTTA
Statistics
Matches: 103, Mismatches: 6, Indels: 13
0.84 0.05 0.11
Matches are distributed among these distances:
50 14 0.14
51 44 0.43
52 6 0.06
53 39 0.38
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (50 bp):
TTTATTTAAATTATTTTGTTCAGATATGATGTTTTTATAAAAAATAAATA
Found at i:229207 original size:53 final size:50
Alignment explanation
Indices: 229094--229323 Score: 234
Period size: 50 Copynumber: 4.5 Consensus size: 50
229084 TTAGATCTTG
*
229094 TTTATCTAAATTATTTTGTTCAGATATGATGTTTT-TATAAAAAATAAATA
1 TTTATTTAAATTATTTTGTTCAGATATG-TGTTTTATATAAAAAATAAATA
*
229144 TTTATTTAAATTACTTTTGTTCAGATCTAGTGTTTTATATAAAAAAATAAATA
1 TTTATTTAAATTA-TTTTGTTCAGATAT-GTGTTTTATAT-AAAAAATAAATA
* *
229197 TTTATTTAAATTGTTTTTGTTCAGATATGGTGTTTTATAT-AAATATAAATA
1 TTTATTTAAATT-ATTTTGTTCAGATAT-GTGTTTTATATAAAAAATAAATA
* *** * * * *
229248 TTTATTTAAATTGTTCAATTTAGATTTGGTGTTTTACAT-AAATATAAATA
1 TTTATTTAAATTATTTTGTTCAGATAT-GTGTTTTATATAAAAAATAAATA
* * *
229298 TTTATTTATATT-GTTTGTTCAAATAT
1 TTTATTTAAATTATTTTGTTCAGATAT
229324 TTTATTCTAC
Statistics
Matches: 154, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
49 7 0.05
50 54 0.35
51 41 0.27
52 4 0.03
53 48 0.31
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (50 bp):
TTTATTTAAATTATTTTGTTCAGATATGTGTTTTATATAAAAAATAAATA
Found at i:229296 original size:50 final size:51
Alignment explanation
Indices: 229110--229312 Score: 207
Period size: 53 Copynumber: 4.0 Consensus size: 51
229100 TAAATTATTT
* * * * *
229110 TGTTCAGATATGATGTTTT-TATAAAAAATAAATATTTATTTAAATTACTT-T
1 TGTTCAGATATGGTGTTTTACAT-AAATATAAATATTTATTTAAATT-GTTAA
* * * * **
229161 TGTTCAGATCTAGTGTTTTATATAAAAAAATAAATATTTATTTAAATTGTTTT
1 TGTTCAGATATGGTGTTTTACAT--AAATATAAATATTTATTTAAATTGTTAA
*
229214 TGTTCAGATATGGTGTTTTATATAAATATAAATATTTATTTAAATTGTTCAA
1 TGTTCAGATATGGTGTTTTACATAAATATAAATATTTATTTAAATTGTT-AA
* *
229266 T-TT-AGATTTGGTGTTTTACATAAATATAAATATTTATTTATATTGTT
1 TGTTCAGATATGGTGTTTTACATAAATATAAATATTTATTTAAATTGTT
229313 TGTTCAAATA
Statistics
Matches: 136, Mismatches: 12, Indels: 9
0.87 0.08 0.06
Matches are distributed among these distances:
50 41 0.30
51 43 0.32
52 6 0.04
53 46 0.34
ACGTcount: A:0.36, C:0.03, G:0.10, T:0.50
Consensus pattern (51 bp):
TGTTCAGATATGGTGTTTTACATAAATATAAATATTTATTTAAATTGTTAA
Found at i:236412 original size:37 final size:37
Alignment explanation
Indices: 236362--236471 Score: 175
Period size: 37 Copynumber: 3.0 Consensus size: 37
236352 GCATACACAA
*
236362 TTTCAAGCTATGTGTCTAGTAGGCTTCGTGCCGGTGT
1 TTTCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
236399 TTTCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
1 TTTCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
* ** *
236436 TTTCAGGCTATGTGCCTAGTAAACTTCGTGCTGGTG
1 TTTCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTG
236472 AATTCGGGCT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.15, C:0.20, G:0.29, T:0.36
Consensus pattern (37 bp):
TTTCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
Found at i:236482 original size:37 final size:37
Alignment explanation
Indices: 236362--236507 Score: 166
Period size: 37 Copynumber: 3.9 Consensus size: 37
236352 GCATACACAA
* *
236362 TTTCAAGCTATGTGTCTAGTAGGCTTCGTGCCGGTGT
1 TTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
*
236399 TTTCAAGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
1 TTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
** * *
236436 TTTCAGGCTATGTGCCTAGTAAACTTCGTGCTGGTGA
1 TTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
* * * * ** *
236473 ATTCGGGCTATATGCTTAACAGGCTTTGTGCCGGT
1 TTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGT
236508 AATCCAAAAA
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 93 1.00
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.36
Consensus pattern (37 bp):
TTTCAGGCTATGTGCCTAGTAGGCTTCGTGCCGGTGT
Found at i:242077 original size:119 final size:119
Alignment explanation
Indices: 241866--242104 Score: 469
Period size: 119 Copynumber: 2.0 Consensus size: 119
241856 CTTGGTTCAC
241866 TATGGTTGTTTTGGTTTTCCTATTGTACCTCCTACAATATCTCGTTTGCACTAGATATTTAGAGT
1 TATGGTTGTTTTGGTTTTCCTATTGTACCTCCTACAATATCTCGTTTGCACTAGATATTTAGAGT
241931 ATATCCATCACATCTTGCCATGTCTTGGTCCAAATGCTACCTCCTGTCATGATA
66 ATATCCATCACATCTTGCCATGTCTTGGTCCAAATGCTACCTCCTGTCATGATA
241985 TATGGTTGTTTTGGTTTTCCTATTGTACCTCCTACAATATCTCGTTTGCACTAGATATTTAGAGT
1 TATGGTTGTTTTGGTTTTCCTATTGTACCTCCTACAATATCTCGTTTGCACTAGATATTTAGAGT
*
242050 ATATCCATCACATCTTGCCATGTCTTGGTCCAAATGCTACCTCTTGTCATGATA
66 ATATCCATCACATCTTGCCATGTCTTGGTCCAAATGCTACCTCCTGTCATGATA
242104 T
1 T
242105 CCACCTTCCT
Statistics
Matches: 119, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 119 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (119 bp):
TATGGTTGTTTTGGTTTTCCTATTGTACCTCCTACAATATCTCGTTTGCACTAGATATTTAGAGT
ATATCCATCACATCTTGCCATGTCTTGGTCCAAATGCTACCTCCTGTCATGATA
Found at i:250624 original size:19 final size:19
Alignment explanation
Indices: 250596--250634 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
250586 TTTATGGTTT
250596 TAAATAATTTTTGGGTAAAA
1 TAAATAA-TTTTGGGTAAAA
*
250616 TAAAT-ATTTTGGGTTAAA
1 TAAATAATTTTGGGTAAAA
250634 T
1 T
250635 TGGAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 1 0.06
20 5 0.28
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (19 bp):
TAAATAATTTTGGGTAAAA
Found at i:252444 original size:22 final size:22
Alignment explanation
Indices: 252416--252501 Score: 102
Period size: 22 Copynumber: 3.9 Consensus size: 22
252406 GATGTAATAT
*
252416 GCCAATATAATTGATCGATTGC
1 GCCAATATAATTGATTGATTGC
*
252438 GCCAATACAATTGATTGATTGC
1 GCCAATATAATTGATTGATTGC
*
252460 ACCAAGT-TAATTGATTGATTGC
1 GCCAA-TATAATTGATTGATTGC
* * *
252482 GCCACTTTAATTGAATGATT
1 GCCAATATAATTGATTGATT
252502 TTTTATGCTA
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
21 1 0.02
22 53 0.96
23 1 0.02
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (22 bp):
GCCAATATAATTGATTGATTGC
Found at i:255303 original size:27 final size:26
Alignment explanation
Indices: 255253--255303 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
255243 GTGTCGTATC
*
255253 TTGTTTTGGCTTCTGCACTGTGGAAT
1 TTGTTTTGGCTTCTGCAATGTGGAAT
* *
255279 TTGTTTTGTGCTTCTTCAATTTGGA
1 TTGTTTTG-GCTTCTGCAATGTGGA
255304 CTGTGACACG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 8 0.38
27 13 0.62
ACGTcount: A:0.12, C:0.14, G:0.24, T:0.51
Consensus pattern (26 bp):
TTGTTTTGGCTTCTGCAATGTGGAAT
Found at i:264065 original size:14 final size:13
Alignment explanation
Indices: 264048--264085 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
264038 ATTTAAAACA
264048 AAACAAGTAAAATG
1 AAACAAGTAAAA-G
*
264062 AAACAAATAAAAG
1 AAACAAGTAAAAG
264075 AAA-AAGTAAAA
1 AAACAAGTAAAA
264086 ATGCATTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 11 0.50
ACGTcount: A:0.74, C:0.05, G:0.11, T:0.11
Consensus pattern (13 bp):
AAACAAGTAAAAG
Found at i:271185 original size:60 final size:60
Alignment explanation
Indices: 271117--271236 Score: 195
Period size: 60 Copynumber: 2.0 Consensus size: 60
271107 GCTGATCTTG
** *
271117 TGGCTGCATTCTTCTTTTAGCATTTATCTTCTGATAAGAGTTTCTGCGCTGACAATTCTA
1 TGGCTGCATTCTTCTTCCAGCATTAATCTTCTGATAAGAGTTTCTGCGCTGACAATTCTA
* *
271177 TGGCTGCATTCTTCTTCCAGCATTAATCTTTTGATATGAGTTTCTGCGCTGACAATTCTA
1 TGGCTGCATTCTTCTTCCAGCATTAATCTTCTGATAAGAGTTTCTGCGCTGACAATTCTA
271237 AGGCGCAATA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.20, C:0.21, G:0.17, T:0.42
Consensus pattern (60 bp):
TGGCTGCATTCTTCTTCCAGCATTAATCTTCTGATAAGAGTTTCTGCGCTGACAATTCTA
Found at i:286744 original size:21 final size:21
Alignment explanation
Indices: 286701--286745 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
286691 GGATTTTTAA
* *
286701 TATCGGTAGAAGCATGTCGAG
1 TATCGGTAGAACCATGTCAAG
286722 TATCGGTAGAACCAT-TACAAG
1 TATCGGTAGAACCATGT-CAAG
286743 TAT
1 TAT
286746 TGAATAGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (21 bp):
TATCGGTAGAACCATGTCAAG
Found at i:292431 original size:15 final size:14
Alignment explanation
Indices: 292407--292436 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
292397 AAAATTCCTC
292407 ATAGCAAGGGAGTT
1 ATAGCAAGGGAGTT
292421 ATAGACAAGGGAGTT
1 ATAG-CAAGGGAGTT
292436 A
1 A
292437 CAACAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.40, C:0.07, G:0.33, T:0.20
Consensus pattern (14 bp):
ATAGCAAGGGAGTT
Found at i:300415 original size:17 final size:18
Alignment explanation
Indices: 300393--300430 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
300383 TTACATTTTT
300393 ATTTGTCACTGCATTT-C
1 ATTTGTCACTGCATTTGC
* *
300410 ATTTGTTAGTGCATTTGC
1 ATTTGTCACTGCATTTGC
300428 ATT
1 ATT
300431 GTAGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (18 bp):
ATTTGTCACTGCATTTGC
Found at i:300447 original size:17 final size:16
Alignment explanation
Indices: 300402--300443 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
300392 TATTTGTCAC
300402 TGCATTTCATTTGTTAG
1 TGCATTTCA-TTGTTAG
300419 TGCATTTGCATTG-TAG
1 TGCATTT-CATTGTTAG
300435 TTGCATTTC
1 -TGCATTTC
300444 CATTCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (16 bp):
TGCATTTCATTGTTAG
Found at i:301033 original size:15 final size:14
Alignment explanation
Indices: 301008--301050 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 14
300998 AAAATTCACA
301008 AAAG-AAAGAAAAG
1 AAAGAAAAGAAAAG
301021 AAAGAAGAAGAAAAG
1 AAAGAA-AAGAAAAG
301036 --AGAAAAGAAAAG
1 AAAGAAAAGAAAAG
301048 AAA
1 AAA
301051 TATATTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
12 8 0.31
13 8 0.31
14 2 0.08
15 8 0.31
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAGAAAAGAAAAG
Found at i:305754 original size:18 final size:18
Alignment explanation
Indices: 305690--305756 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
305680 ACAAAAGAAA
* * *
305690 TAGCATAATAGCTTGTTT
1 TAGCATACTGGCTCGTTT
* * *
305708 GAGCATATTGCCTC-TTT
1 TAGCATACTGGCTCGTTT
305725 TAAGCATACTGGCTCGTTT
1 T-AGCATACTGGCTCGTTT
305744 TAGCATACTGGCT
1 TAGCATACTGGCT
305757 TGAAAGAGCA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
17 3 0.08
18 32 0.82
19 4 0.10
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (18 bp):
TAGCATACTGGCTCGTTT
Found at i:308266 original size:22 final size:21
Alignment explanation
Indices: 308239--308306 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 21
308229 ATTTTTATGC
308239 TGTTTTTTACTGTTATGGTTGT
1 TGTTTTTTACTGTT-TGGTTGT
** *
308261 TGTTTTTTGTTGTTT--TGGT
1 TGTTTTTTACTGTTTGGTTGT
*
308280 T-TTTTTTACTGTTTTGGTTGC
1 TGTTTTTTACTG-TTTGGTTGT
308301 TGTTTT
1 TGTTTT
308307 GGTGCTCTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
18 8 0.23
19 7 0.20
21 4 0.11
22 16 0.46
ACGTcount: A:0.04, C:0.04, G:0.22, T:0.69
Consensus pattern (21 bp):
TGTTTTTTACTGTTTGGTTGT
Found at i:308359 original size:12 final size:12
Alignment explanation
Indices: 308338--308448 Score: 68
Period size: 12 Copynumber: 9.1 Consensus size: 12
308328 GATGCTGTTA
*
308338 TTTTTATTGCTT
1 TTTTTGTTGCTT
308350 TTTTTGTTGCTT
1 TTTTTGTTGCTT
**
308362 TTTTCCATCTG-TT
1 TTTT-TGT-TGCTT
*
308375 ATTTTTGTTGCTG
1 -TTTTTGTTGCTT
*
308388 TTTTTGTTACTAT
1 TTTTTGTTGCT-T
*
308401 TTTTT-CTG-TT
1 TTTTTGTTGCTT
308411 ATTTTTGTTG-TT
1 -TTTTTGTTGCTT
*
308423 GTTTTTGTTGCTA
1 -TTTTTGTTGCTT
*
308436 TTTTTATTGCTT
1 TTTTTGTTGCTT
308448 T
1 T
308449 CGTTGTTGTT
Statistics
Matches: 76, Mismatches: 15, Indels: 16
0.71 0.14 0.15
Matches are distributed among these distances:
10 1 0.01
11 6 0.08
12 52 0.68
13 11 0.14
14 6 0.08
ACGTcount: A:0.07, C:0.09, G:0.14, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGCTT
Found at i:308365 original size:24 final size:24
Alignment explanation
Indices: 308338--308448 Score: 77
Period size: 24 Copynumber: 4.5 Consensus size: 24
308328 GATGCTGTTA
308338 TTTTTATTGCTTTTTTTGTTGCTT
1 TTTTTATTGCTTTTTTTGTTGCTT
* *
308362 TTTTCCATCTG-TTATTTTTGTTGCTG
1 TTTT-TAT-TGCTT-TTTTTGTTGCTT
* * *
308388 TTTTTGTTACTATTTTTT-CTG-TT
1 TTTTTATTGCT-TTTTTTGTTGCTT
* *
308411 ATTTTTGTTG-TTGTTTTTGTTGCTA
1 -TTTTTATTGCTT-TTTTTGTTGCTT
308436 TTTTTATTGCTTT
1 TTTTTATTGCTTT
308449 CGTTGTTGTT
Statistics
Matches: 66, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
22 1 0.02
23 7 0.11
24 26 0.39
25 14 0.21
26 18 0.27
ACGTcount: A:0.07, C:0.09, G:0.14, T:0.70
Consensus pattern (24 bp):
TTTTTATTGCTTTTTTTGTTGCTT
Found at i:308405 original size:86 final size:85
Alignment explanation
Indices: 308291--308448 Score: 192
Period size: 86 Copynumber: 1.8 Consensus size: 85
308281 TTTTTTACTG
* * *
308291 TTTTGGTTGCTGTTTTGGTGCTCTTTTTTACTGTT-TTGATGCTGTTATTTTTATTGCTTTTTTT
1 TTTTGGTTGCTGTTTTGGTACTATTTTTT-CTGTTATTGATGCTGTTATTTTTATTGCTATTTTT
*
308355 GTTGCTTTTTTCCATCTGTTA
65 ATTGCTTTTTTCCATCTGTTA
* * ** * * *
308376 TTTTTGTTGCTGTTTTTGTTACTATTTTTTCTGTTATTTTTGTTGTTGTTTTTGTTGCTATTTTT
1 TTTTGGTTGCTG-TTTTGGTACTATTTTTTCTGTTATTGATGCTGTTATTTTTATTGCTATTTTT
308441 ATTGCTTT
65 ATTGCTTT
308449 CGTTGTTGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
85 16 0.27
86 44 0.73
ACGTcount: A:0.07, C:0.09, G:0.16, T:0.67
Consensus pattern (85 bp):
TTTTGGTTGCTGTTTTGGTACTATTTTTTCTGTTATTGATGCTGTTATTTTTATTGCTATTTTTA
TTGCTTTTTTCCATCTGTTA
Found at i:308417 original size:36 final size:37
Alignment explanation
Indices: 308332--308440 Score: 150
Period size: 36 Copynumber: 2.9 Consensus size: 37
308322 TGTTTTGATG
* *
308332 CTGTTATTTTTATTGCTTTTTTTGTTGCT-TTTTTCCAT
1 CTGTTATTTTTGTTGCTGTTTTTGTTGCTATTTTT-C-T
*
308370 CTGTTATTTTTGTTGCTGTTTTTGTTACTATTTTT-T
1 CTGTTATTTTTGTTGCTGTTTTTGTTGCTATTTTTCT
*
308406 CTGTTATTTTTGTTGTTGTTTTTGTTGCTATTTTT
1 CTGTTATTTTTGTTGCTGTTTTTGTTGCTATTTTT
308441 ATTGCTTTCG
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
36 34 0.52
38 26 0.40
39 5 0.08
ACGTcount: A:0.07, C:0.09, G:0.14, T:0.70
Consensus pattern (37 bp):
CTGTTATTTTTGTTGCTGTTTTTGTTGCTATTTTTCT
Found at i:308455 original size:36 final size:36
Alignment explanation
Indices: 308369--308458 Score: 94
Period size: 36 Copynumber: 2.5 Consensus size: 36
308359 CTTTTTTCCA
** *
308369 TCTGTTATTTTTGTTGCTGTTTTTGTTACTATTTTT
1 TCTGTTATCGTTGTTGTTGTTTTTGTTACTATTTTT
** *
308405 TCTGTTATTTTTGTTGTTGTTTTTGTTGCTATTTTT
1 TCTGTTATCGTTGTTGTTGTTTTTGTTACTATTTTT
308441 AT-TGCTT-TCGTTGTTGTT
1 -TCTG-TTATCGTTGTTGTT
308459 TTGCTGTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 45 0.94
37 3 0.06
ACGTcount: A:0.07, C:0.08, G:0.17, T:0.69
Consensus pattern (36 bp):
TCTGTTATCGTTGTTGTTGTTTTTGTTACTATTTTT
Found at i:308662 original size:12 final size:12
Alignment explanation
Indices: 308645--308669 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
308635 AAGTTGTTTA
308645 TGTTTTAATGTT
1 TGTTTTAATGTT
308657 TGTTTTAATGTT
1 TGTTTTAATGTT
308669 T
1 T
308670 TTAAGTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TGTTTTAATGTT
Found at i:308669 original size:20 final size:20
Alignment explanation
Indices: 308647--308685 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
308637 GTTGTTTATG
*
308647 TTTTAATGTTTGTTTTAATGT
1 TTTTAA-GTTTATTTTAATGT
308668 TTTTAAGTTTATTTTAAT
1 TTTTAAGTTTATTTTAAT
308686 ATATTATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (20 bp):
TTTTAAGTTTATTTTAATGT
Found at i:308678 original size:27 final size:27
Alignment explanation
Indices: 308620--308677 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
308610 TATAAAGAAT
*
308620 TTTTAATGTTTTTTAAAGTTGTTTATG
1 TTTTAATGTTTTTTAAAGTTGTTTAAG
*
308647 TTTTAATGTTTGTTTTAATGTT-TTTAAG
1 TTTTAATG-TT-TTTTAAAGTTGTTTAAG
308675 TTT
1 TTT
308678 ATTTTAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 8 0.30
28 10 0.37
29 9 0.33
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.66
Consensus pattern (27 bp):
TTTTAATGTTTTTTAAAGTTGTTTAAG
Found at i:318688 original size:56 final size:56
Alignment explanation
Indices: 318625--318901 Score: 450
Period size: 56 Copynumber: 5.0 Consensus size: 56
318615 TTTCCTTCAA
*
318625 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAG
1 ATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAG
* *
318681 ATTTTCTCAAACTTTCTCTCTTTCCAAACATCCATTTCCTCTCATTA-TTTTCTAG
1 ATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAG
* * * *
318736 ATTTTCTCAGACTTTCTCTCTTTCCAAACACTCATTTTCCCTCATTATTTTTTTAG
1 ATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAG
* *
318792 ATTTTCTCAAACTTTCTCTGTTTCCAAACATCCATTTTCTCTCATTATTTTTCTAG
1 ATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAG
*
318848 ATTTTCTCAAACTTTTTCTCTTTCCAAACACCCATTTTCTCTCATT-TTTTTCTA
1 ATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTA
318902 TTTTCTAGGC
Statistics
Matches: 202, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
55 58 0.29
56 144 0.71
ACGTcount: A:0.21, C:0.27, G:0.03, T:0.49
Consensus pattern (56 bp):
ATTTTCTCAAACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAG
Found at i:318753 original size:111 final size:112
Alignment explanation
Indices: 318625--318901 Score: 477
Period size: 111 Copynumber: 2.5 Consensus size: 112
318615 TTTCCTTCAA
318625 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAGATTTTCTCA
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAGATTTTCTCA
318690 AACTTTCTCTCTTTCCAAACATCCATTTCCTCTCATTA-TTTTCTAG
66 AACTTTCTCTCTTTCCAAACATCCATTTCCTCTCATTATTTTTCTAG
* * *
318736 ATTTTCTCAGACTTTCTCTCTTTCCAAACACTCATTTTCCCTCATTATTTTTTTAGATTTTCTCA
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAGATTTTCTCA
* *
318801 AACTTTCTCTGTTTCCAAACATCCATTTTCTCTCATTATTTTTCTAG
66 AACTTTCTCTCTTTCCAAACATCCATTTCCTCTCATTATTTTTCTAG
* *
318848 ATTTTCTCAAACTTTTTCTCTTTCCAAACACCCATTTTCTCTCATT-TTTTTCTA
1 ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTA
318902 TTTTCTAGGC
Statistics
Matches: 155, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
111 105 0.68
112 50 0.32
ACGTcount: A:0.21, C:0.27, G:0.03, T:0.49
Consensus pattern (112 bp):
ATTTTCTCAGACTTTCTCTCTTTCCAAACACCCATTTTCTCTCATTATTTTTCTAGATTTTCTCA
AACTTTCTCTCTTTCCAAACATCCATTTCCTCTCATTATTTTTCTAG
Found at i:327371 original size:12 final size:12
Alignment explanation
Indices: 327354--327388 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
327344 TTTTGAGAGC
327354 ATAAAATAAAAG
1 ATAAAATAAAAG
*
327366 ATAAAATAAAAT
1 ATAAAATAAAAG
*
327378 AGAAAATAAAA
1 ATAAAATAAAA
327389 ACAAAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Done.