Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011909.1 Kokia drynarioides strain JFW-HI SEQ_126907, 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: 268014
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 469 characters in sequence are not A, C, G, or T
Found at i:450 original size:94 final size:95
Alignment explanation
Indices: 347--625 Score: 470
Period size: 95 Copynumber: 2.9 Consensus size: 95
337 TTAAGGGTAT
* * * *
347 TTTAGTAAATAATATATTGTTAAATCAACATATTATTTGATAAAAATTAAAATATTATAATAAT-
1 TTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATA
*
411 TTTTTTATTTAAATAAATTTAAAATTTAAA
66 TTTTTTATTTAAATAATTTTAAAATTTAAA
*
441 TTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATC
1 TTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATA
* *
506 TTTTTTATTTAAATAATTTTAAATTTTGAA
66 TTTTTTATTTAAATAATTTTAAAATTTAAA
*
536 TTTGGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATA
1 TTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATA
601 TTTTTTATTTAAATAATTTTAAAAT
66 TTTTTTATTTAAATAATTTTAAAAT
626 AATTTTAAAA
Statistics
Matches: 174, Mismatches: 10, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
94 60 0.34
95 114 0.66
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (95 bp):
TTTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTGAAATATTATAATAATA
TTTTTTATTTAAATAATTTTAAAATTTAAA
Found at i:627 original size:11 final size:11
Alignment explanation
Indices: 611--635 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
601 TTTTTTATTT
611 AAATAATTTTA
1 AAATAATTTTA
622 AAATAATTTTA
1 AAATAATTTTA
633 AAA
1 AAA
636 GTGATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AAATAATTTTA
Found at i:825 original size:17 final size:16
Alignment explanation
Indices: 799--833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
789 AATTTTGAAA
*
799 TTAATTTCAACTTAAT
1 TTAATTTCAAATTAAT
815 TTAATTTTCAAATTAAT
1 TTAA-TTTCAAATTAAT
832 TT
1 TT
834 TTACACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (16 bp):
TTAATTTCAAATTAAT
Found at i:4904 original size:56 final size:56
Alignment explanation
Indices: 4715--4913 Score: 195
Period size: 59 Copynumber: 3.4 Consensus size: 56
4705 CATGACCAAC
* * * * *
4715 TTTTTTTTATTAGATAAAAAAGGTACTGTCGGCCAATGCATGACGAACACAAAAAAAAT
1 TTTTTTTTATCAGATAAAAAAGGTGCTGTCGGCCAATGCATGGCCAACAC---CAAAAT
* * * * *
4774 TATTTTTTTATCAAATAAAAAA-GTGGTGTTGGCCAATGCATGGTCAACA-CAATTTTTAT
1 T-TTTTTTTATCAGATAAAAAAGGTGCTGTCGGCCAATGCATGGCCAACACCAA----AAT
* * *
4833 TTTATTTTATCAGATAAAAAAGGTGCTGTCGGCCAAAGTATGGCCAACACCAAAAT
1 TTTTTTTTATCAGATAAAAAAGGTGCTGTCGGCCAATGCATGGCCAACACCAAAAT
4889 TTTTTTTTATCAGATAAAAAAGGTG
1 TTTTTTTTATCAGATAAAAAAGGTG
4914 GTGTTGAAAA
Statistics
Matches: 114, Mismatches: 19, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
55 2 0.02
56 26 0.23
58 18 0.16
59 47 0.41
60 21 0.18
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (56 bp):
TTTTTTTTATCAGATAAAAAAGGTGCTGTCGGCCAATGCATGGCCAACACCAAAAT
Found at i:5181 original size:112 final size:108
Alignment explanation
Indices: 4924--5316 Score: 438
Period size: 112 Copynumber: 3.6 Consensus size: 108
4914 GTGTTGAAAA
* * * * **
4924 AAATTATTTTTTATCAGATAAAAAAGTGGTATCAGCCAAGCATTGACCAACAAAAAAATATTTTT
1 AAATT-TTTTTTATCTGATAAAAAGGTGGTGTCGGCCAAGCATTGACCAAC-ACCAAAT-TTTTT
** * *
4989 TTATCTGATAAAAGGT-GT--TGTC-AGTCAATGCATGGCCAACACC
63 TTATCTGATAAAAAATACTAGTGTCGA-CCAATGCATGGCCAACACC
*
5032 -AATTTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGCA-TGACCAACACCAAGATTTTTT
1 AAATTTTTTTTATCTGAT-AAAAAGGTGGTGTCGGCCAA-GCATTGACCAACACCAA-ATTTTTT
* * *
5095 TTATCTGATAAAAAAATATTGGTGTCGACCAATGCATGGTCAACACC
63 TTATCTGAT-AAAAAATACTAGTGTCGACCAATGCATGGCCAACACC
*
5142 AAAATTTTTTTTTATCTAATAAAAAGGTGGTGTCGGCCAAGCATTGACCAACACCAAATAAATTT
1 -AAA-TTTTTTTTATCTGATAAAAAGGTGGTGTCGGCCAAGCATTGACCAACACCAAAT---TTT
* *
5207 TTTTATCTGATAAAAAATACTAGTGTCGGCTAATGCATGGCCAACACC
61 TTTTATCTGATAAAAAATACTAGTGTCGACCAATGCATGGCCAACACC
* * *
5255 AAATTTTTTTTATCTGACAAAAGAGGTGGTGTCGGCCAAACATTGGCCAACACCAAATTTTT
1 AAATTTTTTTTATCTGATAAAA-AGGTGGTGTCGGCCAAGCATTGACCAACACCAAATTTTT
5317 ATTTCAAAAT
Statistics
Matches: 248, Mismatches: 21, Indels: 31
0.83 0.07 0.10
Matches are distributed among these distances:
106 29 0.12
107 37 0.15
108 4 0.02
109 4 0.02
110 21 0.08
111 23 0.09
112 70 0.28
113 46 0.19
114 14 0.06
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (108 bp):
AAATTTTTTTTATCTGATAAAAAGGTGGTGTCGGCCAAGCATTGACCAACACCAAATTTTTTTTA
TCTGATAAAAAATACTAGTGTCGACCAATGCATGGCCAACACC
Found at i:5288 original size:54 final size:54
Alignment explanation
Indices: 4924--5316 Score: 379
Period size: 55 Copynumber: 7.1 Consensus size: 54
4914 GTGTTGAAAA
* * * * **
4924 AAATTATTTTTTATCAGATAAAAAA-GTGGTATCAGCCAA-GCATTGACCAACAAAA
1 AAATT-TTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAATGCA-TGGCCAAC-ACC
* * *
4979 AAATATTTTTTTATCTGAT--AAAAGGTGTTGTCAGTCAATGCATGGCCAACACC
1 AAAT-TTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACC
* *
5032 -AATTTTTTTTATCTGATAAAAAAGGTGGTGTCAGCCAATGCATGACCAACACC
1 AAATTTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACC
** * *
5085 AAGATTTTTTTTATCTGATAAAAAAATATTGGTGTCGACCAATGCATGGTCAACACC
1 AA-ATTTTTTTTATCTGAT-AAAAAA-GGTGGTGTCGGCCAATGCATGGCCAACACC
* *
5142 AAAATTTTTTTTTATCTAAT-AAAAAGGTGGTGTCGGCCAA-GCATTGACCAACACC
1 -AAA-TTTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAATGCA-TGGCCAACACC
** * *
5197 AAATAAATTTTTTTATCTGATAAAAAATACTAGTGTCGGCTAATGCATGGCCAACACC
1 AAAT---TTTTTTTATCTGATAAAAAA-GGTGGTGTCGGCCAATGCATGGCCAACACC
* * *
5255 AAATTTTTTTTATCTGACAAAAGAGGTGGTGTCGGCCAA-ACATTGGCCAACACC
1 AAATTTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAATGCA-TGGCCAACACC
5309 AAATTTTT
1 AAATTTTT
5317 ATTTCAAAAT
Statistics
Matches: 284, Mismatches: 35, Indels: 39
0.79 0.10 0.11
Matches are distributed among these distances:
51 14 0.05
52 3 0.01
53 39 0.14
54 55 0.19
55 74 0.26
56 25 0.09
57 30 0.11
58 41 0.14
59 3 0.01
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (54 bp):
AAATTTTTTTTATCTGATAAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACC
Found at i:8027 original size:20 final size:21
Alignment explanation
Indices: 7997--8035 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
7987 TGTATGATAT
*
7997 ATTTGAAAATATTAATTTAAA
1 ATTTGAAAATATAAATTTAAA
8018 ATTT-AAAATATAAATTTA
1 ATTTGAAAATATAAATTTA
8036 TGAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (21 bp):
ATTTGAAAATATAAATTTAAA
Found at i:10421 original size:3 final size:3
Alignment explanation
Indices: 10413--10444 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
10403 AAAACCATGA
10413 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10445 AAAGAAAAGA
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:15161 original size:43 final size:43
Alignment explanation
Indices: 15095--15189 Score: 165
Period size: 43 Copynumber: 2.2 Consensus size: 43
15085 CACAAGACAG
*
15095 AGGACGCTATGTGGAAAAAGCCACATT-CAAGAAACGACAAAGA
1 AGGAAGCTATGTGGAAAAAGCCAC-TTCCAAGAAACGACAAAGA
15138 AGGAAGCTATGTGGAAAAAGCCACTTCCAAGAAACGACAAAGA
1 AGGAAGCTATGTGGAAAAAGCCACTTCCAAGAAACGACAAAGA
15181 AGGAAGCTA
1 AGGAAGCTA
15190 CGAGGAAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
42 2 0.04
43 48 0.96
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.12
Consensus pattern (43 bp):
AGGAAGCTATGTGGAAAAAGCCACTTCCAAGAAACGACAAAGA
Found at i:17051 original size:3 final size:3
Alignment explanation
Indices: 17045--17085 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
17035 TATATACATA
17045 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
17086 GTGACTGAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17651 original size:17 final size:17
Alignment explanation
Indices: 17629--17662 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
17619 CATTAATACT
17629 AAAATGCAATGACAATG
1 AAAATGCAATGACAATG
17646 AAAATGCAATGACAATG
1 AAAATGCAATGACAATG
17663 CTTACTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAATGCAATGACAATG
Found at i:20393 original size:39 final size:39
Alignment explanation
Indices: 20339--20418 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
20329 CTACCAGTAG
*
20339 TTCCATATTGTAATCTTATCCACCGTCCTCTCCCTGTAA
1 TTCCATATTGTAATCTTATCCACCATCCTCTCCCTGTAA
*
20378 TTCCATATTGTAATCTTATCCACCATCCTTTCCCTGTAA
1 TTCCATATTGTAATCTTATCCACCATCCTCTCCCTGTAA
20417 TT
1 TT
20419 GGTATCATAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.31, G:0.06, T:0.41
Consensus pattern (39 bp):
TTCCATATTGTAATCTTATCCACCATCCTCTCCCTGTAA
Found at i:22874 original size:30 final size:30
Alignment explanation
Indices: 22838--23062 Score: 253
Period size: 29 Copynumber: 7.6 Consensus size: 30
22828 ATTTTACCCA
* **
22838 AAAATCACATTTCGACCCTCAAACTTTTTC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* *
22868 AAAATCACATTTTAACCCT-AAACTTACCC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
*
22897 AAAATCACATTTTGACCC-CTAAACATTCCC
1 AAAATCACATTTTGACCCTC-AAACTTTCCC
* * *
22927 AAAATCACATTTTGATCCTCAAAC-TTACT
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* *
22956 AAAATCACATTTTGACCCTAAAACTTTTCC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
*
22986 AAAATCACATTTTGACCCCCAAAC-TTCCC
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* * *
23015 AAAATCATATTTTAACCCT-AAACTTTCCA
1 AAAATCACATTTTGACCCTCAAACTTTCCC
* *
23044 AAAATTACATTTTAACCCT
1 AAAATCACATTTTGACCCT
23063 TGAATTTTTT
Statistics
Matches: 166, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
28 4 0.02
29 90 0.54
30 71 0.43
31 1 0.01
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (30 bp):
AAAATCACATTTTGACCCTCAAACTTTCCC
Found at i:22930 original size:59 final size:59
Alignment explanation
Indices: 22831--23062 Score: 265
Period size: 59 Copynumber: 3.9 Consensus size: 59
22821 AGCCCCTATT
* * **
22831 TTACCCAAAAATCACATTTCGACCCTCAAACTTTTTCAAAATCACATTTTAACCCTAAAC
1 TTACCC-AAAATCACATTTTGACCCTAAAACTTTCCCAAAATCACATTTTAACCCTAAAC
* * *
22891 TTACCCAAAATCACATTTTGACCCCT-AAACATTCCCAAAATCACATTTTGATCCTCAAAC
1 TTACCCAAAATCACATTTTGA-CCCTAAAACTTTCCCAAAATCACATTTTAACCCT-AAAC
* * * *
22951 TTA-CTAAAATCACATTTTGACCCTAAAACTTTTCCAAAATCACATTTTGACCCCCAAAC
1 TTACCCAAAATCACATTTTGACCCTAAAACTTTCCCAAAATCACATTTT-AACCCTAAAC
* * * *
23010 TT-CCCAAAATCATATTTTAACCCT-AAACTTTCCAAAAATTACATTTTAACCCT
1 TTACCCAAAATCACATTTTGACCCTAAAACTTTCCCAAAATCACATTTTAACCCT
23063 TGAATTTTTT
Statistics
Matches: 146, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
57 4 0.03
58 24 0.16
59 99 0.68
60 19 0.13
ACGTcount: A:0.38, C:0.29, G:0.02, T:0.31
Consensus pattern (59 bp):
TTACCCAAAATCACATTTTGACCCTAAAACTTTCCCAAAATCACATTTTAACCCTAAAC
Found at i:24819 original size:11 final size:11
Alignment explanation
Indices: 24803--24834 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
24793 TCGAAACATT
24803 TAATAAATAAA
1 TAATAAATAAA
*
24814 TAATAAATACA
1 TAATAAATAAA
24825 TAATAAATAA
1 TAATAAATAA
24835 CAAAAAGGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:25770 original size:30 final size:30
Alignment explanation
Indices: 25736--25994 Score: 220
Period size: 30 Copynumber: 8.6 Consensus size: 30
25726 GTTTTATTTA
* *
25736 AAAATCACATTTTAACTCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
** *
25766 AAAATTGTATTTTAACCCCTAAACTTTTCA
1 AAAATTACATTTTAACCCCTAAACTTTTCC
25796 AAAATTA-ATTTTTAACCCCTAAACTTTTCC
1 AAAATTACA-TTTTAACCCCTAAACTTTTCC
* * *
25826 AAAATTGCATTTTAACCCCTTAATTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * * **
25856 AAAATTTCATGTTGATACCTAAAC-TTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * * **
25885 AAAAATTACATTTTGATCCC-AAATTTTTTG
1 -AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
25915 AAAATCACATTTTGACCTCTAAAC-TTTCAC
1 AAAATTACATTTTAACCCCTAAACTTTTC-C
* ** * *
25945 AAAATCACATTTTGGCGCCCAAAAATTTTCC
1 AAAATTACATTTTAAC-CCCTAAACTTTTCC
25976 AAAATTACATTTTAACCCC
1 AAAATTACATTTTAACCCC
25995 AAATTCTCTA
Statistics
Matches: 185, Mismatches: 36, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
29 28 0.15
30 133 0.72
31 20 0.11
32 4 0.02
ACGTcount: A:0.36, C:0.23, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:26007 original size:28 final size:30
Alignment explanation
Indices: 25967--26025 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 30
25957 TGGCGCCCAA
*
25967 AAATTTTCCAAAA-TTACA-TTTT-AACCCC
1 AAATTCTCCAAAACTT-CATTTTTCAACCCC
*
25995 AAATTCTCTAAAACTTCATTTTTCAACCCC
1 AAATTCTCCAAAACTTCATTTTTCAACCCC
26025 A
1 A
26026 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 13 0.50
29 6 0.23
30 7 0.27
ACGTcount: A:0.37, C:0.27, G:0.00, T:0.36
Consensus pattern (30 bp):
AAATTCTCCAAAACTTCATTTTTCAACCCC
Found at i:38644 original size:14 final size:15
Alignment explanation
Indices: 38625--38656 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
38615 ATATATTTCC
38625 TTTTCTT-TTCTTTT
1 TTTTCTTCTTCTTTT
38639 TTTTCTTCTTCTTTT
1 TTTTCTTCTTCTTTT
38654 TTT
1 TTT
38657 ATATGTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTCTTCTTCTTTT
Found at i:42004 original size:18 final size:18
Alignment explanation
Indices: 41983--42022 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
41973 CAAATGCAGT
41983 CACATAA-CTAGATGCAAC
1 CACATAATC-AGATGCAAC
*
42001 CACATAATCGGATGCAAC
1 CACATAATCAGATGCAAC
42019 CACA
1 CACA
42023 ATAGACTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 19 0.95
19 1 0.05
ACGTcount: A:0.42, C:0.30, G:0.12, T:0.15
Consensus pattern (18 bp):
CACATAATCAGATGCAAC
Found at i:58259 original size:21 final size:22
Alignment explanation
Indices: 58235--58275 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
58225 ATTATACTTA
*
58235 TATCGATAGAACTA-GCACAGG
1 TATCGATAGAAATATGCACAGG
58256 TATCGATAGAAATATGCACA
1 TATCGATAGAAATATGCACA
58276 ATTTAGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (22 bp):
TATCGATAGAAATATGCACAGG
Found at i:66367 original size:19 final size:20
Alignment explanation
Indices: 66333--66374 Score: 77
Period size: 19 Copynumber: 2.1 Consensus size: 20
66323 TATTTATACT
66333 TTAATTAATATAGTTTAATC
1 TTAATTAATATAGTTTAATC
66353 TTAATTAAT-TAGTTTAATC
1 TTAATTAATATAGTTTAATC
66372 TTA
1 TTA
66375 GTTTAGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (20 bp):
TTAATTAATATAGTTTAATC
Found at i:69224 original size:23 final size:24
Alignment explanation
Indices: 69196--69241 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
69186 ACCCCACCAT
69196 CGGCCAC-CCGATCAACTCACTAC
1 CGGCCACACCGATCAACTCACTAC
69219 CGGCCACTACCGATCAACTCACT
1 CGGCCAC-ACCGATCAACTCACT
69242 GGAGGACACC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 7 0.33
25 14 0.67
ACGTcount: A:0.26, C:0.46, G:0.13, T:0.15
Consensus pattern (24 bp):
CGGCCACACCGATCAACTCACTAC
Found at i:70515 original size:41 final size:41
Alignment explanation
Indices: 70430--70581 Score: 164
Period size: 41 Copynumber: 3.7 Consensus size: 41
70420 AAACACAGCA
* * * **
70430 AAAGGT-AAAGCAATAGCGGCATTTAT-AGGAAAAACGTCTTT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGG--AAGCGTCGCT
*
70471 AAAGGTTAAAGCATTAGCGGCGTTTATGAGGAAGCGTCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGGAAGCGTCGCT
* * *
70512 AAAGGTCAGAGCATTAGTGGCGTTTATGAGGAAGCGCCGCT
1 AAAGGTCAAAGCATTAGCGGCGTTTATGAGGAAGCGTCGCT
* * *
70553 AAAGATCAGAGCATTAACGGCGTTTATGA
1 AAAGGTCAAAGCATTAGCGGCGTTTATGA
70582 AAAAAGCCAC
Statistics
Matches: 97, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
41 76 0.78
42 18 0.19
43 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.28, T:0.24
Consensus pattern (41 bp):
AAAGGTCAAAGCATTAGCGGCGTTTATGAGGAAGCGTCGCT
Found at i:70639 original size:16 final size:17
Alignment explanation
Indices: 70618--70656 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
70608 TAATGATATA
*
70618 TTAATCAGTA-TAATAG
1 TTAATCAATATTAATAG
70634 TTAATCAATATTTAATAG
1 TTAATCAATA-TTAATAG
70652 TTAAT
1 TTAAT
70657 TGACTCAGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
18 11 0.55
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (17 bp):
TTAATCAATATTAATAG
Found at i:70845 original size:28 final size:28
Alignment explanation
Indices: 70813--70869 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
70803 AAAGAAAAAG
70813 AACAAGCATTTTAACCAATTAAGCCGAA
1 AACAAGCATTTTAACCAATTAAGCCGAA
70841 AACAAGCATTTTAACCAATTAAGCCGAA
1 AACAAGCATTTTAACCAATTAAGCCGAA
70869 A
1 A
70870 TTATTTAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.21, G:0.11, T:0.21
Consensus pattern (28 bp):
AACAAGCATTTTAACCAATTAAGCCGAA
Found at i:73402 original size:18 final size:21
Alignment explanation
Indices: 73381--73422 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
73371 AATTATACTG
73381 AATAAATT-TC-A-TATATAA
1 AATAAATTATCAATTATATAA
73399 AAT-AATTATCAATTATATAA
1 AATAAATTATCAATTATATAA
73419 AATA
1 AATA
73423 TTCATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.20
18 5 0.25
19 1 0.05
20 10 0.50
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
AATAAATTATCAATTATATAA
Found at i:75433 original size:15 final size:15
Alignment explanation
Indices: 75413--75441 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
75403 GAAGTTATTG
75413 GTTGGATTTGAATTA
1 GTTGGATTTGAATTA
75428 GTTGGATTTGAATT
1 GTTGGATTTGAATT
75442 TACAGGACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (15 bp):
GTTGGATTTGAATTA
Found at i:75557 original size:43 final size:42
Alignment explanation
Indices: 75494--75732 Score: 300
Period size: 43 Copynumber: 5.5 Consensus size: 42
75484 AATTTTAGTG
* *
75494 GCGTTTGTGGGGAAAA-CGCCGCTAAAGACCATGTTCTTTAGC
1 GCGTTTGT-GAGAAAAGCGCCGCTAAAGACTATGTTCTTTAGC
* * *
75536 GTCATTTTTGAGAAAAGCGCCGCTAAAGACTATGTTCTTTAGTA
1 G-CGTTTGTGAGAAAAGCGCCGCTAAAGACTATGTTCTTTAG-C
*
75580 GCGTTTGTGAGAAAAGCGCTTGCTAAAGACTATGTTCTTTAGC
1 GCGTTTGTGAGAAAAGCGC-CGCTAAAGACTATGTTCTTTAGC
* *
75623 AGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTG
1 -GCGTTTGTGAGAAAAGCGCCGCTAAAGACTATGTTCTTTAG-C
* * * *
75667 GCGTTTGTGAGGAAAGCGCTGTTAAAGACTATGTACTTTAGC
1 GCGTTTGTGAGAAAAGCGCCGCTAAAGACTATGTTCTTTAGC
75709 GACGTTTGTGAGAAAAGCGCCGCT
1 G-CGTTTGTGAGAAAAGCGCCGCT
75733 TCTTTAGCGG
Statistics
Matches: 169, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
42 8 0.05
43 120 0.71
44 41 0.24
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.29
Consensus pattern (42 bp):
GCGTTTGTGAGAAAAGCGCCGCTAAAGACTATGTTCTTTAGC
Found at i:75616 original size:87 final size:85
Alignment explanation
Indices: 75487--75732 Score: 350
Period size: 87 Copynumber: 2.8 Consensus size: 85
75477 ATCTATTAAT
* * * * *
75487 TTTAGTGGCGTTTGTGGGGAAAA-CGCCGCTAAAGACCATGTTCTTTAGCGTCATTTTTGAGAAA
1 TTTAGTGGCGTTTGT-GAGAAAAGCGCTGCTAAAGACTATGTTCTTTAGCG-CGTTTGTGAGAAA
*
75551 AGCGCCGCTAAAGACTATGTTC
64 AGCGCCGCTAAAGACCATGTTC
*
75573 TTTAGTAGCGTTTGTGAGAAAAGCGCTTGCTAAAGACTATGTTCTTTAGCAGCGTTTGTGAGAAA
1 TTTAGTGGCGTTTGTGAGAAAAGCGC-TGCTAAAGACTATGTTCTTTAGC-GCGTTTGTGAGAAA
75638 AGCGCCGCTAAAGACCATGTTC
64 AGCGCCGCTAAAGACCATGTTC
* * *
75660 TTTAGTGGCGTTTGTGAGGAAAGCGCTGTTAAAGACTATGTACTTTAGCGACGTTTGTGAGAAAA
1 TTTAGTGGCGTTTGTGAGAAAAGCGCTGCTAAAGACTATGTTCTTTAGCG-CGTTTGTGAGAAAA
75725 GCGCCGCT
65 GCGCCGCT
75733 TCTTTAGCGG
Statistics
Matches: 145, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
85 7 0.05
86 60 0.41
87 77 0.53
88 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (85 bp):
TTTAGTGGCGTTTGTGAGAAAAGCGCTGCTAAAGACTATGTTCTTTAGCGCGTTTGTGAGAAAAG
CGCCGCTAAAGACCATGTTC
Found at i:75720 original size:130 final size:130
Alignment explanation
Indices: 75494--75728 Score: 348
Period size: 130 Copynumber: 1.8 Consensus size: 130
75484 AATTTTAGTG
* * *
75494 GCGTTTGTGGGGAAAACGCCGCTAAAGACCATGTTCTTTAGCGTCATTTTTGAGAAAAGCGCCGC
1 GCGTTTGTGGAGAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGAGAAAAGCGCCGC
* *
75559 TAAAGACTATGTTCTTTAGTAGCGTTTGTGAGAAAAGCGCTTGCTAAAGACTATGTTCTTTAGCA
66 TAAAGACTATGTACTTTAGGAGCGTTTGTGAGAAAAGCGCTTGCTAAAGACTATGTTCTTTAGCA
* * * *
75624 GCGTTTGT-GAGAAAAGCGCCGCTAAAGACCATGTTCTTTAGTGGCGTTTGTGAGGAAAGCGCTG
1 GCGTTTGTGGAGAAAA-CGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGAGAAAAGCGCCG
*
75688 TTAAAGACTATGTACTTTAGCGA-CGTTTGTGAGAAAAGCGC
65 CTAAAGACTATGTACTTTAG-GAGCGTTTGTGAGAAAAGCGC
75729 CGCTTCTTTA
Statistics
Matches: 93, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
129 6 0.06
130 86 0.92
131 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (130 bp):
GCGTTTGTGGAGAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCATTTGTGAGAAAAGCGCCGC
TAAAGACTATGTACTTTAGGAGCGTTTGTGAGAAAAGCGCTTGCTAAAGACTATGTTCTTTAGCA
Found at i:81799 original size:18 final size:18
Alignment explanation
Indices: 81776--81821 Score: 92
Period size: 18 Copynumber: 2.6 Consensus size: 18
81766 AATCAGCCCA
81776 TCATCAATTAAAAATTAG
1 TCATCAATTAAAAATTAG
81794 TCATCAATTAAAAATTAG
1 TCATCAATTAAAAATTAG
81812 TCATCAATTA
1 TCATCAATTA
81822 GAATTTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (18 bp):
TCATCAATTAAAAATTAG
Found at i:85787 original size:50 final size:50
Alignment explanation
Indices: 85732--85831 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
85722 AACAAAAACA
85732 CCAAAGCAATTCAAGCATATACTTGTATTCATAATCAAATAGAAAAACTT
1 CCAAAGCAATTCAAGCATATACTTGTATTCATAATCAAATAGAAAAACTT
85782 CCAAAGCAATTCAAGCATATACTTGTATTCATAATCAAATAGAAAAACTT
1 CCAAAGCAATTCAAGCATATACTTGTATTCATAATCAAATAGAAAAACTT
85832 ACCTTGAATA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (50 bp):
CCAAAGCAATTCAAGCATATACTTGTATTCATAATCAAATAGAAAAACTT
Found at i:87381 original size:17 final size:17
Alignment explanation
Indices: 87356--87390 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
87346 TAACTACTGG
*
87356 AGTATCTACACATATTT
1 AGTAACTACACATATTT
87373 AGTAACTACACATATTT
1 AGTAACTACACATATTT
87390 A
1 A
87391 TCTCATACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.06, T:0.37
Consensus pattern (17 bp):
AGTAACTACACATATTT
Found at i:99471 original size:20 final size:21
Alignment explanation
Indices: 99427--99489 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
99417 ACTTCAATCA
* *
99427 TTAAGCCTTAATTTAATCATTT
1 TTAAG-CTTAATTAAATCATAT
*
99449 TTAATCTTAATTAAATC-TAT
1 TTAAGCTTAATTAAATCATAT
*
99469 TTACGCTTAATATAAATCATA
1 TTAAGCTTAAT-TAAATCATA
99490 CCAATCCACT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 11 0.32
21 17 0.50
22 6 0.18
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (21 bp):
TTAAGCTTAATTAAATCATAT
Found at i:105583 original size:20 final size:21
Alignment explanation
Indices: 105546--105601 Score: 64
Period size: 20 Copynumber: 2.7 Consensus size: 21
105536 ATTATTAAAC
*
105546 CTTAATT-AATCATTTTTA-A
1 CTTAATTAAATCATATTTATA
105565 TCTTAATTAAATC-TATTTATA
1 -CTTAATTAAATCATATTTATA
105586 CTTAATATAAATCATA
1 CTTAAT-TAAATCATA
105602 CCAATCCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 18 0.58
21 11 0.35
22 2 0.06
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (21 bp):
CTTAATTAAATCATATTTATA
Found at i:106508 original size:28 final size:28
Alignment explanation
Indices: 106468--106523 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
106458 AATATCTGAT
*
106468 TTACTCCATGTTGACCCAAAGGTCATGC
1 TTACTCCATGTTGACCCAAAAGTCATGC
*
106496 TTACTCCCTGTTGACCCAAAAGTCATGC
1 TTACTCCATGTTGACCCAAAAGTCATGC
106524 ATGTTACCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (28 bp):
TTACTCCATGTTGACCCAAAAGTCATGC
Found at i:111803 original size:45 final size:45
Alignment explanation
Indices: 111732--111907 Score: 181
Period size: 45 Copynumber: 3.9 Consensus size: 45
111722 ACTTTCGAAG
* * * *
111732 GATGTCATAGCGTCTTTCAGCCATGGTCTTACTCACTTCCGTCAT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
* * * *
111777 GTTGTCATAGCATCTTTTAGCTATGGTCTTACTCATTTATATCAT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
* * * ** *
111822 GATGTCATAACATCTTTCAGCTATGATCTTACTCATTTTTATCCT
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
* * * * *
111867 TATGTCATAGCATTTTTCAACTATGATCTTACTCATTTACA
1 GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACA
111908 AGTGTATAAC
Statistics
Matches: 111, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 111 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (45 bp):
GATGTCATAGCATCTTTCAGCTATGGTCTTACTCACTTACATCAT
Found at i:111903 original size:23 final size:23
Alignment explanation
Indices: 111836--111904 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
111826 TCATAACATC
*
111836 TTTCAGCTATGATCTTACTCATT
1 TTTCAACTATGATCTTACTCATT
* * *
111859 TTT-ATCCTTATG-TCATA-GCATT
1 TTTCA-AC-TATGATCTTACTCATT
111881 TTTCAACTATGATCTTACTCATT
1 TTTCAACTATGATCTTACTCATT
111904 T
1 T
111905 ACAAGTGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 10
0.69 0.12 0.20
Matches are distributed among these distances:
21 4 0.11
22 13 0.37
23 14 0.40
24 4 0.11
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.49
Consensus pattern (23 bp):
TTTCAACTATGATCTTACTCATT
Found at i:115510 original size:31 final size:31
Alignment explanation
Indices: 115474--115541 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
115464 ATAAAAATAA
115474 TCACTTTTGTTTGCCTCAGATTATATTTTAG
1 TCACTTTTGTTTGCCTCAGATTATATTTTAG
115505 TCACTTTTGTTTGCCTCAGATTATATTTTAG
1 TCACTTTTGTTTGCCTCAGATTATATTTTAG
115536 TCACTT
1 TCACTT
115542 ATATTTGAAA
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:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (31 bp):
TCACTTTTGTTTGCCTCAGATTATATTTTAG
Found at i:117137 original size:20 final size:20
Alignment explanation
Indices: 117109--117150 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
117099 TGCAGCGAAA
117109 TTTTGTTCTGTCTGATAAGT
1 TTTTGTTCTGTCTGATAAGT
*
117129 TTTTTTTCTGTCTGATAAGT
1 TTTTGTTCTGTCTGATAAGT
117149 TT
1 TT
117151 ATTTACTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.17, T:0.60
Consensus pattern (20 bp):
TTTTGTTCTGTCTGATAAGT
Found at i:122116 original size:3 final size:3
Alignment explanation
Indices: 122110--122167 Score: 71
Period size: 3 Copynumber: 19.3 Consensus size: 3
122100 ATAACTACTC
* * * *
122110 TGA TGA TGA CGA TGA CGT TGG TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
*
122158 TGG TGA TGA T
1 TGA TGA TGA T
122168 AGCTAAAGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:125506 original size:56 final size:56
Alignment explanation
Indices: 125438--125550 Score: 199
Period size: 56 Copynumber: 2.0 Consensus size: 56
125428 TCTATGATAA
125438 ATGGTTCACAATTGTCCATAACTTAATGCCAAGCAATCAATTTTCACTAGTAAGAC
1 ATGGTTCACAATTGTCCATAACTTAATGCCAAGCAATCAATTTTCACTAGTAAGAC
* * *
125494 ATGGTTCTCAATTGTCCATAACTTAATGCCAAGCAATCGATTTTCACTAGTCAGAC
1 ATGGTTCACAATTGTCCATAACTTAATGCCAAGCAATCAATTTTCACTAGTAAGAC
125550 A
1 A
125551 ACAGGAGAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 54 1.00
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (56 bp):
ATGGTTCACAATTGTCCATAACTTAATGCCAAGCAATCAATTTTCACTAGTAAGAC
Found at i:127458 original size:17 final size:17
Alignment explanation
Indices: 127436--127494 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
127426 AATGGTTCAT
127436 TGAATGCTATATGAAAA
1 TGAATGCTATATGAAAA
* * * * *
127453 TGAATGATAAAAGTATCAT
1 TGAATGCTATATG-A-AAA
127472 TGAATGCTATATGAAAA
1 TGAATGCTATATGAAAA
127489 TGAATG
1 TGAATG
127495 ATAAAAGTAT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
17 17 0.57
18 2 0.07
19 11 0.37
ACGTcount: A:0.46, C:0.05, G:0.19, T:0.31
Consensus pattern (17 bp):
TGAATGCTATATGAAAA
Found at i:127472 original size:36 final size:36
Alignment explanation
Indices: 127432--127506 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
127422 GGAAAATGGT
127432 TCATTGAATGCTATATGAAAATGAATGATAAAAGTA
1 TCATTGAATGCTATATGAAAATGAATGATAAAAGTA
127468 TCATTGAATGCTATATGAAAATGAATGATAAAAGTA
1 TCATTGAATGCTATATGAAAATGAATGATAAAAGTA
127504 TCA
1 TCA
127507 AGAAAGCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.47, C:0.07, G:0.16, T:0.31
Consensus pattern (36 bp):
TCATTGAATGCTATATGAAAATGAATGATAAAAGTA
Found at i:138675 original size:21 final size:21
Alignment explanation
Indices: 138646--138719 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
138636 GGTACCTGGT
138646 AAAAGGTATCGATACTCTTTG
1 AAAAGGTATCGATACTCTTTG
* * *
138667 AAAATGTATCGATACTTTTTAT
1 AAAAGGTATCGATACTCTTT-G
138689 AAAAGGTATCGATACTCTTTG
1 AAAAGGTATCGATACTCTTTG
*
138710 AAAATGTATC
1 AAAAGGTATC
138720 AATATTTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
21 27 0.60
22 18 0.40
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (21 bp):
AAAAGGTATCGATACTCTTTG
Found at i:138693 original size:43 final size:43
Alignment explanation
Indices: 138645--138731 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
138635 CGGTACCTGG
*
138645 TAAAAGGTATCGATACTCTTTGAAAATGTATCGATACTTTTTA
1 TAAAAGGTATCGATACTCTTTGAAAATGTATCAATACTTTTTA
*
138688 TAAAAGGTATCGATACTCTTTGAAAATGTATCAATATTTTTTA
1 TAAAAGGTATCGATACTCTTTGAAAATGTATCAATACTTTTTA
138731 T
1 T
138732 CATTATCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (43 bp):
TAAAAGGTATCGATACTCTTTGAAAATGTATCAATACTTTTTA
Found at i:139064 original size:30 final size:31
Alignment explanation
Indices: 139028--139088 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
139018 ATAGATTGCT
* *
139028 CCCCTTA-ATGAAAGTCATATTCAATTTAAG
1 CCCCTTACATAAAAATCATATTCAATTTAAG
*
139058 CCCCTTACATAAAAATCATTTTCAATTTAAG
1 CCCCTTACATAAAAATCATATTCAATTTAAG
139089 GCATAAAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (31 bp):
CCCCTTACATAAAAATCATATTCAATTTAAG
Found at i:144575 original size:30 final size:32
Alignment explanation
Indices: 144516--144578 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 32
144506 GAGATAAGAA
144516 AACCACTTGAAAATGTGGGGGAGGAGGTGTCTTAG
1 AACCACTTGAAAATGT---GGAGGAGGTGTCTTAG
144551 AACCACTTGAAAATGT-GAGG-GGTGTCTT
1 AACCACTTGAAAATGTGGAGGAGGTGTCTT
144579 GTTAACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 8 0.29
31 4 0.14
35 16 0.57
ACGTcount: A:0.29, C:0.13, G:0.33, T:0.25
Consensus pattern (32 bp):
AACCACTTGAAAATGTGGAGGAGGTGTCTTAG
Found at i:146256 original size:11 final size:11
Alignment explanation
Indices: 146229--146264 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
146219 TTATTTGTTT
*
146229 TTAAATTTATTA
1 TTAAATTTA-AA
146241 TTAAATTTAAA
1 TTAAATTTAAA
146252 TTAAATTTAAA
1 TTAAATTTAAA
146263 TT
1 TT
146265 TTTTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:148170 original size:29 final size:29
Alignment explanation
Indices: 148128--148184 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
148118 TCGTATATAG
*
148128 GGGTTCACATACCTAGGATTCACACATAA
1 GGGTTCACACACCTAGGATTCACACATAA
* *
148157 GGGTTCACACACCTAGGGTTCACTCATA
1 GGGTTCACACACCTAGGATTCACACATA
148185 CAGTTCTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (29 bp):
GGGTTCACACACCTAGGATTCACACATAA
Found at i:148176 original size:15 final size:15
Alignment explanation
Indices: 148128--148179 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
148118 TCGTATATAG
*
148128 GGGTTCACATACCTA
1 GGGTTCACACACCTA
*
148143 GGATTCACACA--TAA
1 GGGTTCACACACCT-A
148157 GGGTTCACACACCTA
1 GGGTTCACACACCTA
148172 GGGTTCAC
1 GGGTTCAC
148180 TCATACAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 1 0.03
14 11 0.35
15 18 0.58
16 1 0.03
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (15 bp):
GGGTTCACACACCTA
Found at i:160772 original size:5 final size:5
Alignment explanation
Indices: 160756--160806 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
160746 AAGTCGAATA
* *
160756 AAAAG AAGAG AAAAG -AAAG AAAAAGGG AAGAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG -AAAA--G AAAAG AAAAG AAAAG AAAAG
160803 AAAA
1 AAAA
160807 TTAAGTTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.11
5 27 0.71
6 3 0.08
7 3 0.08
8 1 0.03
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:161149 original size:13 final size:13
Alignment explanation
Indices: 161131--161155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
161121 CCCATTATAT
161131 CATTTTTAGCATG
1 CATTTTTAGCATG
161144 CATTTTTAGCAT
1 CATTTTTAGCAT
161156 TTTATATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CATTTTTAGCATG
Found at i:165973 original size:3 final size:3
Alignment explanation
Indices: 165967--165995 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
165957 CTTTTTCTGC
165967 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
165996 TAAACACTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:174704 original size:15 final size:16
Alignment explanation
Indices: 174686--174728 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
174676 GAAAGGTAAT
174686 AAAGAGGAGAAGGA-G
1 AAAGAGGAGAAGGATG
*
174701 AAAGAGAAGAAGGATG
1 AAAGAGGAGAAGGATG
174717 -AAGAGGACGAAG
1 AAAGAGGA-GAAG
174729 ATGTCCAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.53, C:0.02, G:0.42, T:0.02
Consensus pattern (16 bp):
AAAGAGGAGAAGGATG
Found at i:177325 original size:23 final size:24
Alignment explanation
Indices: 177299--177345 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
177289 AACTATTCAT
177299 TTTATCTTA-ATTTGC-TCTAACAA
1 TTTATCTTATATTTGCGT-TAACAA
*
177322 TTTATTTTATATTTGCGTTAACAA
1 TTTATCTTATATTTGCGTTAACAA
177346 ATTAATTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.30, C:0.13, G:0.06, T:0.51
Consensus pattern (24 bp):
TTTATCTTATATTTGCGTTAACAA
Found at i:180800 original size:36 final size:36
Alignment explanation
Indices: 180746--180882 Score: 134
Period size: 36 Copynumber: 3.8 Consensus size: 36
180736 TCAAAGGAAA
*
180746 GCATACGTCTCGGTTAGAGCGTATTGCTATGATATT
1 GCATAAGTCTCGGTTAGAGCGTATTGCTATGATATT
* * *** *
180782 GCATAAGTCTCAGCTAGAGCGTATCATTATGATGTT
1 GCATAAGTCTCGGTTAGAGCGTATTGCTATGATATT
180818 GCATACA-TCTCGGTTAGAGCGTATTGCTATGA-ATTT
1 GCATA-AGTCTCGGTTAGAGCGTATTGCTATGATA-TT
* * * * *
180854 ACTTACGTCTCGGTTAGAGCATAATGCTA
1 GCATAAGTCTCGGTTAGAGCGTATTGCTA
180883 AGTGATTGCT
Statistics
Matches: 80, Mismatches: 18, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
36 79 0.99
37 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.34
Consensus pattern (36 bp):
GCATAAGTCTCGGTTAGAGCGTATTGCTATGATATT
Found at i:207187 original size:36 final size:36
Alignment explanation
Indices: 207140--207211 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
207130 AAAAAGTGAT
207140 AGCTTATGCCTCTTGATAGTTACAGCTTCATGAGAA
1 AGCTTATGCCTCTTGATAGTTACAGCTTCATGAGAA
207176 AGCTTATGCCTCTTGATAGTTACAGCTTCATGAGAA
1 AGCTTATGCCTCTTGATAGTTACAGCTTCATGAGAA
207212 GAATTATCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (36 bp):
AGCTTATGCCTCTTGATAGTTACAGCTTCATGAGAA
Found at i:210188 original size:13 final size:13
Alignment explanation
Indices: 210170--210196 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
210160 TGATATTGCA
210170 TACGACAAGGTAT
1 TACGACAAGGTAT
210183 TACGACAAGGTAT
1 TACGACAAGGTAT
210196 T
1 T
210197 TTATAGATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (13 bp):
TACGACAAGGTAT
Found at i:218090 original size:17 final size:17
Alignment explanation
Indices: 218068--218171 Score: 129
Period size: 17 Copynumber: 6.1 Consensus size: 17
218058 CATTTTTAAA
*
218068 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
218085 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
* * *
218102 GAATTT-GTTTAAATTT
1 AAATTTATTTTAAGTTT
218118 AAATTTATTTTAAGTTT
1 AAATTTATTTTAAGTTT
*
218135 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAGTTT
* *
218153 AAAATTATTTTAAATTT
1 AAATTTATTTTAAGTTT
218170 AA
1 AA
218172 TTAATAATGT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
16 13 0.17
17 48 0.63
18 15 0.20
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:218118 original size:6 final size:6
Alignment explanation
Indices: 218109--218171 Score: 58
Period size: 6 Copynumber: 10.8 Consensus size: 6
218099 TTTGAATTTG
* * **
218109 TTTAAA TTTAAA TTT-AT TTTAAG TTTAAA TTTATT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
218156 ATT-AT TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
218172 TTAATAATGT
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
5 7 0.16
6 37 0.84
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:218120 original size:33 final size:33
Alignment explanation
Indices: 218083--218174 Score: 123
Period size: 35 Copynumber: 2.7 Consensus size: 33
218073 TATTTTAAGG
218083 TTAAATTTATTTTAAGTTTGAATT-TGTTTAAAT
1 TTAAATTTATTTTAAGTTT-AATTATGTTTAAAT
*
218116 TTAAATTTATTTTAAGTTTAAATTTATTTTTAAAT
1 TTAAATTTATTTTAAGTTT-AA-TTATGTTTAAAT
* *
218151 TTAAAATTATTTTAAATTTAATTA
1 TTAAATTTATTTTAAGTTTAATTA
218175 ATAATGTCCC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
33 24 0.45
34 4 0.08
35 25 0.47
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (33 bp):
TTAAATTTATTTTAAGTTTAATTATGTTTAAAT
Found at i:218128 original size:50 final size:52
Alignment explanation
Indices: 218068--218171 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 52
218058 CATTTTTAAA
* *
218068 AAATTTATTTTAAGGTTAAATTTA-TTTTAAGTTT-GAATT-TGTTTAAATTT
1 AAATTTATTTTAAGGTTAAATTTATTTTTAAATTTAAAATTAT-TTTAAATTT
*
218118 AAATTTATTTTAAGTTTAAATTTATTTTTAAATTTAAAATTATTTTAAATTT
1 AAATTTATTTTAAGGTTAAATTTATTTTTAAATTTAAAATTATTTTAAATTT
218170 AA
1 AA
218172 TTAATAATGT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
50 23 0.48
51 9 0.19
52 15 0.31
53 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (52 bp):
AAATTTATTTTAAGGTTAAATTTATTTTTAAATTTAAAATTATTTTAAATTT
Found at i:218743 original size:21 final size:21
Alignment explanation
Indices: 218719--218760 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
218709 TAAATGCATA
218719 ATTA-ATAAATATATAATATTT
1 ATTACATAAATA-ATAATATTT
*
218740 ATTACATATATAATAATATTT
1 ATTACATAAATAATAATATTT
218761 TTTTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
ATTACATAAATAATAATATTT
Found at i:219817 original size:30 final size:28
Alignment explanation
Indices: 219778--220007 Score: 157
Period size: 29 Copynumber: 8.0 Consensus size: 28
219768 CACAAAAGGT
219778 CCCT-AAACTTTCCAAAAATCACATTTTG
1 CCCTCAAAC-TTCCAAAAATCACATTTTG
* * *
219806 ACCCTTAAACTTCTCAAAAATTACACTTTTT
1 -CCCTCAAACTTC-CAAAAATCACA-TTTTG
* *
219837 CCC-CTAAACTTCCAAAAATTACATTTTTT
1 CCCTC-AAACTTCCAAAAATCACA-TTTTG
* *
219866 CCCTCAAACTTCC-AATATAACATTTTTG
1 CCCTCAAACTTCCAAAAATCACA-TTTTG
* *
219894 -CCTCCAAACTTCCAAAAATCATATTCTTA
1 CCCT-CAAACTTCCAAAAATCACATT-TTG
* **
219923 CCCTCGAACTTTTAAAAATCACATTTTTG
1 CCCTCAAACTTCCAAAAATCACA-TTTTG
*
219952 -CCTCCAAACTTTCAAAAATCACATTTTTG
1 CCCT-CAAACTTCCAAAAATCACA-TTTTG
** *
219981 -CCTCGGACTTCTCAAAAATAACATTTT
1 CCCTCAAACTTC-CAAAAATCACATTTT
220008 TACCCTGAAC
Statistics
Matches: 167, Mismatches: 22, Indels: 25
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.02
28 35 0.21
29 95 0.57
30 30 0.18
31 4 0.02
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (28 bp):
CCCTCAAACTTCCAAAAATCACATTTTG
Found at i:220028 original size:58 final size:58
Alignment explanation
Indices: 219782--220008 Score: 239
Period size: 58 Copynumber: 3.9 Consensus size: 58
219772 AAAGGTCCCT
* ** *
219782 AAACTTTCCAAAAATCACATTTTGACCCTTAAACTTCTCAAAAATTACACTTTTT-CC-CC
1 AAAC-TTCCAAAAATCACATTTT-TCCCTCGAACTTCTCAAAAATAACA-TTTTTGCCTCC
* * *
219841 TAAACTTCCAAAAATTACATTTTTTCCCTCAAACTTC-C-AATATAACATTTTTGCCTCC
1 -AAACTTCCAAAAATCACA-TTTTTCCCTCGAACTTCTCAAAAATAACATTTTTGCCTCC
* * * *
219899 AAACTTCCAAAAATCATATTCTTACCCTCGAACTT-TTAAAAATCACATTTTTGCCTCC
1 AAACTTCCAAAAATCACATT-TTTCCCTCGAACTTCTCAAAAATAACATTTTTGCCTCC
* * *
219957 AAACTTTCAAAAATCACATTTTTGCCTCGGACTTCTCAAAAATAACATTTTT
1 AAACTTCCAAAAATCACATTTTTCCCTCGAACTTCTCAAAAATAACATTTTT
220009 ACCCTGAACT
Statistics
Matches: 141, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
56 7 0.05
57 48 0.34
58 54 0.38
59 24 0.17
60 8 0.06
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.36
Consensus pattern (58 bp):
AAACTTCCAAAAATCACATTTTTCCCTCGAACTTCTCAAAAATAACATTTTTGCCTCC
Found at i:220028 original size:87 final size:85
Alignment explanation
Indices: 219782--220057 Score: 252
Period size: 87 Copynumber: 3.2 Consensus size: 85
219772 AAAGGTCCCT
* * * *
219782 AAACTTTCCAAAAATCACA-TTTTGACCCTTAAACTTCTCAAAAATTACACTTTTTCCCCTAAAC
1 AAACTTT-CAAAAATCACATTTTTG--CCTCAAACTTCTCAAAAATAACA-TTTTTACCCTGAAC
* *
219846 TTCCAAAAATTACATTTTTTCCCTC
62 TTCCAAAAATCACATTTTTACCC-C
* * * * * *
219871 AAAC-TTCCAATATAACATTTTTGCCTCCAAACTTC-CAAAAATCATATTCTTACCCTCGAACTT
1 AAACTTTCAAAAATCACATTTTTGCCT-CAAACTTCTCAAAAATAACATTTTTACCCT-GAACTT
** *
219934 TTAAAAATCACATTTTTGCCTCC
64 CCAAAAATCACATTTTTACC-CC
**
219957 AAACTTTCAAAAATCACATTTTTGCCTCGGACTTCTCAAAAATAACATTTTTACCCTGAACTCTC
1 AAACTTTCAAAAATCACATTTTTGCCTCAAACTTCTCAAAAATAACATTTTTACCCTGAACT-TC
* * *
220022 CCAAAATGACACTTTTACCCC
65 CAAAAATCACATTTTTACCCC
*
220043 AAAACTTTCTAAAAT
1 -AAACTTTCAAAAAT
220058 TACGTTTTAA
Statistics
Matches: 151, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
85 8 0.05
86 51 0.34
87 81 0.54
88 7 0.05
89 4 0.03
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (85 bp):
AAACTTTCAAAAATCACATTTTTGCCTCAAACTTCTCAAAAATAACATTTTTACCCTGAACTTCC
AAAAATCACATTTTTACCCC
Found at i:220056 original size:29 final size:28
Alignment explanation
Indices: 220022--220084 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
220012 CTGAACTCTC
220022 CCAAAATGACACTTTT-ACCCCAAAACTTT
1 CCAAAATGAC-CTTTTAACCCC-AAACTTT
* * *
220051 CTAAAATTACGTTTTAACCCCAAACTTT
1 CCAAAATGACCTTTTAACCCCAAACTTT
220079 CCAAAA
1 CCAAAA
220085 CTTCATTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 16 0.55
29 13 0.45
ACGTcount: A:0.40, C:0.29, G:0.03, T:0.29
Consensus pattern (28 bp):
CCAAAATGACCTTTTAACCCCAAACTTT
Found at i:220214 original size:28 final size:26
Alignment explanation
Indices: 220159--220214 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 26
220149 TTAATTAATT
220159 TTTTATTTTCTCATTTATTTTTTTGTA
1 TTTTATTTTCTCA-TTATTTTTTTGTA
220186 TTTTACTTTTCTCA-TATTTATTTTCGTA
1 TTTTA-TTTTCTCATTATTT-TTTT-GTA
220214 T
1 T
220215 ATTTGTTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
26 5 0.19
27 9 0.35
28 12 0.46
ACGTcount: A:0.16, C:0.11, G:0.04, T:0.70
Consensus pattern (26 bp):
TTTTATTTTCTCATTATTTTTTTGTA
Found at i:220218 original size:30 final size:27
Alignment explanation
Indices: 220159--220218 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 27
220149 TTAATTAATT
** *
220159 TTTTATTTTCTCATTTATTTTTTTGTA
1 TTTTATTTTCTCATTTATTTTCGTATA
220186 TTTTACTTTTCTCATATTTATTTTCGTATA
1 TTTTA-TTTTCTC--ATTTATTTTCGTATA
220216 TTT
1 TTT
220219 GTTCATTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.19
28 7 0.26
30 15 0.56
ACGTcount: A:0.17, C:0.10, G:0.03, T:0.70
Consensus pattern (27 bp):
TTTTATTTTCTCATTTATTTTCGTATA
Found at i:220452 original size:98 final size:97
Alignment explanation
Indices: 220348--220532 Score: 298
Period size: 98 Copynumber: 1.9 Consensus size: 97
220338 TTTAAAATCG
* *
220348 AGACAATATTCCTTTATTTCGAGTTTTGAAAATTCGTGCCTTAACTTACTAGGCGCGATTTTTTC
1 AGACAATATTCCTTTATTTCGAGTTTTGAAAATTCGTGCATTAACTTACTAGGCGCGA-CTTTTC
220413 TTCAAATCGAGATAATCGAATACTCTTAAATTA
65 TTCAAATCGAGATAATCGAATACTCTTAAATTA
* * * *
220446 AGACAATATTCCTTTATTTCGGGTTTTGAAAATTTGTGCATTTACTTATTAGGCGCGACTTTTCT
1 AGACAATATTCCTTTATTTCGAGTTTTGAAAATTCGTGCATTAACTTACTAGGCGCGACTTTTCT
*
220511 TCAAATCGGGATAATCGAATAC
66 TCAAATCGAGATAATCGAATAC
220533 CCTTTTTCAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
97 27 0.34
98 53 0.66
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (97 bp):
AGACAATATTCCTTTATTTCGAGTTTTGAAAATTCGTGCATTAACTTACTAGGCGCGACTTTTCT
TCAAATCGAGATAATCGAATACTCTTAAATTA
Found at i:231723 original size:39 final size:39
Alignment explanation
Indices: 231634--231740 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
231624 NNNNNNNNNN
* * * *
231634 CAATCTCTTACACTGAGCCTAGGGCAGATTACAGCCATT
1 CAATCTCTTACCCTGAGCCTGGGGCAGATCACAGCCATC
* * *
231673 CGATCTTTTACCCTGAGCCTGGGGCAGATCATCA-TCATC
1 CAATCTCTTACCCTGAGCCTGGGGCAGATCA-CAGCCATC
* * *
231712 CAATCTCTTACCCCGATCGTGGGGCAGAT
1 CAATCTCTTACCCTGAGCCTGGGGCAGAT
231741 TGCAGTCACT
Statistics
Matches: 55, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 53 0.96
40 2 0.04
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (39 bp):
CAATCTCTTACCCTGAGCCTGGGGCAGATCACAGCCATC
Found at i:232170 original size:17 final size:17
Alignment explanation
Indices: 232148--232269 Score: 145
Period size: 17 Copynumber: 7.1 Consensus size: 17
232138 CATTTTTTTA
*
232148 AAATTTATTTTAAGGTT
1 AAATTTATTTTAAGTTT
*
232165 AAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTT
*
232182 AAATTTATTTCAAGTTT
1 AAATTTATTTTAAGTTT
* *
232199 AAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTT
*
232216 AAATTTAATTTAAGTTT
1 AAATTTATTTTAAGTTT
*
232233 AAATTTATTTTTAAATTT
1 AAATTTA-TTTTAAGTTT
* * *
232251 AAAATTATTCTAAATTT
1 AAATTTATTTTAAGTTT
232268 AA
1 AA
232270 TTAATAATGT
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
17 76 0.84
18 14 0.16
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (17 bp):
AAATTTATTTTAAGTTT
Found at i:232182 original size:6 final size:6
Alignment explanation
Indices: 232163--232253 Score: 75
Period size: 6 Copynumber: 15.8 Consensus size: 6
232153 TATTTTAAGG
* * **
232163 TTAAAT TT-ATT TTAAAT TTAAAT TT--AT TTCAAGT TTAAAT TT-GTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT
* **
232208 TTAAAT TTAAAT TT-AAT TTAAGT TTAAAT TTATTT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
232254 ATTATTCTAA
Statistics
Matches: 65, Mismatches: 14, Indels: 12
0.71 0.15 0.13
Matches are distributed among these distances:
4 4 0.06
5 12 0.18
6 46 0.71
7 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (6 bp):
TTAAAT
Found at i:232187 original size:34 final size:34
Alignment explanation
Indices: 232148--232269 Score: 172
Period size: 34 Copynumber: 3.6 Consensus size: 34
232138 CATTTTTTTA
*
232148 AAATTTATTTTAAGGTTAAATTTATTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
* *
232182 AAATTTATTTCAAGTTTAAATTTGTTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
*
232216 AAATTTAATTTAAGTTTAAATTTATTTTTAAATTT
1 AAATTTATTTTAAGTTTAAATTTA-TTTTAAATTT
* * *
232251 AAAATTATTCTAAATTTAA
1 AAATTTATTTTAAGTTTAA
232270 TTAATAATGT
Statistics
Matches: 77, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
34 52 0.68
35 25 0.32
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (34 bp):
AAATTTATTTTAAGTTTAAATTTATTTTAAATTT
Found at i:233911 original size:30 final size:30
Alignment explanation
Indices: 233877--234332 Score: 173
Period size: 29 Copynumber: 15.8 Consensus size: 30
233867 AAACTGTCTA
* * *
233877 AAAATCACATTTTGACCCTTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
** *
233907 AAAATTACA-TTTAACCCCTAAGTTTTTTC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
**
233936 AAAATTTTATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * * * *
233966 AAAATTATATTTTAACCTC-GAACTTCTCA
1 AAAATTACATTTTAACCCCTAAACTTTTCC
*
233995 AAAATTACACTTTT-A-CCCTCGAAC--TTCC
1 AAAATTACA-TTTTAACCCCT-AAACTTTTCC
** *
234023 AAAAATTACATTTT-TGCCCTCGAAC--TTCC
1 -AAAATTACATTTTAACCCCT-AAACTTTTCC
* *
234052 AAAATTACATTTTTACCCCCAAAC--TTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
234080 AAAAATAACATTTTTA-CCCTCGAAC--TTCC
1 -AAAATTACATTTTAACCCCT-AAACTTTTCC
* *
234109 AAAATTACATTTTTACCCCCAAAC--TTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* *
234137 AAAAATAACATTTT-A-CCCTCGAAC--TTCC
1 -AAAATTACATTTTAACCCCT-AAACTTTTCC
** *
234165 AAAAATTACATTTT--TTCCTAAAC-TTTCA
1 -AAAATTACATTTTAACCCCTAAACTTTTCC
* * * * * *
234193 AAAATCAAATTTTTA-CCCTCGAACTTCT-A
1 AAAATTACATTTTAACCCCT-AAACTTTTCC
* * * * *
234222 AAAATCACATTTTTACCCAT-GA-TCTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
234250 AAAAAATACATTTTTA-CCCTAAAC-TCTCC
1 -AAAATTACATTTTAACCCCTAAACTTTTCC
* * *
234279 CAAATGACATTTTTACCCCTAAAAC-TTTCC
1 AAAATTACATTTTAACCCCT-AAACTTTTCC
234309 AAAATTACATTTTAACCCC-AAACT
1 AAAATTACATTTTAACCCCTAAACT
234333 CTCTGAAACT
Statistics
Matches: 338, Mismatches: 62, Indels: 53
0.75 0.14 0.12
Matches are distributed among these distances:
27 19 0.06
28 102 0.30
29 138 0.41
30 79 0.23
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.35
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTCC
Found at i:233938 original size:29 final size:30
Alignment explanation
Indices: 233885--233982 Score: 126
Period size: 30 Copynumber: 3.3 Consensus size: 30
233875 TAAAAATCAC
* * *
233885 ATTTTGACCCTTAAACTTTTCCAAAATTAC
1 ATTTTAACCCCTAAACTTTTCCAAAATTAT
** * *
233915 A-TTTAACCCCTAAGTTTTTTCAAAATTTT
1 ATTTTAACCCCTAAACTTTTCCAAAATTAT
233944 ATTTTAACCCCTAAACTTTTCCAAAATTAT
1 ATTTTAACCCCTAAACTTTTCCAAAATTAT
233974 ATTTTAACC
1 ATTTTAACC
233983 TCGAACTTCT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
29 22 0.39
30 34 0.61
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (30 bp):
ATTTTAACCCCTAAACTTTTCCAAAATTAT
Found at i:234060 original size:57 final size:57
Alignment explanation
Indices: 233962--234326 Score: 395
Period size: 57 Copynumber: 6.4 Consensus size: 57
233952 CCCTAAACTT
* * * *
233962 TTCC-AAAATTATA-TTTTAACCTCGAACTTCTCAAAAATTACACTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTC-C-AAAATTACATTTTTACCCTCAAAC
* *
234019 TTCCAAAAATTACATTTTTGCCCTCGAACTTCCAAAATTACATTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAATTACATTTTTACCCTCAAAC
* *
234076 TTCCAAAAATAACATTTTTACCCTCGAACTTCCAAAATTACATTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAATTACATTTTTACCCTCAAAC
* *
234133 TTCCAAAAATAACA-TTTTACCCTCGAACTTCCAAAAATTACATTTTT-TCCT-AAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTCC-AAAATTACATTTTTACCCTCAAAC
* * * * * * *
234188 TTTCAAAAATCAAATTTTTACCCTCGAACTTCTAAAAATCACATTTTTACCCAT-GATC
1 TTCCAAAAATTACATTTTTACCCTCGAACTTC-CAAAATTACATTTTTACCC-TCAAAC
* * * * *
234246 TTCCAAAAAATACATTTTTACCCT-AAACTCTCCCAAATGACATTTTTACCCCTAAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAACT-TCCAAAATTACATTTTTA-CCCTCAAAC
*
234304 TTTCC-AAAATTACATTTTAACCC
1 -TTCCAAAAATTACATTTTTACCC
234327 CAAACTCTCT
Statistics
Matches: 267, Mismatches: 30, Indels: 21
0.84 0.09 0.07
Matches are distributed among these distances:
55 15 0.06
56 50 0.19
57 128 0.48
58 55 0.21
59 19 0.07
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (57 bp):
TTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAATTACATTTTTACCCTCAAAC
Found at i:234224 original size:29 final size:29
Alignment explanation
Indices: 233962--234326 Score: 383
Period size: 29 Copynumber: 12.8 Consensus size: 29
233952 CCCTAAACTT
* *
233962 TTCC-AAAATTATA-TTTTAACCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
233989 TTCTCAAAAATTACACTTTTACCCTCGAAC
1 TTC-CAAAAATTACATTTTTACCCTCGAAC
*
234019 TTCCAAAAATTACATTTTTGCCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* *
234048 TTCC-AAAATTACATTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
234076 TTCCAAAAATAACATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* *
234105 TTCC-AAAATTACATTTTTACCCCCAAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
*
234133 TTCCAAAAATAACA-TTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* *
234161 TTCCAAAAATTACATTTTT-TCCT-AAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* * *
234188 TTTCAAAAATCAAATTTTTACCCTCGAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* * *
234217 TTCTAAAAATCACATTTTTACCCAT-GATC
1 TTCCAAAAATTACATTTTTACCC-TCGAAC
* *
234246 TTCCAAAAAATACATTTTTACCCT-AAAC
1 TTCCAAAAATTACATTTTTACCCTCGAAC
* * **
234274 TCTCC-CAAATGACATTTTTACCCCTAAAAC
1 T-TCCAAAAATTACATTTTTA-CCCTCGAAC
*
234304 TTTCC-AAAATTACATTTTAACCC
1 -TTCCAAAAATTACATTTTTACCC
234327 CAAACTCTCT
Statistics
Matches: 286, Mismatches: 39, Indels: 24
0.82 0.11 0.07
Matches are distributed among these distances:
27 22 0.08
28 98 0.34
29 129 0.45
30 36 0.13
31 1 0.00
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (29 bp):
TTCCAAAAATTACATTTTTACCCTCGAAC
Found at i:234416 original size:29 final size:28
Alignment explanation
Indices: 234384--234446 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 28
234374 CTTTTAATTA
234384 ATTTTGTATTTT-CTCACTTATT-TTTTCGT
1 ATTTT-TATTTTCCTCA--TATTATTTTCGT
234413 A-TTTTATTTTCCTCATATTATTTTCGT
1 ATTTTTATTTTCCTCATATTATTTTCGT
234440 ATATTTT
1 AT-TTTT
234447 TTCATTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
26 4 0.13
27 14 0.47
28 7 0.23
29 5 0.17
ACGTcount: A:0.17, C:0.13, G:0.05, T:0.65
Consensus pattern (28 bp):
ATTTTTATTTTCCTCATATTATTTTCGT
Found at i:234422 original size:13 final size:13
Alignment explanation
Indices: 234402--234449 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
234392 TTTTCTCACT
234402 TATT-TTTTCGTA
1 TATTATTTTCGTA
* *
234414 TTTTATTTTCCTCA
1 TATTATTTTCGT-A
234428 TATTATTTTCGTA
1 TATTATTTTCGTA
234441 TATT-TTTTC
1 TATTATTTTC
234450 ATTCTTTTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
12 8 0.27
13 11 0.37
14 11 0.37
ACGTcount: A:0.17, C:0.12, G:0.04, T:0.67
Consensus pattern (13 bp):
TATTATTTTCGTA
Found at i:234736 original size:97 final size:98
Alignment explanation
Indices: 234565--234761 Score: 297
Period size: 97 Copynumber: 2.0 Consensus size: 98
234555 TCCAAAATAT
*
234565 TTAAGATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAATTTGTGCCTTAACTTACTAGGCAC
1 TTAAGATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAAATTGTGCCTTAACTTACTAGGCAC
* *
234630 GATTTTTCTTCAAACCGGGATAATTGAATACCC
66 GACTTTTCTTCAAACCGGGATAATAGAATACCC
* * **
234663 TTAA-ATCGAGGCAATATTCCTTTATTTCGGGTTTTGAAAAATTGTGCCTTAAGTTACTAGGTGC
1 TTAAGATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAAATTGTGCCTTAACTTACTAGGCAC
** *
234727 GACTTTTCTTCAAATGGGGATAATAGAATATCC
66 GACTTTTCTTCAAACCGGGATAATAGAATACCC
234760 TT
1 TT
234762 TTTCAAGGTT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
97 85 0.96
98 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (98 bp):
TTAAGATCGAGGCAATATTCCTTTATTTCGAGTTTTGAAAAATTGTGCCTTAACTTACTAGGCAC
GACTTTTCTTCAAACCGGGATAATAGAATACCC
Found at i:239480 original size:24 final size:24
Alignment explanation
Indices: 239428--239480 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
239418 ATTTTTTCTC
*
239428 TTATTGAGTTTTGTTGTTATTTAA
1 TTATTGAGTTTTGTTGTTATATAA
239452 TTATTGA-TTTATGTTG-TATATAA
1 TTATTGAGTTT-TGTTGTTATATAA
239475 TGTATT
1 T-TATT
239481 ACTTCATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 10 0.38
24 16 0.62
ACGTcount: A:0.25, C:0.00, G:0.15, T:0.60
Consensus pattern (24 bp):
TTATTGAGTTTTGTTGTTATATAA
Found at i:240010 original size:17 final size:18
Alignment explanation
Indices: 239989--240039 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
239979 CATGCGTTCG
239989 CACAACATATGGGTTCAT
1 CACAACATATGGGTTCAT
* *
240007 -ACAATATAAGGGTTC-T
1 CACAACATATGGGTTCAT
*
240023 CATAACATATGGGTTCA
1 CACAACATATGGGTTCA
240040 CACTTTATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (18 bp):
CACAACATATGGGTTCAT
Found at i:240096 original size:37 final size:38
Alignment explanation
Indices: 240030--240111 Score: 103
Period size: 37 Copynumber: 2.1 Consensus size: 38
240020 TCTCATAACA
240030 TATGGGTTCACACTTTATAATATAACAGGGTTCACACATG
1 TATGGGTTCACA--TTATAATATAACAGGGTTCACACATG
** * *
240070 TATGGGTTCACA-TATAATATGGCAGGGTTCGCAGATG
1 TATGGGTTCACATTATAATATAACAGGGTTCACACATG
240107 TATGG
1 TATGG
240112 TAGGGTTCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 26 0.68
40 12 0.32
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (38 bp):
TATGGGTTCACATTATAATATAACAGGGTTCACACATG
Found at i:240099 original size:21 final size:21
Alignment explanation
Indices: 240073--240151 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
240063 ACACATGTAT
*
240073 GGGTTCACATATAATATGGCA
1 GGGTTCGCATATAATATGGCA
* * *
240094 GGGTTCGCAGAT-GTATGGTA
1 GGGTTCGCATATAATATGGCA
* *
240114 GGGTTCGCATGATACTATAGCA
1 GGGTTCGCAT-ATAATATGGCA
* *
240136 GGGTTTGCATGTAATA
1 GGGTTCGCATATAATA
240152 CAACAGGGTT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 15 0.33
21 16 0.36
22 14 0.31
ACGTcount: A:0.27, C:0.13, G:0.30, T:0.30
Consensus pattern (21 bp):
GGGTTCGCATATAATATGGCA
Found at i:246851 original size:12 final size:12
Alignment explanation
Indices: 246836--246877 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
246826 GTTTAGTTAT
*
246836 ATGTTCATGAAC
1 ATGTTCGTGAAC
**
246848 ATGTTCGTTTA-
1 ATGTTCGTGAAC
246859 ATGTTCGTGAAC
1 ATGTTCGTGAAC
246871 ATGTTCG
1 ATGTTCG
246878 ATTAAGTTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.40
Consensus pattern (12 bp):
ATGTTCGTGAAC
Found at i:246869 original size:23 final size:22
Alignment explanation
Indices: 246813--246882 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 22
246803 CCATTAACTT
* *
246813 TGTTCGTGAATATGTTTAGTTATA
1 TGTTCGTGAACATG-TTCGTTA-A
*
246837 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCG-TTAA
246860 TGTTCGTGAACATGTTCGATTAA
1 TGTTCGTGAACATGTTCG-TTAA
246883 GTTAAATGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
23 25 0.62
24 15 0.38
ACGTcount: A:0.26, C:0.10, G:0.20, T:0.44
Consensus pattern (22 bp):
TGTTCGTGAACATGTTCGTTAA
Found at i:246892 original size:23 final size:23
Alignment explanation
Indices: 246836--246895 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 23
246826 GTTTAGTTAT
* *
246836 ATGTTCATGAACATGTTCGTTTA
1 ATGTTAATGAACATGTTCGATTA
**
246859 ATGTTCGTGAACATGTTCGATTA
1 ATGTTAATGAACATGTTCGATTA
246882 A-GTTAAATGAACAT
1 ATGTT-AATGAACAT
246896 ATTTGTGAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 3 0.09
23 29 0.91
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (23 bp):
ATGTTAATGAACATGTTCGATTA
Found at i:248642 original size:17 final size:18
Alignment explanation
Indices: 248612--248645 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
248602 AAATTTTTTA
248612 TTTATTTATCTTTTAATT
1 TTTATTTATCTTTTAATT
*
248630 TTTATTT-TTTTTTAAT
1 TTTATTTATCTTTTAAT
248646 ATTGTATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTATTTATCTTTTAATT
Found at i:254638 original size:7 final size:7
Alignment explanation
Indices: 254626--254684 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
254616 AATTGAACCC
254626 AATTTTA
1 AATTTTA
254633 AATTTTA
1 AATTTTA
254640 AATTTTA
1 AATTTTA
*
254647 AATTATTTT
1 AA-T-TTTA
*
254656 AAGTTTA
1 AATTTTA
254663 AA-TTT-
1 AATTTTA
254668 -ATTTTA
1 AATTTTA
254674 AA-TTTA
1 AATTTTA
254680 AATTT
1 AATTT
254685 ATTTTGAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
4 1 0.02
5 3 0.07
6 9 0.21
7 24 0.56
8 1 0.02
9 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (7 bp):
AATTTTA
Found at i:254654 original size:17 final size:17
Alignment explanation
Indices: 254634--254702 Score: 104
Period size: 17 Copynumber: 4.1 Consensus size: 17
254624 CCAATTTTAA
254634 ATTTTAAATTTTAAA-TT
1 ATTTTAAA-TTTAAATTT
*
254651 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
254668 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
254685 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
254702 A
1 A
254703 AAGTTTAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
16 6 0.12
17 42 0.88
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:254679 original size:23 final size:24
Alignment explanation
Indices: 254636--254710 Score: 66
Period size: 23 Copynumber: 3.2 Consensus size: 24
254626 AATTTTAAAT
* * *
254636 TTTAAATTTTAAATT-ATTTTAAG
1 TTTAAATTTGAATTTAAATTTAAG
* *
254659 TTTAAATTT-ATTTTAAATTTAAA
1 TTTAAATTTGAATTTAAATTTAAG
*
254682 TTT-ATTTTGAATTTAAATTTAAAG
1 TTTAAATTTGAATTTAAATTT-AAG
254706 TTTAA
1 TTTAA
254711 TTAAAAGTCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
22 7 0.17
23 28 0.68
24 5 0.12
25 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (24 bp):
TTTAAATTTGAATTTAAATTTAAG
Found at i:254709 original size:7 final size:6
Alignment explanation
Indices: 254629--254710 Score: 64
Period size: 6 Copynumber: 13.8 Consensus size: 6
254619 TGAACCCAAT
* * *
254629 TTTAAA TTTTAAA TTTTAAA -TT-AT TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
254676 TTTAAA TTT-AT TTTGAA TTTAAA TTTAAA GTTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAA
254711 TTAAAAGTCC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
4 1 0.02
5 12 0.19
6 31 0.50
7 18 0.29
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:255375 original size:13 final size:14
Alignment explanation
Indices: 255337--255377 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
255327 TTCGAAACTG
255337 AAAACATATTAAAT
1 AAAACATATTAAAT
*
255351 AAATAGATATTAAAT
1 AAA-ACATATTAAAT
255366 AAAA-ATATTAAA
1 AAAACATATTAAA
255378 AGAGTTGAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 4 0.16
15 13 0.52
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (14 bp):
AAAACATATTAAAT
Found at i:256173 original size:25 final size:26
Alignment explanation
Indices: 256134--256200 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
256124 CTTCTTCTCT
256134 TTTTTTTTCATTTTTATAATTTAATC
1 TTTTTTTTCATTTTTATAATTTAATC
256160 TTTTTTTTCATTTTTATAATTTAATC
1 TTTTTTTTCATTTTTATAATTTAATC
*
256186 TTTTTTAT-ATTTTTA
1 TTTTTTTTCATTTTTA
256201 ATTTATTTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
25 7 0.17
26 33 0.82
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTTTTTCATTTTTATAATTTAATC
Found at i:256650 original size:58 final size:58
Alignment explanation
Indices: 256541--256941 Score: 259
Period size: 58 Copynumber: 6.9 Consensus size: 58
256531 GTTGCCCTAC
* * ** * * *
256541 ACTTCT-AAAAATTAC-TTTTTTCCCCCGAACTTC-CAAAATCACTTTTTACCCCCAA
1 ACTTCTCAAAAATTACATTTTTGCCTCTAAACTTCTAAAAATTACATTTTACCCCCAA
* * * *
256596 ACTTCTCAAAAATTACATTTTTGCTTGTAAACTTTTAAAAATTACATTTTACCCCCGA
1 ACTTCTCAAAAATTACATTTTTGCCTCTAAACTTCTAAAAATTACATTTTACCCCCAA
* * * * * * * *
256654 ACAT-TCAAAAATCACTTTTTTACCT-TCGAACTTCTCAAAAATTACATTTTTTCCCTCGA
1 ACTTCTCAAAAATTACATTTTTGCCTCT-AAACTTCT-AAAAATTACA-TTTTACCCCCAA
* * ** *
256713 ACTTCT-AAAAATTACA-TTTTACCTCTAAACTTCTAAAAATCACATCTTTACCCTTAC
1 ACTTCTCAAAAATTACATTTTTGCCTCTAAACTTCTAAAAATTACAT-TTTACCCCCAA
* * ** * * *
256770 ACTTCTAAAAAATTACATTTTTGCCCCCGAAGTTCTAAAAATTACATTTTGCCCACAA
1 ACTTCTCAAAAATTACATTTTTGCCTCTAAACTTCTAAAAATTACATTTTACCCCCAA
* * * * **
256828 ACTTC-CAAAAATCACATTTTTACC-CTTAAACTTCTCAAAAATTACTTTTTTTCCCCTGA
1 ACTTCTCAAAAATTACATTTTTGCCTC-TAAACTTCT-AAAAATTAC-ATTTTACCCCCAA
* * * *
256887 ACTTC-CAAAAATCATATTTTTATCCTC-AAACTCCTTAAAAATT-CATTTTTACCCC
1 ACTTCTCAAAAATTACATTTTT-GCCTCTAAACTTC-TAAAAATTACA-TTTTACCCC
256942 TAAAACTTTC
Statistics
Matches: 273, Mismatches: 55, Indels: 33
0.76 0.15 0.09
Matches are distributed among these distances:
55 6 0.02
56 12 0.04
57 78 0.29
58 86 0.32
59 86 0.32
60 4 0.01
61 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (58 bp):
ACTTCTCAAAAATTACATTTTTGCCTCTAAACTTCTAAAAATTACATTTTACCCCCAA
Found at i:256664 original size:29 final size:28
Alignment explanation
Indices: 256541--256898 Score: 229
Period size: 29 Copynumber: 12.4 Consensus size: 28
256531 GTTGCCCTAC
* *
256541 ACTTCTAAAAATTACTTTTTTCCCCCGA
1 ACTTCTAAAAATTACATTTTACCCCCGA
* * * *
256569 ACTTC-CAAAATCACTTTTTACCCCCAA
1 ACTTCTAAAAATTACATTTTACCCCCGA
** **
256596 ACTTCTCAAAAATTACATTTT-TGCTTGTAA
1 ACTTCT-AAAAATTACATTTTACCCCCG--A
*
256626 ACTTTTAAAAATTACATTTTACCCCCGA
1 ACTTCTAAAAATTACATTTTACCCCCGA
* * **
256654 ACATTC-AAAAATCACTTTTTTACCTTCGA
1 AC-TTCTAAAAATTAC-ATTTTACCCCCGA
* *
256683 ACTTCTCAAAAATTACATTTTTTCCCTCGA
1 ACTTCT-AAAAATTACA-TTTTACCCCCGA
* **
256713 ACTTCTAAAAATTACATTTTACCTCTAA
1 ACTTCTAAAAATTACATTTTACCCCCGA
* **
256741 ACTTCTAAAAATCACATCTTTA-CCCTTA
1 ACTTCTAAAAATTACAT-TTTACCCCCGA
*
256769 CACTTCTAAAAAATTACATTTTTGCCCCCGA
1 -ACTTCT-AAAAATTACA-TTTTACCCCCGA
* * * *
256800 AGTTCTAAAAATTACATTTTGCCCACAA
1 ACTTCTAAAAATTACATTTTACCCCCGA
* * ***
256828 ACTTCCAAAAATCACATTTTTACCCTTAA
1 ACTTCTAAAAATTACA-TTTTACCCCCGA
* * *
256857 ACTTCTCAAAAATTACTTTTTTTCCCCTGA
1 ACTTCT-AAAAATTAC-ATTTTACCCCCGA
*
256887 ACTTCCAAAAAT
1 ACTTCTAAAAAT
256899 CATATTTTTA
Statistics
Matches: 258, Mismatches: 54, Indels: 35
0.74 0.16 0.10
Matches are distributed among these distances:
27 23 0.09
28 70 0.27
29 89 0.34
30 71 0.28
31 5 0.02
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (28 bp):
ACTTCTAAAAATTACATTTTACCCCCGA
Found at i:256906 original size:29 final size:29
Alignment explanation
Indices: 256568--256945 Score: 111
Period size: 29 Copynumber: 13.1 Consensus size: 29
256558 TTTTCCCCCG
* *
256568 AACTTCC-AAAATCA-CTTTTTACCCCCA
1 AACTTCCAAAAATCATATTTTTACCCCTA
* * * ***
256595 AACTTCTCAAAAATTACATTTTTGCTTGTA
1 AACTTC-CAAAAATCATATTTTTACCCCTA
** * * **
256625 AACTTTTAAAAATTACA-TTTTACCCCCG
1 AACTTCCAAAAATCATATTTTTACCCCTA
* *
256653 AACATT-CAAAAATCACT-TTTTTA-CCTTCG
1 AAC-TTCCAAAAATCA-TATTTTTACCCCT-A
* * * *
256682 AACTTCTCAAAAATTACATTTTT-TCCCTCG
1 AACTTC-CAAAAATCATATTTTTACCCCT-A
* * * *
256712 AACTTCTAAAAATTACA-TTTTACCTCTA
1 AACTTCCAAAAATCATATTTTTACCCCTA
* * * *
256740 AACTTCTAAAAATCACATCTTTACCCTTA
1 AACTTCCAAAAATCATATTTTTACCCCTA
* * * * * **
256769 CACTTCTAAAAAATTACATTTTTGCCCCCG
1 AACTTC-CAAAAATCATATTTTTACCCCTA
* * * * *
256799 AAGTTCTAAAAATTACA-TTTTGCCCAC-A
1 AACTTCCAAAAATCATATTTTTACCC-CTA
* *
256827 AACTTCCAAAAATCACATTTTTACCCTTA
1 AACTTCCAAAAATCATATTTTTACCCCTA
* * *
256856 AACTTCTCAAAAATTACT-TTTTTTCCCCTG
1 AACTTC-CAAAAATCA-TATTTTTACCCCTA
*
256886 AACTTCCAAAAATCATATTTTTA-TCCTCA
1 AACTTCCAAAAATCATATTTTTACCCCT-A
256915 AAC-TCCTTAAAAAT--TCATTTTTACCCCTA
1 AACTTCC--AAAAATCAT-ATTTTTACCCCTA
256944 AA
1 AA
256946 ACTTTCTAAA
Statistics
Matches: 268, Mismatches: 58, Indels: 48
0.72 0.16 0.13
Matches are distributed among these distances:
27 6 0.02
28 70 0.26
29 104 0.39
30 88 0.33
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.37
Consensus pattern (29 bp):
AACTTCCAAAAATCATATTTTTACCCCTA
Found at i:256906 original size:87 final size:87
Alignment explanation
Indices: 256491--256898 Score: 427
Period size: 87 Copynumber: 4.7 Consensus size: 87
256481 GAATTATCTG
* * * * * *
256491 AAAATCATATTTTGACCCTTAAACTTTTCCAAAATTACA--TGTTGCCCT-ACACTTCTAAAAAT
1 AAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTTTCCCCTGA-ACTTCTAAAAAT
* * *
256553 TACTTTTTTCCCCCGAACTTCC-
65 TACATTTTACCCCCAAACTTCCA
** * *** * *
256575 AAAATCAC-TTTTTACCCCCAAACTTCTCAAAAATTACATTTTTGCTTGTAAACTTTTAAAAATT
1 AAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTTTCCCCTGAACTTCTAAAAATT
*
256639 ACATTTTACCCCCGAACATT-CA
66 ACATTTTACCCCCAAAC-TTCCA
* *
256661 AAAATCACTTTTTTA-CCTTCGAACTTCTCAAAAATTACATTTTTT-CCCTCGAACTTCTAAAAA
1 AAAATCACATTTTTACCCTT-AAACTTCTCAAAAATTACATTTTTTCCCCT-GAACTTCTAAAAA
* * *
256724 TTACATTTTACCTCTAAACTTCTA
64 TTACATTTTACCCCCAAACTTCCA
* * * * * *
256748 AAAATCACATCTTTACCCTTACACTTCTAAAAAATTACATTTTTGCCCCCGAAGTTCTAAAAATT
1 AAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTTTCCCCTGAACTTCTAAAAATT
* *
256813 ACATTTTGCCCACAAACTTCCA
66 ACATTTTACCCCCAAACTTCCA
* *
256835 AAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACTTTTTTTCCCCTGAACTTCCAAAAAT
1 AAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTTTCCCCTGAACTTCTAAAAAT
256899 CATATTTTTA
Statistics
Matches: 264, Mismatches: 49, Indels: 19
0.80 0.15 0.06
Matches are distributed among these distances:
83 25 0.09
84 7 0.03
85 31 0.12
86 16 0.06
87 178 0.67
88 7 0.03
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.37
Consensus pattern (87 bp):
AAAATCACATTTTTACCCTTAAACTTCTCAAAAATTACATTTTTTCCCCTGAACTTCTAAAAATT
ACATTTTACCCCCAAACTTCCA
Found at i:256907 original size:30 final size:30
Alignment explanation
Indices: 256826--256907 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
256816 TTTTGCCCAC
* *
256826 AAACTTCCAAAAATCACA-TTTTTACCCTT
1 AAACTTCCAAAAATCATATTTTTTACCCCT
*
256855 AAACTTCTCAAAAAT--TACTTTTTTTCCCCT
1 AAACTTC-CAAAAATCATA-TTTTTTACCCCT
*
256885 GAACTTCCAAAAATCATATTTTT
1 AAACTTCCAAAAATCATATTTTT
256908 ATCCTCAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
28 1 0.02
29 14 0.32
30 27 0.61
31 2 0.05
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.39
Consensus pattern (30 bp):
AAACTTCCAAAAATCATATTTTTTACCCCT
Found at i:256962 original size:30 final size:28
Alignment explanation
Indices: 256904--256993 Score: 83
Period size: 28 Copynumber: 3.1 Consensus size: 28
256894 AAAATCATAT
* * *
256904 TTTTATCCTCAAACTC-CTTAAAAATTCA
1 TTTTAACCCCAAACTCTC-TAAAACTTCA
* * **
256932 TTTTTACCCCTAAAACTTTCTAAATTTTCA
1 TTTTAACCCC--AAACTCTCTAAAACTTCA
256962 TTTTAACCCCAAACTCTCTAAAACTTCA
1 TTTTAACCCCAAACTCTCTAAAACTTCA
256990 TTTT
1 TTTT
256994 CGACCCCATT
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
28 26 0.53
30 22 0.45
31 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTTAACCCCAAACTCTCTAAAACTTCA
Found at i:257143 original size:16 final size:16
Alignment explanation
Indices: 257122--257156 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
257112 TCCTATTTTT
257122 TTCGTATATTTATTCA
1 TTCGTATATTTATTCA
*
257138 TTCGTATATTTGTTCA
1 TTCGTATATTTATTCA
257154 TTC
1 TTC
257157 TTTGTGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.14, G:0.09, T:0.57
Consensus pattern (16 bp):
TTCGTATATTTATTCA
Found at i:267371 original size:39 final size:39
Alignment explanation
Indices: 267286--267451 Score: 110
Period size: 39 Copynumber: 4.3 Consensus size: 39
267276 GAAGATTTCG
* * * **
267286 ATCTCTTCCCCCGAGCCT-AGGCA-ATCACCATCATCTG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
*
267323 ATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * *
267362 ATCTCTTACCTCGAACCTAGGGTAGATTGCAGCCATTC-G---
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCA-TCAGCCA
* *** * *
267401 ATCTTTTACCTTAAGCCTGGGGTAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
267440 ATCTCTTACCCC
1 ATCTCTTACCCC
267452 TATCATGGGG
Statistics
Matches: 99, Mismatches: 20, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
35 2 0.02
36 3 0.03
37 18 0.18
38 5 0.05
39 62 0.63
40 1 0.01
41 2 0.02
42 4 0.04
43 2 0.02
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:267479 original size:78 final size:78
Alignment explanation
Indices: 267322--267471 Score: 210
Period size: 78 Copynumber: 1.9 Consensus size: 78
267312 ACCATCATCT
* * *
267322 GATCTTTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCTCGAACCTAGGGTAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAACATAGGGTAG
267387 ATTGCAGCCATTC
66 ATTGCAGCCATTC
** * * * * *
267400 GATCTTTTACCTTAAGCCTGGGGTAGATCATCATCAGCCAATCTCTTACCCCTATCATGGGGTAG
1 GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAACATAGGGTAG
267465 ATTGCAG
66 ATTGCAG
267472 TTATTCGAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 62 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (78 bp):
GATCTTTTACCCCAAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAACATAGGGTAG
ATTGCAGCCATTC
Found at i:267911 original size:17 final size:17
Alignment explanation
Indices: 267891--267976 Score: 118
Period size: 17 Copynumber: 5.1 Consensus size: 17
267881 CCAATTTTAA
*
267891 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
267908 ATTTTAAGTTTAAACTT
1 ATTTTAAATTTAAATTT
* *
267925 ATTTTGAGTTTAAATTT
1 ATTTTAAATTTAAATTT
267942 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
267959 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
267976 A
1 A
267977 AAGTTTAATT
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.36, C:0.01, G:0.05, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:267983 original size:7 final size:6
Alignment explanation
Indices: 267886--267984 Score: 62
Period size: 6 Copynumber: 16.8 Consensus size: 6
267876 TGAACCCAAT
* * * * * * *
267886 TTTAAA TTTTAAA TTTTAA TTT-AT TTTAAG TTTAAA CTT-AT TTTGAG
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
267933 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
267979 GTTTAA
1 -TTTAA
267985 TTAAAAGTCC
Statistics
Matches: 72, Mismatches: 15, Indels: 10
0.74 0.15 0.10
Matches are distributed among these distances:
5 15 0.21
6 46 0.64
7 11 0.15
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (6 bp):
TTTAAA
Done.