Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015196.1 Kokia drynarioides strain JFW-HI SEQ_130240, 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: 599855
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 661 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:7983 original size:30 final size:30
Alignment explanation
Indices: 7949--8306 Score: 242
Period size: 30 Copynumber: 12.1 Consensus size: 30
7939 ATTTTATTTT
* * *
7949 AAAATTATATTTTAACCCTCTAACTTTTCA
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* * *
7979 AAAATTACATTTTAACTCTCAAATTTTTCT
1 AAAATTACATTTTAACCCTCAAACTTTTCC
*
8009 AAAATTACATTTTAACCC-CTAAACTTTTCT
1 AAAATTACATTTTAACCCTC-AAACTTTTCC
* *
8039 AAAATCACATTTTCACCCT-AAACTTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* *
8068 AAAATTACATTTTAACCCCCAAAATTTTCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
* * *
8098 AAAATCACATTTTCACCCTCAAAC-TTCCC
1 AAAATTACATTTTAACCCTCAAACTTTTCC
** * * *
8127 TAAAATCCCGTTTTGACCC-CAAACTTCTCC
1 -AAAATTACATTTTAACCCTCAAACTTTTCC
* * *
8157 AAAATTATGATTTTATCCCT-AAACTTCTCC
1 AAAATTA-CATTTTAACCCTCAAACTTTTCC
* * * * * *
8187 AAAATTATGATTTT-GCCCTCGAACATCT-A
1 AAAATTA-CATTTTAACCCTCAAACTTTTCC
*
8216 AAAATTACCATTTTACCCCT-AAA-TTTT-C
1 AAAATTA-CATTTTAACCCTCAAACTTTTCC
*
8244 AAAATTCACATTTTCAA-CTTCAAA-TTTTCC
1 AAAATT-ACATTTT-AACCCTCAAACTTTTCC
* *
8274 GAAAGTT-CAATTTTAATCC-CAAA-TTTTCC
1 -AAAATTAC-ATTTTAACCCTCAAACTTTTCC
8303 AAAA
1 AAAA
8307 AAATTCAATT
Statistics
Matches: 266, Mismatches: 46, Indels: 34
0.77 0.13 0.10
Matches are distributed among these distances:
28 19 0.07
29 80 0.30
30 162 0.61
31 5 0.02
ACGTcount: A:0.36, C:0.25, G:0.02, T:0.37
Consensus pattern (30 bp):
AAAATTACATTTTAACCCTCAAACTTTTCC
Found at i:8080 original size:89 final size:89
Alignment explanation
Indices: 7970--8163 Score: 246
Period size: 89 Copynumber: 2.2 Consensus size: 89
7960 TTAACCCTCT
* * * * * *
7970 AACTTTTCAAAAATTACATTTTAACTCTCAAATTTTTCTAAAATTACATTTTAACCC-CTAAACT
1 AACTTTTCCAAAATTACATTTTAACCCCCAAAATTTTCCAAAATCACATTTTAACCCTC-AAACT
** *
8034 TTTCTAAAATCACATTTTCACCCTA
65 TCCCTAAAATCACATTTTCACCCCA
*
8059 AACTTTTCCAAAATTACATTTTAACCCCCAAAATTTTCCAAAATCACATTTTCACCCTCAAACTT
1 AACTTTTCCAAAATTACATTTTAACCCCCAAAATTTTCCAAAATCACATTTTAACCCTCAAACTT
* * *
8124 CCCTAAAATCCCGTTTTGACCCCA
66 CCCTAAAATCACATTTTCACCCCA
*
8148 AACTTCTCCAAAATTA
1 AACTTTTCCAAAATTA
8164 TGATTTTATC
Statistics
Matches: 90, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
89 89 0.99
90 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (89 bp):
AACTTTTCCAAAATTACATTTTAACCCCCAAAATTTTCCAAAATCACATTTTAACCCTCAAACTT
CCCTAAAATCACATTTTCACCCCA
Found at i:8086 original size:59 final size:60
Alignment explanation
Indices: 7949--8193 Score: 241
Period size: 59 Copynumber: 4.1 Consensus size: 60
7939 ATTTTATTTT
* * * * * * *
7949 AAAATTATATTTTAACCCTCT-AACTTTTCAAAAATTACATTTTAACTCTCAAATTTTTCT
1 AAAATTACATTTTAACCC-CTAAACTTTTCCAAAATCACATTTTCACCCTCAAACTTTTCC
*
8009 AAAATTACATTTTAACCCCTAAACTTTTCTAAAATCACATTTTCACCCT-AAACTTTTCC
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTCACCCTCAAACTTTTCC
* * *
8068 AAAATTACATTTTAACCCCCAAAATTTTCCAAAATCACATTTTCACCCTCAAAC-TTCCC
1 AAAATTACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTCACCCTCAAACTTTTCC
** * * * * * *
8127 TAAAATCCCGTTTTGACCCC-AAACTTCTCCAAAATTATGATTTT-ATCCCT-AAACTTCTCC
1 -AAAATTACATTTTAACCCCTAAACTTTTCCAAAATCA-CATTTTCA-CCCTCAAACTTTTCC
8187 AAAATTA
1 AAAATTA
8194 TGATTTTGCC
Statistics
Matches: 156, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
59 84 0.54
60 72 0.46
ACGTcount: A:0.36, C:0.26, G:0.01, T:0.37
Consensus pattern (60 bp):
AAAATTACATTTTAACCCCTAAACTTTTCCAAAATCACATTTTCACCCTCAAACTTTTCC
Found at i:8188 original size:89 final size:89
Alignment explanation
Indices: 7970--8191 Score: 223
Period size: 89 Copynumber: 2.5 Consensus size: 89
7960 TTAACCCTCT
* * * * * * * *
7970 AACTTTTCAAAAATTACATTTTAACTCTCAAATTTTTCTAAAATTACATTTTAACCCCTAAACTT
1 AACTTCTCCAAAATTACATTTTAACCCCCAAAATTCTCCAAAATCACATTTTAACCCCTAAACTT
** *
8035 TTCTAAAATCACATTTTCACCCTA
66 CCCTAAAATCACATTTTCACCCCA
* * *
8059 AACTTTTCCAAAATTACATTTTAACCCCCAAAATTTTCCAAAATCACATTTTCA-CCCTCAAACT
1 AACTTCTCCAAAATTACATTTTAACCCCCAAAATTCTCCAAAATCACATTTTAACCCCT-AAACT
* * *
8123 TCCCTAAAATCCCGTTTTGACCCCA
65 TCCCTAAAATCACATTTTCACCCCA
* * * *
8148 AACTTCTCCAAAATTATGATTTT-ATCCCTAAACTTCTCCAAAAT
1 AACTTCTCCAAAATTA-CATTTTAACCCCCAAAATTCTCCAAAAT
8192 TATGATTTTG
Statistics
Matches: 112, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
88 4 0.04
89 103 0.92
90 5 0.04
ACGTcount: A:0.36, C:0.27, G:0.01, T:0.36
Consensus pattern (89 bp):
AACTTCTCCAAAATTACATTTTAACCCCCAAAATTCTCCAAAATCACATTTTAACCCCTAAACTT
CCCTAAAATCACATTTTCACCCCA
Found at i:8296 original size:29 final size:30
Alignment explanation
Indices: 8215--8329 Score: 87
Period size: 31 Copynumber: 3.8 Consensus size: 30
8205 TCGAACATCT
*
8215 AAAAATTACCATTTT-ACCCCTAAATTTT-C-
1 AAAAATT-CAATTTTAACCCC-AAATTTTCCA
**
8244 -AAAATTCACATTTTCAACTTCAAATTTTCC-
1 AAAAATTCA-ATTTT-AACCCCAAATTTTCCA
* * *
8274 GAAAGTTCAATTTTAATCCCAAATTTTCCAA
1 AAAAATTCAATTTTAACCCCAAATTTTCC-A
*
8305 AAAAATTCAATTTTGACCCCAAATT
1 AAAAATTCAATTTTAACCCCAAATT
8330 CCTCGAAAAT
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.01
28 11 0.16
29 19 0.28
30 9 0.13
31 28 0.41
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAAATTCAATTTTAACCCCAAATTTTCCA
Found at i:16921 original size:15 final size:16
Alignment explanation
Indices: 16891--16929 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
16881 TAATAAAAAT
16891 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
16908 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
16923 ATAATTT
1 ATAATTT
16930 TTAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:17877 original size:21 final size:21
Alignment explanation
Indices: 17852--17906 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 21
17842 CAAAAAATTT
17852 TAAAATTATTTTTTATTTTTA
1 TAAAATTATTTTTTATTTTTA
*
17873 TAAAATGATTTTTTTTTATTTTTA
1 T-AAA--ATTATTTTTTATTTTTA
*
17897 TAAAACTATT
1 TAAAATTATT
17907 ATGATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
21 5 0.18
22 3 0.11
23 3 0.11
24 17 0.61
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
TAAAATTATTTTTTATTTTTA
Found at i:18022 original size:17 final size:17
Alignment explanation
Indices: 18000--18054 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
17990 TCGTCTCCGA
*
18000 TCTTCTTCCTCGTTGTT
1 TCTTCTTCCACGTTGTT
18017 TCTTCTTTCCACAGTT-TT
1 TCTTC-TTCCAC-GTTGTT
* *
18035 T-TTCTTCCCCATTGTT
1 TCTTCTTCCACGTTGTT
18051 TCTT
1 TCTT
18055 TGGAAACCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 2 0.06
16 8 0.26
17 10 0.32
18 8 0.26
19 3 0.10
ACGTcount: A:0.05, C:0.29, G:0.07, T:0.58
Consensus pattern (17 bp):
TCTTCTTCCACGTTGTT
Found at i:18743 original size:27 final size:27
Alignment explanation
Indices: 18705--18756 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
18695 ATGATGATAG
18705 TTTTATAAAAATAAAAAATAATTTTCA
1 TTTTATAAAAATAAAAAATAATTTTCA
18732 TTTTATAAAAATAAAAAATAATTTT
1 TTTTATAAAAATAAAAAATAATTTT
18757 AATAATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
TTTTATAAAAATAAAAAATAATTTTCA
Found at i:21052 original size:28 final size:28
Alignment explanation
Indices: 21012--21069 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
21002 ACATGCCACA
21012 TAACCAAACTTTAGAACGTTTGAAAGAC
1 TAACCAAACTTTAGAACGTTTGAAAGAC
21040 TAACCAAACTTTAGAACGTTTGAAAGAC
1 TAACCAAACTTTAGAACGTTTGAAAGAC
21068 TA
1 TA
21070 CCGAATCAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (28 bp):
TAACCAAACTTTAGAACGTTTGAAAGAC
Found at i:23558 original size:28 final size:28
Alignment explanation
Indices: 23522--23577 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
23512 TTGGTAAGAG
23522 GCATGACCTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
23550 GCATGACCTTTGGGTCAACAGGGAGTAA
1 GCATGACCTTTGGGTCAACAGGGAGTAA
23578 ATCAGATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.32, T:0.21
Consensus pattern (28 bp):
GCATGACCTTTGGGTCAACAGGGAGTAA
Found at i:24283 original size:21 final size:21
Alignment explanation
Indices: 24244--24283 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
24234 TTTTTAGTAC
*
24244 TGGTAGAAGCATAATTTGTTT
1 TGGTAGAAGCATAACTTGTTT
* *
24265 TGGTAGAAGCTTCACTTGT
1 TGGTAGAAGCATAACTTGT
24284 ATCAGTAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (21 bp):
TGGTAGAAGCATAACTTGTTT
Found at i:47806 original size:40 final size:40
Alignment explanation
Indices: 47751--47840 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
47741 GATGATCAAA
47751 AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
1 AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
* **
47791 AAATGATATTTGACTAATAATTTGAAATTGTAATTTTATT
1 AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
*
47831 AAATAATATT
1 AAATGATATT
47841 GGGATAATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.43, C:0.02, G:0.11, T:0.43
Consensus pattern (40 bp):
AAATGATATTTGACTAATAATGTGAAAAGGTAATTTTATT
Found at i:51500 original size:8 final size:9
Alignment explanation
Indices: 51471--51499 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
51461 TCTTTATTAA
51471 TTTAAAAAT
1 TTTAAAAAT
51480 TTTAAAAAT
1 TTTAAAAAT
51489 TTTAAAAAT
1 TTTAAAAAT
51498 TT
1 TT
51500 AGAATATCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:52493 original size:6 final size:6
Alignment explanation
Indices: 52484--52511 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
52474 AAAAAAATGA
52484 AAATTT AAATTT AAATTT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAAT
52512 ATTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
AAATTT
Found at i:58589 original size:158 final size:157
Alignment explanation
Indices: 58301--58623 Score: 452
Period size: 158 Copynumber: 2.0 Consensus size: 157
58291 TTTTGTATCA
* * **
58301 TGTAATGCTCACACGAACTGTGAAATGGGCCTACTCACACAAGTTGTGGGTTGAGATGTTAGGCT
1 TGTAATGCTCACACGAACTATGAAATGGGCCTACTCACACAAGTTGTGAGTCAAGATGTTAGGCT
* * * *
58366 ATACGATACTGCTCACACGAGCTTTGGAGAATCTACTATAAATGTTGAATCTTAACCATCGGTAG
66 ACACCATACTGCTCACACGAGCTGTGGAGAATCTAC-ATAAATGTCGAATCTTAACCATCGGTAG
*
58431 GACATCTAAGACTAGCACCCACATAACC
130 GACATCTAAGACCAGCACCCACATAACC
* * *
58459 TGTAATGCTCACACGAGCTATGAAATGGGCCTGCTCACATGAA-TTGTGAGTCAAGATGTTAGGC
1 TGTAATGCTCACACGAACTATGAAATGGGCCTACTCACA-CAAGTTGTGAGTCAAGATGTTAGGC
* * *
58523 TACACCATGCTGCTGACACGAGCTGTGGAGAATCCGTA-ATAAATGTCGAATCTTAGCCATCGGT
65 TACACCATACTGCTCACACGAGCTGTGGAGAAT-C-TACATAAATGTCGAATCTTAACCATCGGT
*
58587 AGGACATCTAAGACCAGCACCCATATAACC
128 AGGACATCTAAGACCAGCACCCACATAACC
58617 TGTAATG
1 TGTAATG
58624 TAACACCCAA
Statistics
Matches: 146, Mismatches: 16, Indels: 6
0.87 0.10 0.04
Matches are distributed among these distances:
158 141 0.97
159 3 0.02
160 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (157 bp):
TGTAATGCTCACACGAACTATGAAATGGGCCTACTCACACAAGTTGTGAGTCAAGATGTTAGGCT
ACACCATACTGCTCACACGAGCTGTGGAGAATCTACATAAATGTCGAATCTTAACCATCGGTAGG
ACATCTAAGACCAGCACCCACATAACC
Found at i:59822 original size:82 final size:82
Alignment explanation
Indices: 59673--59827 Score: 197
Period size: 82 Copynumber: 1.9 Consensus size: 82
59663 AACTAGTATG
* * * * *
59673 CGATGCTGCTTACATAAGTTGATGAGAATCCGTAAAATATGCAGAAACTCAGCCATCGATACGGT
1 CGATGCTGCTCACACAAGCTGATGAGAATCCGTAAAATACGCAGAAACTCAGCCATCGAGACGGT
*
59738 CCAGAATTACCCACTCA
66 CCACAATTACCCACTCA
* * *
59755 CGATGCTGCTCACACAAGCTGATGAGAATTCGTAACATACGC-GAAGACTCAGCCATC-AGAGGA
1 CGATGCTGCTCACACAAGCTGATGAGAATCCGTAAAATACGCAGAA-ACTCAGCCATCGAGACG-
59818 GTCCACAATT
64 GTCCACAATT
59828 CAGTATTTGT
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
81 6 0.10
82 56 0.90
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (82 bp):
CGATGCTGCTCACACAAGCTGATGAGAATCCGTAAAATACGCAGAAACTCAGCCATCGAGACGGT
CCACAATTACCCACTCA
Found at i:64467 original size:12 final size:13
Alignment explanation
Indices: 64434--64471 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
64424 CTAGCTACCG
64434 CTCCACGTCAGCA
1 CTCCACGTCAGCA
*
64447 CCGCCACGTCAGCA
1 -CTCCACGTCAGCA
64461 -TCCACGTCAGC
1 CTCCACGTCAGC
64472 CACGTGACCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
14 12 0.55
ACGTcount: A:0.21, C:0.47, G:0.18, T:0.13
Consensus pattern (13 bp):
CTCCACGTCAGCA
Found at i:69011 original size:28 final size:29
Alignment explanation
Indices: 68964--69030 Score: 100
Period size: 28 Copynumber: 2.3 Consensus size: 29
68954 AATGAACATC
*
68964 ATTTCATTTTCCATTAAAATCACTCGTTG
1 ATTTCTTTTTCCATTAAAATCACTCGTTG
* *
68993 ATTT-TTTTTCTATTGAAATCACTCGTTG
1 ATTTCTTTTTCCATTAAAATCACTCGTTG
69021 ATTTCTTTTT
1 ATTTCTTTTT
69031 TTGTCCAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 25 0.74
29 9 0.26
ACGTcount: A:0.22, C:0.16, G:0.07, T:0.54
Consensus pattern (29 bp):
ATTTCTTTTTCCATTAAAATCACTCGTTG
Found at i:73942 original size:30 final size:31
Alignment explanation
Indices: 73890--73947 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
73880 CCAGATTCGT
*
73890 TTTAAATAAGTGTAAATTTATAAAAAAAAAA
1 TTTAAATAAGTGTAAAGTTATAAAAAAAAAA
73921 TTTAAA-AA-TGTAAAAGTTATAAAAAAA
1 TTTAAATAAGTGT-AAAGTTATAAAAAAA
73948 TATAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 3 0.12
30 16 0.64
31 6 0.24
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (31 bp):
TTTAAATAAGTGTAAAGTTATAAAAAAAAAA
Found at i:73963 original size:19 final size:19
Alignment explanation
Indices: 73924--73963 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
73914 AAAAAAATTT
* * *
73924 AAAAATGTAAAAGTTATAA
1 AAAAATATAAAAATTAGAA
73943 AAAAATATAAAAATTAGAA
1 AAAAATATAAAAATTAGAA
73962 AA
1 AA
73964 TGTAAAAGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (19 bp):
AAAAATATAAAAATTAGAA
Found at i:82104 original size:21 final size:21
Alignment explanation
Indices: 82080--82124 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
82070 CTACAACTTG
82080 CAAGAACTT-TACATGTTTCTT
1 CAAGAACTTCTACA-GTTTCTT
*
82101 CAAGAACTTCTGCAGTTTCTT
1 CAAGAACTTCTACAGTTTCTT
82122 CAA
1 CAA
82125 CCTTCCCACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.38
Consensus pattern (21 bp):
CAAGAACTTCTACAGTTTCTT
Found at i:91065 original size:25 final size:28
Alignment explanation
Indices: 91013--91079 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 28
91003 AAGTCTAATG
91013 TAAATCTA-AAAAAAGAAAACTTTCATCA
1 TAAATCTACAAAAAAGAAAAC-TTCATCA
91041 TAAATCTACAAAAAA-AAAA-TT-ATCA
1 TAAATCTACAAAAAAGAAAACTTCATCA
*
91066 TGAATCTACAAAAA
1 TAAATCTACAAAAA
91080 TCAAAATTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 17 0.46
26 2 0.05
28 12 0.32
29 6 0.16
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (28 bp):
TAAATCTACAAAAAAGAAAACTTCATCA
Found at i:92387 original size:28 final size:29
Alignment explanation
Indices: 92355--92414 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
92345 CCCGCCCCCC
92355 CTTTTAAT-ATT-TTCCCTCCAAAATTTTA
1 CTTTTAATAATTATTCCC-CCAAAATTTTA
* *
92383 CTTTTCATAATTACTTTCCCCAAAATTTTA
1 CTTTTAATAATTA-TTCCCCCAAAATTTTA
92413 CT
1 CT
92415 CTCCAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 7 0.26
29 3 0.11
30 13 0.48
31 4 0.15
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.48
Consensus pattern (29 bp):
CTTTTAATAATTATTCCCCCAAAATTTTA
Found at i:97588 original size:19 final size:19
Alignment explanation
Indices: 97560--97596 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
97550 TAAAAACAAT
*
97560 AAATTTGGGCCCTTAAAAA
1 AAATTGGGGCCCTTAAAAA
97579 AAATTGGGGCCCTTAAAA
1 AAATTGGGGCCCTTAAAA
97597 GTTGGTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (19 bp):
AAATTGGGGCCCTTAAAAA
Found at i:101428 original size:22 final size:23
Alignment explanation
Indices: 101384--101428 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
101374 AAAAAAATTT
* **
101384 TAAAATTAAAAACATAATTAAAA
1 TAAAATTAAAAAAATAAAAAAAA
101407 TAAAA-TAAAAAAATAAAAAAAA
1 TAAAATTAAAAAAATAAAAAAAA
101429 CATAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (23 bp):
TAAAATTAAAAAAATAAAAAAAA
Found at i:105040 original size:22 final size:23
Alignment explanation
Indices: 105002--105044 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
104992 ATTAGAATTA
*
105002 ATTAATTGTTATTATTGTATAAT
1 ATTAATTGTTATAATTGTATAAT
105025 ATTAATT-TTATAATTGTATA
1 ATTAATTGTTATAATTGTATA
105045 TTTTATGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (23 bp):
ATTAATTGTTATAATTGTATAAT
Found at i:107766 original size:17 final size:17
Alignment explanation
Indices: 107712--107766 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
107702 TTAATTTATT
107712 TTTTTAGTTTATATAAG
1 TTTTTAGTTTATATAAG
* * * *
107729 TTTTAAAATTT-TAAAAA
1 TTTT-TAGTTTATATAAG
107746 TTTTTAGTTTATATAAG
1 TTTTTAGTTTATATAAG
107763 TTTT
1 TTTT
107767 AAAATAATTG
Statistics
Matches: 28, Mismatches: 8, Indels: 4
0.70 0.20 0.10
Matches are distributed among these distances:
16 4 0.14
17 20 0.71
18 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (17 bp):
TTTTTAGTTTATATAAG
Found at i:107932 original size:41 final size:41
Alignment explanation
Indices: 107873--108041 Score: 214
Period size: 41 Copynumber: 4.1 Consensus size: 41
107863 ATTGTTCTGA
* *
107873 AAGCGCCGCTATTGCTCTGACCTTTAGTGGTGCTTTCCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCAT
* * * *
107914 AAGCGCCTCTATTTCTCTGACTTTTAGCGGCG-TTTGCCCGT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTT-CCCAT
* * *
107955 AAGCGCCGTTATTGCTCTGACCTTTAGCGGCGCTTGCCCGT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCAT
* * *
107996 AAGCGCCGCTATTGCCCTAACCTTTAGCGACGCTTTCCCAT
1 AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCAT
108037 AAGCG
1 AAGCG
108042 TAAGCGCGGC
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
40 3 0.03
41 104 0.95
42 2 0.02
ACGTcount: A:0.15, C:0.31, G:0.22, T:0.31
Consensus pattern (41 bp):
AAGCGCCGCTATTGCTCTGACCTTTAGCGGCGCTTTCCCAT
Found at i:113283 original size:16 final size:17
Alignment explanation
Indices: 113250--113287 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
113240 GAAAAAATGG
*
113250 AGAAGAAACGTGGAAAA
1 AGAAGAAACGTCGAAAA
113267 AGAAGAAACG-CGAAAA
1 AGAAGAAACGTCGAAAA
113283 AGAAG
1 AGAAG
113288 GATAAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.61, C:0.08, G:0.29, T:0.03
Consensus pattern (17 bp):
AGAAGAAACGTCGAAAA
Found at i:115082 original size:18 final size:18
Alignment explanation
Indices: 115059--115103 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
115049 GTGGTGAGAG
115059 AAGCAGTTGTTGTCGACA
1 AAGCAGTTGTTGTCGACA
115077 AAGCAGTTGTTGTCGACA
1 AAGCAGTTGTTGTCGACA
115095 AAGCAGTTG
1 AAGCAGTTG
115104 CAAAGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (18 bp):
AAGCAGTTGTTGTCGACA
Found at i:120043 original size:40 final size:40
Alignment explanation
Indices: 119999--120238 Score: 268
Period size: 40 Copynumber: 6.0 Consensus size: 40
119989 TGGTGGTCTA
* * * *
119999 GCAGTTTTTACATTGTCACGGCTAGTTCAGTAATAATATT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATT
* * *
120039 GCAGTGTTTACAGTGTCACTGTCAG-TCTAGTAGTAATATC
1 GCAGTGTTTACAGTGTCACTGCCAGTTC-AGTAATAATATT
*
120079 GCAGTGTTTACAGTGTCACTGCCAGATT-AGTGATAATATT
1 GCAGTGTTTACAGTGTCACTGCCAG-TTCAGTAATAATATT
* * * *
120119 GTAGTGTTTACAATGTCACTGGCAGTTCAATAATAATATT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATT
* * * *
120159 GCAGTATTTACAATGTCATTGCCAGTTCAATAATAATATT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATT
* * * *
120199 GTAGTGTTTACAGTGTCATTGCCAGTTTAGTAAAAATATT
1 GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATT
120239 CCCAAGTGGT
Statistics
Matches: 170, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
39 4 0.02
40 165 0.97
42 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (40 bp):
GCAGTGTTTACAGTGTCACTGCCAGTTCAGTAATAATATT
Found at i:120199 original size:20 final size:19
Alignment explanation
Indices: 120140--120199 Score: 50
Period size: 20 Copynumber: 3.1 Consensus size: 19
120130 AATGTCACTG
120140 GCAGTTCAATAATAATATT
1 GCAGTTCAATAATAATATT
** * *
120159 GCAGTATTTACAAT-GTCATT
1 GCAGT-TCAATAATAAT-ATT
120179 GCCAGTTCAATAATAATATT
1 G-CAGTTCAATAATAATATT
120199 G
1 G
120200 TAGTGTTTAC
Statistics
Matches: 29, Mismatches: 8, Indels: 7
0.66 0.18 0.16
Matches are distributed among these distances:
19 6 0.21
20 18 0.62
21 5 0.17
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (19 bp):
GCAGTTCAATAATAATATT
Found at i:120222 original size:120 final size:120
Alignment explanation
Indices: 120005--120238 Score: 310
Period size: 120 Copynumber: 1.9 Consensus size: 120
119995 TCTAGCAGTT
* * * * * *
120005 TTTACATTGTCACGGCTAGTTCAGTAATAATATTGCAGTGTTTACAGTGTCACTGTCAGTCTAGT
1 TTTACAATGTCACGGCTAGTTCAATAATAATATTGCAGTATTTACAATGTCACTGCCAGTCTAAT
* * *
120070 AGTAATATCGCAGTGTTTACAGTGTCACTGCCAGATTAGTGATAATATTGTAGTG
66 AATAATATCGCAGTGTTTACAGTGTCACTGCCAGATTAGTAAAAATATTGTAGTG
*
120125 TTTACAATGTCACTGGC-AGTTCAATAATAATATTGCAGTATTTACAATGTCATTGCCAGT-TCA
1 TTTACAATGTCAC-GGCTAGTTCAATAATAATATTGCAGTATTTACAATGTCACTGCCAGTCT-A
* * * *
120188 ATAATAATATTGTAGTGTTTACAGTGTCATTGCCAGTTTAGTAAAAATATT
64 ATAATAATATCGCAGTGTTTACAGTGTCACTGCCAGATTAGTAAAAATATT
120239 CCCAAGTGGT
Statistics
Matches: 98, Mismatches: 14, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
119 1 0.01
120 94 0.96
121 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (120 bp):
TTTACAATGTCACGGCTAGTTCAATAATAATATTGCAGTATTTACAATGTCACTGCCAGTCTAAT
AATAATATCGCAGTGTTTACAGTGTCACTGCCAGATTAGTAAAAATATTGTAGTG
Found at i:120846 original size:56 final size:56
Alignment explanation
Indices: 120727--120846 Score: 132
Period size: 56 Copynumber: 2.1 Consensus size: 56
120717 CACACATGGT
* ** **
120727 CTGACACACGACTATGTGCGCAGCCCATAAGTCATAAACCAATATGCACATGCGGT
1 CTGACACACGACTATGTGCACAGCCCATAAGTCATAAACCAATATGCACACACGAC
* ** * * **
120783 CTAACACACGTTTGTGTGCACAGCCCGTAAGTCATAAACCCGTATGCACACACGAC
1 CTGACACACGACTATGTGCACAGCCCATAAGTCATAAACCAATATGCACACACGAC
120839 CTGACACA
1 CTGACACA
120847 TGCCCGTGTG
Statistics
Matches: 51, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.32, C:0.31, G:0.18, T:0.19
Consensus pattern (56 bp):
CTGACACACGACTATGTGCACAGCCCATAAGTCATAAACCAATATGCACACACGAC
Found at i:122536 original size:18 final size:18
Alignment explanation
Indices: 122510--122549 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
122500 TGCATGATTC
122510 TTTTCTCTTTTTTGCAT-T
1 TTTTCTC-TTTTTGCATGT
*
122528 TTTTTTCTTTTTGCATGT
1 TTTTCTCTTTTTGCATGT
122546 TTTT
1 TTTT
122550 ACAGAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.05, C:0.12, G:0.07, T:0.75
Consensus pattern (18 bp):
TTTTCTCTTTTTGCATGT
Found at i:130456 original size:11 final size:11
Alignment explanation
Indices: 130440--130470 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
130430 ATATTAATTT
130440 TTTTCTTTTTC
1 TTTTCTTTTTC
130451 TTTTCTTTTTC
1 TTTTCTTTTTC
130462 -TTTCTTTTT
1 TTTTCTTTTT
130471 ATGTGACTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:142710 original size:21 final size:21
Alignment explanation
Indices: 142686--142739 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
142676 CCTAAAACAA
* *
142686 TTCTACCTATACAAGT-GTGAC
1 TTCTACCGATACAAGTCATG-C
*
142707 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATGC
142728 TTCTACCGATAC
1 TTCTACCGATAC
142740 TAAAAACTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:146913 original size:9 final size:9
Alignment explanation
Indices: 146899--146936 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
146889 GCAAAGACAG
146899 CATCAACAA
1 CATCAACAA
146908 CATCAACAA
1 CATCAACAA
*
146917 CATCAGCAA
1 CATCAACAA
*
146926 CATCAGCAA
1 CATCAACAA
146935 CA
1 CA
146937 GTTTTCTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.50, C:0.34, G:0.05, T:0.11
Consensus pattern (9 bp):
CATCAACAA
Found at i:151208 original size:20 final size:20
Alignment explanation
Indices: 151183--151226 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
151173 TATCAACTCA
151183 TTTTTACATTTAATTTTATC
1 TTTTTACATTTAATTTTATC
* * *
151203 TTTTTACTTTTATTTTTTTC
1 TTTTTACATTTAATTTTATC
151223 TTTT
1 TTTT
151227 AAATCTTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (20 bp):
TTTTTACATTTAATTTTATC
Found at i:161583 original size:19 final size:19
Alignment explanation
Indices: 161546--161609 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
161536 CAAAATAATC
161546 AAAATAATTTTCAAAAATTT
1 AAAATAATTTT-AAAAATTT
* *
161566 AAAATAATTTTTAAAATTA
1 AAAATAATTTTAAAAATTT
161585 AAAAT-ATTTATAAAAATTCT
1 AAAATAATTT-TAAAAATT-T
161605 AAAAT
1 AAAAT
161610 TTATATTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.11
19 18 0.47
20 16 0.42
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
AAAATAATTTTAAAAATTT
Found at i:161653 original size:21 final size:21
Alignment explanation
Indices: 161629--161669 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
161619 ATATATATAT
*
161629 ATATATTAAAAA-TATAAAAAA
1 ATATATAAAAAAGT-TAAAAAA
161650 ATATATAAAAAAGTTAAAAA
1 ATATATAAAAAAGTTAAAAA
161670 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (21 bp):
ATATATAAAAAAGTTAAAAAA
Found at i:161661 original size:11 final size:11
Alignment explanation
Indices: 161629--161661 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
161619 ATATATATAT
*
161629 ATATATTAAAA
1 ATATATAAAAA
161640 ATATA-AAAAA
1 ATATATAAAAA
161650 ATATATAAAAA
1 ATATATAAAAA
161661 A
1 A
161662 GTTAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
ATATATAAAAA
Found at i:174113 original size:31 final size:28
Alignment explanation
Indices: 174073--174145 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
174063 ATTTTAAAAT
*
174073 TATACATGAATTATGATTTAATGTGCAATTG
1 TATATATGAATT-TGATTT--TGTGCAATTG
* * *
174104 TATATATGAACTTTGGTTTTGTGTAATTT
1 TATATATGAA-TTTGATTTTGTGCAATTG
174133 TATATATGAATTT
1 TATATATGAATTT
174146 TTTATTTGAT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.08
29 18 0.49
31 14 0.38
32 2 0.05
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (28 bp):
TATATATGAATTTGATTTTGTGCAATTG
Found at i:185580 original size:96 final size:96
Alignment explanation
Indices: 185398--185582 Score: 239
Period size: 96 Copynumber: 1.9 Consensus size: 96
185388 AAAAAGGATG
* **
185398 TTCGATTATCTCAATTTGAGGAAATGTTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
1 TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
* * *
185463 AGTTAAGGAAACATTGCCTCGATTAAGGGTA
66 AATAAAAGAAACATTGCCTCGATTAAGGGTA
* * *
185494 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAGTTTTC-GAAACTC
1 TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TC
* *
185558 GAAATAAAAG-AATATTGTCTCGATT
64 GAAATAAAAGAAACATTGCCTCGATT
185583 TTAAAGTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
95 1 0.01
96 66 0.87
97 9 0.12
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGCAAATTTTCAGAATCGA
AATAAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:185648 original size:18 final size:18
Alignment explanation
Indices: 185625--185666 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
185615 CAAACATGCG
*
185625 AGTTAAATATGATTAAGC
1 AGTTAAATATGAATAAGC
185643 AGTTAAATATGAATAAGC
1 AGTTAAATATGAATAAGC
185661 AGTTAA
1 AGTTAA
185667 TAATGGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.48, C:0.05, G:0.17, T:0.31
Consensus pattern (18 bp):
AGTTAAATATGAATAAGC
Found at i:185910 original size:29 final size:29
Alignment explanation
Indices: 185845--186122 Score: 265
Period size: 29 Copynumber: 9.5 Consensus size: 29
185835 GTAAAATGTT
* * *
185845 AATTTTGGGAAAGTTCGAGGTTAAAAGATGA
1 AATTTTTGG-AAGTTCGAGGGTAAAA-ATGG
* * *
185876 AATTTTTAGACA-TTTGGGGGTAAAAATGG
1 AATTTTTGGA-AGTTCGAGGGTAAAAATGG
*
185905 AATTTTTGGAAGTTCGAGGGTAATAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
* *
185934 AATTTTTGGAAGATTAG-GGGCAAAAATGG
1 AATTTTTGGAAG-TTCGAGGGTAAAAATGG
* * * *
185963 AATTTTTGGAAATTTTG-GGATCGAAAATGG
1 AATTTTTGG-AAGTTCGAGGGT-AAAAATGG
* **
185993 AATTTTTGGATGTTCGACAGTAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
* * *
186022 AATTTTTGGAAGTTCGGGGGCAAAAAGGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
** *
186051 AATTTTTGGAAGTTTAAGTGTAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
*
186080 GATTTTTGGAAGTTCGAGGGTAAAAATGG
1 AATTTTTGGAAGTTCGAGGGTAAAAATGG
*
186109 GATTTTTGGAAGTT
1 AATTTTTGGAAGTT
186123 TCGGGATCGA
Statistics
Matches: 200, Mismatches: 41, Indels: 14
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.00
29 158 0.79
30 33 0.17
31 8 0.04
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AATTTTTGGAAGTTCGAGGGTAAAAATGG
Found at i:185990 original size:88 final size:87
Alignment explanation
Indices: 185893--186122 Score: 311
Period size: 88 Copynumber: 2.6 Consensus size: 87
185883 AGACATTTGG
*
185893 GGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAATAATGGAATTTTTGGAAGATT-AGGGGCAA
1 GGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAG-TTCAGGGGCAA
* *
185957 AAATGGAATTTTTGGAAATTT-T
65 AAAGGGAATTTTTGGAAATTTAA
* * ** *
185979 GGGATCGAAAATGGAATTTTTGGATGTTCGACAGTAAAAATGGAATTTTTGGAAGTTCGGGGGCA
1 GGG-T-AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCAGGGGCA
*
186044 AAAAGGGAATTTTTGGAAGTTTAA
64 AAAAGGGAATTTTTGGAAATTTAA
* * *
186068 GTGTAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTT
1 GGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTT
186123 TCGGGATCGA
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
86 3 0.02
87 48 0.39
88 71 0.57
89 2 0.02
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (87 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTCAGGGGCAAA
AAGGGAATTTTTGGAAATTTAA
Found at i:187387 original size:19 final size:19
Alignment explanation
Indices: 187363--187404 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
187353 CAAATGTCTT
187363 TTTATTTA-ATATTATAATA
1 TTTATTTATATATTAT-ATA
*
187382 TTTA-TTATTTATTATATA
1 TTTATTTATATATTATATA
187400 TTTAT
1 TTTAT
187405 GGTTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTATATATTATATA
Found at i:188155 original size:17 final size:17
Alignment explanation
Indices: 188117--188157 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
188107 TAAATCCATT
* *
188117 TAAATTTTAATTTAAAG
1 TAAATTTAAATTTAAAA
*
188134 CAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
188151 TAAATTT
1 TAAATTT
188158 GAATCAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:188947 original size:158 final size:158
Alignment explanation
Indices: 188655--188996 Score: 540
Period size: 158 Copynumber: 2.2 Consensus size: 158
188645 GCTTCGACCT
* * * * *
188655 GCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCGTGGGTTTGAT
1 GCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCGTAGGTTTGAT
* *
188720 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCGTTTGTTTCAATTCACTTCTCTG
66 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTA
* *
188785 TATCTCATTAGGAAGACGAATTTGGTCC
131 TATCTCATCAGGAAGACAAATTTGGTCC
* *
188813 GCTTCTCAGTATCTCATCAGGAAGCTGGGATTTGAAGATTTTCTCACATCGAGCGTAGGTTTGAT
1 GCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCGTAGGTTTGAT
* * *
188878 TTGGTCTTCTTCTCAGTATCTTATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTA
66 TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTA
*
188943 TATCTCATCAGGAAGACAAATTTGGTCT
131 TATCTCATCAGGAAGACAAATTTGGTCC
*
188971 ACTTCTCAGTATCTCATCAGGAAGCT
1 GCTTCTCAGTATCTCATCAGGAAGCT
188997 AACCTTTTAT
Statistics
Matches: 168, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
158 168 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (158 bp):
GCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGCTCACATCGAGCGTAGGTTTGAT
TTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATTCACTTCTCTA
TATCTCATCAGGAAGACAAATTTGGTCC
Found at i:189504 original size:204 final size:205
Alignment explanation
Indices: 189141--189709 Score: 908
Period size: 204 Copynumber: 2.8 Consensus size: 205
189131 NNNNNNNNNN
*
189141 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
1 CTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
* * *
189206 GGAAGCTAGGATTCAAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTATCAGTAT
66 GGAAGCTAAGATTCGAAGATTTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTATCAGTAT
* *
189271 CTCATCAGGAAGATGATCGTGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGA
131 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGA
* *
189336 ATTTTGTCTA
196 ATTTGGTCCA
* *
189346 C-TCTCAGTATCTCATTAGGAAGCTAACCTTTTATTACTTCGCCTTGCTTCTCAGTATCTCATCA
1 CTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
* *
189410 GGAAGCTAAGATTCGAGGATTTGCTCACATCGAGTGTGAGTTTGATTTGGTCTTCTTATCAGTAT
66 GGAAGCTAAGATTCGAAGATTTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTATCAGTAT
* * *
189475 CTCATTAGGAAGATGACCGCGTTGTTTGTTTTAATTCGCTTCTCTGTATCTCATCAGGAAGACGA
131 CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGA
189540 ATTTGGTCCA
196 ATTTGGTCCA
* *
189550 CTTCTTAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTACTTCTCAGTATCTCATCA
1 CTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
* * * * * *
189615 GGAAGCTGAGATTTGAAGATTTGCTCATATCGAGCGTGTGTTTGATTTGGTCTTCTTCTCAGTAC
66 GGAAGCTAAGATTCGAAGATTTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTATCAGTAT
*
189680 CTCATCAGGAAGATGACTGCGTCG-TTGTTT
131 CTCATCAGGAAGATGACCGCGTCGTTTGTTT
189710 ATGGATAATC
Statistics
Matches: 333, Mismatches: 30, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
204 195 0.59
205 138 0.41
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.37
Consensus pattern (205 bp):
CTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
GGAAGCTAAGATTCGAAGATTTGCTCACATCGAGCGTGAGTTTGATTTGGTCTTCTTATCAGTAT
CTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTGTATCTCATCAGGAAGACGA
ATTTGGTCCA
Found at i:201472 original size:29 final size:29
Alignment explanation
Indices: 201403--201806 Score: 419
Period size: 29 Copynumber: 13.7 Consensus size: 29
201393 ACCCGGGGAC
* *
201403 AAAATGGTAATTTTGGGAAAGTTCGAGGTTA
1 AAAATGG-AATTTTTGG-AAGTTCGAGGGTA
* *
201434 AAAGATGGAATTTTTAGACA-TTAGAGGGTA
1 AAA-ATGGAATTTTTGGA-AGTTCGAGGGTA
201464 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
201493 AAAATGGAATTTTTGGAAATTTTTG-GGGTCG
1 AAAATGGAATTTTTGG-AA-GTTCGAGGGT-A
* *
201524 AAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
201553 AAAATGGAATTTTTGGAAATTTCGA-AGTCA
1 AAAATGGAATTTTTGG-AAGTTCGAGGGT-A
*
201583 AAAAT-GAATTTTTTGGAAGTTCGGGGGTA
1 AAAATGGAA-TTTTTGGAAGTTCGAGGGTA
*
201612 AAAATGGAATTTTTGGAAGTTTCG-GGGTCG
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* *
201642 AAAATGGAAATTTTGGAAGTTCGAGGGCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
201671 AAAAGGGAATTTTTGGAAGTT-TAGAGGTA
1 AAAATGGAATTTTTGGAAGTTCGAG-GGTA
* * *
201700 AAAAAGGAA-TTTTGGAAGTTCGGGGGCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
201728 AAAATGGAATTTTTGGAAGTTCGGGGGCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
201757 AAAATGGAATTTTTAGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
201786 AAAAT-GAGATTTTTGGAAGTT
1 AAAATGGA-ATTTTTGGAAGTT
201807 TTGGGGTCGA
Statistics
Matches: 319, Mismatches: 35, Indels: 40
0.81 0.09 0.10
Matches are distributed among these distances:
28 27 0.08
29 186 0.58
30 72 0.23
31 30 0.09
32 4 0.01
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:201495 original size:59 final size:59
Alignment explanation
Indices: 201403--201822 Score: 441
Period size: 59 Copynumber: 7.1 Consensus size: 59
201393 ACCCGGGGAC
* * * *
201403 AAAATGGTAATTTTGGGAAAGTTCGAGGTTAAAAGATGGAATTTTTAGACA-TTAGAGGGT-A
1 AAAATGG-AATTTTTGG-AAGTTCGAGGGTAAAA-ATGGAATTTTTGGA-ATTTCGAGGGTCA
* *
201464 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAATTTTTG-GGGTCG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGG-AA-TTTCGAGGGTCA
* * *
201524 AAAATGGAATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAATTTCGA-AGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGG-AATTTCGAGGGTCA
* *
201583 AAAAT-GAATTTTTTGGAAGTTCGGGGGTAAAAATGGAATTTTTGGAAGTTTCG-GGGTCG
1 AAAATGGAA-TTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAA-TTTCGAGGGTCA
* * * *
201642 AAAATGGAAATTTTGGAAGTTCGAGGGCAAAAAGGGAATTTTTGGAAGTTTAGA-GGT-A
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAA-TTTCGAGGGTCA
* * * * *
201700 AAAAAGGAA-TTTTGGAAGTTCGGGGGCAAAAATGGAATTTTTGGAAGTTCG-GGGGCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAATTTCGAGGGTCA
* * *
201757 AAAATGGAATTTTTAGAAGTTCGAGGGTAAAAAT-GAGATTTTTGGAAGTTTTG-GGGTCG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGA-ATTTTTGGAA-TTTCGAGGGTCA
201816 AAAATGG
1 AAAATGG
201823 TTTCTAAACA
Statistics
Matches: 311, Mismatches: 33, Indels: 32
0.83 0.09 0.09
Matches are distributed among these distances:
56 5 0.02
57 46 0.15
58 57 0.18
59 136 0.44
60 60 0.19
61 7 0.02
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.31
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAATTTCGAGGGTCA
Found at i:203099 original size:19 final size:19
Alignment explanation
Indices: 203075--203116 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
203065 CAAATTTCTT
203075 TTTATTTA-ATATTATAATA
1 TTTATTTATATATTAT-ATA
*
203094 TTTA-TTATTTATTATATA
1 TTTATTTATATATTATATA
203112 TTTAT
1 TTTAT
203117 GGTTAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTATTTATATATTATATA
Found at i:203856 original size:17 final size:17
Alignment explanation
Indices: 203831--203886 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
203821 GGATTTTTAA
*
203831 TTAAGTTTTAAATCAAT
1 TTAAATTTTAAATCAAT
* *
203848 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATCAAT
*
203865 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAATC-AAT
203882 TTAAA
1 TTAAA
203887 ATTAAAAGAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 5 0.16
17 27 0.84
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.45
Consensus pattern (17 bp):
TTAAATTTTAAATCAAT
Found at i:203860 original size:6 final size:6
Alignment explanation
Indices: 203845--203917 Score: 69
Period size: 6 Copynumber: 12.3 Consensus size: 6
203835 GTTTTAAATC
* ** *
203845 AATTTA AATTTT AA-TTA AATTTA AATTTA AA-GCA AATTTAA AATTAA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTT-A AATTTA
**
203892 AAGATA AATTTA AATTTA AATTTA AA
1 AATTTA AATTTA AATTTA AATTTA AA
203918 AATAAATTTG
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
5 7 0.13
6 40 0.77
7 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (6 bp):
AATTTA
Found at i:203894 original size:18 final size:19
Alignment explanation
Indices: 203861--203911 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
203851 AATTTTAATT
*
203861 AAATTT-AAATTTAAAG-C
1 AAATTTAAAATTAAAAGAC
*
203878 AAATTTAAAATTAAAAGAT
1 AAATTTAAAATTAAAAGAC
*
203897 AAATTTAAATTTAAA
1 AAATTTAAAATTAAA
203912 TTTAAAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 6 0.21
18 9 0.31
19 14 0.48
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (19 bp):
AAATTTAAAATTAAAAGAC
Found at i:203923 original size:12 final size:12
Alignment explanation
Indices: 203883--203926 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
203873 AAAGCAAATT
*
203883 TAAAATTAAAAGA
1 TAAATTTAAAA-A
**
203896 TAAATTTAAATT
1 TAAATTTAAAAA
203908 TAAATTTAAAAA
1 TAAATTTAAAAA
203920 TAAATTT
1 TAAATTT
203927 GAATCAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
12 17 0.65
13 9 0.35
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:206285 original size:2 final size:2
Alignment explanation
Indices: 206278--206309 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
206268 ATCAAATCTG
206278 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
206310 CCGAGTCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208424 original size:20 final size:20
Alignment explanation
Indices: 208375--208470 Score: 70
Period size: 20 Copynumber: 4.7 Consensus size: 20
208365 ACGGTTTACG
*
208375 GTTTAAGGTTTAGAA-TTTAGA
1 GTTTAGGGTTTA-AAGTTTA-A
*
208396 GTTTTGGGTTTAAAGTTTAA
1 GTTTAGGGTTTAAAGTTTAA
*
208416 GTTTAGGGTTTAATGTTT-A
1 GTTTAGGGTTTAAAGTTTAA
* ** *
208435 GATTTAGAGTTCGAAGTTTGAT
1 G-TTTAGGGTTTAAAGTTT-AA
*
208457 GTTTGGGGTTTAAA
1 GTTTAGGGTTTAAA
208471 ATTTTAGATT
Statistics
Matches: 58, Mismatches: 13, Indels: 8
0.73 0.16 0.10
Matches are distributed among these distances:
19 2 0.03
20 32 0.55
21 23 0.40
22 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.27, T:0.46
Consensus pattern (20 bp):
GTTTAGGGTTTAAAGTTTAA
Found at i:208544 original size:69 final size:69
Alignment explanation
Indices: 208411--208544 Score: 148
Period size: 69 Copynumber: 1.9 Consensus size: 69
208401 GGGTTTAAAG
* * * * * * *
208411 TTTAAGTTTAGGGTTTAATGTTTAGATTTAGAGTTCGAAGTTTGATGTTTGGGGTTTAAAATTTT
1 TTTAAGTTTAAGGTTCAATGTTTAAATTTAGAGTTCGAAGATTGATGTTTAGAGTTCAAAATTTT
208476 AGAT
66 AGAT
*
208480 TTTAAGTTTAAGGTTCAATGTTTAAAGTTTA-AGGTTC-AAGATTGA-GTTTTAGAGTTCAAGAT
1 TTTAAGTTTAAGGTTCAATGTTTAAA-TTTAGA-GTTCGAAGATTGATG-TTTAGAGTTCAAAAT
208542 TTT
63 TTT
208545 TATTCAGAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
68 1 0.02
69 45 0.83
70 8 0.15
ACGTcount: A:0.28, C:0.03, G:0.22, T:0.46
Consensus pattern (69 bp):
TTTAAGTTTAAGGTTCAATGTTTAAATTTAGAGTTCGAAGATTGATGTTTAGAGTTCAAAATTTT
AGAT
Found at i:208672 original size:21 final size:18
Alignment explanation
Indices: 208642--208680 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
208632 CAAAATTGTG
208642 TATTAATAATATGAAAAAAT
1 TATTAATAATA--AAAAAAT
208662 TATTAAATAATAAAAAAAT
1 TATT-AATAATAAAAAAAT
208681 ATGAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 4 0.22
21 7 0.39
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TATTAATAATAAAAAAAT
Found at i:208678 original size:20 final size:20
Alignment explanation
Indices: 208642--208679 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
208632 CAAAATTGTG
*
208642 TATTAATAATATGAAAAAAT
1 TATTAATAATATAAAAAAAT
208662 TATTAAATAATA-AAAAAA
1 TATT-AATAATATAAAAAA
208680 TATGAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (20 bp):
TATTAATAATATAAAAAAAT
Found at i:217510 original size:26 final size:28
Alignment explanation
Indices: 217480--217550 Score: 110
Period size: 26 Copynumber: 2.6 Consensus size: 28
217470 TCTTGAATGA
217480 TTTGAGATTTAGGGTTTGGGTTTAAT-G
1 TTTGAGATTTAGGGTTTGGGTTTAATAG
*
217507 -TTGAGATTTAGGGTTTGGGTTTTATAG
1 TTTGAGATTTAGGGTTTGGGTTTAATAG
*
217534 TTTAAGATTTAGGGTTT
1 TTTGAGATTTAGGGTTT
217551 AGTGTTTGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 24 0.60
27 1 0.03
28 15 0.38
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (28 bp):
TTTGAGATTTAGGGTTTGGGTTTAATAG
Found at i:218057 original size:29 final size:29
Alignment explanation
Indices: 217999--218057 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
217989 TACTTTTTTT
* * *
217999 AATAATTTTAATCATTTTAAATTTTAAAA
1 AATAATTTTAATCACTATAAAGTTTAAAA
* *
218028 AATAATTTTAATCACTATAGAGTTTCAAA
1 AATAATTTTAATCACTATAAAGTTTAAAA
218057 A
1 A
218058 CCCTAAACCT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (29 bp):
AATAATTTTAATCACTATAAAGTTTAAAA
Found at i:218102 original size:20 final size:20
Alignment explanation
Indices: 218077--218129 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
218067 TCAAGCCTCA
*
218077 AACCTCAAATCTTAAACTCG
1 AACCTCGAATCTTAAACTCG
218097 AACCTCGAATCTTAAACTCG
1 AACCTCGAATCTTAAACTCG
218117 AACCTCGAATCTT
1 AACCTCGAATCTT
218130 GAACCTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.30, G:0.08, T:0.26
Consensus pattern (20 bp):
AACCTCGAATCTTAAACTCG
Found at i:218177 original size:27 final size:27
Alignment explanation
Indices: 218147--218228 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
218137 GAATACTTTG
*
218147 AGGTTCCGAGTTTGAGTTTGAGGTTTA
1 AGGTTCCGAGTTTGAGTTTAAGGTTTA
* * * *
218174 AGGTT-CGGGTTTAGGGTTTAATGTTTG
1 AGGTTCCGAGTTT-GAGTTTAAGGTTTA
* *
218201 AGGTTCGGAGTTTAAGGTTTAAGGTTTA
1 AGGTTCCGAGTTTGA-GTTTAAGGTTTA
218229 TTATTCAAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
26 6 0.15
27 20 0.49
28 15 0.37
ACGTcount: A:0.20, C:0.05, G:0.34, T:0.41
Consensus pattern (27 bp):
AGGTTCCGAGTTTGAGTTTAAGGTTTA
Found at i:218643 original size:13 final size:13
Alignment explanation
Indices: 218625--218649 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
218615 TTAATGATTT
218625 TAAATTTTAAAAA
1 TAAATTTTAAAAA
218638 TAAATTTTAAAA
1 TAAATTTTAAAA
218650 TTTTAAAAAA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAAATTTTAAAAA
Found at i:239247 original size:16 final size:16
Alignment explanation
Indices: 239222--239259 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
239212 AACCTTGTCA
239222 TTAATAATATTA-TAAT
1 TTAATAATATTAGT-AT
*
239238 TTAATCATATTAGTAT
1 TTAATAATATTAGTAT
239254 TTAATA
1 TTAATA
239260 TCAGTTAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAATAATATTAGTAT
Found at i:242684 original size:6 final size:6
Alignment explanation
Indices: 242673--242697 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
242663 GCCTTTTGGG
242673 ACCGCC ACCGCC ACCGCC ACCGCC A
1 ACCGCC ACCGCC ACCGCC ACCGCC A
242698 TTTCTCATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.64, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCGCC
Found at i:243002 original size:20 final size:20
Alignment explanation
Indices: 242959--243002 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
242949 ATATTAGTAC
* * *
242959 TGTTCATTATATGATTTCAT
1 TGTTCATGATATGATTCCAA
*
242979 TGTTCATGATTTGATTCCAA
1 TGTTCATGATATGATTCCAA
242999 TGTT
1 TGTT
243003 TTTAGGACTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.52
Consensus pattern (20 bp):
TGTTCATGATATGATTCCAA
Found at i:245379 original size:22 final size:22
Alignment explanation
Indices: 245325--245370 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 22
245315 AAATAATTAC
245325 AAAAT-TTAA-ATT-TTATATT
1 AAAATATTAATATTATTATATT
245344 AAAATATTAATATTATTATATTT
1 AAAATATTAATATTATTATA-TT
245367 AAAA
1 AAAA
245371 GTTAGTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 3 0.13
22 5 0.22
23 6 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAAATATTAATATTATTATATT
Found at i:246700 original size:31 final size:32
Alignment explanation
Indices: 246651--246712 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 32
246641 TTTTGTCTAA
* * * *
246651 CTAGATACTTAAATTTGGTTTTCTGGTTCAAC
1 CTAGATACATAAACTTGGTTTTATAGTTCAAC
246683 CTAG-TACATAAACTTGGTTTTATAGTTCAA
1 CTAGATACATAAACTTGGTTTTATAGTTCAA
246713 TTTTATTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.42
Consensus pattern (32 bp):
CTAGATACATAAACTTGGTTTTATAGTTCAAC
Found at i:249002 original size:109 final size:109
Alignment explanation
Indices: 248811--249029 Score: 384
Period size: 109 Copynumber: 2.0 Consensus size: 109
248801 CTGTCAATCT
* * *
248811 CCTTAGATACCCCTAATACACAACATAATATGAATATGTGAATGAGTCAAATTACAAATTAACCA
1 CCTTAAATACCACTAATACACAACATAATACGAATATGTGAATGAGTCAAATTACAAATTAACCA
248876 TGAACTTGTTGTCATAAAATCATCTCTTCAAATTACAAATTTAC
66 TGAACTTGTTGTCATAAAATCATCTCTTCAAATTACAAATTTAC
* *
248920 CCTTAAATACCACTAATACACAATATAATACGAATATGTGAATGTGTCAAATTACAAATTAACCA
1 CCTTAAATACCACTAATACACAACATAATACGAATATGTGAATGAGTCAAATTACAAATTAACCA
*
248985 TTAACTTGTTGTCATAAAATCATCTCTTCAAATTACAAATTTAC
66 TGAACTTGTTGTCATAAAATCATCTCTTCAAATTACAAATTTAC
249029 C
1 C
249030 AACCCATTAA
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
109 104 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (109 bp):
CCTTAAATACCACTAATACACAACATAATACGAATATGTGAATGAGTCAAATTACAAATTAACCA
TGAACTTGTTGTCATAAAATCATCTCTTCAAATTACAAATTTAC
Found at i:252625 original size:6 final size:6
Alignment explanation
Indices: 252614--252647 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
252604 TTCTTCTTCC
*
252614 CCATCA CCATCA CCATCA CCATTCA TCATCA CCA
1 CCATCA CCATCA CCATCA CCA-TCA CCATCA CCA
252648 AAACCTGTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.32, C:0.47, G:0.00, T:0.21
Consensus pattern (6 bp):
CCATCA
Found at i:255183 original size:35 final size:34
Alignment explanation
Indices: 255134--255202 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 34
255124 GTTTAAATTT
255134 AAAAAATAATTTTATATACTTTAAAATAAAAATA
1 AAAAAATAATTTTATATACTTTAAAATAAAAATA
* * *
255168 AAAAATATAATTTTATTTGCTTTAAAATGAAAATA
1 AAAAA-ATAATTTTATATACTTTAAAATAAAAATA
255203 TAATAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
34 5 0.16
35 26 0.84
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (34 bp):
AAAAAATAATTTTATATACTTTAAAATAAAAATA
Found at i:259401 original size:6 final size:6
Alignment explanation
Indices: 259390--259427 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
259380 TAACTTTGGA
259390 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TT
259428 GATAGGATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTATTT
Found at i:266146 original size:3 final size:3
Alignment explanation
Indices: 266138--266171 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
266128 GAGAGACATG
*
266138 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCC GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
266172 TGATTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.35, G:0.35, T:0.29
Consensus pattern (3 bp):
GCT
Found at i:269589 original size:2 final size:2
Alignment explanation
Indices: 269582--269622 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
269572 AGCTGTTTCC
269582 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
269623 GAACAGTAGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:270308 original size:23 final size:22
Alignment explanation
Indices: 270271--270313 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
270261 TCCTGTTACC
* *
270271 AAAAAAATGTGTTTAATTTTAAA
1 AAAAAAATATATTT-ATTTTAAA
270294 AAAAAAATATATTTATTTTA
1 AAAAAAATATATTTATTTTA
270314 CTTCATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
AAAAAAATATATTTATTTTAAA
Found at i:278713 original size:13 final size:13
Alignment explanation
Indices: 278695--278719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
278685 GTATAAACTG
278695 AAAATTATATATC
1 AAAATTATATATC
278708 AAAATTATATAT
1 AAAATTATATAT
278720 GGACTGTGAT
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTATATATC
Found at i:280961 original size:20 final size:19
Alignment explanation
Indices: 280934--280972 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
280924 CATGTCTAAA
280934 TTTTATTTTACT-TAATTTT
1 TTTTA-TTTACTATAATTTT
280953 TTTTCATTTACTATAATTTT
1 TTTT-ATTTACTATAATTTT
280973 GATTTATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTATTTACTATAATTTT
Found at i:281869 original size:75 final size:78
Alignment explanation
Indices: 281784--281959 Score: 205
Period size: 82 Copynumber: 2.2 Consensus size: 78
281774 AAAAGTATTG
* * *
281784 TACAGGACAGGTTTCTTGACATTCTTCGACA-T-A-TATTCATCCAAGGGATAAAAGAAGCATAA
1 TACAGGACAGGATTCTTAACATTCTTCGACAGTAACTACTCATCCAAGGGATAAAAGAAGCATAA
*
281846 CAAACTAGTATCA
66 CAAACTAGTACCA
** * *
281859 TACAGGACAGGATTCTTAATGTTTTTCGACATGTAACCTGTACTCATCCAAGGGTTAAAAGAAGC
1 TACAGGACAGGATTCTTAACATTCTTCGACA-GTAA-C--TACTCATCCAAGGGATAAAAGAAGC
*
281924 ATTACAAACTAGTACCA
62 ATAACAAACTAGTACCA
*
281941 TACAGGTCAGGATTCTTAA
1 TACAGGACAGGATTCTTAA
281960 TGTTTTTGAC
Statistics
Matches: 84, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
75 26 0.31
77 1 0.01
78 1 0.01
82 56 0.67
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (78 bp):
TACAGGACAGGATTCTTAACATTCTTCGACAGTAACTACTCATCCAAGGGATAAAAGAAGCATAA
CAAACTAGTACCA
Found at i:281921 original size:82 final size:81
Alignment explanation
Indices: 281820--281976 Score: 260
Period size: 82 Copynumber: 1.9 Consensus size: 81
281810 CGACATATAT
*
281820 TCATCCAAGGGATAAAAGAAGCATAACAAACTAGTATCATACAGGACAGGATTCTTAATGTTTTT
1 TCATCCAAGGGATAAAAGAAGCATAACAAACTAGTACCATACAGGACAGGATTCTTAATGTTTTT
*
281885 CGACATGTAACCTGTAC
66 -GACATATAACCTGTAC
* * *
281902 TCATCCAAGGGTTAAAAGAAGCATTACAAACTAGTACCATACAGGTCAGGATTCTTAATGTTTTT
1 TCATCCAAGGGATAAAAGAAGCATAACAAACTAGTACCATACAGGACAGGATTCTTAATGTTTTT
281967 GACATATAAC
66 GACATATAAC
281977 TAGCATTACG
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
81 9 0.13
82 61 0.87
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (81 bp):
TCATCCAAGGGATAAAAGAAGCATAACAAACTAGTACCATACAGGACAGGATTCTTAATGTTTTT
GACATATAACCTGTAC
Found at i:282009 original size:57 final size:57
Alignment explanation
Indices: 281921--282034 Score: 192
Period size: 57 Copynumber: 2.0 Consensus size: 57
281911 GGTTAAAAGA
**
281921 AGCATTACAAACTAGTACCATACAGGTCAGGATTCTTAATGTTTTTGACATATAACT
1 AGCATTACAAACTAGTACCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACT
* *
281978 AGCATTACGAACTAGTATCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACT
1 AGCATTACAAACTAGTACCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACT
282035 TGTACTCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (57 bp):
AGCATTACAAACTAGTACCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACT
Found at i:282090 original size:138 final size:141
Alignment explanation
Indices: 281839--282117 Score: 429
Period size: 138 Copynumber: 2.0 Consensus size: 141
281829 GGATAAAAGA
* *
281839 AGCATAACAAACTAGTATCATACAGGACAGGATTCTTAATGTTTTTCGACATGTAACCTGTACTC
1 AGCATAACAAACTAGTATCATACAGGACAGGATTCTTAATGTTTTTCAACATATAACCTGTACTC
* * * *
281904 ATCCAAGGGTTAAAAGAAGCATTACAAACTAGTACCATACAGGTCAGGATTCTT-AATGTTTTT-
66 ATCCAAGAGTAAAAAGAACCATTACAAACTAGTACCATACAGGACAGGATTCTTAAATGTTTTTC
281967 GACATATAACT
131 GACATATAACT
* * * *
281978 AGCATTACGAACTAGTATCATACAGGTCAGGATTCTTAATG-TTTTCAACATATAACTTGTACTC
1 AGCATAACAAACTAGTATCATACAGGACAGGATTCTTAATGTTTTTCAACATATAACCTGTACTC
* *
282042 ATCCAAGAGTAAAAAGATCCATTACAAACTAGTATCATACAGGACAGGATTCTTAAATGTTTTTC
66 ATCCAAGAGTAAAAAGAACCATTACAAACTAGTACCATACAGGACAGGATTCTTAAATGTTTTTC
282107 GACATATAACT
131 GACATATAACT
282118 TGTATTCATC
Statistics
Matches: 126, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
138 68 0.54
139 47 0.37
140 11 0.09
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.31
Consensus pattern (141 bp):
AGCATAACAAACTAGTATCATACAGGACAGGATTCTTAATGTTTTTCAACATATAACCTGTACTC
ATCCAAGAGTAAAAAGAACCATTACAAACTAGTACCATACAGGACAGGATTCTTAAATGTTTTTC
GACATATAACT
Found at i:282142 original size:83 final size:81
Alignment explanation
Indices: 281980--282380 Score: 567
Period size: 80 Copynumber: 5.0 Consensus size: 81
281970 ATATAACTAG
* * *
281980 CATTACGAACTAGTATCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACTTGTACTCATC
1 CATTACAAACTAGTATCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACTCGTATTCATC
* *
282045 CAAGAGTAAAAAGATC
66 CAAGGGTTAAAAGATC
* * *
282061 CATTACAAACTAGTATCATACAGGACAGGATTCTTAAATGTTTTTCGACATATAACTTGTATTCA
1 CATTACAAACTAGTATCATACAGGTCAGGATTCTT-AATG-TTTTCAACATATAACTCGTATTCA
282126 TCCAAGGGTTAAAAGATC
64 TCCAAGGGTTAAAAGATC
* ** *
282144 CGTTACAAACTAGTATCATACAGGTCAGGATTCTT-ATCGTCATCAACATATAACTCATATTCAT
1 CATTACAAACTAGTATCATACAGGTCAGGATTCTTAAT-GTTTTCAACATATAACTCGTATTCAT
282208 CCAA-GGTTAAAAGATC
65 CCAAGGGTTAAAAGATC
* ** *
282224 CGTTACAAACTAGTATCATACAGGTCAGGATTCTT-ATCGTCATCAACATATAACTCATATTCAT
1 CATTACAAACTAGTATCATACAGGTCAGGATTCTTAAT-GTTTTCAACATATAACTCGTATTCAT
282288 CCAA-GGTTAAAAGATC
65 CCAAGGGTTAAAAGATC
* *
282304 CATTACAAACTAGTATCATACAGGACAGGATTCTTAATGTTTTCAAAATATAACTCGTATTCATC
1 CATTACAAACTAGTATCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACTCGTATTCATC
*
282369 CAGGGGTTAAAA
66 CAAGGGTTAAAA
282381 AAGTTACCTT
Statistics
Matches: 295, Mismatches: 20, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
80 150 0.51
81 69 0.23
82 5 0.02
83 71 0.24
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (81 bp):
CATTACAAACTAGTATCATACAGGTCAGGATTCTTAATGTTTTCAACATATAACTCGTATTCATC
CAAGGGTTAAAAGATC
Found at i:292374 original size:28 final size:27
Alignment explanation
Indices: 292302--292388 Score: 79
Period size: 28 Copynumber: 3.0 Consensus size: 27
292292 CATAGATTTC
292302 TTTATTTTTTACAAATTTAAAATTTAATT
1 TTTA-TTTTT-CAAATTTAAAATTTAATT
*
292331 ATTATATTTTT--TATTTAGAAATTTAATT
1 -TT-TATTTTTCAAATTTA-AAATTTAATT
*
292359 TTTATTTTTCAGATTTTAAAATTTAGATT
1 TTTATTTTTCA-AATTTAAAATTTA-ATT
292388 T
1 T
292389 AATTATTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
26 7 0.15
27 7 0.15
28 17 0.35
29 8 0.17
30 7 0.15
31 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.60
Consensus pattern (27 bp):
TTTATTTTTCAAATTTAAAATTTAATT
Found at i:294234 original size:2 final size:2
Alignment explanation
Indices: 294227--294255 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
294217 ACTAACTTGG
294227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
294256 GGTTATGTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:295039 original size:4 final size:4
Alignment explanation
Indices: 295030--295054 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
295020 ATAAACCCTA
295030 TATG TATG TATG TATG TATG TATG T
1 TATG TATG TATG TATG TATG TATG T
295055 GTATGCACTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:295582 original size:4 final size:4
Alignment explanation
Indices: 295573--295602 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
295563 GATTTACAGG
295573 TACA TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TA
295603 AAATGTTTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:299977 original size:15 final size:14
Alignment explanation
Indices: 299952--299991 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
299942 TTGGATTCTA
299952 ATCATTTTTAAATT
1 ATCATTTTTAAATT
299966 ATCATATTTTAAATT
1 ATCAT-TTTTAAATT
299981 A-C-TTTTTAAAT
1 ATCATTTTTAAAT
299992 ATTTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.32
13 1 0.04
14 6 0.24
15 10 0.40
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
ATCATTTTTAAATT
Found at i:305013 original size:10 final size:10
Alignment explanation
Indices: 304998--305024 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
304988 TTTGCTAATT
304998 TTTTTTTTTA
1 TTTTTTTTTA
305008 TTTTTTTTTA
1 TTTTTTTTTA
305018 TTTTTTT
1 TTTTTTT
305025 AAGTTTTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.00, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:307297 original size:14 final size:14
Alignment explanation
Indices: 307262--307297 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
307252 CTGAGATTGC
*
307262 ATATATAGACATGT
1 ATATATATACATGT
*
307276 ATATATATATATGT
1 ATATATATACATGT
307290 ATATATAT
1 ATATATAT
307298 GAAGTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.44
Consensus pattern (14 bp):
ATATATATACATGT
Found at i:314758 original size:68 final size:68
Alignment explanation
Indices: 314686--314821 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
314676 CTATTTTTTT
314686 AAAAAAATTAAAAATTATATTACTTTTAATATAATATCTAACCTTTTTTCATTTATTAAAATTTT
1 AAAAAAATTAAAAATTATATTACTTTTAATATAATATCTAACCTTTTTTCATTTATTAAAATTTT
314751 ATA
66 ATA
314754 AAAAAAATTAAAAATTATATTACTTTTAATATAATATCTAACCTTTTTTCATTTATTAAAATTTT
1 AAAAAAATTAAAAATTATATTACTTTTAATATAATATCTAACCTTTTTTCATTTATTAAAATTTT
314819 ATA
66 ATA
314822 CACCAGCAAC
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (68 bp):
AAAAAAATTAAAAATTATATTACTTTTAATATAATATCTAACCTTTTTTCATTTATTAAAATTTT
ATA
Found at i:315200 original size:20 final size:22
Alignment explanation
Indices: 315151--315193 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
315141 TTAGATAAAT
*
315151 TTAAAAAAATATAAGTTTTTAA
1 TTAAATAAATATAAGTTTTTAA
*
315173 TTAAATAAATATAATTTTTTA
1 TTAAATAAATATAAGTTTTTA
315194 TACATAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTAAATAAATATAAGTTTTTAA
Found at i:316662 original size:208 final size:208
Alignment explanation
Indices: 316295--316719 Score: 744
Period size: 208 Copynumber: 2.0 Consensus size: 208
316285 ATTCTTGCCT
* *
316295 GATTTTGATCCCCTTATGAAATTACACCCAATTTGTAAATTTCAATGTTCCATCAACCATTTTGT
1 GATTTTGATCCCCTTATGAAATTACACCCAATTTGTAAATTTCAATGCTACATCAACCATTTTGT
* * *
316360 GAATAAATATGTTCTTGATTGTTGCTTGTCAAATTTAAAATATTTTGGCATGAAACAAAATTTGG
66 GAATAAATACGTTCTTGATTGTTGCTTGTCAAATTTAAAATATATGGGCATGAAACAAAATTTGG
* * *
316425 TGTTCCTGTATGAACAACTAAAACTGCCAATGTGAGGAAATGCTTAAGTTGAGAGTCTTCTGCGA
131 TGTTCCTGTATGAACAACTAAAACTGCCAATGTGAGGAAATGCTTAAGCTGAGAATCTTCTCCGA
316490 GTGAGCAAAAGGA
196 GTGAGCAAAAGGA
*
316503 GATTTTGAT-CCCTTATGAAATTACACCCAATTTGTAAATTTCAATGCTACATGAACCATTTTGT
1 GATTTTGATCCCCTTATGAAATTACACCCAATTTGTAAATTTCAATGCTACATCAACCATTTTGT
316567 GAATAAATACGTTCTTGATTGTTGCTTGTCAAATTTAAAATACTATGGGCATGAAACAAAATTTG
66 GAATAAATACGTTCTTGATTGTTGCTTGTCAAATTTAAAATA-TATGGGCATGAAACAAAATTTG
316632 GTGTTCCTGTATGAACAACTAAAACTGCCAATGTGAGGAAATGCTTAAGCTGAGAATCTTCTCCG
130 GTGTTCCTGTATGAACAACTAAAACTGCCAATGTGAGGAAATGCTTAAGCTGAGAATCTTCTCCG
316697 AGTGAGCAAAAGGA
195 AGTGAGCAAAAGGA
*
316711 GATATTGAT
1 GATTTTGAT
316720 TGAGCTTTTA
Statistics
Matches: 206, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
207 93 0.45
208 113 0.55
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (208 bp):
GATTTTGATCCCCTTATGAAATTACACCCAATTTGTAAATTTCAATGCTACATCAACCATTTTGT
GAATAAATACGTTCTTGATTGTTGCTTGTCAAATTTAAAATATATGGGCATGAAACAAAATTTGG
TGTTCCTGTATGAACAACTAAAACTGCCAATGTGAGGAAATGCTTAAGCTGAGAATCTTCTCCGA
GTGAGCAAAAGGA
Found at i:320064 original size:72 final size:72
Alignment explanation
Indices: 319988--320122 Score: 198
Period size: 72 Copynumber: 1.9 Consensus size: 72
319978 ACGTCGAATA
* * * *
319988 CTTCCAGAAATGTAAGTTTTGTTAATTCTGGACATAGTTCGCCAAAGAGCTTGTTGTGGGAGACA
1 CTTCCAGAAACGTAAGTTTTGTTAATTCTGGACACAGTTCACCAAAGAGCTTGTTATGGGAGACA
320053 TCCAAGG
66 TCCAAGG
** * *
320060 CTTCCAGAGCCGTAAGTTTTGTTAATTCTGGAGACGGTTCACCAAAGAGCTTGTTATGGGAGA
1 CTTCCAGAAACGTAAGTTTTGTTAATTCTGGACACAGTTCACCAAAGAGCTTGTTATGGGAGA
320123 GATTCAACGC
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (72 bp):
CTTCCAGAAACGTAAGTTTTGTTAATTCTGGACACAGTTCACCAAAGAGCTTGTTATGGGAGACA
TCCAAGG
Found at i:324966 original size:2 final size:2
Alignment explanation
Indices: 324961--324990 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
324951 GTGTGTGTAA
324961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
324991 TAATCGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339842 original size:20 final size:20
Alignment explanation
Indices: 339817--339861 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
339807 ACAAAAATTT
* *
339817 AAAAAACCTATTTTTT-TTA
1 AAAAAAACTATTTTTTAATA
*
339836 AAAAAAAGTATTTTTTAATA
1 AAAAAAACTATTTTTTAATA
339856 AAAAAA
1 AAAAAA
339862 TCCCCTTAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAAAAACTATTTTTTAATA
Found at i:348196 original size:9 final size:9
Alignment explanation
Indices: 348182--348248 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
348172 AAGCCCTTTT
*
348182 AAATTTTAA
1 AAATTATAA
348191 AAATT-TAA
1 AAATTATAA
*
348199 AAATCATAA
1 AAATTATAA
348208 AAATTATAAACA
1 AAATTAT--A-A
348220 AAATTTATTAA
1 AAA-TTA-TAA
348231 AAATT-T-A
1 AAATTATAA
348238 AAATTATAA
1 AAATTATAA
348247 AA
1 AA
348249 TTTTTATTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
7 6 0.12
8 9 0.19
9 17 0.35
10 2 0.04
11 5 0.10
12 5 0.10
13 3 0.06
14 1 0.02
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:348619 original size:13 final size:13
Alignment explanation
Indices: 348584--348621 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
348574 TACCTTTAAT
*
348584 TACATATTCACTA
1 TACATATTCAATA
*
348597 TA-AAATTCAATA
1 TACATATTCAATA
348609 TACATATTCAATA
1 TACATATTCAATA
348622 ATTTTAATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (13 bp):
TACATATTCAATA
Found at i:356314 original size:14 final size:14
Alignment explanation
Indices: 356297--356324 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
356287 CTACTTTTCA
356297 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
356311 TTCTTTTTTTTTTT
1 TTCTTTTTTTTTTT
356325 GTTAATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTCTTTTTTTTTTT
Found at i:368511 original size:2 final size:2
Alignment explanation
Indices: 368493--368528 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
368483 AGATGCAACG
* *
368493 AT AT AC AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
368529 TTGAAGTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:372425 original size:102 final size:102
Alignment explanation
Indices: 372267--372470 Score: 399
Period size: 102 Copynumber: 2.0 Consensus size: 102
372257 ATAAAACACA
372267 AAAAAAATAAACACTAAATTTAAAAAGTGAGTCGATTTTACATATTGGAGTTTAAGCTTGACTTG
1 AAAAAAATAAACACTAAATTTAAAAAGTGAGTCGATTTTACATATTGGAGTTTAAGCTTGACTTG
372332 TATTTTAAACCATTCTAATATTTTTGTTCAATTTTTT
66 TATTTTAAACCATTCTAATATTTTTGTTCAATTTTTT
*
372369 AAAAAAATAAACACTAAATTTAAAAAGTGAGTCTATTTTACATATTGGAGTTTAAGCTTGACTTG
1 AAAAAAATAAACACTAAATTTAAAAAGTGAGTCGATTTTACATATTGGAGTTTAAGCTTGACTTG
372434 TATTTTAAACCATTCTAATATTTTTGTTCAATTTTTT
66 TATTTTAAACCATTCTAATATTTTTGTTCAATTTTTT
372471 TTAAAATTTA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 101 1.00
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.43
Consensus pattern (102 bp):
AAAAAAATAAACACTAAATTTAAAAAGTGAGTCGATTTTACATATTGGAGTTTAAGCTTGACTTG
TATTTTAAACCATTCTAATATTTTTGTTCAATTTTTT
Found at i:374727 original size:29 final size:29
Alignment explanation
Indices: 374638--374828 Score: 178
Period size: 29 Copynumber: 6.5 Consensus size: 29
374628 AACTATCAAA
* * *
374638 AAAATTATATTTTGACCCCCAAACTTTTCC
1 AAAATTACATTTTTACCCCTAAAC-TTTCC
*
374668 AAAATTATATTTTTGACCCCTAAACTTTCC
1 AAAATTACATTTTT-ACCCCTAAACTTTCC
*
374698 AAAAATTACATTTTTACCCTTAAAC-TTCC
1 -AAAATTACATTTTTACCCCTAAACTTTCC
374727 AAAAATT-C-TATTTTACCCCTAAACTTTCC
1 -AAAATTACAT-TTTTACCCCTAAACTTTCC
* **
374756 AAAATTCCATTTTTGA-CCCTAATTTTTCC
1 AAAATTACATTTTT-ACCCCTAAACTTTCC
*
374785 AAAATTACCA-TTTTACTCCTAAAC-TTCTC
1 AAAATTA-CATTTTTACCCCTAAACTTTC-C
*
374814 AAAATTCCATTTTTA
1 AAAATTACATTTTTA
374829 ACCTCGCTTT
Statistics
Matches: 138, Mismatches: 12, Indels: 23
0.80 0.07 0.13
Matches are distributed among these distances:
27 1 0.01
28 26 0.19
29 58 0.42
30 31 0.22
31 22 0.16
ACGTcount: A:0.34, C:0.25, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAATTACATTTTTACCCCTAAACTTTCC
Found at i:374840 original size:58 final size:58
Alignment explanation
Indices: 374685--374919 Score: 200
Period size: 58 Copynumber: 4.1 Consensus size: 58
374675 TATTTTTGAC
* ** *
374685 CCCTAAACTT-TCCAAAAATTACATTTTT-ACCCTTAA-ACTTCCAAAAATT-CTATTTTA
1 CCCTAAACTTCT-C-AAAATTCCATTTTTAACCC-TAATTTTTCCAAAAATTACCATTTTA
*
374742 CCCCTAAACTT-TCCAAAATTCCATTTTTGACCCTAATTTTTCC-AAAATTACCATTTTA
1 -CCCTAAACTTCT-CAAAATTCCATTTTTAACCCTAATTTTTCCAAAAATTACCATTTTA
**
374800 CTCCTAAACTTCTCAAAATTCCATTTTTAA-CCTCGCTTTTTCCAAAAATTACCA-TTTA
1 C-CCTAAACTTCTCAAAATTCCATTTTTAACCCT-AATTTTTCCAAAAATTACCATTTTA
* * * ** * * *
374858 CCCACAAACTTCTAAAAATTCCATTTTTGACCC-AAACTTTCCCAAGATTACCATTTTG
1 CCC-TAAACTTCTCAAAATTCCATTTTTAACCCTAATTTTTCCAAAAATTACCATTTTA
374916 CCCT
1 CCCT
374920 CGAGTGTCCA
Statistics
Matches: 149, Mismatches: 18, Indels: 21
0.79 0.10 0.11
Matches are distributed among these distances:
57 42 0.28
58 94 0.63
59 13 0.09
ACGTcount: A:0.32, C:0.28, G:0.02, T:0.37
Consensus pattern (58 bp):
CCCTAAACTTCTCAAAATTCCATTTTTAACCCTAATTTTTCCAAAAATTACCATTTTA
Found at i:374893 original size:28 final size:28
Alignment explanation
Indices: 374676--374896 Score: 116
Period size: 29 Copynumber: 7.6 Consensus size: 28
374666 CCAAAATTAT
* *
374676 ATTTTTGACCCCTAAACTTTCCAAAAATTAC
1 ATTTTT-A-CCCTAAAC-TTCTAAAAATTCC
* *
374707 ATTTTTACCCTTAAACTTCCAAAAATTCT
1 ATTTTTACCC-TAAACTTCTAAAAATTCC
*
374736 A-TTTTACCCCTAAACTT-TCCAAAATTCC
1 ATTTTTA-CCCTAAACTTCT-AAAAATTCC
* * *
374764 ATTTTTGACCCT-AATTTTTCCAAAATTACC
1 ATTTTT-ACCCTAAACTTCT-AAAAATT-CC
*
374794 A-TTTTACTCCTAAACTTCTCAAAATTCC
1 ATTTTTAC-CCTAAACTTCTAAAAATTCC
* ** *
374822 ATTTTTAACCT-CGCTTTTTCCAAAAATTACC
1 ATTTTTACCCTAAAC---TTCTAAAAATT-CC
*
374853 A--TTTACCCACAAACTTCTAAAAATTCC
1 ATTTTTACCC-TAAACTTCTAAAAATTCC
374880 ATTTTTGACCC-AAACTT
1 ATTTTT-ACCCTAAACTT
374897 TCCCAAGATT
Statistics
Matches: 153, Mismatches: 18, Indels: 41
0.72 0.08 0.19
Matches are distributed among these distances:
27 4 0.03
28 48 0.31
29 63 0.41
30 28 0.18
31 10 0.07
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (28 bp):
ATTTTTACCCTAAACTTCTAAAAATTCC
Found at i:374957 original size:28 final size:28
Alignment explanation
Indices: 374899--374970 Score: 67
Period size: 28 Copynumber: 2.6 Consensus size: 28
374889 CCAAACTTTC
* * * *
374899 CCAAGATTACCATTTTGCCCTCGAGTGT
1 CCAAAATTACCATTTTACCCCCGAGTAT
374927 CCAAAATTACCATTTTACCCCC-AGGTAT
1 CCAAAATTACCATTTTACCCCCGA-GTAT
*
374955 CCAGAAATCA-CATTTT
1 CCA-AAATTACCATTTT
374971 CAACTCCGAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 31 0.84
29 5 0.14
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGTAT
Found at i:381672 original size:21 final size:22
Alignment explanation
Indices: 381646--381686 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
381636 TTTTATAACT
381646 TTATATGTATTTTA-TAAAATC
1 TTATATGTATTTTATTAAAATC
381667 TTATATGTATTTTATTAAAA
1 TTATATGTATTTTATTAAAA
381687 ACGAACTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (22 bp):
TTATATGTATTTTATTAAAATC
Found at i:382155 original size:29 final size:32
Alignment explanation
Indices: 382113--382171 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 32
382103 TGCTCTTTTT
382113 TTTGGTCACTTAAC-TATC-A-ATTTTTTTAA
1 TTTGGTCACTTAACTTATCGAGATTTTTTTAA
382142 TTTGGTCAGC-TAACTTATCGAGATTTTTTT
1 TTTGGTCA-CTTAACTTATCGAGATTTTTTT
382172 TTGCTCCCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
29 12 0.46
30 5 0.19
31 1 0.04
32 8 0.31
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.51
Consensus pattern (32 bp):
TTTGGTCACTTAACTTATCGAGATTTTTTTAA
Found at i:382174 original size:29 final size:27
Alignment explanation
Indices: 382108--382173 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
382098 ACTATTGCTC
382108 TTTTTTTTGGTCACTTAACTATCAATT
1 TTTTTTTTGGTCACTTAACTATCAATT
382135 TTTTTAATTTGGTCAGC-TAACTTATCGAGATT
1 TTTTT--TTTGGTCA-CTTAAC-TATC-A-ATT
382167 TTTTTTT
1 TTTTTTT
382174 GCTCCCTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
27 5 0.15
29 12 0.36
30 7 0.21
31 1 0.03
32 8 0.24
ACGTcount: A:0.21, C:0.12, G:0.11, T:0.56
Consensus pattern (27 bp):
TTTTTTTTGGTCACTTAACTATCAATT
Found at i:382389 original size:6 final size:6
Alignment explanation
Indices: 382380--382405 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
382370 ATCACTGTTG
382380 CCTCCA CCTCCA CCTCCA CCTCCA CC
1 CCTCCA CCTCCA CCTCCA CCTCCA CC
382406 ACTACTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.69, G:0.00, T:0.15
Consensus pattern (6 bp):
CCTCCA
Found at i:382764 original size:31 final size:30
Alignment explanation
Indices: 382722--382828 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 30
382712 TAACAAATTG
*
382722 ATAGTTAGGTGACCAAAAAAGAAAAGGGATA
1 ATAGTTGGGTGACCAAAAAAGAAAA-GGATA
* *
382753 ATAGTTGGGTGACCAAATTAAA-AAAA-AACTG
1 ATAGTTGGGTGACCAAA--AAAGAAAAGGA-TA
* *
382784 GTAGTTGGGTGACCAAAAAAGAAAACGGACA
1 ATAGTTGGGTGACCAAAAAAGAAAA-GGATA
382815 ATAGTTGGGTGACC
1 ATAGTTGGGTGACC
382829 TATGTTGTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
29 3 0.05
30 5 0.08
31 46 0.74
32 5 0.08
33 3 0.05
ACGTcount: A:0.45, C:0.10, G:0.26, T:0.19
Consensus pattern (30 bp):
ATAGTTGGGTGACCAAAAAAGAAAAGGATA
Found at i:384547 original size:21 final size:19
Alignment explanation
Indices: 384469--384557 Score: 58
Period size: 19 Copynumber: 4.6 Consensus size: 19
384459 TTTTAGGCAA
* *
384469 TTTTT-AAATTTTTAGAAAA
1 TTTTTAAAAATTTTAG-AAT
*
384488 TTTTT-AAAATTTTA-ACT
1 TTTTTAAAAATTTTAGAAT
* *
384505 TTCTTTATACATCTTTAGAATT
1 TT-TTTAAAAAT-TTTAGAA-T
*
384527 CTTTTTAAAAATTTTATAAT
1 -TTTTTAAAAATTTTAGAAT
384547 TTTTTAAAAAT
1 TTTTTAAAAAT
384558 ATATATTTTG
Statistics
Matches: 55, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
17 3 0.05
18 3 0.05
19 27 0.49
20 5 0.09
21 7 0.13
22 8 0.15
23 2 0.04
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (19 bp):
TTTTTAAAAATTTTAGAAT
Found at i:384562 original size:18 final size:18
Alignment explanation
Indices: 384528--384566 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
384518 TTTAGAATTC
*
384528 TTTTTAAAAATTTTATAAT
1 TTTTTAAAAATTATAT-AT
384547 TTTTTAAAAA-TATATAT
1 TTTTTAAAAATTATATAT
384564 TTT
1 TTT
384567 GGATTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 4 0.21
19 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTTAAAAATTATATAT
Found at i:391610 original size:17 final size:17
Alignment explanation
Indices: 391590--391635 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
391580 TCGGGGCCCA
*
391590 ATAAATTTAAATTTATT
1 ATAAATTTAAATTTAAT
391607 ATAAATTTAAATTTAAT
1 ATAAATTTAAATTTAAT
**
391624 ATTCATTTAAAT
1 ATAAATTTAAAT
391636 AATGTTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
ATAAATTTAAATTTAAT
Found at i:391621 original size:23 final size:23
Alignment explanation
Indices: 391591--391635 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
391581 CGGGGCCCAA
*
391591 TAAATTTAA-ATTTATTATAAATT
1 TAAATTTAATATTCATT-TAAATT
391614 TAAATTTAATATTCATTTAAAT
1 TAAATTTAATATTCATTTAAAT
391636 AATGTTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAAATTTAATATTCATTTAAATT
Found at i:392325 original size:13 final size:13
Alignment explanation
Indices: 392306--392345 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
392296 GGTGATAACT
392306 ATATTAATAATTA
1 ATATTAATAATTA
* *
392319 TTATTAATAATCA
1 ATATTAATAATTA
*
392332 ATATTAATTATTA
1 ATATTAATAATTA
392345 A
1 A
392346 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATTAATAATTA
Done.