Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 40 of 226
Found at i:17202938 original size:29 final size:28
Alignment explanation
Indices: 17202896--17202967 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 28
17202886 TTTAGTTTAT
17202896 TTAATATATAATAATATA-ATATAATATAA
1 TTAATATAT-ATAATATATATATAATA-AA
17202925 TTAATATTATATAATATATTATATAATAAA
1 TTAATA-TATATAATATA-TATATAATAAA
*
17202955 ATAATATATATAA
1 TTAATATATATAA
17202968 AACATAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
29 21 0.54
30 10 0.26
31 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (28 bp):
TTAATATATATAATATATATATAATAAA
Found at i:17202943 original size:12 final size:12
Alignment explanation
Indices: 17202909--17202952 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
17202899 ATATATAATA
17202909 ATATAATATA--
1 ATATAATATATT
17202919 ATATAATTAATATT
1 ATATAA-T-ATATT
17202933 ATATAATATATT
1 ATATAATATATT
17202945 ATATAATA
1 ATATAATA
17202953 AAATAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.20
11 1 0.03
12 16 0.53
13 1 0.03
14 6 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATAATATATT
Found at i:17202957 original size:17 final size:17
Alignment explanation
Indices: 17202892--17202967 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
17202882 TCTATTTAGT
*
17202892 TTATTTAATAT-ATA-A
1 TTATATAATATAATATA
*
17202907 TAATATAATATAATATAA
1 TTATATAATATAATAT-A
*
17202925 TTAATATTATATAATATA
1 TT-ATATAATATAATATA
*
17202943 TTATATAATAAAATA-A
1 TTATATAATATAATATA
17202959 TATATATAA
1 T-TATATAA
17202968 AACATAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
15 9 0.18
16 5 0.10
17 18 0.36
18 5 0.10
19 13 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTATATAATATAATATA
Found at i:17204511 original size:20 final size:20
Alignment explanation
Indices: 17204486--17204552 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
17204476 CTGTTTAACC
17204486 CTTATGGTTTCCGTTCAGCT
1 CTTATGGTTTCCGTTCAGCT
*
17204506 CTTATGAGCTTCCGTTCA-CT
1 CTTATG-GTTTCCGTTCAGCT
* * *
17204526 CTTATAGGTTTCTGTTTAGCA
1 CTTAT-GGTTTCCGTTCAGCT
17204547 CTTATG
1 CTTATG
17204553 TGCTTCTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (20 bp):
CTTATGGTTTCCGTTCAGCT
Found at i:17204520 original size:21 final size:21
Alignment explanation
Indices: 17204456--17204530 Score: 73
Period size: 20 Copynumber: 3.7 Consensus size: 21
17204446 AATGGGTTTT
* *
17204456 CGTTGAGCTCTTTTGAGCTTC
1 CGTTCAGCTCTTATGAGCTTC
* * * * *
17204477 TGTTTAACCCTTATG-GTTTC
1 CGTTCAGCTCTTATGAGCTTC
17204497 CGTTCAGCTCTTATGAGCTTC
1 CGTTCAGCTCTTATGAGCTTC
17204518 CGTTCA-CTCTTAT
1 CGTTCAGCTCTTAT
17204531 AGGTTTCTGT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 22 0.52
21 20 0.48
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.44
Consensus pattern (21 bp):
CGTTCAGCTCTTATGAGCTTC
Found at i:17204536 original size:41 final size:41
Alignment explanation
Indices: 17204450--17204558 Score: 112
Period size: 41 Copynumber: 2.7 Consensus size: 41
17204440 AAACCTAATG
* * * *
17204450 GGTTTTCGTTGAGCTCTTTTGAGCTTCTGTTTAACCCTTAT
1 GGTTTCCGTTCAGCTCTTATGAGCTTCCGTTTAACCCTTAT
* *
17204491 GGTTTCCGTTCAGCTCTTATGAGCTTCCG-TTCACTCTTAT
1 GGTTTCCGTTCAGCTCTTATGAGCTTCCGTTTAACCCTTAT
* * * *
17204531 AGGTTTCTGTTTAGCACTTATGTGCTTC
1 -GGTTTCCGTTCAGCTCTTATGAGCTTC
17204559 TATTCAGCCT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 9 0.16
41 48 0.84
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (41 bp):
GGTTTCCGTTCAGCTCTTATGAGCTTCCGTTTAACCCTTAT
Found at i:17207304 original size:38 final size:38
Alignment explanation
Indices: 17207204--17207334 Score: 131
Period size: 38 Copynumber: 3.4 Consensus size: 38
17207194 CCTTGAGTCA
* * *
17207204 ATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATTCG
1 ATGAGACACTGGGTGTCA--ACTTTACTTCGGCTAG-TCCG
* * *
17207245 ATGAGATACTGGGTATC-ACTTTACTTCGGCTAGGCCG
1 ATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTCCG
* *
17207282 ATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TCCG
1 ATGAGACACTGGGTGTCAACTTTACTTCG-GCTAGTCCG
*
17207320 ATGAGGCACTGGGTG
1 ATGAGACACTGGGTG
17207335 CCAATCTGGT
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 17 0.22
38 41 0.54
39 3 0.04
41 15 0.20
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (38 bp):
ATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTCCG
Found at i:17209902 original size:16 final size:16
Alignment explanation
Indices: 17209865--17209904 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
17209855 TTAATAAAAT
* *
17209865 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
17209881 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
17209897 TAAAATTA
1 TAAAATTA
17209905 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:17209904 original size:22 final size:22
Alignment explanation
Indices: 17209837--17209889 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
17209827 TAATTAAAAT
* * *
17209837 TAAAATTAAAATTATTTTTTAA
1 TAAAATTAAAACTAATTGTTAA
*
17209859 TAAAATTAAAACTAATTGTTAT
1 TAAAATTAAAACTAATTGTTAA
17209881 TAAAATTAA
1 TAAAATTAA
17209890 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAAATTAAAACTAATTGTTAA
Found at i:17209963 original size:66 final size:67
Alignment explanation
Indices: 17209893--17210035 Score: 243
Period size: 68 Copynumber: 2.1 Consensus size: 67
17209883 AAATTAATTG
*
17209893 TTAGTAAAATTATCAAATTATTAATTG-TTAATTGTATTAATTGTTGCAATAAAATCTAACATTT
1 TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGCAACAAAATCTAACATTT
17209957 GA
66 GA
* *
17209959 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAAATTATCAAATTATTAATTG-ATTAATTGTATTAATTGTTGCAACAAAATCTAACATT
17210024 TGA
65 TGA
17210027 TTAGTAAAA
1 TTAGTAAAA
17210036 CAAACTTGAT
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
66 26 0.37
68 45 0.63
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (67 bp):
TTAGTAAAATTATCAAATTATTAATTGATTAATTGTATTAATTGTTGCAACAAAATCTAACATTT
GA
Found at i:17209989 original size:9 final size:9
Alignment explanation
Indices: 17209977--17210004 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
17209967 TTTATCAAAT
17209977 TATTAATTG
1 TATTAATTG
17209986 TATTAATTG
1 TATTAATTG
17209995 TATTAATTG
1 TATTAATTG
17210004 T
1 T
17210005 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:17210141 original size:22 final size:24
Alignment explanation
Indices: 17210101--17210144 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17210091 AAATAAACTT
17210101 AAAATAAAAAACTATTATATTTTA
1 AAAATAAAAAACTATTATATTTTA
17210125 AAAATAAAAAA-TA-TATATTT
1 AAAATAAAAAACTATTATATTT
17210145 AATATTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 7 0.35
23 2 0.10
24 11 0.55
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATAAAAAACTATTATATTTTA
Found at i:17213161 original size:11 final size:13
Alignment explanation
Indices: 17213141--17213172 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
17213131 AATAAATTAA
17213141 TAAAATATCAT-T
1 TAAAATATCATAT
17213153 TAAAA-ATCATAT
1 TAAAATATCATAT
17213165 TAAAATAT
1 TAAAATAT
17213173 TAATAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATATCATAT
Found at i:17214045 original size:9 final size:9
Alignment explanation
Indices: 17214031--17214067 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
17214021 TATAGTTTGA
17214031 TATTCGAAT
1 TATTCGAAT
17214040 TATTCGAAT
1 TATTCGAAT
*
17214049 TATTCGAGT
1 TATTCGAAT
*
17214058 TATTAGAAT
1 TATTCGAAT
17214067 T
1 T
17214068 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:17225204 original size:18 final size:18
Alignment explanation
Indices: 17225181--17225247 Score: 98
Period size: 18 Copynumber: 3.7 Consensus size: 18
17225171 TTTGGTTAAA
* *
17225181 AATTAACCGAATTATCTG
1 AATTAACCGAATTACCCG
*
17225199 AATTAACCGGATTACCCG
1 AATTAACCGAATTACCCG
*
17225217 AATTAACTGAATTACCCG
1 AATTAACCGAATTACCCG
17225235 AATTAACCGAATT
1 AATTAACCGAATT
17225248 GAATCACTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:17225212 original size:9 final size:9
Alignment explanation
Indices: 17225181--17225247 Score: 80
Period size: 9 Copynumber: 7.4 Consensus size: 9
17225171 TTTGGTTAAA
17225181 AATTAACCG
1 AATTAACCG
* *
17225190 AATTATCTG
1 AATTAACCG
17225199 AATTAACCG
1 AATTAACCG
* *
17225208 GATTACCCG
1 AATTAACCG
*
17225217 AATTAACTG
1 AATTAACCG
*
17225226 AATTACCCG
1 AATTAACCG
17225235 AATTAACCG
1 AATTAACCG
17225244 AATT
1 AATT
17225248 GAATCACTAC
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 46 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (9 bp):
AATTAACCG
Found at i:17225217 original size:27 final size:27
Alignment explanation
Indices: 17225181--17225247 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
17225171 TTTGGTTAAA
*
17225181 AATTAACCGAATTATCTGAATTAACCG
1 AATTAACCGAATTAACTGAATTAACCG
* * *
17225208 GATTACCCGAATTAACTGAATTACCCG
1 AATTAACCGAATTAACTGAATTAACCG
17225235 AATTAACCGAATT
1 AATTAACCGAATT
17225248 GAATCACTAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.28
Consensus pattern (27 bp):
AATTAACCGAATTAACTGAATTAACCG
Found at i:17242535 original size:20 final size:19
Alignment explanation
Indices: 17242483--17242534 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
17242473 TTTTAGAAAA
17242483 TTTTA-AAATTTTTAACTT
1 TTTTATAAATTTTTAACTT
*
17242501 TCTTTATATATTTTTAGA-TT
1 T-TTTATAAATTTTTA-ACTT
17242521 TTTTATAAATTTTT
1 TTTTATAAATTTTT
17242535 TTACAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 11 0.38
21 1 0.03
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATAAATTTTTAACTT
Found at i:17242571 original size:19 final size:19
Alignment explanation
Indices: 17242547--17242596 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
17242537 ACAAATAAAT
17242547 TTTTGAAATTTAAAAATTA
1 TTTTGAAATTTAAAAATTA
* * *
17242566 TTTTGAATTTTTTAAAATTT
1 TTTTGAA-ATTTAAAAATTA
*
17242586 TTTTAAAATTT
1 TTTTGAAATTT
17242597 TTTTGTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
TTTTGAAATTTAAAAATTA
Found at i:17242609 original size:11 final size:11
Alignment explanation
Indices: 17242573--17242600 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17242563 TTATTTTGAA
17242573 TTTTTTAAAAT
1 TTTTTTAAAAT
17242584 TTTTTTAAAAT
1 TTTTTTAAAAT
17242595 TTTTTT
1 TTTTTT
17242601 GTAATTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTAAAAT
Found at i:17243220 original size:31 final size:31
Alignment explanation
Indices: 17243185--17243243 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
17243175 ATATGTACAA
* *
17243185 TTGAATCAAAA-CTAAAGTTTCATGTATACGT
1 TTGAACCAAAATC-AAAGTTCCATGTATACGT
*
17243216 TTGAACCACAATCAAAGTTCCATGTATA
1 TTGAACCAAAATCAAAGTTCCATGTATA
17243244 TAATTGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 23 0.96
32 1 0.04
ACGTcount: A:0.39, C:0.17, G:0.12, T:0.32
Consensus pattern (31 bp):
TTGAACCAAAATCAAAGTTCCATGTATACGT
Found at i:17244437 original size:25 final size:25
Alignment explanation
Indices: 17244385--17244455 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
17244375 TTTTGTTTAA
*
17244385 TTTACTTTTTGTAT-ATTTTTATA-CT
1 TTTA-TTTTT-TATAATTTTAATATCT
*
17244410 TTTATTTTTATATAATTTTAATATTT
1 TTTATTTTT-TATAATTTTAATATCT
*
17244436 TTTAGTTTTTATAATTTTAA
1 TTTATTTTTTATAATTTTAA
17244456 AAGAAAATCA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.20
25 23 0.57
26 9 0.22
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.68
Consensus pattern (25 bp):
TTTATTTTTTATAATTTTAATATCT
Found at i:17248906 original size:50 final size:50
Alignment explanation
Indices: 17248835--17248935 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
17248825 AGAACCTTAA
17248835 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
*
17248885 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATTCTAAT
1 TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
17248935 T
1 T
17248936 GAAACTCACA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.19, C:0.16, G:0.10, T:0.55
Consensus pattern (50 bp):
TTTTTTGCTTATTCTTCTCTTTAATCTTTTTCATGGTGCAAGATACTAAT
Found at i:17252047 original size:15 final size:15
Alignment explanation
Indices: 17252022--17252056 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
17252012 AACTCTATTT
*
17252022 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
17252036 TAATTAATATTAAGA
1 TAATTAATATTAAGA
17252051 TAATTA
1 TAATTA
17252057 TGAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:17252926 original size:17 final size:17
Alignment explanation
Indices: 17252901--17252936 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17252891 GATCCAAACC
17252901 TTTAATTTTGTTATTTT
1 TTTAATTTTGTTATTTT
* *
17252918 TTTATTTTTTTTATTTT
1 TTTAATTTTGTTATTTT
17252935 TT
1 TT
17252937 CAGGAACGCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.03, T:0.83
Consensus pattern (17 bp):
TTTAATTTTGTTATTTT
Found at i:17255173 original size:21 final size:22
Alignment explanation
Indices: 17255141--17255186 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
17255131 AATTTTATGT
17255141 TAAAAATAAAAATTTAA-TTAGA
1 TAAAAATAAAAATTTAAGTTA-A
17255163 TAAAAAT-AAAATTTAAGTTAA
1 TAAAAATAAAAATTTAAGTTAA
17255184 TAA
1 TAA
17255187 TTTAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (22 bp):
TAAAAATAAAAATTTAAGTTAA
Found at i:17255224 original size:29 final size:29
Alignment explanation
Indices: 17255168--17255224 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
17255158 TTAGATAAAA
*
17255168 ATAAAATTTAAGTTAATAATTTAAATTAT
1 ATAAAATTTAAGTTAATAAATTAAATTAT
* * * *
17255197 ATAAAATTTTATTTATTAAATTATATTA
1 ATAAAATTTAAGTTAATAAATTAAATTA
17255225 CCTATTTTCC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATAAAATTTAAGTTAATAAATTAAATTAT
Found at i:17255504 original size:21 final size:21
Alignment explanation
Indices: 17255458--17255520 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
17255448 CCCCGAACCA
*
17255458 TGAACTCTAAATCTTGAATCT
1 TGAACTCTAAATATTGAATCT
*
17255479 CGAACTTCTAAATATTGAA-CT
1 TGAAC-TCTAAATATTGAATCT
* * *
17255500 TGAACCCTAAACACTGAATCT
1 TGAACTCTAAATATTGAATCT
17255521 CAAACCCCAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.29
21 12 0.35
22 12 0.35
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.32
Consensus pattern (21 bp):
TGAACTCTAAATATTGAATCT
Found at i:17264037 original size:23 final size:24
Alignment explanation
Indices: 17264011--17264069 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
17264001 AAATTTTAAA
17264011 AATATTTATATTATTT-TAAATTT
1 AATATTTATATTATTTATAAATTT
17264034 AATATTTA-A-TATTTAATAAATTT
1 AATATTTATATTATTT-ATAAATTT
*
17264057 ATATATTTTTATT
1 A-ATATTTATATT
17264070 GATTAAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.17
22 1 0.03
23 16 0.53
24 6 0.20
25 1 0.03
26 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AATATTTATATTATTTATAAATTT
Found at i:17264047 original size:14 final size:15
Alignment explanation
Indices: 17264011--17264051 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
17264001 AAATTTTAAA
17264011 AATATTTATATTATTTT
1 AATATTTA-A-TATTTT
17264028 AA-ATTTAATA-TTT
1 AATATTTAATATTTT
17264041 AATATTTAATA
1 AATATTTAATA
17264052 AATTTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
14 10 0.43
15 1 0.04
16 5 0.22
17 2 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATATTTAATATTTT
Found at i:17264076 original size:23 final size:23
Alignment explanation
Indices: 17264026--17264076 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
17264016 TTATATTATT
*
17264026 TTAAATTTAATATTTAATATTTA
1 TTAAATTTAATATTTAATATTGA
* *
17264049 ATAAATTTATATATTT-TTATTGA
1 TTAAATTTA-ATATTTAATATTGA
17264072 TTAAA
1 TTAAA
17264077 ATTTTAAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAATTTAATATTTAATATTGA
Found at i:17268724 original size:13 final size:13
Alignment explanation
Indices: 17268708--17268732 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17268698 TGGAAATTAA
17268708 AAAAATAAAAAAT
1 AAAAATAAAAAAT
17268721 AAAAATAAAAAA
1 AAAAATAAAAAA
17268733 GGGAAACAAA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:17270388 original size:2 final size:2
Alignment explanation
Indices: 17270376--17270417 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
17270366 AAAATAATTG
*
17270376 GA GA CA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17270418 TAAAGTAGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17272940 original size:15 final size:16
Alignment explanation
Indices: 17272920--17272949 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17272910 CATCATACAA
17272920 TTATTC-TCTTCTTTC
1 TTATTCTTCTTCTTTC
17272935 TTATTCTTCTTCTTT
1 TTATTCTTCTTCTTT
17272950 GCAAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTCTTCTTCTTTC
Found at i:17273350 original size:24 final size:25
Alignment explanation
Indices: 17273290--17273352 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
17273280 ATATGTATTA
17273290 AAAATATTTATAAATATCAAATAAT
1 AAAATATTTATAAATATCAAATAAT
* * ** *
17273315 GAGAT-TAAATAAATCTCAAAT-AT
1 AAAATATTTATAAATATCAAATAAT
17273338 AAAATATTTATAAAT
1 AAAATATTTATAAAT
17273353 TATATAAAAG
Statistics
Matches: 28, Mismatches: 9, Indels: 3
0.70 0.22 0.08
Matches are distributed among these distances:
23 5 0.18
24 20 0.71
25 3 0.11
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (25 bp):
AAAATATTTATAAATATCAAATAAT
Found at i:17277151 original size:21 final size:21
Alignment explanation
Indices: 17277099--17277145 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
17277089 AAATATACAG
17277099 TATATG-GCATTTAAACTATA
1 TATATGAGCATTTAAACTATA
**
17277119 TATATGAGCATTTAATGTATA
1 TATATGAGCATTTAAACTATA
17277140 TATATG
1 TATATG
17277146 CTCATTAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (21 bp):
TATATGAGCATTTAAACTATA
Found at i:17285398 original size:2 final size:2
Alignment explanation
Indices: 17285391--17285435 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17285381 TTTTATTTAG
17285391 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17285433 TA T
1 TA T
17285436 GTTGAAGAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17293670 original size:14 final size:14
Alignment explanation
Indices: 17293651--17293684 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17293641 TCAGAAATTT
17293651 AAAAAAAAAAAAGA
1 AAAAAAAAAAAAGA
*
17293665 AAAAAAAACAAAGA
1 AAAAAAAAAAAAGA
17293679 ACAAAA
1 A-AAAA
17293685 GAATAGGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAGA
Found at i:17296675 original size:5 final size:5
Alignment explanation
Indices: 17296667--17296766 Score: 68
Period size: 5 Copynumber: 20.0 Consensus size: 5
17296657 ATTTAAAATA
* *
17296667 TATAT TATAT TATA- TATACG TA-AT TAATGAT TATGT T-T-T TATAT
1 TATAT TATAT TATAT TATA-T TATAT T-AT-AT TATAT TATAT TATAT
* *
17296711 TGTAT TATTAT TA-A- TATAT TATAT TATAT TATAT TATAT TACAT ATATAT
1 TATAT TA-TAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT -TATAT
17296761 ATATAT
1 -TATAT
17296767 AACAGAAGAA
Statistics
Matches: 78, Mismatches: 6, Indels: 21
0.74 0.06 0.20
Matches are distributed among these distances:
3 4 0.05
4 9 0.12
5 43 0.55
6 19 0.24
7 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (5 bp):
TATAT
Found at i:17296730 original size:19 final size:18
Alignment explanation
Indices: 17296666--17296751 Score: 57
Period size: 19 Copynumber: 4.4 Consensus size: 18
17296656 AATTTAAAAT
17296666 ATATATTATATTATATATA
1 ATATATTATATTATAT-TA
* * *
17296685 CGTA-ATTAATGATTATGTTT
1 -ATATATT-AT-ATTATATTA
* *
17296705 TTATATTGTATTATTATTA
1 ATATATTATATTA-TATTA
17296724 ATATATTATATTATATTA
1 ATATATTATATTATATTA
17296742 TATTATATTA
1 -A-TATATTA
17296752 CATATATATA
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
18 9 0.18
19 21 0.41
20 15 0.29
21 6 0.12
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (18 bp):
ATATATTATATTATATTA
Found at i:17296767 original size:29 final size:29
Alignment explanation
Indices: 17296705--17296764 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
17296695 GATTATGTTT
*
17296705 TTATATTGTATTATTATTAATATATTATA
1 TTATATTATATTATTATTAATATATTATA
17296734 TTATATTATATTA-TATTACATATATATATA
1 TTATATTATATTATTATTA-ATATAT-TATA
17296764 T
1 T
17296765 ATAACAGAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
28 5 0.18
29 18 0.64
30 5 0.18
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (29 bp):
TTATATTATATTATTATTAATATATTATA
Found at i:17296844 original size:35 final size:34
Alignment explanation
Indices: 17296787--17296853 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
17296777 AGCATAGAAA
* *
17296787 TGAGAAAGAAAGAAACAGAGAAGCAAAACGAAAAT
1 TGAGAAAGAAAGAAACAAAGAAG-AAAAAGAAAAT
*
17296822 TGAGAAAGAAA-AAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAGAA-ACAAAGAAGAAAAAGAAA
17296854 GAGAGCCACG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.67, C:0.04, G:0.24, T:0.04
Consensus pattern (34 bp):
TGAGAAAGAAAGAAACAAAGAAGAAAAAGAAAAT
Found at i:17311576 original size:6 final size:6
Alignment explanation
Indices: 17311569--17311607 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
17311559 CTCTCTCGAA
*
17311569 AAAAAA AAAAAG AAAAAG AAAAAG AAAAAG AAAAA- AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
17311608 GATAAAAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
5 4 0.12
6 28 0.88
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:17315732 original size:15 final size:15
Alignment explanation
Indices: 17315712--17315747 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
17315702 AGTGTTGAAC
*
17315712 AAAAAACAAAAAC-A
1 AAAAAAAAAAAACGA
17315726 AAAAAAAAAAAACGA
1 AAAAAAAAAAAACGA
17315741 AAAAAAA
1 AAAAAAA
17315748 GAAGAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAACGA
Found at i:17323055 original size:34 final size:34
Alignment explanation
Indices: 17323007--17323076 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
17322997 GCCATGGTGG
*
17323007 TAGCAGAGTCCCTAGTTGAGTCCCCCAAGAACCA
1 TAGCAGAGTCCCTAGTCGAGTCCCCCAAGAACCA
*
17323041 TAGCGGAGTCCCTAGTCGAGTCCCCCAAGAACCA
1 TAGCAGAGTCCCTAGTCGAGTCCCCCAAGAACCA
17323075 TA
1 TA
17323077 TTAAGTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.17
Consensus pattern (34 bp):
TAGCAGAGTCCCTAGTCGAGTCCCCCAAGAACCA
Found at i:17324204 original size:20 final size:20
Alignment explanation
Indices: 17324179--17324219 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17324169 CTCAAGGCAC
17324179 CTCACTAACACATCATAAAT
1 CTCACTAACACATCATAAAT
17324199 CTCACTAACACATCATAAAT
1 CTCACTAACACATCATAAAT
17324219 C
1 C
17324220 AAGTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (20 bp):
CTCACTAACACATCATAAAT
Found at i:17327499 original size:7 final size:7
Alignment explanation
Indices: 17327487--17327521 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
17327477 ACTAAGGCAT
17327487 CTCATGG
1 CTCATGG
17327494 CTCATGG
1 CTCATGG
17327501 CTCATGG
1 CTCATGG
17327508 CTCATGG
1 CTCATGG
17327515 CTCATGG
1 CTCATGG
17327522 TGGCACTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.29, G:0.29, T:0.29
Consensus pattern (7 bp):
CTCATGG
Found at i:17332219 original size:3 final size:3
Alignment explanation
Indices: 17332206--17332333 Score: 229
Period size: 3 Copynumber: 42.7 Consensus size: 3
17332196 ACCCCATAGC
*
17332206 AAG ATG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
17332254 AAG AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
*
17332302 AAG AAG AAA AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
17332334 ATGGACATAC
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 119 1.00
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (3 bp):
AAG
Found at i:17332880 original size:15 final size:17
Alignment explanation
Indices: 17332856--17332892 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17332846 TTTTGGATGC
*
17332856 TTGTTATTTGGT-ATTT
1 TTGTTATTTGCTGATTT
17332872 TTGTT-TTTGCTGATTT
1 TTGTTATTTGCTGATTT
17332888 TTGTT
1 TTGTT
17332893 GTTTTGTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 5 0.26
16 14 0.74
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (17 bp):
TTGTTATTTGCTGATTT
Found at i:17334353 original size:2 final size:2
Alignment explanation
Indices: 17334341--17334372 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17334331 GTTCTTGGTG
*
17334341 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17334373 ATTCTGAAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:17371307 original size:18 final size:19
Alignment explanation
Indices: 17371284--17371321 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
17371274 AGAACTCAAC
*
17371284 TAAAAA-TAATTTTAAATA
1 TAAAAACTAATTTAAAATA
17371302 TAAAAACTAATTTAAAATA
1 TAAAAACTAATTTAAAATA
17371321 T
1 T
17371322 GAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAACTAATTTAAAATA
Found at i:17377304 original size:4 final size:4
Alignment explanation
Indices: 17377295--17377319 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
17377285 CATTCGCATG
17377295 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
17377320 TCCACATGTG
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:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:17380619 original size:2 final size:2
Alignment explanation
Indices: 17380612--17380667 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
17380602 NNNNNNNNNN
17380612 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17380654 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
17380668 GTAGATGAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17382340 original size:23 final size:23
Alignment explanation
Indices: 17382282--17382340 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 23
17382272 ATTTTTAAAA
* *
17382282 ATATTTAAAATTATTAAAATATT
1 ATATTTAATATTATTAAAATATC
17382305 ATATTTTTCAATATTATTAAACATA-C
1 ATA--TTT-AATATTATTAAA-ATATC
17382331 ATATTTAATA
1 ATATTTAATA
17382341 ATTTATATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
23 7 0.23
24 3 0.10
25 3 0.10
26 14 0.47
27 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
ATATTTAATATTATTAAAATATC
Found at i:17382414 original size:20 final size:22
Alignment explanation
Indices: 17382374--17382415 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
17382364 ATTAAGAATA
*
17382374 TAATAAATATAATTTATTATTT
1 TAATAAATATAATTTAATATTT
17382396 TAATAAAT-T-ATTTAATATTT
1 TAATAAATATAATTTAATATTT
17382416 CAATTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 1 0.05
22 8 0.42
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATAAATATAATTTAATATTT
Found at i:17382463 original size:16 final size:17
Alignment explanation
Indices: 17382427--17382463 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
17382417 AATTTTATTT
*
17382427 TAATAATAAATTTTGAA
1 TAATAATAAATTTTAAA
17382444 -AATAATAAA-TTTAAA
1 TAATAATAAATTTTAAA
17382459 TAATA
1 TAATA
17382464 TTATTCACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:17382516 original size:15 final size:15
Alignment explanation
Indices: 17382496--17382552 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
17382486 ATTCAATATT
17382496 AATATTTTAATAATA
1 AATATTTTAATAATA
*
17382511 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
* *
17382530 AACATATTAATAATA
1 AATATTTTAATAATA
17382545 AATATTTT
1 AATATTTT
17382553 GTAGTATAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
17 4 0.12
18 1 0.03
19 9 0.28
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:17383027 original size:14 final size:14
Alignment explanation
Indices: 17383008--17383044 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17382998 CTAGAAAAGT
17383008 AAATTATTTTCCAA
1 AAATTATTTTCCAA
*
17383022 AAATTATTTTCCGA
1 AAATTATTTTCCAA
*
17383036 AAATCATTT
1 AAATTATTT
17383045 CAGTGAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.41, C:0.14, G:0.03, T:0.43
Consensus pattern (14 bp):
AAATTATTTTCCAA
Found at i:17391988 original size:19 final size:19
Alignment explanation
Indices: 17391944--17391988 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
17391934 ATAATTTTAT
17391944 TATTATTACTAATATATAA
1 TATTATTACTAATATATAA
* *
17391963 TAATATTAACTAATTTA-AA
1 TATTATT-ACTAATATATAA
17391982 TATTATT
1 TATTATT
17391989 TAAATGCATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTATTACTAATATATAA
Found at i:17409431 original size:24 final size:22
Alignment explanation
Indices: 17409387--17409431 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
17409377 ATCTTTTTAT
*
17409387 TTTTATTTTAAAAATTTAGTCA
1 TTTTATTTTAAAAATTAAGTCA
*
17409409 TTTTACTTTTCAAAATTCAAGTC
1 TTTTA-TTTTAAAAATT-AAGTC
17409432 TAATTGTTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 5 0.26
23 10 0.53
24 4 0.21
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTATTTTAAAAATTAAGTCA
Found at i:17412024 original size:24 final size:24
Alignment explanation
Indices: 17411997--17412046 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
17411987 AGAACTATGC
17411997 ACAATAAAACAAATAAAAGAACTT
1 ACAATAAAACAAATAAAAGAACTT
17412021 ACAATAAAACAAATAAAAGAACTT
1 ACAATAAAACAAATAAAAGAACTT
17412045 AC
1 AC
17412047 TTGCCAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.66, C:0.14, G:0.04, T:0.16
Consensus pattern (24 bp):
ACAATAAAACAAATAAAAGAACTT
Found at i:17420879 original size:31 final size:31
Alignment explanation
Indices: 17420841--17420940 Score: 103
Period size: 39 Copynumber: 3.0 Consensus size: 31
17420831 GACCCATTTT
17420841 TATTTTAAAAATTTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATTTTAAAAAATTAAAAAAAG
17420872 TATTTTAAAAATATTTTAAAATTAAAAAATTAAAAAAAG
1 TATTTT-AAAA-A--TT----TTAAAAAATTAAAAAAAG
*
17420911 TATTTTAAAAATATTT-TAAAATTAAAAAAA
1 TATTTTAAAAAT-TTTAAAAAATTAAAAAAA
17420941 ATTTAAAAAA
Statistics
Matches: 59, Mismatches: 1, Indels: 18
0.76 0.01 0.23
Matches are distributed among these distances:
31 19 0.32
32 6 0.10
33 1 0.02
35 3 0.05
36 1 0.02
37 1 0.02
38 4 0.07
39 24 0.41
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
TATTTTAAAAATTTTAAAAAATTAAAAAAAG
Found at i:17420902 original size:39 final size:40
Alignment explanation
Indices: 17420867--17421002 Score: 172
Period size: 39 Copynumber: 3.4 Consensus size: 40
17420857 AAAAATTAAA
17420867 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAA-TTAAA
1 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAGTTAAA
*
17420906 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAAATTTAAA
1 AAAAGTATTTTAAAAATATTTTAAAATT--AAAAAAGTTAAA
* *
17420948 AAAAGTATTTT-AAAAT-TTTAAAAAATTAAAAAAGTATGTAA
1 AAAAGTATTTTAAAAATATTT-TAAAATTAAAAAAGT-T-AAA
17420989 AAAA-TATTTTAAAA
1 AAAAGTATTTTAAAA
17421003 TTAAAAAAAT
Statistics
Matches: 87, Mismatches: 3, Indels: 12
0.85 0.03 0.12
Matches are distributed among these distances:
39 35 0.40
40 10 0.11
41 26 0.30
42 16 0.18
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (40 bp):
AAAAGTATTTTAAAAATATTTTAAAATTAAAAAAGTTAAA
Found at i:17420993 original size:30 final size:30
Alignment explanation
Indices: 17420936--17421010 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
17420926 TTAAAATTAA
**
17420936 AAAAAATTTAAAAAAAGTATTTTAAAAT-TTT
1 AAAAAA-TT-AAAAAAGTATTAAAAAATATTT
17420967 AAAAAATTAAAAAAGTATGTAAAAAATATTT
1 AAAAAATTAAAAAAGTAT-TAAAAAATATTT
*
17420998 -TAAAATTAAAAAA
1 AAAAAATTAAAAAA
17421011 ATAAATATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.26
30 20 0.51
31 9 0.23
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (30 bp):
AAAAAATTAAAAAAGTATTAAAAAATATTT
Found at i:17421002 original size:11 final size:11
Alignment explanation
Indices: 17420841--17420931 Score: 65
Period size: 10 Copynumber: 8.9 Consensus size: 11
17420831 GACCCATTTT
17420841 TATTTT-AAAA
1 TATTTTAAAAA
17420851 -ATTTTAAAAA
1 TATTTTAAAAA
**
17420861 -ATTAAAAAAA
1 TATTTTAAAAA
17420871 GTATTTTAAAAA
1 -TATTTTAAAAA
17420883 TATTTT--AAA
1 TATTTTAAAAA
17420892 -A--TTAAAAA
1 TATTTTAAAAA
**
17420900 -ATTAAAAAAA
1 TATTTTAAAAA
17420910 GTATTTTAAAAA
1 -TATTTTAAAAA
17420922 TATTTTAAAA
1 TATTTTAAAA
17420932 TTAAAAAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
6 2 0.03
8 5 0.08
9 8 0.12
10 17 0.27
11 16 0.25
12 16 0.25
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:17424508 original size:7 final size:6
Alignment explanation
Indices: 17424491--17424571 Score: 60
Period size: 6 Copynumber: 13.2 Consensus size: 6
17424481 TCATTCTTTC
* *
17424491 TTTCTT TTTCTCT TTTC-- TTTCTT TCATTCTT TGTT-TT GTTTCTT TCTCTC
1 TTTCTT TTTCT-T TTTCTT TTTCTT T--TTCTT T-TTCTT -TTTCTT TTTCTT
* *
17424541 ATTCTT TTTCTA TTTCTT TTTCTT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
17424572 ATCATCATAA
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
4 4 0.07
6 39 0.66
7 10 0.17
8 6 0.10
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTCTT
Found at i:17424508 original size:21 final size:20
Alignment explanation
Indices: 17424484--17424571 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 20
17424474 ATTTTTCTCA
17424484 TTCTTTCTTTCTTTTTCTCTT
1 TTCTTTCTTTCTTTTTCT-TT
*
17424505 TTCTTTCTTTCATTCTTT-GTT
1 TTCTTTCTTTC-TT-TTTCTTT
* *
17424526 TTGTTTCTTTCTCTCATTCTTT
1 TTCTTTCTTTCT-T-TTTCTTT
*
17424548 TTC--TATTTCTTTTTCTTT
1 TTCTTTCTTTCTTTTTCTTT
17424566 TTCTTT
1 TTCTTT
17424572 ATCATCATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
18 9 0.17
19 1 0.02
20 8 0.15
21 27 0.50
22 6 0.11
23 3 0.06
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.74
Consensus pattern (20 bp):
TTCTTTCTTTCTTTTTCTTT
Found at i:17424514 original size:25 final size:24
Alignment explanation
Indices: 17424503--17424559 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 24
17424493 TCTTTTTCTC
17424503 TTTTCTTTCTTTCATTCTTTGTT-T
1 TTTTCTTTCTTTCATTCTTT-TTCT
*
17424527 TGTTTCTTTCTCTCATTCTTTTTCT
1 T-TTTCTTTCTTTCATTCTTTTTCT
*
17424552 ATTTCTTT
1 TTTTCTTT
17424560 TTCTTTTTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.72
Consensus pattern (24 bp):
TTTTCTTTCTTTCATTCTTTTTCT
Found at i:17424644 original size:28 final size:29
Alignment explanation
Indices: 17424580--17424655 Score: 111
Period size: 28 Copynumber: 2.7 Consensus size: 29
17424570 TTATCATCAT
*
17424580 AATATAATAATATATATACTTAACTTTTA
1 AATATTATAATATATATACTTAACTTTTA
*
17424609 AATATTATAATATATAT-TTTAAC-TTTA
1 AATATTATAATATATATACTTAACTTTTA
17424636 AATATTTATAATATATATAC
1 AATA-TTATAATATATATAC
17424656 ACTTATGCCG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 8 0.19
28 18 0.43
29 16 0.38
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (29 bp):
AATATTATAATATATATACTTAACTTTTA
Found at i:17426902 original size:24 final size:24
Alignment explanation
Indices: 17426875--17426926 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
17426865 TTAGTAAGTC
* *
17426875 AAATAAACTATCCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
17426899 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
17426923 AAAT
1 AAAT
17426927 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:17427188 original size:13 final size:14
Alignment explanation
Indices: 17427172--17427213 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
17427162 TTTCAATTTT
17427172 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
17427185 ATTTTAAGAATAATA
1 ATTTTAATAAT-ATA
17427200 ATTTTAAATAATAT
1 ATTTT-AATAATAT
17427214 TCAACATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:17427204 original size:15 final size:16
Alignment explanation
Indices: 17427177--17427206 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17427167 ATTTTATTTT
17427177 AATAATAAATTTTAAG
1 AATAATAAATTTTAAG
17427193 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
17427207 ATAATATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAG
Found at i:17446714 original size:3 final size:3
Alignment explanation
Indices: 17446706--17446771 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
17446696 GTTATATTGC
17446706 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
17446754 ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT
17446772 TCTATACATA
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:17447125 original size:6 final size:6
Alignment explanation
Indices: 17447105--17447136 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17447095 TATGTCATAC
17447105 TTTTTA -TTTTA -TTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
17447137 ATATATATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.40
6 15 0.60
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:17447125 original size:11 final size:11
Alignment explanation
Indices: 17447105--17447138 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
17447095 TATGTCATAC
17447105 TTTTTATTTTA
1 TTTTTATTTTA
17447116 -TTTTATTTTTA
1 TTTTTA-TTTTA
17447127 TTTTTATTTTA
1 TTTTTATTTTA
17447138 T
1 T
17447139 ATATATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 5 0.24
11 11 0.52
12 5 0.24
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:17448292 original size:46 final size:45
Alignment explanation
Indices: 17448225--17448364 Score: 235
Period size: 46 Copynumber: 3.0 Consensus size: 45
17448215 ACAATGCTAT
*
17448225 AACTCAGTATGGTTTCTTTCACTAAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTC-TTCACTGAAACACCATACCTACTTTTCAC
17448271 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGG-TTTCTTCACTGAAACACCATACCTACTTTTCAC
*
17448317 AACTCAATATGGCTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGG-TTTCTTCACTGAAACACCATACCTACTTTTCAC
17448363 AA
1 AA
17448365 TTTTCCATGG
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
46 86 0.96
47 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.07, T:0.34
Consensus pattern (45 bp):
AACTCAGTATGGTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:17449399 original size:29 final size:30
Alignment explanation
Indices: 17449340--17449397 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
17449330 TCCGAGCCTT
*
17449340 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
17449370 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
17449398 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:17449628 original size:13 final size:13
Alignment explanation
Indices: 17449610--17449640 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
17449600 TTCCAGCAAC
17449610 TATGAATTTATTT
1 TATGAATTTATTT
17449623 TATGAATTTATTT
1 TATGAATTTATTT
*
17449636 GATGA
1 TATGA
17449641 TGATCTAAGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (13 bp):
TATGAATTTATTT
Found at i:17452371 original size:17 final size:17
Alignment explanation
Indices: 17452349--17452396 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
17452339 AAATTCTTTT
17452349 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAC
*
17452366 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
17452383 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
17452397 TTCTAAATTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.50, C:0.21, G:0.02, T:0.27
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:17454504 original size:30 final size:30
Alignment explanation
Indices: 17454410--17454504 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
17454400 ATTTAAAATC
* * *
17454410 TAATGTGAGAAAATTTATCAAATTCAAATCCC
1 TAAT-TGAAAAAAATTATCAAATTCAAA-CCT
* * * * *
17454442 AATATTG-AAATAATTATCAAGTTTAAAACT
1 TA-ATTGAAAAAAATTATCAAATTCAAACCT
17454472 TAATTGAAAAAAATTATCAAATTCAAACCT
1 TAATTGAAAAAAATTATCAAATTCAAACCT
17454502 TAA
1 TAA
17454505 ATAATAATTG
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
29 4 0.08
30 24 0.50
31 15 0.31
32 3 0.06
33 2 0.04
ACGTcount: A:0.49, C:0.12, G:0.06, T:0.33
Consensus pattern (30 bp):
TAATTGAAAAAAATTATCAAATTCAAACCT
Found at i:17469952 original size:3 final size:3
Alignment explanation
Indices: 17469932--17470016 Score: 95
Period size: 3 Copynumber: 28.3 Consensus size: 3
17469922 TTTGTTAACT
* *
17469932 TTA TTA TT- TTA ATG TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
*
17469977 TTA TTA TTA TTA TTA TTA -TA TT- TTCA TTAA TAA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TT-A TTA TTA TTA T
17470017 GTAATATTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 10
0.80 0.08 0.11
Matches are distributed among these distances:
2 6 0.09
3 57 0.81
4 7 0.10
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17470307 original size:12 final size:12
Alignment explanation
Indices: 17470260--17470330 Score: 52
Period size: 12 Copynumber: 5.8 Consensus size: 12
17470250 ATAATTTTTT
*
17470260 TTTATTTTTATG
1 TTTATTTATATG
* * *
17470272 TTCATTTATGTA
1 TTTATTTATATG
*
17470284 TTTGTTTATATG
1 TTTATTTATATG
*
17470296 TTTATTTTTATG
1 TTTATTTATATG
* *
17470308 CTTTAGTTTATTTA
1 -TTTA-TTTATATG
17470322 TTTATTTAT
1 TTTATTTAT
17470331 TTGCTATGGA
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
12 31 0.70
13 8 0.18
14 5 0.11
ACGTcount: A:0.20, C:0.03, G:0.08, T:0.69
Consensus pattern (12 bp):
TTTATTTATATG
Found at i:17473994 original size:29 final size:29
Alignment explanation
Indices: 17473962--17474036 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
17473952 AATGAAAATG
*
17473962 AAAATGAA-AAAAATAAAAAAACAAAAAAC
1 AAAAAGAAGAAAAA-AAAAAAACAAAAAAC
* *
17473991 AAAAAGAAGAAAGAAGAAAAACAAAAAGA-
1 AAAAAGAAGAAAAAAAAAAAACAAAAA-AC
* *
17474020 AGAAAGAAGGAAAAAAA
1 AAAAAGAAGAAAAAAAA
17474037 TCAAAATCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 32 0.86
30 5 0.14
ACGTcount: A:0.80, C:0.04, G:0.13, T:0.03
Consensus pattern (29 bp):
AAAAAGAAGAAAAAAAAAAAACAAAAAAC
Found at i:17474010 original size:22 final size:23
Alignment explanation
Indices: 17473985--17474034 Score: 93
Period size: 22 Copynumber: 2.2 Consensus size: 23
17473975 TAAAAAAACA
17473985 AAAAACAAAAAGAAGAAAGAA-G
1 AAAAACAAAAAGAAGAAAGAAGG
17474007 AAAAACAAAAAGAAGAAAGAAGG
1 AAAAACAAAAAGAAGAAAGAAGG
17474030 AAAAA
1 AAAAA
17474035 AATCAAAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 21 0.78
23 6 0.22
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (23 bp):
AAAAACAAAAAGAAGAAAGAAGG
Found at i:17474071 original size:6 final size:6
Alignment explanation
Indices: 17474033--17474067 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
17474023 AAGAAGGAAA
*
17474033 AAAATC AAAATC AAAATC AAAATC AAAATG AAAAT
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAAT
17474068 GAAACTGAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.69, C:0.11, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:17475015 original size:7 final size:7
Alignment explanation
Indices: 17475003--17475063 Score: 54
Period size: 7 Copynumber: 9.0 Consensus size: 7
17474993 CACTCTGAAA
17475003 AAAAATG
1 AAAAATG
17475010 AAAAATG
1 AAAAATG
* *
17475017 -AGAATT
1 AAAAATG
*
17475023 AAAAAGG
1 AAAAATG
17475030 AAAAA-G
1 AAAAATG
*
17475036 GAAAATG
1 AAAAATG
17475043 AAAAATG
1 AAAAATG
* *
17475050 AAAGATA
1 AAAAATG
17475057 AAAAATG
1 AAAAATG
17475064 GAGAGGCTAA
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
6 9 0.22
7 32 0.78
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:17475046 original size:20 final size:20
Alignment explanation
Indices: 17475003--17475052 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
17474993 CACTCTGAAA
* * *
17475003 AAAAATGAAAAATGAGAATT
1 AAAAATGAAAAAGGAAAATG
*
17475023 AAAAAGGAAAAAGGAAAATG
1 AAAAATGAAAAAGGAAAATG
17475043 AAAAATGAAA
1 AAAAATGAAA
17475053 GATAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.18, T:0.12
Consensus pattern (20 bp):
AAAAATGAAAAAGGAAAATG
Found at i:17476349 original size:44 final size:44
Alignment explanation
Indices: 17476278--17477150 Score: 187
Period size: 44 Copynumber: 19.8 Consensus size: 44
17476268 GGAAGACACT
* *
17476278 ATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAAG
* * * * * ** *
17476322 ATCTTATCTCCCTGAGGTTACAATGGAGCAGATTGACACCAGAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAAG
* * * ** * * **
17476366 ATCTTATTTCCCTG-AGATTACAGCGGAGCAGA-TCGAAGACACT
1 ATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATTAAAATAAAAG
* * *
17476409 ATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAAG
* ** * * *
17476453 ATCCTATCTCTCTGAAGTTACAGCAGAGCAG-GTCACAT--AA-
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAAG
* * * * **
17476493 ACCCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAG
1 ATCC-TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATAAAAG
* * * * ** ***
17476539 -TCTTATCTCCCTGAGGTTACAGTGAAGTAGACCGAAGAATTTCAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AATAAAAG
* * * * *** *
17476584 ATCTTATCTCCCTG-AGATTACAGAGGAGTAGATCGAAGCCACAA-
1 ATCCTATCTCCCTGAAG-TTACAGTGGAGCAGAT-TAAAATAAAAG
* * * **
17476628 A-CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAG
1 ATCC-TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATAAAAG
* * * ** ***
17476673 -TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AATAAAAG
* * * *** *
17476718 ATCTTATCTCCCTG-AGATTACAGAGGAGCAGATCGAAGCCACAA-
1 ATCCTATCTCCCTGAAG-TTACAGTGGAGCAGAT-TAAAATAAAAG
* * **
17476762 A-CCTTATCTCCCTGAAGTTACAGTAGG-GCAGGTTGAATATGCAAG
1 ATCC-TATCTCCCTGAAGTTACAGT-GGAGCAGATT-AAAATAAAAG
* * * ** ***
17476807 -TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AATAAAAG
* ** *** *
17476852 ATCTTATCTCCCTG-AGATTACAGAAGAGCAGATTGAAGCCACAA-
1 ATCCTATCTCCCTGAAG-TTACAGTGGAGCAGATT-AAAATAAAAG
** * *** *
17476896 A-CCTTATCTCCCTG-AGATTACAGAAGAGCAGATCGAAGCCACAA-
1 ATCC-TATCTCCCTGAAG-TTACAGTGGAGCAGAT-TAAAATAAAAG
* * * **
17476940 A-CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAG
1 ATCC-TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATAAAAG
** * * ** **
17476985 -TTTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAA-
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGA-TTAA-AA-TAAAAG
* * * ** **
17477030 ATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGGAGCTAGTA-
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAATAAAAG
* * *
17477074 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAGAATAAAGG
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAAG
* * *
17477118 AT-CTCATCTCTCTGAAGTTACAGTAGAGTAGAT
1 ATCCT-ATCTCCCTGAAGTTACAGTGGAGCAGAT
17477151 CGCATCAGGT
Statistics
Matches: 600, Mismatches: 180, Indels: 98
0.68 0.21 0.11
Matches are distributed among these distances:
40 3 0.00
41 24 0.04
42 1 0.00
43 43 0.07
44 378 0.63
45 32 0.05
46 119 0.20
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
ATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAATAAAAG
Found at i:17476651 original size:134 final size:134
Alignment explanation
Indices: 17476495--17476918 Score: 787
Period size: 134 Copynumber: 3.2 Consensus size: 134
17476485 TCACATAAAC
17476495 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
1 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
* *
17476560 GTGAAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGTAGATCGAAGCCA
66 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCA
17476625 CAAA
131 CAAA
17476629 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
1 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
17476694 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCA
66 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCA
17476759 CAAA
131 CAAA
*
17476763 CCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
1 CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
* *
17476828 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCCA
66 GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCA
17476893 CAAA
131 CAAA
17476897 CCTTATCTCCCTG-AGATTACAG
1 CCTTATCTCCCTGAAG-TTACAG
17476919 AAGAGCAGAT
Statistics
Matches: 284, Mismatches: 5, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
133 2 0.01
134 282 0.99
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (134 bp):
CCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACA
GTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCA
CAAA
Found at i:17476770 original size:178 final size:176
Alignment explanation
Indices: 17476586--17477061 Score: 449
Period size: 178 Copynumber: 2.7 Consensus size: 176
17476576 AATTTCAGAT
* *
17476586 CTTATCTCCCTG-AGATTACAG-AGGAGTAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTAC
1 CTTATCTCCCTGAAG-TTACAGTAGG-GCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTAC
* ** * ** *
17476649 AGTGGGGCAG-GTTGAATATGCA-AGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-A
64 AGTGGAGCAGCGAAGAAT-TGCAGA-TCTTATCTCCCTGAGATTACAGAAGAGCAGACCGAAGCA
* * *
17476711 ATTTCAGATCTTATCTCCCTGAGATTACAGAGGAGCAGATCGAAGCCACAAAC
127 A---CAAACCTTATCTCCCTGAGATTACAGAAGAGCAGATCGAAGCCACAAAC
* * * ** ** *
17476764 CTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAATATGCAAGTCTTATCTCCCTGAGGTTACAG
1 CTTATCTCCCTGAAGTTACAGTAGGGCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTACAG
* * ** *
17476829 TGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCCAC
66 TGGAGCAG--CGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGACCGAAGCAAC
17476894 AAACCTTATCTCCCTGAGATTACAGAAGAGCAGATCGAAGCCACAAAC
129 AAACCTTATCTCCCTGAGATTACAGAAGAGCAGATCGAAGCCACAAAC
* * * * ** *** *
17476942 CTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGCAAGTTTTATCTCCCTGAGGTTACAG
1 CTTATCTCCCTGAAGTTACAGTAGGGCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTACAG
* * * * **
17477007 TGGAGTAGACCGAAGAATTTCAAATCTTATCTCCCTGAGGTTACAGTGGAGCAGA
66 TGGAGCAG--CGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGA
17477062 TTGGAGCTAG
Statistics
Matches: 260, Mismatches: 31, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
178 214 0.82
179 5 0.02
180 34 0.13
181 7 0.03
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.25
Consensus pattern (176 bp):
CTTATCTCCCTGAAGTTACAGTAGGGCAGATCGAAGACACAAACCTTATCTCCCTGAAGTTACAG
TGGAGCAGCGAAGAATTGCAGATCTTATCTCCCTGAGATTACAGAAGAGCAGACCGAAGCAACAA
ACCTTATCTCCCTGAGATTACAGAAGAGCAGATCGAAGCCACAAAC
Found at i:17477062 original size:178 final size:179
Alignment explanation
Indices: 17476673--17477235 Score: 716
Period size: 178 Copynumber: 3.2 Consensus size: 179
17476663 AATATGCAAG
* ** * *
17476673 TCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAG-AATTTCAGATCTTATCTCCCTGAGATT
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAA--TCAAACCTTATCTCCCTGAGATT
17476737 ACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAATAT
64 ACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAATAT
17476802 GCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
129 GCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
* ** *
17476853 TCTTATCTCCCTGAGATTACAGAAGAGCAGATTGAAGCCA-CAAACCTTATCTCCCTGAGATTAC
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAATCAAACCTTATCTCCCTGAGATTAC
* *
17476917 AGAAGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATGC
66 AGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAATATGC
* *
17476982 AAGTTTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAAA
131 AAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
* * *
17477031 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGGAGCTAGT-AATCC-TATCTCCCTGA-AGTT
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-AATCAAACCTTATCTCCCTGAGA-TT
* * * * * * * * * * *
17477093 ACAGTGGAGCGGATTAGAA--TA-AAGGATCTCATCTCTCTGAAGTTACAGTAGAGTAGATCG--
64 ACAGAGGAGCAGA-TCGAAGCCACAA--ACCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAA
* * *
17477153 CAT-CAGGTCTTATCTCCCTGAGGTTACAGTGGAGTAAACCGAAGAATTTCAGA
126 TATGCAAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
17477206 TCTTATCTCCCTGAGGTTACAGTGGAGCAG
1 TCTTATCTCCCTGAGGTTACAGTGGAGCAG
17477236 GTCAAAGATG
Statistics
Matches: 338, Mismatches: 38, Indels: 19
0.86 0.10 0.05
Matches are distributed among these distances:
175 76 0.22
176 4 0.01
177 2 0.01
178 216 0.64
179 8 0.02
180 31 0.09
181 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (179 bp):
TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCAATCAAACCTTATCTCCCTGAGATTAC
AGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTAGGGCAGGTTGAATATGC
AAGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGA
Found at i:17477127 original size:134 final size:129
Alignment explanation
Indices: 17476278--17477186 Score: 635
Period size: 134 Copynumber: 6.9 Consensus size: 129
17476268 GGAAGACACT
* *
17476278 ATCCTATCTCTCTGAAGTTACAGTGGAGCGGATTAAAATAAAAGATCTTATCTCCCTGAGGTTAC
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAGAAT-AAAGATCTTATCTCCCTGAGGTTAC
* * * * * * * * * * **
17476343 A-ATGGAGCAGATTGACACCAGAGATCTTATTTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
65 AGA-GGAGCAGATCGA-AGCACAAACCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAATATG
*
17476407 CT
128 CA
* * * * *
17476409 ATCCTATCTCCCTGAAGTTATAGTGGAGCGGATTAAAATAAAGGATCCTATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAGAATAAA-GATCTTATCTCCCTGAGGTTAC
* * * * *
17476474 AGCA-GAGCAGGTC--A-CATAAACCCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAATATG
65 AG-AGGAGCAGATCGAAGCACAAA-CCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAATATG
17476535 CA
128 CA
* * * **
17476537 AGTCTTATCTCCCTGAGGTTACAGTGAAGTAGACCGA--AGAATTTCAGATCTTATCTCCCTGAG
1 A-TCCTATCTCCCTGAAGTTACAGTG--G-AG-CGGATTAGAA-TAAAGATCTTATCTCCCTGAG
* * * * *
17476600 ATTACAGAGGAGTAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTGGGGCAGGTTGAA
60 GTTACAGAGGAGCAGATCGAAG-CACAAACCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAA
17476665 TATGCA
124 TATGCA
* * ** ** ** *
17476671 AGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGAT
1 A-TCCTATCTCCCTGAAGTTACAGTGGAGCGGA--TTAGAA-TAAAGATCTTATCTCCCTGAGGT
* *
17476736 TACAGAGGAGCAGATCGAAGCCACAAACCTTATCTCCCTGAAGTTACAGTAGG-GCAGGTTGAAT
62 TACAGAGGAGCAGATCGAAG-CACAAACCTTATCTCCCTGAGGTTACAGT-GGAGCAGATTGAAT
17476800 ATGCA
125 ATGCA
* * ** ** ** *
17476805 AGTCTTATCTCCCTGAGGTTACAGTGGAGTAGACCGAAGAATTTCAGATCTTATCTCCCTGAGAT
1 A-TCCTATCTCCCTGAAGTTACAGTGGAGCGGA--TTAGAA-TAAAGATCTTATCTCCCTGAGGT
* * * ** * **
17476870 TACAGAAGAGCAGATTGAAGCCACAAACCTTATCTCCCTGAGATTACAGAAGAGCAGATCGAAGC
62 TACAGAGGAGCAGATCGAAG-CACAAACCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAATA
**
17476935 CACA
126 TGCA
* * *
17476939 AACCTTATCTCCCTGAAGTTACAGTGGGGCAGG-TT-GAATATGCAAG-TTTTATCTCCCTGAGG
1 ATCC-TATCTCCCTGAAGTTACAGTGGAGC-GGATTAGAATA---AAGATCTTATCTCCCTGAGG
* * * * *
17477001 TTACAGTGGAGTAGACCGAAGAATTTCAAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGG
61 TTACAGAGGAGCAGATCGAAGCA---CAAACCTTATCTCCCTGAGGTTACAGTGGAGCAGATT-G
* *
17477066 AGCTA-GTA
122 A-ATATGCA
* * *
17477074 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAGAATAAAGGATCTCATCTCTCTGAAGTTAC
1 ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAGAATAAA-GATCTTATCTCCCTGAGGTTAC
* ***
17477139 AGTA-GAGTAGATC---GCATCAGGTCTTATCTCCCTGAGGTTACAGTGGAG
65 AG-AGGAGCAGATCGAAGCA-CAAACCTTATCTCCCTGAGGTTACAGTGGAG
17477187 TAAACCGAAG
Statistics
Matches: 653, Mismatches: 89, Indels: 74
0.80 0.11 0.09
Matches are distributed among these distances:
127 4 0.01
128 32 0.05
129 51 0.08
130 7 0.01
131 103 0.16
132 37 0.06
133 12 0.02
134 388 0.59
135 19 0.03
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (129 bp):
ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAGAATAAAGATCTTATCTCCCTGAGGTTACA
GAGGAGCAGATCGAAGCACAAACCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAATATGCA
Found at i:17477396 original size:40 final size:40
Alignment explanation
Indices: 17477254--17477398 Score: 125
Period size: 43 Copynumber: 3.5 Consensus size: 40
17477244 TGGTAGATCC
**
17477254 TATCTCCCTAAGCAGTAGTGGGGCAGATCGAAAATGGCGAA-TCT
1 TATCTCCCTAAGCAGTAGTGAAGCAGATC---AAT-GC-AAGTCT
* * * *
17477298 TATCTTCCTAAACAGTAGTGAAGCAGATTTAA-GCTACCAGTCC
1 TATCTCCCTAAGCAGTAGTGAAGCAGA-TCAATGC-A--AGTCT
17477341 TATCTCCCTAAGCAGTAGTGAAGCAGATCACAT-CAAGTCT
1 TATCTCCCTAAGCAGTAGTGAAGCAGATCA-ATGCAAGTCT
17477381 TATCTCCCTAAGCAGTAG
1 TATCTCCCTAAGCAGTAG
17477399 CGGAGTAGAC
Statistics
Matches: 84, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
40 25 0.30
42 6 0.07
43 29 0.35
44 23 0.27
45 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (40 bp):
TATCTCCCTAAGCAGTAGTGAAGCAGATCAATGCAAGTCT
Found at i:17478893 original size:3 final size:3
Alignment explanation
Indices: 17478873--17478918 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
17478863 TTTGTTAACT
* *
17478873 TTA TTA TT- TTA ATG TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA
17478918 T
1 T
17478919 AATATTTTCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17478939 original size:36 final size:37
Alignment explanation
Indices: 17478873--17478951 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 37
17478863 TTTGTTAACT
* * * *
17478873 TTATTATTTTAATGTTATTATTTATTATTATTAT-TA
1 TTATTATTATAATATTATTATTAATAATTATTATGTA
17478909 TTATTATTATAATATT-TTCATTAATAATTATTATGTA
1 TTATTATTATAATATTATT-ATTAATAATTATTATGTA
*
17478946 ATATTA
1 TTATTA
17478952 AATATATGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
35 2 0.06
36 27 0.75
37 7 0.19
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (37 bp):
TTATTATTATAATATTATTATTAATAATTATTATGTA
Found at i:17480108 original size:26 final size:26
Alignment explanation
Indices: 17480075--17480124 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
17480065 AATCACCTTT
17480075 TTTTTAATGTTTGTAGGGTTAAGACC
1 TTTTTAATGTTTGTAGGGTTAAGACC
17480101 TTTTTAATGTTTGTAGGGTTAAGA
1 TTTTTAATGTTTGTAGGGTTAAGA
17480125 ACTCAACATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (26 bp):
TTTTTAATGTTTGTAGGGTTAAGACC
Found at i:17483107 original size:43 final size:41
Alignment explanation
Indices: 17483045--17483162 Score: 121
Period size: 43 Copynumber: 2.8 Consensus size: 41
17483035 CAAATCAACC
*
17483045 AATTGTTTCGGTTTATCCAATGATGCACTATGCGAGCTAATAT
1 AATTGTTTCGATTTATCCAATGATGCACTATGCG-GC-AATAT
* * *
17483088 AATTGTTTCGATTTGTCCAA-GAATGCACCTTATGTGTCAATAT
1 AATTGTTTCGATTTATCCAATG-ATGCA-C-TATGCGGCAATAT
* **
17483131 AATTGCTTCGATTTATCTGATGATGCACTATG
1 AATTGTTTCGATTTATCCAATGATGCACTATG
17483163 TGTGTCAGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
41 4 0.06
42 2 0.03
43 49 0.78
44 3 0.05
45 5 0.08
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (41 bp):
AATTGTTTCGATTTATCCAATGATGCACTATGCGGCAATAT
Found at i:17483167 original size:43 final size:42
Alignment explanation
Indices: 17483045--17483177 Score: 119
Period size: 43 Copynumber: 3.1 Consensus size: 42
17483035 CAAATCAACC
* * *
17483045 AATTGTTTCGGTTTATCCAATGATGCACTATGCGAG-CTAATAT
1 AATTGTTTCGATTTAT-CAATGATGCACTATGTGTGTC-AATAT
* *
17483088 AATTGTTTCGATTTGTCCAA-GAATGCACCT-TATGTGTCAATAT
1 AATTGTTTCGATTTAT-CAATG-ATGCA-CTATGTGTGTCAATAT
* * *
17483131 AATTGCTTCGATTTATCTGATGATGCACTATGTGTGTCAGTAT
1 AATTGTTTCGATTTATC-AATGATGCACTATGTGTGTCAATAT
17483174 AATT
1 AATT
17483178 ACTCTGGTTT
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
42 4 0.05
43 66 0.89
44 4 0.05
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (42 bp):
AATTGTTTCGATTTATCAATGATGCACTATGTGTGTCAATAT
Found at i:17489540 original size:16 final size:16
Alignment explanation
Indices: 17489521--17489553 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17489511 AGGGTATATT
*
17489521 GTGATAATTATCTTAG
1 GTGATAATTACCTTAG
17489537 GTGATAATTACCTTAG
1 GTGATAATTACCTTAG
17489553 G
1 G
17489554 GTTTTTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (16 bp):
GTGATAATTACCTTAG
Found at i:17491357 original size:108 final size:105
Alignment explanation
Indices: 17491164--17491369 Score: 277
Period size: 108 Copynumber: 1.9 Consensus size: 105
17491154 AAATTCAAGA
* * * * *
17491164 GGATATTTGGCAATTTGGTTAAACGAGACATCGAAACCCAGCACCTTAGGGCACGTTCCTCGAAT
1 GGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGACAAGTTCCTCGAAT
*
17491229 TTCCAAACGCAAAACATTGCCTTATTTTGAAATTTTGGAG
66 TCCCAAACGCAAAACATTGCCTTATTTTGAAATTTTGGAG
* * * * *
17491269 GGATATTTAGCTATTTGGTTGAACGAGAAAAATCGACACCCAGCACATTAGGACATATTTTCTCG
1 GGATATTTAGCAATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGACA-AGTTCCTCG
*
17491334 AATTCCCAGACGCAAAACATTGCCTTATTTTGAAAT
63 AATTCCCAAACGCAAAACATTGCCTTATTTTGAAAT
17491370 ATTTTCCTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
105 24 0.28
107 22 0.26
108 40 0.47
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (105 bp):
GGATATTTAGCAATTTGGTTAAACGAGAAATCGAAACCCAGCACATTAGGACAAGTTCCTCGAAT
TCCCAAACGCAAAACATTGCCTTATTTTGAAATTTTGGAG
Found at i:17491825 original size:3 final size:3
Alignment explanation
Indices: 17491798--17491877 Score: 87
Period size: 3 Copynumber: 27.3 Consensus size: 3
17491788 TTAATATTAC
*
17491798 ATA ATA ATTA TTA ATGA A-A AT- ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA A-TA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
17491843 A-A ATA ATA ATA ATA ATA ATA ACA TTA A-A ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17491878 AGTTAACAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
2 8 0.12
3 53 0.82
4 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17491870 original size:26 final size:26
Alignment explanation
Indices: 17491819--17491877 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
17491809 TAATGAAAAT
*
17491819 ATAATAATAATAATAATAATAATAAA
1 ATAATAATAATAATAATAACAATAAA
*
17491845 ATAATAATAATAATAATAACATTAAA
1 ATAATAATAATAATAATAACAATAAA
17491871 ATAATAA
1 ATAATAA
17491878 AGTTAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
ATAATAATAATAATAATAACAATAAA
Found at i:17494361 original size:33 final size:33
Alignment explanation
Indices: 17494319--17494386 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
17494309 TTTTTTTAGT
* * *
17494319 TTTTTTTTTTTC-AGATT-TTAGAATATTTTCAA
1 TTTTTATTTTTCTAGATTCTTAAAAT-TTTTAAA
17494351 TTTTTATTTTTCTAGATTCTTAAAATTTTTAAA
1 TTTTTATTTTTCTAGATTCTTAAAATTTTTAAA
17494384 TTT
1 TTT
17494387 CATAGTTTCT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
32 11 0.35
33 14 0.45
34 6 0.19
ACGTcount: A:0.26, C:0.06, G:0.04, T:0.63
Consensus pattern (33 bp):
TTTTTATTTTTCTAGATTCTTAAAATTTTTAAA
Found at i:17494387 original size:25 final size:25
Alignment explanation
Indices: 17494349--17494400 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
17494339 GAATATTTTC
**
17494349 AATTTTTATTTTTC-TAGATTCTTAA
1 AATTTTTAAATTTCATAGATTC-TAA
*
17494374 AATTTTTAAATTTCATAGTTTCTAA
1 AATTTTTAAATTTCATAGATTCTAA
17494399 AA
1 AA
17494401 GCTATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (25 bp):
AATTTTTAAATTTCATAGATTCTAA
Found at i:17494512 original size:14 final size:14
Alignment explanation
Indices: 17494469--17494519 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
17494459 AAATTTAATA
*
17494469 TTTAAAATATTATTT
1 TTTAAATTA-TATTT
*
17494484 TTT-AATTTTAGTTT
1 TTTAAATTATA-TTT
17494498 TTTAAATTATATTT
1 TTTAAATTATATTT
*
17494512 TTAAAATT
1 TTTAAATT
17494520 TAAAACTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 2 0.07
14 19 0.63
15 9 0.30
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (14 bp):
TTTAAATTATATTT
Found at i:17494519 original size:29 final size:28
Alignment explanation
Indices: 17494447--17494520 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 28
17494437 TTAATATCTT
17494447 ATATATTTTTGAAAA-TTTAATATTTAAA
1 ATATATTTTT-AAAATTTTAATATTTAAA
* * *
17494475 ATATTATTTTT-TAATTTTAGTTTTTTAAA
1 ATA-TATTTTTAAAATTTTA-ATATTTAAA
*
17494504 TTATATTTTTAAAATTT
1 ATATATTTTTAAAATTT
17494521 AAAACTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.05
28 14 0.38
29 21 0.57
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (28 bp):
ATATATTTTTAAAATTTTAATATTTAAA
Found at i:17494521 original size:28 final size:27
Alignment explanation
Indices: 17494447--17494522 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
17494437 TTAATATCTT
17494447 ATATATTTTTGAAAATTTAATATTTAAA
1 ATATATTTTT-AAAATTTAATATTTAAA
* * * *
17494475 ATATTATTTTTTAATTTTAGTTTTTTAAA
1 ATA-TATTTTTAAAATTTA-ATATTTAAA
*
17494504 TTATATTTTTAAAATTTAA
1 ATATATTTTTAAAATTTAA
17494523 AACTTTTATT
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
28 22 0.58
29 16 0.42
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (27 bp):
ATATATTTTTAAAATTTAATATTTAAA
Found at i:17494946 original size:19 final size:18
Alignment explanation
Indices: 17494931--17494966 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17494921 TATAAAAACT
*
17494931 GAAAAATCATAAAAAATAA
1 GAAAAACCATAAAAAA-AA
17494950 GAAAAACCATAAAAAAA
1 GAAAAACCATAAAAAAA
17494967 TTTAAAAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 1 0.06
19 15 0.94
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.11
Consensus pattern (18 bp):
GAAAAACCATAAAAAAAA
Found at i:17495052 original size:17 final size:17
Alignment explanation
Indices: 17495029--17495102 Score: 57
Period size: 16 Copynumber: 4.4 Consensus size: 17
17495019 TGAAAATTGA
17495029 TATAAATTTATAAATAT
1 TATAAATTTATAAATAT
17495046 TATAAA-TTATAAA-ATT
1 TATAAATTTATAAATA-T
* *
17495062 CTAATAAATTATAAAAAAAT
1 -T-ATAAATT-TATAAATAT
*
17495082 TATAAAATTA-AAATAT
1 TATAAATTTATAAATAT
17495098 T-TAAA
1 TATAAA
17495103 CTTTTGTAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
15 5 0.10
16 14 0.29
17 9 0.19
18 11 0.23
19 2 0.04
20 6 0.12
21 1 0.02
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (17 bp):
TATAAATTTATAAATAT
Found at i:17495086 original size:18 final size:18
Alignment explanation
Indices: 17495029--17495087 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
17495019 TGAAAATTGA
*
17495029 TATAAATT-TATAAATAT
1 TATAAATTATAAAAATAT
* *
17495046 TATAAATTATAAAATTCT
1 TATAAATTATAAAAATAT
* *
17495064 AATAAATTATAAAAAAAT
1 TATAAATTATAAAAATAT
17495082 TATAAA
1 TATAAA
17495088 ATTAAAATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 8 0.24
18 25 0.76
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TATAAATTATAAAAATAT
Found at i:17495090 original size:8 final size:8
Alignment explanation
Indices: 17494987--17495091 Score: 70
Period size: 8 Copynumber: 11.9 Consensus size: 8
17494977 AGAAAGTAAA
17494987 AAAATTAT
1 AAAATTAT
*
17494995 AAAACTAT
1 AAAATTAT
17495003 AAAA-TAT
1 AAAATTAT
17495010 AAAAATATAT
1 -AAAAT-TAT
17495020 GAAAATTGAT
1 -AAAATT-AT
17495030 ATAAATTTAT
1 A-AAA-TTAT
17495040 AAATATTAT
1 AAA-ATTAT
17495049 -AAATTAT
1 AAAATTAT
*
17495056 AAAATTCT
1 AAAATTAT
17495064 AATAAATTAT
1 -A-AAATTAT
17495074 AAAAAAATTAT
1 ---AAAATTAT
17495085 AAAATTA
1 AAAATTA
17495092 AAATATTTAA
Statistics
Matches: 81, Mismatches: 4, Indels: 24
0.74 0.04 0.22
Matches are distributed among these distances:
7 8 0.10
8 30 0.37
9 9 0.11
10 23 0.28
11 9 0.11
12 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (8 bp):
AAAATTAT
Found at i:17495123 original size:21 final size:22
Alignment explanation
Indices: 17495091--17495140 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
17495081 TTATAAAATT
* *
17495091 AAAAT-AT-TTAAACTTTTGTA
1 AAAATCATATTAAACTTCTATA
17495111 AAAA-CATATTAAACTTCTATA
1 AAAATCATATTAAACTTCTATA
17495132 AAAATCATA
1 AAAATCATA
17495141 ACTATTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 6 0.24
21 15 0.60
22 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.02, T:0.36
Consensus pattern (22 bp):
AAAATCATATTAAACTTCTATA
Found at i:17495689 original size:19 final size:20
Alignment explanation
Indices: 17495648--17495689 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
17495638 CAATTTTAAT
*
17495648 ATTTTTATATTTTTTTTACA
1 ATTTTTATATTATTTTTACA
*
17495668 ATTTTT-TATTATTTTTAGA
1 ATTTTTATATTATTTTTACA
17495687 ATT
1 ATT
17495690 CTAAAACGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.69
Consensus pattern (20 bp):
ATTTTTATATTATTTTTACA
Found at i:17495745 original size:27 final size:26
Alignment explanation
Indices: 17495671--17495746 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
17495661 TTTTACAATT
* * *
17495671 TTTTATTATTTTTAGAATTCTAAAACG
1 TTTTATTAATTTTAAAATT-TAAAAAG
*
17495698 TTTTTTTAATTTTAAATATTTAAACAAG
1 TTTTATTAATTTTAAA-ATTTAAA-AAG
*
17495726 TTTTATTAATTTTATAATTTA
1 TTTTATTAATTTTAAAATTTA
17495747 TTAGATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (26 bp):
TTTTATTAATTTTAAAATTTAAAAAG
Found at i:17495757 original size:28 final size:28
Alignment explanation
Indices: 17495670--17495792 Score: 71
Period size: 28 Copynumber: 4.5 Consensus size: 28
17495660 TTTTTACAAT
* * * *
17495670 TTTTTATTATTTTTAGAAT-TCTAAAACG
1 TTTTTATTAATTTTATAATATATATAA-G
* *
17495698 TTTTT-TTAATTTTA-AATATTTAAACAAG
1 TTTTTATTAATTTTATAATA--TATATAAG
* *
17495726 -TTTTATTAATTTTATAATTTAT-TAGAT
1 TTTTTATTAATTTTATAATATATATA-AG
*
17495753 TTTTTGTT--TTTTATAATATATATAAG
1 TTTTTATTAATTTTATAATATATATAAG
*
17495779 TTTTTATAAATTTT
1 TTTTTATTAATTTT
17495793 TTTATAATTT
Statistics
Matches: 72, Mismatches: 13, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
26 23 0.32
27 17 0.24
28 25 0.35
29 7 0.10
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.59
Consensus pattern (28 bp):
TTTTTATTAATTTTATAATATATATAAG
Found at i:17495797 original size:31 final size:31
Alignment explanation
Indices: 17495759--17495822 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
17495749 AGATTTTTTG
*
17495759 TTTTTTATAA-TATATATAAGTTTTTATAAAT
1 TTTTTTATAATTATA-ATAAGTTTATATAAAT
* *
17495790 TTTTTTATAATTTTAATAAGTTTATATCAAT
1 TTTTTTATAATTATAATAAGTTTATATAAAT
17495821 TT
1 TT
17495823 AAATAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (31 bp):
TTTTTTATAATTATAATAAGTTTATATAAAT
Found at i:17495803 original size:9 final size:9
Alignment explanation
Indices: 17495726--17495885 Score: 50
Period size: 9 Copynumber: 17.7 Consensus size: 9
17495716 TTTAAACAAG
17495726 TTTTATTAA-
1 TTTTA-TAAT
17495735 TTTTATAAT
1 TTTTATAAT
*
17495744 TTATTA-GAT
1 TT-TTATAAT
**
17495753 TTTT-TGTT
1 TTTTATAAT
17495761 TTTTATAAT
1 TTTTATAAT
* *
17495770 ATATATAAGT
1 TTTTATAA-T
17495780 TTTTATAAATTT
1 TTTTAT-AA--T
17495792 TTTTATAAT
1 TTTTATAAT
*
17495801 TTTAATAAGT
1 TTTTATAA-T
*
17495811 TTATATCAAT
1 TTTTAT-AAT
**
17495821 TTAAATAA-
1 TTTTATAAT
17495829 TTTT-T-AT
1 TTTTATAAT
*
17495836 TTTTATACT
1 TTTTATAAT
17495845 TTATCTA-AAT
1 TT-T-TATAAT
17495855 TTTTAT--T
1 TTTTATAAT
* *
17495862 TTTAATATT
1 TTTTATAAT
*
17495871 TTTTATGAT
1 TTTTATAAT
17495880 TTTTAT
1 TTTTAT
17495886 GGGAAAATAT
Statistics
Matches: 113, Mismatches: 21, Indels: 34
0.67 0.12 0.20
Matches are distributed among these distances:
6 1 0.01
7 11 0.10
8 16 0.14
9 46 0.41
10 24 0.21
11 8 0.07
12 7 0.06
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:17497938 original size:23 final size:25
Alignment explanation
Indices: 17497895--17497947 Score: 58
Period size: 23 Copynumber: 2.2 Consensus size: 25
17497885 AATTTTATAT
*
17497895 TTTTATGATTAAAAAA-TTAAAT-A
1 TTTTATGATTAAAAAAGTAAAATAA
*
17497918 TTTTAT-ATTTAAAATAGTAAAATAA
1 TTTTATGA-TTAAAAAAGTAAAATAA
17497943 TTTTA
1 TTTTA
17497948 AAATATTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
22 1 0.04
23 13 0.52
24 5 0.20
25 6 0.24
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTTATGATTAAAAAAGTAAAATAA
Found at i:17509725 original size:14 final size:15
Alignment explanation
Indices: 17509702--17509748 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
17509692 AAATTTAATT
*
17509702 TTAAAAAAAATTAAA
1 TTAATAAAAATTAAA
17509717 TTAATAAAAATATAAA
1 TTAATAAAAAT-TAAA
*
17509733 -TATTAAAAATTAAA
1 TTAATAAAAATTAAA
17509747 TT
1 TT
17509749 TATCATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 4 0.14
15 20 0.71
16 4 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TTAATAAAAATTAAA
Found at i:17510120 original size:20 final size:18
Alignment explanation
Indices: 17510068--17510120 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
17510058 TTTCCGATAA
17510068 TTGGATTTGATTTTAGGTT
1 TTGGATTT-ATTTTAGGTT
** *
17510087 TTTTATTTAATTTAGGGTT
1 TTGGATTTATTTTA-GGTT
17510106 TTAGGATTTATTTTA
1 TT-GGATTTATTTTA
17510121 ATAATATGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 5 0.19
19 12 0.46
20 9 0.35
ACGTcount: A:0.21, C:0.00, G:0.19, T:0.60
Consensus pattern (18 bp):
TTGGATTTATTTTAGGTT
Done.