Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 3 of 133
Found at i:524983 original size:15 final size:15
Alignment explanation
Indices: 524894--524983 Score: 55
Period size: 15 Copynumber: 6.0 Consensus size: 15
524884 TTATTTAATT
*
524894 TTTAAAATTAATAAA
1 TTTAAAATTAATTAA
*
524909 TTTAATTCAATTAATAAA
1 TTTAA---AATTAATTAA
**
524927 AATAAAA-TAA-TAA
1 TTTAAAATTAATTAA
524940 TTT--AATTAATTTAA
1 TTTAAAATTAA-TTAA
*
524954 TTTTAAA-TAATTTAA
1 TTTAAAATTAA-TTAA
524969 TTTAAAATTAATTAA
1 TTTAAAATTAATTAA
524984 ATCGATCGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
11 2 0.03
12 3 0.05
13 3 0.05
14 9 0.15
15 25 0.42
16 5 0.08
18 13 0.22
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTAAAATTAATTAA
Found at i:524983 original size:24 final size:23
Alignment explanation
Indices: 524935--524985 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
524925 AAAATAAAAT
*
524935 AATAATTTAATTAATTTAATTTTA
1 AATAATTTAATTAAATTAA-TTTA
524959 AATAATTTAATTTAAAATTAA-TTA
1 AATAATTTAA-TT-AAATTAATTTA
524983 AAT
1 AAT
524986 CGATCGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 16 0.67
25 2 0.08
26 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATAATTTAATTAAATTAATTTA
Found at i:525144 original size:13 final size:13
Alignment explanation
Indices: 525126--525173 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
525116 TCATGTCAAT
525126 TAATTTAATAAAA
1 TAATTTAATAAAA
*
525139 TAATTTTATAAAA
1 TAATTTAATAAAA
525152 TGTAATTTAATAAAA
1 --TAATTTAATAAAA
525167 T-ATTTAA
1 TAATTTAA
525174 AATATCAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 6 0.19
13 13 0.42
15 12 0.39
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TAATTTAATAAAA
Found at i:525159 original size:15 final size:14
Alignment explanation
Indices: 525123--525167 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 14
525113 ATATCATGTC
525123 AATTAATTTAATAA
1 AATTAATTTAATAA
*
525137 AA-TAATTTTATAA
1 AATTAATTTAATAA
525150 AATGTAATTTAATAA
1 AAT-TAATTTAATAA
525165 AAT
1 AAT
525168 ATTTAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
13 12 0.44
14 2 0.07
15 13 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (14 bp):
AATTAATTTAATAA
Found at i:527028 original size:12 final size:13
Alignment explanation
Indices: 527011--527039 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
527001 TGTTTTGTGG
527011 TTTTA-TTTTATT
1 TTTTATTTTTATT
527023 TTTTATTTTTATT
1 TTTTATTTTTATT
527036 TTTT
1 TTTT
527040 TATTGTGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTATTTTTATT
Found at i:532109 original size:14 final size:14
Alignment explanation
Indices: 532092--532121 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
532082 TATTAAAAAA
532092 TTTTTTCAAACTTT
1 TTTTTTCAAACTTT
*
532106 TTTTTTCGAACTTT
1 TTTTTTCAAACTTT
532120 TT
1 TT
532122 CTCCAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.13, G:0.03, T:0.67
Consensus pattern (14 bp):
TTTTTTCAAACTTT
Found at i:533801 original size:63 final size:63
Alignment explanation
Indices: 533680--533803 Score: 146
Period size: 63 Copynumber: 2.0 Consensus size: 63
533670 ATATTAAATA
* **
533680 TAAATTCATAAAAAACCTCCTCTAGATTATCTCATTTATGACTTTAACATGGGTTGTTCGATG
1 TAAATTCATAAAAAACCTCCTCTAGATTATCTCATCTATGACTACAACATGGGTTGTTCGATG
* * *
533743 TAAATTCATAAAATAA-C-CCTCCTGGGTTATCTCATCTATGACTACAACGTGCGG-TGTTCGA
1 TAAATTCATAAAA-AACCTCCT-CTAGATTATCTCATCTATGACTACAACATG-GGTTGTTCGA
533804 CCAGTTGCAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
62 3 0.06
63 45 0.87
64 4 0.08
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.35
Consensus pattern (63 bp):
TAAATTCATAAAAAACCTCCTCTAGATTATCTCATCTATGACTACAACATGGGTTGTTCGATG
Found at i:534054 original size:19 final size:19
Alignment explanation
Indices: 534030--534072 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
534020 ATTCGGATCA
534030 CTGACTTTTTACCATTTAC
1 CTGACTTTTTACCATTTAC
534049 CTGACTTTTTACCATTTAC
1 CTGACTTTTTACCATTTAC
534068 CTGAC
1 CTGAC
534073 AGAAATAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (19 bp):
CTGACTTTTTACCATTTAC
Found at i:539912 original size:22 final size:23
Alignment explanation
Indices: 539860--539904 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
539850 AACATACACG
*
539860 AAAAAACACACACAAATAGGAAA
1 AAAAAACACACACAAAGAGGAAA
*
539883 AAAAAACACA-ACAGAGAGGAAA
1 AAAAAACACACACAAAGAGGAAA
539905 CATAAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.69, C:0.16, G:0.13, T:0.02
Consensus pattern (23 bp):
AAAAAACACACACAAAGAGGAAA
Found at i:550174 original size:9 final size:9
Alignment explanation
Indices: 550144--550177 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
550134 TGTATTGACT
550144 ATGCTCATAA
1 ATGC-CATAA
*
550154 ATACCATAA
1 ATGCCATAA
550163 ATGCCATAA
1 ATGCCATAA
550172 ATGCCA
1 ATGCCA
550178 GATATATGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 19 0.86
10 3 0.14
ACGTcount: A:0.44, C:0.24, G:0.09, T:0.24
Consensus pattern (9 bp):
ATGCCATAA
Found at i:551130 original size:23 final size:23
Alignment explanation
Indices: 551100--551163 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
551090 GTACTATGCT
551100 TGAAAAAAAAGAAAAAAATGAAA
1 TGAAAAAAAAGAAAAAAATGAAA
*
551123 TGAAAAAAATGAAAAAAATGAAA
1 TGAAAAAAAAGAAAAAAATGAAA
551146 --AAAATGAAAAGAAAAAAA
1 TGAAAA--AAAAGAAAAAAA
551164 AAGTGAATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.11
23 33 0.89
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (23 bp):
TGAAAAAAAAGAAAAAAATGAAA
Found at i:551140 original size:32 final size:32
Alignment explanation
Indices: 551100--551163 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
551090 GTACTATGCT
*
551100 TGAAAAAAAAGAAAAAAATGAAATGAAAAAAA
1 TGAAAAAAAAGAAAAAAATGAAAAGAAAAAAA
*
551132 TGAAAAAAATGAAAAAAATGAAAAGAAAAAAA
1 TGAAAAAAAAGAAAAAAATGAAAAGAAAAAAA
551164 AAGTGAATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (32 bp):
TGAAAAAAAAGAAAAAAATGAAAAGAAAAAAA
Found at i:551177 original size:16 final size:16
Alignment explanation
Indices: 551111--551170 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 16
551101 GAAAAAAAAG
*
551111 AAAAAAATGAAATG--
1 AAAAAAATGAAAAGAA
*
551125 AAAAAAATGAAAAAAA
1 AAAAAAATGAAAAGAA
551141 TGAAAAAAATGAAAAGAA
1 --AAAAAAATGAAAAGAA
551159 AAAAAAAGTGAA
1 AAAAAAA-TGAA
551171 TGAAAAAGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
14 12 0.32
16 7 0.18
17 4 0.11
18 15 0.39
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.10
Consensus pattern (16 bp):
AAAAAAATGAAAAGAA
Found at i:552301 original size:43 final size:42
Alignment explanation
Indices: 552197--552313 Score: 119
Period size: 43 Copynumber: 2.7 Consensus size: 42
552187 GCATTTACAT
* ** *
552197 CCAAAGTTGTGGTGCCTCTGTTTAGAAAAGCAATTTATTTTT
1 CCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTATTTTC
* *
552239 CAAAAGTCATG-GTTGCCTCTGTTTAGAGGAGCAATTTATTGTTC
1 CCAAAGT--TGTGATGCCTCTGTTTAGAGGAGCAATTTATT-TTC
* **
552283 CCAAAGTTGTGATACCTCTAATTAGAGGAGC
1 CCAAAGTTGTGATGCCTCTGTTTAGAGGAGC
552314 TTTGTTTATT
Statistics
Matches: 61, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
42 8 0.13
43 43 0.70
44 10 0.16
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.35
Consensus pattern (42 bp):
CCAAAGTTGTGATGCCTCTGTTTAGAGGAGCAATTTATTTTC
Found at i:552345 original size:44 final size:43
Alignment explanation
Indices: 552297--552657 Score: 255
Period size: 44 Copynumber: 8.5 Consensus size: 43
552287 AGTTGTGATA
* *
552297 CCTCTAATTAGAGGAGCTTTGTTTATTTTTTTAAAGTCATTAAG
1 CCTCTGATTAGAGGAGCTTTGTTTATTTTTTT-AAGTCATTGAG
* * * * *
552341 CCTCTGTTTAGAGGAGCTTTATTT-GTTGTTTAAGTCATTGAA
1 CCTCTGATTAGAGGAGCTTTGTTTATTTTTTTAAGTCATTGAG
* ** *
552383 CCTCTGATTAGAAGAGC--CATTTATTTTTTTAAGTCGTTGAG
1 CCTCTGATTAGAGGAGCTTTGTTTATTTTTTTAAGTCATTGAG
*
552424 CCTCT-ATTTAGAGGAGC-TTGATTTATTTTTTCAAAGTCATTGAG
1 CCTCTGA-TTAGAGGAGCTTTG-TTTATTTTTT-TAAGTCATTGAG
** * *
552468 CCTCTGATTAGAGGAGC--CATTTA-TTTTTTAAGTCGTTGAA
1 CCTCTGATTAGAGGAGCTTTGTTTATTTTTTTAAGTCATTGAG
* * * *
552508 CTTCTGTTTAGAGGAG-TTTGATTTATTTTTTCAAAGTCATCGAG
1 CCTCTGATTAGAGGAGCTTTG-TTTATTTTTT-TAAGTCATTGAG
** * * *
552552 CCTCTGATTAGAGGAGC--CATTTA-TTTTTTAGGTCGTGGAG
1 CCTCTGATTAGAGGAGCTTTGTTTATTTTTTTAAGTCATTGAG
* * * *
552592 CTTCT-ATTTAGAGAAACTTTGTTTATTTTTTTTAAAGTCGTTGAG
1 CCTCTGA-TTAGAGGAGCTTTGTTTA-TTTTTTT-AAGTCATTGAG
* *
552637 CCT-TTACTTAGAAGAGCTTTG
1 CCTCTGA-TTAGAGGAGCTTTG
552658 ATCAAAATTT
Statistics
Matches: 246, Mismatches: 52, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
39 1 0.00
40 48 0.20
41 38 0.15
42 40 0.16
43 20 0.08
44 75 0.30
45 24 0.10
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (43 bp):
CCTCTGATTAGAGGAGCTTTGTTTATTTTTTTAAGTCATTGAG
Found at i:552451 original size:127 final size:126
Alignment explanation
Indices: 552297--552580 Score: 326
Period size: 127 Copynumber: 2.2 Consensus size: 126
552287 AGTTGTGATA
* * *
552297 CCTCTAATTAGAGGAGCTTTG-TTTATTTTTTTAAAGTCATTAAGCCTCTGTTTAGAGGAGCTTT
1 CCTCT-ATTAGAGGAGC-TTGATTTATTTTTTCAAAGTCATTAAGCCTCTGATTAGAGGAGC--C
* * * *
552361 ATTTGTTGTTTAAGTCATTGAACCTCTGATTAGAAGAG-CCATTTATTTTTT-TAAGTCGTTGAG
62 ATTTATTGTTTAAGTCATTGAACCTCTGATTAGAAGAGTCCATTTATTTTTTCAAAGTCATCGAG
*
552424 CCTCTATTTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCATT
1 CCTCTA-TTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTAAGCCTCTGATTAGAGGAGCCATT
* * * * * **
552489 TATTTTTTAAGTCGTTGAACTTCTGTTTAGAGGAGTTTGATTTATTTTTTCAAAGTCATCGAG
65 TATTGTTTAAGTCATTGAACCTCTGATTAGAAGAG-TCCATTTATTTTTTCAAAGTCATCGAG
*
552552 CCTCTGATTAGAGGAGC--CATTTATTTTTT
1 CCTCT-ATTAGAGGAGCTTGATTTATTTTTT
552581 AGGTCGTGGA
Statistics
Matches: 135, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
125 32 0.24
126 15 0.11
127 63 0.47
128 24 0.18
129 1 0.01
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (126 bp):
CCTCTATTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTAAGCCTCTGATTAGAGGAGCCATTT
ATTGTTTAAGTCATTGAACCTCTGATTAGAAGAGTCCATTTATTTTTTCAAAGTCATCGAG
Found at i:552485 original size:85 final size:84
Alignment explanation
Indices: 552318--552639 Score: 398
Period size: 84 Copynumber: 3.8 Consensus size: 84
552308 AGGAGCTTTG
* * * * * *
552318 TTTATTTTTTTAAAGTCATTAAGCCTCTGTTTAGAGGAGCTTTATTTGTTGTTT--AAGTCATTG
1 TTTA-TTTTTT-AAGTCGTTGAGCCTCTATTTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTG
* *
552381 AACCTCTGATTAGAAGAGCCA
64 AGCCTCTGATTAGAGGAGCCA
552402 TTTATTTTTTTAAGTCGTTGAGCCTCTATTTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTGA
1 TTTA-TTTTTTAAGTCGTTGAGCCTCTATTTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTGA
552467 GCCTCTGATTAGAGGAGCCA
65 GCCTCTGATTAGAGGAGCCA
* * * * *
552487 TTTATTTTTTAAGTCGTTGAACTTCTGTTTAGAGGAGTTTGATTTATTTTTTCAAAGTCATCGAG
1 TTTATTTTTTAAGTCGTTGAGCCTCTATTTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTGAG
552552 CCTCTGATTAGAGGAGCCA
66 CCTCTGATTAGAGGAGCCA
* * * * * * *
552571 TTTATTTTTTAGGTCGTGGAGCTTCTATTTAGAGAAACTTTG-TTTATTTTTTTTAAAGTCGTTG
1 TTTATTTTTTAAGTCGTTGAGCCTCTATTTAGAGGAGC-TTGATTTA-TTTTTTCAAAGTCATTG
552635 AGCCT
64 AGCCT
552640 TTACTTAGAA
Statistics
Matches: 211, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
83 36 0.17
84 121 0.57
85 54 0.26
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (84 bp):
TTTATTTTTTAAGTCGTTGAGCCTCTATTTAGAGGAGCTTGATTTATTTTTTCAAAGTCATTGAG
CCTCTGATTAGAGGAGCCA
Found at i:552496 original size:169 final size:168
Alignment explanation
Indices: 552318--552639 Score: 420
Period size: 169 Copynumber: 1.9 Consensus size: 168
552308 AGGAGCTTTG
* *
552318 TTTATTTTTTTAAAGTCATT-AAGCCTCTGTTTAGAGGAGCTTT-ATTTGTTGTTT-AAGTCATT
1 TTTA-TTTTTT-AAGTCATTGAA-CCTCTGTTTAGAGGAG-TTTGATTTATTGTTTAAAGTCATC
* * *
552380 GAACCTCTGATTAGAAGAGCCATTTATTTTTTTAAGTCGTTGAGCCTCTATTTAGAGGAGC-TTG
62 GAACCTCTGATTAGAAGAGCCATTTA-TTTTTTAAGTCGTGGAGCCTCTATTTAGAGAAACTTTG
552444 ATTTA-TTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCA
126 -TTTATTTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCA
* * * *
552487 TTTATTTTTTAAGTCGTTGAACTTCTGTTTAGAGGAGTTTGATTTATTTTTTCAAAGTCATCGAG
1 TTTATTTTTTAAGTCATTGAACCTCTGTTTAGAGGAGTTTGATTTATTGTTT-AAAGTCATCGAA
* * *
552552 CCTCTGATTAGAGGAGCCATTTATTTTTTAGGTCGTGGAGCTTCTATTTAGAGAAACTTTGTTTA
65 CCTCTGATTAGAAGAGCCATTTATTTTTTAAGTCGTGGAGCCTCTATTTAGAGAAACTTTGTTTA
* *
552617 TTTTTTTTAAAGTCGTTGAGCCT
130 TTTTTTTCAAAGTCATTGAGCCT
552640 TTACTTAGAA
Statistics
Matches: 133, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
166 3 0.02
167 31 0.23
168 41 0.31
169 58 0.44
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (168 bp):
TTTATTTTTTAAGTCATTGAACCTCTGTTTAGAGGAGTTTGATTTATTGTTTAAAGTCATCGAAC
CTCTGATTAGAAGAGCCATTTATTTTTTAAGTCGTGGAGCCTCTATTTAGAGAAACTTTGTTTAT
TTTTTTCAAAGTCATTGAGCCTCTGATTAGAGGAGCCA
Found at i:552986 original size:57 final size:53
Alignment explanation
Indices: 552845--552986 Score: 139
Period size: 52 Copynumber: 2.7 Consensus size: 53
552835 TTATTTTTTA
* * * *
552845 TTTTTATTTATTTATAAATATATTTAT-TATTATTATTATTTATCTTTTAATT
1 TTTTTATTTATCTATCAATATATTTATCTATTTTTATTATTTATCTTATAATT
* * * *
552897 TTTTTATTTATCTATTAATATATATA-C-GTTTTTATTATTTAT-TAATATATTT
1 TTTTTATTTATCTATCAATATATTTATCTATTTTTATTATTTATCT--TATAATT
552949 TTTGTTATTTATCTATCAATGTATATTTATCTATTTTT
1 TTT-TTATTTATCTATCAA--TATATTTATCTATTTTT
552987 TTTTTTAGGT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
50 1 0.01
51 13 0.18
52 31 0.43
53 14 0.19
55 7 0.10
56 1 0.01
57 5 0.07
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (53 bp):
TTTTTATTTATCTATCAATATATTTATCTATTTTTATTATTTATCTTATAATT
Found at i:553835 original size:5 final size:5
Alignment explanation
Indices: 553825--553852 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
553815 TTTAGTACTC
553825 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
553853 TTAAATGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:553958 original size:58 final size:59
Alignment explanation
Indices: 553882--554097 Score: 237
Period size: 58 Copynumber: 3.7 Consensus size: 59
553872 TAAAATTCCA
*
553882 AAAAATATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGTTTTCT
1 AAAAAGATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGTTTTCT
* *
553941 AAAAA-ATATTTTCGAGGAAAAGTTAAAAGTATCAATTTTCTTTGAAAATAA-TTTTCT
1 AAAAAGATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGTTTTCT
* * * * *
553998 AAAAAAGGATTTTTTTTTAGGAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAG-TTTC-
1 -AAAAA-GA-TATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAAT-AAGTTTTCT
* * * *
554059 AGAAAA-ACA-TCTTGGGGAAAAGTTGAAAGTATCAATTTT
1 A-AAAAGATATTTTTGAGGAAAAGTTAAAAGTATCAATTTT
554098 TTTTGTACAA
Statistics
Matches: 135, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
57 32 0.24
58 49 0.36
59 6 0.04
60 2 0.01
61 40 0.30
62 6 0.04
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (59 bp):
AAAAAGATATTTTTGAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATAAGTTTTCT
Found at i:559970 original size:6 final size:6
Alignment explanation
Indices: 559951--559981 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
559941 AGGTTGCACA
*
559951 ACCATG ACCTTG ACCATG ACCATG ACCATG A
1 ACCATG ACCATG ACCATG ACCATG ACCATG A
559982 TGTTGAATAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.32, C:0.32, G:0.16, T:0.19
Consensus pattern (6 bp):
ACCATG
Found at i:560133 original size:21 final size:21
Alignment explanation
Indices: 560088--560133 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
560078 ACTGGTCATG
* *
560088 AAAACAGCAAAACATGATTAA
1 AAAAAAGCAAAACATGATGAA
* *
560109 AAAAAAGCAGAACATGATGAC
1 AAAAAAGCAAAACATGATGAA
560130 AAAA
1 AAAA
560134 TCCCTTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.63, C:0.13, G:0.13, T:0.11
Consensus pattern (21 bp):
AAAAAAGCAAAACATGATGAA
Found at i:562338 original size:28 final size:28
Alignment explanation
Indices: 562284--562339 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
562274 AATTCATTAG
*
562284 ATTATCAATTTATCACTTATTTTTTATT
1 ATTATCAATTTATCACTTATTTGTTATT
562312 ATTATCAA-TTATCATCATTA-TTGTTATT
1 ATTATCAATTTATCA-C-TTATTTGTTATT
562340 TTTTCGTTAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 16 0.64
29 3 0.12
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTATCAATTTATCACTTATTTGTTATT
Found at i:563647 original size:43 final size:43
Alignment explanation
Indices: 563599--563683 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
563589 TTTGTACAAA
* * *
563599 GAAAATTGATACTTTCAATTTTTCCTTAAAATATTTTTTTAAG
1 GAAAATTGATACTTCCAACTTTTCCCTAAAATATTTTTTTAAG
*
563642 GAAAATTGGTACTTCCAACTTTTCCCTAAAATATTTTTTTAA
1 GAAAATTGATACTTCCAACTTTTCCCTAAAATATTTTTTTAA
563684 AACTTTAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (43 bp):
GAAAATTGATACTTCCAACTTTTCCCTAAAATATTTTTTTAAG
Found at i:563795 original size:58 final size:58
Alignment explanation
Indices: 563631--563817 Score: 226
Period size: 57 Copynumber: 3.3 Consensus size: 58
563621 TCCTTAAAAT
* * *
563631 ATTT-TTTT-AAGGAAAATTGGTACTTCCAACTTTTCCCT-AAAATATTTTTTTA-AA
1 ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAGAA
* * *
563685 ACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCTTAAAAATA-TTTTTTAGAA
1 A-TTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAGAA
* * *
563743 AATTATTTTCAAGGAAAATTAATACTTTTAACTTTTCCTTAAAAATATTTTTTTAGAA
1 ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAGAA
*
563801 TTTTATTTT-AA-GAAAAT
1 ATTTATTTTCAAGGAAAAT
563818 CATTTAAAAA
Statistics
Matches: 113, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
54 1 0.01
55 3 0.03
56 9 0.08
57 74 0.65
58 26 0.23
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.46
Consensus pattern (58 bp):
ATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTCCTTAAAAATATTTTTTTAGAA
Found at i:564643 original size:16 final size:16
Alignment explanation
Indices: 564622--564705 Score: 58
Period size: 16 Copynumber: 5.6 Consensus size: 16
564612 AAAATAAAAA
564622 TAATAGATAAATATAT
1 TAATAGATAAATATAT
*
564638 TAATAGAT-AA-CTA-
1 TAATAGATAAATATAT
564651 -AA-AGA-AAATA-AT
1 TAATAGATAAATATAT
* *
564663 TAGATAAATAAAAAATAT
1 TA-ATAGAT-AAATATAT
*
564681 TAATAGATAAATATAA
1 TAATAGATAAATATAT
564697 TAATA-ATAA
1 TAATAGATAA
564706 TAATCATAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 19
0.67 0.09 0.24
Matches are distributed among these distances:
11 6 0.12
12 2 0.04
13 1 0.02
14 3 0.06
15 8 0.15
16 19 0.37
17 9 0.17
18 4 0.08
ACGTcount: A:0.63, C:0.01, G:0.06, T:0.30
Consensus pattern (16 bp):
TAATAGATAAATATAT
Found at i:564679 original size:19 final size:20
Alignment explanation
Indices: 564655--564703 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
564645 TAACTAAAAG
564655 AAAATAATTAGATAAATA-A
1 AAAATAATTAGATAAATATA
*
564674 AAAATATTAATAGATAAATATA
1 AAAATA--ATTAGATAAATATA
*
564696 ATAATAAT
1 AAAATAAT
564704 AATAATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 11 0.46
22 6 0.25
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (20 bp):
AAAATAATTAGATAAATATA
Found at i:564701 original size:22 final size:21
Alignment explanation
Indices: 564610--564729 Score: 86
Period size: 22 Copynumber: 5.6 Consensus size: 21
564600 ATCTCAGCCA
* *
564610 AAAAAATAAAAATA-ATAGAT
1 AAAAAATAATAATAGATAAAT
* * *
564630 -AAATATATTAATAGATAACT
1 AAAAAATAATAATAGATAAAT
564650 AAAAGAA-AATAATTAGATAAAT
1 AAAA-AATAATAA-TAGATAAAT
*
564672 AAAAAATATTAATAGATAAAT
1 AAAAAATAATAATAGATAAAT
*
564693 ATAATAATAATAATA-ATCATAAT
1 A-AAAAATAATAATAGAT-A-AAT
*
564716 AATAAAAAAATAAT
1 AA-AAAATAATAAT
564730 TAAATTAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
19 10 0.13
20 4 0.05
21 21 0.27
22 30 0.38
23 13 0.17
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAAATAATAATAGATAAAT
Found at i:565129 original size:43 final size:41
Alignment explanation
Indices: 564935--565408 Score: 240
Period size: 41 Copynumber: 11.2 Consensus size: 41
564925 TTTTAGTCAA
** * * *
564935 AGCTCCTCTAAGTAGAAGCTTAACGACTTTGAATAAAATAAACAA
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTG-A-AAAAT-AA-AT
* * * * *
564980 AGGTCTTCTAAACAGAGGCTCCATGACTTTG-AAAGTAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * ** *
565020 GGCTCATCTAATCAGAAACTTAACGACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
* * * *
565061 GGCTCATCTAATCAGAGGCTTAACGACTTTGAAAAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
*
565102 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTAAAAAATAGAAT
1 --AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATA-AAT
** *
565146 -GCT-CTCCTAGTCAGAGGCTCAACGACTTTTG-AAAATAAACAA
1 AGCTCCT-CTAAACAGAGGCTCAACGAC-TTTGAAAAAT-AA-AT
* ** * *
565188 AACTCCTCTAATGAGAGGCTCAATGAC-TTGAAAGAAAATAAACAA
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTG--A-AAAAT-AA-AT
* * * *
565233 AGCTTCTCTAATCAAAGGCTCAACGACTTTGGGAACAATAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTT--GAAAAATAAAT
* * * * * * *
565276 TGCTCCTTTAAATAGAGGCAACCATGACTTTTGAAAGATAAAT
1 AGCTCCTCTAAACAGAGGC-TCAACGAC-TTTGAAAAATAAAT
* * * * * *
565319 TGCTTCTCTAAACAGAAGCACCACAACTTTGAAAAAGTAAAT
1 AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAA-TAAAT
* * * * *
565361 TGTTTCTCTAAACAGAGGCATC-ACAACTTTGAAAGATAAAT
1 AGCTCCTCTAAACAGAGGC-TCAACGACTTTGAAAAATAAAT
*
565402 TGCTCCT
1 AGCTCCT
565409 TGACAATCAT
Statistics
Matches: 342, Mismatches: 66, Indels: 46
0.75 0.15 0.10
Matches are distributed among these distances:
40 25 0.07
41 97 0.28
42 50 0.15
43 91 0.27
44 12 0.04
45 63 0.18
46 3 0.01
48 1 0.00
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (41 bp):
AGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAT
Found at i:565160 original size:84 final size:84
Alignment explanation
Indices: 565041--565262 Score: 236
Period size: 84 Copynumber: 2.6 Consensus size: 84
565031 TCAGAAACTT
* * *
565041 AACGACTTTGAAAAATAAATGGCTCATCTAATCAGAGGCTTAACGAC-TTTGAAAAATAAATAAA
1 AACGACTTTAAAAAATAAATGGCTCATCTAATCAGAGGCTCAACGACTTTTG-AAAATAAACAAA
*
565105 GCTCCTCTAAACAGAGGCTC
65 ACTCCTCTAAACAGAGGCTC
*
565125 AACGACTTTAAAAAATAGAAT-GCTC-TCCTAGTCAGAGGCTCAACGACTTTTGAAAATAAACAA
1 AACGACTTTAAAAAATA-AATGGCTCAT-CTAATCAGAGGCTCAACGACTTTTGAAAATAAACAA
**
565188 AACTCCTCTAATGAGAGGCTC
64 AACTCCTCTAAACAGAGGCTC
* * ** *
565209 AATGACTTGAAAGAAAATAAACAAAGCTTC-TCTAATCAAAGGCTCAACGACTTT
1 AACGACTT-TAA-AAAAT-AA-ATGGC-TCATCTAATCAGAGGCTCAACGACTTT
565263 GGGAACAATA
Statistics
Matches: 117, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
83 1 0.01
84 73 0.62
85 9 0.08
86 6 0.05
87 2 0.02
88 23 0.20
89 3 0.03
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (84 bp):
AACGACTTTAAAAAATAAATGGCTCATCTAATCAGAGGCTCAACGACTTTTGAAAATAAACAAAA
CTCCTCTAAACAGAGGCTC
Found at i:565242 original size:45 final size:45
Alignment explanation
Indices: 565067--565261 Score: 131
Period size: 43 Copynumber: 4.5 Consensus size: 45
565057 AAATGGCTCA
* * * *
565067 TCTAATCAGAGGCTTAACGACTTTG--A-AAAATAAATAAAGCTCC
1 TCTAATCAAAGGCTCAACGAC-TTGAAAGAAAATAAACAAAACTCC
* * * * **
565110 TCTAAACAGAGGCTCAACGACTT-TAA-AAAAT--AGAATGCT-C
1 TCTAATCAAAGGCTCAACGACTTGAAAGAAAATAAACAAAACTCC
* * **
565150 TCCTAGTCAGAGGCTCAACGACTT--TTGAAAATAAACAAAACTCC
1 T-CTAATCAAAGGCTCAACGACTTGAAAGAAAATAAACAAAACTCC
* * * * *
565194 TCTAATGAGAGGCTCAATGACTTGAAAGAAAATAAACAAAGCTTC
1 TCTAATCAAAGGCTCAACGACTTGAAAGAAAATAAACAAAACTCC
565239 TCTAATCAAAGGCTCAACGACTT
1 TCTAATCAAAGGCTCAACGACTT
565262 TGGGAACAAT
Statistics
Matches: 122, Mismatches: 21, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
40 2 0.02
41 31 0.25
42 2 0.02
43 49 0.40
44 2 0.02
45 36 0.30
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (45 bp):
TCTAATCAAAGGCTCAACGACTTGAAAGAAAATAAACAAAACTCC
Found at i:565361 original size:42 final size:41
Alignment explanation
Indices: 565305--565405 Score: 157
Period size: 42 Copynumber: 2.4 Consensus size: 41
565295 AACCATGACT
565305 TTTGAAAGATAAATTGCTTCTCTAAACAGAAGCACCACAAC
1 TTTGAAAGATAAATTGCTTCTCTAAACAGAAGCACCACAAC
* * * *
565346 TTTGAAAAAGTAAATTGTTTCTCTAAACAGAGGCATCACAAC
1 TTTGAAAGA-TAAATTGCTTCTCTAAACAGAAGCACCACAAC
565388 TTTGAAAGATAAATTGCT
1 TTTGAAAGATAAATTGCT
565406 CCTTGACAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
41 16 0.30
42 37 0.70
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.29
Consensus pattern (41 bp):
TTTGAAAGATAAATTGCTTCTCTAAACAGAAGCACCACAAC
Found at i:572836 original size:126 final size:128
Alignment explanation
Indices: 572706--572941 Score: 343
Period size: 129 Copynumber: 1.8 Consensus size: 128
572696 ATTTTTTTAT
* * *
572706 AAAAAAAATTATTTTTCAGGAAAATCGATACTTTCAAC-TTTTCTCCAAAATATTTTTT-AAAAA
1 AAAAAAAATTATTTTTAAGAAAAATCGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAA
* *
572769 CTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCT-AAAACAAAAAAACCTCTTTTTAAA
66 C-TTAATTTCAAGAAAAATTGATACTTGCAACTTTTCCTCAAAACAAAAAAACCTCTTTTTAAA
* * *
572832 AAAAAAACTTATTTTTAAGAAAAATTGTTACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAA
1 AAAAAAAATTATTTTTAAGAAAAATCGATACTTTCAACTTTTTCTCAAAAATATTTTTT--AAAA
*
572897 AACTTATTTTCAAGAAAAATTGATACTTGCAACTTTTCCTCAAAA
64 AACTTAATTTCAAGAAAAATTGATACTTGCAACTTTTCCTCAAAA
572942 ATATTTTTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
126 33 0.34
127 19 0.20
129 34 0.35
130 10 0.10
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.38
Consensus pattern (128 bp):
AAAAAAAATTATTTTTAAGAAAAATCGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAAA
CTTAATTTCAAGAAAAATTGATACTTGCAACTTTTCCTCAAAACAAAAAAACCTCTTTTTAAA
Found at i:572837 original size:19 final size:20
Alignment explanation
Indices: 572813--572855 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
572803 TTCCTAAAAC
*
572813 AAAAAAACCTCTTTTTAA-A
1 AAAAAAACCTATTTTTAAGA
*
572832 AAAAAAACTTATTTTTAAGA
1 AAAAAAACCTATTTTTAAGA
572852 AAAA
1 AAAA
572856 TTGTTACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAAAACCTATTTTTAAGA
Found at i:572988 original size:58 final size:58
Alignment explanation
Indices: 572707--573123 Score: 400
Period size: 58 Copynumber: 7.0 Consensus size: 58
572697 TTTTTTTATA
* * * *
572707 AAAAAAATTATTTTTC-AGGAAAATCGATACTTTCAACTTTT-CTCCAAAATATTTTTT
1 AAAAAACTTA-TTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
* * *
572764 -AAAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTCCTAAAACAAAAAAACCTCTTTT
1 AAAAAAC-TTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCT----CAAAAATA--T-TTTT
572828 T
58 T
* * *
572829 AAAAAAAAAACTTATTTTTAAGAAAAATTGTTACTTTCAACTTTTTCTCAAAAATATTTTTT
1 ----AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
*
572891 AGAAAAAACTTATTTTCAAGAAAAATTGATACTTGCAACTTTTCCTCAAAAATATTTTTT
1 --AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
* * *
572951 AAAAAGCTTATTTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT
1 AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
*** *
573009 AGAAATTTTTATTTTCAA-AGAAAATTGATACTTTCAA-TTTT-TTCAAAAATATTTTTT
1 A-AAAAACTTATTTTCAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
*** * *
573066 AAAATTTTTACTTTCAA-AAGAAATTGATACTTTCAAC-TTTCTTTCAAAAATATTTTTT
1 AAAAAACTTATTTTCAAGAA-AAATTGATACTTTCAACTTTTC-CTCAAAAATATTTTTT
573124 TTAAAAAAAT
Statistics
Matches: 312, Mismatches: 27, Indels: 41
0.82 0.07 0.11
Matches are distributed among these distances:
55 1 0.00
56 44 0.14
57 42 0.13
58 78 0.25
59 29 0.09
60 55 0.18
62 11 0.04
63 1 0.00
64 1 0.00
65 12 0.04
69 32 0.10
70 6 0.02
ACGTcount: A:0.41, C:0.12, G:0.05, T:0.43
Consensus pattern (58 bp):
AAAAAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTT
Found at i:573135 original size:15 final size:15
Alignment explanation
Indices: 573111--573144 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
573101 ACTTTCTTTC
* *
573111 AAAAATATTTTTTTT
1 AAAAAAATTTATTTT
573126 AAAAAAATTTATTTT
1 AAAAAAATTTATTTT
573141 AAAA
1 AAAA
573145 GAATCATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AAAAAAATTTATTTT
Found at i:574905 original size:20 final size:20
Alignment explanation
Indices: 574882--574940 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
574872 AGAAAAAAAT
574882 AAATCATAAAATAAAAATAA
1 AAATCATAAAATAAAAATAA
*
574902 AAATGATAAATATGAAATAA-AA
1 AAATCATAAA-AT-AAA-AATAA
574924 AAATC-TAAAATAAAAAT
1 AAATCATAAAATAAAAAT
574941 GAATAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 11 0.33
21 6 0.18
22 9 0.27
23 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (20 bp):
AAATCATAAAATAAAAATAA
Found at i:575223 original size:44 final size:43
Alignment explanation
Indices: 575141--575512 Score: 341
Period size: 42 Copynumber: 8.7 Consensus size: 43
575131 AATTTTGATT
* *
575141 AAAGCTCCTCTAATCAGAGGTTCAACGACTTTTAAAAAAATAAAC
1 AAAGCTCCTCTAATCAGAGGCTCAACGAC-TTT-GAAAAATAAAC
* * * *
575186 AAAGCTCCTCTAATCAAAGG-TCAACAACTTTTGAAAAATCAAT
1 AAAGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAAATAAAC
* * *
575229 AAGGTTCTTCTAATCAGAGGCTCAACGACTTTGAAAAGATAAAC
1 AAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA-ATAAAC
* * * * *
575273 AAGGCTCCTCTAATTAGAGGCTCAATGACTTTG-AAATTAAAA
1 AAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAC
* * * * *
575315 AAAGCTCCTCTAAACAGAGGTTTAACGACTTTG-AAATTAAAT
1 AAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAC
*
575357 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTTTG-AAAATAAA-
1 AAAGCTCCTCTAATCAGAGGCTCAACGAC--TTTGAAAAATAAAC
** *
575400 TGA-CTCCTCTAATCAGAGGTTCAACGACTTTG-AAAAT-AA-
1 AAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAC
** * * *
575439 ATGGCTCATCTAATCAGAGGCTCAACGACTTTG-AAATTAAAT
1 AAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAC
* * *
575481 AAAGCTCCTTTAAACAGAGGTTCAACGACTTT
1 AAAGCTCCTCTAATCAGAGGCTCAACGACTTT
575513 TTTAAAAATA
Statistics
Matches: 276, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.01
40 40 0.14
41 2 0.01
42 115 0.42
43 36 0.13
44 62 0.22
45 19 0.07
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (43 bp):
AAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAAC
Found at i:575387 original size:84 final size:85
Alignment explanation
Indices: 575141--575512 Score: 389
Period size: 84 Copynumber: 4.4 Consensus size: 85
575131 AATTTTGATT
* *
575141 AAAGCTCCTCTAATCAGAGGTTCAACGACTTTTAAAAAAATAAACAAAGCTCCTCTAATCAAAGG
1 AAAGCTCCTCTAATCAGAGGTTCAACGAC-TTT--GAAAATAAACAAAGCTCCTCTAATCAGAGG
* * *
575206 -TCAACAACTTTTGAAAAATCAAT
63 CTCAACGACTTTTG-AAAATAAAA
* * * * * *
575229 AAGGTTCTTCTAATCAGAGGCTCAACGACTTTGAAAAGATAAACAAGGCTCCTCTAATTAGAGGC
1 AAAGCTCCTCTAATCAGAGGTTCAACGACTTTG-AAA-ATAAACAAAGCTCCTCTAATCAGAGGC
* *
575294 TCAATGAC-TTTGAAATTAAAA
64 TCAACGACTTTTGAAAATAAAA
* * * * *
575315 AAAGCTCCTCTAAACAGAGGTTTAACGACTTTGAAATTAAATAAAGCTCCTCTAAACAGAGGCTC
1 AAAGCTCCTCTAATCAGAGGTTCAACGACTTTGAAAATAAACAAAGCTCCTCTAATCAGAGGCTC
575380 AACGACTTTTTGAAAAT-AAA
66 AACGAC-TTTTGAAAATAAAA
** ** *
575400 TGA-CTCCTCTAATCAGAGGTTCAACGACTTTGAAAAT-AA-ATGGCTCATCTAATCAGAGGCTC
1 AAAGCTCCTCTAATCAGAGGTTCAACGACTTTGAAAATAAACAAAGCTCCTCTAATCAGAGGCTC
* *
575462 AACGAC-TTTGAAATTAAAT
66 AACGACTTTTGAAAATAAAA
* *
575481 AAAGCTCCTTTAAACAGAGGTTCAACGACTTT
1 AAAGCTCCTCTAATCAGAGGTTCAACGACTTT
575513 TTTAAAAATA
Statistics
Matches: 236, Mismatches: 41, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
80 8 0.03
81 3 0.01
82 51 0.22
83 2 0.01
84 60 0.25
85 7 0.03
86 44 0.19
87 30 0.13
88 31 0.13
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (85 bp):
AAAGCTCCTCTAATCAGAGGTTCAACGACTTTGAAAATAAACAAAGCTCCTCTAATCAGAGGCTC
AACGACTTTTGAAAATAAAA
Found at i:575483 original size:124 final size:123
Alignment explanation
Indices: 575144--575532 Score: 413
Period size: 124 Copynumber: 3.0 Consensus size: 123
575134 TTTGATTAAA
* *
575144 GCTCCTCTAATCAGAGGTTCAACGACTTTTAAAAAAATAAACAAAGCTCCTCTAATCAAAGGTCA
1 GCTCCTCTAATCAGAGGTTCAACGAC-TTT--GAAAAT-AA-AAAGCTCCTCTAATCAGAGGTCA
* * * * * * *
575209 ACAACTTTTGAAAAATCAATAAGGTTCTTCTAATCAGAGGCTCAACGAC--TTTGAAAAGATAAA
61 ACGAC-TTTG-AAATTAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTTG-AAA-AT-AA
*
575272 CAAG
121 -ATG
* * * * * *
575276 GCTCCTCTAATTAGAGGCTCAATGACTTTGAAATTAAAAAAAGCTCCTCTAAACAGAGGTTTAAC
1 GCTCCTCTAATCAGAGGTTCAACGACTTTGAAA--ATAAAAAGCTCCTCTAATCAGAGG-TCAAC
575341 GACTTTGAAATTAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTTGAAAATAAATG
63 GACTTTGAAATTAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTTGAAAATAAATG
* ** *
575402 ACTCCTCTAATCAGAGGTTCAACGACTTTGAAAATAAATGGCTCATCTAATCAGAGGCTCAACGA
1 GCTCCTCTAATCAGAGGTTCAACGACTTTGAAAATAAAAAGCTCCTCTAATCAGAGG-TCAACGA
* * *
575467 CTTTGAAATTAAATAAAGCTCCTTTAAACAGAGGTTCAACGACTTTTTTAAAAATAAATG
65 CTTTGAAATTAAATAAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTTTGAAAATAAATG
575527 GCTCCT
1 GCTCCT
575533 TGATGATTGT
Statistics
Matches: 220, Mismatches: 31, Indels: 19
0.81 0.11 0.07
Matches are distributed among these distances:
124 66 0.30
125 20 0.09
126 31 0.14
127 2 0.01
128 34 0.15
129 28 0.13
130 12 0.05
131 4 0.02
132 23 0.10
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.27
Consensus pattern (123 bp):
GCTCCTCTAATCAGAGGTTCAACGACTTTGAAAATAAAAAGCTCCTCTAATCAGAGGTCAACGAC
TTTGAAATTAAATAAAGCTCCTCTAAACAGAGGCTCAACGACTTTTTGAAAATAAATG
Found at i:576141 original size:22 final size:21
Alignment explanation
Indices: 576097--576153 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
576087 TTCACTCCTT
576097 AAAGATTCTCATTTTGAAACTC
1 AAAGATTCTCA-TTTGAAACTC
**
576119 AAAGATTCTCATTTGAGTTCTC
1 AAAGATTCTCATTTGA-AACTC
*
576141 AAAAATTCTCATT
1 AAAGATTCTCATT
576154 AAAATATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 5 0.16
22 26 0.84
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.39
Consensus pattern (21 bp):
AAAGATTCTCATTTGAAACTC
Found at i:576657 original size:63 final size:63
Alignment explanation
Indices: 576553--576672 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
576543 GCTTATTAGC
** *
576553 ACTAACCATTTCAAAATAAATTTCATGTTCTATCACTTGGTCATCGTTCATAAGCTTTTCAAT
1 ACTAACCATTTCAAAATAAATTTCATCATCTATCACTTGGTCATCATTCATAAGCTTTTCAAT
* *
576616 ACTAGCCATTTCAAAATAAATTTCATCATCTGTCACTTGGTCATCATTCATAAGCTT
1 ACTAACCATTTCAAAATAAATTTCATCATCTATCACTTGGTCATCATTCATAAGCTT
576673 CTCAGCATCA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (63 bp):
ACTAACCATTTCAAAATAAATTTCATCATCTATCACTTGGTCATCATTCATAAGCTTTTCAAT
Found at i:577397 original size:22 final size:22
Alignment explanation
Indices: 577372--577416 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
577362 CTTTTTTTCA
*
577372 TTTTCT-CATTTTTTTCTTTTTT
1 TTTTCTCCA-TTTTTTCATTTTT
577394 TTTTCTCCATTTTTTCATTTTT
1 TTTTCTCCATTTTTTCATTTTT
577416 T
1 T
577417 CATCATCTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCTCCATTTTTTCATTTTT
Found at i:577412 original size:8 final size:8
Alignment explanation
Indices: 577364--577419 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
577354 ATTTGAATCT
577364 TTTTTTCA
1 TTTTTTCA
*
577372 TTTTCTCA
1 TTTTTTCA
577380 TTTTTTTC-
1 -TTTTTTCA
577388 TTTTTT--
1 TTTTTTCA
*
577394 TTTTCTCCA
1 TTTT-TTCA
577403 TTTTTTCA
1 TTTTTTCA
577411 TTTTTTCA
1 TTTTTTCA
577419 T
1 T
577420 CATCTTCTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
6 4 0.10
7 7 0.17
8 19 0.47
9 10 0.25
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTTTCA
Found at i:577428 original size:39 final size:39
Alignment explanation
Indices: 577364--577446 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
577354 ATTTGAATCT
** *
577364 TTTTTTCATTTTCTCATTTTTTTCTTTT-TTTTTTCTCCA
1 TTTTTTCATTTTCTCATCATCTTCTTTTCTTTTTTCT-CA
*
577403 TTTTTTCATTTTTTCATCATCTTCTTTTCTTTTTTCTCA
1 TTTTTTCATTTTCTCATCATCTTCTTTTCTTTTTTCTCA
577442 TTTTT
1 TTTTT
577447 CATCCATTGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 31 0.79
40 8 0.21
ACGTcount: A:0.08, C:0.18, G:0.00, T:0.73
Consensus pattern (39 bp):
TTTTTTCATTTTCTCATCATCTTCTTTTCTTTTTTCTCA
Found at i:581733 original size:58 final size:58
Alignment explanation
Indices: 581467--581814 Score: 378
Period size: 58 Copynumber: 5.9 Consensus size: 58
581457 CGTTTTTTTT
* * * *
581467 AAACTTATTTTTAAGAAAAATTGATACTTTCAAC-TTTTTCCCAAAATATTTTTTAGA
1 AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAAA
** * ** * * *
581524 AATTTTAATTTCGTGAAAAATTGATACTTTCAACTTTTTCTCAAAACTTTTTTTTAAAAAAA
1 AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTT----AAA
* * * * *
581586 AAACTTATTTTTAAGTAAAATTGATACTTTCAACTTTTTCTCGAATATATTTTTTAGAAA
1 AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTT--AAA
* *
581646 AAATTTATTTTCAAGGAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAAA
1 AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAAA
* *
581704 AAACTTATTTTTAAGGAAAATTGATACTTTC-A-TTTTTTTCAAAAATATTTTTTAAA
1 AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAAA
*** * * *
581760 ATTTTTACTTTCAAAAAAAATTGATACTTTCAACTTTCTTTCAAAAATATTTTTT
1 AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTT
581815 TTAAAAAAAA
Statistics
Matches: 244, Mismatches: 40, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
56 48 0.20
57 30 0.12
58 67 0.27
60 53 0.22
62 46 0.19
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (58 bp):
AAACTTATTTTCAAGAAAAATTGATACTTTCAACTTTTTTTCAAAAATATTTTTTAAA
Found at i:583621 original size:21 final size:20
Alignment explanation
Indices: 583584--583622 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
583574 CATAAAATAA
*
583584 AAATAAAAATGATAAATATG
1 AAATAAAAATGAAAAATATG
*
583604 AAATAAAAAATTAAAAATA
1 AAAT-AAAAATGAAAAATA
583623 AAAATGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (20 bp):
AAATAAAAATGAAAAATATG
Found at i:587006 original size:64 final size:64
Alignment explanation
Indices: 586905--587032 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
586895 GTAAATTTAT
586905 TTATGATCAACAAAACTTTGTCTTAGCTATTAAAAGAAACTTGTTATTTTTACGACTGTTTCTA
1 TTATGATCAACAAAACTTTGTCTTAGCTATTAAAAGAAACTTGTTATTTTTACGACTGTTTCTA
586969 TTATGATCAACAAAACTTTGTCTTAGCTATTAAAAGAAACTTGTTATTTTTACGACTGTTTCTA
1 TTATGATCAACAAAACTTTGTCTTAGCTATTAAAAGAAACTTGTTATTTTTACGACTGTTTCTA
587033 AATTTAAGAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (64 bp):
TTATGATCAACAAAACTTTGTCTTAGCTATTAAAAGAAACTTGTTATTTTTACGACTGTTTCTA
Found at i:590716 original size:30 final size:30
Alignment explanation
Indices: 590668--590743 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
590658 TATATTTTTA
* *
590668 TTATATTTAAAT-AATTTTTTAATTTTTAAT
1 TTATA-TTAAATAAATTTTTAAATTTGTAAT
*
590698 TTGTATTAAATAAATTTTTAAATTTGTAAT
1 TTATATTAAATAAATTTTTAAATTTGTAAT
590728 TTATATTCAAATAAAT
1 TTATATT-AAATAAAT
590744 CTGTAATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 6 0.15
30 26 0.65
31 8 0.20
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATATTAAATAAATTTTTAAATTTGTAAT
Found at i:591961 original size:2 final size:2
Alignment explanation
Indices: 591954--591984 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
591944 AACAGCCTCG
*
591954 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
591985 CCTTTAGTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:592102 original size:12 final size:12
Alignment explanation
Indices: 592085--592109 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
592075 AGCCTATGCT
592085 GGCCATAGTCAG
1 GGCCATAGTCAG
592097 GGCCATAGTCAG
1 GGCCATAGTCAG
592109 G
1 G
592110 ATTCACCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (12 bp):
GGCCATAGTCAG
Found at i:597629 original size:56 final size:56
Alignment explanation
Indices: 597508--597954 Score: 387
Period size: 56 Copynumber: 7.7 Consensus size: 56
597498 TTTTGTGCAT
* *
597508 GAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTTAGAAATTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGA-AAACTTTAATTTCGA
* * *
597565 -AGAAAATTGATACTTTCGACTTTTTCCCAAAATATTTTTGAAAATTTTAATTTCAA
1 GA-AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGAAAACTTTAATTTCGA
* *
597621 AAAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGAAAACTTTAATTTCGA
* * * **
597677 GGAAAATTGATACTTTCAACTTTTTCTCAAAA-ACCTTTTTTGAAAA-TTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTCCCAAAATA---TTTTTGAAAACTTTAATTTCGA
* * * **
597734 GGAAAATTAACACTTTCAACTTTACCCCAAAAATATTTTTTAGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTTCCC-AAAATA-TTTTT-GAAAACTTTAATTTCGA
** * * * * **
597793 GAAAAATTGATACTTTCAACTTTTTCTAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTC--CCAAAATA--TTTTTGAAAACTTTAATTTCGA
* ** * * * * **
597853 GGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAAACCTTGTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTTC---CCAAAATA--TT-TTTGAAAACTTTAATTTCGA
*
597915 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTT
1 GAAAAATTGATACTTTCAACTTTTTCCC-AAAATATTTTT
597955 TTTGGATTTA
Statistics
Matches: 332, Mismatches: 43, Indels: 30
0.82 0.11 0.07
Matches are distributed among these distances:
55 1 0.00
56 93 0.28
57 78 0.23
58 21 0.06
59 30 0.09
60 47 0.14
61 18 0.05
62 44 0.13
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (56 bp):
GAAAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGAAAACTTTAATTTCGA
Found at i:597889 original size:62 final size:60
Alignment explanation
Indices: 597676--597938 Score: 322
Period size: 62 Copynumber: 4.4 Consensus size: 60
597666 TTTAATTTCG
* *
597676 AGGAAAATTGATACTTTCAACTTTTTCT---CAAAAACCTTTTTTGAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAACCTTTTTTAAAAATTTATTTTTA
* * * *** * * **
597733 AGGAAAATTAACACTTTCAAC-TTTACCCCAAAAATA--TTTTTTAGAAAACTTTAATTTCG
1 AGGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAACCTTTTTTA-AAAA-TTTATTTTTA
*
597792 AGAAAAATTGATACTTTCAACTTTTTCTAAAAAAAAACCTTTTTTAAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAACCTTTTTTAAAAATTTATTTTTA
597852 AGGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAAACCTTGTTTTAAAAATTTATTTTTA
1 AGGAAAATTGATACTTTCAACTTTTTCT-AAAAAAAAACCTT-TTTTAAAAATTTATTTTTA
*
597914 AGAAAAATTGATACTTTCAACTTTT
1 AGGAAAATTGATACTTTCAACTTTT
597939 CCCCAAAAAT
Statistics
Matches: 173, Mismatches: 23, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
56 4 0.02
57 25 0.14
58 4 0.02
59 29 0.17
60 44 0.25
61 17 0.10
62 50 0.29
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.41
Consensus pattern (60 bp):
AGGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAACCTTTTTTAAAAATTTATTTTTA
Found at i:597947 original size:62 final size:61
Alignment explanation
Indices: 597508--597947 Score: 327
Period size: 57 Copynumber: 7.5 Consensus size: 61
597498 TTTTGTGCAT
* * * **
597508 GAAAAATTGATACTTTCAACTTTTTCCC---AAAATA--TTTTTTAGAAATTTTAATTTCGAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTA-AAAATTT-ATTTTTAA
* * * * * * *
597566 G-AAAATTGATACTTTCGACTTTTTCCC---AAAATA--TTTTTGAAAATTTTAATTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
* * * * * **
597621 AAAAAATTGATACTTTCAACTTTTCCCC---AAAATA--TTTTTGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
* * * *
597677 GGAAAATTGATACTTTCAACTTTTTCTC----AAAAACCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
* * * * * * **
597734 GGAAAATTAACACTTTCAACTTTACCCC--AAAAATA--TTTTTTAGAAAACTTTAATTTCGA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTA-AAAA-TTTATTTTTAA
* *
597793 GAAAAATTGATACTTTCAACTTTT-TCTAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
* * **
597853 GGAAAATTGATACTTTCAACTTTTTCTAAAAAAAAAACCTTGTTTTAAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTT-TTTTAAAAATTTATTTTTAA
597915 GAAAAATTGATACTTTCAACTTTTCCCCAAAAA
1 GAAAAATTGATACTTTCAACTTTTCCCCAAAAA
597948 TATTTTTTTT
Statistics
Matches: 320, Mismatches: 49, Indels: 22
0.82 0.13 0.06
Matches are distributed among these distances:
55 9 0.03
56 81 0.25
57 82 0.26
58 6 0.02
59 32 0.10
60 37 0.12
61 17 0.05
62 56 0.17
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.41
Consensus pattern (61 bp):
GAAAAATTGATACTTTCAACTTTTCCCCAAAAAAAAACCTTTTTTAAAAATTTATTTTTAA
Found at i:597967 original size:119 final size:116
Alignment explanation
Indices: 597536--597955 Score: 345
Period size: 113 Copynumber: 3.6 Consensus size: 116
597526 ACTTTTTCCC
* * *
597536 AAAATATTTTTTAG-AAATTTTAATTTCGAAG-AAAATTGATACTTTCGACTTTTTCC-C-AAAA
1 AAAAAATTTTTTAGAAAACTTTAATTTC-AAGAAAAATTGATACTTTCAAC-TTTTCCACAAAAA
* * * * * ** * * * ***
597597 TATTTTTGAAAATTTTAATTTCAAAAAAAATTGATACTTTCAACTTTTC-CCC
64 AATTTTTTAAAAATTTATTTTTAAGGAAAATTAACACTTTCAACTTTACAAAA
* * * * * **
597649 AAAATA-TTTTT-GAAAACTTTAATTTCGAGGAAAATTGATACTTTCAACTTTTTCTCAAAAACC
1 AAAAAATTTTTTAGAAAACTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTCCACAAAAAAA
* ***
597712 TTTTTTGAAAATTTATTTTTAAGGAAAATTAACACTTTCAACTTTACCCCA
66 TTTTTTAAAAATTTATTTTTAAGGAAAATTAACACTTTCAACTTTACAAAA
* * * *
597763 AAAATATTTTTTAGAAAACTTTAATTTCGAGAAAAATTGATACTTTCAACTTTTTCTAAAAAAAA
1 AAAAAATTTTTTAGAAAACTTTAATTTCAAGAAAAATTGATACTTTCAAC-TTTTCCACAAAAAA
* * *
597828 ACCTTTTTTAAAAATTTATTTTTAAGGAAAATTGATACTTTCAACTTTTTCTAAAA
65 A--TTTTTTAAAAATTTATTTTTAAGGAAAATTAACACTTTCAAC-TTTAC-AAAA
* * *
597884 AAAAAACCTTGTTTTA-AAAA-TTTATTTTTAAGAAAAATTGATACTTTCAACTTTTCCCCAAAA
1 AAAAAA--TT-TTTTAGAAAACTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTCCACAAAA
*
597947 ATATTTTTT
63 AAATTTTTT
597956 TTGGATTTAT
Statistics
Matches: 253, Mismatches: 39, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
111 8 0.03
112 35 0.14
113 47 0.19
114 8 0.03
115 5 0.02
116 36 0.14
117 9 0.04
119 45 0.18
120 4 0.02
121 17 0.07
122 28 0.11
123 6 0.02
124 5 0.02
ACGTcount: A:0.40, C:0.13, G:0.06, T:0.42
Consensus pattern (116 bp):
AAAAAATTTTTTAGAAAACTTTAATTTCAAGAAAAATTGATACTTTCAACTTTTCCACAAAAAAA
TTTTTTAAAAATTTATTTTTAAGGAAAATTAACACTTTCAACTTTACAAAA
Found at i:597982 original size:5 final size:5
Alignment explanation
Indices: 597972--598059 Score: 62
Period size: 5 Copynumber: 17.8 Consensus size: 5
597962 TTATTTAAAG
*
597972 AAAAT AAAAT --AAT AAAAT AAAA- AAAGT GAAAAT AAAAAT AAAGA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAA-AT
* *
598016 AAAGT AAAAT AAAA- AATA- AAAAT AAAAT AAAGAT AAAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT -AAAAT AAAA
598060 GAATATTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
3 3 0.04
4 9 0.13
5 38 0.57
6 14 0.21
7 3 0.04
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:598009 original size:6 final size:6
Alignment explanation
Indices: 597972--598059 Score: 61
Period size: 6 Copynumber: 13.5 Consensus size: 6
597962 TTATTTAAAG
* * *
597972 AAAATAA AATAATA AAATAAA AAAAGTG AAAATA AAAATA AAGAAAA GTAAAATAA
1 AAAAT-A AA-AATA AAA-ATA AAAA-TA AAAATA AAAATA AA-AATA --AAAAT-A
*
598028 AAAATA AAAAT- AAAATA AAGATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
598060 GAATATTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 17
0.72 0.09 0.19
Matches are distributed among these distances:
5 5 0.08
6 30 0.46
7 22 0.34
8 5 0.08
9 3 0.05
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:598047 original size:28 final size:30
Alignment explanation
Indices: 598000--598064 Score: 91
Period size: 28 Copynumber: 2.2 Consensus size: 30
597990 AAAAAAAGTG
598000 AAAATAAAAATAAAGAAAAG-T-AAAATAA
1 AAAATAAAAATAAAGAAAAGATAAAAATAA
598028 AAAATAAAAATAAA-ATAAAGATAAAAATAA
1 AAAATAAAAATAAAGA-AAAGATAAAAATAA
598058 AAGAATA
1 AA-AATA
598065 TTAAACAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
27 1 0.03
28 18 0.55
29 1 0.03
30 9 0.27
31 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.15
Consensus pattern (30 bp):
AAAATAAAAATAAAGAAAAGATAAAAATAA
Found at i:598509 original size:21 final size:20
Alignment explanation
Indices: 598471--598564 Score: 77
Period size: 21 Copynumber: 4.7 Consensus size: 20
598461 AATATATTAA
*
598471 TAGATAACACAAAAAAATAAT
1 TAGATAA-ATAAAAAAATAAT
*
598492 TAGATAAAT-AAAAGA-AA-
1 TAGATAAATAAAAAAATAAT
* *
598509 TAGATAAATAATAAAAAAAAG
1 TAGATAAATAA-AAAAATAAT
*
598530 TAGATAAATAATAAAAATATT
1 TAGATAAATAA-AAAAATAAT
*
598551 ATAGAAAAATAAAA
1 -TAGATAAATAAAA
598565 TATATATTAA
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
17 9 0.15
18 3 0.05
19 9 0.15
20 3 0.05
21 27 0.44
22 10 0.16
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.21
Consensus pattern (20 bp):
TAGATAAATAAAAAAATAAT
Found at i:598525 original size:38 final size:38
Alignment explanation
Indices: 598456--598548 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 38
598446 CAAAATAAAA
** * *
598456 AGATAAAT-ATATTAATAGATAACACAAAAAAATAATT
1 AGATAAATAATAAAAATAGATAACACAAAAAAAAAAGT
*
598493 AGATAAATAA-AAGAAATAGATAA-ATAATAAAAAAAAGT
1 AGATAAATAATAA-AAATAGATAACACAA-AAAAAAAAGT
598531 AGATAAATAATAAAAATA
1 AGATAAATAATAAAAATA
598549 TTATAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
37 12 0.26
38 33 0.70
39 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (38 bp):
AGATAAATAATAAAAATAGATAACACAAAAAAAAAAGT
Found at i:598536 original size:17 final size:18
Alignment explanation
Indices: 598482--598546 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 18
598472 AGATAACACA
*
598482 AAAAAATAATTAGATAAAT
1 AAAAAA-AAGTAGATAAAT
*
598501 AAAAGAAA-TAGATAAATAAT
1 AAAAAAAAGTAGAT--A-AAT
598521 AAAAAAAAGTAGATAAAT
1 AAAAAAAAGTAGATAAAT
598539 AATAAAAA
1 AA-AAAAA
598547 TATTATAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.13
18 7 0.18
19 12 0.31
20 10 0.26
21 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (18 bp):
AAAAAAAAGTAGATAAAT
Found at i:598584 original size:20 final size:17
Alignment explanation
Indices: 598533--598586 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
598523 AAAAAAGTAG
598533 ATAAATAATAAAAATATT
1 ATAAATAAT-AAAATATT
*
598551 ATAGAAAAATAAAATATAT
1 ATA-AATAATAAAATAT-T
598570 ATTAAATAATGAAAATA
1 A-TAAATAAT-AAAATA
598587 AAAATAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 10 0.33
19 12 0.40
20 8 0.27
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
ATAAATAATAAAATATT
Found at i:605858 original size:30 final size:30
Alignment explanation
Indices: 605775--605850 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
605765 TATATTTTTA
* *
605775 TTATATTTAAATAATTTTTTAATTTTTAAT
1 TTATATTTAAATAAATTTTTAATTTGTAAT
*
605805 TTGTATTTAAATAAATTTTTAATTTGTAAT
1 TTATATTTAAATAAATTTTTAATTTGTAAT
*
605835 TTATATTCAAATAAAT
1 TTATATTTAAATAAAT
605851 CTGTAATTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.39, C:0.01, G:0.03, T:0.57
Consensus pattern (30 bp):
TTATATTTAAATAAATTTTTAATTTGTAAT
Found at i:606077 original size:20 final size:20
Alignment explanation
Indices: 606052--606089 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
606042 TTGGCTACAA
606052 TAAAAATAT-AAAAATTTACT
1 TAAAAA-ATGAAAAATTTACT
606072 TAAAAAATGAAAAATTTA
1 TAAAAAATGAAAAATTTA
606090 AACACTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.32
Consensus pattern (20 bp):
TAAAAAATGAAAAATTTACT
Found at i:607148 original size:12 final size:12
Alignment explanation
Indices: 607131--607155 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
607121 CAGCCTTGCT
607131 GGCCATAGTCAG
1 GGCCATAGTCAG
607143 GGCCATAGTCAG
1 GGCCATAGTCAG
607155 G
1 G
607156 ATTCACCAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.36, T:0.16
Consensus pattern (12 bp):
GGCCATAGTCAG
Found at i:614939 original size:11 final size:11
Alignment explanation
Indices: 614915--614970 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
614905 ATTAGATTTA
614915 ATAATATAATAAT
1 ATAATAT-A-AAT
614928 ATAATATAAAT
1 ATAATATAAAT
614939 ATAATA-AGAAT
1 ATAATATA-AAT
* *
614950 ATAAGATAAAAA
1 ATAATAT-AAAT
614962 ATAATATAA
1 ATAATATAA
614971 CTTAAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 1 0.03
11 19 0.51
12 9 0.24
13 8 0.22
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:614967 original size:17 final size:17
Alignment explanation
Indices: 614917--614970 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
614907 TAGATTTAAT
614917 AATATAATAATATAATATA
1 AATATAA-AA-ATAATATA
* *
614936 AATATAATAAGAATATA
1 AATATAAAAATAATATA
614953 AGATA-AAAAATAATATA
1 A-ATATAAAAATAATATA
614970 A
1 A
614971 CTTAAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 19 0.63
18 4 0.13
19 7 0.23
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.30
Consensus pattern (17 bp):
AATATAAAAATAATATA
Found at i:628261 original size:39 final size:39
Alignment explanation
Indices: 628207--628281 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
628197 TTATACCATC
* *
628207 GGTTGCTTCGCAAGCCCGG-TGACTGACCTTTTCCTTATT
1 GGTTGCTTCGCAAG-CCGGTTGAATAACCTTTTCCTTATT
*
628246 GGTTGCTTCGGAAGCCGGTTGAATAACCTTTTCCTT
1 GGTTGCTTCGCAAGCCGGTTGAATAACCTTTTCCTT
628282 TACCTTCTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 4 0.12
39 28 0.88
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (39 bp):
GGTTGCTTCGCAAGCCGGTTGAATAACCTTTTCCTTATT
Found at i:637420 original size:39 final size:39
Alignment explanation
Indices: 637369--637523 Score: 128
Period size: 39 Copynumber: 4.1 Consensus size: 39
637359 ACTGCTGCTT
*
637369 CTCTCTCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCC
1 CTCTCCCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCC
* *
637408 CTCTCCCTCCTCTCTCTCTCCTTTTCCCTCT-C-TCT-C
1 CTCTCCCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCC
* * *
637444 CTCTCCCT-ATC-C-CTCT--CTTTCCCCTTATCCTTATCC
1 CTCTCCCTCCTCTCTCTCTCCCTTT--CCTTCTCCTTCTCC
* * * * * *
637480 CTATCTCTCCTTTCTCTGTCCCTTTCCTTTTCCTTTTCC
1 CTCTCCCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCC
637519 CTCTC
1 CTCTC
637524 TCTACTGCTC
Statistics
Matches: 90, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
31 3 0.03
33 8 0.09
34 2 0.02
35 4 0.04
36 16 0.18
37 4 0.04
38 2 0.02
39 47 0.52
41 4 0.04
ACGTcount: A:0.03, C:0.50, G:0.01, T:0.46
Consensus pattern (39 bp):
CTCTCCCTCCTCTCTCTCTCCCTTTCCTTCTCCTTCTCC
Found at i:637564 original size:18 final size:18
Alignment explanation
Indices: 637543--637577 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
637533 CCTCTCTAAA
637543 TCCCTATCCCTCTCTCTC
1 TCCCTATCCCTCTCTCTC
* *
637561 TCCCTTTCCCTTTCTCT
1 TCCCTATCCCTCTCTCT
637578 ATCGCGGCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (18 bp):
TCCCTATCCCTCTCTCTC
Found at i:643223 original size:17 final size:17
Alignment explanation
Indices: 643201--643239 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
643191 TCTTCATCAG
643201 TAATAAAAAATTTAAAA
1 TAATAAAAAATTTAAAA
* **
643218 TAATAATATTTTTAAAA
1 TAATAAAAAATTTAAAA
643235 TAATA
1 TAATA
643240 TTAATTAGTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAAAAAATTTAAAA
Found at i:651621 original size:21 final size:20
Alignment explanation
Indices: 651597--651637 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
651587 TAAAAAATTT
651597 TTAATATAAATTAAATAAATA
1 TTAATATAAA-TAAATAAATA
*
651618 TTAATATATATAAATAAATA
1 TTAATATAAATAAATAAATA
651638 AATAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
TTAATATAAATAAATAAATA
Found at i:651643 original size:21 final size:21
Alignment explanation
Indices: 651598--651643 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
651588 AAAAAATTTT
*
651598 TAATATAAATTAAATAAATAT
1 TAATATAAATTAAATAAATAA
*
651619 TAATATATA-TAAATAAATAAA
1 TAATATAAATTAAATAAAT-AA
651640 TAAT
1 TAAT
651644 TTTATATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATATAAATTAAATAAATAA
Found at i:651649 original size:24 final size:24
Alignment explanation
Indices: 651580--651653 Score: 80
Period size: 24 Copynumber: 3.0 Consensus size: 24
651570 ATCTGATTTA
* *
651580 AAATTAATAAAAAATTTT-TAATAT
1 AAATAAATAAATAATTTTAT-ATAT
*
651604 AAATTAAATAAAT-ATTAATATATAT
1 AAA-TAAATAAATAATT-TTATATAT
651629 AAATAAATAAATAATTTTATATAT
1 AAATAAATAAATAATTTTATATAT
651653 A
1 A
651654 TCAAGTTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 23 0.55
25 18 0.43
26 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
AAATAAATAAATAATTTTATATAT
Found at i:652469 original size:2 final size:2
Alignment explanation
Indices: 652462--652505 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
652452 TTAGGATGTG
** *
652462 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GC GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
652504 AT
1 AT
652506 GCGAGTGTCT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:654505 original size:46 final size:46
Alignment explanation
Indices: 654437--654528 Score: 166
Period size: 46 Copynumber: 2.0 Consensus size: 46
654427 TCTTAAGGCC
*
654437 GAAGCTAGTACCGCCAGTTAGCAAGTTGACAACATGTTTAATGTAT
1 GAAGCTAGTACCGCCAGATAGCAAGTTGACAACATGTTTAATGTAT
*
654483 GAAGCTAGTACTGCCAGATAGCAAGTTGACAACATGTTTAATGTAT
1 GAAGCTAGTACCGCCAGATAGCAAGTTGACAACATGTTTAATGTAT
654529 TACATTGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 44 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (46 bp):
GAAGCTAGTACCGCCAGATAGCAAGTTGACAACATGTTTAATGTAT
Found at i:661466 original size:29 final size:29
Alignment explanation
Indices: 661424--661501 Score: 106
Period size: 29 Copynumber: 2.8 Consensus size: 29
661414 TTTATAAGAA
661424 AATA-AAT-TTTAAATTATAAAAAAATTT
1 AATATAATATTTAAATTATAAAAAAATTT
* * *
661451 AATATGATATTTAAATTTTAAAAATATTT
1 AATATAATATTTAAATTATAAAAAAATTT
*
661480 AATATAATATTTAAATTGTAAA
1 AATATAATATTTAAATTATAAA
661502 TTTTTTAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 4 0.09
28 2 0.05
29 38 0.86
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
AATATAATATTTAAATTATAAAAAAATTT
Found at i:666356 original size:24 final size:24
Alignment explanation
Indices: 666321--666371 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
666311 AACTTAAATT
* * *
666321 TTTAAAATATTTATTAAAATTAAA
1 TTTAAAAAATTTAATAAAATAAAA
666345 TTTAAAAAATTTAATAAAATAAAA
1 TTTAAAAAATTTAATAAAATAAAA
666369 TTT
1 TTT
666372 CGAGCCTGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAAAAATTTAATAAAATAAAA
Found at i:674709 original size:2 final size:2
Alignment explanation
Indices: 674702--674727 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
674692 ATGAACAACC
674702 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
674728 TGTGCACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:693510 original size:3 final size:3
Alignment explanation
Indices: 693502--693541 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
693492 TAAAAAGTAA
693502 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
693542 GTAATCAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:694391 original size:22 final size:20
Alignment explanation
Indices: 694330--694399 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
694320 ATTAGATATT
694330 TAATT-TTTAAT-TTATTTA
1 TAATTATTTAATATTATTTA
* *
694348 AAATTATTAAATATTATTTA
1 TAATTATTTAATATTATTTA
*
694368 TATTTATTTAATATCTAATTTA
1 TAATTATTTAATAT-T-ATTTA
694390 TAATTATTTA
1 TAATTATTTA
694400 TGTAAATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
18 4 0.10
19 5 0.12
20 18 0.43
21 1 0.02
22 14 0.33
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (20 bp):
TAATTATTTAATATTATTTA
Found at i:697954 original size:19 final size:20
Alignment explanation
Indices: 697930--697968 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
697920 AAGTGTGAAA
697930 AAAATTATAAAATTA-ATTT
1 AAAATTATAAAATTAGATTT
*
697949 AAAATTATAATATTAGATTT
1 AAAATTATAAAATTAGATTT
697969 GATTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AAAATTATAAAATTAGATTT
Found at i:698086 original size:17 final size:18
Alignment explanation
Indices: 698065--698109 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
698055 AAATTAAATC
698065 AAATTATATAT-TATTTT
1 AAATTATATATATATTTT
* *
698082 TAATT-TTTATATATTTT
1 AAATTATATATATATTTT
698099 AAATTAT-TATA
1 AAATTATATATA
698110 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 4 0.17
17 18 0.78
18 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AAATTATATATATATTTT
Found at i:698173 original size:17 final size:17
Alignment explanation
Indices: 698147--698191 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
698137 ATTTACTTAA
* *
698147 ATATATTAAAATAATAT
1 ATATAATAAAAAAATAT
698164 ATATAATAAAAAAATAT
1 ATATAATAAAAAAATAT
*
698181 AAATCAATAAA
1 ATAT-AATAAA
698192 TCAAATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 18 0.75
18 6 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (17 bp):
ATATAATAAAAAAATAT
Found at i:702253 original size:115 final size:114
Alignment explanation
Indices: 702051--702284 Score: 344
Period size: 115 Copynumber: 2.0 Consensus size: 114
702041 TAGACTTTAG
** *
702051 CATTACCTGTATGCAGAAGTATAACACCTTTCTAATGGGAGAGCTTTTATTAATAGATGAAGGTT
1 CATTACCTGTACACAGAAGTATAACACCTTTCTAATGGGAGAGCTTTTATTAATAGATGAAGGCT
* * *
702116 AAGAAGTGAACAGAACTTTTTACGGTCGGAA-AAAAGTAGAAGTTGTATTT
66 AAGAACTAAACAGAACTTTTTACAGTC-GAATAAAA-TAGAAGTTGTATTT
* **
702166 CATTACCTGTACACAGAGGTATAATGCCTTTCTAATGGGAGAGCTTTTATTAATAGATGAAGGCT
1 CATTACCTGTACACAGAAGTATAACACCTTTCTAATGGGAGAGCTTTTATTAATAGATGAAGGCT
* *
702231 AAGAACTAAACAGAACTTTTTACAGTCGAATAACATAGAAGTTGTCTTT
66 AAGAACTAAACAGAACTTTTTACAGTCGAATAAAATAGAAGTTGTATTT
702280 CATTA
1 CATTA
702285 GCAATCTTTT
Statistics
Matches: 107, Mismatches: 11, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
114 21 0.20
115 86 0.80
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (114 bp):
CATTACCTGTACACAGAAGTATAACACCTTTCTAATGGGAGAGCTTTTATTAATAGATGAAGGCT
AAGAACTAAACAGAACTTTTTACAGTCGAATAAAATAGAAGTTGTATTT
Found at i:706020 original size:21 final size:22
Alignment explanation
Indices: 705991--706034 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
705981 TCGAATCAAG
705991 ATTTATAAGATCAAA-CGCAAAT
1 ATTTATAAGA-CAAATCGCAAAT
*
706013 ATTT-TAAGACAAATTGCAAAT
1 ATTTATAAGACAAATCGCAAAT
706034 A
1 A
706035 CGTGAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (22 bp):
ATTTATAAGACAAATCGCAAAT
Found at i:708538 original size:22 final size:24
Alignment explanation
Indices: 708503--708546 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
708493 TTTTTTTATT
*
708503 ATTTAAATATTATTTTAATAAAAA
1 ATTTAAATATTATTTAAATAAAAA
708527 ATTT-AATA-TATTTAAATAAA
1 ATTTAAATATTATTTAAATAAA
708547 TATATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
23 4 0.21
24 4 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
ATTTAAATATTATTTAAATAAAAA
Found at i:708598 original size:9 final size:10
Alignment explanation
Indices: 708572--708603 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
708562 ATTATTTTAT
708572 TTTAAAAATA
1 TTTAAAAATA
708582 TTTAAAAATA
1 TTTAAAAATA
708592 TTTAAAATATA
1 TTTAAAA-ATA
708603 T
1 T
708604 AATTAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 17 0.81
11 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAATA
Found at i:715325 original size:13 final size:14
Alignment explanation
Indices: 715301--715333 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
715291 GAAATTCTTT
715301 GAAGATAAGAAGAA
1 GAAGATAAGAAGAA
715315 GAAGA-AAGAAGAA
1 GAAGATAAGAAGAA
*
715328 GCAGAT
1 GAAGAT
715334 GTTGATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.30, T:0.06
Consensus pattern (14 bp):
GAAGATAAGAAGAA
Found at i:717726 original size:21 final size:20
Alignment explanation
Indices: 717700--717744 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
717690 TATTTAAAGA
717700 TATTAAAAA-ATAAATTTTAAT
1 TATTAAAAATA-AAATTTT-AT
*
717721 TATTAAAATTAAAATTTTAT
1 TATTAAAAATAAAATTTTAT
717741 TATT
1 TATT
717745 TTATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 15 0.68
22 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAAAAATAAAATTTTAT
Found at i:717733 original size:20 final size:21
Alignment explanation
Indices: 717700--717744 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
717690 TATTTAAAGA
717700 TATTAAAAAAT-AAATTTTAAT
1 TATTAAAAAATAAAATTTT-AT
*
717721 TATT-AAAATTAAAATTTTAT
1 TATTAAAAAATAAAATTTTAT
717741 TATT
1 TATT
717745 TTATTAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAAAAAATAAAATTTTAT
Found at i:718729 original size:13 final size:11
Alignment explanation
Indices: 718703--718736 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 11
718693 TTTATATTCG
718703 TATCATATTTA
1 TATCATATTTA
718714 TATCATATCATTA
1 TATCATAT--TTA
718727 TATCATATTT
1 TATCATATTT
718737 TAAATTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.48
13 11 0.52
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (11 bp):
TATCATATTTA
Found at i:722364 original size:2 final size:2
Alignment explanation
Indices: 722357--722393 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
722347 ATGAAACAAC
*
722357 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
722394 TTATTCTGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:725806 original size:16 final size:16
Alignment explanation
Indices: 725785--725829 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
725775 GTTTCTAGAG
725785 AGAGAAAAAAAGAAAA
1 AGAGAAAAAAAGAAAA
* * *
725801 AGAGAATAAAAGAGAT
1 AGAGAAAAAAAGAAAA
725817 AGAGAAAAGAAAG
1 AGAGAAAA-AAAG
725830 GAGATATGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 20 0.83
17 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.04
Consensus pattern (16 bp):
AGAGAAAAAAAGAAAA
Found at i:727630 original size:14 final size:14
Alignment explanation
Indices: 727595--727631 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
727585 AAAGTTCAAA
*
727595 ATTTTAAAATAAAT
1 ATTTTAATATAAAT
*
727609 ATTTTAATATTAAT
1 ATTTTAATATAAAT
727623 ATTTTAATA
1 ATTTTAATA
727632 ATTTTAAATA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTTAATATAAAT
Found at i:727647 original size:5 final size:5
Alignment explanation
Indices: 727637--727663 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
727627 TAATAATTTT
727637 AAATA AAATA AAATA AAATA AAATA AA
1 AAATA AAATA AAATA AAATA AAATA AA
727664 TTTTTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAATA
Found at i:727889 original size:52 final size:53
Alignment explanation
Indices: 727789--727893 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 53
727779 TAGTTTATTA
* * *
727789 AGGAATAATTACAATAGTACTTATTCATTATCTAATTAATGCATAAAACTACG
1 AGGAAAAATTACAACAGTACTTATTCATTATCTAATTAATGCAGAAAACTACG
727842 AGGAAAAATTACAACAGTACTTA-TCATTATCTAATTAATGCAGAAAACTACG
1 AGGAAAAATTACAACAGTACTTATTCATTATCTAATTAATGCAGAAAACTACG
727894 TACTAAGTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
52 28 0.57
53 21 0.43
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.30
Consensus pattern (53 bp):
AGGAAAAATTACAACAGTACTTATTCATTATCTAATTAATGCAGAAAACTACG
Found at i:732773 original size:22 final size:21
Alignment explanation
Indices: 732744--732784 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
732734 TTGAATTTTT
*
732744 AAAAAATTAAGCCTGAAAAGA
1 AAAAAATTAAACCTGAAAAGA
*
732765 AAAATAATTAAACTTGAAAA
1 AAAA-AATTAAACCTGAAAA
732785 AATTATACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (21 bp):
AAAAAATTAAACCTGAAAAGA
Found at i:733534 original size:46 final size:45
Alignment explanation
Indices: 733456--733546 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 45
733446 TTTGAAATCC
* ** *
733456 TTATTTATAACAAATCTAAACATGTCGCGAGGTAGCATGAGGTAG
1 TTATTTATAACAAATCCAAACATGTCAAGAGGTAGCATAAGGTAG
* * *
733501 TTATTTATTAATAAATCCAAACCTGTCAAGAGGTTGCATAAGGTAG
1 TTATTTA-TAACAAATCCAAACATGTCAAGAGGTAGCATAAGGTAG
733547 GTAGGATACA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
45 7 0.18
46 31 0.82
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (45 bp):
TTATTTATAACAAATCCAAACATGTCAAGAGGTAGCATAAGGTAG
Found at i:733573 original size:2 final size:2
Alignment explanation
Indices: 733566--733596 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
733556 AAAACAAATC
*
733566 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
733597 AATGTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:735837 original size:62 final size:62
Alignment explanation
Indices: 735627--735829 Score: 180
Period size: 63 Copynumber: 3.3 Consensus size: 62
735617 CTTTCAATTT
* * * * * *
735627 TTATTGAAGGCATTTTTGGTAAAAAATACCTTGAGTAATC--CTTCTAATTTTTTAGAAGGGA
1 TTATTGAAGGCGTTTTTAGTAAAAAATGCTTTGAGTAATCTGTTTC-AATTTTTAAGAAGGGA
* * * **
735688 TTATTGAAGGCGTTTTTAGTAAAAAATGCTTTCAAT-ATTTCGCTTTC-ATTTTTATTAAGGGGA
1 TTATTGAAGGCGTTTTTAGTAAAAAATGCTTTGAGTAATCT-G-TTTCAATTTTTAAGAA-GGGA
* * * ** * *
735751 TTATTCAAGGTGATTTTAGCCAAAAACGCTTTGAGTAATCTGTTTCAATTTTTAAGAAGAGA
1 TTATTGAAGGCGTTTTTAGTAAAAAATGCTTTGAGTAATCTGTTTCAATTTTTAAGAAGGGA
735813 TTATTGAAGGCGTTTTT
1 TTATTGAAGGCGTTTTT
735830 GATCAAAAGT
Statistics
Matches: 109, Mismatches: 26, Indels: 13
0.74 0.18 0.09
Matches are distributed among these distances:
60 2 0.02
61 30 0.28
62 29 0.27
63 42 0.39
64 6 0.06
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (62 bp):
TTATTGAAGGCGTTTTTAGTAAAAAATGCTTTGAGTAATCTGTTTCAATTTTTAAGAAGGGA
Found at i:740537 original size:20 final size:20
Alignment explanation
Indices: 740509--740547 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
740499 TAGATAATTG
* *
740509 TTTATAATTTAATACTATTA
1 TTTAAAATTTAAAACTATTA
740529 TTTAAAATTTAAAACTATT
1 TTTAAAATTTAAAACTATT
740548 TTATTTTAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTAAAATTTAAAACTATTA
Found at i:744889 original size:21 final size:21
Alignment explanation
Indices: 744851--744890 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
744841 GGTAAATAAA
*
744851 ATTAAATTTTATATTAATTTT
1 ATTAAATTTTATAATAATTTT
744872 ATTAATATTTTA-AATAATT
1 ATTAA-ATTTTATAATAATT
744891 ATCATATGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTAAATTTTATAATAATTTT
Found at i:757375 original size:23 final size:23
Alignment explanation
Indices: 757318--757378 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
757308 TGTTTTTAGA
* * *
757318 AAAATGCCGCTAAGTTTTATCAT
1 AAAACGCCACTAAATTTTATCAT
**
757341 AAAACGTTACTAAATTTTATCAT
1 AAAACGCCACTAAATTTTATCAT
757364 AAAACGCCACTAAAT
1 AAAACGCCACTAAAT
757379 ATAAAAACGT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (23 bp):
AAAACGCCACTAAATTTTATCAT
Found at i:757400 original size:34 final size:34
Alignment explanation
Indices: 757362--757436 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 34
757352 AAATTTTATC
757362 ATAAAACGCCACTAAATATAAAAACGTTTATAGT
1 ATAAAACGCCACTAAATATAAAAACGTTTATAGT
* * * ***
757396 ATAAAATGTCACTAAATTTAGTGACGTTTATAGT
1 ATAAAACGCCACTAAATATAAAAACGTTTATAGT
*
757430 AGAAAAC
1 ATAAAAC
757437 ACCATTATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (34 bp):
ATAAAACGCCACTAAATATAAAAACGTTTATAGT
Found at i:758748 original size:62 final size:60
Alignment explanation
Indices: 758608--758752 Score: 141
Period size: 62 Copynumber: 2.4 Consensus size: 60
758598 TTTTTACAAA
* * *
758608 AAAAATACCTTCAATAATCCTCTCTATTTTTTATGAAAGGATTATTGAAGGCATTTCAAGC
1 AAAAATACCTTCAATAAT-CTCTCTAATTTTGATGAAAGGATTATTGAAAGCATTTCAAGC
* * * * * *
758669 -AAAAGACGTCTTTAATAATCTCTTTAAATTTTGATGAGAA-GATTATTGAAAGCGTTTTTAATC
1 AAAAATAC--CTTCAATAATCTCTCT-AATTTTGATGA-AAGGATTATTGAAAGC-ATTTCAAGC
758732 AAAAATACCTTCAATAATCTC
1 AAAAATACCTTCAATAATCTC
758753 CTATAAAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
60 6 0.09
61 5 0.07
62 42 0.63
63 8 0.12
64 6 0.09
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (60 bp):
AAAAATACCTTCAATAATCTCTCTAATTTTGATGAAAGGATTATTGAAAGCATTTCAAGC
Found at i:758989 original size:62 final size:59
Alignment explanation
Indices: 758800--759001 Score: 217
Period size: 62 Copynumber: 3.3 Consensus size: 59
758790 GTTTTCTGTC
* * * * *
758800 AAAAATGCCTTTAATAATCCTTTTCATTTTTTAGAAGGGATTATTGAAGGCGTTTAGGTA
1 AAAAATACCTTCAATAATCCTTTTAATTTTTTAG-AGGGATTATTGAAAGCGTTTAGGCA
* * * * * *
758860 AAAAA-ACGCCTTCAATAATCCCTTTCAATTTTTTAGAGTGGATTATTAAAAACATTTTAAGCC
1 AAAAATA--CCTTCAATAAT-CCTTTTAATTTTTTAGAG-GGATTATTGAAAGC-GTTTAGGCA
758923 AAAAATACCTTCAATAATCTCTTTTAATTTTTTAGACGGGATTATTGAAAGCGTTTCAGGCA
1 AAAAATACCTTCAATAATC-CTTTTAATTTTTTAGA-GGGATTATTGAAAGCGTTT-AGGCA
758985 AAAAATACCTTCAATAA
1 AAAAATACCTTCAATAA
759002 CCATCAATAA
Statistics
Matches: 116, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
60 5 0.04
61 16 0.14
62 83 0.72
63 11 0.09
64 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (59 bp):
AAAAATACCTTCAATAATCCTTTTAATTTTTTAGAGGGATTATTGAAAGCGTTTAGGCA
Found at i:768735 original size:17 final size:17
Alignment explanation
Indices: 768713--768747 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
768703 CACTTCTTAA
768713 TTTTTT-AAATTCATATT
1 TTTTTTAAAATT-ATATT
768730 TTTTTTAAAATTATATT
1 TTTTTTAAAATTATATT
768747 T
1 T
768748 AAGAAAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTTAAAATTATATT
Found at i:777804 original size:128 final size:128
Alignment explanation
Indices: 777449--777975 Score: 649
Period size: 130 Copynumber: 4.1 Consensus size: 128
777439 TTTTCATACC
* *
777449 TTGAAAGCTCAATAATTTGAATTTTCTTTTTTTTTTTCTATTGGGTGAAGTAAAAATGGTGCGGT
1 TTGAAAGTTCAATAATTTG-AGTTT-TTTTTTTTTTTCTATTGGGTGAAGTAAAAATGGTGCGGT
* * * *
777514 CCAAAAATAATATTTATTAGTTAGTAACTAATAATGACCAGGCATGATCACCAGAATTTCATGCT
64 CCAAAAATAATATTTATTAGTTAGTAACTAATAATGATCACGCATGATCACGAGAATTTCACGCT
* **
777579 TTGAAAGTTCAATAATTTGAGTTTTTTTTTTCTTTTTTTATTGGGTGAAGTAAAAATGGTATGGT
1 TTGAAAGTTCAATAATTTGAG-TTTTTTTTT-TTTTTCTATTGGGTGAAGTAAAAATGGTGCGGT
* * * * *
777644 TCAAAAATAATATTTATTAGTTAGTAATTAATAATAATCACGCATGATCATGAGAATTTCACGTT
64 CCAAAAATAATATTTATTAGTTAGTAACTAATAATGATCACGCATGATCACGAGAATTTCACGCT
777709 TTGAAAGTTCAATAATTTGAGTTTTTTTTTTTTTTCTATTGGGTGAAGTAAAAATGGTGCGGTCC
1 TTGAAAGTTCAATAATTTGAGTTTTTTTTTTTTTTCTATTGGGTGAAGTAAAAATGGTGCGGTCC
* *
777774 AAAAATAATATTTATTAGTTAGTAACTAATAATGATGACGCATGATCACGAGGATTTCACGCT
66 AAAAATAATATTTATTAGTTAGTAACTAATAATGATCACGCATGATCACGAGAATTTCACGCT
* * * **
777837 TTAAAAGCTT-AATAATTTGAG--TTTTTTTTTTAT-TAAT---TGAA-TAAAAATAATGCGGTC
1 TTGAAAG-TTCAATAATTTGAGTTTTTTTTTTTTTTCTATTGGGTGAAGTAAAAATGGTGCGGTC
* * * * * ** * *
777894 TAAAATTAATATTTATTAGTTAGTAACTAACAATGA-CTAGGTAAAATCACGAGGATTTCTCGCT
65 CAAAAATAATATTTATTAGTTAGTAACTAATAATGATC-ACGCATGATCACGAGAATTTCACGCT
*
777958 TTGGAAAGCTCAATAATT
1 TT-GAAAGTTCAATAATT
777976 ATATTCCATA
Statistics
Matches: 351, Mismatches: 40, Indels: 20
0.85 0.10 0.05
Matches are distributed among these distances:
121 71 0.20
122 15 0.04
125 3 0.01
126 11 0.03
128 105 0.30
129 18 0.05
130 128 0.36
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (128 bp):
TTGAAAGTTCAATAATTTGAGTTTTTTTTTTTTTTCTATTGGGTGAAGTAAAAATGGTGCGGTCC
AAAAATAATATTTATTAGTTAGTAACTAATAATGATCACGCATGATCACGAGAATTTCACGCT
Found at i:783485 original size:3 final size:3
Alignment explanation
Indices: 783470--783642 Score: 163
Period size: 3 Copynumber: 61.7 Consensus size: 3
783460 CAACCGATAT
* **
783470 TTA TTA TTG TTA TTA TTA TT- TTA TTA GCA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
783516 TTT TTA TTA GTA TTA -TA TTA CTA -TA GTA -TA TTA -TA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
** * *
783559 TCC TTA -TA TTA -TA TTA -TA GTA -TA TTA -TA TTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
783602 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
783643 TTCTTTACTG
Statistics
Matches: 141, Mismatches: 17, Indels: 24
0.77 0.09 0.13
Matches are distributed among these distances:
2 24 0.17
3 117 0.83
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:784118 original size:20 final size:20
Alignment explanation
Indices: 784093--784130 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
784083 TTGAGATTAT
* *
784093 GAAAAAATTTGAAGAATTTG
1 GAAAAAATCTGAAAAATTTG
784113 GAAAAAATCTGAAAAATT
1 GAAAAAATCTGAAAAATT
784131 ATAGGTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.16, T:0.26
Consensus pattern (20 bp):
GAAAAAATCTGAAAAATTTG
Found at i:784156 original size:8 final size:8
Alignment explanation
Indices: 784143--784167 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
784133 AGGTTTGAGA
784143 TGAATTTT
1 TGAATTTT
784151 TGAATTTT
1 TGAATTTT
784159 TGAATTTT
1 TGAATTTT
784167 T
1 T
784168 CGATTGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TGAATTTT
Found at i:784534 original size:11 final size:11
Alignment explanation
Indices: 784470--784534 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
784460 GATCGCAAGT
*
784470 TTTTTTTTTCTA
1 TTTTATTTT-TA
* *
784482 TTTTAATTGTA
1 TTTTATTTTTA
*
784493 TTTTAATTTTA
1 TTTTATTTTTA
784504 TTTTATTTTATA
1 TTTTATTTT-TA
784516 TTTATATTTTTA
1 TTT-TATTTTTA
784528 TTTTATT
1 TTTTATT
784535 ATCAGTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
11 24 0.52
12 16 0.35
13 6 0.13
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:784536 original size:16 final size:16
Alignment explanation
Indices: 784475--784560 Score: 54
Period size: 19 Copynumber: 5.3 Consensus size: 16
784465 CAAGTTTTTT
*
784475 TTTTCTATTTTAATTGTA
1 TTTT-TATTTT-ATTATA
* *
784493 TTTTAATTTTATTTTA
1 TTTTTATTTTATTATA
*
784509 -TTTTA-TAT-TTATA
1 TTTTTATTTTATTATA
784522 TTTTTATTTTATTATCA
1 TTTTTATTTTATTAT-A
*
784539 GTTTTTTATTTTACTA-A
1 --TTTTTATTTTATTATA
784556 TTTTT
1 TTTTT
784561 GTTATTTATT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
13 4 0.07
14 7 0.13
15 11 0.20
16 9 0.16
17 7 0.13
18 4 0.07
19 13 0.24
ACGTcount: A:0.23, C:0.03, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTTATTTTATTATA
Found at i:784551 original size:5 final size:5
Alignment explanation
Indices: 784480--784534 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 5
784470 TTTTTTTTTC
* *
784480 TATTT TAATTG TATTT TAATTT TATTT TATTT TATATT TA-TA T-TTT
1 TATTT T-ATTT TATTT T-ATTT TATTT TATTT TAT-TT TATTT TATTT
784526 TATTT TATT
1 TATTT TATT
784535 ATCAGTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
4 4 0.10
5 24 0.59
6 13 0.32
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (5 bp):
TATTT
Found at i:785733 original size:17 final size:17
Alignment explanation
Indices: 785697--785729 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
785687 ATAAAAGTAA
*
785697 ATATTTTTATTAATTTT
1 ATATTTTTATAAATTTT
785714 ATATTTTT-TAAATTTT
1 ATATTTTTATAAATTTT
785730 TATAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
ATATTTTTATAAATTTT
Found at i:785789 original size:12 final size:12
Alignment explanation
Indices: 785772--785807 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
785762 TCTATTTAAA
785772 TATATTAAAAAT
1 TATATTAAAAAT
*
785784 TATATTAAAAAA
1 TATATTAAAAAT
785796 TATA-TAAAAAT
1 TATATTAAAAAT
785807 T
1 T
785808 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TATATTAAAAAT
Found at i:785805 original size:24 final size:25
Alignment explanation
Indices: 785769--785828 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
785759 AAATCTATTT
* *
785769 AAATATATTAAAAATT-ATATTAAA
1 AAATATATAAAAAATTAAAATTAAA
* *
785793 AAATATATAAAAATTTAAAATTTAA
1 AAATATATAAAAAATTAAAATTAAA
*
785818 AAATAAATAAA
1 AAATATATAAA
785829 TCAAAAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 14 0.47
25 16 0.53
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AAATATATAAAAAATTAAAATTAAA
Found at i:788075 original size:30 final size:30
Alignment explanation
Indices: 788005--788076 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 30
787995 ACCACACCCG
* * * *
788005 AAATTAAT-AAAATATTATTTTTTAAATAT
1 AAATAAATAAAAATATCATTATATAAATAT
**
788034 AAATATTTAAAAATATCATTATATAAATAT
1 AAATAAATAAAAATATCATTATATAAATAT
*
788064 ATATAAATAAAAA
1 AAATAAATAAAAA
788077 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
29 5 0.15
30 28 0.85
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (30 bp):
AAATAAATAAAAATATCATTATATAAATAT
Done.