Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold226
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: 763807
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 17558 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:370042 original size:40 final size:40
Alignment explanation
Indices: 369918--370057 Score: 151
Period size: 40 Copynumber: 3.5 Consensus size: 40
369908 GACTTCGAGT
* * *
369918 CGATGAGACACTAGGTGACAAATTATTACTTCGGATATATT
1 CGATGAGACACTGGGTGCCAAATTATTACTTCGGAT-TATC
* * * *
369959 CGATGAGGCACTGGGTGCC-GA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGCCAAATTATTACTTCGGATTATC
* *
369996 CGATGAGACATTGGGTGCCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGCCAAATTATTACTTCGGATTATC
* *
370036 CAATGAGGCACTGGGTGCCAAA
1 CGATGAGACACTGGGTGCCAAA
370058 CTGGTGTGTT
Statistics
Matches: 80, Mismatches: 16, Indels: 7
0.78 0.16 0.07
Matches are distributed among these distances:
37 19 0.24
38 11 0.14
39 2 0.03
40 32 0.40
41 16 0.20
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.29
Consensus pattern (40 bp):
CGATGAGACACTGGGTGCCAAATTATTACTTCGGATTATC
Found at i:379615 original size:15 final size:16
Alignment explanation
Indices: 379588--379622 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
379578 ATTGTGTATC
379588 ATATTATTTAATATAA
1 ATATTATTTAATATAA
379604 ATATTA-TTAATATAA
1 ATATTATTTAATATAA
379619 ATAT
1 ATAT
379623 AATCTTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATATTATTTAATATAA
Found at i:380178 original size:25 final size:26
Alignment explanation
Indices: 380141--380190 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
380131 TCACAAACAA
380141 TAAATCAAACAAACAAACAAAATTTT
1 TAAATCAAACAAACAAACAAAATTTT
* *
380167 TAAAT-AAACAAACCAACTAAATTT
1 TAAATCAAACAAACAAACAAAATTT
380191 AAATATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (26 bp):
TAAATCAAACAAACAAACAAAATTTT
Found at i:382553 original size:241 final size:241
Alignment explanation
Indices: 382128--382614 Score: 911
Period size: 241 Copynumber: 2.0 Consensus size: 241
382118 GGGTTTTAGT
*
382128 ATCGATTTTAATTATGCACTTTTGTGTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
1 ATCGATTTTAATTATGCACTTTTGTCTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
*
382193 CAACCATTTAAACTGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
66 CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
* *
382258 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATTATTACTGATTTGAGCAT
131 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
382323 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
196 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
* * *
382369 ATCGATTTTAGTTATGCACTTTTGTCTGCTGCCAGGAGAGGATTGAGAGGAAATTGGTGCTCCTC
1 ATCGATTTTAATTATGCACTTTTGTCTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
382434 CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
66 CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
382499 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
131 CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
382564 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
196 GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
382610 ATCGA
1 ATCGA
382615 AATTGGATCA
Statistics
Matches: 239, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
241 239 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (241 bp):
ATCGATTTTAATTATGCACTTTTGTCTGCTACCAAGAGAGGATTGAGAGGAAATTGGTGCTCCTC
CAACCATTTAAACGGCAGGTTGTTGTTGTTCACTGTTGCATAAGTATTTTAACATTTTTGGAAGC
CGAATATGGGCATTTTTGTGGCATATTTAATTTAGTTTCCGTACAATCATTACTGATTTGAACAT
GTTAAATGACGATTTTAGGTTCTGGGAGTTTCGTGGTGGCATTTAC
Found at i:384086 original size:18 final size:18
Alignment explanation
Indices: 384063--384100 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
384053 TGAACCTTTA
*
384063 ATAATTTTAAAATTTTTT
1 ATAATTTTAAAATTATTT
*
384081 ATAATTTTTAAATTATTT
1 ATAATTTTAAAATTATTT
384099 AT
1 AT
384101 TGGCATGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATAATTTTAAAATTATTT
Found at i:385289 original size:14 final size:14
Alignment explanation
Indices: 385270--385309 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
385260 TTGATTGCCA
385270 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
385284 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
385298 GGAAAATGTTTT
1 GTAAAATGTTTT
385310 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:385318 original size:20 final size:20
Alignment explanation
Indices: 385293--385332 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
385283 CGTAAAATGA
*
385293 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
385313 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
385333 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:385322 original size:34 final size:35
Alignment explanation
Indices: 385278--385344 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
385268 CAGTAAAATG
*
385278 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
385312 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
385345 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:385348 original size:14 final size:15
Alignment explanation
Indices: 385272--385348 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
385262 GATTGCCAGT
* *
385272 AAAATG-TTTTCCGT
1 AAAATGATTTTCTGG
385286 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
385300 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
385320 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
385335 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
385349 TGTTTGATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.09, G:0.16, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:385602 original size:34 final size:32
Alignment explanation
Indices: 385554--385616 Score: 108
Period size: 34 Copynumber: 1.9 Consensus size: 32
385544 TGAAAACAAC
385554 TAATATCAATATTTGTAATTGTGTTAAAATAA
1 TAATATCAATATTTGTAATTGTGTTAAAATAA
385586 TAATACTCAATTATTTGTAATTGTGTTAAAA
1 TAATA-TCAA-TATTTGTAATTGTGTTAAAA
385617 ACAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 5 0.17
33 4 0.14
34 20 0.69
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (32 bp):
TAATATCAATATTTGTAATTGTGTTAAAATAA
Found at i:388105 original size:12 final size:11
Alignment explanation
Indices: 388091--388132 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
388081 CCAGATCAAG
388091 GGAGAACGAAA
1 GGAGAACGAAA
388102 GG-G-A-GAAA
1 GGAGAACGAAA
388110 GGAGAACGAAA
1 GGAGAACGAAA
388121 GGGAGAACGAAA
1 -GGAGAACGAAA
388133 CCAGATCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
8 6 0.22
9 2 0.07
10 2 0.07
11 6 0.22
12 11 0.41
ACGTcount: A:0.52, C:0.07, G:0.40, T:0.00
Consensus pattern (11 bp):
GGAGAACGAAA
Found at i:388115 original size:19 final size:19
Alignment explanation
Indices: 388091--388127 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
388081 CCAGATCAAG
388091 GGAGAACGAAAGGGAGAAA
1 GGAGAACGAAAGGGAGAAA
388110 GGAGAACGAAAGGGAGAA
1 GGAGAACGAAAGGGAGAA
388128 CGAAACCAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.43, T:0.00
Consensus pattern (19 bp):
GGAGAACGAAAGGGAGAAA
Found at i:402124 original size:18 final size:17
Alignment explanation
Indices: 402101--402134 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
402091 CGCCGCACGT
402101 CCCACGTCGCAGCAACCG
1 CCCACGT-GCAGCAACCG
*
402119 CCCACGTTCAGCAACC
1 CCCACGTGCAGCAACC
402135 CCGCACGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.50, G:0.18, T:0.09
Consensus pattern (17 bp):
CCCACGTGCAGCAACCG
Found at i:402132 original size:17 final size:17
Alignment explanation
Indices: 402110--402143 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
402100 TCCCACGTCG
402110 CAGCAACCGCC-CACGTT
1 CAGCAACC-CCGCACGTT
402127 CAGCAACCCCGCACGTT
1 CAGCAACCCCGCACGTT
402144 GTGCACATCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.24, C:0.47, G:0.18, T:0.12
Consensus pattern (17 bp):
CAGCAACCCCGCACGTT
Found at i:402978 original size:18 final size:16
Alignment explanation
Indices: 402957--403002 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 16
402947 GATTGTATCC
402957 TTATTATTATATTATTTA
1 TTATT-TTATATTA-TTA
402975 TTATTTTTATCATTATTA
1 TTA-TTTTAT-ATTATTA
402993 TTATTTTATA
1 TTATTTTATA
403003 CATATACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.04
17 6 0.23
18 13 0.50
19 6 0.23
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTTATATTATTA
Found at i:403055 original size:25 final size:25
Alignment explanation
Indices: 403018--403066 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
403008 ACACACGCAT
*
403018 TTTTTTAATAATATATATGCATATA
1 TTTTTTAATAATACATATGCATATA
*
403043 TTTTTT-ATAAATACATGTGCATAT
1 TTTTTTAAT-AATACATATGCATAT
403067 TTTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (25 bp):
TTTTTTAATAATACATATGCATATA
Found at i:403091 original size:11 final size:12
Alignment explanation
Indices: 403063--403096 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
403053 ATACATGTGC
403063 ATATTTTATATAT
1 ATATTTTAT-TAT
403076 ATATTTTATTAT
1 ATATTTTATTAT
403088 -TATTTTATT
1 ATATTTTATT
403097 CTCATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 3 0.14
13 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:403142 original size:18 final size:17
Alignment explanation
Indices: 403105--403143 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
403095 TTCTCATAGT
* *
403105 TTTTATATACATTTATA
1 TTTTATATACATATACA
403122 TTTTATAATACATATACA
1 TTTTAT-ATACATATACA
403140 TTTT
1 TTTT
403144 CCTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATATACATATACA
Found at i:403349 original size:13 final size:14
Alignment explanation
Indices: 403331--403359 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
403321 TTTCAAGATT
403331 TACTTATATAT-TA
1 TACTTATATATATA
403344 TACTTATATATATA
1 TACTTATATATATA
403358 TA
1 TA
403360 TTGCAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TACTTATATATATA
Found at i:413370 original size:20 final size:20
Alignment explanation
Indices: 413347--413385 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
413337 TGAAATAATC
*
413347 AAAAATG-AATAAAATTTTA
1 AAAAATGAAACAAAATTTTA
413366 AAAAATGAAACAAAATTTTA
1 AAAAATGAAACAAAATTTTA
413386 TAAATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (20 bp):
AAAAATGAAACAAAATTTTA
Found at i:415322 original size:44 final size:42
Alignment explanation
Indices: 415250--415643 Score: 195
Period size: 44 Copynumber: 8.8 Consensus size: 42
415240 ATCTGATGCG
* * * *
415250 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTTACTTTA
* * * *
415294 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTTA
* * *
415338 ATCTGCTCC-GTAGTAATCTCAGGGAGATAAGATTTCTGGCTTCA
1 ATCTGCTCCACT-GTAATCTCAGGGAGATAAGATTT-T-ACTTTA
** *
415382 ATCTGATGCGATCTACACTACTGTAA-CTTCAGAAAGATAAGATCTTTTATTTTA
1 ATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGA--TTTTACTTTA
* * * * *
415436 ATCCGCTCCACTGTAATCTCAGAGAGATAGGATTACTAGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTTA
* ** * * *
415480 ATCTACTCCGTTGTAATCTCAGGGAGATAAGATTTGA-TGTG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTACTTTA
* * * *
415521 ATCTACTCCACTGTAA-CTTCAGAGAGATAAGATCCCTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TTTACTTTA
* * *
415565 ATCTGCTCCACTGTAATCTCGGGGAGATAGGATTACTAGCTTTA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATT-TTA-CTTTA
* *
415609 ATCTACTCCACTGTAATCTCAAGGAGATAAGATTT
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTT
415644 CTGACTTCAG
Statistics
Matches: 265, Mismatches: 55, Indels: 61
0.70 0.14 0.16
Matches are distributed among these distances:
40 1 0.00
41 29 0.11
42 3 0.01
43 10 0.04
44 180 0.68
45 4 0.02
46 1 0.00
47 3 0.01
49 2 0.01
51 2 0.01
52 1 0.00
53 2 0.01
54 22 0.08
55 2 0.01
56 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (42 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTTACTTTA
Found at i:415407 original size:142 final size:141
Alignment explanation
Indices: 415101--415652 Score: 772
Period size: 142 Copynumber: 4.0 Consensus size: 141
415091 GAGATAAGAC
* * * *
415101 CTGATGCGATCTACTCAACTGTAACTTCAGAAAGATAAGATTCTTTACTTTAATTCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* *
415166 TAATCTCAGAGAGATAGGATTACT-GCTTCAATCTGCTCCGCTGTAATCTCAAGGAGGTAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCG-TGTAATCTCAAGGAGATAAGATT
415230 TCTGGCTTCAAT
130 TCTGGCTTCAAT
*
415242 CTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAAGATCCTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * *
415307 TAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCTCCGTAGTAATCTCAGGGAGATAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGT-GTAATCTCAAGGAGATAAGATT
415372 TCTGGCTTCAAT
130 TCTGGCTTCAAT
* *
415384 CTGATGCGATCTACACTACTGTAACTTCAGAAAGATAAGATCTTTTATTTTAATCCGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
*
415449 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGTTGTAATCTCAGGGAGATAAGA-T
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCG-TGTAATCTCAAGGAGATAAGATT
415513 T-T-G-----A-
130 TCTGGCTTCAAT
* * * *
415517 -TG-T--GATCTACTCCACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCTGCTCCACTG
1 CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
* * * *
415578 TAATCTCGGGGAGATAGGATTACTAGCTTTAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
66 TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCC-GTGTAATCTCAAGGAGATAAGATT
*
415643 TCTGACTTCA
130 TCTGGCTTCA
415653 GTTTGTTCCA
Statistics
Matches: 374, Mismatches: 25, Indels: 28
0.88 0.06 0.07
Matches are distributed among these distances:
129 109 0.29
130 2 0.01
131 2 0.01
132 2 0.01
134 1 0.00
139 1 0.00
140 1 0.00
141 86 0.23
142 169 0.45
143 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.33
Consensus pattern (141 bp):
CTGATGCGATCTACTCTACTGTAACTTCAGAAAGATAAGATCCTTTATTTTAATCCGCTCCACTG
TAATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGTGTAATCTCAAGGAGATAAGATTT
CTGGCTTCAAT
Found at i:415615 original size:129 final size:129
Alignment explanation
Indices: 415385--415643 Score: 401
Period size: 129 Copynumber: 2.0 Consensus size: 129
415375 GGCTTCAATC
* **
415385 TGATGCGATCTACACTACTGTAACTTCAGAAAGATAAGATCTTTTATTTTAATCCGCTCCACTGT
1 TGATGCGATCTACACCACTGTAACTTCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
** *
415450 AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCGTTGTAATCTCAGGGAGATAAGATT
66 AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
* * * *
415514 TGATGTGATCTACTCCACTGTAACTTCAGAGAGATAAGATCCCTTATTTTAATCTGCTCCACTGT
1 TGATGCGATCTACACCACTGTAACTTCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
* * *
415579 AATCTCGGGGAGATAGGATTACTAGCTTTAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
66 AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
415643 T
1 T
415644 CTGACTTCAG
Statistics
Matches: 117, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
129 117 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (129 bp):
TGATGCGATCTACACCACTGTAACTTCAGAAAGATAAGATCCCTTATTTTAATCCGCTCCACTGT
AATCTCAGAGAGATAGGATTACTAGCTTCAATCTACTCCACTGTAATCTCAAGGAGATAAGATT
Found at i:430695 original size:22 final size:19
Alignment explanation
Indices: 430657--430697 Score: 55
Period size: 22 Copynumber: 2.0 Consensus size: 19
430647 AAATTATTGG
430657 AAAGATGACTGAGAATTAC
1 AAAGATGACTGAGAATTAC
430676 AAAGACTGACATGAGAAATTAC
1 AAAGA-TGAC-TGAG-AATTAC
430698 CATTCTCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 4 0.21
21 4 0.21
22 6 0.32
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (19 bp):
AAAGATGACTGAGAATTAC
Found at i:432603 original size:50 final size:50
Alignment explanation
Indices: 432535--432652 Score: 157
Period size: 50 Copynumber: 2.4 Consensus size: 50
432525 AATACACCAG
* * * * *
432535 TCTTATCGCCTTGACGTTGCAATGGAATAGATTGAAGCCACAGCGGCGAA
1 TCTTATCTCCCTGGCGTTGCAATGGAATAGATTGAAGCCACAACGGCAAA
* *
432585 TCTTA-CTTCCCTGGCGTTGCAGTGGAGTAGATTGAAGCCACAACGGCAAA
1 TCTTATC-TCCCTGGCGTTGCAATGGAATAGATTGAAGCCACAACGGCAAA
432635 TCTTATCTCCCTGGCGTT
1 TCTTATCTCCCTGGCGTT
432653 AAGACTTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.02
50 57 0.97
51 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.27
Consensus pattern (50 bp):
TCTTATCTCCCTGGCGTTGCAATGGAATAGATTGAAGCCACAACGGCAAA
Found at i:432852 original size:100 final size:100
Alignment explanation
Indices: 432731--433037 Score: 427
Period size: 100 Copynumber: 3.1 Consensus size: 100
432721 CAGTGGAACG
* * * * *
432731 GATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGTGGTGTAGTGGAACAGATTAAAGTTACGAC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
432796 GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
66 GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
* * * ** *
432831 TATTGAAGCCACAACGGTGAATCTTACTTCTCTGACGGTGTAGTGGAATAGATTGAAGCTGTGGC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
* *
432896 GGCGGATCTGATTTCCCCGACATTGCAATTAAAAA
66 GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
* *
432931 GATTGAAGCCACAACTGTGAATCTTACTTTCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
1 GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
* * * *
432996 GGTGAATATTG-TTTCCTCGACATTGCAGTTAAACA
66 GGTGAAT-CTGATTTCCCCGACATTGCAATTAAAAA
433031 GATTGAA
1 GATTGAA
433038 AATGGCGAAT
Statistics
Matches: 179, Mismatches: 27, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
100 177 0.99
101 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (100 bp):
GATTGAAGCCACAACGGTGAATCTTACTTCCCTGGCGGTGTAGTGGAATAGATTGAAGCTACGAC
GGTGAATCTGATTTCCCCGACATTGCAATTAAAAA
Found at i:433001 original size:50 final size:50
Alignment explanation
Indices: 432722--433002 Score: 145
Period size: 50 Copynumber: 5.6 Consensus size: 50
432712 TTGGCATTAC
** * * **
432722 AGTGGAACGGATTGAAGCCACAACGGTGAATCTTGCTTCCCTGGTGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGACGGTGT
* * ** * * * ** *
432772 AGTGGAACAGATTAAAGTTACGACGGTGAATCTGA-TTTCCCCGACATTGC
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTT-CCTGACGGTGT
* ** *
432822 AATTAAAAATATTGAAGCCACAACGGTGAATCTTAC-TTCTCTGACGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTC-CTGACGGTGT
* ***** * * * * ** *
432872 AGTGGAATAGATTGAAGCTGTGGCGGCGGATCTGA-TTTCCCCGACATTGC
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTT-CCTGACGGTGT
* ** * *
432922 AATTAAAAAGATTGAAGCCACAACTGTGAATCTTACTTTCCTGGCGGTGT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGACGGTGT
* * *
432972 AGTGGAATAGATTGAAGCTACGACGGTGAAT
1 AGTGGAAAAGATTGAAGCCACAACGGTGAAT
433003 ATTGTTTCCT
Statistics
Matches: 155, Mismatches: 70, Indels: 12
0.65 0.30 0.05
Matches are distributed among these distances:
49 3 0.02
50 148 0.95
51 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (50 bp):
AGTGGAAAAGATTGAAGCCACAACGGTGAATCTTACTTTCCTGACGGTGT
Found at i:434614 original size:3 final size:3
Alignment explanation
Indices: 434606--434656 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
434596 GATTGTATCC
* *
434606 TTA TTA TTA -TA TTA TTTA TTA TTT TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
434651 TT- TTA T
1 TTA TTA T
434657 ACATATACAC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 4 0.10
3 34 0.83
4 3 0.07
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:434699 original size:25 final size:25
Alignment explanation
Indices: 434673--434720 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
434663 ACACACGCAT
*
434673 TTTTTTAT-AATATATATGCATATA
1 TTTTTTATAAATACATATGCATATA
*
434697 TTTTTTATAAATACATGTGCATAT
1 TTTTTTATAAATACATATGCATAT
434721 TTTATATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTTTTATAAATACATATGCATATA
Found at i:434745 original size:11 final size:12
Alignment explanation
Indices: 434717--434750 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
434707 ATACATGTGC
434717 ATATTTTATATAT
1 ATATTTTAT-TAT
434730 ATATTTTATTAT
1 ATATTTTATTAT
434742 -TATTTTATT
1 ATATTTTATT
434751 CTCATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 3 0.14
13 9 0.43
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTTTATTAT
Found at i:434796 original size:18 final size:17
Alignment explanation
Indices: 434759--434797 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
434749 TTCTCATAGT
* *
434759 TTTTATATACATTTATA
1 TTTTATATACATATACA
434776 TTTTATAATACATATACA
1 TTTTAT-ATACATATACA
434794 TTTT
1 TTTT
434798 CCTTATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATATACATATACA
Found at i:435005 original size:13 final size:14
Alignment explanation
Indices: 434987--435015 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
434977 TCTCAAGATT
434987 TACTTATATAT-TA
1 TACTTATATATATA
435000 TACTTATATATATA
1 TACTTATATATATA
435014 TA
1 TA
435016 TTGCAAATAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
TACTTATATATATA
Found at i:436668 original size:7 final size:7
Alignment explanation
Indices: 436656--436682 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
436646 AAATTATCAT
436656 TTTAAAC
1 TTTAAAC
436663 TTTAAAC
1 TTTAAAC
436670 TTTAAAC
1 TTTAAAC
436677 TTTAAA
1 TTTAAA
436683 TTTCCTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (7 bp):
TTTAAAC
Found at i:437755 original size:29 final size:30
Alignment explanation
Indices: 437692--437769 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 30
437682 GTTTTTGTAC
*
437692 TCTTTATAAATTTA-GAATTTAGTCTCAGTA
1 TCTTT-TATATTTAGGAATTTAGTCTCAGTA
* *
437722 -CTTTTATTTTTAGGAATTTAGTGCTTA-TA
1 TCTTTTATATTTAGGAATTTAGT-CTCAGTA
* *
437751 TTTTTTATATTTCGGAATT
1 TCTTTTATATTTAGGAATT
437770 CAGATCCAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 6 0.15
29 15 0.38
30 18 0.46
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (30 bp):
TCTTTTATATTTAGGAATTTAGTCTCAGTA
Found at i:438732 original size:2 final size:2
Alignment explanation
Indices: 438725--438757 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
438715 TTCTTTTCTT
438725 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
438758 GAAATGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:441257 original size:16 final size:16
Alignment explanation
Indices: 441236--441268 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
441226 TACTTAGTTC
441236 ATAATGATGCTTCTAA
1 ATAATGATGCTTCTAA
441252 ATAATGATGCTTCTAA
1 ATAATGATGCTTCTAA
441268 A
1 A
441269 ATTGGTATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (16 bp):
ATAATGATGCTTCTAA
Found at i:446644 original size:27 final size:26
Alignment explanation
Indices: 446601--446697 Score: 70
Period size: 27 Copynumber: 3.6 Consensus size: 26
446591 GTGTTTTAAT
* *
446601 AAAAAAA-TATAACTACTTAATTAGGA
1 AAAAAAACT-TAAATACTTAAATAGGA
* *
446627 CAAAAAAACTTAAATACTAAAATATTGA
1 -AAAAAAACTTAAATACTTAAATA-GGA
*** *
446655 AGTCAAACTAAAATACTTAAATAGGA
1 AAAAAAACTTAAATACTTAAATAGGA
446681 TAAAAAGAACTTAAATA
1 -AAAAA-AACTTAAATA
446698 TCATTTTTTT
Statistics
Matches: 52, Mismatches: 14, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
26 2 0.04
27 38 0.73
28 12 0.23
ACGTcount: A:0.59, C:0.09, G:0.07, T:0.25
Consensus pattern (26 bp):
AAAAAAACTTAAATACTTAAATAGGA
Found at i:450664 original size:489 final size:489
Alignment explanation
Indices: 449746--450724 Score: 1958
Period size: 489 Copynumber: 2.0 Consensus size: 489
449736 CACAAATTTA
449746 TTCTTCGAAACTACAAGTATCGCACCATGTTAAACTGTTGAAGACATCCAAATACTGAGTATATG
1 TTCTTCGAAACTACAAGTATCGCACCATGTTAAACTGTTGAAGACATCCAAATACTGAGTATATG
449811 TAGCAGGAAAGGCAGCTAAAATTTGGTGCTCATGGTTGTTGAAAGCCACCACATGTATTGACCTA
66 TAGCAGGAAAGGCAGCTAAAATTTGGTGCTCATGGTTGTTGAAAGCCACCACATGTATTGACCTA
449876 TGTTACTAGAACTTGCTTGTGTCAAACACAGGTATGTGTCCTACATAGGCATGCTCAATCCTTTC
131 TGTTACTAGAACTTGCTTGTGTCAAACACAGGTATGTGTCCTACATAGGCATGCTCAATCCTTTC
449941 CAAGCTTTTTATGTATTTGAAAGATTCTTGAAGGATCACATCCTCATACCCATGTTCATATATGT
196 CAAGCTTTTTATGTATTTGAAAGATTCTTGAAGGATCACATCCTCATACCCATGTTCATATATGT
450006 ATTGGACAGGTCTTGGACACAGACACAGTCCTTCAAGAAAAATGAAGTTTTGAAGCAACATGGGT
261 ATTGGACAGGTCTTGGACACAGACACAGTCCTTCAAGAAAAATGAAGTTTTGAAGCAACATGGGT
450071 ATTGATTGACAAGCAAGTCGCCAAAAATGTTAGTTGGAAAGAAGGATTACCACTTTGTGATTTGA
326 ATTGATTGACAAGCAAGTCGCCAAAAATGTTAGTTGGAAAGAAGGATTACCACTTTGTGATTTGA
450136 ATGTCAAGAAAACATAAACATTGTGCGGCATTGATAAGTAGCATACCATTTTAAAGCTTTTTGGA
391 ATGTCAAGAAAACATAAACATTGTGCGGCATTGATAAGTAGCATACCATTTTAAAGCTTTTTGGA
450201 GTTCGTACACTATTTTCGTAATGAACATCATCGT
456 GTTCGTACACTATTTTCGTAATGAACATCATCGT
450235 TTCTTCGAAACTACAAGTATCGCACCATGTTAAACTGTTGAAGACATCCAAATACTGAGTATATG
1 TTCTTCGAAACTACAAGTATCGCACCATGTTAAACTGTTGAAGACATCCAAATACTGAGTATATG
450300 TAGCAGGAAAGGCAGCTAAAATTTGGTGCTCATGGTTGTTGAAAGCCACCACATGTATTGACCTA
66 TAGCAGGAAAGGCAGCTAAAATTTGGTGCTCATGGTTGTTGAAAGCCACCACATGTATTGACCTA
450365 TGTTACTAGAACTTGCTTGTGTCAAACACAGGTATGTGTCCTACATAGGCATGCTCAATCCTTTC
131 TGTTACTAGAACTTGCTTGTGTCAAACACAGGTATGTGTCCTACATAGGCATGCTCAATCCTTTC
450430 CAAGCTTTTTATGTATTTGAAAGATTCTTGAAGGATCACATCCTCATACCCATGTTCATATATGT
196 CAAGCTTTTTATGTATTTGAAAGATTCTTGAAGGATCACATCCTCATACCCATGTTCATATATGT
450495 ATTGGACAGGTCTTGGACACAGACACAGTCCTTCAAGAAAAATGAAGTTTTGAAGCAACATGGGT
261 ATTGGACAGGTCTTGGACACAGACACAGTCCTTCAAGAAAAATGAAGTTTTGAAGCAACATGGGT
450560 ATTGATTGACAAGCAAGTCGCCAAAAATGTTAGTTGGAAAGAAGGATTACCACTTTGTGATTTGA
326 ATTGATTGACAAGCAAGTCGCCAAAAATGTTAGTTGGAAAGAAGGATTACCACTTTGTGATTTGA
450625 ATGTCAAGAAAACATAAACATTGTGCGGCATTGATAAGTAGCATACCATTTTAAAGCTTTTTGGA
391 ATGTCAAGAAAACATAAACATTGTGCGGCATTGATAAGTAGCATACCATTTTAAAGCTTTTTGGA
450690 GTTCGTACACTATTTTCGTAATGAACATCATCGT
456 GTTCGTACACTATTTTCGTAATGAACATCATCGT
450724 T
1 T
450725 ACCAGCCAAC
Statistics
Matches: 490, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
489 490 1.00
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (489 bp):
TTCTTCGAAACTACAAGTATCGCACCATGTTAAACTGTTGAAGACATCCAAATACTGAGTATATG
TAGCAGGAAAGGCAGCTAAAATTTGGTGCTCATGGTTGTTGAAAGCCACCACATGTATTGACCTA
TGTTACTAGAACTTGCTTGTGTCAAACACAGGTATGTGTCCTACATAGGCATGCTCAATCCTTTC
CAAGCTTTTTATGTATTTGAAAGATTCTTGAAGGATCACATCCTCATACCCATGTTCATATATGT
ATTGGACAGGTCTTGGACACAGACACAGTCCTTCAAGAAAAATGAAGTTTTGAAGCAACATGGGT
ATTGATTGACAAGCAAGTCGCCAAAAATGTTAGTTGGAAAGAAGGATTACCACTTTGTGATTTGA
ATGTCAAGAAAACATAAACATTGTGCGGCATTGATAAGTAGCATACCATTTTAAAGCTTTTTGGA
GTTCGTACACTATTTTCGTAATGAACATCATCGT
Found at i:452139 original size:1 final size:1
Alignment explanation
Indices: 452133--452157 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
452123 GCAGTAAAAT
452133 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
452158 AAGACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:452834 original size:16 final size:16
Alignment explanation
Indices: 452813--452864 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
452803 TTTGGTTCGC
452813 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
452829 TGTATTGAATTAGAGG
1 TGTATTGGATTAGAGG
* * *
452845 TATAATGGATTAGAGA
1 TGTATTGGATTAGAGG
452861 TGTA
1 TGTA
452865 ATAACAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:453524 original size:20 final size:22
Alignment explanation
Indices: 453488--453528 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
453478 ATGGCTATGC
453488 TTAAATAATATTTTTTAATTAT
1 TTAAATAATATTTTTTAATTAT
453510 TTAAA-AATA-TTTTTAATTA
1 TTAAATAATATTTTTTAATTA
453529 AGAGAATAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAAATAATATTTTTTAATTAT
Found at i:454110 original size:23 final size:23
Alignment explanation
Indices: 454080--454140 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
454070 TGGACAAATG
454080 AAGGCCATGTTCCTGTTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
*
454103 AAGGCCATGTTCCTATTTTTATT
1 AAGGCCATGTTCCTGTTTTTATT
**
454126 GTGGCCATGTTCCTG
1 AAGGCCATGTTCCTG
454141 AGTTGAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (23 bp):
AAGGCCATGTTCCTGTTTTTATT
Found at i:454682 original size:41 final size:41
Alignment explanation
Indices: 454625--454707 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
454615 CGAGCCTAAA
454625 TATAAATTACAACTGAAATGAATGTTTAAGAAACTTACAGT
1 TATAAATTACAACTGAAATGAATGTTTAAGAAACTTACAGT
*
454666 TATAAATTACAGCTGAAATGAATGTTTAAGAAACTTACAGT
1 TATAAATTACAACTGAAATGAATGTTTAAGAAACTTACAGT
454707 T
1 T
454708 GCTCGAGTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.45, C:0.10, G:0.13, T:0.33
Consensus pattern (41 bp):
TATAAATTACAACTGAAATGAATGTTTAAGAAACTTACAGT
Found at i:457088 original size:3 final size:3
Alignment explanation
Indices: 457080--457109 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
457070 TCAATATTTG
457080 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
457110 GTTTAATTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:458293 original size:58 final size:60
Alignment explanation
Indices: 458184--458332 Score: 205
Period size: 63 Copynumber: 2.5 Consensus size: 60
458174 ACCCTAATTC
* * *
458184 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAAGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAAGGCTATATCAATA
* *
458242 -GATCACCCGTCCGGGCTAGATCTTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAAGGCTATATC-A-ATA
458304 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
458333 ACCGTCAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 7
0.86 0.07 0.08
Matches are distributed among these distances:
57 25 0.32
58 25 0.32
61 1 0.01
62 1 0.01
63 27 0.34
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAAGGCTATATCAATA
Found at i:460281 original size:102 final size:102
Alignment explanation
Indices: 460162--460360 Score: 346
Period size: 102 Copynumber: 1.9 Consensus size: 102
460152 TCCTAATCCA
460162 TCCATTTTCCTTAGTTTCTAGATCATTCCACCCTTAAAATATTTACACCATTGGTCCTTCAACTT
1 TCCATTTTCCTTAGTTTCTAGATCATTCCACCCTTAAAATATTTACACCATTGGTCCTTCAACTT
460227 TTTCATATTTACACTTT-AACCCCTCAATTTTTGAGG
66 TTTCATATTTACACTTTAAACCCCTCAATTTTTGAGG
* * *
460263 TCCATTTTTTCTTAGTTTCTAGATTATTCCACCCTTAAAATATTTACACCATTGGTCCTTCAATT
1 TCCA-TTTTCCTTAGTTTCTAGATCATTCCACCCTTAAAATATTTACACCATTGGTCCTTCAACT
460328 TTTTCATATTTACACTTTAAAACCCCTCAATTT
65 TTTTCATATTTACACTTT-AAACCCCTCAATTT
460361 AAGTATTTAC
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
101 4 0.04
102 75 0.82
104 13 0.14
ACGTcount: A:0.26, C:0.25, G:0.06, T:0.44
Consensus pattern (102 bp):
TCCATTTTCCTTAGTTTCTAGATCATTCCACCCTTAAAATATTTACACCATTGGTCCTTCAACTT
TTTCATATTTACACTTTAAACCCCTCAATTTTTGAGG
Found at i:465331 original size:869 final size:853
Alignment explanation
Indices: 463668--465390 Score: 3207
Period size: 869 Copynumber: 2.0 Consensus size: 853
463658 ATTTTAAATT
463668 ATTTTCACTATTTTAAGTACAAAATATTTAATGTTATATAATAAAAATAAAATATTTATAAAATA
1 ATTTTCACTATTTTAAGTACAAAATATTTAATGTTATATAATAAAAATAAAATATTTATAAAATA
463733 AAAAATATAATTCGATTTGGTTTCGGGAAATCGTAGTTTTTAAACTTGCATTCCATAAACCGTCC
66 AAAAATATAATTCGATTTGGTTTCGGGAAATCGTAGTTTTTAAACTTGCATTCCATAAACCGTCC
463798 AAGTACATTGATTCAAATAATTGAGTTGATCAAATAATAAAAAGAATAATCACAAATCTAAAAAT
131 AAGTACATTGATTCAAATAATTGAGTTGATCAAATAATAAAAAGAATAATCACAAATCTAAAAAT
463863 TACGTTTTTTTATATTATTGTTTAGTTAGGTTTAGGGATAAAAAATTAGATTTAAGTGAATAATA
196 TACGTTTTTTTATATTATTGTTTAGTTAGGTTTAGGGATAAAAAATTAGATTTAAGTGAATAATA
* ** * *
463928 GAATAAAATATTAAAGATAATCAAAGTTAAATACTAGCTTTGGTGTTGGGATGGGAAAGAATTAC
261 GAATAAAATATTAAAGATAATCAAAGTTAAATAATA-CTTTAATATTAGGATGGGAAAGAATTAC
463993 GAATAAAAGTAGATTTTGTATAAAAATGTAATAAATTAAAAAACTTCAAATTCAGACCACAACTA
325 GAATAAAAGTAGATTTTGTATAAAAATGTAATAAATTAAAAAACTTCAAATTCAGACCACAACTA
464058 AAATAAAATTAGATTTATAAAAATTAAAAAAAATTATAGTGTGTTTTAAATGAAATAAAAATTCA
390 AAATAAAATTAGATTTATAAAAATTAAAAAAAATTATAGTGTGTTTTAAATGAAATAAAAATTCA
464123 ATTATATAAAAATAAAAAATAGAAAAAATATTAATGTGTGGGTTTTAAATGATTATAGATAAATA
455 ATTATATAAAAATAAAAAATAGAAAAAATATTAATGTGTGGGTTTTAAATGATTATAGATAAATA
464188 AAATTTGAAAACCTAATGTAGGAAGGAATCCCTCACGTGGGGTAAGGAGGGAGAAATGAAGTAGC
520 AAATTTGAAAACCTAATGTAGGAAGGAATCCCTCACGTGGGGTAAGGAGGGAGAAATGAAGTAGC
464253 AGTCAGAAGTTTAGTTTAGTGACGGCTTTTCTTAAAACAAAAGTACAAAACAAAGTTTGTCTCTC
585 AGTCAGAAGTTTAGTTTAGTGACGGCTTTTCTTAAAACAAAAGTACAAAACAAAGTTTGTCTCTC
464318 CTCCTCTGCTGTGCTGTGTTTCCAACGTTTTACAAATGTGGAAGCAGTTTTAATAATGTAAACGG
650 CTCCTCTGCTGTGCTGTGTTTCCAACGTTTTACAAATGTGGAAGCAGTTTTAATAATGTAAACGG
464383 TTTACAACGTTTTCTTCAAGTTTCCCGACTCTCTCTTCTCTGCTTTGCTGTGTTGACACAATACA
715 TTTACAACGTTTTCTTCAAGTTTCCCGACTCTCTCTTCTCTGCTTTGCTGTGTTGACACAATACA
464448 AACAAAACAAAACAAAACCACCCCCAGCTACCTTCTTCTACACTTTCCTTTAACTTCATCCCTCT
780 AACAAAACAAAACAAAACCACCCCCAGCTACCTTCTTCTACACTTTCCTTTAACTTCATCCCTCT
464513 CTCTTTCCC
845 CTCTTTCCC
464522 ATTTTCACTATTTTAAGTACAAAATATTTAATGTTATATAATAAAAATAAAATATTTATAAAATA
1 ATTTTCACTATTTTAAGTACAAAATATTTAATGTTATATAATAAAAATAAAATATTTATAAAATA
464587 AAAAATATAATTCGATTTGGTTTCGGGAAATCGTAGTTTTTAAACTTGCATTCCATAAACCGTCC
66 AAAAATATAATTCGATTTGGTTTCGGGAAATCGTAGTTTTTAAACTTGCATTCCATAAACCGTCC
464652 AAGTACATTGATTCAAATAATTGAGTTGATCAAATAATAAAAAGAATAATCACAAATCTAAAAAT
131 AAGTACATTGATTCAAATAATTGAGTTGATCAAATAATAAAAAGAATAATCACAAATCTAAAAAT
464717 TACGTTTTTTTATATTATTGTTTAGTTAGGTTTAGGGATAAAAAATTAGATTTAAGTGAATAATA
196 TACGTTTTTTTATATTATTGTTTAGTTAGGTTTAGGGATAAAAAATTAGATTTAAGTGAATAATA
*
464782 GAATAAAATATTAAAGAAAAAATATTTTTCTCATGAAGAAATTAAA-AATA-TTTAAAAATATTA
261 GAATAAAATATTAAAG-----ATA-----ATCA--AAG---TTAAATAATACTTT---AATATTA
464845 GGATGGGAAAGAATTACGAATAAAAGTAGATTTTGTATAAAAATGTAATAAATTAAAAAACTTCA
308 GGATGGGAAAGAATTACGAATAAAAGTAGATTTTGTATAAAAATGTAATAAATTAAAAAACTTCA
464910 AATTCAGACCACAACTAAAATAAAATTAGATTTATAAAAATTAAAAAAAATTATAGTGTGTTTTA
373 AATTCAGACCACAACTAAAATAAAATTAGATTTATAAAAATTAAAAAAAATTATAGTGTGTTTTA
464975 AATGAAATAAAAATTCAATTATATAAAAATAAAAAATAGAAAAAATATTAATGTGTGGGTTTTAA
438 AATGAAATAAAAATTCAATTATATAAAAATAAAAAATAGAAAAAATATTAATGTGTGGGTTTTAA
465040 ATGATTATAGATAAATAAAATTTGAAAACCTAATGTAGGAAGGAATCCCTCACGTGGGGTAAGGA
503 ATGATTATAGATAAATAAAATTTGAAAACCTAATGTAGGAAGGAATCCCTCACGTGGGGTAAGGA
465105 GGGAGAAATGAAGTAGCAGTCAGAAGTTTAGTTTAGTGACGGCTTTTCTTAAAACAAAAGTACAA
568 GGGAGAAATGAAGTAGCAGTCAGAAGTTTAGTTTAGTGACGGCTTTTCTTAAAACAAAAGTACAA
465170 AACAAAGTTTGTCTCTCCTCCTCTGCTGTGCTGTGTTTCCAACGTTTTACAAATGTGGAAGCAGT
633 AACAAAGTTTGTCTCTCCTCCTCTGCTGTGCTGTGTTTCCAACGTTTTACAAATGTGGAAGCAGT
465235 TTTAATAATGTAAACGGTTTACAACGTTTTCTTCAAGTTTCCCGACTCTCTCTTCTCTGCTTTGC
698 TTTAATAATGTAAACGGTTTACAACGTTTTCTTCAAGTTTCCCGACTCTCTCTTCTCTGCTTTGC
465300 TGTGTTGACACAATACAAACAAAACAAAACAAAACCACCCCCAGCTACCTTCTTCTACACTTTCC
763 TGTGTTGACACAATACAAACAAAACAAAACAAAACCACCCCCAGCTACCTTCTTCTACACTTTCC
465365 TTTAACTTCATCCCTCTCTCTTTCCC
828 TTTAACTTCATCCCTCTCTCTTTCCC
465391 TTCTCCATTA
Statistics
Matches: 845, Mismatches: 6, Indels: 21
0.97 0.01 0.02
Matches are distributed among these distances:
854 276 0.33
859 3 0.00
864 3 0.00
866 6 0.01
868 3 0.00
869 554 0.66
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (853 bp):
ATTTTCACTATTTTAAGTACAAAATATTTAATGTTATATAATAAAAATAAAATATTTATAAAATA
AAAAATATAATTCGATTTGGTTTCGGGAAATCGTAGTTTTTAAACTTGCATTCCATAAACCGTCC
AAGTACATTGATTCAAATAATTGAGTTGATCAAATAATAAAAAGAATAATCACAAATCTAAAAAT
TACGTTTTTTTATATTATTGTTTAGTTAGGTTTAGGGATAAAAAATTAGATTTAAGTGAATAATA
GAATAAAATATTAAAGATAATCAAAGTTAAATAATACTTTAATATTAGGATGGGAAAGAATTACG
AATAAAAGTAGATTTTGTATAAAAATGTAATAAATTAAAAAACTTCAAATTCAGACCACAACTAA
AATAAAATTAGATTTATAAAAATTAAAAAAAATTATAGTGTGTTTTAAATGAAATAAAAATTCAA
TTATATAAAAATAAAAAATAGAAAAAATATTAATGTGTGGGTTTTAAATGATTATAGATAAATAA
AATTTGAAAACCTAATGTAGGAAGGAATCCCTCACGTGGGGTAAGGAGGGAGAAATGAAGTAGCA
GTCAGAAGTTTAGTTTAGTGACGGCTTTTCTTAAAACAAAAGTACAAAACAAAGTTTGTCTCTCC
TCCTCTGCTGTGCTGTGTTTCCAACGTTTTACAAATGTGGAAGCAGTTTTAATAATGTAAACGGT
TTACAACGTTTTCTTCAAGTTTCCCGACTCTCTCTTCTCTGCTTTGCTGTGTTGACACAATACAA
ACAAAACAAAACAAAACCACCCCCAGCTACCTTCTTCTACACTTTCCTTTAACTTCATCCCTCTC
TCTTTCCC
Found at i:474984 original size:16 final size:16
Alignment explanation
Indices: 474963--474993 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
474953 AAAACATTTA
*
474963 TAATATATATGTATAT
1 TAATATATATATATAT
474979 TAATATATATATATA
1 TAATATATATATATA
474994 GGCGAACACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TAATATATATATATAT
Found at i:477942 original size:18 final size:18
Alignment explanation
Indices: 477915--477968 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
477905 ATAAAATTCA
* *
477915 ATAAAATTTATT-AAATT
1 ATAAATTTTATTAAAAAT
*
477932 ATTAAATTTTAATAAAAAT
1 A-TAAATTTTATTAAAAAT
*
477951 ATAAATTTTATTTAAAAT
1 ATAAATTTTATTAAAAAT
477969 TAGAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 1 0.03
18 24 0.80
19 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATTTTATTAAAAAT
Found at i:477997 original size:20 final size:19
Alignment explanation
Indices: 477974--478036 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
477964 AAAATTAGAA
*
477974 AAAAATTTATAAAAATCGTT
1 AAAAATTTAAAAAAATCG-T
* *
477994 AAAAATATAAAAAAATTGT
1 AAAAATTTAAAAAAATCGT
* * *
478013 AAAATTTTACAAAAATCAT
1 AAAAATTTAAAAAAATCGT
478032 AAAAA
1 AAAAA
478037 AATGCTCTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATTTAAAAAAATCGT
Found at i:478320 original size:29 final size:28
Alignment explanation
Indices: 478240--478342 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 28
478230 CTTTATATTT
* *
478240 TTTTATAATTTTCTTACGACTTTATAAAA
1 TTTTATAATTTTTTTATGA-TTTATAAAA
* * *
478269 TTTTGTAATTTTTTTCTAT-ATTTCTACATA
1 TTTTATAA-TTTTTT-TATGATTTATA-AAA
478299 TTTTATAATTTTTTTATGATTTTTTATAAAA
1 TTTTATAATTTTTTTATGA---TTTATAAAA
*
478330 TTTTACAATTTTT
1 TTTTATAATTTTT
478343 CTATAAATTT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
28 3 0.05
29 19 0.33
30 15 0.26
31 16 0.28
32 5 0.09
ACGTcount: A:0.29, C:0.07, G:0.03, T:0.61
Consensus pattern (28 bp):
TTTTATAATTTTTTTATGATTTATAAAA
Found at i:478367 original size:20 final size:21
Alignment explanation
Indices: 478299--478376 Score: 79
Period size: 22 Copynumber: 3.7 Consensus size: 21
478289 TTTCTACATA
*
478299 TTTTATAATTTTTTTA-TGATT
1 TTTTATAAATTTTTTACT-ATT
* *
478320 TTTTATAAA-ATTTTACAATT
1 TTTTATAAATTTTTTACTATT
478340 TTTCTATAAATTTTTTACTATT
1 TTT-TATAAATTTTTTACTATT
*
478362 TTTATATATATTTTT
1 TTT-TATAAATTTTT
478377 AGTTTTTAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
20 11 0.23
21 14 0.30
22 22 0.47
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (21 bp):
TTTTATAAATTTTTTACTATT
Found at i:478377 original size:21 final size:21
Alignment explanation
Indices: 478276--478377 Score: 68
Period size: 20 Copynumber: 4.9 Consensus size: 21
478266 AAATTTTGTA
* * *
478276 ATTTTTTTCTATATTTCTAC-
1 ATTTTTATATATATTTTTACT
*
478296 ATATTTTATA-ATTTTTTTA-T
1 AT-TTTTATATATATTTTTACT
* * *
478316 GATTTTT-TATAAAATTTTACA
1 -ATTTTTATATATATTTTTACT
* *
478337 ATTTTTCTATAAATTTTTTACT
1 ATTTTTATATATA-TTTTTACT
478359 ATTTTTATATATATTTTTA
1 ATTTTTATATATATTTTTA
478378 GTTTTTAATA
Statistics
Matches: 63, Mismatches: 12, Indels: 13
0.72 0.14 0.15
Matches are distributed among these distances:
19 2 0.03
20 25 0.40
21 19 0.30
22 17 0.27
ACGTcount: A:0.29, C:0.06, G:0.01, T:0.64
Consensus pattern (21 bp):
ATTTTTATATATATTTTTACT
Found at i:478383 original size:20 final size:19
Alignment explanation
Indices: 478299--478383 Score: 55
Period size: 21 Copynumber: 4.2 Consensus size: 19
478289 TTTCTACATA
*
478299 TTTTATAATTTTTTTATGATT
1 TTTTATAATATTTTTA-G-TT
* * *
478320 TTTTATAAAATTTTACAATT
1 TTTTATAATATTTT-TAGTT
*
478340 TTTCTATAA-ATTTTTTACTAT
1 TTT-TATAATA-TTTTTAGT-T
478361 TTTTATATATATTTTTAGTT
1 TTTTATA-ATATTTTTAGTT
478381 TTT
1 TTT
478384 AATATTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 16 0.31
21 33 0.65
22 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTATAATATTTTTAGTT
Found at i:478383 original size:61 final size:61
Alignment explanation
Indices: 478260--478377 Score: 139
Period size: 61 Copynumber: 1.9 Consensus size: 61
478250 TTCTTACGAC
** * * * *
478260 TTTATAAAATTTTGTAATTTTTTTCTATATTTCTACATATTTTATAATTTTTTTATGATTT
1 TTTATAAAATTTTACAATTTTTCTATAAATTTCTACATATTTTATAATATTTTTATGATTT
*
478321 TTTATAAAATTTTACAATTTTTCTATAAATTTTTTAC-TATTTTTATATATATTTTTA
1 TTTATAAAATTTTACAATTTTTCTATAAA-TTTCTACATA-TTTTATA-ATATTTTTA
478378 GTTTTTAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
61 26 0.55
62 13 0.28
63 8 0.17
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (61 bp):
TTTATAAAATTTTACAATTTTTCTATAAATTTCTACATATTTTATAATATTTTTATGATTT
Found at i:478388 original size:18 final size:18
Alignment explanation
Indices: 478360--478394 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
478350 TTTTTTACTA
478360 TTTTTATATATATTTTTAG
1 TTTTTATATAT-TTTTTAG
478379 TTTTTA-ATATTTTTTA
1 TTTTTATATATTTTTTA
478395 NNNNNNNNNN
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTATATATTTTTTAG
Found at i:481034 original size:10 final size:10
Alignment explanation
Indices: 481021--481054 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
481011 TTTTCATTTC
481021 TTTTT-TTTT
1 TTTTTGTTTT
*
481030 GTTTTGTTTT
1 TTTTTGTTTT
481040 TTTTTGTTTT
1 TTTTTGTTTT
481050 TTTTT
1 TTTTT
481055 TGCGACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:481045 original size:15 final size:14
Alignment explanation
Indices: 481021--481055 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
481011 TTTTCATTTC
481021 TTTTTTTTTGTTTT
1 TTTTTTTTTGTTTT
481035 GTTTTTTTTTGTTTT
1 -TTTTTTTTTGTTTT
481050 TTTTTT
1 TTTTTT
481056 GCGACTCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (14 bp):
TTTTTTTTTGTTTT
Found at i:481542 original size:10 final size:10
Alignment explanation
Indices: 481527--481600 Score: 50
Period size: 11 Copynumber: 7.5 Consensus size: 10
481517 CGGTAGAGGT
481527 TTTTTGTTTC
1 TTTTTGTTTC
481537 TTTTTGTTTC
1 TTTTTGTTTC
481547 ---TTG-TTC
1 TTTTTGTTTC
481553 TTTTTGTTCTC
1 TTTTTGTT-TC
* *
481564 TTTTCTATTTT
1 TTTT-TGTTTC
*
481575 TTTCTTTTTTC
1 TTT-TTGTTTC
481586 TATTTT-TTTC
1 T-TTTTGTTTC
481596 TTTTT
1 TTTTT
481601 TTCTATTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 17
0.71 0.05 0.23
Matches are distributed among these distances:
6 3 0.06
7 3 0.06
9 7 0.13
10 16 0.31
11 17 0.33
12 6 0.12
ACGTcount: A:0.03, C:0.12, G:0.05, T:0.80
Consensus pattern (10 bp):
TTTTTGTTTC
Found at i:481550 original size:17 final size:18
Alignment explanation
Indices: 481525--481609 Score: 76
Period size: 17 Copynumber: 5.0 Consensus size: 18
481515 CCCGGTAGAG
*
481525 GTTTTTTGTTTCT-TTTT
1 GTTTCTTGTTTCTATTTT
481542 GTTTCTTG-TTCT-TTTT
1 GTTTCTTGTTTCTATTTT
481558 G-TTCTCT-TTTCTATTTT
1 GTTTCT-TGTTTCTATTTT
*
481575 -TTTCTTTTTTCTATTTT
1 GTTTCTTGTTTCTATTTT
*
481592 -TTTCTTTTTTTCTATTTT
1 GTTTC-TTGTTTCTATTTT
481610 TTTTGTTTTT
Statistics
Matches: 61, Mismatches: 1, Indels: 11
0.84 0.01 0.15
Matches are distributed among these distances:
15 4 0.07
16 15 0.25
17 29 0.48
18 13 0.21
ACGTcount: A:0.04, C:0.12, G:0.06, T:0.79
Consensus pattern (18 bp):
GTTTCTTGTTTCTATTTT
Found at i:481555 original size:16 final size:15
Alignment explanation
Indices: 481533--481627 Score: 71
Period size: 16 Copynumber: 6.6 Consensus size: 15
481523 AGGTTTTTTG
481533 TTTCTTTTTGTTTCT
1 TTTCTTTTTGTTTCT
481548 TGTTCTTTTTGTTCTCT
1 T-TTCTTTTTGTT-TCT
481565 TTTCTATTTT-TTTC-
1 TTTCT-TTTTGTTTCT
* *
481579 TTT-TTTCTATTT-T
1 TTTCTTTTTGTTTCT
481592 TTTC-TTTT-TTTCT
1 TTTCTTTTTGTTTCT
481605 ATTT-TTTTTGTTT-T
1 -TTTCTTTTTGTTTCT
*
481619 TTTATTTTT
1 TTTCTTTTT
481628 TTTTGAACTG
Statistics
Matches: 67, Mismatches: 2, Indels: 23
0.73 0.02 0.25
Matches are distributed among these distances:
12 6 0.09
13 14 0.21
14 16 0.24
15 6 0.09
16 17 0.25
17 8 0.12
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (15 bp):
TTTCTTTTTGTTTCT
Found at i:481575 original size:1 final size:1
Alignment explanation
Indices: 481571--481631 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
481561 CTCTTTTCTA
* * * * * * * *
481571 TTTTTTTCTTTTTTCTATTTTTTTCTTTTTTTCTATTTTTTTTGTTTTTTTATTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
481632 GAACTGAATC
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.05, C:0.07, G:0.02, T:0.87
Consensus pattern (1 bp):
T
Found at i:481579 original size:26 final size:26
Alignment explanation
Indices: 481527--481583 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
481517 CGGTAGAGGT
*
481527 TTTTTGTTTCTTTTTGTTTCTTGTTC
1 TTTTTGTTTCTTTTTATTTCTTGTTC
481553 TTTTTGTTCTCTTTTCTATTT-TT-TTC
1 TTTTTGTT-TCTTTT-TATTTCTTGTTC
481579 TTTTT
1 TTTTT
481584 TCTATTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 16 0.57
27 8 0.29
28 4 0.14
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (26 bp):
TTTTTGTTTCTTTTTATTTCTTGTTC
Found at i:481592 original size:18 final size:18
Alignment explanation
Indices: 481553--481630 Score: 99
Period size: 17 Copynumber: 4.4 Consensus size: 18
481543 TTTCTTGTTC
* *
481553 TTTTTGTTCTCTTTTCTA
1 TTTTTTTTCTTTTTTCTA
481571 -TTTTTTTCTTTTTTCTA
1 TTTTTTTTCTTTTTTCTA
481588 -TTTTTTTCTTTTTTTCTA
1 TTTTTTTTC-TTTTTTCTA
*
481606 TTTTTTTTGTTTTTT-TA
1 TTTTTTTTCTTTTTTCTA
481623 TTTTTTTT
1 TTTTTTTT
481631 TGAACTGAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
17 33 0.60
18 15 0.27
19 7 0.13
ACGTcount: A:0.05, C:0.09, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTTTTCTTTTTTCTA
Found at i:481601 original size:10 final size:10
Alignment explanation
Indices: 481526--481631 Score: 62
Period size: 10 Copynumber: 10.7 Consensus size: 10
481516 CCGGTAGAGG
481526 TTTTTTGTTTC
1 TTTTTT-TTTC
*
481537 TTTTTGTTTC
1 TTTTTTTTTC
*
481547 TTGTTCTTTTTG
1 TT-TT-TTTTTC
* *
481559 TTCTCTTTTC
1 TTTTTTTTTC
*
481569 TATTTTTTTC
1 TTTTTTTTTC
481579 ---TTTTTTC
1 TTTTTTTTTC
*
481586 TATTTTTTTC
1 TTTTTTTTTC
481596 --TTTTTTTC
1 TTTTTTTTTC
*
481604 TATTTTTTTTG
1 T-TTTTTTTTC
481615 TTTTTTTATT-
1 TTTTTTT-TTC
481625 TTTTTTT
1 TTTTTTT
481632 GAACTGAATC
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 7 0.09
8 8 0.11
10 37 0.49
11 18 0.24
12 6 0.08
ACGTcount: A:0.04, C:0.09, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:486122 original size:14 final size:14
Alignment explanation
Indices: 486100--486135 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
486090 CATAGGTATC
486100 TAAAAAAATGGAAA
1 TAAAAAAATGGAAA
* *
486114 TAAATAAATGTAAA
1 TAAAAAAATGGAAA
486128 TAAAAAAA
1 TAAAAAAA
486136 AAGTAAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (14 bp):
TAAAAAAATGGAAA
Found at i:486293 original size:23 final size:23
Alignment explanation
Indices: 486265--486309 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
486255 ATATATTTGG
486265 ACTATA-AAATATACATAAAACAA
1 ACTATACAAATAT-CATAAAACAA
*
486288 ACTATACAAATATTATAAAACA
1 ACTATACAAATATCATAAAACA
486310 GAAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTATACAAATATCATAAAACAA
Found at i:489287 original size:18 final size:18
Alignment explanation
Indices: 489260--489313 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
489250 ATAAAATTCA
* *
489260 ATAAAATTTATT-AAATT
1 ATAAATTTTATTAAAAAT
*
489277 ATTAAATTTTAATAAAAAT
1 A-TAAATTTTATTAAAAAT
*
489296 ATAAATTTTATTTAAAAT
1 ATAAATTTTATTAAAAAT
489314 TAGAAAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
17 1 0.03
18 24 0.80
19 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
ATAAATTTTATTAAAAAT
Found at i:489342 original size:20 final size:19
Alignment explanation
Indices: 489319--489381 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 19
489309 AAAATTAGAA
*
489319 AAAAATTTATAAAAATCGTT
1 AAAAATTTAAAAAAATCG-T
* *
489339 AAAAATATAAAAAAATTGT
1 AAAAATTTAAAAAAATCGT
* * *
489358 AAAATTTTACAAAAATCAT
1 AAAAATTTAAAAAAATCGT
489377 AAAAA
1 AAAAA
489382 AATGCTCTTT
Statistics
Matches: 34, Mismatches: 9, Indels: 1
0.77 0.20 0.02
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
AAAAATTTAAAAAAATCGT
Found at i:492852 original size:683 final size:683
Alignment explanation
Indices: 491547--493598 Score: 4104
Period size: 683 Copynumber: 3.0 Consensus size: 683
491537 GTGAATGGTG
491547 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
1 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
491612 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
66 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
491677 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
131 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
491742 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
196 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
491807 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
261 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
491872 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
326 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
491937 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
391 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
492002 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
456 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
492067 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
521 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
492132 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
586 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
492197 AAATTTTAACAAAAGAAAAACATATAAAAATAT
651 AAATTTTAACAAAAGAAAAACATATAAAAATAT
492230 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
1 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
492295 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
66 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
492360 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
131 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
492425 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
196 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
492490 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
261 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
492555 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
326 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
492620 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
391 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
492685 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
456 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
492750 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
521 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
492815 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
586 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
492880 AAATTTTAACAAAAGAAAAACATATAAAAATAT
651 AAATTTTAACAAAAGAAAAACATATAAAAATAT
492913 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
1 AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
492978 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
66 GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
493043 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
131 GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
493108 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
196 TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
493173 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
261 AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
493238 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
326 TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
493303 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
391 ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
493368 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
456 TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
493433 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
521 AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
493498 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
586 TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
493563 AAATTTTAACAAAAGAAAAACATATAAAAATAT
651 AAATTTTAACAAAAGAAAAACATATAAAAATAT
493596 AAT
1 AAT
493599 TAATAATTAA
Statistics
Matches: 1369, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
683 1369 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (683 bp):
AATAAAAATTCACTATGTTTCTAACAGAAGAGAGAAAGACTTAATGTTACACGAAAATGTTAAGA
GGAAAGTCTCTTATCTCTATGTCTAATCTATCAAGACAAACTTTTTGAAACATCCCAAGAGTGAA
GGCAACCCAAGAACTTTACCATATTCTAAGGTTATTTTCACTTCTTCCATTTCAGTGAAGCAGTA
TTATGTAAAACATTTCCCCGAAACTTTTGTTGAAATGCAAAACGTTAATGGTTAAATATAACTCA
AAAAAGAATAAGGACCAAATTGATTAAAAAATATAAACATTGAGAGCTAAATTTATCATTATATC
TTGAATAATGAATATTGTGTATGAATGTTAATTTTTTTACTATTATTTTTTAGTGTTGACATATT
ATTGTATTAGTAATGGTGTTAATATATTTTAATTAAAGTTAAAATATGTCATAAATAGATGTAGT
TTTTATAAATTTAGAATTTAGTTACTGTACTTTAATTTATAAGAATTTAGTTTGTTTGTTTTTTA
AAATTTAAAATTTAAGTCAAATAATTATTAAATTATTTTATTATTTTATTTTTAGGAATAAATTG
TTTTTATTTTTATATGCTATGCCATTTATATAAAATAAAATTAAATATTTAATGCTTTATGGTTA
AAATTTTAACAAAAGAAAAACATATAAAAATAT
Found at i:494956 original size:17 final size:17
Alignment explanation
Indices: 494930--494962 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
494920 AAAATTATAA
*
494930 ATAAAGTATTAAAAAAT
1 ATAAAATATTAAAAAAT
494947 ATAAAATATTAAAAAA
1 ATAAAATATTAAAAAA
494963 GTAATCAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
ATAAAATATTAAAAAAT
Found at i:498170 original size:14 final size:14
Alignment explanation
Indices: 498153--498183 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
498143 TTAAATTATG
*
498153 AAAATAAAATCTCT
1 AAAACAAAATCTCT
498167 AAAACAAAATCTCT
1 AAAACAAAATCTCT
498181 AAA
1 AAA
498184 CTAAGTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAACAAAATCTCT
Found at i:499327 original size:16 final size:16
Alignment explanation
Indices: 499290--499329 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
499280 TTAATAAAAT
* *
499290 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
499306 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
499322 TAAAATTA
1 TAAAATTA
499330 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:499490 original size:23 final size:24
Alignment explanation
Indices: 499456--499503 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
499446 GTAAATAAAC
*
499456 TTAAAACAAAAAACTAT-TATATT
1 TTAAAACAAAAAAATATATATATT
499479 TTAAAA-ATAAAAAATATATATATT
1 TTAAAACA-AAAAAATATATATATT
499503 T
1 T
499504 AATATTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 1 0.05
23 14 0.64
24 7 0.32
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAACAAAAAAATATATATATT
Found at i:499505 original size:23 final size:24
Alignment explanation
Indices: 499458--499503 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
499448 AAATAAACTT
499458 AAAACAAAAAACTATTATATTTTA
1 AAAACAAAAAACTATTATATTTTA
*
499482 AAAATAAAAAA-TATATATATTT
1 AAAACAAAAAACTAT-TATATTT
499504 AATATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAACAAAAAACTATTATATTTTA
Found at i:514814 original size:6 final size:6
Alignment explanation
Indices: 514803--514847 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
514793 ATTCCCACTC
* * * *
514803 ATAATA ATAATA ATACTA ATAATA ATATTA ATACTA ATATTA ATA
1 ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATAATA ATA
514848 CTTACCTCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAATA
Found at i:514826 original size:18 final size:18
Alignment explanation
Indices: 514803--514847 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
514793 ATTCCCACTC
514803 ATAATAATAATAATACTA
1 ATAATAATAATAATACTA
*
514821 ATAATAATATTAATACTA
1 ATAATAATAATAATACTA
*
514839 ATATTAATA
1 ATAATAATA
514848 CTTACCTCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAATAATAATACTA
Found at i:514849 original size:12 final size:12
Alignment explanation
Indices: 514807--514847 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
514797 CCACTCATAA
*
514807 TAATAATAATAC
1 TAATAATAATAT
514819 TAATAATAATAT
1 TAATAATAATAT
*
514831 TAATACTAATAT
1 TAATAATAATAT
514843 TAATA
1 TAATA
514848 CTTACCTCAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (12 bp):
TAATAATAATAT
Found at i:515782 original size:14 final size:17
Alignment explanation
Indices: 515763--515800 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
515753 ATTTATTTCT
515763 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
515777 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
515794 TAATATA
1 TAATATA
515801 CTTTATAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.38
15 1 0.05
16 4 0.19
17 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:515808 original size:12 final size:11
Alignment explanation
Indices: 515780--515823 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
515770 ATATTTATAA
515780 TATAATTAATT
1 TATAATTAATT
*
515791 TAATAATATACTT
1 T-ATAAT-TAATT
515804 TATAATTAATT
1 TATAATTAATT
515815 TATATATTA
1 TATA-ATTA
515824 TATAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 9 0.32
12 14 0.50
13 5 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TATAATTAATT
Found at i:515827 original size:20 final size:23
Alignment explanation
Indices: 515775--515837 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
515765 ATATAATATT
515775 TATA-ATATAATTAATTTAATAA
1 TATATATATAATTAATTTAATAA
* *
515797 TATACTTTATAATTAATTTATATAT
1 TATA-TATATAATTAATTTA-ATAA
* *
515822 TATATAAATAAATAAT
1 TATATATATAATTAAT
515838 ATAAATATCT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
22 4 0.12
24 22 0.67
25 7 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TATATATATAATTAATTTAATAA
Found at i:515839 original size:20 final size:20
Alignment explanation
Indices: 515792--515840 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
515782 TAATTAATTT
*
515792 AATAATATACTTTATAATTA
1 AATAATATACTTTATAAATA
* *
515812 ATTTATATA-TTATATAAATA
1 AATAATATACTT-TATAAATA
515832 AATAATATA
1 AATAATATA
515841 AATATCTAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 2 0.09
20 21 0.91
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATAATATACTTTATAAATA
Found at i:523081 original size:157 final size:157
Alignment explanation
Indices: 522779--523072 Score: 342
Period size: 157 Copynumber: 1.9 Consensus size: 157
522769 CCAAAAAAGG
* * * * * * * * *
522779 AAAATGGGTGTTGTGATTAGGGATTAATACGATGGCTTGAAATCTAGCATAAGTTGTGGATTCTT
1 AAAATGGGTATTGTGATTAGGAATTAATACGATGACTGGAAATCCAACATAAGTTGCGGATCCTC
* ** *
522844 TGAAGCTAGTGTTAGTAGCATCGTACTAAGCTAGTGTTAGCAACCCTGATCTGAAGCTAGTGCTA
66 TGAAGCTAGTGTTAGTAGAATCAAACTAAACTAGTGTTAGCAACCCTGATCTGAAGCTAGTGCTA
** *
522909 GTAGCTCAAATATGTCGACTTGTATAA
131 ACAGCCCAAATATGTCGACTTGTATAA
* * *
522936 AAAATGGGTATTGTGATT-GAGAATTAATTCGATGACTGGAGATCCAACATATGTTGCGGATCCT
1 AAAATGGGTATTGTGATTAG-GAATTAATACGATGACTGGAAATCCAACATAAGTTGCGGATCCT
* *
523000 CTGAAGCTAGTGTTCGTA-AATTCAAACTAAACTAGTGTTAGCAA-CCTGGATTTGAAGCTAGTG
65 CTGAAGCTAGTGTTAGTAGAA-TCAAACTAAACTAGTGTTAGCAACCCT-GATCTGAAGCTAGTG
*
523063 TTAACAGCCC
128 CTAACAGCCC
523073 GATAATGTCA
Statistics
Matches: 112, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
156 5 0.04
157 107 0.96
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (157 bp):
AAAATGGGTATTGTGATTAGGAATTAATACGATGACTGGAAATCCAACATAAGTTGCGGATCCTC
TGAAGCTAGTGTTAGTAGAATCAAACTAAACTAGTGTTAGCAACCCTGATCTGAAGCTAGTGCTA
ACAGCCCAAATATGTCGACTTGTATAA
Found at i:524859 original size:18 final size:19
Alignment explanation
Indices: 524824--524859 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
524814 TTTTTTATAA
*
524824 TTTTTTAAAAATTTTAATT
1 TTTTTTAAAAATTATAATT
524843 TTTTTTAAAAA-TATAAT
1 TTTTTTAAAAATTATAAT
524860 CTTTGAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTTAAAAATTATAATT
Found at i:544414 original size:13 final size:15
Alignment explanation
Indices: 544395--544427 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
544385 GACTAAAATT
544395 CTAAAAATA-AAAAA
1 CTAAAAATATAAAAA
544409 -TAAAAATATAAAAA
1 CTAAAAATATAAAAA
544423 CTAAA
1 CTAAA
544428 TTCTATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 8 0.47
14 5 0.29
15 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
CTAAAAATATAAAAA
Found at i:544955 original size:15 final size:15
Alignment explanation
Indices: 544898--544956 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
544888 TATACTTCAT
*
544898 TTTTCTTTTTATTTTA
1 TTTT-TTTTTCTTTTA
*
544914 TTTTTTATTTTCTTTCA
1 -TTTTT-TTTTCTTTTA
**
544931 TTTTCGTTTCTTTTA
1 TTTTTTTTTCTTTTA
544946 TTTTTTTTTCT
1 TTTTTTTTTCT
544957 GGGTCTTCTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
15 17 0.50
16 5 0.15
17 12 0.35
ACGTcount: A:0.08, C:0.10, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTTTCTTTTA
Found at i:550072 original size:17 final size:19
Alignment explanation
Indices: 550038--550078 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
550028 TAAAATATTG
550038 AAAAATTATAAGAATTAAA
1 AAAAATTATAAGAATTAAA
*
550057 AAAAATT-TAA-ATTTAAA
1 AAAAATTATAAGAATTAAA
550074 AAAAA
1 AAAAA
550079 AAACTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 11 0.52
18 3 0.14
19 7 0.33
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
AAAAATTATAAGAATTAAA
Found at i:550437 original size:21 final size:21
Alignment explanation
Indices: 550411--550468 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 21
550401 CCTTAAAACG
550411 AGATGTCTCGATACATCCCTT
1 AGATGTCTCGATACATCCCTT
* * *
550432 AGATGT-TCAATATATCCTTT
1 AGATGTCTCGATACATCCCTT
*
550452 AGTTGTGC-CGATACATC
1 AGATGT-CTCGATACATC
550469 TTTAAATGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (21 bp):
AGATGTCTCGATACATCCCTT
Found at i:551667 original size:46 final size:46
Alignment explanation
Indices: 551600--551694 Score: 181
Period size: 46 Copynumber: 2.1 Consensus size: 46
551590 AAGAAAACCC
*
551600 TTTGTGGGATCAATGCTTGTGATATTATGTATAGTTTTTATGCATG
1 TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
551646 TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
1 TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
551692 TTT
1 TTT
551695 ATTATATCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.21, C:0.06, G:0.24, T:0.48
Consensus pattern (46 bp):
TTTGTGGGATCAATGCTTGTGATATTAGGTATAGTTTTTATGCATG
Found at i:558049 original size:13 final size:13
Alignment explanation
Indices: 558031--558055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
558021 TTAAACGGTA
558031 AAATTTTCACACG
1 AAATTTTCACACG
558044 AAATTTTCACAC
1 AAATTTTCACAC
558056 ATAAATTAAC
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:0.40, C:0.24, G:0.04, T:0.32
Consensus pattern (13 bp):
AAATTTTCACACG
Found at i:563741 original size:20 final size:21
Alignment explanation
Indices: 563716--563756 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
563706 ATTGTGAGAG
563716 TTAAAA-ATAAAACGAAATAA
1 TTAAAACATAAAACGAAATAA
* *
563736 TTAAAACATGAAACGAGATAA
1 TTAAAACATAAAACGAAATAA
563757 AATTAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.63, C:0.07, G:0.10, T:0.20
Consensus pattern (21 bp):
TTAAAACATAAAACGAAATAA
Found at i:566013 original size:224 final size:225
Alignment explanation
Indices: 565623--566062 Score: 846
Period size: 224 Copynumber: 2.0 Consensus size: 225
565613 TAATTAGATC
* *
565623 ATTCAACAAAACAAGAAATTTGAATCCTATGTTTTTCGGATTTGGGTGAGTTTGTGTTCAGTTTT
1 ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
565688 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
66 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
565753 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCA-C
131 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
565817 CATATTGGTAATAATAATGAATCCTATGTT
196 CATATTGGTAATAATAATGAATCCTATGTT
565847 ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
1 ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
*
565912 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGTATACAGG
66 TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
565977 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
131 TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
566042 CATATTGGTAATAATAATGAA
196 CATATTGGTAATAATAATGAA
566063 ACTACGATGC
Statistics
Matches: 212, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
224 190 0.90
225 22 0.10
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.37
Consensus pattern (225 bp):
ATTCAACAAAACAAGAAATTTGAATCCTATGTTATTCGGATTTGGGTGAGTTTGAGTTCAGTTTT
TCATGTATTTGGTGGGTTCTTGGGGTCCTATCCCTATATATATGTCGAAATGTGTTGAATACAGG
TATTTCAGTCAGAATGAACAGTTGAAGCAGCACAGTCTGAATTTTCTAGTAGTTTTAGCACCATC
CATATTGGTAATAATAATGAATCCTATGTT
Found at i:569404 original size:26 final size:24
Alignment explanation
Indices: 569367--569420 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
569357 GAAAATAAAC
569367 AAATTTGAATTTCAAAGCAAATTTGT
1 AAATTTGAATTTCAAAG--AATTTGT
* *
569393 AAATTT-ATATTTTATAGAATTTGT
1 AAATTTGA-ATTTCAAAGAATTTGT
569417 AAAT
1 AAAT
569421 ATCCAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 11 0.44
25 1 0.04
26 13 0.52
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (24 bp):
AAATTTGAATTTCAAAGAATTTGT
Found at i:572869 original size:56 final size:57
Alignment explanation
Indices: 572796--572908 Score: 219
Period size: 56 Copynumber: 2.0 Consensus size: 57
572786 AAATGGCTTA
572796 ATCGCGTAAAATAAAAATTTAGGGGTTAAATCTAAAGGTACCAAATTGTTGTTATCT
1 ATCGCGTAAAATAAAAATTTAGGGGTTAAATCTAAAGGTACCAAATTGTTGTTATCT
572853 ATCGCGT-AAATAAAAATTTAGGGGTTAAATCTAAAGGTACCAAATTGTTGTTATCT
1 ATCGCGTAAAATAAAAATTTAGGGGTTAAATCTAAAGGTACCAAATTGTTGTTATCT
572909 TTATAAAATG
Statistics
Matches: 56, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
56 49 0.88
57 7 0.12
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (57 bp):
ATCGCGTAAAATAAAAATTTAGGGGTTAAATCTAAAGGTACCAAATTGTTGTTATCT
Found at i:572988 original size:2 final size:2
Alignment explanation
Indices: 572981--573016 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
572971 AGTATAGCCT
*
572981 TA TA TA TA TA TA TA TA TG 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
573017 AAGGTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:574658 original size:41 final size:41
Alignment explanation
Indices: 574596--574715 Score: 145
Period size: 41 Copynumber: 2.9 Consensus size: 41
574586 CCGGATTTAT
* * * *
574596 TGCCAGTGAAATAATTCAGACTTTAGGTCTAGCAGGCTTGA
1 TGCCAGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
* * *
574637 TGCCGGTGAAATTATTCAGACTATACGTCTAGCAAGCTTAA
1 TGCCAGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
574678 TGCCAGTGATACA-T-TTCAGACTATAAGTCTAGCAGGCT
1 TGCCAGTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCT
574716 AAAAGACGGT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
41 65 0.96
42 2 0.03
43 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (41 bp):
TGCCAGTGAAATTATTCAGACTATAAGTCTAGCAGGCTTAA
Found at i:580892 original size:2 final size:2
Alignment explanation
Indices: 580885--580909 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
580875 CTAGAGTTAA
580885 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
580910 TTATTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:584285 original size:16 final size:15
Alignment explanation
Indices: 584260--584290 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
584250 ACTTTATTTT
584260 TAAAATATTTTTTAA
1 TAAAATATTTTTTAA
584275 TAAATATATTTTTTAA
1 TAAA-ATATTTTTTAA
584291 AATTTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAAAATATTTTTTAA
Found at i:584306 original size:12 final size:13
Alignment explanation
Indices: 584286--584321 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
584276 AAATATATTT
584286 TTTAAAATTTT-A
1 TTTAAAATTTTGA
584298 TTTAAAATTTTGA
1 TTTAAAATTTTGA
*
584311 CTTAAAATTTT
1 TTTAAAATTTT
584322 TAAATTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (13 bp):
TTTAAAATTTTGA
Found at i:584317 original size:13 final size:12
Alignment explanation
Indices: 584287--584321 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
584277 AATATATTTT
*
584287 TTAAAATTTTAT
1 TTAAAATTTTAC
584299 TTAAAATTTTGAC
1 TTAAAATTTT-AC
584312 TTAAAATTTT
1 TTAAAATTTT
584322 TAAATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (12 bp):
TTAAAATTTTAC
Found at i:586171 original size:75 final size:76
Alignment explanation
Indices: 586088--586238 Score: 250
Period size: 76 Copynumber: 2.0 Consensus size: 76
586078 ATCATTGAAG
* * *
586088 CAAT-AAAAAAAACATGCAAGGTTTCGTGATTTCATCCCAATAAGTTTCACCCAAAACATTGCCC
1 CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCCAAATAAGTTTCACCCAAAACATTGCCC
586152 ATATCAAAAGA
66 ATATCAAAAGA
* *
586163 CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCTAAATAAGTTTCATCCAAAACATTGCCC
1 CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCCAAATAAGTTTCACCCAAAACATTGCCC
586228 ATATCAAAAGA
66 ATATCAAAAGA
586239 GGGATATGCA
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
75 4 0.06
76 66 0.94
ACGTcount: A:0.45, C:0.21, G:0.09, T:0.25
Consensus pattern (76 bp):
CAATAAAAAAAAACATGCAAGATTTCATGATTTCATCCAAATAAGTTTCACCCAAAACATTGCCC
ATATCAAAAGA
Found at i:595634 original size:30 final size:30
Alignment explanation
Indices: 595600--595700 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 30
595590 TTATTTTTAT
595600 TTTTTAATTTTAAAATACTTTTAAAATATA
1 TTTTTAATTTTAAAATACTTTTAAAATATA
* * * ** *
595630 -TTTT--TTATAAATATATATTTTTATTTTTA
1 TTTTTAATTTTAAA-ATA-CTTTTAAAATATA
595659 TTTTTTAATTTTAAAATACTTTTAAAATATA
1 -TTTTTAATTTTAAAATACTTTTAAAATATA
*
595690 TTTTTTATTTT
1 TTTTTAATTTT
595701 TTTATTTTTA
Statistics
Matches: 52, Mismatches: 13, Indels: 12
0.68 0.17 0.16
Matches are distributed among these distances:
27 6 0.12
28 3 0.06
29 12 0.23
30 10 0.19
31 12 0.23
32 3 0.06
33 6 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTAATTTTAAAATACTTTTAAAATATA
Found at i:595643 original size:15 final size:16
Alignment explanation
Indices: 595618--595653 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
595608 TTTAAAATAC
595618 TTTTA-AAATATAT-T
1 TTTTATAAATATATAT
595632 TTTTATAAATATATAT
1 TTTTATAAATATATAT
595648 TTTTAT
1 TTTTAT
595654 TTTTATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 5 0.25
15 8 0.40
16 7 0.35
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTATAAATATATAT
Found at i:595662 original size:60 final size:61
Alignment explanation
Indices: 595575--595697 Score: 239
Period size: 60 Copynumber: 2.0 Consensus size: 61
595565 CCCGAATATA
595575 ATAAATATATATTTTTTATTTTTATTTTTTAATTTTAAAATACTTTTAAAATATATTTTTT
1 ATAAATATATATTTTTTATTTTTATTTTTTAATTTTAAAATACTTTTAAAATATATTTTTT
595636 ATAAATATATA-TTTTTATTTTTATTTTTTAATTTTAAAATACTTTTAAAATATATTTTTT
1 ATAAATATATATTTTTTATTTTTATTTTTTAATTTTAAAATACTTTTAAAATATATTTTTT
595696 AT
1 AT
595698 TTTTTTATTT
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 51 0.82
61 11 0.18
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (61 bp):
ATAAATATATATTTTTTATTTTTATTTTTTAATTTTAAAATACTTTTAAAATATATTTTTT
Found at i:598501 original size:39 final size:39
Alignment explanation
Indices: 598447--598525 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
598437 AAGCTTGGCC
598447 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
1 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
598486 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
1 AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
598525 A
1 A
598526 GGAAGAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (39 bp):
AAATACTTCCTGGCTTCAACCATGGTGTTTGGGGTTTTT
Found at i:603021 original size:20 final size:19
Alignment explanation
Indices: 602972--603062 Score: 53
Period size: 20 Copynumber: 4.6 Consensus size: 19
602962 TAACAGATGA
*
602972 ATCGAAGTGCTAACAGAGGC
1 ATCGAAGTGC-AACAGAAGC
*
602992 AT-GATTGTGCAATCAGAAGC
1 ATCGA-AGTGCAA-CAGAAGC
*
603012 ATCGAAGTGCAA-ACGTAGAC
1 ATCGAAGTGCAACA-GAAG-C
* * *
603032 ACCGAAGTGTAACAGAGGC
1 ATCGAAGTGCAACAGAAGC
603051 A-CTGAAGTGCAA
1 ATC-GAAGTGCAA
603063 AAAGAGGCAC
Statistics
Matches: 55, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
18 2 0.04
19 17 0.31
20 33 0.60
21 3 0.05
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.16
Consensus pattern (19 bp):
ATCGAAGTGCAACAGAAGC
Found at i:604859 original size:42 final size:42
Alignment explanation
Indices: 604741--604859 Score: 130
Period size: 42 Copynumber: 2.8 Consensus size: 42
604731 TTGTGCTTGT
* * *
604741 GCCACAAGGGCATGTGTCCAGGTCATGTGAGCCACTGACTTAA
1 GCCACAAGGGCGTGTGT-CAGGCCGTGTGAGCCACTGACTTAA
* * * * *
604784 GCCACACGGGTGTGTGCCAGGCCGTGTAAGCCACTGACTTGA
1 GCCACAAGGGCGTGTGTCAGGCCGTGTGAGCCACTGACTTAA
* * *
604826 TCCACAAGGGCGTGTGTGAGGCCGTGTGGGCCAC
1 GCCACAAGGGCGTGTGTCAGGCCGTGTGAGCCAC
604860 ATGAGCCGGC
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
42 48 0.79
43 13 0.21
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.19
Consensus pattern (42 bp):
GCCACAAGGGCGTGTGTCAGGCCGTGTGAGCCACTGACTTAA
Found at i:612588 original size:19 final size:20
Alignment explanation
Indices: 612492--612627 Score: 139
Period size: 20 Copynumber: 6.8 Consensus size: 20
612482 GTAGATGCGT
* *
612492 AACAGATGCACCAAAGTGCT
1 AACAGAGGCACCAAAGTGCA
* * * **
612512 GATAGAGGCACGATTGTGCA
1 AACAGAGGCACCAAAGTGCA
*
612532 ATCAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
* * *
612552 AACATAGACACCAAAGTG-T
1 AACAGAGGCACCAAAGTGCA
* *
612571 AATAGAGGCACTAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
612591 AACAGAGGCACCAAAGTGCA
1 AACAGAGGCACCAAAGTGCA
*
612611 AACAGAGGCACCGAAGT
1 AACAGAGGCACCAAAGT
612628 TCAATCCTGT
Statistics
Matches: 90, Mismatches: 25, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
19 14 0.16
20 76 0.84
ACGTcount: A:0.41, C:0.21, G:0.25, T:0.12
Consensus pattern (20 bp):
AACAGAGGCACCAAAGTGCA
Found at i:612597 original size:59 final size:60
Alignment explanation
Indices: 612500--612614 Score: 178
Period size: 59 Copynumber: 1.9 Consensus size: 60
612490 GTAACAGATG
* ** *
612500 CACCAAAGTGCTGATAGAGGCACGATTGTGCAATCAGAGGCACCAAAGTGCAAACATAGA
1 CACCAAAGTGCTAATAGAGGCACGAAAGTGCAAACAGAGGCACCAAAGTGCAAACATAGA
*
612560 CACCAAAGTG-TAATAGAGGCACTAAAGTGCAAACAGAGGCACCAAAGTGCAAACA
1 CACCAAAGTGCTAATAGAGGCACGAAAGTGCAAACAGAGGCACCAAAGTGCAAACA
612615 GAGGCACCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 40 0.80
60 10 0.20
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (60 bp):
CACCAAAGTGCTAATAGAGGCACGAAAGTGCAAACAGAGGCACCAAAGTGCAAACATAGA
Found at i:612791 original size:77 final size:77
Alignment explanation
Indices: 612664--612820 Score: 305
Period size: 77 Copynumber: 2.0 Consensus size: 77
612654 ACCCTATTGG
612664 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
1 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
612729 ATACACATTCTT
66 ATACACATTCTT
*
612741 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTTGTTACTTT
1 CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
612806 ATACACATTCTT
66 ATACACATTCTT
612818 CAT
1 CAT
612821 CCGGAATTAC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (77 bp):
CATTCCAATTGTATCCTAAACGTTTACTATGTTCAACCGAGCATTAAGCATAATTTCGTTACTTT
ATACACATTCTT
Found at i:619095 original size:19 final size:19
Alignment explanation
Indices: 619050--619098 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
619040 TCTAAAACTG
619050 ATATTACA-GAACATAAAT
1 ATATTACATGAACATAAAT
* *
619068 ATATAACATGAACA-CAAT
1 ATATTACATGAACATAAAT
619086 ATGATTACATGAA
1 AT-ATTACATGAA
619099 TTTTTCAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.53, C:0.12, G:0.08, T:0.27
Consensus pattern (19 bp):
ATATTACATGAACATAAAT
Found at i:624987 original size:6 final size:6
Alignment explanation
Indices: 624976--625000 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
624966 ATTATTTGTG
624976 TCATGT TCATGT TCATGT TCATGT T
1 TCATGT TCATGT TCATGT TCATGT T
625001 TTTCTTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TCATGT
Found at i:628736 original size:16 final size:15
Alignment explanation
Indices: 628694--628739 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
628684 AAAATCAAGG
628694 GAAGATAAAA-GATT
1 GAAGATAAAATGATT
628708 G-AGATTAAAATGATT
1 GAAGA-TAAAATGATT
628723 GAAGATAAAGATGATT
1 GAAGATAAA-ATGATT
628739 G
1 G
628740 GTTGATCACA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
13 3 0.11
14 6 0.21
15 9 0.32
16 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (15 bp):
GAAGATAAAATGATT
Found at i:629643 original size:6 final size:6
Alignment explanation
Indices: 629632--629656 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
629622 TTTATTTGTG
629632 TCATGT TCATGT TCATGT TCATGT T
1 TCATGT TCATGT TCATGT TCATGT T
629657 TTTCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TCATGT
Found at i:640032 original size:15 final size:15
Alignment explanation
Indices: 640012--640045 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
640002 GTTTACTTTC
*
640012 AATAAATTGGTTATT
1 AATAAATTGGTGATT
640027 AATAAATTGGTGATT
1 AATAAATTGGTGATT
640042 AATA
1 AATA
640046 TATAGGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (15 bp):
AATAAATTGGTGATT
Found at i:640781 original size:103 final size:105
Alignment explanation
Indices: 640667--640866 Score: 264
Period size: 105 Copynumber: 1.9 Consensus size: 105
640657 ATCATACTAG
*
640667 GAAAATAAAATA-TTATTTTTTTAGAAAATGGTT-CGACCATT-TTTCATCCAGCTGTAAACTAA
1 GAAAATAAAATACTTATTTTTTTAGAAAATGGTTAC-ACCATTGTTT-ATCCAGCTATAAACTAA
* * * * *
640729 TTTATACTTCTCTTTTATTGTT-TTTTTTCCATATTTTGGAC
64 TTCACACTTCCCTTTTATGGTTCTTTATTCCATATTTTGGAC
* * *
640770 GAAAATAAAATATCTTTTTTTTTTAGAAAATGGTTACATCATTGTTTATCCAGCTATACACTAAT
1 GAAAATAAAATA-CTTATTTTTTTAGAAAATGGTTACACCATTGTTTATCCAGCTATAAACTAAT
640835 TCACACTTCCCTTTTATGGTTCTTTATTCCAT
65 TCACACTTCCCTTTTATGGTTCTTTATTCCAT
640867 GCTTTGAATT
Statistics
Matches: 83, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
103 12 0.14
105 58 0.70
106 13 0.16
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.46
Consensus pattern (105 bp):
GAAAATAAAATACTTATTTTTTTAGAAAATGGTTACACCATTGTTTATCCAGCTATAAACTAATT
CACACTTCCCTTTTATGGTTCTTTATTCCATATTTTGGAC
Found at i:663322 original size:22 final size:21
Alignment explanation
Indices: 663257--663323 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
663247 GTGAATATCT
*
663257 ACACACCCATGTGAAAGAGGC
1 ACACGCCCATGTGAAAGAGGC
* * *
663278 ACACGCCCCTTTGAAAGAAGC
1 ACACGCCCATGTGAAAGAGGC
663299 ACACGCCCATGTGAAAAGAGGC
1 ACACGCCCATGTG-AAAGAGGC
663321 ACA
1 ACA
663324 TGGCCGTGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
21 28 0.74
22 10 0.26
ACGTcount: A:0.37, C:0.30, G:0.22, T:0.10
Consensus pattern (21 bp):
ACACGCCCATGTGAAAGAGGC
Found at i:664155 original size:7 final size:7
Alignment explanation
Indices: 664137--664178 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
664127 TTCCCAAGTA
664137 AAATAA-
1 AAATAAT
664143 AAATAAT
1 AAATAAT
664150 AAATAAT
1 AAATAAT
664157 AAATAGAT
1 AAATA-AT
*
664165 AAAAATAT
1 AAATA-AT
664173 AAATAA
1 AAATAA
664179 GTATCTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
6 6 0.19
7 13 0.42
8 12 0.39
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:664159 original size:16 final size:17
Alignment explanation
Indices: 664138--664178 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
664128 TCCCAAGTAA
664138 AATAAA-AATAATAAAT
1 AATAAATAATAATAAAT
664154 AATAAATAGATAA-AAAT
1 AATAAATA-ATAATAAAT
664171 -ATAAATAA
1 AATAAATAA
664179 GTATCTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 13 0.57
17 5 0.22
18 4 0.17
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AATAAATAATAATAAAT
Found at i:668281 original size:4 final size:4
Alignment explanation
Indices: 668267--668326 Score: 59
Period size: 4 Copynumber: 14.5 Consensus size: 4
668257 TTAAACTAAG
* * *
668267 TAAA AAAA TAAA TAAA TAAA TAAA TATAA -AACTT TAAA AAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TA-AA TAA--A TAAA TAAA TAAA TAAA
668317 TAAA TAAA TA
1 TAAA TAAA TA
668327 TAAAACTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
3 1 0.02
4 41 0.89
5 2 0.04
6 2 0.04
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Done.