Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008797.1 Hibiscus syriacus cultivar Beakdansim tig00111942_pilon, 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: 1112200
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 3 of 5
Found at i:383646 original size:2 final size:2
Alignment explanation
Indices: 383641--383680 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
383631 ACACACACAG
383641 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
383681 GTTTGGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:384872 original size:67 final size:67
Alignment explanation
Indices: 384764--384959 Score: 349
Period size: 67 Copynumber: 2.9 Consensus size: 67
384754 ATCTAAGGGT
384764 GAGTTGAAGTCCTATTTTATAATTCAACACGGGTAATCAAATCGGAGAAGACTAAACTCACCAAG
1 GAGTTGAAGTCCTATTTTATAATTCAACACGGGTAATCAAATCGGAGAAGACTAAACTCACCAAG
384829 TC
66 TC
*
384831 GAGTTGAAGTCCTATTTTATAATTTAACACGGGTAATCAAATCGGAGAAGACTAAACTCACCAAG
1 GAGTTGAAGTCCTATTTTATAATTCAACACGGGTAATCAAATCGGAGAAGACTAAACTCACCAAG
384896 TC
66 TC
*
384898 GAGTTGAAGTCCTATTTTATAATTCAACACAGGGGTAGTCAAAT-GGAGAAGACTAAACTCAC
1 GAGTTGAAGTCCTATTTTATAATTCAACAC--GGGTAATCAAATCGGAGAAGACTAAACTCAC
384960 TAATTCAACT
Statistics
Matches: 124, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
67 95 0.77
68 18 0.15
69 11 0.09
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (67 bp):
GAGTTGAAGTCCTATTTTATAATTCAACACGGGTAATCAAATCGGAGAAGACTAAACTCACCAAG
TC
Found at i:390614 original size:31 final size:31
Alignment explanation
Indices: 390578--390638 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
390568 AACTTAAAAG
* **
390578 AGTTTTGCAATACTGAGCTTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
390609 AGTTTTACAATACTGAAATTTAAATAATTT
1 AGTTTTACAATACTGAAATTTAAATAATTT
390639 ATACAACTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:391140 original size:18 final size:18
Alignment explanation
Indices: 391112--391162 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
391102 AAATAATTAA
391112 AATAA-ATATAAAATTTT
1 AATAATATATAAAATTTT
*
391129 AATAATATATAAATAATTT
1 AATAATATATAAA-ATTTT
391148 -AT-ATGATATAAAATT
1 AATAAT-ATATAAAATT
391163 AAATATCTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 9 0.31
18 16 0.55
19 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (18 bp):
AATAATATATAAAATTTT
Found at i:391146 original size:20 final size:19
Alignment explanation
Indices: 391102--391148 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
391092 ACTTAAATCA
*
391102 AAATAATTAAAATAAATAT
1 AAATAATTTAAATAAATAT
*
391121 -AA-AATTTTAATAATATAT
1 AAATAATTTAAATAA-ATAT
391139 AAATAATTTA
1 AAATAATTTA
391149 TATGATATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 5
0.73 0.10 0.17
Matches are distributed among these distances:
17 9 0.41
18 6 0.27
19 2 0.09
20 5 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AAATAATTTAAATAAATAT
Found at i:391220 original size:12 final size:12
Alignment explanation
Indices: 391205--391284 Score: 69
Period size: 12 Copynumber: 6.7 Consensus size: 12
391195 AATTTATTTA
391205 AAAATTAATATT
1 AAAATTAATATT
391217 AAAATTAATATCT
1 AAAATTAATAT-T
* *
391230 ATAATATAAT-TA
1 AAAAT-TAATATT
391242 AAAATTAATATT
1 AAAATTAATATT
*
391254 --AATTTAT-TT
1 AAAATTAATATT
391263 AAAAAATTAATATT
1 --AAAATTAATATT
391277 AAAATTAA
1 AAAATTAA
391285 AATCAATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
9 2 0.04
10 6 0.11
11 4 0.07
12 24 0.44
13 12 0.22
14 6 0.11
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (12 bp):
AAAATTAATATT
Found at i:391222 original size:24 final size:23
Alignment explanation
Indices: 391157--391222 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
391147 TATATGATAT
*
391157 AAAATTAAATATCTATAATATATTA
1 AAAATT-AATAT-TATAATTTATTA
*
391182 AAAAATAATATT-TAATTTATTTA
1 AAAATTAATATTATAATTTA-TTA
*
391205 AAAATTAATATTAAAATT
1 AAAATTAATATTATAATT
391223 AATATCTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 6 0.17
23 15 0.43
24 9 0.26
25 5 0.14
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAAATTAATATTATAATTTATTA
Found at i:391223 original size:60 final size:60
Alignment explanation
Indices: 391156--391299 Score: 222
Period size: 60 Copynumber: 2.4 Consensus size: 60
391146 TTATATGATA
391156 TAAAATTAAATATCTATAATATATTAAAAAATAATATTTAATTTATTT-AAAAATTAATAT
1 TAAAATTAAATATCTATAATATATTAAAAAATAATA-TTAATTTATTTAAAAAATTAATAT
*
391216 TAAAATT-AATATCTATAATATAATTAAAAATTAATATTAATTTATTTAAAAAATTAATAT
1 TAAAATTAAATATCTATAATAT-ATTAAAAAATAATATTAATTTATTTAAAAAATTAATAT
391276 TAAAATTAAA-ATCAATATAATATA
1 TAAAATTAAATATC--TATAATATA
391300 ATATAATATA
Statistics
Matches: 78, Mismatches: 1, Indels: 9
0.89 0.01 0.10
Matches are distributed among these distances:
59 25 0.32
60 42 0.54
61 3 0.04
62 8 0.10
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (60 bp):
TAAAATTAAATATCTATAATATATTAAAAAATAATATTAATTTATTTAAAAAATTAATAT
Found at i:391247 original size:37 final size:35
Alignment explanation
Indices: 391176--391255 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 35
391166 TATCTATAAT
* *
391176 ATATTAAAAAATAATATTTAATTTATTTAAAAATTA
1 ATATT-AAAAATAATATTTAATATAATTAAAAATTA
*
391212 ATATTAAAATTAATATCTATAATATAATTAAAAATTA
1 ATATTAAAAATAATAT-T-TAATATAATTAAAAATTA
391249 ATATTAA
1 ATATTAA
391256 TTTATTTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 10 0.26
36 6 0.15
37 23 0.59
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (35 bp):
ATATTAAAAATAATATTTAATATAATTAAAAATTA
Found at i:391299 original size:5 final size:5
Alignment explanation
Indices: 391289--391375 Score: 142
Period size: 5 Copynumber: 17.4 Consensus size: 5
391279 AATTAAAATC
391289 AATAT AATAT AATAT AATAT -ATAT AATAT AATAT AATATAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT -A-ATAT AATAT AATAT
391340 AATAT -ATAT AATAT AATAT AATAT AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA
391376 AATTAAATTA
Statistics
Matches: 78, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
4 8 0.10
5 64 0.82
6 2 0.03
7 4 0.05
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATAT
Found at i:391314 original size:19 final size:19
Alignment explanation
Indices: 391290--391375 Score: 149
Period size: 19 Copynumber: 4.6 Consensus size: 19
391280 ATTAAAATCA
391290 ATATAATATAATATAATAT
1 ATATAATATAATATAATAT
391309 ATATAATATAATAT-A-AT
1 ATATAATATAATATAATAT
391326 ATATAATATAATATAATAT
1 ATATAATATAATATAATAT
391345 ATATAATATAATATAATAT
1 ATATAATATAATATAATAT
391364 AATATAATATAA
1 -ATATAATATAA
391376 AATTAAATTA
Statistics
Matches: 64, Mismatches: 0, Indels: 5
0.93 0.00 0.07
Matches are distributed among these distances:
17 16 0.25
18 2 0.03
19 35 0.55
20 11 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATATAATATAATATAATAT
Found at i:391331 original size:36 final size:34
Alignment explanation
Indices: 391289--391375 Score: 156
Period size: 36 Copynumber: 2.5 Consensus size: 34
391279 AATTAAAATC
391289 AATATAATATAATATAATATATATAATATAATAT
1 AATATAATATAATATAATATATATAATATAATAT
391323 AATATATAATATAATATAATATATATAATATAATAT
1 -A-ATATAATATAATATAATATATATAATATAATAT
391359 AATATAATATAATATAA
1 AATATAATATAATATAA
391376 AATTAAATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
34 16 0.31
35 2 0.04
36 33 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AATATAATATAATATAATATATATAATATAATAT
Found at i:391393 original size:11 final size:11
Alignment explanation
Indices: 391289--391393 Score: 70
Period size: 12 Copynumber: 9.2 Consensus size: 11
391279 AATTAAAATC
*
391289 AATATAATATA
1 AATAAAATATA
*
391300 ATATAATATATA
1 A-ATAAAATATA
*
391312 TAATATAATATA
1 -AATAAAATATA
*
391324 ATATATAATATA
1 A-ATAAAATATA
*
391336 ATATAATATATA
1 A-ATAAAATATA
*
391348 TAATATAATAT-
1 -AATAAAATATA
*
391359 AATATAATATA
1 AATAAAATATA
391370 ATATAAAAT-TA
1 A-ATAAAATATA
*
391381 AATTAAATATA
1 AATAAAATATA
391392 AA
1 AA
391394 ACCTCTTTGA
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
10 16 0.21
11 10 0.13
12 49 0.64
13 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATAAAATATA
Found at i:392990 original size:19 final size:20
Alignment explanation
Indices: 392966--393024 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
392956 CGTTATATGC
*
392966 CTTA-GGGTATCGGTACCAT
1 CTTAGGGGTATCGATACCAT
392985 CTTAGGGGTATCGATACCATT
1 CTTAGGGGTATCGATACCA-T
* *
393006 GCATGGGGGTATCGATACC
1 -CTTAGGGGTATCGATACC
393025 TATGGGAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 4 0.12
20 13 0.38
21 1 0.03
22 16 0.47
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (20 bp):
CTTAGGGGTATCGATACCAT
Found at i:392995 original size:20 final size:19
Alignment explanation
Indices: 392966--393004 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
392956 CGTTATATGC
*
392966 CTTAGGGTATCGGTACCAT
1 CTTAGGGTATCGATACCAT
392985 CTTAGGGGTATCGATACCAT
1 CTTA-GGGTATCGATACCAT
393005 TGCATGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (19 bp):
CTTAGGGTATCGATACCAT
Found at i:394513 original size:21 final size:22
Alignment explanation
Indices: 394482--394531 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
394472 AAACATTCAT
*
394482 AATCCATCAAACAAA-TTCAAAC
1 AATCCAACAAACAAAGTT-AAAC
394504 -ATCCAACAAACAAAGTTAAAC
1 AATCCAACAAACAAAGTTAAAC
394525 AATCCAA
1 AATCCAA
394532 AAGCATTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 17 0.68
22 8 0.32
ACGTcount: A:0.56, C:0.26, G:0.02, T:0.16
Consensus pattern (22 bp):
AATCCAACAAACAAAGTTAAAC
Found at i:395382 original size:44 final size:46
Alignment explanation
Indices: 395333--395509 Score: 166
Period size: 44 Copynumber: 3.8 Consensus size: 46
395323 TATAAAATCT
*
395333 CTTACCATTT-A-TCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * *
395377 CTTACCGTTTAAAATTTCATAAGCT-GTAAGCTTATATTTTTTTTCCAATATA
1 CTTACCATTT--AATTCCATAAGCTCGTAAGC-T-TA---TTTTACCAATATA
* * *
395429 CTTACCATTTAAATTCTATAAGCTCATAAGCTTATTTTACCCATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
395476 CTTGCCA-TT-ATTCCAAAAGCTCGTAAGCTTATTT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTT
395510 GTATGCTTAC
Statistics
Matches: 109, Mismatches: 14, Indels: 20
0.76 0.10 0.14
Matches are distributed among these distances:
44 31 0.28
46 2 0.02
47 24 0.22
48 10 0.09
49 2 0.02
50 2 0.02
51 13 0.12
52 25 0.23
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:395440 original size:52 final size:52
Alignment explanation
Indices: 395364--395463 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
395354 CGTAAGCTTA
* *
395364 TTTTACCAAAATACTTACCGTTTAAAATT-TCATAAGCT-GTAAGCTTATATTT
1 TTTTACCAAAATACTTACCATTT-AAATTCT-ATAAGCTCATAAGCTTATATTT
* *
395416 TTTTTCCAATATACTTACCATTTAAATTCTATAAGCTCATAAGCTTAT
1 TTTTACCAAAATACTTACCATTTAAATTCTATAAGCTCATAAGCTTAT
395464 TTTACCCATA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
51 12 0.29
52 30 0.71
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (52 bp):
TTTTACCAAAATACTTACCATTTAAATTCTATAAGCTCATAAGCTTATATTT
Found at i:395669 original size:40 final size:40
Alignment explanation
Indices: 395614--395775 Score: 306
Period size: 40 Copynumber: 4.0 Consensus size: 40
395604 ACCGTAGTGC
*
395614 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
395654 TACACATAAGGTCGTGCCCACCATATACAGCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
395694 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
395734 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
395774 TA
1 TA
395776 TAAACCTGCA
Statistics
Matches: 119, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 119 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:402462 original size:50 final size:47
Alignment explanation
Indices: 402361--402524 Score: 192
Period size: 44 Copynumber: 3.5 Consensus size: 47
402351 ATCATTTATC
* *
402361 CCATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCGTTTAAAATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTT-AAATT
*
402409 CCATAAGCTCGTAAGCTTATATTTTTTCCAATATACTTACCATTTAAATT
1 CCATAAGCTCGTAAGC-T-TA-TTTTACCAATATACTTACCATTTAAATT
** * *
402459 CCATAAGCTTATAAGCTTATTTTACCCATATACTTGCCA-TT--ATT
1 CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAATT
402503 CCGA-AAGCTCGTAAGCTTATTT
1 CC-ATAAGCTCGTAAGCTTATTT
402525 GTATGCTTAC
Statistics
Matches: 102, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
44 21 0.21
45 1 0.01
46 2 0.02
47 17 0.17
48 18 0.18
49 2 0.02
50 21 0.21
51 20 0.20
ACGTcount: A:0.32, C:0.21, G:0.09, T:0.38
Consensus pattern (47 bp):
CCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTAAATT
Found at i:402673 original size:40 final size:40
Alignment explanation
Indices: 402629--402710 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
402619 ACCGTAGTGC
*
402629 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTCTAT
*
402669 TACACATAAGGTCGTGCCCACCATATGCACCGAAGTCTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTCTAT
402709 TA
1 TA
402711 TAAACCTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.32, C:0.28, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTCTAT
Found at i:406594 original size:23 final size:22
Alignment explanation
Indices: 406548--406711 Score: 137
Period size: 23 Copynumber: 7.6 Consensus size: 22
406538 ACCCCGATAA
406548 GGGTATCGATA-CCA-TC-AGG
1 GGGTATCGATACCCATTCAAGG
406567 GGGTATCGATACCCATTCAAGG
1 GGGTATCGATACCCATTCAAGG
* * *
406589 ATGGTATCGATACCTATTGAA-G
1 -GGGTATCGATACCCATTCAAGG
*
406611 GGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACCCATTC-AAGG
* * *
406634 GGGTATCGATA-CTAGTGCTA-G
1 GGGTATCGATACCCA-TTCAAGG
*
406655 GGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACCCATTC-AAGG
* *
406678 GGGTATCGATA-CCAGTGCTA-G
1 GGGTATCGATACCCA-TTCAAGG
406699 GGGTATCGATACC
1 GGGTATCGATACC
406712 TAATGCACAA
Statistics
Matches: 121, Mismatches: 12, Indels: 21
0.79 0.08 0.14
Matches are distributed among these distances:
19 11 0.09
20 3 0.02
21 44 0.36
22 18 0.15
23 45 0.37
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (22 bp):
GGGTATCGATACCCATTCAAGG
Found at i:406617 original size:21 final size:21
Alignment explanation
Indices: 406548--406713 Score: 142
Period size: 21 Copynumber: 7.7 Consensus size: 21
406538 ACCCCGATAA
* *
406548 GGGTATCGATACC-A-TCAGG
1 GGGTATCGATACCTATTGAAG
* *
406567 GGGTATCGATACCCATTCAAG
1 GGGTATCGATACCTATTGAAG
406588 GATGGTATCGATACCTATTGAAG
1 G--GGTATCGATACCTATTGAAG
*
406611 GGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACCTATT-GAA-G
* *
406634 GGGTATCGATA-CTAGTGCTAG
1 GGGTATCGATACCTATTG-AAG
*
406655 GGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACCTATT-GAA-G
* *
406678 GGGTATCGATACC-AGTGCTAG
1 GGGTATCGATACCTATTG-AAG
406699 GGGTATCGATACCTA
1 GGGTATCGATACCTA
406714 ATGCACAAAA
Statistics
Matches: 122, Mismatches: 13, Indels: 21
0.78 0.08 0.13
Matches are distributed among these distances:
19 13 0.11
20 1 0.01
21 47 0.39
22 16 0.13
23 45 0.37
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (21 bp):
GGGTATCGATACCTATTGAAG
Found at i:406621 original size:44 final size:44
Alignment explanation
Indices: 406548--406713 Score: 223
Period size: 44 Copynumber: 3.8 Consensus size: 44
406538 ACCCCGATAA
* *
406548 GGGTATCGATACCA-T-CAGGGGGTATCGATACCCATTC-AAGG
1 GGGTATCGATACCAGTGCAAGGGGTATCGATACCTATTCAAAGG
* *
406589 ATGGTATCGATACCTATTG-AAGGGGTATCGATACCTATTCAAAGG
1 -GGGTATCGATACC-AGTGCAAGGGGTATCGATACCTATTCAAAGG
* *
406634 GGGTATCGATACTAGTGCTAGGGGTATCGATACCTATTCAAAGG
1 GGGTATCGATACCAGTGCAAGGGGTATCGATACCTATTCAAAGG
*
406678 GGGTATCGATACCAGTGCTAGGGGTATCGATACCTA
1 GGGTATCGATACCAGTGCAAGGGGTATCGATACCTA
406714 ATGCACAAAA
Statistics
Matches: 111, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
42 12 0.11
43 4 0.04
44 91 0.82
45 4 0.04
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (44 bp):
GGGTATCGATACCAGTGCAAGGGGTATCGATACCTATTCAAAGG
Found at i:408823 original size:20 final size:20
Alignment explanation
Indices: 408798--408838 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
408788 ACTCTTCTAC
408798 AACTAAAGTTCTTTTATTAA
1 AACTAAAGTTCTTTTATTAA
408818 AACTAAAGTTCTTTTATTAA
1 AACTAAAGTTCTTTTATTAA
408838 A
1 A
408839 TAATCGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (20 bp):
AACTAAAGTTCTTTTATTAA
Found at i:412492 original size:19 final size:20
Alignment explanation
Indices: 412468--412547 Score: 72
Period size: 22 Copynumber: 3.9 Consensus size: 20
412458 TGTTATATGC
*
412468 CTTA-GGGTATCGGTACCAT
1 CTTAGGGGTATCGATACCAT
412487 CTTAGGGGTATCGATACCATT
1 CTTAGGGGTATCGATACCA-T
* *
412508 GCATGGGGGTATCGATACCTAT
1 -CTTAGGGGTATCGATACC-AT
***
412530 GGGAGGGGTATCGATACC
1 CTTAGGGGTATCGATACC
412548 TTTCGAGCGT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
19 4 0.08
20 13 0.26
21 15 0.30
22 17 0.34
23 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.28
Consensus pattern (20 bp):
CTTAGGGGTATCGATACCAT
Found at i:412497 original size:20 final size:19
Alignment explanation
Indices: 412468--412506 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
412458 TGTTATATGC
*
412468 CTTAGGGTATCGGTACCAT
1 CTTAGGGTATCGATACCAT
412487 CTTAGGGGTATCGATACCAT
1 CTTA-GGGTATCGATACCAT
412507 TGCATGGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.31
Consensus pattern (19 bp):
CTTAGGGTATCGATACCAT
Found at i:412539 original size:21 final size:21
Alignment explanation
Indices: 412490--412548 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
412480 GTACCATCTT
*
412490 AGGGGTATCGATACC-ATTGC
1 AGGGGTATCGATACCTATGGC
*
412510 ATGGGGGTATCGATACCTATGGG
1 A--GGGGTATCGATACCTATGGC
412533 AGGGGTATCGATACCT
1 AGGGGTATCGATACCT
412549 TTCGAGCGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 1 0.03
21 15 0.44
22 14 0.41
23 4 0.12
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (21 bp):
AGGGGTATCGATACCTATGGC
Found at i:424230 original size:20 final size:20
Alignment explanation
Indices: 424196--424233 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
424186 ATTTTTACAG
424196 AAAAATCCCCGAACGGCTCC
1 AAAAATCCCCGAACGGCTCC
424216 AAAATATCCCC-AACGGCT
1 AAAA-ATCCCCGAACGGCT
424234 AGATACGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.37, C:0.37, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAAATCCCCGAACGGCTCC
Found at i:424504 original size:33 final size:32
Alignment explanation
Indices: 424449--424515 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 32
424439 TTTGTAAAGG
*
424449 GGAAAGGTTCTAGCTAAGCCCGTGTAAAAGCTA
1 GGAAAGGTTCTAGCTAAGCCCGTG-AAAAACTA
* * *
424482 GGAAAGGTTCTAGTTTATCCCGTGAAAAACTA
1 GGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
424514 GG
1 GG
424516 GTTGTAAAGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
32 9 0.30
33 21 0.70
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (32 bp):
GGAAAGGTTCTAGCTAAGCCCGTGAAAAACTA
Found at i:427563 original size:32 final size:33
Alignment explanation
Indices: 427520--427585 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
427510 AATGCAAAAA
*
427520 GGGTATCGATACCCCT-ATGGGTATCTATACCC
1 GGGTATCGATACCCCTCATGGGTATCAATACCC
* *
427552 GGGTATTGATACCCCTGCCTGGGTATCAATACCC
1 GGGTATCGATACCCCT-CATGGGTATCAATACCC
427586 CCTGGCTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 15 0.52
34 14 0.48
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (33 bp):
GGGTATCGATACCCCTCATGGGTATCAATACCC
Found at i:428227 original size:20 final size:20
Alignment explanation
Indices: 428202--428246 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
428192 CCCAACAAAA
*
428202 ACTTTA-GCATGAGTATCGAT
1 ACTTTAGGCAT-AATATCGAT
*
428222 ACTTTAGGGATAATATCGAT
1 ACTTTAGGCATAATATCGAT
428242 ACTTT
1 ACTTT
428247 CAATCAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 19 0.86
21 3 0.14
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (20 bp):
ACTTTAGGCATAATATCGAT
Found at i:429258 original size:12 final size:12
Alignment explanation
Indices: 429243--429285 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
429233 GTTATTTAAA
429243 CGGGTATTGGGT
1 CGGGTATTGGGT
*
429255 CGGGTATTGGGC
1 CGGGTATTGGGT
* * *
429267 CGAGAATCGGGT
1 CGGGTATTGGGT
429279 CGGGTAT
1 CGGGTAT
429286 ATATATATAT
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.14, C:0.14, G:0.47, T:0.26
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:436948 original size:9 final size:8
Alignment explanation
Indices: 436914--436959 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
436904 TTAGAACTAA
436914 AAATATTT
1 AAATATTT
436922 AAATA--T
1 AAATATTT
436928 -AATAATTT
1 AAAT-ATTT
436936 AAATATTT
1 AAATATTT
436944 AAAATATTT
1 -AAATATTT
436953 AAATATT
1 AAATATT
436960 ACAACTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
5 3 0.09
6 2 0.06
8 17 0.52
9 11 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATATTT
Found at i:444308 original size:20 final size:21
Alignment explanation
Indices: 444278--444316 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
444268 TAAGTGGTCT
444278 GATTGATAAAATTAAAAGATC
1 GATTGATAAAATTAAAAGATC
444299 GATT-ATAAAATTAAAAGA
1 GATTGATAAAATTAAAAGA
444317 GCTAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.56, C:0.03, G:0.13, T:0.28
Consensus pattern (21 bp):
GATTGATAAAATTAAAAGATC
Found at i:448306 original size:17 final size:17
Alignment explanation
Indices: 448284--448325 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
448274 TCTTTTTTTT
448284 TTTCATCCTTGATTTGC
1 TTTCATCCTTGATTTGC
448301 TTTCATCCTTGATTTGC
1 TTTCATCCTTGATTTGC
448318 TTTCATCC
1 TTTCATCC
448326 ATTTCTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.12, C:0.26, G:0.10, T:0.52
Consensus pattern (17 bp):
TTTCATCCTTGATTTGC
Found at i:449571 original size:26 final size:26
Alignment explanation
Indices: 449539--449595 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
449529 GGCCCCCTTC
*
449539 TTTAAATATTATCGAATTAACATCTT
1 TTTAAATATTATCGAATTAACATCAT
449565 TTTAAATATTATCGAATTAACATCAT
1 TTTAAATATTATCGAATTAACATCAT
449591 TTTAA
1 TTTAA
449596 CAAAACGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.46
Consensus pattern (26 bp):
TTTAAATATTATCGAATTAACATCAT
Found at i:449930 original size:13 final size:13
Alignment explanation
Indices: 449912--449937 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
449902 TTTCACACTT
449912 TTCCTTCTATCAA
1 TTCCTTCTATCAA
449925 TTCCTTCTATCAA
1 TTCCTTCTATCAA
449938 GCTAAGTAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (13 bp):
TTCCTTCTATCAA
Found at i:450560 original size:23 final size:24
Alignment explanation
Indices: 450503--450563 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
450493 CTCGAATGAA
*
450503 AATTAAATAAAAACATTACAAACT
1 AATTAAATAAAAACAATACAAACT
* *
450527 AAAT-AAGAAAAACAATA-AAA-T
1 AATTAAATAAAAACAATACAAACT
450548 CAATTAAATAAAAACA
1 -AATTAAATAAAAACA
450564 TTAACTATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 6 0.20
23 20 0.67
24 3 0.10
ACGTcount: A:0.69, C:0.10, G:0.02, T:0.20
Consensus pattern (24 bp):
AATTAAATAAAAACAATACAAACT
Found at i:450643 original size:19 final size:19
Alignment explanation
Indices: 450619--450666 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
450609 AAGAACAAAA
450619 TAAATAAAAAGTCCATAAT
1 TAAATAAAAAGTCCATAAT
*
450638 TAAATAAAAAGTCTATAAT
1 TAAATAAAAAGTCCATAAT
450657 TAAATAAAAA
1 TAAATAAAAA
450667 CATTAAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.27
Consensus pattern (19 bp):
TAAATAAAAAGTCCATAAT
Found at i:451111 original size:21 final size:21
Alignment explanation
Indices: 451088--451167 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
451078 ACCCTGTGGT
**
451088 GGTGGCATCTGAAATGGCTTT
1 GGTGGCATCTGAAATGGCTGC
* *
451109 GGTGGCATC-GAAAACGACTGC
1 GGTGGCATCTG-AAATGGCTGC
* *
451130 AGTGCCATCTGAAATGGCTGC
1 GGTGGCATCTGAAATGGCTGC
*
451151 GGTGGCATCTAAAATGG
1 GGTGGCATCTGAAATGG
451168 TTGTGGAATA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 44 0.96
22 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.24
Consensus pattern (21 bp):
GGTGGCATCTGAAATGGCTGC
Found at i:453075 original size:24 final size:24
Alignment explanation
Indices: 453043--453091 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
453033 GGGAACGGAT
*
453043 GGTTGGACGGTATTTATGGAGGAC
1 GGTTAGACGGTATTTATGGAGGAC
453067 GGTTAGACGGTATTTATGGAGGAC
1 GGTTAGACGGTATTTATGGAGGAC
453091 G
1 G
453092 ATTATATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.41, T:0.29
Consensus pattern (24 bp):
GGTTAGACGGTATTTATGGAGGAC
Found at i:457859 original size:14 final size:14
Alignment explanation
Indices: 457842--457868 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
457832 ATTATTTAAA
457842 ATAAAATTTTAATT
1 ATAAAATTTTAATT
457856 ATAAAATTTTAAT
1 ATAAAATTTTAAT
457869 AATTTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATAAAATTTTAATT
Found at i:460280 original size:7 final size:7
Alignment explanation
Indices: 460268--460316 Score: 68
Period size: 7 Copynumber: 7.3 Consensus size: 7
460258 ACAATCTTCT
460268 TTATATA
1 TTATATA
460275 TTATATTA
1 TTATA-TA
460283 TTATATA
1 TTATATA
460290 TTATATA
1 TTATATA
460297 -TATATA
1 TTATATA
460303 -T-TATA
1 TTATATA
460308 TTATATA
1 TTATATA
460315 TT
1 TT
460317 GGAGATATTC
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
5 4 0.10
6 8 0.21
7 20 0.51
8 7 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
TTATATA
Found at i:460281 original size:5 final size:5
Alignment explanation
Indices: 460271--460313 Score: 56
Period size: 5 Copynumber: 9.0 Consensus size: 5
460261 ATCTTCTTTA
460271 TATAT TATAT TAT-T ATATAT TATA- TATA- TATAT TATAT TATAT
1 TATAT TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT
460314 ATTGGAGATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 9 0.26
5 25 0.71
6 1 0.03
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:460289 original size:2 final size:2
Alignment explanation
Indices: 460269--460315 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
460259 CAATCTTCTT
460269 TA TA TA T- TA TA T- TA T- TA TA TA T- TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
460306 TA T- TA TA TA T
1 TA TA TA TA TA T
460316 TGGAGATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
1 6 0.15
2 33 0.85
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (2 bp):
TA
Found at i:465022 original size:34 final size:30
Alignment explanation
Indices: 464984--465052 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 30
464974 TTGATATAAC
*
464984 AATTTAAGGCAAAATGATTTTTGGACTTGAATTG
1 AATTTAA--CAAAATG-TATTTGGACTT-AATTG
465018 AATTT-ACAAAATGTATTTGGACTTAATTG
1 AATTTAACAAAATGTATTTGGACTTAATTG
465047 AATTTA
1 AATTTA
465053 TTCAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 10 0.30
30 10 0.30
31 7 0.21
33 1 0.03
34 5 0.15
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (30 bp):
AATTTAACAAAATGTATTTGGACTTAATTG
Found at i:465060 original size:31 final size:31
Alignment explanation
Indices: 464993--465052 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
464983 CAATTTAAGG
*
464993 CAAAATGATTTTTGGACTTGAATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
465024 CAAAATG-TATTTGGACTT-AATTGAATTTA
1 CAAAATGATATTTGGACTTGAATTGAATTTA
465053 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 10 0.36
31 7 0.25
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.42
Consensus pattern (31 bp):
CAAAATGATATTTGGACTTGAATTGAATTTA
Found at i:481372 original size:12 final size:12
Alignment explanation
Indices: 481355--481397 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
481345 TTTTCATTAA
481355 ATATAATTTTTT
1 ATATAATTTTTT
***
481367 ATATAAATTTAAA
1 ATAT-AATTTTTT
481380 ATATAATTTTTT
1 ATATAATTTTTT
481392 ATATAA
1 ATATAA
481398 ATTTAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
12 15 0.62
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATAATTTTTT
Found at i:481381 original size:25 final size:25
Alignment explanation
Indices: 481353--481407 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
481343 TTTTTTCATT
481353 AAATATAATTTTTTATATAAATTTA
1 AAATATAATTTTTTATATAAATTTA
481378 AAATATAATTTTTTATATAAATTTA
1 AAATATAATTTTTTATATAAATTTA
481403 AAATA
1 AAATA
481408 AATATAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (25 bp):
AAATATAATTTTTTATATAAATTTA
Found at i:486940 original size:33 final size:32
Alignment explanation
Indices: 486913--486972 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
486903 TATTAAATTT
486913 TTTAAATTAATATAA-GATAAAATTATTAAAA
1 TTTAAATTAATATAATGATAAAATTATTAAAA
* * *
486944 TTTATATTATTATAATGTTAAAATTATTA
1 TTTAAATTAATATAATGATAAAATTATTA
486973 TTTCATAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
TTTAAATTAATATAATGATAAAATTATTAAAA
Found at i:488109 original size:31 final size:30
Alignment explanation
Indices: 488053--488110 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
488043 ACAAATTAAA
**
488053 TTACTTTCAGATTAAGTTTGAGGTTTTAGC
1 TTACTTTCAGATTAAGCATGAGGTTTTAGC
488083 TTACTTTCAGATTAATGCATGAGGTTTT
1 TTACTTTCAGATTAA-GCATGAGGTTTT
488111 TGATCAATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 15 0.60
31 10 0.40
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.47
Consensus pattern (30 bp):
TTACTTTCAGATTAAGCATGAGGTTTTAGC
Found at i:490318 original size:60 final size:60
Alignment explanation
Indices: 490225--490387 Score: 229
Period size: 60 Copynumber: 2.7 Consensus size: 60
490215 AGTCGATGTG
490225 AACTTTTAATAGTTAAGGGACTTAATAAAGTAATTACTTATAGCCGGATGATCATTTTAT
1 AACTTTTAATAGTTAAGGGACTTAATAAAGTAATTACTTATAGCCGGATGATCATTTTAT
* * *
490285 AACTTTTAATAGTTAAGGGACTTAATAAAGTAATTTCTTATAGTCGGATGATCGTTTTAT
1 AACTTTTAATAGTTAAGGGACTTAATAAAGTAATTACTTATAGCCGGATGATCATTTTAT
* * *** *
490345 AATTTTTAATAATTAAATAACTTAATAAAATAA-TATCTTATAG
1 AACTTTTAATAGTTAAGGGACTTAATAAAGTAATTA-CTTATAG
490388 TCGAAGATCA
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
59 1 0.01
60 91 0.99
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.40
Consensus pattern (60 bp):
AACTTTTAATAGTTAAGGGACTTAATAAAGTAATTACTTATAGCCGGATGATCATTTTAT
Found at i:494141 original size:74 final size:75
Alignment explanation
Indices: 494060--494208 Score: 255
Period size: 75 Copynumber: 2.0 Consensus size: 75
494050 AAAAATTCTT
* * *
494060 AATTTCTTCTCTTT-CCCTTAATATATTGAACTATATTTAATAACTTATTCAAAATAATGGTTAT
1 AATTTCTTCTCTTTCCCCTTAATATATTAAACTATATTTAATAACTTATCCAAAATAATGGGTAT
494124 GCACTTGGCC
66 GCACTTGGCC
494134 AATTTCTTCTCTTTCCCCTTAATATATTAAACTATATTTAATAACTTATCCAAAATAATGGGTAT
1 AATTTCTTCTCTTTCCCCTTAATATATTAAACTATATTTAATAACTTATCCAAAATAATGGGTAT
*
494199 GCATTTGGCC
66 GCACTTGGCC
494209 CTCTAGAGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
74 14 0.20
75 56 0.80
ACGTcount: A:0.32, C:0.18, G:0.08, T:0.42
Consensus pattern (75 bp):
AATTTCTTCTCTTTCCCCTTAATATATTAAACTATATTTAATAACTTATCCAAAATAATGGGTAT
GCACTTGGCC
Found at i:494379 original size:5 final size:5
Alignment explanation
Indices: 494369--494421 Score: 106
Period size: 5 Copynumber: 10.6 Consensus size: 5
494359 ACCAACCCAT
494369 TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA
1 TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA TGGTA
494419 TGG
1 TGG
494422 AAGCAATTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.19, C:0.00, G:0.42, T:0.40
Consensus pattern (5 bp):
TGGTA
Found at i:494684 original size:31 final size:31
Alignment explanation
Indices: 494639--494743 Score: 138
Period size: 31 Copynumber: 3.4 Consensus size: 31
494629 AAATCAGATT
* * *
494639 GGTTGGTTTTCGAGTCGGATTAATATCGGATC
1 GGTTGG-TTTCGAGTCGGGTTAGTATCGGACC
*
494671 GGTTGGTTTCGAGTCGGGTTAGTTTCGGACC
1 GGTTGGTTTCGAGTCGGGTTAGTATCGGACC
*
494702 GGTTGGTTTCGAGTCGGGTTAGTATCGGGCC
1 GGTTGGTTTCGAGTCGGGTTAGTATCGGACC
* *
494733 AGTTTGTTTCG
1 GGTTGGTTTCG
494744 GTTCAGGTCA
Statistics
Matches: 65, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
31 59 0.91
32 6 0.09
ACGTcount: A:0.12, C:0.14, G:0.36, T:0.37
Consensus pattern (31 bp):
GGTTGGTTTCGAGTCGGGTTAGTATCGGACC
Found at i:494690 original size:16 final size:16
Alignment explanation
Indices: 494671--494721 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
494661 ATATCGGATC
494671 GGTTGGTTTCGAGTCG
1 GGTTGGTTTCGAGTCG
* * *
494687 GGTTAGTTTCG-GACC
1 GGTTGGTTTCGAGTCG
494702 GGTTGGTTTCGAGTCG
1 GGTTGGTTTCGAGTCG
494718 GGTT
1 GGTT
494722 AGTATCGGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
15 12 0.43
16 16 0.57
ACGTcount: A:0.08, C:0.14, G:0.41, T:0.37
Consensus pattern (16 bp):
GGTTGGTTTCGAGTCG
Found at i:495232 original size:17 final size:18
Alignment explanation
Indices: 495210--495247 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
495200 ACCCTAGAAT
495210 TTTTTATATTATTTTA-A
1 TTTTTATATTATTTTATA
495227 TTTTTATATTATTTTATA
1 TTTTTATATTATTTTATA
495245 TTT
1 TTT
495248 ACATTCTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTATATTATTTTATA
Found at i:495241 original size:10 final size:10
Alignment explanation
Indices: 495211--495246 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
495201 CCCTAGAATT
495211 TTTTATATTA
1 TTTTATATTA
495221 TTTTA-A-T-
1 TTTTATATTA
495228 TTTTATATTA
1 TTTTATATTA
495238 TTTTATATT
1 TTTTATATT
495247 TACATTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
7 5 0.22
8 2 0.09
9 2 0.09
10 14 0.61
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTATATTA
Found at i:507417 original size:21 final size:21
Alignment explanation
Indices: 507391--507448 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
507381 ATTTATTCTA
* *
507391 GATTGTATGGCGACTTTTGGG
1 GATTGTATGGCGACCTTTAGG
507412 GATTGTATGGCGACCTTTAGG
1 GATTGTATGGCGACCTTTAGG
* **
507433 GACTACATGGCGACCT
1 GATTGTATGGCGACCT
507449 AGTAGGTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (21 bp):
GATTGTATGGCGACCTTTAGG
Found at i:523513 original size:21 final size:20
Alignment explanation
Indices: 523472--523528 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
523462 AACCCAACAC
523472 TAAATATTAATATTATTAAA
1 TAAATATTAATATTATTAAA
*
523492 TAAATATTAATATTTTTTAAA
1 TAAATATTAATA-TTATTAAA
523513 TAAA-A-TAA-ATTATTAA
1 TAAATATTAATATTATTAA
523529 TATATCACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
17 6 0.18
18 1 0.03
19 3 0.09
20 13 0.38
21 11 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATATTAATATTATTAAA
Found at i:523909 original size:59 final size:59
Alignment explanation
Indices: 523799--523974 Score: 200
Period size: 59 Copynumber: 3.0 Consensus size: 59
523789 GTGGATTTGG
*
523799 GGATGAAATTTGAATATTCAAAAGTTT-AGGACCAATTTAGAAAGAGGGTCATAGTTT-A
1 GGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGA-GGTCATAGTTTAA
* *
523857 GGAATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATTGA-GTCATAGTTTAA
1 GG-ATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAA-AGAGGTCATAGTTTAA
* * * *
523917 GGATGTAATTAGAATATTTAAAAGTTT-AGGAATCAATTTA-AAACAAGAGTCATAGTTT
1 GGATGAAATTAGAATATTCAAAAGTTTAAGG-ACCAATTTAGAAA-GAG-GTCATAGTTT
523975 GGAGATATAG
Statistics
Matches: 101, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
58 8 0.08
59 64 0.63
60 27 0.27
61 2 0.02
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (59 bp):
GGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAAAGAGGTCATAGTTTAA
Found at i:523929 original size:30 final size:29
Alignment explanation
Indices: 523846--523931 Score: 79
Period size: 30 Copynumber: 2.9 Consensus size: 29
523836 TAGAAAGAGG
*
523846 GTCATAGTTT-AGGAATGAAATTAGAA-TA
1 GTCATAGTTTAAGG-ATGTAATTAGAATTA
* * *
523874 TTCAAAAGTTTAAGGA-CTAATTTAGAATTGA
1 GTC-ATAGTTTAAGGATGTAA-TTAGAATT-A
523905 GTCATAGTTTAAGGATGTAATTAGAAT
1 GTCATAGTTTAAGGATGTAATTAGAAT
523932 ATTTAAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.09
29 13 0.29
30 22 0.49
31 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.35
Consensus pattern (29 bp):
GTCATAGTTTAAGGATGTAATTAGAATTA
Found at i:524144 original size:3 final size:3
Alignment explanation
Indices: 524138--524203 Score: 132
Period size: 3 Copynumber: 22.0 Consensus size: 3
524128 GTATAATAAC
524138 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
524186 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
524204 CGGAACAAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:526749 original size:21 final size:21
Alignment explanation
Indices: 526725--526859 Score: 127
Period size: 21 Copynumber: 6.5 Consensus size: 21
526715 GTTTTCAGAT
* *
526725 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTGGACTA
*
526746 TCGCAATGCGAGCTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
526767 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
526787 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
* *
526808 TCGCAATGCGAA-TATGTA-AA
1 TCGCAATGCGAACT-TGGACTA
* *
526828 TCGCAATGCGATA-GTCGACTA
1 TCGCAATGCGA-ACTTGGACTA
526849 TCGCAATGCGA
1 TCGCAATGCGA
526860 TTTACATATT
Statistics
Matches: 94, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
20 32 0.34
21 62 0.66
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:526791 original size:20 final size:20
Alignment explanation
Indices: 526766--526838 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
526756 AGCTTGGACT
526766 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
526786 ATCGCAATGCGAACT-TGGACT
1 ATCGCAATGCGAA-TATGTA-A
526807 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
526827 ATCGCAATGCGA
1 ATCGCAATGCGA
526839 TAGTCGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 29 0.63
21 17 0.37
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:526796 original size:41 final size:41
Alignment explanation
Indices: 526745--526859 Score: 187
Period size: 41 Copynumber: 2.8 Consensus size: 41
526735 AACTTCGACT
*
526745 ATCGCAATGCGAGCTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
526786 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
* *
526827 ATCGCAATGCGATA-GTCGACTATCGCAATGCGA
1 ATCGCAATGCGA-ACTTGGACTATCGCAATGCGA
526860 TTTACATATT
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
41 69 0.99
42 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.23
Consensus pattern (41 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAA
Found at i:527027 original size:5 final size:6
Alignment explanation
Indices: 526977--527024 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
526967 GACACGTATT
526977 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC-CG ACC-CG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
527022 ACC
1 ACC
527025 CGAGACGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 15 0.36
6 27 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:527661 original size:21 final size:21
Alignment explanation
Indices: 527636--527770 Score: 136
Period size: 21 Copynumber: 6.4 Consensus size: 21
527626 ATTTTGGACT
527636 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
527657 ATCGCAACGAATTTAGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
527678 ATCGCAACGCAAACTTCGACT--
1 ATCGCAACG--AACTTGGAATAA
*
527699 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
527720 ATCGCAACGCGAACTT-CAACT--
1 ATCGCAA--CGAACTTGGAA-TAA
527741 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
527762 ATCGCAACG
1 ATCGCAACG
527771 CGAACTTGAA
Statistics
Matches: 93, Mismatches: 11, Indels: 20
0.75 0.09 0.16
Matches are distributed among these distances:
19 15 0.16
20 2 0.02
21 60 0.65
22 2 0.02
23 14 0.15
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:527703 original size:42 final size:42
Alignment explanation
Indices: 527657--527785 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
527647 CTTGGAATAA
* *
527657 ATCGCAACGAATTTAGAATAAATCGCAACGCAAACTTCGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
527699 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCAACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
*
527741 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT-GAACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCG-ACT
527783 ATC
1 ATC
527786 ACAATGCGAA
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
42 81 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACT
Found at i:528047 original size:14 final size:14
Alignment explanation
Indices: 528028--528054 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
528018 ATATTAAATA
528028 ATAACTATAATTAT
1 ATAACTATAATTAT
528042 ATAACTATAATTA
1 ATAACTATAATTA
528055 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAACTATAATTAT
Found at i:528269 original size:24 final size:24
Alignment explanation
Indices: 528242--528303 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
528232 CTATTATTTC
* *
528242 ACTTCAATTAAGCTCGAATTTTAG
1 ACTTCAATCAAGCTCGAATTTCAG
528266 ACTTCAATCAAGCTCGAATTTCAG
1 ACTTCAATCAAGCTCGAATTTCAG
*
528290 ACTTCAATCGAGCT
1 ACTTCAATCAAGCT
528304 TCTAAATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (24 bp):
ACTTCAATCAAGCTCGAATTTCAG
Found at i:528778 original size:13 final size:13
Alignment explanation
Indices: 528760--528798 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
528750 TAAAATTAGT
528760 TAAAATTTTAAAA
1 TAAAATTTTAAAA
528773 TAAAATTATTTAAAA
1 TAAAA-T-TTTAAAA
*
528788 TAAAATATTAA
1 TAAAATTTTAA
528799 TTACATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 2 0.09
15 12 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAAATTTTAAAA
Found at i:536255 original size:28 final size:29
Alignment explanation
Indices: 536224--536281 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 29
536214 GCGACCTCCT
536224 AGGTCGCCATGCACGC-CGGCGACCAAGG
1 AGGTCGCCATGCACGCGCGGCGACCAAGG
* *
536252 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCGCGGCGACCAAGG
536281 A
1 A
536282 TTCATGCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.22, C:0.33, G:0.36, T:0.09
Consensus pattern (29 bp):
AGGTCGCCATGCACGCGCGGCGACCAAGG
Found at i:536523 original size:29 final size:29
Alignment explanation
Indices: 536488--536574 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
536478 GTTGGCTGGT
*
536488 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
536517 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
536546 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
536575 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:536951 original size:31 final size:31
Alignment explanation
Indices: 536905--536978 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
536895 TATTTTTGAT
* * *
536905 TCATCTTA-GTGTCTAACGTTTTCTCCGTTA
1 TCATTTTAGGTGTCTAACGTTTTCTACATTA
* *
536935 TTATTTTAGGTGTCTAACGTTTTTTACATTA
1 TCATTTTAGGTGTCTAACGTTTTCTACATTA
536966 TCATTTTAGGTGT
1 TCATTTTAGGTGT
536979 TCGGCCATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 6 0.16
31 31 0.84
ACGTcount: A:0.19, C:0.15, G:0.15, T:0.51
Consensus pattern (31 bp):
TCATTTTAGGTGTCTAACGTTTTCTACATTA
Found at i:538789 original size:53 final size:53
Alignment explanation
Indices: 538678--538780 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
538668 GGTATAAATT
** *
538678 AAATTTCAGGGCGGACACTATCCCTAAAATAAGTAACCAATCGAAGAAAACTC
1 AAATTTCAGGGCGGACACTATCAATAAAATAAATAACCAATCGAAGAAAACTC
* * * **
538731 AAATTTTAGGGTGGATACTATCAATAAAATAAATAATTAATCGAAGAAAA
1 AAATTTCAGGGCGGACACTATCAATAAAATAAATAACCAATCGAAGAAAA
538781 TTTGAATTTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.23
Consensus pattern (53 bp):
AAATTTCAGGGCGGACACTATCAATAAAATAAATAACCAATCGAAGAAAACTC
Found at i:542894 original size:2 final size:2
Alignment explanation
Indices: 542887--542917 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
542877 TGTGTAACTC
542887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
542918 CACTCTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:546190 original size:27 final size:27
Alignment explanation
Indices: 546152--546208 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
546142 TGCAAATCAA
*
546152 GGAAGCGGTGGAACATGAGGAAGTGCT
1 GGAAGCGGTGGAACACGAGGAAGTGCT
*
546179 GGAAGCGGTGGAACACGAGGTAGTGCT
1 GGAAGCGGTGGAACACGAGGAAGTGCT
546206 GGA
1 GGA
546209 TCACGTACTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.28, C:0.12, G:0.46, T:0.14
Consensus pattern (27 bp):
GGAAGCGGTGGAACACGAGGAAGTGCT
Found at i:549712 original size:60 final size:60
Alignment explanation
Indices: 549648--549761 Score: 167
Period size: 60 Copynumber: 1.9 Consensus size: 60
549638 ATTTAAGATG
*
549648 ATCATTTTATAACTTTTAATAGTCG-AGGACTTAATCAAACAATATTCTATAGTTTAAAGA
1 ATCATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAACAATA-TCTATAGTTTAAAGA
* * * *
549708 ATCATTTTGTAACTTTTAATAGTCGAATGACTTAATAAAATAGTATCTATAGTT
1 ATCATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAACAATATCTATAGTT
549762 GGGGTCAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
60 33 0.69
61 15 0.31
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (60 bp):
ATCATTTTATAACTTTTAATAGTCGAAGGACTTAATAAAACAATATCTATAGTTTAAAGA
Found at i:552298 original size:51 final size:49
Alignment explanation
Indices: 552222--552347 Score: 146
Period size: 51 Copynumber: 2.5 Consensus size: 49
552212 TTAGTAGTAA
* * ** * *
552222 AGCGCACCCCCTGCACTGCGTTATACGATGATTTGGCGCCACGTGCGGTAT
1 AGCGCGCCCCCTGCAC-GCGCTATACGATGAGCTGGCGCCACAT-AGGTAT
*
552273 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTGGCGCCACATAGGTAT
1 AGCGCGCCCCCTGCA-CGCGCTATACGATGAGCTGGCGCCACATAGGTAT
*
552323 AGCGCGGCCCCTGCA-GCGCTATACG
1 AGCGCGCCCCCTGCACGCGCTATACG
552348 CCACGTAGGG
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 10 0.15
50 19 0.29
51 36 0.55
52 1 0.02
ACGTcount: A:0.17, C:0.35, G:0.29, T:0.18
Consensus pattern (49 bp):
AGCGCGCCCCCTGCACGCGCTATACGATGAGCTGGCGCCACATAGGTAT
Found at i:552442 original size:49 final size:49
Alignment explanation
Indices: 552359--552479 Score: 174
Period size: 49 Copynumber: 2.5 Consensus size: 49
552349 CACGTAGGGG
** *
552359 TATAGCGCGGATCAGGTACCACGCTATACATTTACTCCTA-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACATTTACTCC-ACATAATTTTA
*
552408 TATAGCGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACATTTACTCCACATAATTTTA
552457 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
552480 TTTTGTATAA
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
48 1 0.02
49 64 0.97
50 1 0.02
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (49 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACATTTACTCCACATAATTTTA
Found at i:556117 original size:25 final size:24
Alignment explanation
Indices: 556044--556123 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
556034 AAAGTCCAAC
556044 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAA--ATT
* **
556070 AAA-TGAGA-AATAATAAAAAAAATT
1 AAATTTA-ACAA-AATAAAGTAAATT
556094 ACAATTTAACAAAATAAAGTAAATGT
1 A-AATTTAACAAAATAAAGTAAAT-T
556120 AAAT
1 AAAT
556124 ATAATTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
24 4 0.10
25 20 0.48
26 18 0.43
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.26
Consensus pattern (24 bp):
AAATTTAACAAAATAAAGTAAATT
Found at i:558358 original size:110 final size:111
Alignment explanation
Indices: 558177--558384 Score: 355
Period size: 110 Copynumber: 1.9 Consensus size: 111
558167 ATTCTTAATC
* *
558177 TAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTAAATTAAAACGTTA
1 TAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAACGTTA
* *
558242 AAATGTTACTGTATCAGCAAAGTGTCGAGATATTTAATTATTATTA
66 AAATGTTACCGTATCAGCAAAGTGTAGAGATATTTAATTATTATTA
* *
558288 TAATAATCATGCATTAAATAAAT-AACTAAATATTACTGATAATTTAAATTAAATTAAAACGTTA
1 TAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAACGTTA
558352 AAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AAATGTTACCGTATCAGCAAAGTGTAGAGATAT
558385 ATGATTTCCA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 69 0.76
111 22 0.24
ACGTcount: A:0.46, C:0.09, G:0.10, T:0.36
Consensus pattern (111 bp):
TAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTAAATTAAAACGTTA
AAATGTTACCGTATCAGCAAAGTGTAGAGATATTTAATTATTATTA
Found at i:558688 original size:36 final size:37
Alignment explanation
Indices: 558641--558716 Score: 127
Period size: 38 Copynumber: 2.1 Consensus size: 37
558631 CTATACCCCA
*
558641 CGTGTCAG-ATATATATGTATAGCGCACTGCAGGGGC
1 CGTGTCAGAATATATATGTATAGCGCACTACAGGGGC
558677 CGTGTCAGATATATATATGTATAGCGCACTACAGGGGC
1 CGTGTCAGA-ATATATATGTATAGCGCACTACAGGGGC
558715 CG
1 CG
558717 CGCTATACCC
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
36 8 0.22
38 29 0.78
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (37 bp):
CGTGTCAGAATATATATGTATAGCGCACTACAGGGGC
Found at i:558770 original size:50 final size:51
Alignment explanation
Indices: 558708--558821 Score: 140
Period size: 51 Copynumber: 2.3 Consensus size: 51
558698 TAGCGCACTA
* ** *
558708 CAGGGGCCGCGCTATA-CCCACGTAGCACCAGCTCACCGTATAGCACGGTG
1 CAGGGGGCGCGCTATACCCCACGTAGCACCAAATCACCGTATAGCACGATG
* * * * *
558758 CAGGGTGCGCGCTATACCCCACGTGGCGCCAAATCATCGTATAGCGCGATG
1 CAGGGGGCGCGCTATACCCCACGTAGCACCAAATCACCGTATAGCACGATG
558809 CAGGGGGCGCGCT
1 CAGGGGGCGCGCT
558822 TTACTGCTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
50 14 0.26
51 39 0.74
ACGTcount: A:0.20, C:0.33, G:0.32, T:0.15
Consensus pattern (51 bp):
CAGGGGGCGCGCTATACCCCACGTAGCACCAAATCACCGTATAGCACGATG
Found at i:563559 original size:34 final size:35
Alignment explanation
Indices: 563516--563598 Score: 123
Period size: 34 Copynumber: 2.3 Consensus size: 35
563506 TTGGCGGTTG
563516 GTTTTAGGGTTTTACATATTGAATGA-GTTTTCAT
1 GTTTTAGGGTTTTACATATTGAATGATGTTTTCAT
* *
563550 GTTTTAGGGTTTTACATATTGAATGATTTTTTTTTAT
1 GTTTTAGGGTTTTACATATTGAATGA--TGTTTTCAT
563587 GTTTTAGGGTTT
1 GTTTTAGGGTTT
563599 CACAGTGAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
34 26 0.59
37 18 0.41
ACGTcount: A:0.20, C:0.04, G:0.20, T:0.55
Consensus pattern (35 bp):
GTTTTAGGGTTTTACATATTGAATGATGTTTTCAT
Found at i:565116 original size:13 final size:13
Alignment explanation
Indices: 565098--565124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
565088 GAAGTTAAAT
565098 GATTCATATTTTA
1 GATTCATATTTTA
565111 GATTCATATTTTA
1 GATTCATATTTTA
565124 G
1 G
565125 GTACTATGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (13 bp):
GATTCATATTTTA
Found at i:570659 original size:2 final size:2
Alignment explanation
Indices: 570652--570686 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
570642 AAAACACAAG
570652 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
570687 ATGTAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:572028 original size:6 final size:6
Alignment explanation
Indices: 572019--572048 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
572009 ACAGCTGCAG
*
572019 GAGGAG GAGGAA GAGGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
572049 AAATAGTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (6 bp):
GAGGAA
Found at i:572235 original size:8 final size:8
Alignment explanation
Indices: 572222--572247 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
572212 CCTTTTTCAT
572222 CTCTCTCG
1 CTCTCTCG
572230 CTCTCTCG
1 CTCTCTCG
572238 CTCTCTCG
1 CTCTCTCG
572246 CT
1 CT
572248 AGCTTCAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.50, G:0.12, T:0.38
Consensus pattern (8 bp):
CTCTCTCG
Found at i:574419 original size:31 final size:31
Alignment explanation
Indices: 574331--574426 Score: 106
Period size: 31 Copynumber: 3.1 Consensus size: 31
574321 AAACCTCGAC
* *
574331 AACTGTCCATA-GATCCCGAAGAACCTAGGTA
1 AACTGTCCATATG-TCCCTAAGAACATAGGTA
** *
574362 AACTGTCCATATGTTTCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCTAAGAACATAGGTA
*
574393 TACTGTCCATATGTCCCTAA-AGACATAGGTA
1 AACTGTCCATATGTCCCTAAGA-ACATAGGTA
574424 AAC
1 AAC
574427 CCTCGACTCT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
30 1 0.02
31 51 0.96
32 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCTAAGAACATAGGTA
Found at i:579598 original size:21 final size:21
Alignment explanation
Indices: 579572--579612 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
579562 TGCCATGAAC
579572 ATTGCTACAGTGCATCGATGT
1 ATTGCTACAGTGCATCGATGT
*
579593 ATTGCTACAGTGCATTGATG
1 ATTGCTACAGTGCATCGATG
579613 CACCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
ATTGCTACAGTGCATCGATGT
Found at i:580271 original size:31 final size:31
Alignment explanation
Indices: 580233--580328 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
580223 AAACCTCGGC
* * *
580233 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCCCTAAGAACATAGGTA
* *
580264 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCTAAGAACATAGGTA
* *
580295 TACTGTTCATATGTCCCTAA-AGACATAGGTA
1 AACTGTCCATATGTCCCTAAGA-ACATAGGTA
580326 AAC
1 AAC
580329 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.02
31 53 0.98
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (31 bp):
AACTGTCCATATGTCCCTAAGAACATAGGTA
Found at i:581745 original size:9 final size:9
Alignment explanation
Indices: 581731--581766 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
581721 TTCAATTTGG
581731 AGATGAAGA
1 AGATGAAGA
581740 AGATGAAGA
1 AGATGAAGA
581749 AGATGAAG-
1 AGATGAAGA
581757 AGA-GAAGA
1 AGATGAAGA
581765 AG
1 AG
581767 GAAAAGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 5 0.19
9 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (9 bp):
AGATGAAGA
Found at i:587442 original size:20 final size:20
Alignment explanation
Indices: 587409--587446 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
587399 TCCAATTAAT
587409 TTTATATTTATTCACGTTCG
1 TTTATATTTATTCACGTTCG
* *
587429 TTTATGTTTGTTCACGTT
1 TTTATATTTATTCACGTT
587447 TATTCATTTA
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:0.16, C:0.13, G:0.13, T:0.58
Consensus pattern (20 bp):
TTTATATTTATTCACGTTCG
Found at i:600162 original size:6 final size:6
Alignment explanation
Indices: 600151--600211 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
600141 GACACGTATT
* * *
600151 ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG ACCTCG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
600199 ACCACG ACCACG A
1 ACCACG ACCACG A
600212 GCCGAGCCGA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.30, C:0.49, G:0.16, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:600219 original size:5 final size:5
Alignment explanation
Indices: 600209--600257 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
600199 ACCACGACCA
* * * *
600209 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
600258 ACGGACGGAC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.16, C:0.37, G:0.41, T:0.06
Consensus pattern (5 bp):
CGAGC
Found at i:606118 original size:6 final size:6
Alignment explanation
Indices: 606107--606179 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
606097 GACACGTATT
606107 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
606155 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
606180 GCCGAGCCGA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.34, C:0.49, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:606187 original size:5 final size:5
Alignment explanation
Indices: 606177--606235 Score: 73
Period size: 5 Copynumber: 11.8 Consensus size: 5
606167 ACCACGACCA
* * * *
606177 CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGTGC CGAGC CGAGC
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
*
606227 CGAGA CGAG
1 CGAGC CGAG
606236 ACGGACGGAC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 51 1.00
ACGTcount: A:0.15, C:0.37, G:0.41, T:0.07
Consensus pattern (5 bp):
CGAGC
Found at i:606657 original size:4 final size:4
Alignment explanation
Indices: 606648--607316 Score: 1256
Period size: 4 Copynumber: 168.2 Consensus size: 4
606638 AGAGAAACCT
606648 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606696 TACA TACA TACA TACA TAC- -ACA TACA T--A TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606740 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606788 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606836 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606884 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606932 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
606980 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
607028 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
607076 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
607124 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
607172 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
607220 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACG TACG TACG
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* * *
607268 TACG TACA TACA TACA TACG TACA TACA TACA TACG TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
607316 T
1 T
607317 GGGGTTTTGT
Statistics
Matches: 655, Mismatches: 6, Indels: 8
0.98 0.01 0.01
Matches are distributed among these distances:
2 4 0.01
4 651 0.99
ACGTcount: A:0.49, C:0.25, G:0.01, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:608157 original size:31 final size:30
Alignment explanation
Indices: 608072--608158 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 30
608062 TTCGATAATA
*
608072 TAATAATTATTTTAT-ATTATTTAGATAAATT
1 TAATAA-TATTTTATAATTTTTTA-ATAAATT
* * *
608103 TATTTATAATTTTATAATCTTTTAATAAATT
1 TAATAAT-ATTTTATAATTTTTTAATAAATT
608134 TAATAAGTATTTTATAATTTTTTAA
1 TAATAA-TATTTTATAATTTTTTAA
608159 ACTTTATTGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
30 1 0.02
31 38 0.83
32 7 0.15
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (30 bp):
TAATAATATTTTATAATTTTTTAATAAATT
Found at i:608253 original size:24 final size:24
Alignment explanation
Indices: 608220--608270 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 24
608210 ACTTTATTTG
608220 AAAATATAT-ATTAAACTTAGTAA
1 AAAATATATAATTAAACTTAGTAA
608243 AAAATATTATACAATTAAACTTAGTAA
1 AAAATA-TAT--AATTAAACTTAGTAA
608270 A
1 A
608271 CTTTTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 6 0.25
24 3 0.12
27 15 0.62
ACGTcount: A:0.57, C:0.06, G:0.04, T:0.33
Consensus pattern (24 bp):
AAAATATATAATTAAACTTAGTAA
Found at i:610971 original size:38 final size:39
Alignment explanation
Indices: 610927--611000 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
610917 ATTTTTTAAC
*
610927 ATTTTCAATT-TAA-CTGAAAATATTATGAAAAATGTAAT
1 ATTTTCAATTGTAACCT-AAAATATTACGAAAAATGTAAT
* *
610965 ATTTTCAGTTGTAACCTAAAATGTTACGAAAAATGT
1 ATTTTCAATTGTAACCTAAAATATTACGAAAAATGT
611001 TTGCATCCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 9 0.29
39 20 0.65
40 2 0.06
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (39 bp):
ATTTTCAATTGTAACCTAAAATATTACGAAAAATGTAAT
Found at i:615241 original size:3 final size:3
Alignment explanation
Indices: 615229--615276 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
615219 CATAATAATA
* * *
615229 ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT -ATT ATT
615276 A
1 A
615277 AATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
3 32 0.86
4 5 0.14
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:615263 original size:25 final size:24
Alignment explanation
Indices: 615223--615271 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
615213 TTTTTTCATA
615223 ATAATAATTATAATTATTATTAAT
1 ATAATAATTATAATTATTATTAAT
*
615247 ATAATATATTATTATTATTATTAAT
1 ATAATA-ATTATAATTATTATTAAT
615272 TATTAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
ATAATAATTATAATTATTATTAAT
Found at i:616184 original size:30 final size:30
Alignment explanation
Indices: 616148--616287 Score: 253
Period size: 31 Copynumber: 4.6 Consensus size: 30
616138 GTCCATAGAT
*
616148 TCCGAAGAACCTAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
616178 TCCGAAGAACATAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATG
616208 TCCCGAAGAACATAGGTAAACAGTCCATATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATG
616239 TCCCGAAGAACATAGGTAAACAGTCCATATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATG
616270 TCCGAAGAACATAGGTAA
1 TCCGAAGAACATAGGTAA
616288 CCCTCGACCC
Statistics
Matches: 108, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
30 47 0.44
31 61 0.56
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (30 bp):
TCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:616215 original size:61 final size:61
Alignment explanation
Indices: 616148--616287 Score: 255
Period size: 61 Copynumber: 2.3 Consensus size: 61
616138 GTCCATAGAT
*
616148 TCCGAAGAACCTAGGTAAACAGTCCATATGT-CCGAAGAACATAGGTAAACAGTCCATATG
1 TCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
616208 TCCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
1 T-CCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
616270 TCCGAAGAACATAGGTAA
1 TCCGAAGAACATAGGTAA
616288 CCCTCGACCC
Statistics
Matches: 77, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
60 1 0.01
61 46 0.60
62 30 0.39
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (61 bp):
TCCGAAGAACATAGGTAAACAGTCCATATGTCCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:619383 original size:125 final size:125
Alignment explanation
Indices: 619221--619449 Score: 354
Period size: 125 Copynumber: 1.8 Consensus size: 125
619211 GTTTTATTAC
*
619221 ATTTTTAATATTTATTTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAA-GTCACCTAGAAG
1 ATTTTTAATATTTATTTTTATTTATTAATATCAAAGAAAAGAGATGTCTTAAGGT-ACCTAGAAG
*
619285 CCATTTTCTCATATTTTTAAATAAATAAATATCTTATTTAATTTTTATTTTTTAAGAAAAT
65 CCATTTTCTCATATTTCTAAATAAATAAATATCTTATTTAATTTTTATTTTTTAAGAAAAT
* * *
619346 ATTTTTAGTTATTTA-TTTTATTTTTTAATATCGAAGAAAAGAGATGTCTTAAGGTACCTAGAAG
1 ATTTTTA-ATATTTATTTTTATTTATTAATATCAAAGAAAAGAGATGTCTTAAGGTACCTAGAAG
* * *
619410 CCCTTTTCTGATATTTCTAAATAAGTAAATATCTTATTTA
65 CCATTTTCTCATATTTCTAAATAAATAAATATCTTATTTA
619450 TGTATATTAA
Statistics
Matches: 94, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
125 86 0.91
126 8 0.09
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (125 bp):
ATTTTTAATATTTATTTTTATTTATTAATATCAAAGAAAAGAGATGTCTTAAGGTACCTAGAAGC
CATTTTCTCATATTTCTAAATAAATAAATATCTTATTTAATTTTTATTTTTTAAGAAAAT
Found at i:619941 original size:20 final size:21
Alignment explanation
Indices: 619918--619969 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
619908 AGAAATTAAA
619918 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
619938 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
619960 -ATT-ATTTATT
1 AATTCATTTATT
619970 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:624341 original size:2 final size:2
Alignment explanation
Indices: 624334--624365 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
624324 TTATCCTTTA
624334 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
624366 CCTTTGTTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:627125 original size:114 final size:114
Alignment explanation
Indices: 626925--627148 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
626915 GTGCCATGTT
626925 CTCATAGAAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGAAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
*
626990 GTTTGGTATAAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 GTTTGGTATAAACCCCAAAACCAATCATTGGATTAGAAAGATGAATTTG
*
627039 CTCATAGTAA-AAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
1 CTCATAG-AAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCT
** *
627103 GGTTTGGTA-AGAACCTTAAAACCAATCATTGGATTAGGAAGATGAA
65 GGTTTGGTATA-AACCCCAAAACCAATCATTGGATTAGAAAGATGAA
627149 CTGCATGATC
Statistics
Matches: 103, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
113 1 0.01
114 100 0.97
115 2 0.02
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.30
Consensus pattern (114 bp):
CTCATAGAAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
GTTTGGTATAAACCCCAAAACCAATCATTGGATTAGAAAGATGAATTTG
Found at i:629275 original size:52 final size:52
Alignment explanation
Indices: 629197--629358 Score: 243
Period size: 52 Copynumber: 3.1 Consensus size: 52
629187 CAATGATTGA
629197 GAACATCTGAGCAGAAGCCACAAAAAAATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAATGAATGTGTTGTCAAATGTTTTAC
*
629249 GAACATCTGAGCAGAAGCCACAAAAAAATGAATATGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACAAAAAAATGAATGTGTTGTCAAATGTTTTAC
* * * ***
629301 AAACATCTGAGCAGAGGCCACAGGAAAAGATGAATGCACTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAGCCACA--AAAAAATGAATGTGTTGTCAAATGTTTTAC
629355 GAAC
1 GAAC
629359 CTGTTATTCT
Statistics
Matches: 99, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
52 71 0.72
54 28 0.28
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.23
Consensus pattern (52 bp):
GAACATCTGAGCAGAAGCCACAAAAAAATGAATGTGTTGTCAAATGTTTTAC
Found at i:630533 original size:76 final size:76
Alignment explanation
Indices: 630433--630892 Score: 780
Period size: 76 Copynumber: 6.1 Consensus size: 76
630423 ACTATTTCCC
*
630433 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
630498 AAGCCTTCGGG
66 AAACCTTCGGG
* *
630509 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
630574 AAACCTTCGGG
66 AAACCTTCGGG
630585 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
630650 AAGCCTTCGGG
66 AAACCTTCGGG
630661 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
630726 AAACCTTCGGG
66 AAACCTTCGGG
*
630737 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
630802 AATCC-TCAGGG
66 AAACCTTC-GGG
* * * *
630813 TCATCTGTAAGTCCTGCAGTTCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT-T
1 TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
630877 AAACCCTCGGGG
66 AAACCTTC-GGG
630889 TCAT
1 TCAT
630893 TCATAAGACC
Statistics
Matches: 367, Mismatches: 15, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
75 6 0.02
76 361 0.98
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAACCTTCGGG
Found at i:631077 original size:19 final size:22
Alignment explanation
Indices: 631041--631085 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
631031 AATTTTTTCA
631041 TAATAATAATTATAATTATTAT
1 TAATAATAATTATAATTATTAT
*
631063 TAAT-ATAATATATTATTATTAT
1 TAATAATAAT-TATAATTATTAT
631085 T
1 T
631086 TATTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATAATAATTATAATTATTAT
Found at i:632897 original size:125 final size:125
Alignment explanation
Indices: 632735--632963 Score: 363
Period size: 125 Copynumber: 1.8 Consensus size: 125
632725 GTTTTATTAC
632735 ATTTTTAATATTTATTTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAA-GTCACCTAGAAG
1 ATTTTTAATATTTATTTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGT-ACCTAGAAG
*
632799 CCATTTTCTCATATTTTTAAATAAATAAATATCTTATTTAATTTTTATTTTTTAAGAAAAT
65 CCATTTTCTCATATTTCTAAATAAATAAATATCTTATTTAATTTTTATTTTTTAAGAAAAT
* * *
632860 ATTTTTAGTTATTTA-TTTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGTACCTAGAAG
1 ATTTTTA-ATATTTATTTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAG
* * *
632924 CCCTTTTCTGATATTTCTAAATAAGTAAATATCTTATTTA
65 CCATTTTCTCATATTTCTAAATAAATAAATATCTTATTTA
632964 TGTATATTAA
Statistics
Matches: 95, Mismatches: 7, Indels: 4
0.90 0.07 0.04
Matches are distributed among these distances:
125 87 0.92
126 8 0.08
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (125 bp):
ATTTTTAATATTTATTTTTATTTATTAATATCAAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGC
CATTTTCTCATATTTCTAAATAAATAAATATCTTATTTAATTTTTATTTTTTAAGAAAAT
Found at i:635309 original size:34 final size:34
Alignment explanation
Indices: 635271--635340 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
635261 GTCTTGATTG
635271 GTCGAAAAAGATGTTGGAGAATAATGATTTTGGT
1 GTCGAAAAAGATGTTGGAGAATAATGATTTTGGT
635305 GTCGAAAAAGATGTTGGAGAATAATGATTTTGGT
1 GTCGAAAAAGATGTTGGAGAATAATGATTTTGGT
635339 GT
1 GT
635341 GACAATGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.33
Consensus pattern (34 bp):
GTCGAAAAAGATGTTGGAGAATAATGATTTTGGT
Found at i:640925 original size:24 final size:24
Alignment explanation
Indices: 640884--640938 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
640874 GTTTTTTTTT
* *
640884 AATT-TTATTAATTTAATATATAA
1 AATTATTAATAATTAAATATATAA
*
640907 AATTATTAATAATTAAATATGTAA
1 AATTATTAATAATTAAATATATAA
*
640931 TATTATTA
1 AATTATTA
640939 TATATAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
23 4 0.15
24 23 0.85
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
AATTATTAATAATTAAATATATAA
Found at i:642376 original size:132 final size:134
Alignment explanation
Indices: 642136--642389 Score: 440
Period size: 132 Copynumber: 1.9 Consensus size: 134
642126 CACATGCCCA
* * *
642136 AATCCTTAAACTTGTTTCATTCAATAAGTTCATGCTTAAAAGACTATATTTTAAAAACTTGATAA
1 AATCCTTAAACTTATTTCATTCAATAAGTTCATGCTTAAAAGAC-ATATTTTAAAAACATGAAAA
*
642201 AACTAATGTGAGATTTAAAAATCTCACTGTTAAACTTATTGATTTTGAACTATAAAACGTGCTCA
65 AACTAATGTGAGATTTAAAAATCTCACTGTTAAACTTAATGATTTTGAACTATAAAACGTGCTCA
642266 CCCTG
130 CCCTG
*
642271 AATCCTTAAACTTATTTCATTCAATAAGTTCATGTTTAAAAGAC-TATTTT-AAAACATGAAAAA
1 AATCCTTAAACTTATTTCATTCAATAAGTTCATGCTTAAAAGACATATTTTAAAAACATGAAAAA
642334 ACTAATGTGAGATTTAAAAATCTCACTGTTAAACTTAATGATTTTGAACTATAAAA
66 ACTAATGTGAGATTTAAAAATCTCACTGTTAAACTTAATGATTTTGAACTATAAAA
642390 AGACAAATTC
Statistics
Matches: 114, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
132 66 0.58
133 6 0.05
135 42 0.37
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (134 bp):
AATCCTTAAACTTATTTCATTCAATAAGTTCATGCTTAAAAGACATATTTTAAAAACATGAAAAA
ACTAATGTGAGATTTAAAAATCTCACTGTTAAACTTAATGATTTTGAACTATAAAACGTGCTCAC
CCTG
Found at i:648781 original size:20 final size:21
Alignment explanation
Indices: 648736--648783 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 21
648726 TATTTTATAG
648736 TAAAATAAAATAAAATATATT
1 TAAAATAAAATAAAATATATT
* *
648757 T--AATAAAA-ATAATATTTT
1 TAAAATAAAATAAAATATATT
648775 TAAAATAAA
1 TAAAATAAA
648784 TTTTAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
18 9 0.39
19 7 0.30
20 6 0.26
21 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAATAAAATAAAATATATT
Done.