Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008521.1 Hibiscus syriacus cultivar Beakdansim tig00111388_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: 1601068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:220059 original size:20 final size:20
Alignment explanation
Indices: 220004--220066 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
219994 ATATCTTTAT
* * *
220004 TAAAATATTTTTTAAATATT
1 TAAAAAATTTATTAAATATA
220024 TAAATAATATTATTATTAAATATA
1 TAAA-AA-A-T-TTATTAAATATA
*
220048 TAAAAAATTTATTATATAT
1 TAAAAAATTTATTAAATAT
220067 TATTAAAATA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.40
21 2 0.06
22 2 0.06
23 3 0.09
24 14 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAAAATTTATTAAATATA
Found at i:220070 original size:30 final size:28
Alignment explanation
Indices: 220034--220106 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 28
220024 TAAATAATAT
220034 TATTATTAAATATATAAAA-AATTTAT-TATA
1 TATTATTAAATATA-AAAATAA--TATCT-TA
220064 TATTATTAAA-ATAAAAATAATATCTTA
1 TATTATTAAATATAAAAATAATATCTTA
220091 TATTATTATAATATAA
1 TATTATTA-AATATAA
220107 TTGATTATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
27 13 0.33
28 7 0.18
29 9 0.23
30 10 0.26
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
TATTATTAAATATAAAAATAATATCTTA
Found at i:220106 original size:29 final size:28
Alignment explanation
Indices: 220034--220106 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 28
220024 TAAATAATAT
*
220034 TATTATTA-AATATATAAAAAATTTATTA
1 TATTATTATAATATA-AAAAAATATATTA
* *
220062 TA-TATTATTAAAATAAAAATAATATCTTA
1 TATTATTA-TAATATAAAAA-AATATATTA
220091 TATTATTATAATATAA
1 TATTATTATAATATAA
220107 TTGATTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 5 0.14
28 6 0.16
29 21 0.57
30 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.45
Consensus pattern (28 bp):
TATTATTATAATATAAAAAAATATATTA
Found at i:220139 original size:20 final size:20
Alignment explanation
Indices: 220112--220155 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
220102 TATAATTGAT
220112 TATT-TTATATAATTAAAAA
1 TATTATTATATAATTAAAAA
* *
220131 TATTATTATATTATTATAAA
1 TATTATTATATAATTAAAAA
220151 TATTA
1 TATTA
220156 ATAAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTATATAATTAAAAA
Found at i:220164 original size:4 final size:4
Alignment explanation
Indices: 220155--220179 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
220145 TATAAATATT
220155 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
220180 TATTTTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:220405 original size:42 final size:42
Alignment explanation
Indices: 220357--220476 Score: 186
Period size: 42 Copynumber: 2.9 Consensus size: 42
220347 ATGAATTACA
* * *
220357 TTCCGAAAAACCAATTACTTGAAACAAATACGAAAAAACATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGAAAAAACATT
** *
220399 TTCCGAAAAACGAATTACGTGAAACAAACACGGGAAAATATT
1 TTCCGAAAAACGAATTACGTGAAACAAACACGAAAAAACATT
220441 TTCCGAAAAACGAATTACGTGAAACAAACACGAAAA
1 TTCCGAAAAACGAATTACGTGAAACAAACACGAAAA
220477 TTCGAGGAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 70 1.00
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.18
Consensus pattern (42 bp):
TTCCGAAAAACGAATTACGTGAAACAAACACGAAAAAACATT
Found at i:220786 original size:15 final size:15
Alignment explanation
Indices: 220769--220824 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
220759 TAACCGGTTT
*
220769 CGGTTTTAAAAAAAT
1 CGGTTTTAAAAAAAC
220784 CGGTTTTTTAAAAAAAC
1 CGG--TTTTAAAAAAAC
*
220801 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
220816 CGATTTTAA
1 CGGTTTTAA
220825 TATTCCAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
15 21 0.60
17 14 0.40
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:220794 original size:17 final size:17
Alignment explanation
Indices: 220772--220822 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
220762 CCGGTTTCGG
*
220772 TTTTAAAAAAATCGGTT
1 TTTTAAAAAAACCGGTT
220789 TTTTAAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
220804 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
220821 TT
1 TT
220823 AATATTCCAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 13 0.45
17 16 0.55
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:221017 original size:21 final size:21
Alignment explanation
Indices: 220993--221045 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
220983 ACACTTAGGG
220993 AACCGATTCCCTATGAGAGGA
1 AACCGATTCCCTATGAGAGGA
*
221014 AACCGATTCCCTATGAGAGGG
1 AACCGATTCCCTATGAGAGGA
*
221035 TACCGATTCCC
1 AACCGATTCCC
221046 CCACGCTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.21
Consensus pattern (21 bp):
AACCGATTCCCTATGAGAGGA
Found at i:221377 original size:32 final size:33
Alignment explanation
Indices: 221281--221379 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
221271 AACTCAACAT
* * *
221281 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
221314 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
221347 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
221379 A
1 A
221380 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:221398 original size:21 final size:21
Alignment explanation
Indices: 221374--221413 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
221364 ACTTCAAGTT
221374 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
221395 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
221414 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:223861 original size:28 final size:26
Alignment explanation
Indices: 223821--223878 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
223811 AAAAAACCGG
*
223821 TTTTTCCCAAATCCGAT-TTCGGATATT
1 TTTTTCCAAAATCCGATATTC-GA-ATT
*
223848 TTTTTCGCAAAATCGGATATTCGAATT
1 TTTTTC-CAAAATCCGATATTCGAATT
223875 TTTT
1 TTTT
223879 GTGCACCCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 13 0.48
28 11 0.41
29 3 0.11
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (26 bp):
TTTTTCCAAAATCCGATATTCGAATT
Found at i:225461 original size:27 final size:27
Alignment explanation
Indices: 225423--225477 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
225413 AGGCAGGAAG
225423 AGGTTTACAAAAGAAGCCGTATAACTT
1 AGGTTTACAAAAGAAGCCGTATAACTT
*
225450 AGGTTTACAAAAGAAGCCGTTTAACTT
1 AGGTTTACAAAAGAAGCCGTATAACTT
225477 A
1 A
225478 CTCTGGCACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (27 bp):
AGGTTTACAAAAGAAGCCGTATAACTT
Found at i:232836 original size:22 final size:22
Alignment explanation
Indices: 232773--232843 Score: 101
Period size: 21 Copynumber: 3.3 Consensus size: 22
232763 AGTCGAGGGT
232773 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
232794 CTCATAGGTCCTTC-GGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
232815 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
232837 TTTCATA
1 -TTCATA
232844 TGCCACACAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 4 0.09
21 27 0.63
22 7 0.16
23 5 0.12
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:236076 original size:65 final size:64
Alignment explanation
Indices: 235990--236151 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 64
235980 TTGTTTAAGG
* * * * ** * *
235990 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTTAAATATAAAGCATCGAATATGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAA-CATCGAATAGGATTTA
**
236055 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
**
236119 TGCATCGATGC-TTGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
236152 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.02
64 27 0.33
65 54 0.65
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
Found at i:237548 original size:21 final size:21
Alignment explanation
Indices: 237522--237584 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
237512 GTCGAGGGTT
237522 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
237543 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
237565 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
237585 ATTTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:237575 original size:22 final size:22
Alignment explanation
Indices: 237521--237592 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
237511 AGTCGAGGGT
237521 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
237542 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
237564 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
237586 TTTCATA
1 -TTCATA
237593 TGCCACACAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.40
22 22 0.49
23 5 0.11
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:240826 original size:65 final size:64
Alignment explanation
Indices: 240740--240901 Score: 182
Period size: 65 Copynumber: 2.5 Consensus size: 64
240730 TTGTTTAAGG
* * * * ** * *
240740 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTTAAATATAAAGCATCGAATATGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAA-CATCGAATAGGATTTA
**
240805 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
**
240869 TGCATCGATGC-TTGGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
240902 ACCTTCATTA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
63 2 0.02
64 27 0.33
65 54 0.65
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAACATTAAATACAAACATCGAATAGGATTTA
Found at i:242302 original size:21 final size:21
Alignment explanation
Indices: 242276--242338 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
242266 GTCGAGGGTT
242276 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
242297 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
242319 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
242339 ATTTCATATG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 20 0.51
22 19 0.49
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:242329 original size:22 final size:22
Alignment explanation
Indices: 242275--242346 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
242265 AGTCGAGGGT
242275 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
242296 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
242318 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
242340 TTTCATA
1 -TTCATA
242347 TGCCACACAG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.40
22 22 0.49
23 5 0.11
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:249915 original size:22 final size:22
Alignment explanation
Indices: 249887--249928 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
249877 TTTTCCGCCG
*
249887 TTTGTAACTCATGTAATTACAC
1 TTTGTAACTCATATAATTACAC
*
249909 TTTGTAACTCTTATAATTAC
1 TTTGTAACTCATATAATTAC
249929 TCTGTAACTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (22 bp):
TTTGTAACTCATATAATTACAC
Found at i:255852 original size:21 final size:22
Alignment explanation
Indices: 255827--255867 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
255817 TTTTCAGTCG
255827 TTTGT-ACTCAAGTAATTACAC
1 TTTGTAACTCAAGTAATTACAC
**
255848 TTTGTAACTCTTGTAATTAC
1 TTTGTAACTCAAGTAATTAC
255868 TCTGTAACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.17, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTGTAACTCAAGTAATTACAC
Found at i:264494 original size:20 final size:20
Alignment explanation
Indices: 264444--264502 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
264434 AGGGTATGAG
*
264444 TTTATGATTAGAGTTTA-GGT
1 TTTAT-ATTAGAATTTAGGGT
264464 TTTGGAT-TTAGAATTTAGGGT
1 TTT--ATATTAGAATTTAGGGT
*
264485 TTTATATTAGGATTTAGG
1 TTTATATTAGAATTTAGG
264503 TATAGGATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
19 2 0.06
20 23 0.70
21 6 0.18
22 2 0.06
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.49
Consensus pattern (20 bp):
TTTATATTAGAATTTAGGGT
Found at i:264558 original size:27 final size:29
Alignment explanation
Indices: 264509--264567 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 29
264499 TAGGTATAGG
*
264509 ATGATGCAATTAAATAACTTA-GGACTAAA
1 ATGATGCAA-TAAATAACTTAGGGACAAAA
**
264538 ATGATGCAA-AAATATTTTAGGGACAAAA
1 ATGATGCAATAAATAACTTAGGGACAAAA
264566 AT
1 AT
264568 AATAAATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 8 0.31
28 9 0.35
29 9 0.35
ACGTcount: A:0.49, C:0.08, G:0.15, T:0.27
Consensus pattern (29 bp):
ATGATGCAATAAATAACTTAGGGACAAAA
Found at i:265480 original size:36 final size:36
Alignment explanation
Indices: 265440--265511 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
265430 TAATATTATT
265440 TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
1 TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
* *
265476 TTACTTTTTATGGTTTAGTGTTAATAATAAATCAAA
1 TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
265512 ATTAAATATG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (36 bp):
TTACTTCTTATCGTTTAGTGTTAATAATAAATCAAA
Found at i:272427 original size:37 final size:31
Alignment explanation
Indices: 272386--272472 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 31
272376 CGTATATAGA
272386 ATGGATGAAATATTAATAAAATAAAATTAAACTAAAC
1 ATGGAT-AAATA--AAT-AAATAAAA-T-AACTAAAC
*
272423 ATGGATAAATAAATAAATAAAATAACTAAATG
1 ATGGATAAATAAATAAATAAAATAACTAAA-C
*
272455 AAGG-TAAATAAATAAATA
1 ATGGATAAATAAATAAATA
272473 CAAGAAATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 21 0.45
32 4 0.09
33 8 0.17
34 3 0.06
36 5 0.11
37 6 0.13
ACGTcount: A:0.62, C:0.03, G:0.09, T:0.25
Consensus pattern (31 bp):
ATGGATAAATAAATAAATAAAATAACTAAAC
Found at i:272436 original size:4 final size:4
Alignment explanation
Indices: 272427--272486 Score: 57
Period size: 4 Copynumber: 14.0 Consensus size: 4
272417 CTAAACATGG
* *
272427 ATAA ATAA ATAA ATAAA ATAA CTAA ATGAA GGTAA ATAA ATAA ATACA
1 ATAA ATAA ATAA AT-AA ATAA ATAA AT-AA -ATAA ATAA ATAA ATA-A
*
272475 AGAA ATAA ATAA
1 ATAA ATAA ATAA
272487 CAATGAAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
4 34 0.74
5 11 0.24
6 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.07, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:272556 original size:8 final size:8
Alignment explanation
Indices: 272528--272589 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
272518 TGTAAAACGT
272528 AATATATA
1 AATATATA
*
272536 AAAATATA
1 AATATATA
272544 AATATATA
1 AATATATA
*
272552 TATATATA
1 AATATATA
*
272560 TATATAT-
1 AATATATA
*
272567 AATATTTA
1 AATATATA
272575 AAGTA-A-A
1 AA-TATATA
272582 AATATATA
1 AATATATA
272590 TATTTAATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 2 0.05
7 9 0.20
8 31 0.70
9 2 0.05
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (8 bp):
AATATATA
Found at i:272591 original size:2 final size:2
Alignment explanation
Indices: 272529--272571 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
272519 GTAAAACGTA
* * *
272529 AT AT AT AA AA AT AT AA AT AT AT AT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
272570 AT
1 AT
272572 TTAAAGTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:275342 original size:201 final size:198
Alignment explanation
Indices: 274883--275509 Score: 726
Period size: 201 Copynumber: 3.1 Consensus size: 198
274873 TGAGGAAGTT
*
274883 TAGTCAGTGGACGACATTGTTCCTACTTGATGAAGACATCTAGTCGTATTTGAAAGATTGTATCT
1 TAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACATCTAGTCGTATTTGAAAGATTGTATCT
* * * *
274948 GAAGACAACAT-TGTTCCTTCTTGTTGAGGAAATCTGATTTCTTAGTGATAACTTGATTTTGGGA
66 AAAGAC-ACATAT-TT-CTTCTTGTTGAGGAAATCTGATTGCCTAGAGATAACTTGATTTT-GGA
* * * *
275012 AAAGACACGGCTCCTACGTGATAAGGATATCTGGTCACTTCTGATGATATTGCTCCTTCATGTTG
127 AAAGACAC-GCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGCTCCTTCATGTTG
* *
275077 ATGAGTTC
191 AGGAGTAC
* *
275085 TAGTCAGTGGACGACATTGTTCCTACTTGATTAGGACATCTAGTCGTATCTGAAAGATTGTATCT
1 TAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACATCTAGTCGTATTTGAAAGATTGTATCT
* * *
275150 AAAGACGACACTATTTCTTCTTGTTGAGGAAATCTGATTGCCTGGAGATAACTAGATTTTAGAAA
66 AAAGAC-ACA-TATTTCTTCTTGTTGAGGAAATCTGATTGCCTAGAGATAACTTGATTTTGGAAA
* *
275215 CGACACAGCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGTTCCTTCATGTTGAG
129 AGACAC-GCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGCTCCTTCATGTTGAG
275280 GA-TGAC
193 GAGT-AC
* * * * * * *
275286 TAGTTAGTGGATGACATTATTCTTGCTTGATGAGGA-AGTCTAGTCGTATTTGAAAGAATATATC
1 TAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACA-TCTAGTCGTATTTGAAAGATTGTATC
* * *
275350 TTAAGACA-ATATTGTTCTTTCTTGTTGAGGAAATCTGATTGCCTAAATATAACTTGATTTTGGA
65 TAAAGACACATA-T-TTC-TTCTTGTTGAGGAAATCTGATTGCCTAGAGATAACTTGATTTTGGA
* * * * * * *
275414 AATGACACGACTCTTACGTGATGAGAAGATCTGATCACTTCTGATGACATTGCTCATTTAT-TTG
127 AAAGACACG-CTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGCTCCTTCATGTTG
*
275478 AAGAGGT-C
191 AGGA-GTAC
* * *
275486 TAGTCAATGAACGATATTGTTCCT
1 TAGTCAGTGGACGACATTGTTCCT
275510 TCAAGTTGAG
Statistics
Matches: 364, Mismatches: 51, Indels: 22
0.83 0.12 0.05
Matches are distributed among these distances:
198 2 0.01
199 2 0.01
200 31 0.09
201 215 0.59
202 110 0.30
203 3 0.01
204 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (198 bp):
TAGTCAGTGGACGACATTGTTCCTACTTGATGAGGACATCTAGTCGTATTTGAAAGATTGTATCT
AAAGACACATATTTCTTCTTGTTGAGGAAATCTGATTGCCTAGAGATAACTTGATTTTGGAAAAG
ACACGCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGCTCCTTCATGTTGAGGAG
TAC
Found at i:275613 original size:403 final size:403
Alignment explanation
Indices: 274883--275655 Score: 916
Period size: 403 Copynumber: 1.9 Consensus size: 403
274873 TGAGGAAGTT
* * *
274883 TAGTCAGTGGACGACATTGTTCCTACTTGATGAAGACATCTAGTCGTATTTGAAAGATTGTATCT
1 TAGTCAGTGGACGACATTATTCCTACTTGATGAAGACATCTAGTCGTATTTGAAAGAATATATCT
* * *
274948 GAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTTCTTAGTGATAACTTGATTTTGGGAA
66 GAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTCCTAAATGATAACTTGATTTTGGGAA
* * * * * *
275013 AAGACACGGCTCCTACGTGATAAGGATATCTGGTCACTTCTGATGATATTGCTCCTTCATGTTGA
131 AAGACACGACTCCTACGTGATAAGAAGATCTGATCACTTCTGATGACATTGCTCATTCATGTTGA
* * * * **
275078 TGAGTTCTAGTCAGTGGACGACATTGTTCCTACTTGATTAGGACATCTAGTCGTATCTGAAAGAT
196 AGAGGTCTAGTCAATGAACGACATTGTTCCTACAAGATTAGGACATCTAGTCGTATCTGAAAGAT
* * * ** * * *
275143 TGTATCTAAAGACGACACTATTTCTTCTTGTTGAGGAAATCTGATTGCCTGGAGATAACTAGATT
261 TGCATCTAAAGAAGACAATATTTCTTCGCGTTGAGGAAATCTGATTACCTGAAAATAACTAGATT
* *
275208 TTAGAAACGACACAGCTCCTACGTGATGAGGAGATCTGGTCACTTCTGATGACATCGTTCCTTCA
326 TTAGAAACGACACAGCTCCTACGTGATGAGGAGATATAGTCACTTCTGATGACATCGTTCCTTCA
275273 TGTTGAGGATGAC
391 TGTTGAGGATGAC
* * * * *
275286 TAGTTAGTGGATGACATTATTCTTGCTTGATGAGGA-AGTCTAGTCGTATTTGAAAGAATATATC
1 TAGTCAGTGGACGACATTATTCCTACTTGATGAAGACA-TCTAGTCGTATTTGAAAGAATATATC
* * *
275350 TTAAGACAATATTGTTCTTTCTTGTTGAGGAAATCTGATTGCCTAAAT-ATAACTTGATTTT-GG
65 TGAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATT-CCTAAATGATAACTTGATTTTGGG
* * * *
275413 AAATGACACGACTCTTACGTGATGAGAAGATCTGATCACTTCTGATGACATTGCTCATTTAT-TT
129 AAAAGACACGACTCCTACGTGATAAGAAGATCTGATCACTTCTGATGACATTGCTCATTCATGTT
* * * * **
275477 GAAGAGGTCTAGTCAATGAACGATATTGTTCCTTCAAG-TTGAGGGA-GTCTAGTCGTATTTGGG
194 GAAGAGGTCTAGTCAATGAACGACATTGTTCCTACAAGATT-A-GGACATCTAGTCGTATCTGAA
* * *
275540 TGATTGCA-C-ATATGAAGACAATATTGTTCCTTCGCGTTGAGGAAGTCTGATTACCT-AAAACT
257 AGATTGCATCTA-AAGAAGACAATA-T-TT-CTTCGCGTTGAGGAAATCTGATTACCTGAAAA-T
* * * * *
275602 AATTTGATTTTAGAAACGACACGGCTCCTATGTGATGATGAGATATAGTCACTT
317 AACTAGATTTTAGAAACGACACAGCTCCTACGTGATGAGGAGATATAGTCACTT
275656 TGGTGATTTG
Statistics
Matches: 307, Mismatches: 54, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
399 1 0.00
400 12 0.04
401 53 0.17
402 62 0.20
403 175 0.57
404 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (403 bp):
TAGTCAGTGGACGACATTATTCCTACTTGATGAAGACATCTAGTCGTATTTGAAAGAATATATCT
GAAGACAACATTGTTCCTTCTTGTTGAGGAAATCTGATTCCTAAATGATAACTTGATTTTGGGAA
AAGACACGACTCCTACGTGATAAGAAGATCTGATCACTTCTGATGACATTGCTCATTCATGTTGA
AGAGGTCTAGTCAATGAACGACATTGTTCCTACAAGATTAGGACATCTAGTCGTATCTGAAAGAT
TGCATCTAAAGAAGACAATATTTCTTCGCGTTGAGGAAATCTGATTACCTGAAAATAACTAGATT
TTAGAAACGACACAGCTCCTACGTGATGAGGAGATATAGTCACTTCTGATGACATCGTTCCTTCA
TGTTGAGGATGAC
Found at i:276361 original size:44 final size:44
Alignment explanation
Indices: 276298--276385 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
276288 GAGGTATCAT
276298 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
1 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
276342 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
1 CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
276386 ATTTCTGATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.27, C:0.05, G:0.27, T:0.41
Consensus pattern (44 bp):
CGTGAGAGTGAAGTCTAAGTTTATTATGTTGTATGTGATTATGA
Found at i:276982 original size:19 final size:19
Alignment explanation
Indices: 276942--276982 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
276932 AAAATGTTTT
*
276942 ATGAAAGAATTATGAAATA
1 ATGAAAGAATTATGAAAAA
* *
276961 ATGAAAGAATTTTTAAAAA
1 ATGAAAGAATTATGAAAAA
276980 ATG
1 ATG
276983 TTTAATGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (19 bp):
ATGAAAGAATTATGAAAAA
Found at i:276988 original size:26 final size:25
Alignment explanation
Indices: 276959--277028 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
276949 AATTATGAAA
*
276959 TAATGAAAGAATTTTTAAAAAATGTT
1 TAATGAAAGAATTTTGAAAAAA-GTT
276985 TAATGAAAGAATTTTGAAAAAAGTT
1 TAATGAAAGAATTTTGAAAAAAGTT
* *
277010 TGATG-AAG-TTTTTGAAAAA
1 TAATGAAAGAATTTTGAAAAA
277029 CGGTCTCTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
23 10 0.24
24 3 0.07
25 7 0.17
26 21 0.51
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.36
Consensus pattern (25 bp):
TAATGAAAGAATTTTGAAAAAAGTT
Found at i:282045 original size:27 final size:26
Alignment explanation
Indices: 282002--282057 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
281992 AATATAATAA
* *
282002 AACTAAACATGGATAAATAAATAAAAT
1 AACTAAACAAGGATAAACAAAT-AAAT
282029 AACTAAACAAAGG-TAAACAAATAAAT
1 AACTAAAC-AAGGATAAACAAATAAAT
282055 AAC
1 AAC
282058 AATGAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 7 0.27
27 16 0.62
28 3 0.12
ACGTcount: A:0.64, C:0.11, G:0.07, T:0.18
Consensus pattern (26 bp):
AACTAAACAAGGATAAACAAATAAAT
Found at i:283857 original size:3 final size:3
Alignment explanation
Indices: 283849--283914 Score: 69
Period size: 3 Copynumber: 21.0 Consensus size: 3
283839 AAATAAAAGT
* * *
283849 TAA TAA TAA TAT TAA TAA TAAA CAA GTAA CAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA
*
283896 GAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA
283915 CCCGGGCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
3 45 0.87
4 7 0.13
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:286257 original size:2 final size:2
Alignment explanation
Indices: 286250--286274 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
286240 TTTTTCTAAT
286250 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 T
286275 GGACTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:286524 original size:21 final size:21
Alignment explanation
Indices: 286500--286561 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
286490 GATCATACAT
286500 ATTTAAAATTATTTAAGTTTG
1 ATTTAAAATTATTTAAGTTTG
286521 ATTTAATTAA-TATTTAA-TTTG
1 ATTTAA--AATTATTTAAGTTTG
* *
286542 AATT-AATTTGATTTAAGTTT
1 ATTTAAAATT-ATTTAAGTTT
286562 AAATTTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 7 0.21
21 16 0.47
22 7 0.21
23 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (21 bp):
ATTTAAAATTATTTAAGTTTG
Found at i:286526 original size:11 final size:10
Alignment explanation
Indices: 286510--286557 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
286500 ATTTAAAATT
286510 ATTTAAGTTTG
1 ATTTAA-TTTG
286521 ATTTAATTAAT-
1 ATTTAATT--TG
286532 ATTTAATTTG
1 ATTTAATTTG
*
286542 AATTAATTTG
1 ATTTAATTTG
286552 ATTTAA
1 ATTTAA
286558 GTTTAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
9 1 0.03
10 16 0.50
11 14 0.44
12 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (10 bp):
ATTTAATTTG
Found at i:286566 original size:21 final size:21
Alignment explanation
Indices: 286509--286566 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
286499 TATTTAAAAT
*
286509 TATTTAAGTTTGATTTAATTAA
1 TATTTAAGTTTGAATTAATT-A
286531 TATTTAA-TTTGAATTAATT-
1 TATTTAAGTTTGAATTAATTA
*
286550 TGATTTAAGTTTAAATT
1 T-ATTTAAGTTTGAATT
286567 TGATTCGAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 6 0.19
21 18 0.56
22 7 0.22
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
TATTTAAGTTTGAATTAATTA
Found at i:287561 original size:32 final size:32
Alignment explanation
Indices: 287534--287647 Score: 149
Period size: 32 Copynumber: 3.6 Consensus size: 32
287524 TTATCTCGGA
* * *
287534 GCCTGAGAGCCTACCCAAGAGAGTATCTTAGG
1 GCCTAAGAGCCTACCCAAGAGAGTACCTTGGG
*
287566 GCCTAAGAGCCTACCCAAGAGAGCACCTTGGG
1 GCCTAAGAGCCTACCCAAGAGAGTACCTTGGG
* *
287598 GCCTTAGAGCCTACCCAAG-GAAATACCTTGGG
1 GCCTAAGAGCCTACCCAAGAG-AGTACCTTGGG
*
287630 GCCTCAGAGCCTACCCAA
1 GCCTAAGAGCCTACCCAA
287648 ATGTCACCTT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
31 1 0.01
32 72 0.99
ACGTcount: A:0.28, C:0.31, G:0.25, T:0.16
Consensus pattern (32 bp):
GCCTAAGAGCCTACCCAAGAGAGTACCTTGGG
Found at i:288755 original size:28 final size:28
Alignment explanation
Indices: 288724--288786 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
288714 TAGGGCTTGG
*
288724 GGGTATTTTAGGTCAT-TTCATACTTCAA
1 GGGTATTTTAGGTCATGTT-ACACTTCAA
* * *
288752 GGGTATTTTTGGTTATGTTACAGTTCAA
1 GGGTATTTTAGGTCATGTTACACTTCAA
288780 GGGTATT
1 GGGTATT
288787 ACAGTCCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.22, C:0.10, G:0.24, T:0.44
Consensus pattern (28 bp):
GGGTATTTTAGGTCATGTTACACTTCAA
Found at i:302265 original size:21 final size:21
Alignment explanation
Indices: 302225--302263 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
302215 ATAAATATTG
302225 AATAAATTGAAGAGAAAAATA
1 AATAAATTGAAGAGAAAAATA
*
302246 AATAAATTG-TGAGAAAAA
1 AATAAATTGAAGAGAAAAA
302264 ATGTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.64, C:0.00, G:0.15, T:0.21
Consensus pattern (21 bp):
AATAAATTGAAGAGAAAAATA
Found at i:303280 original size:19 final size:19
Alignment explanation
Indices: 303230--303280 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
303220 TTTAGGCCTG
* *
303230 AAATATGTAATAAAACAAT
1 AAATATATAATATAACAAT
*
303249 AAATAAATAATATAACACAT
1 AAATATATAATATAACA-AT
303269 -AATATATAATAT
1 AAATATATAATAT
303281 GCTTTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 25 0.93
20 2 0.07
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATATATAATATAACAAT
Found at i:303927 original size:84 final size:84
Alignment explanation
Indices: 303800--304516 Score: 660
Period size: 84 Copynumber: 8.7 Consensus size: 84
303790 TGCTTTGGGC
* * * *
303800 TATGTTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
* * *
303864 AACCCTCCTAGCCTTGAGT
66 AACCCTTCTAGACTTAAGT
* * **
303883 TATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTT-G-G-CAGAT
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
* * *
303945 AGCCCTTCTCGACTTAAGC
66 AACCCTTCTAGACTTAAGT
* * * * * * *
303964 TATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGA-AG
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTC-TTTGGT-GACAG
*
304027 ACAACCCTTCTAGACTTAAGT
64 ATAACCCTTCTAGACTTAAGT
* * * * *
304048 TGTACTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
*
304112 AACCCTTCTAGACTTGAGT
66 AACCCTTCTAGACTTAAGT
* * * * * *
304131 TATACTGTGAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTC-AGGGGTCTTT-G-G-CAGA
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGA-AGGTCTTTGGTGACAGA
* * * *
304192 TAGCTCTTCTCGACTTAAGC
65 TAACCCTTCTAGACTTAAGT
* * * * * *
304212 TATGCTGCAAATGATGTGTCGTTG-AGCTGAGCGTAATCGAACTC-AGAGGTCTTTTGTTGGCAG
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGA-AGGTC-TTTGGTGACAG
*
304275 ACAACCCTTCTAGACTTAAGT
64 ATAACCCTTCTAGACTTAAGT
* * * *
304296 TGTGCTGTAAATGATATG-CCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGAT
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
*
304360 AACCCTTCTAGACTTGAGT
66 AACCCTTCTAGACTTAAGT
* * * * **
304379 TATGCTGTGAATGATATGCCCTCGAACCTGAGTGTAATCGAACTCGGGGGTCTTTGGT---AGAT
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
* * * *
304441 AGCTCTTCTCGACTTAAGC
66 AACCCTTCTAGACTTAAGT
* * * * * * *
304460 TATGTTGCAAATGATGTG-TCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGT
1 TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGT
304517 TGGCAAATAG
Statistics
Matches: 511, Mismatches: 106, Indels: 37
0.78 0.16 0.06
Matches are distributed among these distances:
80 75 0.15
81 112 0.22
82 4 0.01
83 113 0.22
84 206 0.40
85 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (84 bp):
TATGCTGTAAATGATATGCCCTTGAAGCTGAGCGTAATCGAACTCGAAGGTCTTTGGTGACAGAT
AACCCTTCTAGACTTAAGT
Found at i:303995 original size:164 final size:164
Alignment explanation
Indices: 303798--304516 Score: 743
Period size: 164 Copynumber: 4.4 Consensus size: 164
303788 CTTGCTTTGG
*
303798 GCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
1 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * * * *
303863 TAACCCTCCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTC
66 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
* * *
303928 GGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
131 GGAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
* * * *
303962 GCTATGCTGCAAATGATGTGCCGTT-GAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGTTGGA-
1 GCTATGCTGTAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT-GAC
* * * * * *
304025 AGACAACCCTTCTAGACTTAAGTTGTACTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAA
63 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAA
* *
304089 CTCGAAGGTCTTTGGTGACAGATAACCCTTCTAGACTTGA
128 CTCGGAGGTCTTT-G-G-CAGATAACCCTTCTAGACTTAA
* * * * * * * * * *
304129 GTTATACTGTGAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTC-AGGGGTCTTT-G-G-CA
1 GCTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGA-AGGTCTTTGGTGACA
* * * * * * * *
304190 GATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTG-AGCTGAGCGTAATCGAAC
64 GATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAAC
* *
304254 TCAGAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAA
129 TCGGAGGTC---T-TTGGCAGATAACCCTTCTAGACTTAA
* * * *
304294 GTTGTGCTGTAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
1 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* ** * *
304359 TAACCCTTCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAACCTGAGTGTAATCGAACTC
66 TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
* * * * *
304424 GGGGGTCTTTGGTAGATAGCTCTTCTCGACTTAA
131 GGAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
* * * *
304458 GCTATGTTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTGGT
1 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
304517 TGGCAAATAG
Statistics
Matches: 449, Mismatches: 86, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
164 233 0.52
165 86 0.19
166 5 0.01
167 78 0.17
168 47 0.10
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (164 bp):
GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
TAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTC
GGAGGTCTTTGGCAGATAACCCTTCTAGACTTAA
Found at i:304521 original size:248 final size:248
Alignment explanation
Indices: 303805--304521 Score: 1211
Period size: 248 Copynumber: 2.9 Consensus size: 248
303795 TGGGCTATGT
*
303805 TGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
1 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
* * *
303870 CCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
66 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
* *
303935 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTGAGCTGAGCGTAG
131 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
* * *
304000 TCAAACTCAAAGGTCTTTTGTTGGAAGACAACCCTTCTAGACTTAAGTTGTAC
196 TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTAC
*
304053 TGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
1 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
* * *
304118 TCTAGACTTGAGTTATACTGTGAATGATATGCCCTCGAAGTTGAGTGTAATCGAACTCAGGGGTC
66 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
*
304183 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAA
131 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
* * *
304248 TCGAACTCAGAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGC
196 TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTAC
*
304301 TGTAAATGATATGCCTTGGAGCTAAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
1 TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
*
304366 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAACCTGAGTGTAATCGAACTCGGGGGTC
66 TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
* *
304431 TTTGGTAGATAGCTCTTCTCGACTTAAGCTATGTTGCAAATGATGTGTC-TTGGAGCTGAGCGTA
131 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTT-GAGCTGAGCGTA
* *
304495 GTCGAACTTGAAGGTCTTTGGTTGGCA
195 GTCGAACTTAAAGGTCTTTTGTTGGCA
304522 AATAGCCCTT
Statistics
Matches: 440, Mismatches: 28, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
247 2 0.00
248 438 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (248 bp):
TGTAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCT
TCTAGACTTGAGTTATGCTGTGAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGGTC
TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGTCGTTGAGCTGAGCGTAG
TCGAACTTAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTAC
Found at i:309004 original size:20 final size:21
Alignment explanation
Indices: 308968--309007 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
308958 ATAAATACTG
308968 AATAAATTGAAGAGAAAAATA
1 AATAAATTGAAGAGAAAAATA
*
308989 AATAAATTG-TGAGAAAAAT
1 AATAAATTGAAGAGAAAAAT
309008 GTTAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (21 bp):
AATAAATTGAAGAGAAAAATA
Found at i:317362 original size:23 final size:23
Alignment explanation
Indices: 317331--317389 Score: 100
Period size: 23 Copynumber: 2.6 Consensus size: 23
317321 TCTAGGCTGG
* *
317331 ACCATTGCCAGCTGCCCAGCAGC
1 ACCACTGCCAGCTGCCCAACAGC
317354 ACCACTGCCAGCTGCCCAACAGC
1 ACCACTGCCAGCTGCCCAACAGC
317377 ACCACTGCCAGCT
1 ACCACTGCCAGCT
317390 CTGCCCGATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.24, C:0.46, G:0.19, T:0.12
Consensus pattern (23 bp):
ACCACTGCCAGCTGCCCAACAGC
Found at i:320472 original size:150 final size:150
Alignment explanation
Indices: 320199--320488 Score: 386
Period size: 150 Copynumber: 1.9 Consensus size: 150
320189 ACAACCAATA
* * * **
320199 AAGGTGAATCCCTATTCTTAATCATACCGAAAGACGTCAGCAGGTCTGGAAAATCAAATGAACAA
1 AAGGTGAATCCCTATTCTTAATCAGACCGAAAGACATCAGCAGGCCTAAAAAATCAAATGAACAA
*
320264 GAAGCTGATATGAACGAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTTGAAAGTGAAAA
66 GAAGCTGATATGAACGAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTCGAAAGTGAAAA
320329 AGAAAGAGAGACAGTTAATG
131 AGAAAGAGAGACAGTTAATG
** * * *
320349 AAGGTGAATCTGTATTCTTAATCAGACCGGAAGACATCATC-GTGCCTAAAAAATCAAATGAAGA
1 AAGGTGAATCCCTATTCTTAATCAGACCGAAAGACATCAGCAG-GCCTAAAAAATCAAATGAACA
* * * * * *
320413 ATAAGCTGATATG-ACTGAAACAGAAACAATTGGAAGTGATTATACAAGCATTGTCGAAAGTGCA
65 AGAAGCTGATATGAAC-GAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTCGAAAGTGAA
*
320477 ATAGAAAGAGAG
129 AAAGAAAGAGAG
320489 GTAAATACAT
Statistics
Matches: 120, Mismatches: 18, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
149 3 0.03
150 117 0.98
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.21
Consensus pattern (150 bp):
AAGGTGAATCCCTATTCTTAATCAGACCGAAAGACATCAGCAGGCCTAAAAAATCAAATGAACAA
GAAGCTGATATGAACGAAACAGAAACAATTGAAAGCGACTATACAAGAATTGTCGAAAGTGAAAA
AGAAAGAGAGACAGTTAATG
Found at i:321925 original size:8 final size:8
Alignment explanation
Indices: 321907--322037 Score: 211
Period size: 8 Copynumber: 17.1 Consensus size: 8
321897 CTTAGTTAGT
321907 TGTAC-TA
1 TGTACGTA
321914 TGTACGTA
1 TGTACGTA
321922 TGTACGTA
1 TGTACGTA
321930 TGTACGTA
1 TGTACGTA
321938 TGTACGTA
1 TGTACGTA
321946 TGTACGTA
1 TGTACGTA
321954 TGTACGTA
1 TGTACGTA
321962 TGTACGTA
1 TGTACGTA
321970 TGTACGTA
1 TGTACGTA
321978 TGTACG--
1 TGTACGTA
321984 TGTA-GTA
1 TGTACGTA
321991 TGTACGTA
1 TGTACGTA
321999 TGTACGTA
1 TGTACGTA
322007 TGT-CGTA
1 TGTACGTA
322014 TGTACGTA
1 TGTACGTA
322022 TGTACG-A
1 TGTACGTA
*
322029 TGTATGTA
1 TGTACGTA
322037 T
1 T
322038 ACATGAAAAC
Statistics
Matches: 117, Mismatches: 1, Indels: 11
0.91 0.01 0.09
Matches are distributed among these distances:
5 1 0.01
6 4 0.03
7 22 0.19
8 90 0.77
ACGTcount: A:0.24, C:0.11, G:0.25, T:0.39
Consensus pattern (8 bp):
TGTACGTA
Found at i:322037 original size:4 final size:4
Alignment explanation
Indices: 321912--322037 Score: 96
Period size: 4 Copynumber: 31.8 Consensus size: 4
321902 TTAGTTGTAC
* * * * * *
321912 TATG TACG TATG TACG TATG TACG TATG TACG TATG TACG TATG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
321960 TATG TACG TATG TACG TATG TACGTG TA-G TATG TACG TATG TACG TATG
1 TATG TATG TATG TATG TATG TA--TG TATG TATG TATG TATG TATG TATG
* * *
322009 T-CG TATG TACG TATG TACG -ATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
322038 ACATGAAAAC
Statistics
Matches: 91, Mismatches: 26, Indels: 10
0.72 0.20 0.08
Matches are distributed among these distances:
3 7 0.08
4 80 0.88
6 4 0.04
ACGTcount: A:0.25, C:0.11, G:0.25, T:0.39
Consensus pattern (4 bp):
TATG
Found at i:322996 original size:20 final size:20
Alignment explanation
Indices: 322971--323010 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
322961 TGAAATTAGT
*
322971 AAAAAATCTACAATATTTTAA
1 AAAAAAT-TAAAATATTTTAA
322992 AAAAAATTAAAATATTTTA
1 AAAAAATTAAAATATTTTA
323011 CACAGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAAATTAAAATATTTTAA
Found at i:323210 original size:31 final size:31
Alignment explanation
Indices: 323172--323240 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
323162 CAGCCACTCT
323172 CAGTTAACATTTGAGGGAAGGACTGAAGTGA
1 CAGTTAACATTTGAGGGAAGGACTGAAGTGA
323203 CAGTTAACATTTGAGGGAAGGACTGAAGTGA
1 CAGTTAACATTTGAGGGAAGGACTGAAGTGA
323234 CAGTTAA
1 CAGTTAA
323241 TAAAATCGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.36, C:0.10, G:0.30, T:0.23
Consensus pattern (31 bp):
CAGTTAACATTTGAGGGAAGGACTGAAGTGA
Found at i:326048 original size:13 final size:13
Alignment explanation
Indices: 326030--326054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
326020 GATTAAATGA
326030 ATTTAAATAATTT
1 ATTTAAATAATTT
326043 ATTTAAATAATT
1 ATTTAAATAATT
326055 AGATGATAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTAAATAATTT
Found at i:337485 original size:138 final size:137
Alignment explanation
Indices: 337276--337544 Score: 317
Period size: 138 Copynumber: 2.0 Consensus size: 137
337266 ACACGGTTTC
* * * ** *
337276 TACGTGATGAGGAAATCCGATTATCTAAGGGTGACACTGCTCCTACGTGATGAAGAGATCTAGTC
1 TACGCGATGAGGAAATCCGACTATCTAAGGATGACACAACTCCTACGTGATGAAGAGACCTAGTC
** * ** *
337341 GATGGATGACATTGTTCTTACATGATGAAGATGTCTGGCCATCTTTAAGGG-TAAATGGAGATAA
66 GATGGATGACACAGTTCATACATGATGAAGACATCTGGCCATCTTT-AGGGAT-AATAGAGATAA
337405 CATGGTTCT
129 CATGGTTCT
* * * * * *
337414 TACGCGATGAGGAAGTCTGACTATCTAAGGATGACGCAACTCCTACGTGATGAGGAGGCCTGGTC
1 TACGCGATGAGGAAATCCGACTATCTAAGGATGACACAACTCCTACGTGATGAAGAGACCTAGTC
* *
337479 -AGTGGATGACACAGTTCATACGTGATGAGGACATCTGGCCATCTTTAGGGATAATAGAGATAAC
66 GA-TGGATGACACAGTTCATACATGATGAAGACATCTGGCCATCTTTAGGGATAATAGAGATAAC
337543 AT
130 AT
337545 AGCTATCTAA
Statistics
Matches: 109, Mismatches: 20, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
137 18 0.17
138 91 0.83
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (137 bp):
TACGCGATGAGGAAATCCGACTATCTAAGGATGACACAACTCCTACGTGATGAAGAGACCTAGTC
GATGGATGACACAGTTCATACATGATGAAGACATCTGGCCATCTTTAGGGATAATAGAGATAACA
TGGTTCT
Found at i:337673 original size:113 final size:113
Alignment explanation
Indices: 337434--337656 Score: 293
Period size: 113 Copynumber: 2.0 Consensus size: 113
337424 GGAAGTCTGA
* * *
337434 CTATCTAAGGATGACGCAACTCCTACGTGATGAGGAGGCCTGGTCAGTGGATGACACAGTTCATA
1 CTATCTAAGGATGACGCAACTCCTACGTGATGAGAAGACCTGGTCAGTGAATGACACAGTTCATA
* * *
337499 CGTGATGAGGACATCTGGCCATCTTTAGGGATAATAGAGATAACATAG
66 CATGATAAGGACATCTGACCATCTTTAGGGATAATAGAGATAACATAG
* * * * ** *
337547 CTATCTAAGGATGACGCGACTCCTACTTGATGAGAAGATCTGGTCATTGAATGACATGGTTCCTA
1 CTATCTAAGGATGACGCAACTCCTACGTGATGAGAAGACCTGGTCAGTGAATGACACAGTTCATA
** * *
337612 CATGATAAGGATGTCTGACCATTTTTAGGGATAATGGAGATAACA
66 CATGATAAGGACATCTGACCATCTTTAGGGATAATAGAGATAACA
337657 CGGTTCCTAC
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
113 93 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (113 bp):
CTATCTAAGGATGACGCAACTCCTACGTGATGAGAAGACCTGGTCAGTGAATGACACAGTTCATA
CATGATAAGGACATCTGACCATCTTTAGGGATAATAGAGATAACATAG
Found at i:337753 original size:250 final size:251
Alignment explanation
Indices: 337297--337791 Score: 592
Period size: 250 Copynumber: 2.0 Consensus size: 251
337287 GAAATCCGAT
* * * *
337297 TATCTAAGGGTGACACTGCTCCTACGTGATGAAGAGATCTAGTCGATGGATGACATTGTTCTTAC
1 TATCTAAGGATGACACTGCTCCTACGTGATGAAGAGATCTAGTCGATGAATGACATGGTTCCTAC
* * *
337362 ATGATGAAGATGTCTGGCCATCTTTAAGGGTAAATGGAGATAACATGGTTCTTACGCGATGAGGA
66 ATGATGAAGATGTCTGACCATCTTTAAGGGTAAATGGAGATAACACGGTTCCTACGCGATGAGGA
* * **
337427 AGTCTGACTATCTAAGGATGACGCAACTCCTACGTGATGAGGAGGCCTGGTCAGTGGATGACACA
131 AGTCTGACTATCTAA-GATGACGCAACTCCTACGTGATGAGGAGACCTGGTCAGTAGACAACACA
337492 GTTCATACGTGATGAGGACATCTGGCCATCTTTAGGGAT-AATAGAGATAACATAGC
195 GTTCATACGTGATGAGGACATCTGGCCATCTTTAGGGATAAATAGAGATAACATAGC
* * *
337548 TATCTAAGGATGACGC-GACTCCTACTTGATG-AGAAGATCTGGTC-ATTGAATGACATGGTTCC
1 TATCTAAGGATGACACTG-CTCCTACGTGATGAAG-AGATCTAGTCGA-TGAATGACATGGTTCC
*
337610 TACATGAT-AAGGATGTCTGACCAT-TTTTAGGG-ATAATGGAGATAACACGGTTCCTACGCGAT
63 TACATGATGAA-GATGTCTGACCATCTTTAAGGGTA-AATGGAGATAACACGGTTCCTACGCGAT
** * ** *
337672 GAGGAAGTCTGGTTATCTAA-ATGTAACGCTACTCCTACGTGATGAGGAGATTTGGTCGGTAGAC
126 GAGGAAGTCTGACTATCTAAGATG--ACGCAACTCCTACGTGATGAGGAGACCTGGTCAGTAGAC
* ** * * * * * *
337736 AATATTGTTCCTACGTGATTAGGACGTTTGGTCATCTTTAGGGATAAATGGAGATA
189 AACACAGTTCATACGTGATGAGGACATCTGGCCATCTTTAGGGATAAATAGAGATA
337792 TCACGGTTCC
Statistics
Matches: 206, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
248 3 0.01
249 1 0.00
250 125 0.61
251 77 0.37
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.28
Consensus pattern (251 bp):
TATCTAAGGATGACACTGCTCCTACGTGATGAAGAGATCTAGTCGATGAATGACATGGTTCCTAC
ATGATGAAGATGTCTGACCATCTTTAAGGGTAAATGGAGATAACACGGTTCCTACGCGATGAGGA
AGTCTGACTATCTAAGATGACGCAACTCCTACGTGATGAGGAGACCTGGTCAGTAGACAACACAG
TTCATACGTGATGAGGACATCTGGCCATCTTTAGGGATAAATAGAGATAACATAGC
Found at i:337828 original size:138 final size:138
Alignment explanation
Indices: 337548--338058 Score: 526
Period size: 138 Copynumber: 3.7 Consensus size: 138
337538 ATAACATAGC
* * * * * ** * * *
337548 TATCTAAGGATGACGC-GACTCCTACTTGATGAGAAGATCTGGTCATTGAATGACATGGTTCCTA
1 TATCTAAGGGTAACGCTG-CTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTA
* * * * * * *
337612 CATGATAAGGATGTCT-GACCATTTTTAGGGAT-AATGGAGATAACACGGTTCCTACGCGATGAG
65 CGTGATGAGGACGTTTGGA-CATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAG
337675 GAAGTCTGGT
129 GAAGTCTGGT
** * * **
337685 TATCTAAATGTAACGCTACTCCTACGTGATGAGGAGATTTGGTCGGTAGACAATATTGTTCCTAC
1 TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
* *
337750 GTGATTAGGACGTTTGGTCATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGGA
66 GTGATGAGGACGTTTGGACATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGGA
*
337815 AGTTTGGT
131 AGTCTGGT
* * * * * ** * *
337823 CATCTAAGGGTAACACTGCTCTTACGTGATGAAGAGATATGGTTTGTGGATGATATTATTTCTAC
1 TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
* * * * *
337888 GTGATGAGGAC-TTCTGGAAATATTTAGGGATAAATGGAGATATTATGGTTCCTACATGATGAGG
66 GTGATGAGGACGTT-TGGACATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGG
*
337952 AAGCCTGGT
130 AAGTCTGGT
* * * *
337961 TATCTAAGGGTGACGCTGCTCCTACGTGATAAGGAGATTTGGTCGGTGGATGACACTGTTCCTAC
1 TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
* * * *
338026 ATGATGAGGACGTCTGGCCATCTTTAGAGATAA
66 GTGATGAGGACGTTTGGACATCTTTAGGGATAA
338059 TTTTTTCAAG
Statistics
Matches: 301, Mismatches: 68, Indels: 9
0.80 0.18 0.02
Matches are distributed among these distances:
137 73 0.24
138 227 0.75
139 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.31
Consensus pattern (138 bp):
TATCTAAGGGTAACGCTGCTCCTACGTGATGAGGAGATTTGGTCGGTGGATGATATTGTTCCTAC
GTGATGAGGACGTTTGGACATCTTTAGGGATAAATGGAGATATCACGGTTCCTACGTGATGAGGA
AGTCTGGT
Found at i:338225 original size:65 final size:65
Alignment explanation
Indices: 338062--338313 Score: 314
Period size: 65 Copynumber: 3.9 Consensus size: 65
338052 GAGATAATTT
* * * * *
338062 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCGAGGGAATTAATCTCAAAGATTTTT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAATAATCTCAAAG-TTTAT
338127 G
65 G
* * * **
338128 TTTTAAGAGAAACTGTCTCAAAAGAGA-TAAATTTGTTTCAAGGAAAATAATCT-AAATGTGCAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAATAATCTCAAA-GTTTAT
338191 G
65 G
* *
338192 TTTCAAGAGAAAGTGTCTCAAGAGATACAAAATTTGTTTCAA-GAGAAATAATCTCAAAGTTTAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAATAATCTCAAAGTTTAT
338256 G
65 G
* *
338257 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAA-GAGAAACAATCTCAA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGA-AAATAATCTCAA
338314 GGGTTTTATG
Statistics
Matches: 161, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
64 31 0.19
65 103 0.64
66 27 0.17
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (65 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGAAAATAATCTCAAAGTTTATG
Found at i:338237 original size:36 final size:35
Alignment explanation
Indices: 338190--338304 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 35
338180 TAAATGTGCA
338190 TGTTTCAAGAGAAAGTGTCTCAAGAGATACAAAATT
1 TGTTTCAAGAGAAA-TGTCTCAAGAGATACAAAATT
*
338226 TGTTTCAAGAGAAATAATCTCAA-AG-T------TT
1 TGTTTCAAGAGAAAT-GTCTCAAGAGATACAAAATT
* *
338254 ATGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACT
1 -TGTTTCAAGAGAAA-TGTCTCAAGAGATACAAAATT
338291 TGTTTCAAGAGAAA
1 TGTTTCAAGAGAAA
338305 CAATCTCAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 22
0.71 0.04 0.24
Matches are distributed among these distances:
28 2 0.03
29 20 0.31
30 3 0.05
34 1 0.02
35 3 0.05
36 34 0.53
37 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (35 bp):
TGTTTCAAGAGAAATGTCTCAAGAGATACAAAATT
Found at i:338295 original size:130 final size:131
Alignment explanation
Indices: 338062--338304 Score: 364
Period size: 130 Copynumber: 1.9 Consensus size: 131
338052 GAGATAATTT
* * * *
338062 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCGAGGGAATTAATCTCAAAGATTTTT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAGATTTAT
* * *
338127 GTTTTAAGAGAAACTGTCTCAAAAGAGATAAATTTGTTTCAAG-GAAAATAATCTAAATGTGCAT
66 GTTTCAAGAGAAACTGTCTCAAAAGAGAAAAACTTGTTTCAAGAGAAAATAATCTAAATGTGCAT
338191 G
131 G
* * *
338192 TTTCAAGAGAAAGTGTCTCAAGAGATACAAAATTTGTTTCAAGAGAAATAATCTCAAAG-TTTAT
1 TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAGATTTAT
*
338256 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAGAAA
66 GTTTCAAGAGAAACTGTCTCAAAAGAGA-AAAACTTGTTTCAAGAGAAA
338305 CAATCTCAAG
Statistics
Matches: 100, Mismatches: 11, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
129 30 0.30
130 66 0.66
131 4 0.04
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.30
Consensus pattern (131 bp):
TTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAATCTCAAAGATTTAT
GTTTCAAGAGAAACTGTCTCAAAAGAGAAAAACTTGTTTCAAGAGAAAATAATCTAAATGTGCAT
G
Found at i:338299 original size:21 final size:20
Alignment explanation
Indices: 338266--338307 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
338256 GTTTCAAGAG
*
338266 AAACTGTCTCAAGAGAGACA
1 AAACTGTCTCAAGAGAAACA
*
338286 AAACTTGTTTCAAGAGAAACA
1 AAAC-TGTCTCAAGAGAAACA
338307 A
1 A
338308 TCTCAAGGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.48, C:0.17, G:0.17, T:0.19
Consensus pattern (20 bp):
AAACTGTCTCAAGAGAAACA
Found at i:338685 original size:36 final size:36
Alignment explanation
Indices: 338641--338749 Score: 146
Period size: 37 Copynumber: 3.0 Consensus size: 36
338631 AAAGGAAAAA
* *
338641 TGTCTCAAGCGAGATGAAATTTGTTTTGAGAGAAAT
1 TGTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAT
* *
338677 TGTCTCAAGCGAGACAAAATTTGTTTTTAAGAAAAAT
1 TGTCTCAAGCGAGACGAAATTTG-TTTTAAGAGAAAT
* *
338714 TGTCTCTAGCGAGACGACAATTTGTTTCAAGAGAAA
1 TGTCTCAAGCGAGACGA-AATTTGTTTTAAGAGAAA
338750 CAATCTCAAA
Statistics
Matches: 63, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
36 21 0.33
37 36 0.57
38 6 0.10
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAT
Found at i:340009 original size:2 final size:2
Alignment explanation
Indices: 340002--340053 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
339992 AGCTTTATTG
340002 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
340044 TA TA TA TA TA
1 TA TA TA TA TA
340054 ATTGCCTTTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:350027 original size:21 final size:21
Alignment explanation
Indices: 349980--350028 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
349970 TTACTATCGT
349980 AATGCGATTTTCCAATTTCGC
1 AATGCGATTTTCCAATTTCGC
**
350001 GTTGCGATTTTCCCAA-TTCGC
1 AATGCGATTTT-CCAATTTCGC
350022 AATGCGA
1 AATGCGA
350029 ATAAGTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.35
Consensus pattern (21 bp):
AATGCGATTTTCCAATTTCGC
Found at i:350061 original size:21 final size:21
Alignment explanation
Indices: 350018--350173 Score: 176
Period size: 21 Copynumber: 7.5 Consensus size: 21
350008 TTTTCCCAAT
** *
350018 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
350038 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
350059 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
350080 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
* **
350101 TCGCAATGCG-ATACT-GACTA
1 TCGCAATGCGAAT-TTGGAAAA
* * **
350121 TCGCAACGCG-ATAATACAAAA
1 TCGCAATGCGAAT-TTGGAAAA
350142 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
350163 TCGCAATGCGA
1 TCGCAATGCGA
350174 TACTGACTAT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
20 30 0.26
21 85 0.73
22 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:350124 original size:62 final size:63
Alignment explanation
Indices: 350076--350254 Score: 258
Period size: 62 Copynumber: 2.9 Consensus size: 63
350066 GCGAATTTGG
350076 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCG-ATAATAC
1 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGAATAATAC
350138 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCG-ATAATAC
1 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGAATAATAC
* * *** * *
350200 AAAATCGCAACGCG-ATACT-GACTTTCGCAACGCGATACTGACTTTCGCAACGCGA
1 AAAATCGCAATGCGAAT-TTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGA
350255 TTCTGACTTT
Statistics
Matches: 108, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
61 32 0.30
62 76 0.70
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (63 bp):
AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACTATCGCAACGCGAATAATAC
Found at i:350186 original size:41 final size:42
Alignment explanation
Indices: 350057--350221 Score: 128
Period size: 41 Copynumber: 4.0 Consensus size: 42
350047 GAATTTGGAA
* * *
350057 AATCGCAATGCGAAT-TTGGAAAATCGCAATGCGA-ATTTGGAA
1 AATCGCAATGCGAATATTGGAAAATCGCAACGCGATA-CT-GAC
* ** *
350099 AATCGCAATGCG-ATACT-GACTATCGCAACGCGATAAT-AC
1 AATCGCAATGCGAATATTGGAAAATCGCAACGCGATACTGAC
*
350138 AAAATCGCAATGCGAAT-TTGGAAAATCGCAATGCGATACTGAC
1 --AATCGCAATGCGAATATTGGAAAATCGCAACGCGATACTGAC
* * * **
350181 TATCGCAACGCG-ATAATACAAAATCGCAACGCGATACTGAC
1 AATCGCAATGCGAATATTGGAAAATCGCAACGCGATACTGAC
350222 TTTCGCAACG
Statistics
Matches: 98, Mismatches: 17, Indels: 17
0.74 0.13 0.13
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 61 0.62
42 32 0.33
43 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (42 bp):
AATCGCAATGCGAATATTGGAAAATCGCAACGCGATACTGAC
Found at i:350187 original size:20 final size:20
Alignment explanation
Indices: 350162--350316 Score: 177
Period size: 20 Copynumber: 7.7 Consensus size: 20
350152 AATTTGGAAA
*
350162 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
350182 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
350203 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
350223 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
350243 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
350263 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* * *
350283 TTCGCAACGAGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
350303 ATCGCAACGAGATA
1 ATCGCAACGCGATA
350317 ATACAGAATC
Statistics
Matches: 122, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
19 2 0.02
20 103 0.84
21 15 0.12
22 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:350207 original size:83 final size:83
Alignment explanation
Indices: 350055--350216 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 83
350045 GCGAATTTGG
* * * *
350055 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGAATTTGGAAAATCGCAATGCGATACTGACT
1 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGAATCTGGAAAATCGCAACGCGATAATGACA
350120 ATCGCAACGCGATAATAC
66 ATCGCAACGCGATAATAC
**
350138 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCG-ATACT-GACTATCGCAACGCGATAAT-AC
1 AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGAAT-CTGGAAAATCGCAACGCGATAATGAC
350200 AAAATCGCAACGCGATA
65 --AATCGCAACGCGATA
350217 CTGACTTTCG
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
81 2 0.03
82 18 0.26
83 50 0.71
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.20
Consensus pattern (83 bp):
AAAATCGCAATGCGAATTTGGAAAATCGCAATGCGAATCTGGAAAATCGCAACGCGATAATGACA
ATCGCAACGCGATAATAC
Found at i:350208 original size:21 final size:21
Alignment explanation
Indices: 350120--350216 Score: 92
Period size: 21 Copynumber: 4.7 Consensus size: 21
350110 GATACTGACT
350120 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* * **
350141 ATCGCAATGCGA-ATTTGGAAA
1 ATCGCAACGCGATA-ATACAAA
* * *
350162 ATCGCAATGCGATACTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
350182 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
350203 ATCGCAACGCGATA
1 ATCGCAACGCGATA
350217 CTGACTTTCG
Statistics
Matches: 60, Mismatches: 11, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
19 2 0.03
20 15 0.25
21 42 0.70
22 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:350290 original size:60 final size:60
Alignment explanation
Indices: 350101--350336 Score: 251
Period size: 62 Copynumber: 3.9 Consensus size: 60
350091 ATTTGGAAAA
* * * ***
350101 TCGCAATGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAATGCGA-ATTTGGAAAA
1 TCGCAACGCGATACTGACTATCGCAACGCGATAATAC-AAATCGCAACGCGATA-CT-GACTT
*
350163 TCGCAATGCGATACTGACTATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAATAC-AAATCGCAACGCGATACTGACTT
* ** ** *
350224 TCGCAACGCGATACTGACTTTCGCAACGCGATTCTGAC-TTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAAT-ACAAATCGCAACGCGATACTGACTT
* * * *
350284 TCGCAACGAGATTCTGACTATCGCAACGAGATAATACAGAATCGCAATGCGAT
1 TCGCAACGCGATACTGACTATCGCAACGCGATAATACA-AATCGCAACGCGAT
350337 TTTCAAAGTT
Statistics
Matches: 149, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
59 2 0.01
60 48 0.32
61 44 0.30
62 54 0.36
63 1 0.01
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (60 bp):
TCGCAACGCGATACTGACTATCGCAACGCGATAATACAAATCGCAACGCGATACTGACTT
Found at i:351073 original size:24 final size:24
Alignment explanation
Indices: 351046--351099 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
351036 GTATTCGAAA
*
351046 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
351070 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
351094 TTTGAT
1 TTTGAT
351100 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:351291 original size:12 final size:12
Alignment explanation
Indices: 351274--351298 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
351264 ATATAATCCT
351274 GAAGAAGAAAAA
1 GAAGAAGAAAAA
351286 GAAGAAGAAAAA
1 GAAGAAGAAAAA
351298 G
1 G
351299 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:353517 original size:19 final size:19
Alignment explanation
Indices: 353492--353622 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
353482 CTTAATGTCT
353492 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
353511 ATTGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
353525 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
353544 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
353558 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
353577 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
353591 ATCGCAAAGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
353610 ATCGCAACGCGAA
1 ATCGCAATGCGAA
353623 TTTAGTTTCG
Statistics
Matches: 86, Mismatches: 11, Indels: 30
0.68 0.09 0.24
Matches are distributed among these distances:
14 28 0.33
15 3 0.03
16 6 0.07
17 6 0.07
18 3 0.03
19 40 0.47
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:353534 original size:33 final size:33
Alignment explanation
Indices: 353492--353618 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
353482 CTTAATGTCT
*
353492 ATCGCAATGCGAAATGAAAATTGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
353525 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
353558 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
353591 ATCGCAAAGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
353619 CGAATTTAGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:353562 original size:14 final size:14
Alignment explanation
Indices: 353514--353597 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
353504 AATGAAAATT
353514 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
353528 GCAATGCGAAATGAAAATC
1 GCAA--CG--A-GAGAATC
353547 GCAACGAGAGAATC
1 GCAACGAGAGAATC
*
353561 GCAATGCGAAATGAAAATC
1 GCAA--CG--A-GAGAATC
*
353580 GCAACGAGGGAATC
1 GCAACGAGAGAATC
353594 GCAA
1 GCAA
353598 AGCGAAATGA
Statistics
Matches: 55, Mismatches: 5, Indels: 20
0.69 0.06 0.25
Matches are distributed among these distances:
14 23 0.42
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 20 0.36
ACGTcount: A:0.44, C:0.19, G:0.26, T:0.11
Consensus pattern (14 bp):
GCAACGAGAGAATC
Found at i:353640 original size:19 final size:19
Alignment explanation
Indices: 353618--353711 Score: 83
Period size: 19 Copynumber: 5.2 Consensus size: 19
353608 AAATCGCAAC
353618 GCGAATTT-AGTTTCGCGTT
1 GCGAATTTCA-TTTCGCGTT
*
353637 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
353656 GTG-A-TTC---TCTCGTT
1 GCGAATTTCATTTCGCGTT
*
353670 GCGATTTTCATTTCGCGTT
1 GCGAATTTCATTTCGCGTT
* *
353689 GCGATTTTCATTTCGCATT
1 GCGAATTTCATTTCGCGTT
353708 GCGA
1 GCGA
353712 TAGTCATTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
14 8 0.13
16 3 0.05
17 3 0.05
19 46 0.75
20 1 0.02
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
GCGAATTTCATTTCGCGTT
Found at i:353712 original size:19 final size:19
Alignment explanation
Indices: 353628--353712 Score: 108
Period size: 19 Copynumber: 4.7 Consensus size: 19
353618 GCGAATTTAG
353628 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
353647 TTTCGCGTTGTGA--TTC-
1 TTTCGCGTTGCGATTTTCA
*
353663 --TCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
353680 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
353699 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
353713 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 9 0.16
16 3 0.05
17 3 0.05
19 41 0.73
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:353718 original size:19 final size:19
Alignment explanation
Indices: 353677--353720 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
353667 GTTGCGATTT
* **
353677 TCATTTCGCGTTGCGATTT
1 TCATTTCGCATTGCGATAG
353696 TCATTTCGCATTGCGATAG
1 TCATTTCGCATTGCGATAG
353715 TCATTT
1 TCATTT
353721 TTTCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.45
Consensus pattern (19 bp):
TCATTTCGCATTGCGATAG
Found at i:353838 original size:14 final size:14
Alignment explanation
Indices: 353819--353855 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
353809 CGTCAATTAA
353819 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
353833 ACAAATCATCTTTT
1 ACAAATCAACTTTT
353847 ACAAATCAA
1 ACAAATCAA
353856 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:355878 original size:94 final size:94
Alignment explanation
Indices: 355717--355931 Score: 403
Period size: 94 Copynumber: 2.3 Consensus size: 94
355707 GAATAGTTTC
*
355717 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
355782 ACAGTGTTAAACAATACACAGTTTAGCAG
66 ACAGTGTTAAACAATACACAGTTTAGCAG
355811 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
*
355876 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGTTAAACAATACACAGTTTAGCAG
*
355905 AATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
355932 AAGCAATATA
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 118 1.00
ACGTcount: A:0.47, C:0.20, G:0.13, T:0.21
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGTTAAACAATACACAGTTTAGCAG
Found at i:357687 original size:14 final size:14
Alignment explanation
Indices: 357668--357755 Score: 68
Period size: 14 Copynumber: 5.6 Consensus size: 14
357658 GAAATGACTT
357668 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
357682 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
357701 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
357715 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
357734 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
357748 TCGCAACG
1 TCGCAACG
357756 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:357704 original size:19 final size:19
Alignment explanation
Indices: 357618--357777 Score: 125
Period size: 19 Copynumber: 9.1 Consensus size: 19
357608 TCTTTTGGTT
*
357618 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
357637 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
***
357657 GGAAATGACTTTCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
357675 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
357691 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
357708 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
357724 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
357741 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
357757 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
357776 GA
1 GA
357778 TTTTGGTTTC
Statistics
Matches: 111, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
14 28 0.25
15 3 0.03
16 6 0.05
17 5 0.05
18 4 0.04
19 36 0.32
20 27 0.24
21 2 0.02
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:357705 original size:33 final size:33
Alignment explanation
Indices: 357618--357772 Score: 220
Period size: 33 Copynumber: 4.5 Consensus size: 33
357608 TCTTTTGGTT
357618 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
***
357657 GGAAATGACTTTCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
357691 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
357724 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
357757 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
357773 TGCGATTTTG
Statistics
Matches: 109, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
33 79 0.72
34 11 0.10
36 1 0.01
37 1 0.01
38 3 0.03
40 14 0.13
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:357795 original size:19 final size:20
Alignment explanation
Indices: 357773--357824 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
357763 AAAATCGCAA
**
357773 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTTCATTTCCGCGT
**
357792 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTTCCGCGT
357812 TGCGATTTTCATT
1 TGCGATTTTCATT
357825 CTCGAAACTA
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.12, C:0.19, G:0.25, T:0.44
Consensus pattern (20 bp):
TGCGATTTTCATTTCCGCGT
Found at i:358151 original size:25 final size:26
Alignment explanation
Indices: 358094--358144 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
358084 TTCCATTTCT
* *
358094 GAATGATTGTGAGGGATTTCTGACCGT
1 GAATGGTTGTGAGGGATTTC-GACCGC
358121 GAATGGTTGTGAGGGATTTC-ACCG
1 GAATGGTTGTGAGGGATTTCGACCG
358145 ACGATGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.17
27 19 0.83
ACGTcount: A:0.22, C:0.12, G:0.35, T:0.31
Consensus pattern (26 bp):
GAATGGTTGTGAGGGATTTCGACCGC
Found at i:358375 original size:20 final size:20
Alignment explanation
Indices: 358350--358400 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
358340 GCTATGTAAA
358350 TCGCATTGCGATAGT-CATAT
1 TCGCATTGCGAT-GTACATAT
* *
358370 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATGTACATAT
358390 TCGCATTGCGA
1 TCGCATTGCGA
358401 ATTATGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (20 bp):
TCGCATTGCGATGTACATAT
Found at i:358421 original size:21 final size:21
Alignment explanation
Indices: 358397--358456 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
358387 TATTCGCATT
*
358397 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
358418 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
358438 GCGAAATT-GGAAAATCGCA
1 GCG-AATTACGAAAATCGCA
358457 TTGCGATAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
20 15 0.47
21 16 0.50
22 1 0.03
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:364343 original size:21 final size:21
Alignment explanation
Indices: 364317--364363 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
364307 AGTTAATTCA
*
364317 GTCGGCCATCGAATTAGTTCG
1 GTCGGCCACCGAATTAGTTCG
364338 GTCGGCCACCGAATTAGTTCG
1 GTCGGCCACCGAATTAGTTCG
364359 GTCGG
1 GTCGG
364364 GAAACTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.26
Consensus pattern (21 bp):
GTCGGCCACCGAATTAGTTCG
Found at i:369581 original size:32 final size:32
Alignment explanation
Indices: 369538--369608 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
369528 TAACAAAGAC
369538 AAAAAAAAAAGAAAATAAACGACACACCAATA
1 AAAAAAAAAAGAAAATAAACGACACACCAATA
* *
369570 AGAAAATAAAGAAAATAAACGACACACCAATA
1 AAAAAAAAAAGAAAATAAACGACACACCAATA
369602 AAAAAAA
1 AAAAAAA
369609 TAAGTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.72, C:0.14, G:0.07, T:0.07
Consensus pattern (32 bp):
AAAAAAAAAAGAAAATAAACGACACACCAATA
Found at i:375482 original size:20 final size:20
Alignment explanation
Indices: 375457--375501 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
375447 AATTTTCTGA
375457 GACACGTCCTAGACTAACCC
1 GACACGTCCTAGACTAACCC
375477 GACACGTCCTAGACTAACCC
1 GACACGTCCTAGACTAACCC
375497 GACAC
1 GACAC
375502 AAAGTAGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.40, G:0.16, T:0.13
Consensus pattern (20 bp):
GACACGTCCTAGACTAACCC
Found at i:384037 original size:10 final size:10
Alignment explanation
Indices: 383998--384037 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
383988 TTTATCACAC
383998 CAAATTCTCT
1 CAAATTCTCT
*
384008 CAATTTCTCT
1 CAAATTCTCT
*
384018 CAACTTCTCT
1 CAAATTCTCT
*
384028 CAAATACTCT
1 CAAATTCTCT
384038 TATAATCTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:384123 original size:17 final size:17
Alignment explanation
Indices: 384086--384121 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
384076 ATATTTTGAG
384086 TTTAATTTATTTAAGTA
1 TTTAATTTATTTAAGTA
384103 TTTAATTTATTTAA-TA
1 TTTAATTTATTTAAGTA
384119 TTT
1 TTT
384122 TACTTAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTTAATTTATTTAAGTA
Found at i:385914 original size:33 final size:33
Alignment explanation
Indices: 385870--385932 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
385860 CAGATGCCAC
* *
385870 GCCGCCGCCTTCACCTG-GTTTTATGACCCCGCT
1 GCCGCCACCTTCA-CAGAGTTTTATGACCCCGCT
385903 GCCGCCACCTTCACAGAGTTTTATGACCCC
1 GCCGCCACCTTCACAGAGTTTTATGACCCC
385933 TCCTGGAGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 2 0.07
33 25 0.93
ACGTcount: A:0.14, C:0.41, G:0.19, T:0.25
Consensus pattern (33 bp):
GCCGCCACCTTCACAGAGTTTTATGACCCCGCT
Found at i:386480 original size:34 final size:34
Alignment explanation
Indices: 386429--386499 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
386419 CGTTATTATG
386429 GTTGGATTTATTTTAATTTATTTTG-TTAAATTT
1 GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
*
386462 GTTGGACTTT-TTGTTAATTTATTTTGCTTAATTTT
1 GTTGGA-TTTATT-TTAATTTATTTTGCTTAAATTT
386497 GTT
1 GTT
386500 TATTACCATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
33 8 0.24
34 16 0.47
35 10 0.29
ACGTcount: A:0.20, C:0.03, G:0.14, T:0.63
Consensus pattern (34 bp):
GTTGGATTTATTTTAATTTATTTTGCTTAAATTT
Found at i:392696 original size:16 final size:16
Alignment explanation
Indices: 392666--392724 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 16
392656 ATTTTTGTAA
* *
392666 AAATAATCTTAATTTT
1 AAATAATTTTTATTTT
392682 AAATAATTTTTATTTT
1 AAATAATTTTTATTTT
* **
392698 -TAT-ATTTTTA-GAT
1 AAATAATTTTTATTTT
392711 AAATAATTTTTATT
1 AAATAATTTTTATT
392725 CCAAATCCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
13 1 0.03
14 9 0.27
15 9 0.27
16 14 0.42
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (16 bp):
AAATAATTTTTATTTT
Found at i:395316 original size:81 final size:81
Alignment explanation
Indices: 395206--395578 Score: 484
Period size: 81 Copynumber: 4.6 Consensus size: 81
395196 GAATTTATTT
* * * *
395206 TTCATCTAACTTGCATGATTGAC-CATTTTCTGCCAAATGCACAGTTAGGCCATTTATTTTTTAC
1 TTCATCTAACTGGCATAATTGACAC-TTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* * *
395270 TCGACAGTCTTTAACGG
65 TCAACGGTCTTTAACCG
* *
395287 TTCATCTAACTGGCATAATTGACACTTTTCTTCCAAATGCACAGGTAGGCCATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
395352 CAACGGTCTTTAACCG
66 CAACGGTCTTTAACCG
* * * * * * *
395368 TTCATCTAACTTGCATAATTGACACCTTTCTTCCAAATACGCAGCTAGACAATTTATCTTTTACT
1 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* *
395433 CAACGTTCTTTAACCA
66 CAACGGTCTTTAACCG
* * * *
395449 TTCATCTAAATGACATAATTGACA-TATTT-TGTCAAATGCACATCTAGGCCATTTATCTTTTAC
1 TTCATCTAACTGGCATAATTGACACT-TTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
395512 TCAACGGTCTTTAACCG
65 TCAACGGTCTTTAACCG
* *
395529 TCCATCTAACT-GCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCC
1 TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCACAGCTAGGCC
395579 TCAAAGGCAC
Statistics
Matches: 252, Mismatches: 36, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
79 14 0.06
80 70 0.28
81 167 0.66
82 1 0.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (81 bp):
TTCATCTAACTGGCATAATTGACACTTTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACGGTCTTTAACCG
Found at i:395445 original size:162 final size:161
Alignment explanation
Indices: 395206--395868 Score: 745
Period size: 162 Copynumber: 4.2 Consensus size: 161
395196 GAATTTATTT
* * *
395206 TTCATCTAACTTGCATGATTGAC-CATTTTCTGCCAAATGCACAGTTAGGCCATTTATTTTTTAC
1 TTCATCTAACTTGCATAATTGACACA-TTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTAC
* ** * *
395270 TCGACAGTCTTTAACGGTTCATCTAACTGGCATAATTGACACTTTTCT-TCCAAATGCACAGGTA
65 TCAACAGTCTTTAACCATTCATCTAACTGACATAATTGACACTTTT-TAT-CAAATGCACAGCTA
395334 GGCCATTTATCTTTTACTCAACGGTCTTTAACCG
128 GGCCATTTATCTTTTACTCAACGGTCTTTAACCG
* * * * * *
395368 TTCATCTAACTTGCATAATTGACACCTTTCTTCCAAATACGCAGCTAGACAATTTATCTTTTACT
1 TTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* * *
395433 CAAC-GTTCTTTAACCATTCATCTAAATGACATAATTGACA-TATTTTGTCAAATGCACATCTAG
66 CAACAG-TCTTTAACCATTCATCTAACTGACATAATTGACACT-TTTTATCAAATGCACAGCTAG
395496 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
129 GCCATTTATCTTTTACTCAACGGTCTTTAACCG
*
395529 TCCATCTAAC-TGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCC-----TC----A--
1 TTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* * * * * *
395582 -AAGGCA--C-TTAGCCTTTCATCTAACTGACATAATTAACACCTTTCTATCAAATGAACAGTTA
66 CAA--CAGTCTTTAACCATTCATCTAACTGACATAATTGACA-CTTTTTATCAAATGCACAGCTA
*
395643 GGCCATTTATCTTTTACTCAACGGTCTTTAACCT
128 GGCCATTTATCTTTTACTCAACGGTCTTTAACCG
* * ** *
395677 TTCATCTAACTGGCATAATTAACATTTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTTACT
1 TTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
* ** ** *
395742 CAACAGTCTTTAACCCTTCATCTAACTGGTATAATTGACACCTTTTTGCCAAATGCAAAGCTAGG
66 CAACAGTCTTTAACCATTCATCTAACTGACATAATTGACA-CTTTTTATCAAATGCACAGCTAGG
* * *
395807 CCATTTATCTTTTAGTCAACGGTCTTTAATCT
130 CCATTTATCTTTTACTCAACGGTCTTTAACCG
*
395839 TTCATCTAACTAGCATAATTGACACATTTC
1 TTCATCTAACTTGCATAATTGACACATTTC
395869 CTTAAGCTTA
Statistics
Matches: 420, Mismatches: 56, Indels: 50
0.80 0.11 0.10
Matches are distributed among these distances:
147 27 0.06
148 60 0.14
149 36 0.09
150 1 0.00
151 1 0.00
154 2 0.00
155 2 0.00
158 1 0.00
159 2 0.00
160 34 0.08
161 61 0.15
162 192 0.46
163 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (161 bp):
TTCATCTAACTTGCATAATTGACACATTTCTGCCAAATGCACAGCTAGGCCATTTATCTTTTACT
CAACAGTCTTTAACCATTCATCTAACTGACATAATTGACACTTTTTATCAAATGCACAGCTAGGC
CATTTATCTTTTACTCAACGGTCTTTAACCG
Found at i:395714 original size:81 final size:81
Alignment explanation
Indices: 395593--395868 Score: 367
Period size: 81 Copynumber: 3.4 Consensus size: 81
395583 AGGCACTTAG
* * ** *
395593 CCTTTCATCTAACTGACATAATTAACACCTTTCTATCAAATGAACAGTTAGGCCATTTATCTTTT
1 CCTTTCATCTAACTGGCATAATTAACACTTTTCTGCCAAATGAACAGCTAGGCCATTTATCTTTT
395658 ACTCAACGGTCTTTAA
66 ACTCAACGGTCTTTAA
* * *
395674 CCTTTCATCTAACTGGCATAATTAACATTTTTCTGCCAAATGCACAACTAGGCCATTTATCTTTT
1 CCTTTCATCTAACTGGCATAATTAACACTTTTCTGCCAAATGAACAGCTAGGCCATTTATCTTTT
*
395739 ACTCAACAGTCTTTAA
66 ACTCAACGGTCTTTAA
* * *
395755 CCCTTCATCTAACTGGTATAATTGACACCTTTT-TGCCAAATGCAA-AGCTAGGCCATTTATCTT
1 CCTTTCATCTAACTGGCATAATTAACA-CTTTTCTGCCAAATG-AACAGCTAGGCCATTTATCTT
*
395818 TTAGTCAACGGTCTTTAA
64 TTACTCAACGGTCTTTAA
* * * *
395836 TCTTTCATCTAACTAGCATAATTGACACATTTC
1 CCTTTCATCTAACTGGCATAATTAACACTTTTC
395869 CTTAAGCTTA
Statistics
Matches: 170, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
80 4 0.02
81 161 0.95
82 5 0.03
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (81 bp):
CCTTTCATCTAACTGGCATAATTAACACTTTTCTGCCAAATGAACAGCTAGGCCATTTATCTTTT
ACTCAACGGTCTTTAA
Found at i:445742 original size:66 final size:66
Alignment explanation
Indices: 445626--445750 Score: 196
Period size: 66 Copynumber: 1.9 Consensus size: 66
445616 GTCCCTTTTT
* *
445626 TTCTTCTGGTTGGTGGGTGCAGCTTCTCTCCCACGTTCCTCAGTAACAGTCGACTCGTTAGTGCT
1 TTCTTCAGGTTGGTGGGTGCAGCTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTTAGTGCT
445691 C
66 C
* * * *
445692 TTCTTCAGGTTGGTGGGTGCAGTTTCTTTCCCACGTCCCTCGGTAGCAGTCGACTCGTT
1 TTCTTCAGGTTGGTGGGTGCAGCTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTT
445751 CGAGTTCCCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 53 1.00
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.35
Consensus pattern (66 bp):
TTCTTCAGGTTGGTGGGTGCAGCTTCTCTCCCACGTCCCTCAGTAACAGTCGACTCGTTAGTGCT
C
Found at i:449168 original size:28 final size:29
Alignment explanation
Indices: 449132--449187 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
449122 GTTGGAAGAT
449132 AATT-TTTTTAACTTTGTTTTTAA-ATTTG
1 AATTATTTTTAA-TTTGTTTTTAATATTTG
*
449160 AATTATTTTTTATTTGTTTTTAATATTT
1 AATTATTTTTAATTTGTTTTTAATATTT
449188 TTCTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (29 bp):
AATTATTTTTAATTTGTTTTTAATATTTG
Found at i:451210 original size:24 final size:24
Alignment explanation
Indices: 451141--451212 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
451131 TTGATGACCT
* *
451141 GAGTTTAAGCACCATAGATATAAG
1 GAGTTTGAGCACCATAGATATCAG
451165 GAGTTTGAGCACCATAGATATCAG
1 GAGTTTGAGCACCATAGATATCAG
*
451189 GTGTTTGAGCACCATAGATATCAG
1 GAGTTTGAGCACCATAGATATCAG
451213 AGGCGTGAGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (24 bp):
GAGTTTGAGCACCATAGATATCAG
Found at i:451221 original size:24 final size:24
Alignment explanation
Indices: 451148--451222 Score: 75
Period size: 24 Copynumber: 3.1 Consensus size: 24
451138 CCTGAGTTTA
451148 AGCACCATAGATAT-A-AGGAGTTTG
1 AGCACCATAGATATCAGAGGAG--TG
**
451172 AGCACCATAGATATCAG-GTGTTTG
1 AGCACCATAGATATCAGAG-GAGTG
*
451196 AGCACCATAGATATCAGAGGCGTG
1 AGCACCATAGATATCAGAGGAGTG
451220 AGC
1 AGC
451223 GTTAATATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 39 0.91
25 3 0.07
26 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.27, T:0.23
Consensus pattern (24 bp):
AGCACCATAGATATCAGAGGAGTG
Found at i:453340 original size:22 final size:21
Alignment explanation
Indices: 453292--453340 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
453282 AACCTAATTT
453292 TTTTTTTGATTTTTTATTAAA
1 TTTTTTTGATTTTTTATTAAA
* * *
453313 TATTTTTGGTATTTTTATTTAA
1 TTTTTTTGAT-TTTTTATTAAA
453335 TTTTTT
1 TTTTTT
453341 AAATAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.73
Consensus pattern (21 bp):
TTTTTTTGATTTTTTATTAAA
Found at i:453891 original size:29 final size:29
Alignment explanation
Indices: 453803--453897 Score: 88
Period size: 29 Copynumber: 3.2 Consensus size: 29
453793 TATTAGTCTC
* * *
453803 TAAATTTTTGAATATTTTAATTTCATCCT
1 TAAACTTTTGATTATTTCAATTTCATCCT
*
453832 TAAACTATTAT-ATT-TATTCTAAATT-ATTCCT
1 TAAACT-TT-TGATTAT-TTC-AATTTCA-TCCT
453863 TAAACTTTTGATTATTTCAATTTCATCCT
1 TAAACTTTTGATTATTTCAATTTCATCCT
453892 TAAACT
1 TAAACT
453898 ATGACATGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
29 21 0.40
30 16 0.30
31 16 0.30
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.52
Consensus pattern (29 bp):
TAAACTTTTGATTATTTCAATTTCATCCT
Found at i:453915 original size:60 final size:60
Alignment explanation
Indices: 453794--453945 Score: 178
Period size: 60 Copynumber: 2.5 Consensus size: 60
453784 CCTCATCTAT
* * * * * * * *
453794 ATTAGTCTCTAAATTTTTGAATATTTTAATTTCATCCTTAAACTATTATATTTATTCTAA
1 ATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCTTAAACTATGACATGTACTATAA
* * *
453854 ATTATTCCTTAAACTTTTGATTATTTCAATTTCATCCTTAAACTATGACATGTACTATAA
1 ATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCTTAAACTATGACATGTACTATAA
* * *
453914 ATTGGTCCCCAAACTTTTAAATATTTCAATTT
1 ATTAGTCCCTAAACTTTTGAATATTTCAATTT
453946 TGTCTCCAAA
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 75 1.00
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (60 bp):
ATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCTTAAACTATGACATGTACTATAA
Found at i:477450 original size:21 final size:21
Alignment explanation
Indices: 477426--477491 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
477416 AATTATGTGA
*
477426 TAGGGTTTATGGTTTAGTATT
1 TAGGGTTTATGGTTTAGGATT
* * *
477447 TAGGGCTTATGGTATAGGGTT
1 TAGGGTTTATGGTTTAGGATT
* *
477468 TAGGGTTTATAGTTTAGGGTT
1 TAGGGTTTATGGTTTAGGATT
477489 TAG
1 TAG
477492 TATTTAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (21 bp):
TAGGGTTTATGGTTTAGGATT
Found at i:477511 original size:7 final size:7
Alignment explanation
Indices: 477426--477491 Score: 60
Period size: 7 Copynumber: 9.4 Consensus size: 7
477416 AATTATGTGA
477426 TAGGGTT
1 TAGGGTT
*
477433 TATGGTT
1 TAGGGTT
**
477440 TAGTATT
1 TAGGGTT
*
477447 TAGGGCT
1 TAGGGTT
* *
477454 TATGGTA
1 TAGGGTT
477461 TAGGGTT
1 TAGGGTT
477468 TAGGGTT
1 TAGGGTT
**
477475 TATAGTT
1 TAGGGTT
477482 TAGGGTT
1 TAGGGTT
477489 TAG
1 TAG
477492 TATTTAATAT
Statistics
Matches: 43, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.20, C:0.02, G:0.33, T:0.45
Consensus pattern (7 bp):
TAGGGTT
Found at i:480436 original size:22 final size:22
Alignment explanation
Indices: 480407--480451 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
480397 ACTTACCCTT
480407 TCAAATAGAATTCAATAA-AAA
1 TCAAATAGAATTCAATAACAAA
* *
480428 TCAAGATAGATTTCTATAACAAA
1 TCAA-ATAGAATTCAATAACAAA
480451 T
1 T
480452 ATATTTCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.53, C:0.11, G:0.07, T:0.29
Consensus pattern (22 bp):
TCAAATAGAATTCAATAACAAA
Found at i:482708 original size:7 final size:7
Alignment explanation
Indices: 482696--482820 Score: 78
Period size: 7 Copynumber: 18.3 Consensus size: 7
482686 AGATTACACT
482696 CTAAACC
1 CTAAACC
482703 CTAAA-C
1 CTAAACC
482709 CTAAACC
1 CTAAACC
*
482716 CTAAAAC
1 CTAAACC
*
482723 TTAAACC
1 CTAAACC
482730 CTAAATCC
1 CTAAA-CC
482738 C-AAACC
1 CTAAACC
* *
482744 TTAAATC
1 CTAAACC
* *
482751 ATAAACA
1 CTAAACC
*
482758 CTAAACT
1 CTAAACC
482765 CTAAACC
1 CTAAACC
**
482772 CTAAGTC
1 CTAAACC
*
482779 TTAAACC
1 CTAAACC
* *
482786 ATAAAGC
1 CTAAACC
*
482793 C-AAAGC
1 CTAAACC
*
482799 CTAAGCC
1 CTAAACC
*
482806 C-AAGCC
1 CTAAACC
482812 CTAAACC
1 CTAAACC
482819 CT
1 CT
482821 TAATCCGATT
Statistics
Matches: 90, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
6 20 0.22
7 67 0.74
8 3 0.03
ACGTcount: A:0.44, C:0.34, G:0.04, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:483891 original size:23 final size:23
Alignment explanation
Indices: 483861--483908 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
483851 CATAATTGAC
*
483861 CTCAAAATCGAGCTTGAATCAAG
1 CTCAAAATCGAGCTTCAATCAAG
*
483884 CTCAAAATCGAGCTTCAATCGAG
1 CTCAAAATCGAGCTTCAATCAAG
483907 CT
1 CT
483909 TGAGTCTCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (23 bp):
CTCAAAATCGAGCTTCAATCAAG
Found at i:483897 original size:12 final size:12
Alignment explanation
Indices: 483842--483897 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
483832 TTTGAGCTTG
*
483842 AATCGAGCTCAT
1 AATCGAGCTCAA
* *
483854 AATTGACCTCAA
1 AATCGAGCTCAA
**
483866 AATCGAGCT-TG
1 AATCGAGCTCAA
*
483877 AATCAAGCTCAA
1 AATCGAGCTCAA
483889 AATCGAGCT
1 AATCGAGCT
483898 TCAATCGAGC
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
11 8 0.25
12 24 0.75
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (12 bp):
AATCGAGCTCAA
Found at i:485028 original size:23 final size:23
Alignment explanation
Indices: 485002--485047 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
484992 ATAAATCACG
485002 TAATCACACCATTAATGAGAAAA
1 TAATCACACCATTAATGAGAAAA
485025 TAATCACACCATTAATGAGAAAA
1 TAATCACACCATTAATGAGAAAA
485048 CAATTGAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.52, C:0.17, G:0.09, T:0.22
Consensus pattern (23 bp):
TAATCACACCATTAATGAGAAAA
Found at i:492552 original size:42 final size:41
Alignment explanation
Indices: 492505--492585 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
492495 TTGGCTTTTG
* *
492505 GGTTAAGTAGATTGAATATC-TAAAAATATCTTTTTAAAATTA
1 GGTTAAGTAGATCGAATA-CATAAAAACAT-TTTTTAAAATTA
*
492547 GGTTAAGTAGGTCGAATACATAAAAACATTTTTTAAAAT
1 GGTTAAGTAGATCGAATACATAAAAACATTTTTTAAAAT
492586 AATTTTAAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 11 0.31
42 24 0.69
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (41 bp):
GGTTAAGTAGATCGAATACATAAAAACATTTTTTAAAATTA
Found at i:494639 original size:13 final size:14
Alignment explanation
Indices: 494609--494653 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
494599 AAAGGAAAAG
494609 AAAAAGAAAATAAC
1 AAAAAGAAAATAAC
*
494623 AAAAAGAAAGTAA-
1 AAAAAGAAAATAAC
*
494636 AAAAA-ATAATAAC
1 AAAAAGAAAATAAC
494649 AAAAA
1 AAAAA
494654 CCAAAAAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
12 5 0.19
13 10 0.37
14 12 0.44
ACGTcount: A:0.80, C:0.04, G:0.07, T:0.09
Consensus pattern (14 bp):
AAAAAGAAAATAAC
Found at i:503713 original size:21 final size:20
Alignment explanation
Indices: 503687--503731 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
503677 TTCAATTAAG
*
503687 AATCAAAGAGCTTTACTTCA
1 AATCAAAGAGCCTTACTTCA
* *
503707 TAATCAAGGCGCCTTACTTCA
1 -AATCAAAGAGCCTTACTTCA
503728 AATC
1 AATC
503732 CATAGCTTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.29
Consensus pattern (20 bp):
AATCAAAGAGCCTTACTTCA
Found at i:507050 original size:81 final size:80
Alignment explanation
Indices: 506941--507107 Score: 226
Period size: 81 Copynumber: 2.1 Consensus size: 80
506931 TTGGGCCTAT
* *
506941 GGCCTACCCAAGGATATCCTTAGATCCGTAGAGTTACCTTAAGCACACAAAAAAAGAAACCAACC
1 GGCCTACCCAAGGATACCCTTAGATCCGTAGAGTTACCCTAAGCACACAAAAAAAGAAACCAACC
*
507006 TAAGGATATGCCTTGG
66 TAAGGATATACCTT-G
* * * ** * * *
507022 GGCCTACCCAAGGGTACCCTTAGGTCCGTAGGGTTACCCTGTGCACACAACAAAGGGAACCAACC
1 GGCCTACCCAAGGATACCCTTAGATCCGTAGAGTTACCCTAAGCACACAAAAAAAGAAACCAACC
507087 TAAGGATATACCTTG
66 TAAGGATATACCTTG
507102 GGCCTA
1 GGCCTA
507108 TGGGCCTACC
Statistics
Matches: 75, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 7 0.09
81 68 0.91
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.19
Consensus pattern (80 bp):
GGCCTACCCAAGGATACCCTTAGATCCGTAGAGTTACCCTAAGCACACAAAAAAAGAAACCAACC
TAAGGATATACCTTG
Found at i:512924 original size:13 final size:12
Alignment explanation
Indices: 512895--512929 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
512885 AGGGTTTTCG
512895 AAATAAAAAACA
1 AAATAAAAAACA
*
512907 AAATAAAAAAGA
1 AAATAAAAAACA
512919 ATAATAAAAAA
1 A-AATAAAAAA
512930 AAACATTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 12 0.57
13 9 0.43
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (12 bp):
AAATAAAAAACA
Done.