Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008925.1 Hibiscus syriacus cultivar Beakdansim tig00112230_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: 2702387
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 11
Found at i:195620 original size:41 final size:37
Alignment explanation
Indices: 195552--195688 Score: 118
Period size: 41 Copynumber: 3.5 Consensus size: 37
195542 AGTATCAATA
* *
195552 TTATATATATATATATATAATTTTTATATTATATGTTAT
1 TTATATATAT-TATATATTATATTTATATTATAT-TTAT
*
195591 TTATATATATTATATATTATATACATTATATAATATTCGTA-
1 TTATATATATTATATATTATAT---TTATATTATATT--TAT
*
195632 TTATATATATTAGATA--ATATTTATATTATATATTAT
1 TTATATATATTATATATTATATTTATATTATAT-TTAT
*
195668 ATAGTATATATATATATATTA
1 TTA-TATATAT-TATATATTA
195689 AGTATAGTAT
Statistics
Matches: 80, Mismatches: 7, Indels: 21
0.74 0.06 0.19
Matches are distributed among these distances:
35 2 0.03
36 12 0.15
37 8 0.10
38 15 0.19
39 14 0.17
40 2 0.03
41 25 0.31
42 2 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (37 bp):
TTATATATATTATATATTATATTTATATTATATTTAT
Found at i:195828 original size:2 final size:2
Alignment explanation
Indices: 195549--195809 Score: 100
Period size: 2 Copynumber: 137.0 Consensus size: 2
195539 TTTAGTATCA
* * *
195549 AT AT -T AT AT AT AT AT AT AT AT A- AT TT TT AT AT -T AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
195588 -T AT TT AT AT AT AT -T AT AT AT -T AT AT AC AT -T 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
* * *
195625 AT -T CGT AT -T AT AT AT AT -T AG AT A- AT AT TT AT AT -T AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
195663 AT -T AT AT AGT AT AT AT AT AT AT AT -T A- AGT AT AGT AT TT TT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT A-T AT AT AT
* **
195703 TT AGT AT AT A- AT AT -T AT AT -T AT GC AT -T AT AT AT AT -T AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
195741 ACT AT TT AT AT AT AGT AT ACT AT AT ACT AT AT AG A- AT AT -T AT
1 A-T AT AT AT AT AT A-T AT A-T AT AT A-T AT AT AT AT AT AT AT AT
* * * *
195783 AT TT TT AGT TT AT AT AT TT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT
195810 TACAGATATA
Statistics
Matches: 199, Mismatches: 27, Indels: 66
0.68 0.09 0.23
Matches are distributed among these distances:
1 23 0.12
2 159 0.80
3 17 0.09
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (2 bp):
AT
Found at i:202309 original size:26 final size:25
Alignment explanation
Indices: 202270--202319 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
202260 AGGTTACTAA
*
202270 GGTCATTTACACTTTAGGGCATTTT
1 GGTCATTTACACTTTAGGACATTTT
*
202295 GGTCATTTTATACTTTAGGACATTT
1 GGTCA-TTTACACTTTAGGACATTT
202320 CTATAAATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.46
Consensus pattern (25 bp):
GGTCATTTACACTTTAGGACATTTT
Found at i:218391 original size:23 final size:23
Alignment explanation
Indices: 218358--218419 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
218348 GCTCATATAA
218358 ATGCACTGAAGTGCCACGTAGA-
1 ATGCACTGAAGTGCCACGTAGAG
* * * *
218380 ATTGCACCGAAGTACCGCTTAGAG
1 A-TGCACTGAAGTGCCACGTAGAG
218404 ATGCACTGAAGTGCCA
1 ATGCACTGAAGTGCCA
218420 TATAAGATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 1 0.03
23 29 0.94
24 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (23 bp):
ATGCACTGAAGTGCCACGTAGAG
Found at i:227312 original size:21 final size:21
Alignment explanation
Indices: 227269--227308 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
227259 GCATCAAGGT
*
227269 TTTTGTTGAAGCCATGAAATC
1 TTTTATTGAAGCCATGAAATC
227290 TTTTATTGAAGCCAT-AAAT
1 TTTTATTGAAGCCATGAAAT
227309 TCTTGCAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (21 bp):
TTTTATTGAAGCCATGAAATC
Found at i:242778 original size:27 final size:29
Alignment explanation
Indices: 242739--242801 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 29
242729 TTGAACTATG
**
242739 TTTAAATAATTAT-TTTAATCATTGAATT
1 TTTAAATAATTATAAATAATCATTGAATT
242767 TTTAAA-AATTATAAATAATCATTGAATT
1 TTTAAATAATTATAAATAATCATTGAATT
*
242795 ATTAAAT
1 TTTAAAT
242802 TTTTATACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTAAATAATTATAAATAATCATTGAATT
Found at i:244996 original size:16 final size:16
Alignment explanation
Indices: 244975--245005 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
244965 TATTATTGAT
244975 ATGATGAAAAATTAAC
1 ATGATGAAAAATTAAC
244991 ATGATGAAAAATTAA
1 ATGATGAAAAATTAA
245006 TAAGCACATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (16 bp):
ATGATGAAAAATTAAC
Found at i:246531 original size:2 final size:2
Alignment explanation
Indices: 246524--246594 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
246514 ACGAGATCTT
246524 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
246566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
246595 TTTTAAATTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:249840 original size:46 final size:48
Alignment explanation
Indices: 249786--249893 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 48
249776 CGATCGTACT
*
249786 TATCACAAAACGA-TTGATATCAACTCCAACCGAGTGATGA-TCTCTAC
1 TATCACAAAACGACTT-ATATCAACTCCAACCAAGTGATGACTCTCTAC
* * *
249833 -ATCACAAAATGACTTATGTCAACTCTAACCAAGTGATGAGCTCTCTAC
1 TATCACAAAACGACTTATATCAACTCCAACCAAGTGATGA-CTCTCTAC
249881 TTATCACAAAACG
1 -TATCACAAAACG
249894 GACATAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
46 32 0.63
47 2 0.04
48 7 0.14
50 10 0.20
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (48 bp):
TATCACAAAACGACTTATATCAACTCCAACCAAGTGATGACTCTCTAC
Found at i:250039 original size:45 final size:45
Alignment explanation
Indices: 249975--250066 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
249965 AAAGATGATT
**
249975 TTGAGAAGGGTATTTAACCCTTTTGTATGCAATGGAATACAATCA
1 TTGAGAAGGGTATTTAACCCTTTTAAATGCAATGGAATACAATCA
*
250020 TTGAGAAGGGTATTTAACCCTTTTAAATTCAATGGAATACAATCA
1 TTGAGAAGGGTATTTAACCCTTTTAAATGCAATGGAATACAATCA
250065 TT
1 TT
250067 AAATACCCTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (45 bp):
TTGAGAAGGGTATTTAACCCTTTTAAATGCAATGGAATACAATCA
Found at i:254380 original size:21 final size:20
Alignment explanation
Indices: 254356--254418 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 20
254346 TGTTAAAACC
254356 TAAATCCTAAACCCTAAACTA
1 TAAA-CCTAAACCCTAAACTA
254377 TAAACCCTAAACCCTAAAC-A
1 TAAA-CCTAAACCCTAAACTA
254397 TTAAACTCTAAACCCT-AACTA
1 -TAAAC-CTAAACCCTAAACTA
254418 T
1 T
254419 TCTCCCTCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 6 0.16
21 32 0.84
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (20 bp):
TAAACCTAAACCCTAAACTA
Found at i:254395 original size:7 final size:7
Alignment explanation
Indices: 254349--254414 Score: 69
Period size: 7 Copynumber: 9.4 Consensus size: 7
254339 TGGTTGTTGT
*
254349 TAAAACC
1 TAAACCC
*
254356 TAAATCC
1 TAAACCC
254363 TAAACCC
1 TAAACCC
**
254370 TAAACTA
1 TAAACCC
254377 TAAACCC
1 TAAACCC
254384 TAAACCC
1 TAAACCC
**
254391 TAAACAT
1 TAAACCC
*
254398 TAAACTC
1 TAAACCC
254405 TAAACCC
1 TAAACCC
254412 TAA
1 TAA
254415 CTATTCTCCC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 48 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCC
Found at i:254780 original size:21 final size:22
Alignment explanation
Indices: 254738--254780 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
254728 AATTTGATTC
* * *
254738 GATATAATCGATTAACATATTA
1 GATAAAATCGATTAAAAAATTA
254760 GATAAAAT-GATTAAAAAATTA
1 GATAAAATCGATTAAAAAATTA
254781 CCTATAATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.09, T:0.33
Consensus pattern (22 bp):
GATAAAATCGATTAAAAAATTA
Found at i:255062 original size:16 final size:16
Alignment explanation
Indices: 255038--255068 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
255028 GGGAGAGCAT
255038 ACTAGTTATAAATTCA
1 ACTAGTTATAAATTCA
*
255054 ACTATTTATAAATTC
1 ACTAGTTATAAATTC
255069 GATTTAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.03, T:0.42
Consensus pattern (16 bp):
ACTAGTTATAAATTCA
Found at i:256352 original size:14 final size:14
Alignment explanation
Indices: 256333--256360 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
256323 TCGAATGACA
256333 TCGGTCGGATGCCC
1 TCGGTCGGATGCCC
256347 TCGGTCGGATGCCC
1 TCGGTCGGATGCCC
256361 AACGTGTTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.36, G:0.36, T:0.21
Consensus pattern (14 bp):
TCGGTCGGATGCCC
Found at i:268385 original size:20 final size:21
Alignment explanation
Indices: 268360--268421 Score: 65
Period size: 22 Copynumber: 3.0 Consensus size: 21
268350 TTTTGGTGCA
268360 GAGGGAATCGAT-CCCCCCTT
1 GAGGGAATCGATACCCCCCTT
* * *
268380 GAGGGAACCGATTCCCCCCCAT
1 GAGGGAATCGA-TACCCCCCTT
268402 -AGGGGAATCGATACCCCCCT
1 GA-GGGAATCGATACCCCCCT
268422 CGGGTTCTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
20 10 0.29
21 9 0.26
22 15 0.44
ACGTcount: A:0.23, C:0.37, G:0.24, T:0.16
Consensus pattern (21 bp):
GAGGGAATCGATACCCCCCTT
Found at i:268397 original size:21 final size:20
Alignment explanation
Indices: 268360--268398 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
268350 TTTTGGTGCA
*
268360 GAGGGAATCGATCCCCCCTT
1 GAGGGAACCGATCCCCCCTT
268380 GAGGGAACCGATTCCCCCC
1 GAGGGAACCGA-TCCCCCC
268399 CATAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.21, C:0.38, G:0.26, T:0.15
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCTT
Found at i:270743 original size:13 final size:14
Alignment explanation
Indices: 270725--270754 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
270715 TAAGGGGGAG
270725 TAATTTCAAAA-CT
1 TAATTTCAAAATCT
270738 TAATTTCAAAATCT
1 TAATTTCAAAATCT
270752 TAA
1 TAA
270755 AATTACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (14 bp):
TAATTTCAAAATCT
Found at i:271948 original size:26 final size:26
Alignment explanation
Indices: 271912--271962 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
271902 TTAGACAATT
271912 AGACTTACTTTAGTAAATCAGAAATC
1 AGACTTACTTTAGTAAATCAGAAATC
271938 AGACTTACTTTAGTAAATCAGAAAT
1 AGACTTACTTTAGTAAATCAGAAAT
271963 AAAACTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (26 bp):
AGACTTACTTTAGTAAATCAGAAATC
Found at i:271969 original size:26 final size:26
Alignment explanation
Indices: 271914--271969 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
271904 AGACAATTAG
* *
271914 ACTTACTTTAGTAAATCAGAAATCAG
1 ACTTACTTTAGTAAATCAGAAATAAA
271940 ACTTACTTTAGTAAATCAGAAATAAA
1 ACTTACTTTAGTAAATCAGAAATAAA
271966 ACTT
1 ACTT
271970 TAGATCAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (26 bp):
ACTTACTTTAGTAAATCAGAAATAAA
Found at i:272609 original size:20 final size:20
Alignment explanation
Indices: 272584--272632 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
272574 CCGATTCGAA
** *
272584 TTGACTCGGTTCGGTTTGGG
1 TTGACTCGGTTCGGTGCGAG
*
272604 TTGACTCGATTCGGTGCGAG
1 TTGACTCGGTTCGGTGCGAG
272624 TTGACTCGG
1 TTGACTCGG
272633 ACCGATTCAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.10, C:0.18, G:0.37, T:0.35
Consensus pattern (20 bp):
TTGACTCGGTTCGGTGCGAG
Found at i:275893 original size:6 final size:6
Alignment explanation
Indices: 275882--275907 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
275872 TTAACTTTTT
275882 AGTCAA AGTCAA AGTCAA AGTCAA AG
1 AGTCAA AGTCAA AGTCAA AGTCAA AG
275908 GCCAACTCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
AGTCAA
Found at i:276021 original size:20 final size:20
Alignment explanation
Indices: 275996--276050 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
275986 GAGTCATGTT
275996 GGTTTGGGTTGACTCAGTTC
1 GGTTTGGGTTGACTCAGTTC
*
276016 GGTTTGGGTTGACTCTGTTC
1 GGTTTGGGTTGACTCAGTTC
* * *
276036 AGTCTGAGTTGACTC
1 GGTTTGGGTTGACTC
276051 GGACCAGTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.16, G:0.33, T:0.40
Consensus pattern (20 bp):
GGTTTGGGTTGACTCAGTTC
Found at i:279147 original size:60 final size:60
Alignment explanation
Indices: 279060--279222 Score: 190
Period size: 60 Copynumber: 2.7 Consensus size: 60
279050 TTATAACCCT
*
279060 CATTTTAAATT-GATCCTTAAA-TTTTGAATATAT-TAATTTCATCC-TCAAACTATGACTCA
1 CATTCTAAATTAG-TCCTTAAACTTTTGAATAT-TCTAATTTCATCCAT-AAACTATGACTCA
* * * * *
279119 CATTCTAGATTAGTTCTTAAACTTTTGAACATTCTAGTTTCATCCATAAACTATGACTCT
1 CATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCATAAACTATGACTCA
* * *
279179 CTTTCTAAATTGGTCCTAAAACTTTTGAATATTCTAATTTCATC
1 CATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATC
279223 TCCAAATTCA
Statistics
Matches: 87, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 17 0.20
60 69 0.79
61 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (60 bp):
CATTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTCATCCATAAACTATGACTCA
Found at i:282325 original size:74 final size:74
Alignment explanation
Indices: 282188--282390 Score: 291
Period size: 74 Copynumber: 2.7 Consensus size: 74
282178 TCTTAAACAA
* *
282188 AAATAACAGATTGCTCGAAGGGTACCGATACCCCCCAAGAGGGTACCGATACCCCCATATAAGAT
1 AAATAACAGATTGCTCGGAGGGTACCGATA--CCCCAAGAGAGTACCGATACCCCCATATAAGAT
*
282253 TTGGCTCCGAG
64 TTGGCTCCAAG
* *
282264 AAATTACAGATTGCTCGGAGGGTACCGATACCCCAAGAGAGTACCGATACCCCCATGTAAGATTT
1 AAATAACAGATTGCTCGGAGGGTACCGATACCCCAAGAGAGTACCGATACCCCCATATAAGATTT
282329 GGCTCCAAG
66 GGCTCCAAG
* * *
282338 AAATAACAGATTGCTAGGAGGGTACCAATACACCCCAG-GAGGTACCGATACCC
1 AAATAACAGATTGCTCGGAGGGTACCGATAC-CCCAAGAGA-GTACCGATACCC
282391 TCATCTCAAA
Statistics
Matches: 116, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
74 71 0.61
75 17 0.15
76 28 0.24
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.18
Consensus pattern (74 bp):
AAATAACAGATTGCTCGGAGGGTACCGATACCCCAAGAGAGTACCGATACCCCCATATAAGATTT
GGCTCCAAG
Found at i:284390 original size:21 final size:21
Alignment explanation
Indices: 284352--284391 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
284342 AAGATTTTAT
*
284352 TTTCAAAATATAATAATGATA
1 TTTCAAAATATAAAAATGATA
284373 TTTCAAAAT-TGAAAAATGA
1 TTTCAAAATAT-AAAAATGA
284392 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (21 bp):
TTTCAAAATATAAAAATGATA
Found at i:288254 original size:20 final size:21
Alignment explanation
Indices: 288190--288262 Score: 85
Period size: 23 Copynumber: 3.3 Consensus size: 21
288180 TCTAGGTATC
*
288190 GATACCCCCCTTGTATGGGTATT
1 GATA-CCCCCTTG-ATGGGTACT
288213 GATACCCCCTTTGAGTGGGTACT
1 GATACCCCC-TTGA-TGGGTACT
*
288236 GATACCCCCTTGA-GGGTACC
1 GATACCCCCTTGATGGGTACT
288256 GATACCC
1 GATACCC
288263 TCCACGGGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
20 13 0.28
22 10 0.22
23 23 0.50
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.27
Consensus pattern (21 bp):
GATACCCCCTTGATGGGTACT
Found at i:290981 original size:76 final size:76
Alignment explanation
Indices: 290820--291028 Score: 327
Period size: 76 Copynumber: 2.8 Consensus size: 76
290810 AAATCTTAAC
*
290820 AGAAATAACAGATTGCTCGGAGGGTACTGATA-CCCCCAAGAGAGTACCGATA-CCCCATGTAAG
1 AGAAATAACAGATTGCTCGGAGGGTACTGATACCCCCCAAGAGGGTACCGATACCCCCATGTAAG
290883 ATTTGGCTCCT
66 ATTTGGCTCCT
* *
290894 AGAAATTACAGATTGCTCGGAGGGTACCGATACCCCCCAAGAGGGTACCGATACCCCCATGTAAG
1 AGAAATAACAGATTGCTCGGAGGGTACTGATACCCCCCAAGAGGGTACCGATACCCCCATGTAAG
290959 ATTTGGCT-CT
66 ATTTGGCTCCT
* * *
290969 GAGAAATAACAGATTGCTCGAAAGGTACTGATACCCCCCAGGA-GGTACCGATACCCCCAT
1 -AGAAATAACAGATTGCTCGGAGGGTACTGATACCCCCCAAGAGGGTACCGATACCCCCAT
291029 CTCATAACGA
Statistics
Matches: 124, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
74 30 0.24
75 38 0.31
76 56 0.45
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.20
Consensus pattern (76 bp):
AGAAATAACAGATTGCTCGGAGGGTACTGATACCCCCCAAGAGGGTACCGATACCCCCATGTAAG
ATTTGGCTCCT
Found at i:296876 original size:319 final size:319
Alignment explanation
Indices: 296297--296934 Score: 1116
Period size: 319 Copynumber: 2.0 Consensus size: 319
296287 AAAATTATAG
* *
296297 AATGGTCCCCAAATTTTTCTAAGGATTGTAGAATTCTTCCTACAACGTTTCCATCCCTTACATAA
1 AATGGTCACCAAATTTTTCTAAGGATTGTAGAATACTTCCTACAACGTTTCCATCCCTTACATAA
*
296362 TTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGTCAAATGGTTCAAAGTTCTAAAACTAGAT
66 TTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGCCAAATGGTTCAAAGTTCTAAAACTAGAT
* * *
296427 TTTTCATGATTTTGCTCGATTTTGATTCGATTTAGGCCTAAAATCAACTTCCATCCAACCTTACA
131 GTTTCATGATTTTGCTCGATTTTGATTCGATTGAAGCCTAAAATCAACTTCCATCCAACCTTACA
* * * *
296492 TCATCCCTACAATCAAAGCCCTAATCAAATTTTATCAAAACGCAAAGTTTCCACAACTTATAATT
196 TCATCCATACAATCAAAGCCCTAATCAAATATCATCAAAACACAAAGTTTCCACAACTTATAATT
296557 TGGCCGAATATCAAAGAAACATTTCTAGAAAGATTGAACATGTTTTAATCATCATACAA
261 TGGCCGAATATCAAAGAAACATTTCTAGAAAGATTGAACATGTTTTAATCATCATACAA
* *
296616 AATGGTCACCAAATTTTTCTAAGGCTTGTAGAATACTTCCTACATCGTTTCCATCCCTTACATAA
1 AATGGTCACCAAATTTTTCTAAGGATTGTAGAATACTTCCTACAACGTTTCCATCCCTTACATAA
*
296681 TTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGCCAAATGGTTCAAAGTTCTAAAACTTGAT
66 TTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGCCAAATGGTTCAAAGTTCTAAAACTAGAT
*
296746 GTTTCATGATTTTTCTCGATTTTGATTCGATTGAAGCCTAAAATCAACTTCCATCCAACCTTACA
131 GTTTCATGATTTTGCTCGATTTTGATTCGATTGAAGCCTAAAATCAACTTCCATCCAACCTTACA
*
296811 TCATCTATACAATCAAAGCCCTAATCAAATATCATCAAAACACAAAGTTTCC-CAAACTTATAAT
196 TCATCCATACAATCAAAGCCCTAATCAAATATCATCAAAACACAAAGTTTCCAC-AACTTATAAT
*
296875 TTGGCCGAATATCAAAGAAACATTTCTAGGAAGATTGAACATGTTTTAATCATCATACAA
260 TTGGCCGAATATCAAAGAAACATTTCTAGAAAGATTGAACATGTTTTAATCATCATACAA
296935 GCTAGAAAAT
Statistics
Matches: 302, Mismatches: 16, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
318 1 0.00
319 301 1.00
ACGTcount: A:0.34, C:0.22, G:0.11, T:0.34
Consensus pattern (319 bp):
AATGGTCACCAAATTTTTCTAAGGATTGTAGAATACTTCCTACAACGTTTCCATCCCTTACATAA
TTTTTGCAGAATTTTCCTCATCCTTTAAGACCAAGGCCAAATGGTTCAAAGTTCTAAAACTAGAT
GTTTCATGATTTTGCTCGATTTTGATTCGATTGAAGCCTAAAATCAACTTCCATCCAACCTTACA
TCATCCATACAATCAAAGCCCTAATCAAATATCATCAAAACACAAAGTTTCCACAACTTATAATT
TGGCCGAATATCAAAGAAACATTTCTAGAAAGATTGAACATGTTTTAATCATCATACAA
Found at i:304118 original size:217 final size:217
Alignment explanation
Indices: 303730--304149 Score: 777
Period size: 217 Copynumber: 1.9 Consensus size: 217
303720 AAATAATATG
* * *
303730 TCATTGAAGAACCTATTCCTGATGTACAAGCAATTAATGCTTCTAGAACTGAAAAAGACAAGTTT
1 TCATTAAAGAACATATTCCTGATGTACAAGCAATTAATACTTCTAGAACTGAAAAAGACAAGTTT
303795 AAGAAACATATGGATGATATGTTAGATGTTGGATGTCTAATGCTTGCCATCATGACTATTGAGCT
66 AAGAAACATATGGATGATATGTTAGATGTTGGATGTCTAATGCTTGCCATCATGACTATTGAGCT
303860 TCAGAAGCAACATGAGGACATGGTTGCATATGAAATAATTCAAAATCTATAGAAAATATATGAAG
131 TCAGAAGCAACATGAGGACATGGTTGCATATGAAATAATTCAAAATCTATAGAAAATATATGAAG
303925 TGAAAGCAGTTCCTGATGTACA
196 TGAAAGCAGTTCCTGATGTACA
*
303947 TCATTAAAGAACATATTCCTGATGTACAAGCAATTAATACTTCTAGAGCTGAAAAAGACAAGTTT
1 TCATTAAAGAACATATTCCTGATGTACAAGCAATTAATACTTCTAGAACTGAAAAAGACAAGTTT
* *
304012 AAGAAACATATGGATGATATGTTAGATGTTGGATGTTTAATGCTTGCCATCATGACTCTTGAGCT
66 AAGAAACATATGGATGATATGTTAGATGTTGGATGTCTAATGCTTGCCATCATGACTATTGAGCT
*
304077 TCAGAAGCAACATGAGGACATGGTTGCATATGAAATAATTCAAAATCTATAGGAAATATATGAAG
131 TCAGAAGCAACATGAGGACATGGTTGCATATGAAATAATTCAAAATCTATAGAAAATATATGAAG
304142 TGAAAGCA
196 TGAAAGCA
304150 CGTAAAGAGA
Statistics
Matches: 196, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
217 196 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.29
Consensus pattern (217 bp):
TCATTAAAGAACATATTCCTGATGTACAAGCAATTAATACTTCTAGAACTGAAAAAGACAAGTTT
AAGAAACATATGGATGATATGTTAGATGTTGGATGTCTAATGCTTGCCATCATGACTATTGAGCT
TCAGAAGCAACATGAGGACATGGTTGCATATGAAATAATTCAAAATCTATAGAAAATATATGAAG
TGAAAGCAGTTCCTGATGTACA
Found at i:309172 original size:10 final size:11
Alignment explanation
Indices: 309148--309172 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
309138 ATTGGCGTGC
309148 AAAACAGAAGA
1 AAAACAGAAGA
309159 AAAACAGAAGA
1 AAAACAGAAGA
309170 AAA
1 AAA
309173 GACTCCTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (11 bp):
AAAACAGAAGA
Found at i:309225 original size:5 final size:5
Alignment explanation
Indices: 309199--309263 Score: 59
Period size: 5 Copynumber: 13.6 Consensus size: 5
309189 TTGGAGTGCA
* *
309199 AAAAG -AAAG AAAAG ACAA- AAAAG AAAAAG AAAAG AAGA- AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAAG AAAAG
309247 --AAG AAAAG AAAAAG AAA
1 AAAAG AAAAG -AAAAG AAA
309264 TTCAAAAAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
3 3 0.06
4 10 0.20
5 26 0.53
6 10 0.20
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:309227 original size:6 final size:6
Alignment explanation
Indices: 309216--309263 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
309206 AGAAAAGACA
309216 AAAAAG AAAAAG AAAAGAAG AAAAAG -AAAAG AAGAAAAG AAAAAG AAA
1 AAAAAG AAAAAG -AAA-AAG AAAAAG AAAAAG -A-AAAAG AAAAAG AAA
309264 TTCAAAAAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.14
6 17 0.46
7 7 0.19
8 8 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:309229 original size:20 final size:20
Alignment explanation
Indices: 309204--309259 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 20
309194 GTGCAAAAAG
309204 AAAGAAAAGACAAAAAAG-AA
1 AAAGAAAAGA-AAAAAAGAAA
309224 AAAGAAAAGAAGAAAAAGAAA
1 AAAGAAAAGAA-AAAAAGAAA
309245 AGAAGAAAAGAAAAA
1 A-AAGAAAAGAAAAA
309260 GAAATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.03
20 16 0.48
21 6 0.18
22 10 0.30
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAGAAAAGAAAAAAAGAAA
Found at i:309239 original size:19 final size:19
Alignment explanation
Indices: 309198--309263 Score: 84
Period size: 19 Copynumber: 3.5 Consensus size: 19
309188 ATTGGAGTGC
309198 AAAAAG-AAAGAAAAGACA-
1 AAAAAGAAAAGAAAAGA-AG
309216 AAAAAGAAAAAGAAAAGAAG
1 AAAAAG-AAAAGAAAAGAAG
309236 AAAAAGAAAAGAAGAA-AAG
1 AAAAAGAAAAGAA-AAGAAG
309255 AAAAAGAAA
1 AAAAAGAAA
309264 TTCAAAAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.14
19 20 0.45
20 18 0.41
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAGAAG
Found at i:309254 original size:8 final size:8
Alignment explanation
Indices: 309199--309256 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 8
309189 TTGGAGTGCA
309199 AAAAGAAAG
1 AAAAG-AAG
*
309208 AAAAG-AC
1 AAAAGAAG
309215 AAAA-AAG
1 AAAAGAAG
309222 -AAA-AAG
1 AAAAGAAG
309228 AAAAGAAG
1 AAAAGAAG
309236 -AAA-AAG
1 AAAAGAAG
309242 AAAAGAAG
1 AAAAGAAG
309250 AAAAGAA
1 AAAAGAA
309257 AAAGAAATTC
Statistics
Matches: 42, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
6 9 0.21
7 15 0.36
8 13 0.31
9 5 0.12
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:309262 original size:14 final size:14
Alignment explanation
Indices: 309199--309258 Score: 79
Period size: 14 Copynumber: 4.3 Consensus size: 14
309189 TTGGAGTGCA
309199 AAAAGAA-AGAAAAG
1 AAAAGAAGA-AAAAG
*
309213 ACAAAAAAGAAAAAG
1 A-AAAGAAGAAAAAG
309228 AAAAGAAGAAAAAG
1 AAAAGAAGAAAAAG
309242 AAAAGAAG-AAAAG
1 AAAAGAAGAAAAAG
309255 AAAA
1 AAAA
309259 AGAAATTCAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
13 9 0.21
14 21 0.50
15 11 0.26
16 1 0.02
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAAAG
Found at i:320192 original size:29 final size:29
Alignment explanation
Indices: 320130--320189 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
320120 TCATGTTAAT
*
320130 ATTATTTTCATTTTTTTCGCTGCTCCTAT
1 ATTATTTTCATTTTTTTCGCTGCTCCTAA
*
320159 ATTATTTTCATTTTTTT-GCTGCTTCTAA
1 ATTATTTTCATTTTTTTCGCTGCTCCTAA
320187 ATT
1 ATT
320190 TATGAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.17, C:0.17, G:0.07, T:0.60
Consensus pattern (29 bp):
ATTATTTTCATTTTTTTCGCTGCTCCTAA
Found at i:321876 original size:16 final size:17
Alignment explanation
Indices: 321855--321888 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
321845 ATTATTTTTA
*
321855 TTTA-TTTATAATATTT
1 TTTATTTTAAAATATTT
321871 TTTATTTTAAAATATTT
1 TTTATTTTAAAATATTT
321888 T
1 T
321889 AGATGGCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTTAAAATATTT
Found at i:323746 original size:49 final size:49
Alignment explanation
Indices: 323612--323747 Score: 146
Period size: 51 Copynumber: 2.7 Consensus size: 49
323602 TCGAGTTTCA
* * ** * *
323612 AAAAAATATTTGTATTCAAACTCGTCACCTCGAGGTAATGAGTTCTAAT
1 AAAAAATATTTTTATTCAAATTCGTCACCTCGAGGTAAAAAATTCAAAT
* * ** *
323661 AAAATATAATTTTTTATTAAAATTTATCACATCGAGGTAAAAAATTCAAAT
1 AAAAAAT-A-TTTTTATTCAAATTCGTCACCTCGAGGTAAAAAATTCAAAT
*
323712 AAAAAATATTTTTATTCGAATTCGTCACCTCGAGGT
1 AAAAAATATTTTTATTCAAATTCGTCACCTCGAGGT
323748 GACAAGTTCC
Statistics
Matches: 68, Mismatches: 17, Indels: 4
0.76 0.19 0.04
Matches are distributed among these distances:
49 29 0.43
50 2 0.03
51 37 0.54
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.35
Consensus pattern (49 bp):
AAAAAATATTTTTATTCAAATTCGTCACCTCGAGGTAAAAAATTCAAAT
Found at i:329317 original size:13 final size:13
Alignment explanation
Indices: 329299--329324 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329289 TATTTCCTAT
329299 AATGTAGGAAGGA
1 AATGTAGGAAGGA
329312 AATGTAGGAAGGA
1 AATGTAGGAAGGA
329325 CAAATCCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.38, T:0.15
Consensus pattern (13 bp):
AATGTAGGAAGGA
Found at i:338776 original size:25 final size:24
Alignment explanation
Indices: 338743--338797 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
338733 TTTCAAGGGT
*
338743 AAAAAAGTCTTTACTATCAAATGGC
1 AAAATAGTC-TTACTATCAAATGGC
*
338768 AAAATAGTCTTGCTATCAAATGGC
1 AAAATAGTCTTACTATCAAATGGC
338792 AAAATA
1 AAAATA
338798 AAGACTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 20 0.71
25 8 0.29
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (24 bp):
AAAATAGTCTTACTATCAAATGGC
Found at i:340039 original size:20 final size:20
Alignment explanation
Indices: 340014--340067 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
340004 ATTCAAGGGT
340014 AGTATCAATACTCTTGGCTG
1 AGTATCAATACTCTTGGCTG
* *
340034 AGTATCAATACTATTGGTTG
1 AGTATCAATACTCTTGGCTG
*
340054 AGTATCTATACTCT
1 AGTATCAATACTCT
340068 AGTTCTAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.39
Consensus pattern (20 bp):
AGTATCAATACTCTTGGCTG
Found at i:345850 original size:29 final size:29
Alignment explanation
Indices: 345796--345852 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
345786 CATTCAAAAC
* *
345796 TTTTCCAAAAATACCAAATTGATCCCCAT
1 TTTTCCAAAAATACAAAATAGATCCCCAT
*
345825 TTTTTCAAAAATTACAAAATAG-TCCCCA
1 TTTTCCAAAAA-TACAAAATAGATCCCCA
345853 AATGTTTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.40, C:0.25, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTTCCAAAAATACAAAATAGATCCCCAT
Found at i:346176 original size:28 final size:28
Alignment explanation
Indices: 346136--346200 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
346126 TCTAGGAAGT
* *
346136 TTGAACATGTTTTAATTATCAATCAAGC
1 TTGAAAATGTTTTAATCATCAATCAAGC
*
346164 TTGAAAATGTTTTAATCGTCAATCAAGC
1 TTGAAAATGTTTTAATCATCAATCAAGC
346192 TTGAAAATG
1 TTGAAAATG
346201 AATCTACAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (28 bp):
TTGAAAATGTTTTAATCATCAATCAAGC
Found at i:357316 original size:45 final size:45
Alignment explanation
Indices: 357107--357308 Score: 345
Period size: 45 Copynumber: 4.5 Consensus size: 45
357097 GGTAAGTATG
* *
357107 AAAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATGTTCGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
357151 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
357196 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
*
357241 AAAATAAGCTTACGAGCTTATAGAAATAAATGGTAAG-ATGTTGGT
1 AAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATGTTGGT
*
357286 AAAATAAGCTTACAAGCTTATGG
1 AAAATAAGCTTACGAGCTTATGG
357309 GATTAAATTG
Statistics
Matches: 151, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
44 27 0.18
45 110 0.73
46 14 0.09
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATGTTGGT
Found at i:362611 original size:29 final size:31
Alignment explanation
Indices: 362556--362618 Score: 94
Period size: 29 Copynumber: 2.1 Consensus size: 31
362546 TTTTGATCCT
*
362556 TAAACTTTTCCAAACTTTATACTTTGGTCAC
1 TAAACTTTTCCAAACATTATACTTTGGTCAC
*
362587 TAAACTTTT-CAAA-ATTATATTTTGGTCAC
1 TAAACTTTTCCAAACATTATACTTTGGTCAC
362616 TAA
1 TAA
362619 CCAAAATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 17 0.57
30 4 0.13
31 9 0.30
ACGTcount: A:0.33, C:0.17, G:0.06, T:0.43
Consensus pattern (31 bp):
TAAACTTTTCCAAACATTATACTTTGGTCAC
Found at i:367813 original size:17 final size:16
Alignment explanation
Indices: 367778--367819 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
367768 TTGCCCAAAT
*
367778 ATGATTTTTA-TGTTG
1 ATGATTTTAATTGTTG
*
367793 ATGAATTTTAATTGTTT
1 ATG-ATTTTAATTGTTG
367810 ATGATTTTAA
1 ATGATTTTAA
367820 GACATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 3 0.13
16 13 0.57
17 7 0.30
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (16 bp):
ATGATTTTAATTGTTG
Found at i:383625 original size:30 final size:30
Alignment explanation
Indices: 383591--383652 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 30
383581 TGAGCATCCG
**
383591 TACACAATACAATGTTGTACTAAGTGTCCT
1 TACACAATACAATAATGTACTAAGTGTCCT
* * *
383621 TACACACTATAGTAATGTACTAAGTGTCCT
1 TACACAATACAATAATGTACTAAGTGTCCT
383651 TA
1 TA
383653 TACACTATAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (30 bp):
TACACAATACAATAATGTACTAAGTGTCCT
Found at i:383658 original size:30 final size:32
Alignment explanation
Indices: 383606--383697 Score: 125
Period size: 30 Copynumber: 2.9 Consensus size: 32
383596 AATACAATGT
*
383606 TGTACTAAGTGTCCTTACACACTATAGT-A-A
1 TGTACTAAGTGTCCTTATACACTATAGTCATA
383636 TGTACTAAGTGTCCTTATACACTATAGTACCATA
1 TGTACTAAGTGTCCTTATACACTATAGT--CATA
* *
383670 TGCACTAAGTGTCCTTATATACTATAGT
1 TGTACTAAGTGTCCTTATACACTATAGT
383698 GCTAACCCGA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
30 27 0.49
33 1 0.02
34 27 0.49
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.36
Consensus pattern (32 bp):
TGTACTAAGTGTCCTTATACACTATAGTCATA
Found at i:383682 original size:34 final size:30
Alignment explanation
Indices: 383609--383697 Score: 115
Period size: 34 Copynumber: 2.8 Consensus size: 30
383599 ACAATGTTGT
* *
383609 ACTAAGTGTCCTTACACACTATAGTAATGT
1 ACTAAGTGTCCTTATACACTATAGTAATGC
383639 ACTAAGTGTCCTTATACACTATAGTACCATATGC
1 ACTAAGTGTCCTTATACACTATAGT---A-ATGC
*
383673 ACTAAGTGTCCTTATATACTATAGT
1 ACTAAGTGTCCTTATACACTATAGT
383698 GCTAACCCGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
30 24 0.46
33 1 0.02
34 27 0.52
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (30 bp):
ACTAAGTGTCCTTATACACTATAGTAATGC
Found at i:383693 original size:17 final size:18
Alignment explanation
Indices: 383639--383698 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 18
383629 ATAGTAATGT
383639 ACTA-AGTGTCCTTATAC
1 ACTATAGTGTCCTTATAC
* * *
383656 ACTATAGT-ACCATATGC
1 ACTATAGTGTCCTTATAC
*
383673 ACTA-AGTGTCCTTATAT
1 ACTATAGTGTCCTTATAC
383690 ACTATAGTG
1 ACTATAGTG
383699 CTAACCCGAT
Statistics
Matches: 33, Mismatches: 7, Indels: 5
0.73 0.16 0.11
Matches are distributed among these distances:
16 3 0.09
17 23 0.70
18 7 0.21
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (18 bp):
ACTATAGTGTCCTTATAC
Found at i:383896 original size:20 final size:21
Alignment explanation
Indices: 383854--383896 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
383844 TGAAATATCA
383854 TTCATGATAAAAATCATATATG
1 TTCATGATAAAAATCA-ATATG
*
383876 TTCATGATAAACATC-ATATG
1 TTCATGATAAAAATCAATATG
383896 T
1 T
383897 AACAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.37
Consensus pattern (21 bp):
TTCATGATAAAAATCAATATG
Found at i:390246 original size:6 final size:7
Alignment explanation
Indices: 390227--390253 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
390217 AGTCACCTTC
390227 TATTTTT
1 TATTTTT
390234 TATTTTT
1 TATTTTT
390241 TATTTTT
1 TATTTTT
390248 TATTTT
1 TATTTT
390254 AAATTATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TATTTTT
Found at i:392354 original size:3 final size:3
Alignment explanation
Indices: 392346--392528 Score: 352
Period size: 3 Copynumber: 61.7 Consensus size: 3
392336 TTTGCCAACA
392346 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
392393 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
392441 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
392488 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
392529 AGGGCTAGTG
Statistics
Matches: 178, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.02
3 174 0.98
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:393294 original size:22 final size:25
Alignment explanation
Indices: 393236--393288 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
393226 TCTTAATTTA
393236 TTATGAGAAAAAAATAATCTCTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
*
393261 TTATGAGAAAAAAATAATCTTTAAC
1 TTATGAGAAAAAAATAATCTCTAAC
393286 TTA
1 TTA
393289 GAAAAACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.51, C:0.09, G:0.08, T:0.32
Consensus pattern (25 bp):
TTATGAGAAAAAAATAATCTCTAAC
Found at i:394522 original size:17 final size:17
Alignment explanation
Indices: 394502--394543 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
394492 TTAAAAATTT
394502 AATTTAATAAAAATAGG
1 AATTTAATAAAAATAGG
394519 AATTTAATAAAAATAGG
1 AATTTAATAAAAATAGG
*
394536 TATTTAAT
1 AATTTAAT
394544 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (17 bp):
AATTTAATAAAAATAGG
Found at i:394544 original size:22 final size:21
Alignment explanation
Indices: 394498--394544 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 21
394488 AAATTTAAAA
394498 ATTTAATTTAATAAAAATAGG
1 ATTTAATTTAATAAAAATAGG
394519 ----AATTTAATAAAAATAGG
1 ATTTAATTTAATAAAAATAGG
394536 TATTTAATT
1 -ATTTAATT
394545 AATTTTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 9
0.70 0.00 0.30
Matches are distributed among these distances:
17 17 0.81
22 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
ATTTAATTTAATAAAAATAGG
Found at i:396960 original size:90 final size:90
Alignment explanation
Indices: 396838--397015 Score: 311
Period size: 90 Copynumber: 2.0 Consensus size: 90
396828 TAATCCTGAA
* * * *
396838 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATTAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
396903 TAGGGGAACTTAGATATAAAAGGAT
66 TAGGGGAACTTAGATATAAAAGGAT
396928 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
396993 TAGGGGAACTTAGCTATAAAAGG
66 TAGGGGAACTTAGATATAAAAGG
397016 GTGTGTTAGG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGGAACTTAGATATAAAAGGAT
Found at i:403571 original size:90 final size:90
Alignment explanation
Indices: 403450--403626 Score: 293
Period size: 90 Copynumber: 2.0 Consensus size: 90
403440 TAATCCCGAA
* *
403450 TATTTAATTTCAATTAATTAAATATAGATTTAATGAATTTGAAATAAT-AAAATCCCTAATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAAAT-CCTAATATGA
403514 TTAGGGGAACTTGGATATAAAAGGAT
65 TTAGGGGAACTTGGATATAAAAGGAT
*
403540 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAATCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAAATCCTAATATGAT
* *
403605 TAGGGTAACTTGGCTATAAAAG
66 TAGGGGAACTTGGATATAAAAG
403627 TGTGTGTTAG
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
90 76 0.94
91 5 0.06
ACGTcount: A:0.45, C:0.06, G:0.12, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATGAATTTGAAATAATAAAAATCCTAATATGAT
TAGGGGAACTTGGATATAAAAGGAT
Found at i:405879 original size:54 final size:54
Alignment explanation
Indices: 405800--406039 Score: 381
Period size: 54 Copynumber: 4.4 Consensus size: 54
405790 ATAAGTTCTT
* * * *
405800 TGGGATGCACACATAGTACCAATACGGTCGTTCATAAACATATTATGAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* * *
405854 TGAGTTGCACACTTAGTGCCGATACGGTCGTTCCTAAACATATTATAAATTCCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
*
405908 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
* *
405962 TGGGTTACACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTTCG
1 TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
*
406016 TGGGTTGCACACTTAGTGCGGATA
1 TGGGTTGCACACTTAGTGCCGATA
406040 GTACACATAG
Statistics
Matches: 172, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 172 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCGATACGGTCGTTCATAAACATATTATGAATTCCG
Found at i:417540 original size:54 final size:54
Alignment explanation
Indices: 417469--417702 Score: 276
Period size: 54 Copynumber: 4.3 Consensus size: 54
417459 ATAAGTTCTT
* *
417469 TGAGGTGCACACATAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCA
1 TGAGTTGCACACTTAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCA
*
417523 TGAGTTGCACACTTAGTG-TCGATACGGTCGTTCATAAACATATTATGAATTCCA
1 TGAGTTGCACACTTAGTGCT-GATACGGTCATTCATAAACATATTATGAATTCCA
* ** * * * * *
417577 TGGGTTATACAGTTAGTGCTGATATGGTCGTTCATAAACATTTTATGAATTCCG
1 TGAGTTGCACACTTAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCA
* * *
417631 TGAGTTGCACACTTAGTGC-CACTATGGTCATTCATAATA-ATATTATGAATTCTA
1 TGAGTTGCACACTTAGTGCTGA-TACGGTCATTCATAA-ACATATTATGAATTCCA
* *
417685 TGGGTTGTACACTTAGTG
1 TGAGTTGCACACTTAGTG
417703 TCGATAGTAC
Statistics
Matches: 155, Mismatches: 21, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
53 2 0.01
54 151 0.97
55 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (54 bp):
TGAGTTGCACACTTAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCA
Found at i:417645 original size:108 final size:108
Alignment explanation
Indices: 417477--417702 Score: 321
Period size: 108 Copynumber: 2.1 Consensus size: 108
417467 TTTGAGGTGC
*
417477 ACACATAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCATGAGTTGCACACTTAGTGT
1 ACACTTAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCATGAGTTGCACACTTAGTG-
* *
417542 CGA-TACGGTCGTTCATAA-ACATATTATGAATTCCATGGGTTAT
65 CCACTACGGTCATTCATAATA-ATATTATGAATTCCATGGGTTAT
* * * * *
417585 ACAGTTAGTGCTGATATGGTCGTTCATAAACATTTTATGAATTCCGTGAGTTGCACACTTAGTGC
1 ACACTTAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCATGAGTTGCACACTTAGTGC
* * *
417650 CACTATGGTCATTCATAATAATATTATGAATTCTATGGGTTGT
66 CACTACGGTCATTCATAATAATATTATGAATTCCATGGGTTAT
417693 ACACTTAGTG
1 ACACTTAGTG
417703 TCGATAGTAC
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
107 2 0.02
108 101 0.97
109 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (108 bp):
ACACTTAGTGCTGATACGGTCATTCATAAACATATTATGAATTCCATGAGTTGCACACTTAGTGC
CACTACGGTCATTCATAATAATATTATGAATTCCATGGGTTAT
Found at i:421443 original size:10 final size:9
Alignment explanation
Indices: 421421--421454 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
421411 AGCAAATCCC
*
421421 TTTTAATTA
1 TTTTTATTA
421430 TTTTTATTA
1 TTTTTATTA
421439 TTTTTATTCA
1 TTTTTATT-A
421449 TTTTTA
1 TTTTTA
421455 ATTTTCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.70
10 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTATTA
Found at i:427471 original size:26 final size:28
Alignment explanation
Indices: 427420--427471 Score: 81
Period size: 26 Copynumber: 1.9 Consensus size: 28
427410 CATGTTATGT
427420 GATGAGTGGAACAACTTCGCTATCCATG
1 GATGAGTGGAACAACTTCGCTATCCATG
*
427448 GATGAGT-GAGCAACTT-GCTATCCA
1 GATGAGTGGAACAACTTCGCTATCCA
427472 ATTTAGGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 8 0.35
28 7 0.30
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (28 bp):
GATGAGTGGAACAACTTCGCTATCCATG
Found at i:434004 original size:29 final size:31
Alignment explanation
Indices: 433935--434005 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 31
433925 AAAACTATAT
* * *
433935 TTTTGGTCCCTTAACTTTTAAAAAATTTATA
1 TTTTGGTCACTAAACTTTTAAAAAATTTACA
* *
433966 TTTT-GCCACTAAAC-TTTCAAAAA-TTACA
1 TTTTGGTCACTAAACTTTTAAAAAATTTACA
433994 TTTTGGTCACTA
1 TTTTGGTCACTA
434006 GATAAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
28 8 0.24
29 14 0.42
30 7 0.21
31 4 0.12
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (31 bp):
TTTTGGTCACTAAACTTTTAAAAAATTTACA
Found at i:434190 original size:2 final size:2
Alignment explanation
Indices: 434183--434209 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
434173 TGTTGTACCA
434183 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
434210 GCAGTTATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:446881 original size:23 final size:24
Alignment explanation
Indices: 446840--446906 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
446830 GAGGTAAGGG
* *
446840 AAAGAAACAAGAGGCAAAAAAATA
1 AAAGAAACAAGAAGAAAAAAAATA
*
446864 AAAGAAA-AAGAAGAAAAAAAACA
1 AAAGAAACAAGAAGAAAAAAAATA
* *
446887 ACAA-AAACAAAAACAAAAAA
1 A-AAGAAACAAGAAGAAAAAA
446907 TGATTGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.79, C:0.09, G:0.10, T:0.01
Consensus pattern (24 bp):
AAAGAAACAAGAAGAAAAAAAATA
Found at i:447443 original size:22 final size:22
Alignment explanation
Indices: 447396--447445 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
447386 ATTTTTCAAA
** *
447396 AAAAATTCCTCAAACATTTGTT
1 AAAAATTAATCAAACATTTGTC
447418 AAAAATTAATCAAACATTT-TC
1 AAAAATTAATCAAACATTTGTC
*
447439 CAAAATT
1 AAAAATT
447446 TCTTTTATCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.48, C:0.16, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATTAATCAAACATTTGTC
Found at i:448680 original size:124 final size:123
Alignment explanation
Indices: 448460--448701 Score: 312
Period size: 124 Copynumber: 2.0 Consensus size: 123
448450 GTCATTCAAA
* * ** *
448460 TACAACTTAGCCTCCTTCAGAGGAAAGAGTAAGATCGTCTCACGACTCAGGGTCTTTTAAAAGAA
1 TACAACTTAGCATCCTTAAGAGGAAAGAGTAAGATCGTCTCAC-ACTCAGCATCTTTCAAAAGAA
*
448525 TGAGTGAGATCGTCACCAGATTCAGCGTCCTTCAGCAAAAGGAGTGGATCACCATGAAT
65 TGAGTGAGATCGTCACCAGATTCAGCATCCTTCAGCAAAAGGAGTGGATCACCATGAAT
448584 TACAACTTAGCATCCTTAAGA-GAAAGGAGTAAGATCGTC-CTACACCTCAGCATCTTTCAGAGA
1 TACAACTTAGCATCCTTAAGAGGAAA-GAGTAAGATCGTCTC-ACA-CTCAGCATCTTTCA-A-A
* * * *
448647 A-AA-GTGTGAGATTGTCACCAGATTCAGCATCCTTCATCAAGAGGAGTGGATCACC
61 AGAATGAGTGAGATCGTCACCAGATTCAGCATCCTTCAGCAAAAGGAGTGGATCACC
448702 TACCAATTAT
Statistics
Matches: 103, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
123 6 0.06
124 92 0.89
125 3 0.03
126 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (123 bp):
TACAACTTAGCATCCTTAAGAGGAAAGAGTAAGATCGTCTCACACTCAGCATCTTTCAAAAGAAT
GAGTGAGATCGTCACCAGATTCAGCATCCTTCAGCAAAAGGAGTGGATCACCATGAAT
Found at i:449410 original size:15 final size:15
Alignment explanation
Indices: 449392--449443 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
449382 TATTTATTTA
*
449392 TATTATTAGTATTAG
1 TATTATTATTATTAG
*
449407 TATTAGTATTATTAG
1 TATTATTATTATTAG
449422 TTATTATT-TTATTA-
1 -TATTATTATTATTAG
449436 TATTATTA
1 TATTATTA
449444 CTAATATCTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 7 0.22
15 19 0.59
16 6 0.19
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
TATTATTATTATTAG
Found at i:449428 original size:3 final size:3
Alignment explanation
Indices: 449392--449443 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
449382 TATTTATTTA
* * *
449392 TAT TAT TAG TAT TAG TAT TAG TAT TAT TAGT TAT TAT T-T TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
449436 TAT TAT TA
1 TAT TAT TA
449444 CTAATATCTT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
2 4 0.10
3 33 0.82
4 3 0.08
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:450720 original size:2 final size:2
Alignment explanation
Indices: 450713--450740 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
450703 ACTCCACGTT
450713 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
450741 ACACCCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:450960 original size:7 final size:7
Alignment explanation
Indices: 450931--450973 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
450921 TTATGAATAA
*
450931 TGAACAA
1 TGAACAG
450938 TGAACAG
1 TGAACAG
* *
450945 T-ACCCG
1 TGAACAG
450951 TGAACAG
1 TGAACAG
450958 TGAACAG
1 TGAACAG
450965 TGAACAG
1 TGAACAG
450972 TG
1 TG
450974 GGAGTATCGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
6 4 0.13
7 26 0.87
ACGTcount: A:0.40, C:0.19, G:0.26, T:0.16
Consensus pattern (7 bp):
TGAACAG
Found at i:452457 original size:154 final size:155
Alignment explanation
Indices: 452137--452467 Score: 414
Period size: 154 Copynumber: 2.1 Consensus size: 155
452127 CATGTACTTT
* ** **
452137 AAATTTAGTAAAAAATTGACTTAAAATAAATCACAAATTCAATGAATAAGGAGATTATGAAAAAT
1 AAATTTGGTAAAAAATAAACTTAAAATAAATCACAAATTCAAAAAATAAGGAGATTATGAAAAAT
* * * *
452202 TGACGGACTAAATTGAAAAATAAAAAAAAAATTATCGGAAAGAAGAATTTAAATTACAAATATAT
66 TGAAGGACTAAATTG---AATAAAAAAAAAATTATCGAAAAGAAGAATTGAAAGTACAAATATAT
* *
452267 TCTACTATGGTTTAGGAGCATGTGACTC
128 TATACTATAGTTTAGGAGCATGTGACTC
* * *
452295 AAATTTGGTAAAAAAATAAACTTAAAATAAATGACGAATTGAAAAAATAAGGAGATTATGAAAAA
1 AAATTTGGT-AAAAAATAAACTTAAAATAAATCACAAATTCAAAAAATAAGGAGATTATGAAAAA
* *** * * *
452360 TTGAAGGATTAAATTG-A-AAAAAAATTGTTATCGAAAAGAGGAATTGAAAGTACACATGTATTA
65 TTGAAGGACTAAATTGAATAAAAAAAAAATTATCGAAAAGAAGAATTGAAAGTACAAATATATTA
*
452423 TACTATAGTTTAGGAGCATGTGATTC
130 TACTATAGTTTAGGAGCATGTGACTC
452449 AAATTTGGTAAAAAATAAA
1 AAATTTGGTAAAAAATAAA
452468 GGACATAAAT
Statistics
Matches: 150, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
153 10 0.07
154 69 0.46
155 1 0.01
158 8 0.05
159 62 0.41
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.28
Consensus pattern (155 bp):
AAATTTGGTAAAAAATAAACTTAAAATAAATCACAAATTCAAAAAATAAGGAGATTATGAAAAAT
TGAAGGACTAAATTGAATAAAAAAAAAATTATCGAAAAGAAGAATTGAAAGTACAAATATATTAT
ACTATAGTTTAGGAGCATGTGACTC
Found at i:454087 original size:35 final size:35
Alignment explanation
Indices: 454048--454118 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 35
454038 AAGAAATAAG
* *
454048 TTTATGGGCTC-TACTTGTAATTTAGTTTATTAATA
1 TTTATGGG-TCATACTTGTAATTTAATATATTAATA
* *
454083 TTTATGGGTCATGCTTTTAATTTAATATATTAATA
1 TTTATGGGTCATACTTGTAATTTAATATATTAATA
454118 T
1 T
454119 AATTTTTAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 2 0.06
35 29 0.94
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (35 bp):
TTTATGGGTCATACTTGTAATTTAATATATTAATA
Found at i:459183 original size:24 final size:24
Alignment explanation
Indices: 459156--459206 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
459146 AAGGGAGGGT
*
459156 TGATTTGAGTTTCATGGCCCTGAA
1 TGATTTGAGTTTCATGGCCATGAA
459180 TGATTTGAGTTTCATGGCCATGAA
1 TGATTTGAGTTTCATGGCCATGAA
459204 TGA
1 TGA
459207 AGGATATGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (24 bp):
TGATTTGAGTTTCATGGCCATGAA
Found at i:464190 original size:153 final size:153
Alignment explanation
Indices: 463912--464218 Score: 587
Period size: 153 Copynumber: 2.0 Consensus size: 153
463902 TTGCAGGAGC
463912 GACATCAAGAGTTTCAGAATCTGGAGCAGGGTAATATGTCTGTTATGGACTATGAGATTAAGTTT
1 GACATCAAGAGTTTCAGAATCTGGAGCAGGGTAATATGTCTGTTATGGACTATGAGATTAAGTTT
*
463977 ATCAGACTGAGTCGTTATGCTACTGGACTTGTTAACATTGAGTCAGATCGGTGCTTGAGGTTTAA
66 ATCAGACTGAGTCGTTATGCTACTGGACTTGTTAACATTGAGTCAGATCGGTGCTTGAGGTTCAA
464042 GAATAGACTCGGGTATGAGATCA
131 GAATAGACTCGGGTATGAGATCA
464065 GACATCAAGAGTTTCAGAATCTGGAGCAGGGTAATATGTCTGTTATGGACTATGAGATTAAGTTT
1 GACATCAAGAGTTTCAGAATCTGGAGCAGGGTAATATGTCTGTTATGGACTATGAGATTAAGTTT
* *
464130 ATTAGACTGAGTCGTTATGCTACTGGACTTGTTAACATTGAGTCAGATCGGTTCTTGAGGTTCAA
66 ATCAGACTGAGTCGTTATGCTACTGGACTTGTTAACATTGAGTCAGATCGGTGCTTGAGGTTCAA
464195 GAATAGACTCGGGTATGAGATCA
131 GAATAGACTCGGGTATGAGATCA
464218 G
1 G
464219 GAGTCGAGTT
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.32
Consensus pattern (153 bp):
GACATCAAGAGTTTCAGAATCTGGAGCAGGGTAATATGTCTGTTATGGACTATGAGATTAAGTTT
ATCAGACTGAGTCGTTATGCTACTGGACTTGTTAACATTGAGTCAGATCGGTGCTTGAGGTTCAA
GAATAGACTCGGGTATGAGATCA
Found at i:468928 original size:15 final size:15
Alignment explanation
Indices: 468908--468936 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
468898 TTGAAAACTG
468908 GTTTGACCCGACCCA
1 GTTTGACCCGACCCA
468923 GTTTGACCCGACCC
1 GTTTGACCCGACCC
468937 GACCACTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.41, G:0.21, T:0.21
Consensus pattern (15 bp):
GTTTGACCCGACCCA
Found at i:472620 original size:27 final size:27
Alignment explanation
Indices: 472570--472666 Score: 115
Period size: 27 Copynumber: 3.4 Consensus size: 27
472560 CTTTATTTTG
*
472570 TTCGGGTC-GGTGTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
472596 TTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTTTTTTAAGTGTGATA
*
472623 TTCGGGTCGGGTCGGGTTTTTTAAGTATGATA
1 -T----TCGGGTCGGGTTTTTTAAGTGTGATA
*
472655 TTCAGGTCGGGT
1 TTCGGGTCGGGT
472667 CGGGTTCGAG
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
26 8 0.13
27 27 0.44
28 1 0.02
31 1 0.02
32 25 0.40
ACGTcount: A:0.14, C:0.09, G:0.35, T:0.41
Consensus pattern (27 bp):
TTCGGGTCGGGTTTTTTAAGTGTGATA
Found at i:472634 original size:32 final size:31
Alignment explanation
Indices: 472571--472672 Score: 133
Period size: 32 Copynumber: 3.4 Consensus size: 31
472561 TTTATTTTGT
*
472571 TCGGGTC-GGTGTTTTAAGTGTGATA-T---
1 TCGGGTCGGGTTTTTTAAGTGTGATATTCGG
472597 TCGGGTCGGGTTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTC-GG
*
472629 TCGGGTCGGGTTTTTTAAGTATGATATTCAGG
1 TCGGGTCGGGTTTTTTAAGTGTGATATTC-GG
472661 TCGGGTCGGGTT
1 TCGGGTCGGGTT
472673 CGAGTTTAGG
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.10
27 17 0.25
28 1 0.01
32 42 0.63
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.40
Consensus pattern (31 bp):
TCGGGTCGGGTTTTTTAAGTGTGATATTCGG
Found at i:473276 original size:17 final size:18
Alignment explanation
Indices: 473251--473297 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
473241 TATAGAATTG
* *
473251 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
473268 GATTTCAATTCCTTCACA
1 GATTTCAATTCCTTCACA
473286 GATTTCAATTCC
1 GATTTCAATTCC
473298 CTCAGAAACA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 11 0.41
18 16 0.59
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:474857 original size:2 final size:2
Alignment explanation
Indices: 474850--474935 Score: 52
Period size: 2 Copynumber: 49.0 Consensus size: 2
474840 GAAAATATTT
*
474850 TA TA TA TA -A T- TA -A TA TA TA -A AA TA T- TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
474886 TA TA TA -A T- TA -A TA TA -A AA AA TA TA -A AA TA T- 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
474922 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
474936 ATCAGGGCGG
Statistics
Matches: 69, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
1 12 0.17
2 57 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:474882 original size:34 final size:34
Alignment explanation
Indices: 474841--474925 Score: 134
Period size: 34 Copynumber: 2.5 Consensus size: 34
474831 CCCAAACCCG
* *
474841 AAAATATTTTATATATAATTAATATATAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
* *
474875 TATATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
474909 AAAATATTATATATATA
1 AAAATATTATATATATA
474926 TATATATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 45 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:474995 original size:13 final size:13
Alignment explanation
Indices: 474977--475002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
474967 ACTCGACCCG
474977 AAAAAATCTCCGA
1 AAAAAATCTCCGA
474990 AAAAAATCTCCGA
1 AAAAAATCTCCGA
475003 TACTCGAACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
AAAAAATCTCCGA
Found at i:475463 original size:23 final size:23
Alignment explanation
Indices: 475430--475477 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
475420 TTCTTACGTG
*
475430 TTCACATATATATTATAAAAGAT
1 TTCACACATATATTATAAAAGAT
475453 TTCACACATATATTATAAAAGAT
1 TTCACACATATATTATAAAAGAT
475476 TT
1 TT
475478 GAAGAAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.46, C:0.10, G:0.04, T:0.40
Consensus pattern (23 bp):
TTCACACATATATTATAAAAGAT
Found at i:476588 original size:148 final size:147
Alignment explanation
Indices: 476401--476796 Score: 559
Period size: 148 Copynumber: 2.7 Consensus size: 147
476391 CTATATTTTT
* *
476401 TTTAT-AAA-TAAGATATTTATTTACTT-AGAAACATCAGAAAATGACTTCTAGGTGCTTTAAGA
1 TTTATAAAAGTAAGATATTTATTTATTTAAGAAA-ATCAGAAAATGACTTCTAGATGCTTTAAGA
476463 CAGCCAATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAAATAATTAA
65 CAGCC-ATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAAATAATTAA
476528 AATAAATTAATATATATAA
129 AATAAATTAATATATATAA
* * *
476547 TTTATAAAAAT-TGAATATTTATTTATTTAAGAATATCAGAAAATGACTTCTAGATGCTTTAAGA
1 TTTATAAAAGTAAG-ATATTTATTTATTTAAGAAAATCAGAAAATGACTTCTAGATGCTTTAAGA
* ** *
476611 CAACTCATTTCTTAATATTAGTAAATAAATAAATACTAATAAAATATTTCTCTAAAAATAATTAA
65 CAGC-CATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAAATAATTAA
*
476676 ACTAAATTAATATATATAA
129 AATAAATTAATATATATAA
* * * *
476695 TTTATAAAAGTAAGATATTTATTTATTTAA-AAAATAAGAAAATGAACATCTAGTTGTTTTAAGA
1 TTTATAAAAGTAAGATATTTATTTATTTAAGAAAATCAGAAAATG-ACTTCTAGATGCTTTAAGA
* * *
476759 CTGCCATTTCTTAATATTGAAAAATAAATATATATTAA
65 CAGCCATTTCTTAATATTAAAAAATAAATAAATATTAA
476797 AATATGATTA
Statistics
Matches: 220, Mismatches: 23, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
146 5 0.02
147 45 0.20
148 164 0.75
149 6 0.03
ACGTcount: A:0.48, C:0.08, G:0.07, T:0.38
Consensus pattern (147 bp):
TTTATAAAAGTAAGATATTTATTTATTTAAGAAAATCAGAAAATGACTTCTAGATGCTTTAAGAC
AGCCATTTCTTAATATTAAAAAATAAATAAATATTAATAAAATATTTCTCTAAAAATAATTAAAA
TAAATTAATATATATAA
Found at i:476975 original size:21 final size:20
Alignment explanation
Indices: 476949--476990 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
476939 TATATCAAAG
476949 ATAATAATAAAACAAAATGAA
1 ATAATAAT-AAACAAAATGAA
*
476970 ATAATAATAATCAAAATGAA
1 ATAATAATAAACAAAATGAA
476990 A
1 A
476991 GAAATTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAATAATAAACAAAATGAA
Found at i:477029 original size:17 final size:17
Alignment explanation
Indices: 476994--477041 Score: 57
Period size: 16 Copynumber: 3.0 Consensus size: 17
476984 AATGAAAGAA
*
476994 ATTAAAA-GCAACA-AT
1 ATTAAAATGCAAAATAT
477009 ATTAAAATGCAAAATAT
1 ATTAAAATGCAAAATAT
*
477026 ATT-AAATGAAAAATAT
1 ATTAAAATGCAAAATAT
477042 CAAACTGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 7 0.24
16 17 0.59
17 5 0.17
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
ATTAAAATGCAAAATAT
Found at i:478319 original size:3 final size:3
Alignment explanation
Indices: 478311--478359 Score: 75
Period size: 3 Copynumber: 16.7 Consensus size: 3
478301 CTTTTTTATT
478311 TAA TAA TAA TAA T-A TATA TAA T-A TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
478355 TAA TA
1 TAA TA
478360 TGAAAATGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:478550 original size:45 final size:45
Alignment explanation
Indices: 478483--478674 Score: 359
Period size: 45 Copynumber: 4.3 Consensus size: 45
478473 GATGGAAGTG
*
478483 TTGAAAACATCATACACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
478528 TTGAAAACATCATGCA-TCGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACT-GAAGGGCTTACAGATGACCCGAAGGTT
478573 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
478618 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
478663 TTGAAAACATCA
1 TTGAAAACATCA
478675 AAAAGCTCCC
Statistics
Matches: 144, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
44 1 0.01
45 142 0.99
46 1 0.01
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:479431 original size:23 final size:22
Alignment explanation
Indices: 479381--479437 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 22
479371 GGACTTGCTT
* *
479381 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAAAATCTA
479403 TCATCTTTGAAGAGATAAATCTA
1 TCATCTTTGAAGAGA-AAATCTA
*
479426 TTATCTTTGAAG
1 TCATCTTTGAAG
479438 GATGTAGATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 14 0.45
23 17 0.55
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (22 bp):
TCATCTTTGAAGAGAAAATCTA
Found at i:479863 original size:54 final size:54
Alignment explanation
Indices: 479797--479954 Score: 185
Period size: 54 Copynumber: 2.9 Consensus size: 54
479787 TAACTGGTTT
*
479797 GTAAAA-TATTTGACAATCCATTTATCATCTCATGTGGTTTCTGCTCAGATGCTA
1 GTAAAACT-TTTGACAATCCATTCATCATCTCATGTGGTTTCTGCTCAGATGCTA
* * * *
479851 GTAAAACTTTTGACAATACATTCATCATCTCATGTGGTTTATGCTCAAATGCTG
1 GTAAAACTTTTGACAATCCATTCATCATCTCATGTGGTTTCTGCTCAGATGCTA
* * * * * *
479905 GTAAAGCATTTGACAA-CACATTCATTATCTCCTGTGGCTTCTGCCCAGAT
1 GTAAAACTTTTGACAATC-CATTCATCATCTCATGTGGTTTCTGCTCAGAT
479955 TTCTCATCAG
Statistics
Matches: 88, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
54 87 0.99
55 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (54 bp):
GTAAAACTTTTGACAATCCATTCATCATCTCATGTGGTTTCTGCTCAGATGCTA
Found at i:488863 original size:61 final size:61
Alignment explanation
Indices: 488793--488913 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
488783 TATTCAATTT
* * *
488793 AGAACTATAGCGTATATAAAGGATACTTAGTGCATATGGTGGGCATGACCTTATGTGTATG
1 AGAACTATAGCGTATATAAAGGACACTTAGTGCATATGGTGGGAACGACCTTATGTGTATG
* *
488854 AGAACTATAGTGTGTATAAAGGACACTTAGTGCATATGGTGGGAACGACCTTATGTGTAT
1 AGAACTATAGCGTATATAAAGGACACTTAGTGCATATGGTGGGAACGACCTTATGTGTAT
488914 TAGCACTTCG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (61 bp):
AGAACTATAGCGTATATAAAGGACACTTAGTGCATATGGTGGGAACGACCTTATGTGTATG
Found at i:492242 original size:82 final size:81
Alignment explanation
Indices: 492087--492311 Score: 273
Period size: 82 Copynumber: 2.8 Consensus size: 81
492077 TATTCAAGAT
* * * *
492087 TTCA-ATTCAA-TTAATTCGATCATGGCAA-CATGCACTAATTTAGAATTTGACTT-AATT-ATA
1 TTCACATTCAACTTAATTCGATCATGG-AAGCATGCAATAATTCATAATTCGA-TTCAATTCA-A
492147 TCATGGTAACATGCAATAA
63 TCATGGTAACATGCAATAA
* *
492166 TTCACCATTCAACTTAATTCAATCATGGAAGCATGCAATAATTCATAATTCGATTCAATTCAATG
1 TTCA-CATTCAACTTAATTCGATCATGGAAGCATGCAATAATTCATAATTCGATTCAATTCAATC
492231 ATGG-AAGCATGCAATAA
65 ATGGTAA-CATGCAATAA
* * *
492248 TTCACAGTTCAACTTAATTCGATCATGGCAGCATGCAATAATCCATAATTCAATTCAATTCAAT
1 TTCACA-TTCAACTTAATTCGATCATGGAAGCATGCAATAATTCATAATTCGATTCAATTCAAT
492312 TCATCATGGA
Statistics
Matches: 128, Mismatches: 10, Indels: 13
0.85 0.07 0.09
Matches are distributed among these distances:
79 4 0.03
81 14 0.11
82 109 0.85
83 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (81 bp):
TTCACATTCAACTTAATTCGATCATGGAAGCATGCAATAATTCATAATTCGATTCAATTCAATCA
TGGTAACATGCAATAA
Found at i:492308 original size:41 final size:40
Alignment explanation
Indices: 492089--492311 Score: 218
Period size: 41 Copynumber: 5.5 Consensus size: 40
492079 TTCAAGATTT
* * *
492089 CAATTCAATTAATTCGATCATGGCAA-CATGCACTAATTTA
1 CAATTCAATTAATTCAATCATGG-AAGCATGCAATAATTCA
* * *
492129 GAATTTGACTTAATT-ATATCATGGTAA-CATGCAATAATTCA
1 CAA-TTCAATTAATTCA-ATCATGG-AAGCATGCAATAATTCA
*
492170 CCATTCAACTTAATTCAATCATGGAAGCATGCAATAATTCA
1 CAATTCAA-TTAATTCAATCATGGAAGCATGCAATAATTCA
* * *
492211 TAATTCGATTCAATTCAATGATGGAAGCATGCAATAATTCA
1 CAATTCAATT-AATTCAATCATGGAAGCATGCAATAATTCA
* * * *
492252 CAGTTCAACTTAATTCGATCATGGCAGCATGCAATAATCCA
1 CAATTCAA-TTAATTCAATCATGGAAGCATGCAATAATTCA
*
492293 TAATTCAATTCAATTCAAT
1 CAATTCAATT-AATTCAAT
492312 TCATCATGGA
Statistics
Matches: 150, Mismatches: 25, Indels: 15
0.79 0.13 0.08
Matches are distributed among these distances:
40 11 0.07
41 136 0.91
42 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.32
Consensus pattern (40 bp):
CAATTCAATTAATTCAATCATGGAAGCATGCAATAATTCA
Found at i:492378 original size:41 final size:40
Alignment explanation
Indices: 492303--492393 Score: 119
Period size: 41 Copynumber: 2.2 Consensus size: 40
492293 TAATTCAATT
*
492303 CAATTCAATTCATCATGGAAACATGCATTTATTCACAAAC
1 CAATTCAATTCATCATGGAAACATGCATTAATTCACAAAC
* * * * *
492343 CAATTCAATTAGATCATTGTAACATGTATTAATTCACAATC
1 CAATTCAATT-CATCATGGAAACATGCATTAATTCACAAAC
492384 CAATTCAATT
1 CAATTCAATT
492394 TAAATCAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 10 0.23
41 34 0.77
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.34
Consensus pattern (40 bp):
CAATTCAATTCATCATGGAAACATGCATTAATTCACAAAC
Found at i:494790 original size:27 final size:27
Alignment explanation
Indices: 494735--494791 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
494725 ATGGTTTGGG
* *
494735 ATGCGTGTTCATACAAGAGGAAAGGTT
1 ATGCGTGTTCACACAAGAGGAAAAGTT
*
494762 ATGCGTGTTCACACAAGAGGAAAATTT
1 ATGCGTGTTCACACAAGAGGAAAAGTT
494789 ATG
1 ATG
494792 GCTTATGCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.26
Consensus pattern (27 bp):
ATGCGTGTTCACACAAGAGGAAAAGTT
Found at i:498427 original size:16 final size:16
Alignment explanation
Indices: 498406--498454 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
498396 AAGTAATATA
498406 AATATAGTTTGAAAAT
1 AATATAGTTTGAAAAT
* * *
498422 AATATAGTATGTATAT
1 AATATAGTTTGAAAAT
498438 -ATATAGTTT-AAAA-
1 AATATAGTTTGAAAAT
498451 AATA
1 AATA
498455 GTATATTAGT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 5 0.19
15 8 0.31
16 13 0.50
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.39
Consensus pattern (16 bp):
AATATAGTTTGAAAAT
Found at i:498502 original size:26 final size:25
Alignment explanation
Indices: 498433--498511 Score: 72
Period size: 26 Copynumber: 3.2 Consensus size: 25
498423 ATATAGTATG
*
498433 TATA-TATATAGTTT-AAAAAATAG
1 TATATTATATAGTTTAAAAAAATAA
* **
498456 TATATTAGTTTTTTTTAAAAAAATAA
1 TATATTA-TATAGTTTAAAAAAATAA
* *
498482 TATATTATATAGTTTAGAAAATATAT
1 TATATTATATAGTTTA-AAAAAATAA
498508 TATA
1 TATA
498512 GGTTTTGAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
23 4 0.09
24 2 0.05
25 11 0.26
26 26 0.60
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (25 bp):
TATATTATATAGTTTAAAAAAATAA
Found at i:498506 original size:21 final size:21
Alignment explanation
Indices: 498480--498537 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
498470 TTAAAAAAAT
498480 AATATATTATATAGTTTAGAA
1 AATATATTATATAGTTTAGAA
* *
498501 AATATATTATA-GGTTTTGAA
1 AATATATTATATAGTTTAGAA
*
498521 AATAGT-GTATATAGTTT
1 AATA-TATTATATAGTTT
498538 TCTTTTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (21 bp):
AATATATTATATAGTTTAGAA
Found at i:498605 original size:22 final size:23
Alignment explanation
Indices: 498554--498609 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
498544 AATATAAATA
* *
498554 TATAGTTTAAAAATAGTATATTT
1 TATAGTTTTAAAATAGAATATTT
*
498577 TCT--TTTTAAAATA-AATATTT
1 TATAGTTTTAAAATAGAATATTT
498597 TATAGTTTTAAAA
1 TATAGTTTTAAAA
498610 CATATATGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 8 0.30
21 9 0.33
22 8 0.30
23 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (23 bp):
TATAGTTTTAAAATAGAATATTT
Found at i:498616 original size:22 final size:22
Alignment explanation
Indices: 498554--498616 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
498544 AATATAAATA
*
498554 TATAGTTTAAAAATAGTATATTT
1 TATAGTTTTAAAATA-TATATTT
* *
498577 TCT--TTTTAAAATAAATATTT
1 TATAGTTTTAAAATATATATTT
*
498597 TATAGTTTTAAAACATATAT
1 TATAGTTTTAAAATATATAT
498617 GCATTTCGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 8 0.25
21 9 0.28
22 13 0.41
23 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.49
Consensus pattern (22 bp):
TATAGTTTTAAAATATATATTT
Found at i:500411 original size:2 final size:2
Alignment explanation
Indices: 500404--500445 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
500394 CAAAGGAAAA
500404 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
500446 GGTTTTATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:501155 original size:22 final size:21
Alignment explanation
Indices: 501116--501174 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 21
501106 CATTTTGTCT
*
501116 TTTATTATTATTATTTTAATTA
1 TTTATTATTATTAATTT-ATTA
501138 TTTATTATT-TGTAATTTATTA
1 TTTATTATTAT-TAATTTATTA
501159 TTAATATATATTATTA
1 TT--TAT-TATTATTA
501175 GAATACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 7 0.23
22 14 0.45
23 3 0.10
24 6 0.19
25 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATTATTATTAATTTATTA
Found at i:501808 original size:19 final size:19
Alignment explanation
Indices: 501764--501835 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 19
501754 CGGCCACCGC
*
501764 CGGTCACTATTCCGACCACCGT
1 CGGTCACTATTCC-A--ACAGT
*
501786 CGGTCACTATTCCAGCAGT
1 CGGTCACTATTCCAACAGT
501805 CGGTCACTATTCCAACAGT
1 CGGTCACTATTCCAACAGT
*
501824 CGATCACTATTC
1 CGGTCACTATTC
501836 ACTGTGGCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 32 0.70
21 1 0.02
22 13 0.28
ACGTcount: A:0.22, C:0.35, G:0.17, T:0.26
Consensus pattern (19 bp):
CGGTCACTATTCCAACAGT
Found at i:502535 original size:3 final size:3
Alignment explanation
Indices: 502529--502598 Score: 86
Period size: 3 Copynumber: 23.3 Consensus size: 3
502519 AATTATTATT
* * * *
502529 TAA TAA TAA TAA TAT TAA TAA TAT TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
502577 TAT TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA T
502599 TTTAAAAATA
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (3 bp):
TAA
Found at i:502547 original size:9 final size:9
Alignment explanation
Indices: 502506--502596 Score: 92
Period size: 9 Copynumber: 9.9 Consensus size: 9
502496 ACTGGGCATG
502506 TAATAATAT
1 TAATAATAT
**
502515 TTGTAATTAT
1 TAATAA-TAT
* *
502525 TATTTAATAA
1 TA-ATAATAT
502535 TAATAATAT
1 TAATAATAT
502544 TAATAATAT
1 TAATAATAT
502553 TAATAATAT
1 TAATAATAT
* *
502562 TTATAATAA
1 TAATAATAT
502571 TAATAATAT
1 TAATAATAT
* *
502580 TTATAATAA
1 TAATAATAT
502589 TAATAATA
1 TAATAATA
502597 ATTTTAAAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
9 55 0.83
10 8 0.12
11 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (9 bp):
TAATAATAT
Found at i:502556 original size:18 final size:18
Alignment explanation
Indices: 502529--502596 Score: 109
Period size: 18 Copynumber: 3.8 Consensus size: 18
502519 AATTATTATT
502529 TAATAATAATAATATTAA
1 TAATAATAATAATATTAA
* *
502547 TAATATTAATAATATTTA
1 TAATAATAATAATATTAA
*
502565 TAATAATAATAATATTTA
1 TAATAATAATAATATTAA
502583 TAATAATAATAATA
1 TAATAATAATAATA
502597 ATTTTAAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
TAATAATAATAATATTAA
Found at i:502608 original size:18 final size:18
Alignment explanation
Indices: 502530--502609 Score: 81
Period size: 18 Copynumber: 4.3 Consensus size: 18
502520 ATTATTATTT
* *
502530 AATAATAATAATATTAAT
1 AATAATAATAATTTTAAA
*
502548 AATATTAATAATATTTATAA
1 AATAATAATAAT-TTTA-AA
*
502568 TAATAATAAT-ATTTATAAT
1 -AATAATAATAATTT-TAAA
502587 AATAATAATAATTTTAAA
1 AATAATAATAATTTTAAA
502605 AATAA
1 AATAA
502610 AATGAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 28 0.55
19 10 0.20
20 5 0.10
21 8 0.16
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATAATAATAATTTTAAA
Found at i:503068 original size:131 final size:132
Alignment explanation
Indices: 502750--503068 Score: 482
Period size: 131 Copynumber: 2.4 Consensus size: 132
502740 TTCTGCCCAA
* * * * * * * * *
502750 AGGTCTTATGAATGGCCCGGATGACTTATCATCTTGCTCGGAAGG-GTTACAGATGA-TCCGGAG
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACTCCGGAA
* *
502813 GATTTAAGATCAAGAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACT
66 GATTTAAGATAAAAAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACT
502878 GG
131 GG
*
502880 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTATAGATGACT-CGGAA
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACTCCGGAA
*
502944 GATTTAAGATAAAAAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCCTGTACT
66 GATTTAAGATAAAAAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACT
503009 GG
131 GG
* *
503011 AGGTCTTATGGATGGCCCTGAGGTCTTATCATTTTGCACTGTAGGTCTTACGGATGAC
1 AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGAC
503069 CCGAAGGCTT
Statistics
Matches: 171, Mismatches: 16, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
130 38 0.22
131 132 0.77
132 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.32
Consensus pattern (132 bp):
AGGTCTTATGGATGGCCCTGAGGTCTTATCATCTTGCACTGTAGGTCTTACAGATGACTCCGGAA
GATTTAAGATAAAAAAACCTTTGAAAATCAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACT
GG
Found at i:503190 original size:45 final size:45
Alignment explanation
Indices: 503045--503430 Score: 565
Period size: 45 Copynumber: 8.5 Consensus size: 45
503035 CTTATCATTT
* * * *
503045 TGCACTGTAGGTCTTACGGATGACCCGAAGGCTTTTTGAAAACATCC
1 TGCACTGAAGGGCTTACAGATGACCCGAAGG--TTTTGAAAACATCA
* * * *
503092 TGCACTGAAGGTCTTACGGATGACCTGAAGGCTTTTTGAAAACATCC
1 TGCACTGAAGGGCTTACAGATGACCCGAAGG--TTTTGAAAACATCA
* *
503139 TACACTGAAGGTCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
*
503184 TGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAAAACATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
* *
503229 TGCACTGAAGGGCTTACAGATGATCCGAATGTTTTGAAAACATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
* *
503274 TGCACTAAAGGGCTTACAAATGACCCGAAGGTTTTGAAAACATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
*
503319 TGCACTGAAGGGCTTACAGATGACTCGAAGGTTTTGAAAACATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
* *
503364 TGAACTGAAGTGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
*
503409 TGCGCTGAAGGGCTTACAGATG
1 TGCACTGAAGGGCTTACAGATG
503431 TTAGAAATAG
Statistics
Matches: 314, Mismatches: 25, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
45 241 0.77
47 73 0.23
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.25
Consensus pattern (45 bp):
TGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
Found at i:503373 original size:25 final size:24
Alignment explanation
Indices: 503300--503373 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 24
503290 CAAATGACCC
503300 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTTGAAAACATCATG-ACT
** *
503325 GAAGGGCTT----ACA-GATGACT
1 GAAGGTTTTGAAAACATCATGACT
503344 CGAAGGTTTTGAAAACATCATGAACT
1 -GAAGGTTTTGAAAACATCATG-ACT
503370 GAAG
1 GAAG
503374 TGCTTACAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
19 3 0.08
20 10 0.28
21 3 0.08
24 3 0.08
25 14 0.39
26 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (24 bp):
GAAGGTTTTGAAAACATCATGACT
Found at i:504116 original size:22 final size:22
Alignment explanation
Indices: 504089--504143 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
504079 CCAATAAATC
504089 TTATCTTTGAAAAGAAAATCTA
1 TTATCTTTGAAAAGAAAATCTA
**
504111 TTATCTTTGAAGGGAAAATCTA
1 TTATCTTTGAAAAGAAAATCTA
*
504133 TCATCTTTGAA
1 TTATCTTTGAA
504144 GAATGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (22 bp):
TTATCTTTGAAAAGAAAATCTA
Found at i:504144 original size:22 final size:21
Alignment explanation
Indices: 504084--504145 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
504074 GAAATCCAAT
*
504084 AAATCT-TATCTTTGAAAAGA
1 AAATCTATATCTTTGAAGAGA
*
504104 AAATCTATTATCTTTGAAGGGA
1 AAATCTA-TATCTTTGAAGAGA
504126 AAATCTATCATCTTTGAAGA
1 AAATCTAT-ATCTTTGAAGA
504146 ATGTAGATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 29 0.81
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (21 bp):
AAATCTATATCTTTGAAGAGA
Found at i:505636 original size:75 final size:76
Alignment explanation
Indices: 505534--505734 Score: 259
Period size: 75 Copynumber: 2.7 Consensus size: 76
505524 TTCAAAATGT
*
505534 TATTCCAATTTCTGATTGAAATAGGCTTTCAGCATACCCCAACATTTGCTAAT-AC-AG-ACATT
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATACCCCAACATTTGCT--TGACGAGAACATT
505596 CAAAATGCGCCAA
64 CAAAATGCGCCAA
* * *
505609 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATGCCCCAGCATTTG-TTGACGTGAACATTCA
1 TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATACCCCAACATTTGCTTGACGAGAACATTCA
*
505673 AAATGCGTCAA
66 AAATGCGCCAA
* * * *
505684 TATTCCTGA-TTATGATTGAAATGGGCTTTCAGCATACCTCATCATTTGCTT
1 TATTCC-AATTTCTGATTGAAATGGGCTTTCAGCATACCCCAACATTTGCTT
505735 CTTATTGATG
Statistics
Matches: 111, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
72 1 0.01
73 2 0.02
74 2 0.02
75 103 0.93
76 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.15, T:0.33
Consensus pattern (76 bp):
TATTCCAATTTCTGATTGAAATGGGCTTTCAGCATACCCCAACATTTGCTTGACGAGAACATTCA
AAATGCGCCAA
Found at i:508373 original size:32 final size:32
Alignment explanation
Indices: 508335--508397 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
508325 GAAGAAATTA
*
508335 TTGTTATGCTTATCTAGTAGAGATACTTCTTG
1 TTGTTATGCTCATCTAGTAGAGATACTTCTTG
*
508367 TTGTTATGCTCATCTTGTAGAGATACTTCTT
1 TTGTTATGCTCATCTAGTAGAGATACTTCTT
508398 ATTTCCAGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (32 bp):
TTGTTATGCTCATCTAGTAGAGATACTTCTTG
Found at i:508868 original size:13 final size:13
Alignment explanation
Indices: 508852--508890 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 13
508842 TTTGATTCAA
508852 TTTTTTTCTTCCT
1 TTTTTTTCTTCCT
508865 TTTTTTTCTTTTTCCT
1 TTTTTTTC---TTCCT
508881 TTTTTTTCTT
1 TTTTTTTCTT
508891 TTTTCTCTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 10 0.43
16 13 0.57
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTTCTTCCT
Found at i:508879 original size:16 final size:16
Alignment explanation
Indices: 508860--508893 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
508850 AATTTTTTTC
508860 TTCCTTTTTTTTCTTT
1 TTCCTTTTTTTTCTTT
508876 TTCCTTTTTTTTCTTT
1 TTCCTTTTTTTTCTTT
508892 TT
1 TT
508894 TCTCTTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTCCTTTTTTTTCTTT
Found at i:514603 original size:26 final size:26
Alignment explanation
Indices: 514574--514628 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
514564 AAAAAAAAAT
514574 ATTGAAATTAAAACTTAAAAAGTCAA
1 ATTGAAATTAAAACTTAAAAAGTCAA
514600 ATTGAAATTAAAACTTAAAAAGTCAA
1 ATTGAAATTAAAACTTAAAAAGTCAA
514626 ATT
1 ATT
514629 CCTTCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.29
Consensus pattern (26 bp):
ATTGAAATTAAAACTTAAAAAGTCAA
Done.