Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 62
Found at i:3734409 original size:41 final size:40
Alignment explanation
Indices: 3734335--3734444 Score: 114
Period size: 41 Copynumber: 2.7 Consensus size: 40
3734325 AATTTCTTTT
* *
3734335 TCGCAACACAAGTTTCCTTTTCGCAACAAGATTTTCTAAA
1 TCGCAACACAATTTTCCTTTTCGCAACAAGATTTTCGAAA
** ** *
3734375 TCGCAACACAAATTTTGTTTTTCGCAACTCGATTTTCGAAT
1 TCGCAACAC-AATTTTCCTTTTCGCAACAAGATTTTCGAAA
**
3734416 TCGCAACACGAATTTT-AATTTCGCAACAA
1 TCGCAACAC-AATTTTCCTTTTCGCAACAA
3734445 CTTTTATTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
40 18 0.32
41 39 0.68
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.34
Consensus pattern (40 bp):
TCGCAACACAATTTTCCTTTTCGCAACAAGATTTTCGAAA
Found at i:3734438 original size:20 final size:20
Alignment explanation
Indices: 3734314--3734462 Score: 78
Period size: 20 Copynumber: 7.5 Consensus size: 20
3734304 GATTTCTGAA
*
3734314 TTCGCAACGCGAATTTCT-TT
1 TTCGCAACACGAATTT-TATT
**
3734334 TTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGAA-TTTTATT
* * *
3734354 TTCGCAACAAG-ATTTTCTAA
1 TTCGCAACACGAATTTTAT-T
* * *
3734374 ATCGCAACACAAATTTTGTTT
1 TTCGCAACACGAATTTT-ATT
* *
3734395 TTCGCAACTCG-ATTTTCGA-A
1 TTCGCAACACGAATTTT--ATT
*
3734415 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTATT
*
3734435 TTCGCAACA--ACTTTTATT
1 TTCGCAACACGAATTTTATT
3734453 TTCGCAACAC
1 TTCGCAACAC
3734463 AAATGTTTTG
Statistics
Matches: 100, Mismatches: 19, Indels: 21
0.71 0.14 0.15
Matches are distributed among these distances:
18 16 0.16
19 8 0.08
20 56 0.56
21 19 0.19
22 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.11, T:0.36
Consensus pattern (20 bp):
TTCGCAACACGAATTTTATT
Found at i:3734628 original size:16 final size:15
Alignment explanation
Indices: 3734600--3734638 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
3734590 TCCCCATCTC
3734600 TAATTTTTTTTTACA
1 TAATTTTTTTTTACA
*
3734615 TAATTTTATTTTTATA
1 TAATTTT-TTTTTACA
3734631 TAATTTTT
1 TAATTTTT
3734639 CAGTGATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TAATTTTTTTTTACA
Found at i:3735229 original size:22 final size:22
Alignment explanation
Indices: 3735201--3735250 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
3735191 CCACAATTTA
3735201 ACCACAAAGAAAATTTTGTTTC
1 ACCACAAAGAAAATTTTGTTTC
3735223 ACCACAAAGAAAATTTTGTTTC
1 ACCACAAAGAAAATTTTGTTTC
3735245 ACCACA
1 ACCACA
3735251 TTTCTAATAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (22 bp):
ACCACAAAGAAAATTTTGTTTC
Found at i:3735460 original size:24 final size:24
Alignment explanation
Indices: 3735400--3735467 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
3735390 GTGAGTACTA
* *
3735400 GTCAATATTCAAAATTTGATCTTG
1 GTCAATACTCAGAATTTGATCTTG
* *
3735424 GTCAATACCCAGACTTTGATCTTG
1 GTCAATACTCAGAATTTGATCTTG
*
3735448 GTCAATACTCAGATTTTGAT
1 GTCAATACTCAGAATTTGAT
3735468 GATGTTTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (24 bp):
GTCAATACTCAGAATTTGATCTTG
Found at i:3740322 original size:20 final size:21
Alignment explanation
Indices: 3740279--3740378 Score: 91
Period size: 21 Copynumber: 4.8 Consensus size: 21
3740269 CATGTGAATC
* *
3740279 GGGCTCTTGAACGGT-AGGAC
1 GGGCTCTTGAACGATGAGGAG
3740299 GGGCTCTTGAACGATGA-GAG
1 GGGCTCTTGAACGATGAGGAG
*
3740319 GGGCCTCTTGAACGATG-GGAT
1 GGG-CTCTTGAACGATGAGGAG
* *
3740340 GGGCTTCTTTAATGAT-AGGAG
1 GGGC-TCTTGAACGATGAGGAG
*
3740361 GGGTATCTTGAACGATGA
1 GGG-CTCTTGAACGATGA
3740379 CAAGTGAATC
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
20 20 0.31
21 43 0.67
22 1 0.02
ACGTcount: A:0.23, C:0.15, G:0.37, T:0.25
Consensus pattern (21 bp):
GGGCTCTTGAACGATGAGGAG
Found at i:3740344 original size:41 final size:42
Alignment explanation
Indices: 3740282--3740377 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
3740272 GTGAATCGGG
* *
3740282 CTCTTGAACGGTAGGACGGGC-TCTTGAACGAT-GAGAGGGGC
1 CTCTTGAACGATGGGACGGGCTTCTTGAACGATAG-GAGGGGC
* * * *
3740323 CTCTTGAACGATGGGATGGGCTTCTTTAATGATAGGAGGGGT
1 CTCTTGAACGATGGGACGGGCTTCTTGAACGATAGGAGGGGC
*
3740365 ATCTTGAACGATG
1 CTCTTGAACGATG
3740378 ACAAGTGAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
41 18 0.39
42 27 0.59
43 1 0.02
ACGTcount: A:0.23, C:0.16, G:0.35, T:0.26
Consensus pattern (42 bp):
CTCTTGAACGATGGGACGGGCTTCTTGAACGATAGGAGGGGC
Found at i:3740805 original size:21 final size:21
Alignment explanation
Indices: 3740781--3740830 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
3740771 ACCATTGTCG
*
3740781 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
3740802 TCACGCAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
3740823 TCACGTAA
1 TCACGTAA
3740831 CTCCCCTAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:3741035 original size:42 final size:42
Alignment explanation
Indices: 3740948--3741043 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
3740938 AGTGAATAGC
* * * * *
3740948 TGATGGCTCTCGGTGTGGAGGTGTATAATTGGCCCGATTAAG
1 TGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCCCGATCAAG
* *
3740990 TGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCTCGATCAGG
1 TGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCCCGATCAAG
*
3741032 TGATGGATCTCG
1 TGATGGCTCTCG
3741044 AAGTGGGGGG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.29
Consensus pattern (42 bp):
TGATGGCTCTCGGTGTCGAGCTGTAGAATCGGCCCGATCAAG
Found at i:3742599 original size:19 final size:20
Alignment explanation
Indices: 3742539--3742601 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
3742529 AAACTTAAAT
*
3742539 TCGCAACACGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
3742559 TCGCAACGCGAAAATGAAAA
1 TCGCAACGCGAAAATGAAAA
* *
3742579 TCGCAATGCGAAACT-AAAA
1 TCGCAACGCGAAAATGAAAA
3742598 TCGC
1 TCGC
3742602 GTTGCGATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 8 0.20
20 32 0.80
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAATGAAAA
Found at i:3743026 original size:22 final size:22
Alignment explanation
Indices: 3742957--3743029 Score: 119
Period size: 22 Copynumber: 3.3 Consensus size: 22
3742947 GATAGAGGGG
* *
3742957 GTCGCCGGATATGGGGATGGAT
1 GTCGCCGGAGATGGGGACGGAT
*
3742979 GTCACCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
3743001 GTCGCCGGAGATGGGGACGGAT
1 GTCGCCGGAGATGGGGACGGAT
3743023 GTCGCCG
1 GTCGCCG
3743030 TAGAGAGTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.18, C:0.19, G:0.47, T:0.16
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACGGAT
Found at i:3743708 original size:24 final size:23
Alignment explanation
Indices: 3743681--3743737 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
3743671 TAAACGAGCG
*
3743681 TAAACAAACACAAACGAACAAAAA
1 TAAACGAACACAAACGAAC-AAAA
* * *
3743705 TAAATGAACATAAACGAACACAA
1 TAAACGAACACAAACGAACAAAA
3743728 TAAACGAACA
1 TAAACGAACA
3743738 ACACAAACAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 12 0.43
24 16 0.57
ACGTcount: A:0.65, C:0.19, G:0.07, T:0.09
Consensus pattern (23 bp):
TAAACGAACACAAACGAACAAAA
Found at i:3744023 original size:14 final size:14
Alignment explanation
Indices: 3744004--3744055 Score: 58
Period size: 14 Copynumber: 4.0 Consensus size: 14
3743994 CCTCTGTTCG
3744004 AACATAAATGAACA
1 AACATAAATGAACA
3744018 AACATAAAT----A
1 AACATAAATGAACA
*
3744028 AACATAAATGAACG
1 AACATAAATGAACA
*
3744042 AACATAAGTGAACA
1 AACATAAATGAACA
3744056 TATAATCGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 10 0.32
14 21 0.68
ACGTcount: A:0.62, C:0.13, G:0.10, T:0.15
Consensus pattern (14 bp):
AACATAAATGAACA
Found at i:3744031 original size:24 final size:24
Alignment explanation
Indices: 3744004--3744066 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
3743994 CCTCTGTTCG
3744004 AACATAAATGAACAAACATAAATA
1 AACATAAATGAACAAACATAAATA
* * *
3744028 AACATAAATGAACGAACATAAGTG
1 AACATAAATGAACAAACATAAATA
3744052 AACATATAATCGAAC
1 AACATA-AAT-GAAC
3744067 GTTCACAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 27 0.79
25 3 0.09
26 4 0.12
ACGTcount: A:0.59, C:0.14, G:0.10, T:0.17
Consensus pattern (24 bp):
AACATAAATGAACAAACATAAATA
Found at i:3745062 original size:182 final size:182
Alignment explanation
Indices: 3744719--3745378 Score: 1022
Period size: 182 Copynumber: 3.6 Consensus size: 182
3744709 GATCCAAATA
* * * *
3744719 AAAAATGTATCGATCCATATCAATATAACAGGTAAAAATATGACAAAACTGGT-T-TAATTATGA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAA--ATGA
* * * * * * *
3744782 CAAAACCGGTAAAGTGCTACCGGATATGTTGAAAGTATCGATTAGATTGAA-ATAAATATTGACA
64 CAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGA-TA-CTTTAATATAAGTATCGACA
3744846 CTTTGGGAATTTAAAAGAGAAGCAGTAA-AGCGCCTATAAAGTGTCGATACTTTAT
127 CTTTGGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* *
3744901 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAAAGACA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
3744966 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
3745031 GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
131 GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * *
3745083 AAAAATATATCGATCCATAACGATATAACATGTAAAAATATGATAAAACCGGTCTCGAAATGACA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* * *
3745148 AAACCGGTAAAGCACTACCGGATATATTGAAAGTTTCAATACTTTAATATAAGTATCGACACTTT
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
*
3745213 GAGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
131 GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
* * * *
3745265 AAAAATGTATCGATCCATAACGATATAACAGGTAAACATATGACAAAACCGATCTCGAAATGACA
1 AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
* *
3745330 AAACCGGTAAAGTGCTACTGGATATATTGAAAGTGTCGATACTTTAATA
66 AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
3745379 AGTACGCGTA
Statistics
Matches: 442, Mismatches: 32, Indels: 8
0.92 0.07 0.02
Matches are distributed among these distances:
180 4 0.01
181 41 0.09
182 394 0.89
183 1 0.00
184 2 0.00
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACA
AAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTTT
GGGAATTTAAAAGAGAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTAT
Found at i:3747876 original size:33 final size:33
Alignment explanation
Indices: 3747839--3747905 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
3747829 AAAAAGATGG
3747839 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
3747872 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
3747905 A
1 A
3747906 CTTAAGATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
Found at i:3748110 original size:18 final size:18
Alignment explanation
Indices: 3748089--3748127 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3748079 GAATAAATAT
*
3748089 GAAGAAGAAAATATGGAG
1 GAAGAAGAAAAGATGGAG
3748107 GAAGAAGAAAAGATGGAG
1 GAAGAAGAAAAGATGGAG
3748125 GAA
1 GAA
3748128 ATGAGGAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (18 bp):
GAAGAAGAAAAGATGGAG
Found at i:3749703 original size:19 final size:19
Alignment explanation
Indices: 3749679--3749727 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3749669 AATGTAGGGT
3749679 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
3749698 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
3749717 TAATTTTGTAT
1 TAATTTTGTAT
3749728 GTGAATGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:3750678 original size:14 final size:14
Alignment explanation
Indices: 3750654--3750689 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3750644 TTTCAATGTA
*
3750654 ACCGATATAAATAT
1 ACCGGTATAAATAT
*
3750668 ATCGGTATAAATAT
1 ACCGGTATAAATAT
3750682 ACCGGTAT
1 ACCGGTAT
3750690 TATGAGAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (14 bp):
ACCGGTATAAATAT
Found at i:3751181 original size:200 final size:201
Alignment explanation
Indices: 3750183--3751351 Score: 1548
Period size: 201 Copynumber: 5.8 Consensus size: 201
3750173 TATGTGTCTC
* ** *
3750183 TACAGTTATAAAAAGTATTGAT-CCAAAAACATCGAAACTCATAATTATAATGTAATAGGTAATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * *
3750247 TTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACA
66 TTTCAATGTAAACAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
* * * **
3750312 CTTGTGAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCCAAAATGGGTGCACGCATAAAG
131 CTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAG
3750376 TGTCGA
196 TGTCGA
* *
3750382 TACATTTATAAAAAAGTATCTATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAGGTAAT
1 TACATTTAT-AAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAT
* * *
3750447 TTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAG-A-A--T-TACATAATGTATCGAC
65 TTTTCAATGTAAACAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGAC
* * ** * * * * *
3750507 AGTTGTGGAATTTGTGTCGATATTTTTTGTCCAGAATAAATACCCAAA--AGGGATGCACACATA
130 ACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTA-AG-TGCACGCATA
*
3750570 AAGTGTAGA
193 AAGTGTCGA
**
3750579 TACATTTATAAAAAGTATCAATCTTAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * *
3750644 TTTCAATGTAACCGATATAAATATATCGGTATAAATATACCGGTATTATGAGAGAATAGGTCTAC
66 TTTCAA--T----G---T--A-A-A-CAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTAC
* * ** *
3750709 ATAATGTAGCGACACTTGTGGAATTTGTGTCGATACTTTTTTTCCAGAATGAATGCCCAAACTAA
117 ATAATGTATCGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAA
3750774 GTGCACGCATAAAGTGTCGA
182 GTGCACGCATAAAGTGTCGA
* ** * *
3750794 TACATTTACAAAAAGTATTGATCCCAAAAACATTGAAAGCCATAATTATAATGTAATAGGTAATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * *
3750859 TTTTAATGTAATCAGTATAAATATACCGGTTTTAAGAGAGAATTGGTCTACATAATGTATCGACA
66 TTTCAATGTAAACAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
* * ** *
3750924 CTTTTTATATTTGTTTCGATACTCCTTGTCCAGAATGAATGCCCAAACTAGGTGCACGCATAAAG
131 CTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAG
*
3750989 TGTTGA
196 TGTCGA
* *
3750995 TACATTTATAAAATGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATATGT-ATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * * *
3751059 TTTCAATTTAAACAATATAAATATACCGGTTTTAAGAGAGAATATGTGTACATAATGTATCGACA
66 TTTCAATGTAAACAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
* *
3751124 TTTTTTAAATTTGTGTCGATACTTTTTGTCCTGAATGAATGCCCAAACTAAGTGCACGCATAAAG
131 CTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAG
3751189 TGTCGA
196 TGTCGA
*
3751195 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTCATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * *
3751260 TTTCAATGTAACCGGTATAAATATATCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
66 TTTCAATGTAAACAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
3751325 CTTTTTAAATTTGTGTCGATACTTTTT
131 CTTTTTAAATTTGTGTCGATACTTTTT
3751352 AAATTTTGCG
Statistics
Matches: 859, Mismatches: 84, Indels: 52
0.86 0.08 0.05
Matches are distributed among these distances:
196 101 0.12
197 44 0.05
198 1 0.00
199 9 0.01
200 195 0.23
201 330 0.38
202 1 0.00
203 1 0.00
204 1 0.00
205 1 0.00
206 1 0.00
207 1 0.00
208 1 0.00
209 1 0.00
210 27 0.03
211 1 0.00
212 1 0.00
213 1 0.00
214 1 0.00
215 138 0.16
216 1 0.00
217 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (201 bp):
TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
TTTCAATGTAAACAGTATAAATATACCGGTTTTAAGAGAGAATAGGTCTACATAATGTATCGACA
CTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAG
TGTCGA
Found at i:3751184 original size:401 final size:398
Alignment explanation
Indices: 3750183--3751347 Score: 1590
Period size: 401 Copynumber: 2.9 Consensus size: 398
3750173 TATGTGTCTC
* ** *
3750183 TACAGTTATAAAAAGTATTGAT-CCAAAAACATCGAAACTCATAATTATAATGTAATAGGTAATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * **
3750247 TTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACA
66 TTTCAATTTAAACAATATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACA
* **
3750312 CTTGTGAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAAAATGGGTGCACGCATAAAGT
131 CTTGTGAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAGT
*
3750377 GTCGATACATTTATAAAAAAGTATCTATCCCAAAAAAATCGAAACCCATAATTATAATGTAATAG
196 GTCGATACATTTA-AAAAAAGTAT-TATCCCAAAAACATCGAAACCCATAATTATAATGTAATAG
*
3750442 GTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTATGAGAGAA---T-TACATAATGTAT
259 GTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAATGGTCTACATAATGTAT
* ** * **
3750503 CGACAGTTGTGGAATTTGTGTCGATATTTTTTGTCCAGAATAAATACCCAAAAGGGATGCACACA
324 CGACACTT-TTTAATTTGTGTCGATACTCCTTGTCCAGAATAAATACCCAAAAGGGATGCACACA
3750568 TAAAGTGTAGA
388 TAAAGTGTAGA
**
3750579 TACATTTATAAAAAGTATCAATCTTAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* *
3750644 TTTCAATGTAACCGATATAAATATATCGGTATAAATATACCGGTATTATGAGAGAATAGGTCTAC
66 TTTCAA--T------T-TAAACA-A----TATAAATATACCGGTTTTATGAGAGAATAGGTCTAC
* *
3750709 ATAATGTAGCGACACTTGTGGAATTTGTGTCGATACTTTTTTTCCAGAATGAATGCCCAAACTAA
117 ATAATGTATCGACACTTGTGAAATTTGTGTCGATAC-TTTTTTCCAGAATGAATGCCCAAACTAA
* * *
3750774 GTGCACGCATAAAGTGTCGATACATTTACAAAAAGTATTGATCCCAAAAACATTGAAAGCCATAA
181 GTGCACGCATAAAGTGTCGATACATTTAAAAAAAGTATT-ATCCCAAAAACATCGAAACCCATAA
* * *
3750839 TTATAATGTAATAGGTAATTTTTTAATGTAATCAGTATAAATATACCGGTTTTAAGAGAGAATTG
245 TTATAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAA-TG
* * *
3750904 GTCTACATAATGTATCGACACTTTTTATATTTGTTTCGATACTCCTTGTCCAGAATGAATGCCCA
309 GTCTACATAATGTATCGACACTTTTTA-ATTTGTGTCGATACTCCTTGTCCAGAATAAATACCCA
* *
3750969 AACTA-GG-TGCACGCATAAAGTGTTGA
373 AA--AGGGATGCACACATAAAGTGTAGA
* *
3750995 TACATTTATAAAATGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATATGT-ATT
1 TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
* * *
3751059 TTTCAATTTAAACAATATAAATATACCGGTTTTAAGAGAGAATATGTGTACATAATGTATCGACA
66 TTTCAATTTAAACAATATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACA
* * * *
3751124 TTTTTTAAATTTGTGTCGATACTTTTTGTCCTGAATGAATGCCCAAACTAAGTGCACGCATAAAG
131 CTTGTGAAATTTGTGTCGATACTTTTT-TCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAG
* *
3751189 TGTCGATACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAG
195 TGTCGATACATTTAAAAAAAGTAT-TATCCCAAAAACATCGAAACCCATAATTATAATGTAATAG
* *
3751254 GTCATTTTTCAATGTAACCGGTATAAATATATCGGTTTTAAGAGAGAATAGGTCTACATAATGTA
259 GTAATTTTTCAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAAT-GGTCTACATAATGTA
3751319 TCGACACTTTTTAAATTTGTGTCGATACT
323 TCGACACTTTTT-AATTTGTGTCGATACT
3751348 TTTTAAATTT
Statistics
Matches: 679, Mismatches: 61, Indels: 53
0.86 0.08 0.07
Matches are distributed among these distances:
396 19 0.03
397 45 0.07
399 1 0.00
400 6 0.01
401 243 0.36
402 1 0.00
405 1 0.00
406 8 0.01
407 1 0.00
410 1 0.00
411 158 0.23
412 53 0.08
413 1 0.00
415 12 0.02
416 126 0.19
417 2 0.00
418 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (398 bp):
TACATTTATAAAAAGTATCAATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATT
TTTCAATTTAAACAATATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATGTATCGACA
CTTGTGAAATTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAAACTAAGTGCACGCATAAAGT
GTCGATACATTTAAAAAAAGTATTATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGT
AATTTTTCAATGTAACCGGTATAAATATACCGGTTTTAAGAGAGAATGGTCTACATAATGTATCG
ACACTTTTTAATTTGTGTCGATACTCCTTGTCCAGAATAAATACCCAAAAGGGATGCACACATAA
AGTGTAGA
Found at i:3751630 original size:22 final size:22
Alignment explanation
Indices: 3751561--3751630 Score: 95
Period size: 22 Copynumber: 3.1 Consensus size: 22
3751551 ATTGGACTCT
*
3751561 TTTTTTCTCTTTAATTTGTTTGTG
1 TTTTTTC-C-TTAATGTGTTTGTG
*
3751585 TATTTTCCTTAATGTGTTTGTG
1 TTTTTTCCTTAATGTGTTTGTG
*
3751607 TTTTTTCGTTAATGTGTTTGTG
1 TTTTTTCCTTAATGTGTTTGTG
3751629 TT
1 TT
3751631 CCAATGTAAC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 35 0.83
23 1 0.02
24 6 0.14
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.66
Consensus pattern (22 bp):
TTTTTTCCTTAATGTGTTTGTG
Found at i:3753262 original size:24 final size:25
Alignment explanation
Indices: 3753235--3753289 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
3753225 TTTCAAGTTC
*
3753235 ATTTCATATGT-AATTGGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
* *
3753259 ATTT-AAATTTCAATTTGAGTTTGA
1 ATTTCAAATGTCAATTGGAGTTTGA
3753283 ATTTCAA
1 ATTTCAA
3753290 TATAAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 4 0.15
24 20 0.77
25 2 0.08
ACGTcount: A:0.33, C:0.05, G:0.15, T:0.47
Consensus pattern (25 bp):
ATTTCAAATGTCAATTGGAGTTTGA
Found at i:3753275 original size:18 final size:18
Alignment explanation
Indices: 3753254--3753290 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
3753244 GTAATTGGAG
3753254 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
3753272 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
3753290 T
1 T
3753291 ATAAATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:3753297 original size:24 final size:24
Alignment explanation
Indices: 3753246--3753298 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
3753236 TTTCATATGT
* * *
3753246 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
*
3753270 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
3753294 AATTT
1 AATTT
3753299 CGGCTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:3755075 original size:199 final size:199
Alignment explanation
Indices: 3754616--3755427 Score: 897
Period size: 199 Copynumber: 4.0 Consensus size: 199
3754606 TCAGTAATCT
* * *
3754616 CCAGAATGAATGCCCAACCGAGGTACACGAATAAATTGTCGATACATTTATTAAAA-GTATCGAT
1 CCAGAAAGAATGCCCAA-CGAGGTGCACGAATAAAGTGTCGATACATTTA-TAAAATGTATCGAT
* * * *
3754680 CCAAAAAATATCGAATA-AGATAATTATAATGTAATAGGTAATTTTTCAATGTAACTGGTATAAA
64 CCCAAAAACATCGAA-ACAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTAGAAA
* * * **
3754744 TATACCGGTTTTATTTGAGAATAGGTCTACATAATGTATTAACACTTTTTAAATTTGTGTCGATA
128 TATACCGG-TTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATA
3754809 CGTTTTGA
192 CGTTTTGA
* * * *
3754817 CCAGAAAGAATGCCCAATGGGGTGTACGAATAAAGTGTCGATACATTTA-AAATTGTATCGATCC
1 CCAGAAAGAATGCCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATGTATCGATCC
* * *
3754881 CAAAAACATCGAAACCGATAATTATAATGTAATAGGTAACTTTACAATGTAACCGGTAGAAATAT
66 CAAAAACATCGAAACAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTAGAAATAT
*
3754946 ACCGATTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTT
131 ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTT
3755011 TTGA
196 TTGA
* * * *
3755015 TCATAATGAATGCCCAACGAGGTGCATGAATAAAGTGTCGATACATTTATAAAATGTATCGATCC
1 CCAGAAAGAATGCCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATGTATCGATCC
* * *
3755080 CAAAAACATC-AAATAAGATAATTGTAATGTAATAGGTAATTTTTCAATGTAACCGGTATAAATA
66 CAAAAACATCGAAA-CAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTAGAAATA
* * *
3755144 TACTGGTT--TTATG----TGAGGTCTATATAATGTATCGACACTTTTTAAATTTGTGTTGATAC
130 TACCGGTTAATTA-GAAAAT-AGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATAC
3755203 GTTTTGA
193 GTTTTGA
* * * *
3755210 CCAGAAAGAATGCCCAACGGGGTGTACGAATAAAGTGTTGATACATTTATAAAAAGTATCGATAC
1 CCAGAAAGAATGCCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATGTATCG----
* * * * *
3755275 ATTTATAAAAACTATCGATCACATAAACATCGAAACCGATAAATATCATGTAATAGGTAAATTTC
62 ----AT-----C---C---CA-A-AAACATCGAAACAGATAATTATAATGTAATAGGTAATTTTT
* * * *
3755340 CAATGTAACCGGTAGAAATATATCGGTTAATTAGAAAATAGGTCTACATAATTTATCGATACGTT
110 CAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTT
* *
3755405 TTAAAGTTGTGTCGATACTTTTT
175 TTAAATTTGTGTCGATACGTTTT
3755428 TAAATTACGC
Statistics
Matches: 514, Mismatches: 63, Indels: 49
0.82 0.10 0.08
Matches are distributed among these distances:
194 1 0.00
195 102 0.20
197 3 0.01
198 109 0.21
199 144 0.28
200 27 0.05
201 16 0.03
203 2 0.00
208 1 0.00
211 1 0.00
214 2 0.00
215 1 0.00
216 55 0.11
217 4 0.01
218 3 0.01
220 42 0.08
221 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (199 bp):
CCAGAAAGAATGCCCAACGAGGTGCACGAATAAAGTGTCGATACATTTATAAAATGTATCGATCC
CAAAAACATCGAAACAGATAATTATAATGTAATAGGTAATTTTTCAATGTAACCGGTAGAAATAT
ACCGGTTAATTAGAAAATAGGTCTACATAATGTATCGACACTTTTTAAATTTGTGTCGATACGTT
TTGA
Found at i:3755298 original size:22 final size:21
Alignment explanation
Indices: 3755249--3755298 Score: 82
Period size: 21 Copynumber: 2.3 Consensus size: 21
3755239 ATAAAGTGTT
*
3755249 GATACATTTATAAAAAGTATC
1 GATACATTTATAAAAACTATC
3755270 GATACATTTATAAAAACTATC
1 GATACATTTATAAAAACTATC
3755291 GATCACAT
1 GAT-ACAT
3755299 AAACATCGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (21 bp):
GATACATTTATAAAAACTATC
Found at i:3758269 original size:198 final size:199
Alignment explanation
Indices: 3757805--3758305 Score: 544
Period size: 200 Copynumber: 2.5 Consensus size: 199
3757795 GGTAAAAAAT
* * * * *
3757805 GTGTCGATACATTTTCTAAAAGTATCGACCCCAACAACATCGAAACCAATAATTATAATGTAATA
1 GTGTCGATACA-TTTATAGAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * *
3757870 GGTAAATTAACAATGTAATCGGTATAAATATACTGGTTAATTACAAAACAGGTAAACATATTGTA
65 GGTAAATTTACAATGTAATCGGTATAAATATACCGGTTAATGACAAAACAGGTAAACATATTGTA
* * * * * *
3757935 TCGACACTTGTGGAATTTGTGTTGACGCTTATTATACAGAATGAATGCCCAAACGAGATGCACAC
130 TCGACACTTGTGAAATATATGTCGACACTTATTATACAGAATGAATGCCCAAACGAGATACACAC
3758000 ATAAA
195 ATAAA
*
3758005 GTGTCGATACATTTATTAGAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATATAATA
1 GTGTCGATACATTTA-TAGAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATA
* * * * * * *
3758070 GGTAAATTTACAATGTGATCGATATAAATATACCGGTTCTATGAGAGAATAGGTCAACAT-TATG
65 GGTAAATTTACAATGTAATCGGTATAAATATACCGGTT-AATGACAAAACAGGTAAACATAT-TG
* * * * * ** * *
3758134 TATCGACACTTTTTAAATATATGTCGATACTT-TTTTCCATCATGAATTCCC-AACGAGGTACAC
128 TATCGACACTTGTGAAATATATGTCGACACTTATTATACAGAATGAATGCCCAAACGAGATACAC
3758197 ACATAAA
193 ACATAAA
* * * * *
3758204 GTTTTGATACATTTA-A-AATTGTATCGATCCCTAAAATATCGAAACTGATAATTATAATGTAAT
1 GTGTCGATACATTTATAGAA--GTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAAT
** * * *
3758267 AGGTAAATTTGTAATGTTACCGGTATAAATAAACCGGTT
64 AGGTAAATTTACAATGTAATCGGTATAAATATACCGGTT
3758306 TAGTTGAAAA
Statistics
Matches: 253, Mismatches: 43, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
196 2 0.01
197 1 0.00
198 72 0.28
199 33 0.13
200 104 0.41
201 41 0.16
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATAGAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAG
GTAAATTTACAATGTAATCGGTATAAATATACCGGTTAATGACAAAACAGGTAAACATATTGTAT
CGACACTTGTGAAATATATGTCGACACTTATTATACAGAATGAATGCCCAAACGAGATACACACA
TAAA
Found at i:3758353 original size:23 final size:23
Alignment explanation
Indices: 3758324--3758371 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
3758314 AAACATGTCA
*
3758324 ATATAAACGCTACCTATTATATT
1 ATATAAACGCTACCTAATATATT
* * *
3758347 ATATAAATGTTACCTAATATGTT
1 ATATAAACGCTACCTAATATATT
3758370 AT
1 AT
3758372 TGTACTTAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (23 bp):
ATATAAACGCTACCTAATATATT
Found at i:3758458 original size:23 final size:23
Alignment explanation
Indices: 3758408--3758452 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3758398 TTCCTATTTT
*
3758408 ATTATATAAACGATACCTATTAC
1 ATTATATAAACGATACCTAATAC
* *
3758431 ATTATATAAGCGTTACCTAATA
1 ATTATATAAACGATACCTAATA
3758453 TGTTATTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGATACCTAATAC
Found at i:3760615 original size:21 final size:22
Alignment explanation
Indices: 3760576--3760629 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3760566 CCCCCTATAT
* * **
3760576 ATATTTTTTTTCGATTAAATCA
1 ATATTTTTATTCGAATAAAAAA
*
3760598 CTATTTTTATT-GAATAAAAAA
1 ATATTTTTATTCGAATAAAAAA
3760619 ATATTTTTATT
1 ATATTTTTATT
3760630 ATTTTGGGTC
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (22 bp):
ATATTTTTATTCGAATAAAAAA
Found at i:3761075 original size:86 final size:86
Alignment explanation
Indices: 3760930--3761094 Score: 276
Period size: 86 Copynumber: 1.9 Consensus size: 86
3760920 GGTTACTATC
3760930 TGCCTCTACAGAAGAGGTGTACATATGTAGTGCCTGGAGGTCATATAGATCGAACCTGGAGCAAT
1 TGCCTCTACAGAAGAGGTGTACATATGTAGTGCCTGGAGGTCATATAGATCGAACCTGGAGCAAT
*
3760995 ATGAATTAAAGTCCTACTGCA
66 ATGAATGAAAGTCCTACTGCA
** * **
3761016 TGCCTCTACAGATTAGGTGTATATATGTAGTGCCTGGAGGTCATATAGATCGAACCTGGAGCTGT
1 TGCCTCTACAGAAGAGGTGTACATATGTAGTGCCTGGAGGTCATATAGATCGAACCTGGAGCAAT
3761081 ATGAATGAAAGTCC
66 ATGAATGAAAGTCC
3761095 GACCCACAGC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 73 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.27
Consensus pattern (86 bp):
TGCCTCTACAGAAGAGGTGTACATATGTAGTGCCTGGAGGTCATATAGATCGAACCTGGAGCAAT
ATGAATGAAAGTCCTACTGCA
Found at i:3764571 original size:35 final size:35
Alignment explanation
Indices: 3764526--3764594 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
3764516 CCTAAAAACA
* *
3764526 AAAATACTTCAATTATATTCAAAACCTCAAATTCC
1 AAAATACTTCAATTACATGCAAAACCTCAAATTCC
**
3764561 AAAATACTTCAATTACATGCCCAACCTCAAATTC
1 AAAATACTTCAATTACATGCAAAACCTCAAATTC
3764595 ATAATCCATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.43, C:0.26, G:0.01, T:0.29
Consensus pattern (35 bp):
AAAATACTTCAATTACATGCAAAACCTCAAATTCC
Found at i:3765115 original size:31 final size:31
Alignment explanation
Indices: 3765078--3765144 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
3765068 TGTAATACAA
3765078 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
* * *
3765109 TCCCCCAATATTTAGTCTGTTTGTAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
3765140 TCCCC
1 TCCCC
3765145 GAAATAACAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.21, C:0.28, G:0.15, T:0.36
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:3768803 original size:15 final size:15
Alignment explanation
Indices: 3768793--3768854 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 15
3768783 GATTTTTAGT
*
3768793 TTTAGTTTTTTTATA
1 TTTAATTTTTTTATA
*
3768808 TTTAATTTTTTGAATA
1 TTTAATTTTTT-TATA
**
3768824 TTTAAATAATTTTATA
1 TTT-AATTTTTTTATA
3768840 TTCATAATTTTTTTA
1 TT--TAATTTTTTTA
3768855 CAAATTAAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
15 10 0.28
16 11 0.31
17 14 0.39
18 1 0.03
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (15 bp):
TTTAATTTTTTTATA
Found at i:3768863 original size:34 final size:32
Alignment explanation
Indices: 3768801--3768866 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 32
3768791 GTTTTAGTTT
*
3768801 TTTTATATTTAATTTTTTGAATATTTAAATAA
1 TTTTATATTTAATTTTTTGAATAATTAAATAA
*
3768833 TTTTATATTCATAATTTTTTTACA-AATTAAATAA
1 TTTTATATT--TAATTTTTTGA-ATAATTAAATAA
3768867 GTCCTTGAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 9 0.31
34 19 0.66
35 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (32 bp):
TTTTATATTTAATTTTTTGAATAATTAAATAA
Found at i:3771316 original size:37 final size:37
Alignment explanation
Indices: 3771271--3771345 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 37
3771261 GTTAGAAAAT
*
3771271 ATTTATAT-ATTTTCTTTAAAAAATTTAAATTAATAAA
1 ATTTATATAATTTTCTTTAAAAAATTTAAAAT-ATAAA
* *
3771308 ATTTATATAATTTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTTTCTTTAAAAAATTTAAAATATAAA
3771345 A
1 A
3771346 AAGTTTAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 14 0.41
38 20 0.59
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATAATTTTCTTTAAAAAATTTAAAATATAAA
Found at i:3774427 original size:351 final size:351
Alignment explanation
Indices: 3773784--3774485 Score: 1404
Period size: 351 Copynumber: 2.0 Consensus size: 351
3773774 TGAAATAATC
3773784 GACTACCATGACTTAAGAAACAAACCACACGCTGTCAAGCAAATTGTCATAATCGTATTTGTGCA
1 GACTACCATGACTTAAGAAACAAACCACACGCTGTCAAGCAAATTGTCATAATCGTATTTGTGCA
3773849 CACATATAATGCATATGCATGATATCATCTCCCCTTCTCTGAGAATGCATGTATAAGATTTCATC
66 CACATATAATGCATATGCATGATATCATCTCCCCTTCTCTGAGAATGCATGTATAAGATTTCATC
3773914 ATTTATCATTGAGCAGAATCTACAAAGTACATGATGAAGCAAAGGACAAAGCCTTTGAACTGGAG
131 ATTTATCATTGAGCAGAATCTACAAAGTACATGATGAAGCAAAGGACAAAGCCTTTGAACTGGAG
3773979 ATGAGTTGGGTATGTGATGAGTCAAAGCAACAACATCAGAAGGTAATTCCCAGCACCCATTATGG
196 ATGAGTTGGGTATGTGATGAGTCAAAGCAACAACATCAGAAGGTAATTCCCAGCACCCATTATGG
3774044 ATATACATCACTTCACTTTCTCCCTTTTTGCCAGCTTGAAAAACTAACAGCAATTACATGCAGAT
261 ATATACATCACTTCACTTTCTCCCTTTTTGCCAGCTTGAAAAACTAACAGCAATTACATGCAGAT
3774109 GGCTTTATGAATTGAATTATGCTGTG
326 GGCTTTATGAATTGAATTATGCTGTG
3774135 GACTACCATGACTTAAGAAACAAACCACACGCTGTCAAGCAAATTGTCATAATCGTATTTGTGCA
1 GACTACCATGACTTAAGAAACAAACCACACGCTGTCAAGCAAATTGTCATAATCGTATTTGTGCA
3774200 CACATATAATGCATATGCATGATATCATCTCCCCTTCTCTGAGAATGCATGTATAAGATTTCATC
66 CACATATAATGCATATGCATGATATCATCTCCCCTTCTCTGAGAATGCATGTATAAGATTTCATC
3774265 ATTTATCATTGAGCAGAATCTACAAAGTACATGATGAAGCAAAGGACAAAGCCTTTGAACTGGAG
131 ATTTATCATTGAGCAGAATCTACAAAGTACATGATGAAGCAAAGGACAAAGCCTTTGAACTGGAG
3774330 ATGAGTTGGGTATGTGATGAGTCAAAGCAACAACATCAGAAGGTAATTCCCAGCACCCATTATGG
196 ATGAGTTGGGTATGTGATGAGTCAAAGCAACAACATCAGAAGGTAATTCCCAGCACCCATTATGG
3774395 ATATACATCACTTCACTTTCTCCCTTTTTGCCAGCTTGAAAAACTAACAGCAATTACATGCAGAT
261 ATATACATCACTTCACTTTCTCCCTTTTTGCCAGCTTGAAAAACTAACAGCAATTACATGCAGAT
3774460 GGCTTTATGAATTGAATTATGCTGTG
326 GGCTTTATGAATTGAATTATGCTGTG
3774486 TTTTATTTAG
Statistics
Matches: 351, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
351 351 1.00
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (351 bp):
GACTACCATGACTTAAGAAACAAACCACACGCTGTCAAGCAAATTGTCATAATCGTATTTGTGCA
CACATATAATGCATATGCATGATATCATCTCCCCTTCTCTGAGAATGCATGTATAAGATTTCATC
ATTTATCATTGAGCAGAATCTACAAAGTACATGATGAAGCAAAGGACAAAGCCTTTGAACTGGAG
ATGAGTTGGGTATGTGATGAGTCAAAGCAACAACATCAGAAGGTAATTCCCAGCACCCATTATGG
ATATACATCACTTCACTTTCTCCCTTTTTGCCAGCTTGAAAAACTAACAGCAATTACATGCAGAT
GGCTTTATGAATTGAATTATGCTGTG
Found at i:3782218 original size:48 final size:48
Alignment explanation
Indices: 3782147--3782240 Score: 127
Period size: 48 Copynumber: 2.0 Consensus size: 48
3782137 TTTTACACTG
** * *
3782147 GTCCTTATCCTTTTAATATTCTAATTTCATCCTTAAACTTTGACTCAA
1 GTCCTTAAACTTTTAATATTCTAATTTCATCCCTAAACTATGACTCAA
*
3782195 GTCCTTAAACTTTTGAA-ATTCTAATTTTATCCCTAAACTATGACTC
1 GTCCTTAAACTTTT-AATATTCTAATTTCATCCCTAAACTATGACTC
3782241 TCTTTCTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 38 0.95
49 2 0.05
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.44
Consensus pattern (48 bp):
GTCCTTAAACTTTTAATATTCTAATTTCATCCCTAAACTATGACTCAA
Found at i:3783928 original size:20 final size:20
Alignment explanation
Indices: 3783903--3783958 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
3783893 ATTTAATTCA
*
3783903 TGGTGCATCGATGCATGGAT
1 TGGTGCATCGGTGCATGGAT
3783923 TGGTGCATCGGTGCATGGAT
1 TGGTGCATCGGTGCATGGAT
3783943 TGGTGCATCGGTGCAT
1 TGGTGCATCGGTGCAT
3783959 CACTCTGAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (20 bp):
TGGTGCATCGGTGCATGGAT
Found at i:3783939 original size:65 final size:64
Alignment explanation
Indices: 3783731--3783938 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
3783721 TACACTAAGA
* * * *
3783731 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGTCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAG-GTGCATCGATGCATGGTTG
* *
3783795 GTGCATCGATGTATCAAATGCATTCGATGTTTTC-ATAAAATCCTCA-GTGCATC-AGTGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAATATAAT--TCAGGTGCATCGA-TGCATGG
3783857 TAT-
62 T-TG
* *
3783860 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCA-GGTGCATCGATGCATGG-TT
3783924 G
64 G
*
3783925 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
3783939 GGATTGGTGC
Statistics
Matches: 121, Mismatches: 11, Indels: 23
0.78 0.07 0.15
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 50 0.41
65 61 0.50
66 1 0.01
67 3 0.02
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAATATAATTCAGGTGCATCGATGCATGGTTG
Found at i:3784386 original size:2 final size:2
Alignment explanation
Indices: 3784379--3784440 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
3784369 GCCAATTGAT
3784379 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
3784421 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
3784441 GCTTAAGCTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3793941 original size:21 final size:21
Alignment explanation
Indices: 3793902--3793942 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3793892 ATTATTTTAT
3793902 ATATATTTTATTCTTAAATTC
1 ATATATTTTATTCTTAAATTC
*
3793923 ATAT-TTTTATTTTTCAAATT
1 ATATATTTTATTCTT-AAATT
3793943 AATACCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (21 bp):
ATATATTTTATTCTTAAATTC
Found at i:3806606 original size:22 final size:24
Alignment explanation
Indices: 3806574--3806631 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 24
3806564 AATATTTAAA
*
3806574 ATATATATTTTTAAATATAATA-T
1 ATATATTTTTTTAAATATAATATT
* *
3806597 A-ATA-TTTTTT-ATTTTAATATT
1 ATATATTTTTTTAAATATAATATT
3806618 ATATATTTTTTTAA
1 ATATATTTTTTTAA
3806632 CATTTTAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
20 7 0.25
21 7 0.25
22 6 0.21
23 7 0.25
24 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATATATTTTTTTAAATATAATATT
Found at i:3806621 original size:25 final size:24
Alignment explanation
Indices: 3806582--3806630 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
3806572 AAATATATAT
3806582 TTTTAAATATAATATAATATTTTTTA
1 TTTTAAATATAATAT-AT-TTTTTTA
*
3806608 TTTT-AATATTATATATTTTTTTA
1 TTTTAAATATAATATATTTTTTTA
3806631 ACATTTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 2 0.09
25 9 0.41
26 4 0.18
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTTAAATATAATATATTTTTTTA
Found at i:3806649 original size:25 final size:26
Alignment explanation
Indices: 3806607--3806656 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
3806597 AATATTTTTT
* *
3806607 ATTTTAATATTATATATTTTTTTAAC
1 ATTTTAATAATATATATTATTTTAAC
*
3806633 ATTTTAGTAATAT-TATTATTTTAA
1 ATTTTAATAATATATATTATTTTAA
3806657 TAAATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTTAATAATATATATTATTTTAAC
Found at i:3806716 original size:27 final size:25
Alignment explanation
Indices: 3806686--3806755 Score: 61
Period size: 25 Copynumber: 2.6 Consensus size: 25
3806676 ATAATACTTT
*
3806686 TATTTTAATAAAATATAATA-ATCTTAA
1 TATTTTAATAAAAT-T-ATAGAT-ATAA
*
3806713 TATTTATTTATAAAATTATAGATATAA
1 TA-TT-TTAATAAAATTATAGATATAA
*
3806740 TATTTTAATAATATTA
1 TATTTTAATAAAATTA
3806756 AATAAATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
25 10 0.28
26 2 0.06
27 10 0.28
28 5 0.14
29 9 0.25
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTTTAATAAAATTATAGATATAA
Found at i:3806719 original size:31 final size:34
Alignment explanation
Indices: 3806648--3806728 Score: 82
Period size: 37 Copynumber: 2.4 Consensus size: 34
3806638 AGTAATATTA
*
3806648 TTATTTTAATAAATAATAAATATAATTTATAATACTT
1 TTATTTTAAT-AA-AATAAATATAATCTATAATAC-T
*
3806685 TTATTTTAATAAAATATA-ATAATCT-TAATA-T
1 TTATTTTAATAAAATAAATATAATCTATAATACT
3806716 TTA-TTT-ATAAAAT
1 TTATTTTAATAAAAT
3806729 TATAGATATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
29 7 0.17
30 3 0.07
31 4 0.10
33 5 0.12
34 6 0.14
35 5 0.12
36 2 0.05
37 10 0.24
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (34 bp):
TTATTTTAATAAAATAAATATAATCTATAATACT
Found at i:3815523 original size:2 final size:2
Alignment explanation
Indices: 3815516--3815542 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3815506 TGGTCATTTC
3815516 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
3815543 CTAATTAATC
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:3817029 original size:26 final size:26
Alignment explanation
Indices: 3817000--3817087 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 26
3816990 TTGACTCGAA
3817000 TATATTAATATTTTAAAATAATATAT
1 TATATTAATATTTTAAAATAATATAT
*
3817026 TATATAATAATATATTTATAAT-ATATTAT
1 TATAT--TAATAT-TTTAAAATAATA-TAT
3817055 TATATTTTAA-ATTATTAAAATAATATAT
1 TATA--TTAATATT-TTAAAATAATATAT
3817083 TATAT
1 TATAT
3817088 ATTTTTATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
26 6 0.12
27 1 0.02
28 24 0.46
29 20 0.38
31 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATTAATATTTTAAAATAATATAT
Found at i:3817096 original size:38 final size:42
Alignment explanation
Indices: 3817031--3817111 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 42
3817021 TATATTATAT
*
3817031 AATAATATATTTATAATATATTATTATATTTTAAATTATTAA
1 AATAATATATTTATAATATATTATTATATTTTAAATAATTAA
*
3817073 AATAATATA-TTAT-ATAT-TT-TTATATTTTTAATAATTAA
1 AATAATATATTTATAATATATTATTATATTTTAAATAATTAA
3817111 A
1 A
3817112 GAATTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 18 0.49
39 2 0.05
40 4 0.11
41 4 0.11
42 9 0.24
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (42 bp):
AATAATATATTTATAATATATTATTATATTTTAAATAATTAA
Found at i:3817097 original size:57 final size:56
Alignment explanation
Indices: 3816999--3817109 Score: 152
Period size: 57 Copynumber: 2.0 Consensus size: 56
3816989 CTTGACTCGA
3816999 ATATATTAATATTTTAAAATAATATATTATATAATAATATATTTATAATATATTATT
1 ATATATTAATATTTTAAAATAATATATTATATAATAATATATTTATAATA-ATTATT
* * ** *
3817056 ATATTTTAA-ATTATTAAAATAATATATTATATATTTTTATATTTTTAATAATTA
1 ATATATTAATATT-TTAAAATAATATATTATATAATAATATATTTATAATAATTA
3817110 AAGAATTTAT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
56 7 0.15
57 41 0.85
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (56 bp):
ATATATTAATATTTTAAAATAATATATTATATAATAATATATTTATAATAATTATT
Found at i:3817104 original size:26 final size:26
Alignment explanation
Indices: 3817018--3817109 Score: 71
Period size: 26 Copynumber: 3.4 Consensus size: 26
3817008 TATTTTAAAA
* ** *
3817018 TAATATATTATATAATAATATATTTA
1 TAATATATTATATATTTTTATATTTT
*
3817044 TAATATATTAT-TATATTTTAAATTATT
1 TAATATATTATATAT-TTTTATATT-TT
3817071 AAAATAATATATTATATATTTTTATATTTT
1 ----TAATATATTATATATTTTTATATTTT
3817101 TAATA-ATTA
1 TAATATATTA
3817110 AAGAATTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
25 6 0.11
26 22 0.42
27 1 0.02
30 2 0.04
31 19 0.36
32 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TAATATATTATATATTTTTATATTTT
Found at i:3819395 original size:89 final size:89
Alignment explanation
Indices: 3819242--3819420 Score: 277
Period size: 89 Copynumber: 2.0 Consensus size: 89
3819232 ATAACCCACA
* * *
3819242 AGGTTGCCATTGAACGTAATTGAATAATGAGGAGTAGTTAAGCAAATTCTGATCCACTCTCAGAA
1 AGGTTGCCATTGAACGTAATTGAATAATGAGGAGTAGTAAAGCAAATTCTAATCCACTCGCAGAA
* *
3819307 TACCACTAGTAATCTCATAGCTTC
66 CACCACTAGTAATCTCACAGCTTC
* *
3819331 AGGTTTCCATTGAACGTAATTGAATAATGAGGCGTAGTAAAGCAAATTCTAATCCACTCGCAGAA
1 AGGTTGCCATTGAACGTAATTGAATAATGAGGAGTAGTAAAGCAAATTCTAATCCACTCGCAGAA
* *
3819396 CACCACTGGTAATTTCACAGCTTC
66 CACCACTAGTAATCTCACAGCTTC
3819420 A
1 A
3819421 AGGACAGTCT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 81 1.00
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (89 bp):
AGGTTGCCATTGAACGTAATTGAATAATGAGGAGTAGTAAAGCAAATTCTAATCCACTCGCAGAA
CACCACTAGTAATCTCACAGCTTC
Found at i:3820953 original size:54 final size:54
Alignment explanation
Indices: 3820887--3821162 Score: 378
Period size: 54 Copynumber: 5.1 Consensus size: 54
3820877 TTACCAAATA
* *
3820887 GGCACTATGTGTGCAAATCACGTAATTCATCATATGTTGATGAATATCCGTTTC
1 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * *
3820941 GGCACTAAGTGTGCAAAGT-ACGAAATTCATCATTTATTGATGAATAACCATTTC
1 GGCACTATGTGTGCAAA-TCACGAAATTCATCATATGTTGATGAATAACCGTTTC
3820995 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
1 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * * * * *
3821049 GACACTATGCGTGTAAATCACGGAATTCATCATATGTTGAT-AGTAACCATTTC
1 GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
* * *
3821102 GGCACTAAGTGTGCAAAGT-ACGTAATTCATCATATGTTGATGAATAACCGTTTT
1 GGCACTATGTGTGCAAA-TCACGAAATTCATCATATGTTGATGAATAACCGTTTC
3821156 GGCACTA
1 GGCACTA
3821163 CGAGTGCATT
Statistics
Matches: 194, Mismatches: 24, Indels: 8
0.86 0.11 0.04
Matches are distributed among these distances:
53 45 0.23
54 148 0.76
55 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (54 bp):
GGCACTATGTGTGCAAATCACGAAATTCATCATATGTTGATGAATAACCGTTTC
Found at i:3828656 original size:27 final size:28
Alignment explanation
Indices: 3828604--3828658 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
3828594 ACAACGTTGC
3828604 TTTCAAGCATTGGCTCGACGAAATAATA
1 TTTCAAGCATTGGCTCGACGAAATAATA
* *
3828632 TTTCAAGCATT-GCTCGAGGACATAATA
1 TTTCAAGCATTGGCTCGACGAAATAATA
3828659 GAAACGGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (28 bp):
TTTCAAGCATTGGCTCGACGAAATAATA
Found at i:3830528 original size:14 final size:14
Alignment explanation
Indices: 3830509--3830540 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
3830499 CATAATCCCT
*
3830509 CTAAATTCTAAACC
1 CTAAATCCTAAACC
3830523 CTAAATCCTAAACC
1 CTAAATCCTAAACC
3830537 CTAA
1 CTAA
3830541 TTTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (14 bp):
CTAAATCCTAAACC
Found at i:3835330 original size:29 final size:29
Alignment explanation
Indices: 3835295--3835376 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
3835285 AAACTAAATT
*
3835295 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
3835324 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
3835353 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
3835377 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:3840103 original size:29 final size:29
Alignment explanation
Indices: 3840032--3840113 Score: 139
Period size: 28 Copynumber: 2.8 Consensus size: 29
3840022 CAAACTAAAT
*
3840032 TGATGTCATTACTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
3840061 -GATGTCATTGCTTACATCATTTAATTAA
1 TGATGTCATTGCTTACATCATTTAATTAA
3840089 TGATGTCATTGCTTACATCAATTTA
1 TGATGTCATTGCTTACATC-ATTTA
3840114 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
28 27 0.54
29 18 0.36
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (29 bp):
TGATGTCATTGCTTACATCATTTAATTAA
Found at i:3841963 original size:30 final size:30
Alignment explanation
Indices: 3841928--3841987 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3841918 GTTTTGAAGC
*
3841928 TATATAATTTTATTGGAGTATCTGTAATTA
1 TATATAATCTTATTGGAGTATCTGTAATTA
3841958 TATATAATCTTATTGGAGTATCTGTAATTA
1 TATATAATCTTATTGGAGTATCTGTAATTA
3841988 GGGTATTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.48
Consensus pattern (30 bp):
TATATAATCTTATTGGAGTATCTGTAATTA
Found at i:3847062 original size:3 final size:3
Alignment explanation
Indices: 3847054--3847092 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3847044 AGTTTTTTCC
3847054 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3847093 TAGTAGAGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3858243 original size:21 final size:20
Alignment explanation
Indices: 3858193--3858251 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
3858183 AAGATTCAAT
3858193 CAAGAACAAAAAAGAAAA-AA
1 CAAGAAC-AAAAAGAAAAGAA
3858213 CAAGAACAAAAAGAAAAGAA
1 CAAGAACAAAAAGAAAAGAA
*
3858233 GCAA-AATCAAAAGGAAAAG
1 -CAAGAA-CAAAAAGAAAAG
3858252 GGACAAAAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
19 10 0.29
20 11 0.31
21 14 0.40
ACGTcount: A:0.73, C:0.10, G:0.15, T:0.02
Consensus pattern (20 bp):
CAAGAACAAAAAGAAAAGAA
Found at i:3859860 original size:36 final size:37
Alignment explanation
Indices: 3859809--3859879 Score: 92
Period size: 36 Copynumber: 1.9 Consensus size: 37
3859799 CTCACCATTG
*
3859809 TCTCTTAAGACAGTTTCCCTT-GAAACAAA-CTTTGTC
1 TCTCTTAAGACAGTTTCACTTGGAAA-AAACCTTTGTC
* *
3859845 TCTCTTGAGATAGTTTCACTTGGAAAAAACCTTTG
1 TCTCTTAAGACAGTTTCACTTGGAAAAAACCTTTG
3859880 AAATTGTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 21 0.70
37 9 0.30
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (37 bp):
TCTCTTAAGACAGTTTCACTTGGAAAAAACCTTTGTC
Found at i:3859990 original size:28 final size:28
Alignment explanation
Indices: 3859959--3860012 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3859949 ATTTTGTCTC
3859959 TTGAGACA-GTTTCCCTTGAAAAAAATCT
1 TTGA-ACATGTTTCCCTTGAAAAAAATCT
* * *
3859987 TTGAATATGTTTTCCTTGGAAAAAAT
1 TTGAACATGTTTCCCTTGAAAAAAAT
3860013 TTCATCTCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 2 0.09
28 20 0.91
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (28 bp):
TTGAACATGTTTCCCTTGAAAAAAATCT
Found at i:3860966 original size:84 final size:82
Alignment explanation
Indices: 3860826--3860984 Score: 246
Period size: 84 Copynumber: 1.9 Consensus size: 82
3860816 AGCGAAGGAT
3860826 ATTGGACTCAAGACAACACAAGTTCACTTCACAACGAAGGGACGCTGGTTCTCAACAAACAATTT
1 ATTGGACTCAAGACAACACAAGTTCACTTCACAACGAAGGGACGCTGGTTCTCAACAAACAATTT
*
3860891 CCCATTTTCAAAAGGGC
66 CCCAATTTCAAAAGGGC
** * * *
3860908 ATTGGACTTGAGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCAAGACAACACAAGTTC-ACTTCACAACGAAGGGAC-GCTGGTTCTCAACAAACAAT
3860973 TTCCCAATTTCA
64 TTCCCAATTTCA
3860985 TAACCAATTT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
82 22 0.32
83 17 0.25
84 30 0.43
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (82 bp):
ATTGGACTCAAGACAACACAAGTTCACTTCACAACGAAGGGACGCTGGTTCTCAACAAACAATTT
CCCAATTTCAAAAGGGC
Found at i:3860983 original size:188 final size:189
Alignment explanation
Indices: 3860730--3861084 Score: 597
Period size: 188 Copynumber: 1.9 Consensus size: 189
3860720 CGCGCCACCC
*
3860730 GAGACAACACAAGTTCAACTTCACAACGAAGGACGACTGGTTGTCAACAAATAACTTCCCAATTT
1 GAGACAACACAAGTTCAACTTCACAACGAAGGACGACTGGTTGTCAACAAACAACTTCCCAATTT
*
3860795 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTC-ACTTCACA
66 CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
3860859 ACGAAGGGAC-GCTGGTTCTCAACAAACAATTTCCCATTTTCAAAAGGGCATTGGACTT
131 ACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCATTTTCAAAAGGGCATTGGACTT
* * * *
3860917 GAGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCAATT
1 GAGACAACACAAGTTCAACTTCACAACGAA-GGACGACTGGTTGTCAACAAACAACTTCCCAATT
* * *
3860982 TCATAACCAATTTCAACTTCACGGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCAC
65 TCAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCAC
*
3861047 AACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCA
130 AACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCA
3861085 GTTCCAGAAC
Statistics
Matches: 155, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
187 28 0.18
188 84 0.54
189 18 0.12
190 25 0.16
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (189 bp):
GAGACAACACAAGTTCAACTTCACAACGAAGGACGACTGGTTGTCAACAAACAACTTCCCAATTT
CAGAACCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACA
ACGAAGGGACGGCTGGTTCTCAACAAACAATTTCCCATTTTCAAAAGGGCATTGGACTT
Found at i:3861096 original size:106 final size:106
Alignment explanation
Indices: 3860908--3861129 Score: 372
Period size: 106 Copynumber: 2.1 Consensus size: 106
3860898 TCAAAAGGGC
* * *
3860908 ATTGGACTTGAGATAACACAAGTTCAACTTTACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* *
3860973 TTCCCAATTTCATAACCAATTTCAACTTCACGGCGAAGGAT
66 TTCCCAATTCCAGAACCAATTTCAACTTCACGGCGAAGGAT
3861014 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
1 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
* * *
3861079 TTCCCAGTTCCAGAACCAATTTCAACTTCACGGTGGAGGAT
66 TTCCCAATTCCAGAACCAATTTCAACTTCACGGCGAAGGAT
3861120 ATTGGACTCG
1 ATTGGACTCG
3861130 GAACAATACA
Statistics
Matches: 108, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 108 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (106 bp):
ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAAT
TTCCCAATTCCAGAACCAATTTCAACTTCACGGCGAAGGAT
Found at i:3862510 original size:21 final size:21
Alignment explanation
Indices: 3862468--3862510 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3862458 TTTTCGGGTT
* * *
3862468 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3862489 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3862510 A
1 A
3862511 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3863295 original size:145 final size:147
Alignment explanation
Indices: 3863031--3863340 Score: 493
Period size: 145 Copynumber: 2.1 Consensus size: 147
3863021 GGTTAGAGGG
* ** * *
3863031 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAGGTCTTGAAAGACCATA
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGCGGAACATGTATGAAGTCTTGAAAGACCATA
* *
3863096 CTTGATCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCA-T-T
65 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTAT
3863159 ATGGCACTACGGTGCAAT
130 ATGGCACTACGGTGCAAT
*
3863177 TCTACGCGGTCCTTCGGG-ATATATATATTCTGCGGAACATGTATGAAGTCTTGGAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGCGGAACATGTATGAAGTCTTGAAAGAC-CATA
3863241 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTAT
65 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTAT
3863306 ATGGCACTACGGTGCAAT
130 ATGGCACTACGGTGCAAT
3863324 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
3863341 TACAATTATA
Statistics
Matches: 152, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
144 35 0.23
145 63 0.41
146 20 0.13
147 34 0.22
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (147 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGCGGAACATGTATGAAGTCTTGAAAGACCATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATA
TGGCACTACGGTGCAAT
Found at i:3863341 original size:23 final size:23
Alignment explanation
Indices: 3863308--3863352 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3863298 ATCATTATAT
* *
3863308 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTACAATTATACGC
*
3863331 GGCACTTCGGTACAATTATACG
1 GGCACTACGGTACAATTATACG
3863353 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTACAATTATACGC
Found at i:3869376 original size:21 final size:21
Alignment explanation
Indices: 3869334--3869376 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
3869324 TTTTCGGGTT
* * *
3869334 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
3869355 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
3869376 A
1 A
3869377 CGAATATGAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:3870151 original size:150 final size:142
Alignment explanation
Indices: 3869898--3870206 Score: 458
Period size: 150 Copynumber: 2.1 Consensus size: 142
3869888 GGGTAGAGGG
* * *
3869898 TCTACGCGGTCCTTCGGGACATAGTATATTCTTTGGAACATGTGAGGTCTTGAAAGACATACTTA
1 TCTACGCGGTCCTTCGGGACATAATATATTCTGTGGAACATGTGAAGTCTTGAAAGACATACTTA
* *
3869963 TCCTTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATATGGC
66 TCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGC
3870028 ACTACGGTGCAAT
131 AC-ACGGTGCAAT
*
3870041 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATA-ATATATTCTGTGGAACA--TGTGAAGTCTT-GAAAG--ACA
* *
3870106 TACTTGATCCCTAGTATATGTATATGATTCTTAAGTAATTATATGTGGTCTTTATGGACATCATT
60 TACTT-ATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
3870171 ATATGGCACACGGTGCAAT
124 ATATGGCACACGGTGCAAT
3870190 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
3870207 TGCAATTATA
Statistics
Matches: 150, Mismatches: 8, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
143 22 0.15
144 15 0.10
146 10 0.07
147 5 0.03
148 1 0.01
149 33 0.22
150 64 0.43
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (142 bp):
TCTACGCGGTCCTTCGGGACATAATATATTCTGTGGAACATGTGAAGTCTTGAAAGACATACTTA
TCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATTATATGGC
ACACGGTGCAAT
Found at i:3879040 original size:21 final size:22
Alignment explanation
Indices: 3878999--3879052 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
3878989 GATTTAAAAT
* *
3878999 ATAAA-TAATTAAATATCGATA
1 ATAAATTAATTTAATATAGATA
3879020 ATAAATTAATTTAATA-AGATA
1 ATAAATTAATTTAATATAGATA
* *
3879041 AGACATTAATTT
1 ATAAATTAATTT
3879053 TTTAAATAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.37
Consensus pattern (22 bp):
ATAAATTAATTTAATATAGATA
Found at i:3879423 original size:22 final size:22
Alignment explanation
Indices: 3879395--3879436 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3879385 AAAAAATTAT
*
3879395 CTAAAACATTAGTTTTTTTTAC
1 CTAAAACATTAATTTTTTTTAC
3879417 CTAAAACATTAATTTTTTTT
1 CTAAAACATTAATTTTTTTT
3879437 CAACATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (22 bp):
CTAAAACATTAATTTTTTTTAC
Found at i:3883982 original size:26 final size:27
Alignment explanation
Indices: 3883953--3884003 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3883943 ATATTTTTAT
*
3883953 TTTTTGTTTCT-ATTTTTAGAAAATAG
1 TTTTTATTTCTAATTTTTAGAAAATAG
* *
3883979 TTTTTATTTTTAATTTTTTGAAAAT
1 TTTTTATTTCTAATTTTTAGAAAAT
3884004 TAAAAATCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 9 0.43
27 12 0.57
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.63
Consensus pattern (27 bp):
TTTTTATTTCTAATTTTTAGAAAATAG
Found at i:3884734 original size:24 final size:23
Alignment explanation
Indices: 3884676--3884739 Score: 58
Period size: 24 Copynumber: 2.7 Consensus size: 23
3884666 AAATATAAAC
*
3884676 AATTATTAAGATATTCAATAAAATA
1 AATTATTAAAATATT--ATAAAATA
* *
3884701 AA-TATAAAAATATTATAGAATTA
1 AATTATTAAAATATTATA-AAATA
*
3884724 AATTATTAAAAAATTA
1 AATTATTAAAATATTA
3884740 ATTTAAGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.09
23 6 0.19
24 21 0.66
25 2 0.06
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (23 bp):
AATTATTAAAATATTATAAAATA
Found at i:3889813 original size:17 final size:19
Alignment explanation
Indices: 3889772--3889814 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
3889762 GCTGAGAGAG
3889772 GAGTATCAATACTCTAATTA
1 GAGTATCAATACTCTAA-TA
*
3889792 GAGTATCGATACTC-AA-A
1 GAGTATCAATACTCTAATA
3889809 GAGTAT
1 GAGTAT
3889815 TGGCACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.30
Consensus pattern (19 bp):
GAGTATCAATACTCTAATA
Found at i:3892056 original size:2 final size:2
Alignment explanation
Indices: 3892051--3892167 Score: 109
Period size: 2 Copynumber: 61.0 Consensus size: 2
3892041 GTGTGTGTGC
*
3892051 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
3892092 A- AT GT -T A- AT AT AT AT AT AT AT AT AT AT AT AT A- AG GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
3892130 GT AA AT AA AA AC AT AT AT AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3892168 GTATGTATAA
Statistics
Matches: 97, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
1 5 0.05
2 92 0.95
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:3892642 original size:20 final size:20
Alignment explanation
Indices: 3892572--3892640 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
3892562 AATGCCACAA
3892572 GAACAATATCGGTATTATAT
1 GAACAATATCGGTATTATAT
3892592 GAACAATATCGGTATTATAT
1 GAACAATATCGGTATTATAT
** * *
3892612 GAATGATATTGGTATTGTAT
1 GAACAATATCGGTATTATAT
3892632 GAACAATAT
1 GAACAATAT
3892641 TGATACCAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.36
Consensus pattern (20 bp):
GAACAATATCGGTATTATAT
Found at i:3898300 original size:26 final size:26
Alignment explanation
Indices: 3898245--3898297 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
3898235 CTTTAAAATC
3898245 TTCTTCATTTGTTGAACTTCATGAAT
1 TTCTTCATTTGTTGAACTTCATGAAT
*
3898271 TTCTTC-TTTGTTGGACTTCATGAAT
1 TTCTTCATTTGTTGAACTTCATGAAT
3898296 TT
1 TT
3898298 TCTAAATCTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 20 0.77
26 6 0.23
ACGTcount: A:0.19, C:0.15, G:0.13, T:0.53
Consensus pattern (26 bp):
TTCTTCATTTGTTGAACTTCATGAAT
Found at i:3911130 original size:16 final size:18
Alignment explanation
Indices: 3911109--3911153 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
3911099 TATGGAATTG
3911109 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
3911125 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
3911143 GATTTCAATTC
1 GATTCCAATTC
3911154 TCTCATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 13 0.50
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:3911943 original size:23 final size:23
Alignment explanation
Indices: 3911913--3911983 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
3911903 ATACTTTACA
*
3911913 ATATAAACACTACCTATTACATT
1 ATATAAACGCTACCTATTACATT
3911936 ATATAAACGCTA-C-ATTACATT
1 ATATAAACGCTACCTATTACATT
* *
3911957 ATATAAGCGCTACCTATTACATC
1 ATATAAACGCTACCTATTACATT
3911980 ATAT
1 ATAT
3911984 TTTACCTATT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 19 0.44
22 2 0.05
23 22 0.51
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAACGCTACCTATTACATT
Found at i:3912347 original size:482 final size:483
Alignment explanation
Indices: 3911520--3912887 Score: 2346
Period size: 482 Copynumber: 2.8 Consensus size: 483
3911510 TTATAATATG
*
3911520 TTGAAAGTGTCCATACTTTTTTATAAAAAGGATCGGTACTTTTTTTAAAGTTATGTAATTTATGT
1 TTGAAAGTGTCCATAC-TTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGT
* * *
3911585 TTCAA-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCA
65 TTCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
3911649 CAAAAAATTATTTGATTGTTTTGATATTTTAT--AAA--ATTTAGAATTTAAATTTAACAATATT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAAATTATTTAGAATTTAAATTTAACAATATT
*
3911710 AACCAAAGATAATAATAAATATGTAATATATATGT-TTTTTTTAATTTAATAATAATATATA-TC
195 AACCAAAGATAATAATAAATATGTAATATATGT-TATTTTTTTAATTTAATAATAATATATACT-
* * * *
3911773 GTAATGTAAAAAATAAATCATTAAACGCCTATAATTACTAAATTAATATTTTAAAACTCACTCAA
258 GTAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
*
3911838 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAATGATAG
323 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT-GACACTTTTATAAAAAAGATAG
3911903 ATACTTTACAATATAAACACTACCTATTACATTATATAAACGCTA-C-ATTACATTATATAAGCG
387 ATACTTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCG
3911966 CTACCTATTACATCATA-TTTTACCTATTATA
452 CTACCTATTACATCATATTTTTACCTATTATA
*
3911997 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
3912062 TCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
3912127 AAAAAATTATTTGATTGTTTTGATATTTTATAAAACATTATTTAGAATTTAAATTTAACAATATT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAA-ATTATTTAGAATTTAAATTTAACAATATT
3912192 AACCAAAGATAATAATAAATATGTAATATATGTTATTTTTTTAATTTAATAATAATATATACTGT
195 AACCAAAGATAATAATAAATATGTAATATATGTTATTTTTTTAATTTAATAATAATATATACTGT
3912257 AACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
260 AACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAA
* *
3912322 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAATTATAGACACTTTTATAAAAAGGATAGAT
325 GATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTAT-GACACTTTTATAAAAAAGATAGAT
*
3912387 ACTTTACAATATAAGCACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCT
389 ACTTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCT
3912452 ACCTATTACATCATATTTTTACCTATTATA
454 ACCTATTACATCATATTTTTACCTATTATA
3912482 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
3912547 TCAATTTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
3912612 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTAAATTTAACAATAT
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAA-ATTATTTAGAATTTAAATTTAACAATAT
3912677 TAACCAAAGATAATAATAAATATGTAATATATATGTTTATTTTTTTTAATTTAATAATAATATAT
194 TAACCAAAGATAATAATAAATATGT-A-ATATATG-TTA-TTTTTTTAATTTAATAATAATATAT
* * *
3912742 -C-GTAACGTAAAAAATAAATTATTAGACGTCTATAATTACTAAATTAATATCTCAAAACTCACA
255 ACTGTAACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACT
* * *
3912805 CAAAAGATAACCTTAAATTAATGTTTTCTATAGTAAAAAAAGTATGACACTTTTATAAAAAAGAT
320 CAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGACACTTTTATAAAAAAGAT
* *
3912870 AAATACTTTGCAATATAA
385 AGATACTTTACAATATAA
3912888 CAGGTAAAAA
Statistics
Matches: 849, Mismatches: 26, Indels: 22
0.95 0.03 0.02
Matches are distributed among these distances:
476 51 0.06
477 104 0.12
479 2 0.00
480 1 0.00
481 1 0.00
482 251 0.30
483 2 0.00
484 34 0.04
485 82 0.10
486 149 0.18
487 36 0.04
488 107 0.13
489 4 0.00
490 25 0.03
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (483 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATATTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAAATTATTTAGAATTTAAATTTAACAATATTA
ACCAAAGATAATAATAAATATGTAATATATGTTATTTTTTTAATTTAATAATAATATATACTGTA
ACGTAAAAAATAAATTATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAAG
ATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGACACTTTTATAAAAAAGATAGATAC
TTTACAATATAAACACTACCTATTACATTATATAAACGCTACCTATTACATTATATAAGCGCTAC
CTATTACATCATATTTTTACCTATTATA
Found at i:3912430 original size:23 final size:23
Alignment explanation
Indices: 3912395--3912467 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
3912385 ATACTTTACA
*
3912395 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3912418 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
3912441 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
3912464 ATAT
1 ATAT
3912468 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:3924756 original size:2 final size:2
Alignment explanation
Indices: 3924749--3924816 Score: 77
Period size: 2 Copynumber: 34.0 Consensus size: 2
3924739 TGATTTTAGG
* * *
3924749 TA TA TA TA TA TA TA TA TA T- TA TGA T- TC GA AA TGA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T-A TA TA TA TA
3924791 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
3924817 ATTTATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
1 2 0.03
2 52 0.90
3 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (2 bp):
TA
Found at i:3929206 original size:30 final size:30
Alignment explanation
Indices: 3929172--3929228 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
3929162 GTGATTAAAA
* * *
3929172 TAAAAGTTTTAAAACTTTAGGGTCTAATTT
1 TAAAAGATTAAAAACTTTAGGGACTAATTT
*
3929202 TAAAAGATTAAAAAGTTTAGGGACTAA
1 TAAAAGATTAAAAACTTTAGGGACTAA
3929229 ATTGGAATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (30 bp):
TAAAAGATTAAAAACTTTAGGGACTAATTT
Found at i:3930828 original size:21 final size:21
Alignment explanation
Indices: 3930780--3930840 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
3930770 GTTCTACGTG
* *
3930780 GTCCTTCGAGATATATATGTA
1 GTCCTTTGGGATATATATGTA
3930801 GTCCTTTGGGATATATATGTA
1 GTCCTTTGGGATATATATGTA
* *
3930822 GTCCTTTGGAACATATATG
1 GTCCTTTGGGATATATATG
3930841 AGGTTCTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.26, C:0.13, G:0.21, T:0.39
Consensus pattern (21 bp):
GTCCTTTGGGATATATATGTA
Found at i:3937057 original size:60 final size:59
Alignment explanation
Indices: 3936991--3937104 Score: 140
Period size: 60 Copynumber: 1.9 Consensus size: 59
3936981 AAACATATGA
* * * * *
3936991 ATAGTCAGATAACTATTTTGTGATTTTTAATAGACAT-GAAACTCAATAAAGCAATGCCCT
1 ATAGTCAGATAACCATTTTATAACTTTTAAT--ACATAGAAACTCAATAAAACAATGCCCT
* *
3937051 ATAGTCAGATGACCATTTTATAACTTTTAATACATAGATACTCAATAAAACAAT
1 ATAGTCAGATAACCATTTTATAACTTTTAATACATAGAAACTCAATAAAACAAT
3937105 ATCATAAATC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
58 4 0.09
59 16 0.35
60 26 0.57
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (59 bp):
ATAGTCAGATAACCATTTTATAACTTTTAATACATAGAAACTCAATAAAACAATGCCCT
Found at i:3939451 original size:3 final size:3
Alignment explanation
Indices: 3939443--3939469 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3939433 CATTCCATGG
3939443 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
3939470 GAAGAATTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3940106 original size:23 final size:25
Alignment explanation
Indices: 3940093--3940170 Score: 68
Period size: 28 Copynumber: 3.0 Consensus size: 25
3940083 AATCAAAAGA
3940093 AAAAAAATGAATGAAATAAAAAAAT
1 AAAAAAATGAATGAAATAAAAAAAT
* * *
3940118 AAAAAAATAAAAAAAGAAGTAAAAAAAT
1 AAAAAAAT---GAATGAAATAAAAAAAT
* * *
3940146 AAATAAATAAATG-AATAAATAAAT
1 AAAAAAATGAATGAAATAAAAAAAT
3940170 A
1 A
3940171 CAAATAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
24 10 0.23
25 12 0.28
28 21 0.49
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAAAAATGAATGAAATAAAAAAAT
Found at i:3940117 original size:8 final size:8
Alignment explanation
Indices: 3940106--3940180 Score: 62
Period size: 8 Copynumber: 9.1 Consensus size: 8
3940096 AAAATGAATG
3940106 AAATAAAA
1 AAATAAAA
3940114 AAATAAAA
1 AAATAAAA
3940122 AAATAAAA
1 AAATAAAA
* *
3940130 AAAGAAGTA
1 AAATAA-AA
*
3940139 AAA-AAAT
1 AAATAAAA
*
3940146 AAATAAAT
1 AAATAAAA
* *
3940154 AAATGAAT
1 AAATAAAA
3940162 AAATAAATA
1 AAATAAA-A
3940171 CAAATAAAA
1 -AAATAAAA
3940180 A
1 A
3940181 GTTAAATTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
7 3 0.05
8 41 0.73
9 5 0.09
10 7 0.12
ACGTcount: A:0.79, C:0.01, G:0.04, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:3940210 original size:16 final size:16
Alignment explanation
Indices: 3940093--3940273 Score: 83
Period size: 16 Copynumber: 11.2 Consensus size: 16
3940083 AATCAAAAGA
*
3940093 AAAAAAATGAATGAAAT
1 AAAAAAAT-AATAAAAT
*
3940110 AAAAAAATAAAAAAAT
1 AAAAAAATAATAAAAT
*
3940126 AAAAAAAGAAGTAAAA-
1 AAAAAAATAA-TAAAAT
*
3940142 AAATAAATAA-ATAAAT
1 AAAAAAATAATA-AAAT
* *
3940158 GAATAAATAAATACAAAT
1 AAAAAAAT-AATA-AAAT
* *
3940176 -AAAAAGT--TAAATT
1 AAAAAAATAATAAAAT
**
3940189 TTAAAAATAATAAAAT
1 AAAAAAATAATAAAAT
*
3940205 AAAAAAACTAA-AAGAT
1 AAAAAAA-TAATAAAAT
*
3940221 AAACATAAATAATACTAAT
1 AAA-A-AAATAATA-AAAT
* *
3940240 -TAAAAATAAT--GAT
1 AAAAAAATAATAAAAT
3940253 AAAAAAATAATAAAAT
1 AAAAAAATAATAAAAT
3940269 GAAAA
1 -AAAA
3940274 TTTAGAGGAG
Statistics
Matches: 124, Mismatches: 23, Indels: 34
0.69 0.13 0.19
Matches are distributed among these distances:
13 5 0.04
14 17 0.14
15 3 0.02
16 56 0.45
17 31 0.25
18 10 0.08
19 2 0.02
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAAAAATAATAAAAT
Found at i:3942491 original size:110 final size:110
Alignment explanation
Indices: 3942362--3942843 Score: 635
Period size: 110 Copynumber: 4.5 Consensus size: 110
3942352 AATCTAAGTA
* * * * **
3942362 TGTGTTGTTTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAA
1 TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA
** * * *
3942427 GTTGTTTGTTGACAGGCAGCCGCCCCTTCACTGTGAAGTTGAGCT
66 GTTGTTTGTTGACAATCAGTCACCCCTTCGCTGTGAAGTTGAGCT
* *
3942472 TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACTATGAATGAAACTGAAAA
1 TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA
*
3942537 GTTGTTTGTTGACAATCAGTCACCCCTTCGTTGTGAAGTTGAGCT
66 GTTGTTTGTTGACAATCAGTCACCCCTTCGCTGTGAAGTTGAGCT
* * **
3942582 TGTGTTGTCTTGAGCCCAATATCCTTCGCTGTGAAGTTGAAATT-AGCTC----TGAAACTGGGA
1 TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGA-CTCTGAATGAAACTGAAA
* * * *
3942642 AGTTATTTGTTGACAACCAGTCGCCCCTTCGTTGT-ATAGTTGAGCT
65 AGTTGTTTGTTGACAATCAGTCACCCCTTCGCTGTGA-AGTTGAGCT
**
3942688 TGTGTTGTCTTAAGTCC-A-A--CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA
1 TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA
3942749 GTTGTTTGTTGA-AAGTCAGTCACCCCTTCGCTGTGAAGTTGAGCT
66 GTTGTTTGTTGACAA-TCAGTCACCCCTTCGCTGTGAAGTTGAGCT
*
3942794 TGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
1 TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCT
3942844 AAAAGCTGTA
Statistics
Matches: 325, Mismatches: 34, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
102 24 0.07
103 1 0.00
104 1 0.00
105 4 0.01
106 125 0.38
107 2 0.01
108 1 0.00
109 1 0.00
110 166 0.51
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (110 bp):
TGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAA
GTTGTTTGTTGACAATCAGTCACCCCTTCGCTGTGAAGTTGAGCT
Found at i:3942770 original size:212 final size:216
Alignment explanation
Indices: 3942362--3942837 Score: 685
Period size: 212 Copynumber: 2.2 Consensus size: 216
3942352 AATCTAAGTA
* * * * *
3942362 TGTGTTGTTTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAATGAAATTGGGAA
1 TGTGTTGTCTCGAGCCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTC---ATGAAACTGGGAA
* ** *
3942427 GTTGTTTGTTGACAGGCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCGAGTCCAAT
63 GTTATTTGTTGACAACCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAAT
3942492 ATCCTTCGCTGTGAAGTTAAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAATCAGT
128 A-CCTTCGCTGTGAAGTTAAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAATCAGT
*
3942557 CACCCCTTCGTTGTGAAGTTGAGCT
192 CACCCCTTCGCTGTGAAGTTGAGCT
*
3942582 TGTGTTGTCTTGAGCCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTC-TGAAACTGGGAAGTT
1 TGTGTTGTCTCGAGCCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCATGAAACTGGGAAGTT
* ** *
3942646 ATTTGTTGACAACCAGTCGCCCCTTCGTTGT-ATAGTTGAGCTTGTGTTGTCTTAAGTCC-A-A-
66 ATTTGTTGACAACCAGCCGCCCCTTCACTGTGA-AGTTGAGCTTGTGTTGTCTCAAGTCCAATAC
* *
3942707 CTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTTGA-AAGTCAGTCA
130 CTTCGCTGTGAAGTTAAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAA-TCAGTCA
3942771 CCCCTTCGCTGTGAAGTTGAGCT
194 CCCCTTCGCTGTGAAGTTGAGCT
* *
3942794 TGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAAATT
1 TGTGTTGTCTCGAGCCCAATATCCTTCGCTGTGAAGTTGAAATT
3942838 GACTCTAAAA
Statistics
Matches: 234, Mismatches: 20, Indels: 12
0.88 0.08 0.05
Matches are distributed among these distances:
211 2 0.01
212 122 0.52
214 1 0.00
215 2 0.01
216 63 0.27
220 44 0.19
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (216 bp):
TGTGTTGTCTCGAGCCCAATATCCTTCGCTGTGAAGTTGAAATTAGCTCATGAAACTGGGAAGTT
ATTTGTTGACAACCAGCCGCCCCTTCACTGTGAAGTTGAGCTTGTGTTGTCTCAAGTCCAATACC
TTCGCTGTGAAGTTAAAATTGACTATGAATGAAACTGAAAAGTTGTTTGTTGACAATCAGTCACC
CCTTCGCTGTGAAGTTGAGCT
Found at i:3946462 original size:6 final size:6
Alignment explanation
Indices: 3946446--3946484 Score: 69
Period size: 6 Copynumber: 6.3 Consensus size: 6
3946436 AAAATGAATG
3946446 AAATAAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
1 AAAT-AA AAATAA AAATAA AAATAA AAATAA AAATAA AA
3946485 GAAGTAAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 28 0.88
7 4 0.12
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:3946472 original size:18 final size:19
Alignment explanation
Indices: 3946446--3946567 Score: 77
Period size: 21 Copynumber: 5.8 Consensus size: 19
3946436 AAAATGAATG
3946446 AAATAAAAAATAAAAATAA
1 AAATAAAAAATAAAAATAA
3946465 AAAT-AAAAATAAAAATAAA
1 AAATAAAAAATAAAAAT-AA
3946484 AGAAGTAAATAAATAAAAAATAA
1 A-AA-TAAA-AAAT-AAAAATAA
*
3946507 ATGAATGAATAAATAAATAA-ATA
1 A--AAT-AAAAAATAAA-AATA-A
* **
3946530 AAATAAAAAGTTAAATCTTAA
1 AAATAAAAA-ATAAA-AATAA
3946551 AAATAATAAAATAAAAA
1 AAATAA-AAAATAAAAA
3946568 CAACTAAAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
18 12 0.15
19 7 0.09
20 6 0.07
21 20 0.24
22 10 0.12
23 16 0.20
24 11 0.13
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.20
Consensus pattern (19 bp):
AAATAAAAAATAAAAATAA
Found at i:3946498 original size:4 final size:4
Alignment explanation
Indices: 3946446--3946536 Score: 66
Period size: 4 Copynumber: 22.8 Consensus size: 4
3946436 AAAATGAATG
* *
3946446 AAAT AAA- AAAT AAA- AATAA AAAT AAA- AATAA AAAT AAA- AGAAGT
1 AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AA-AT AAAT AAAT A-AA-T
* *
3946490 AAAT AAAT AAA- AAAT AAAT GAAT GAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
3946537 AAGTTAAATC
Statistics
Matches: 73, Mismatches: 4, Indels: 20
0.75 0.04 0.21
Matches are distributed among these distances:
3 11 0.15
4 51 0.70
5 10 0.14
6 1 0.01
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (4 bp):
AAAT
Found at i:3947599 original size:28 final size:28
Alignment explanation
Indices: 3947559--3947645 Score: 165
Period size: 28 Copynumber: 3.1 Consensus size: 28
3947549 CTAATATTTA
*
3947559 ATTCCTATCGTGAACTCTGGTTGATGAG
1 ATTCCTATTGTGAACTCTGGTTGATGAG
3947587 ATTCCTATTGTGAACTCTGGTTGATGAG
1 ATTCCTATTGTGAACTCTGGTTGATGAG
3947615 ATTCCTATTGTGAACTCTGGTTGATGAG
1 ATTCCTATTGTGAACTCTGGTTGATGAG
3947643 ATT
1 ATT
3947646 AATCTTACCA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 58 1.00
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (28 bp):
ATTCCTATTGTGAACTCTGGTTGATGAG
Found at i:3949388 original size:21 final size:22
Alignment explanation
Indices: 3949353--3949394 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3949343 TGTGTTATAT
3949353 TATATTTAAAAATATTAATTAG
1 TATATTTAAAAATATTAATTAG
* *
3949375 TATATTT-TAAATATTTATTA
1 TATATTTAAAAATATTAATTA
3949395 AAATATTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
TATATTTAAAAATATTAATTAG
Found at i:3949400 original size:21 final size:22
Alignment explanation
Indices: 3949362--3949419 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
3949352 TTATATTTAA
* **
3949362 AAATATTAATTAGTATATT-TT
1 AAATATTTATTAAAATATTATT
3949383 AAATATTTATTAAAATATTATT
1 AAATATTTATTAAAATATTATT
*
3949405 AGATTATTATATTAA
1 A-AATATT-TATTAA
3949420 TATTAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 16 0.53
22 3 0.10
23 5 0.17
24 6 0.20
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (22 bp):
AAATATTTATTAAAATATTATT
Found at i:3949582 original size:31 final size:28
Alignment explanation
Indices: 3949505--3949612 Score: 76
Period size: 29 Copynumber: 3.7 Consensus size: 28
3949495 AATTTTATTA
* *
3949505 ATAATTTATTAT-ATATTAAAATAAAAAT
1 ATAATTTATTATAATATT-AAATATAATT
* * *
3949533 ATAATATCTTATATTATTATAATATAATT
1 ATAATTTATTATAATATTA-AATATAATT
*
3949562 GATTAATTTATTATAATATTAAAAATAA-T
1 -A-TAATTTATTATAATATTAAATATAATT
* *
3949591 ATTATATTATTAGAAATATTAA
1 ATAAT-TTATTA-TAATATTAA
3949613 TAAATATTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
27 3 0.05
28 18 0.29
29 20 0.32
30 7 0.11
31 15 0.24
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (28 bp):
ATAATTTATTATAATATTAAATATAATT
Found at i:3949595 original size:20 final size:20
Alignment explanation
Indices: 3949570--3949608 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3949560 TTGATTAATT
3949570 TATTATAATATTAAAAATAA
1 TATTATAATATTAAAAATAA
* *
3949590 TATTATATTATTAGAAATA
1 TATTATAATATTAAAAATA
3949609 TTAATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
TATTATAATATTAAAAATAA
Found at i:3949595 original size:23 final size:23
Alignment explanation
Indices: 3949543--3949595 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
3949533 ATAATATCTT
* *
3949543 ATATTATTATAATATAATTGATTA
1 ATATTATTATAATATAA-TAAATA
3949567 AT-TTATTATAATATTAA-AAATA
1 ATATTATTATAATA-TAATAAATA
3949589 ATATTAT
1 ATATTAT
3949596 ATTATTAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
22 5 0.20
23 15 0.60
24 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
ATATTATTATAATATAATAAATA
Found at i:3951355 original size:5 final size:5
Alignment explanation
Indices: 3951345--3951370 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3951335 ATAAAGTTTC
3951345 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
3951371 AATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:3951555 original size:33 final size:33
Alignment explanation
Indices: 3951518--3951626 Score: 155
Period size: 33 Copynumber: 3.2 Consensus size: 33
3951508 CTAAACTCGA
*
3951518 ACCCGACCTGAATATCACACTTAAAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
3951551 ACCCGACCCAAATATCACACTTAAAAAAAACCACCCG
1 ACCCGACCCGAATATCACACTT--AAAAAA--ACCCG
*
3951588 ACCCGACCCGAATATCACACTTAAAAAACCCCG
1 ACCCGACCCGAATATCACACTTAAAAAAACCCG
3951621 ACCCGA
1 ACCCGA
3951627 TCAAAATATG
Statistics
Matches: 68, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
33 30 0.44
35 12 0.18
37 26 0.38
ACGTcount: A:0.42, C:0.38, G:0.08, T:0.12
Consensus pattern (33 bp):
ACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:3951596 original size:37 final size:35
Alignment explanation
Indices: 3951518--3951615 Score: 146
Period size: 37 Copynumber: 2.8 Consensus size: 35
3951508 CTAAACTCGA
*
3951518 ACCCGACCTGAATATCACACTT--AAAAAAACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAAAACCCG
*
3951551 ACCCGACCCAAATATCACACTTAAAAAAAACCACCCG
1 ACCCGACCCGAATATCACACTTAAAAAAAA--ACCCG
3951588 ACCCGACCCGAATATCACACTTAAAAAA
1 ACCCGACCCGAATATCACACTTAAAAAA
3951616 CCCCGACCCG
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
33 20 0.34
35 6 0.10
37 32 0.55
ACGTcount: A:0.45, C:0.35, G:0.07, T:0.13
Consensus pattern (35 bp):
ACCCGACCCGAATATCACACTTAAAAAAAAACCCG
Found at i:3952150 original size:14 final size:14
Alignment explanation
Indices: 3952131--3952161 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3952121 AACGGACATA
3952131 AACGAACACAAACG
1 AACGAACACAAACG
*
3952145 AACGAACATAAACG
1 AACGAACACAAACG
3952159 AAC
1 AAC
3952162 ATAATAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:3952459 original size:10 final size:10
Alignment explanation
Indices: 3952458--3952487 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3952448 ATGAACATAA
*
3952458 ATAAATAAAC
1 ATAAATGAAC
3952468 ATAAATGAAC
1 ATAAATGAAC
3952478 ATAAATGAAC
1 ATAAATGAAC
3952488 GAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (10 bp):
ATAAATGAAC
Found at i:3952463 original size:14 final size:14
Alignment explanation
Indices: 3952444--3952473 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3952434 CTGTTCGAAT
*
3952444 ATAAATGAACATAA
1 ATAAATAAACATAA
3952458 ATAAATAAACATAA
1 ATAAATAAACATAA
3952472 AT
1 AT
3952474 GAACATAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (14 bp):
ATAAATAAACATAA
Found at i:3952492 original size:24 final size:24
Alignment explanation
Indices: 3952439--3952492 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3952429 ACTCTCTGTT
*
3952439 CGAATATAAATGAACATAAATAAA
1 CGAACATAAATGAACATAAATAAA
** *
3952463 TAAACATAAATGAACATAAATGAA
1 CGAACATAAATGAACATAAATAAA
3952487 CGAACA
1 CGAACA
3952493 AACTCTTTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.19
Consensus pattern (24 bp):
CGAACATAAATGAACATAAATAAA
Found at i:3957135 original size:37 final size:37
Alignment explanation
Indices: 3957084--3957160 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
3957074 CCTTCTGCTG
* * *
3957084 CAGTGTAGTTTTCAGTTACGTCATGACGATGTCTGAA
1 CAGTGTAGTCTTCAGTTACATCATGACGATGTCCGAA
*
3957121 CAGTGTAGTCTTCAGTTACATCATGATGATGTCCGAA
1 CAGTGTAGTCTTCAGTTACATCATGACGATGTCCGAA
3957158 CAG
1 CAG
3957161 GTGTGATACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.32
Consensus pattern (37 bp):
CAGTGTAGTCTTCAGTTACATCATGACGATGTCCGAA
Found at i:3964081 original size:15 final size:15
Alignment explanation
Indices: 3964061--3964107 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
3964051 ATAATCTTTC
3964061 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTTGAT
3964076 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTTGAT
* *
3964091 TTTCCCCTTCTGGAT
1 TTTCCCGTTCTTGAT
3964106 TT
1 TT
3964108 GGATCTGTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.06, C:0.28, G:0.13, T:0.53
Consensus pattern (15 bp):
TTTCCCGTTCTTGAT
Found at i:3965850 original size:18 final size:18
Alignment explanation
Indices: 3965824--3965858 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3965814 ACACCAAATT
3965824 TCAAGAATACTTTTAATC
1 TCAAGAATACTTTTAATC
*
3965842 TCAATAATACTTTTAAT
1 TCAAGAATACTTTTAAT
3965859 AGACAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (18 bp):
TCAAGAATACTTTTAATC
Found at i:3971645 original size:29 final size:28
Alignment explanation
Indices: 3971602--3971692 Score: 100
Period size: 29 Copynumber: 3.2 Consensus size: 28
3971592 GTTAGAACAT
3971602 TTATTTTGGGATGTCAAATTTTAAAAAAA
1 TTATTTTGGG-TGTCAAATTTTAAAAAAA
3971631 TTATTTTGTGGTGTCAAA----AAAAAAA
1 TTATTTTG-GGTGTCAAATTTTAAAAAAA
**
3971656 AAATTTTGGGTGTCAAATTTTAAAAAATA
1 TTATTTTGGGTGTCAAATTTTAAAAAA-A
3971685 TATATTTT
1 T-TATTTT
3971693 AAGGTGCTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
24 9 0.18
25 13 0.25
28 6 0.12
29 16 0.31
30 7 0.14
ACGTcount: A:0.42, C:0.03, G:0.13, T:0.42
Consensus pattern (28 bp):
TTATTTTGGGTGTCAAATTTTAAAAAAA
Found at i:3971654 original size:24 final size:24
Alignment explanation
Indices: 3971624--3971672 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
3971614 GTCAAATTTT
**
3971624 AAAAAAATTATTTTGTGGTGTCAAA
1 AAAAAAAAAATTTTG-GGTGTCAAA
3971649 AAAAAAAAAATTTTGGGTGTCAAA
1 AAAAAAAAAATTTTGGGTGTCAAA
3971673 TTTTAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.49, C:0.04, G:0.16, T:0.31
Consensus pattern (24 bp):
AAAAAAAAAATTTTGGGTGTCAAA
Found at i:3971680 original size:24 final size:24
Alignment explanation
Indices: 3971604--3971683 Score: 70
Period size: 24 Copynumber: 3.1 Consensus size: 24
3971594 TAGAACATTT
3971604 ATTTTGGGATGTCAAATTTTAAAAAAA
1 ATTTTGGG-TGTCAAATTTT--AAAAA
****
3971631 TTATTTTGTGGTGTCAAAAAAAAAAAA
1 --ATTTTG-GGTGTCAAATTTTAAAAA
3971658 ATTTTGGGTGTCAAATTTTAAAAA
1 ATTTTGGGTGTCAAATTTTAAAAA
3971682 AT
1 AT
3971684 ATATATTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
24 16 0.38
25 6 0.14
27 5 0.12
29 13 0.31
30 2 0.05
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.38
Consensus pattern (24 bp):
ATTTTGGGTGTCAAATTTTAAAAA
Found at i:3972283 original size:21 final size:21
Alignment explanation
Indices: 3972168--3972283 Score: 60
Period size: 21 Copynumber: 5.6 Consensus size: 21
3972158 GCGAAATAAA
**
3972168 AATCGCAACGCGA-TCCCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
3972188 AATCGCAAATC-AGTTTCCAA
1 AATCGCAACGCGATTTTCCAG
* *
3972208 AATCGCAACGCGATTCTT-GAC
1 AATCGCAACGCGATT-TTCCAG
* ** *
3972229 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
3972249 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
3972271 AATCGCAACGCGA
1 AATCGCAACGCGA
3972284 ATATGAAAAT
Statistics
Matches: 70, Mismatches: 20, Indels: 11
0.69 0.20 0.11
Matches are distributed among these distances:
19 1 0.01
20 25 0.36
21 40 0.57
22 4 0.06
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:3972332 original size:20 final size:20
Alignment explanation
Indices: 3972271--3972499 Score: 230
Period size: 20 Copynumber: 11.4 Consensus size: 20
3972261 GATTTTCCAG
* ** *
3972271 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
3972291 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
3972311 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
3972331 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3972351 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3972371 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3972391 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
3972411 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3972431 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3972451 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
3972471 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
3972491 AATCACAAC
1 AATCGCAAC
3972500 ACTGAAATTT
Statistics
Matches: 175, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 171 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:3973430 original size:12 final size:12
Alignment explanation
Indices: 3973413--3973437 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3973403 ATATAATCCT
3973413 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3973425 GAAGAAGAAAAA
1 GAAGAAGAAAAA
3973437 G
1 G
3973438 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:3975725 original size:20 final size:20
Alignment explanation
Indices: 3975700--3975747 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
3975690 GCATTTGACT
3975700 ATCGCAACACGGAAATTACA
1 ATCGCAACACGGAAATTACA
3975720 ATCGCAACACGGAAATTACA
1 ATCGCAACACGGAAATTACA
3975740 ATCGCAAC
1 ATCGCAAC
3975748 GAGAGAATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.15
Consensus pattern (20 bp):
ATCGCAACACGGAAATTACA
Done.