Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 121 of 172
Found at i:34537842 original size:89 final size:89
Alignment explanation
Indices: 34537793--34538204 Score: 645
Period size: 89 Copynumber: 4.7 Consensus size: 89
34537783 ACCAGTATGG
* * * * * * * *
34537793 GAAGACAAGATCT-ATATATTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCT
1 GAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
34537857 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
* * *
34537881 GAAGACAAGATCT-ATTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAGTATC
1 GAAGACAAGATCTGCTTTT-TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATC
*
34537945 TTTAATCTACTTCACGCCAGTACAT
65 TTTGATCTACTTCACGCCAGTACAT
*
34537970 GAAGACAAGATCTG-TTTTCTACGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATC
1 GAAGACAAGATCTGCTTTT-TTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATC
*
34538034 TTTGATCTACTTCACGCCAATACAT
65 TTTGATCTACTTCACGCCAGTACAT
34538059 GAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCA-C-GTATGGGAAGACAAGATCTGGTATCT
1 GAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
34538122 TTGATCTACTTCACGCCAGTACAT
66 TTGATCTACTTCACGCCAGTACAT
34538146 GAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
1 GAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTG
34538205 TATATTCGAC
Statistics
Matches: 302, Mismatches: 17, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
87 85 0.28
88 18 0.06
89 195 0.65
90 4 0.01
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (89 bp):
GAAGACAAGATCTGCTTTTTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGGTATCT
TTGATCTACTTCACGCCAGTACAT
Found at i:34537997 original size:222 final size:221
Alignment explanation
Indices: 34537589--34538133 Score: 691
Period size: 222 Copynumber: 2.5 Consensus size: 221
34537579 GACTTGTATC
* * * *
34537589 TTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTACTTCGATCTACTTCACGCCAA
1 TTCGATCTACTTCA-CACCAATATAGGAAGACAAGATCTGCTT-CTTTGATCTACTTCACGCCAG
* * * * * *
34537654 TACATGAAGACAATATCTACTTTCTTTGATCTGCTTCTCTACCAGTATGGGAAGGCAAGATCTGG
64 TACATGAAGACAAGATCTACTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG
* * *
34537719 TATCCCTGATCTACTTCACGCCAGTACATAAAGACAGGATCTGCTCTCTTCGATCTACTTCGCCA
129 TATCCCTAATCTACTTCACGCCAGTACATAAAGACAAGATCTGCTCTCTACGATCTACTTCGCCA
34537784 CCAGTATGGGAAGACAAGATCT-ATATA
194 CCAGTATGGGAAGACAAGATCTGATATA
* * * *
34537811 TTCGATCCACTTCGCTACCAATATAGGAAGACAGGATCTGGTATCTTTGATCTACTTCACGCCAG
1 TTCGATCTACTTCAC-ACCAATATAGGAAGACAAGATCTGCT-TCTTTGATCTACTTCACGCCAG
*
34537876 TACATGAAGACAAGATCTATTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG
64 TACATGAAGACAAGATCTACTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAG
** * * *
34537941 TATCTTTAATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTACGATCTACTTCGCCA
129 TATCCCTAATCTACTTCACGCCAGTACATAAAGACAAGATCTGCTCTCTACGATCTACTTCGCCA
* *
34538006 CCAGTATGGGAAGACAAGATCTGGTATC
194 CCAGTATGGGAAGACAAGATCTGATATA
* * * * *
34538034 TTTGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTTTTCGATCTACTT--CGCCACG
1 TTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGCTTCTTT-GATCTACTTCACGCCA-G
*** ** *
34538097 TATGGGAAGACAAGATCTGGTATCTTTGATCTACTTC
64 TACATGAAGACAAGATCTACTTTCTTTGATCTACTTC
34538134 ACGCCAGTAC
Statistics
Matches: 278, Mismatches: 40, Indels: 11
0.84 0.12 0.03
Matches are distributed among these distances:
220 5 0.02
221 37 0.13
222 220 0.79
223 16 0.06
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (221 bp):
TTCGATCTACTTCACACCAATATAGGAAGACAAGATCTGCTTCTTTGATCTACTTCACGCCAGTA
CATGAAGACAAGATCTACTTTCTTTGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTAGTA
TCCCTAATCTACTTCACGCCAGTACATAAAGACAAGATCTGCTCTCTACGATCTACTTCGCCACC
AGTATGGGAAGACAAGATCTGATATA
Found at i:34543724 original size:32 final size:32
Alignment explanation
Indices: 34543678--34543769 Score: 166
Period size: 32 Copynumber: 2.9 Consensus size: 32
34543668 GATATTAACA
*
34543678 AATATGTAAAACTCATATCAAGCAAGAGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
*
34543710 AATATGTAACACTCACATCAAGCAAGAGTGTT
1 AATATGTAAAACTCACATCAAGCAAGAGTGTT
34543742 AATATGTAAAACTCACATCAAGCAAGAG
1 AATATGTAAAACTCACATCAAGCAAGAG
34543770 GACTTTTATC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 57 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (32 bp):
AATATGTAAAACTCACATCAAGCAAGAGTGTT
Found at i:34548412 original size:21 final size:21
Alignment explanation
Indices: 34548388--34548427 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
34548378 TTTTTTTCTA
34548388 TTTTTGAAT-AAATTTTAAATG
1 TTTTT-AATGAAATTTTAAATG
34548409 TTTTTAATGAAATTTTAAA
1 TTTTTAATGAAATTTTAAA
34548428 ATTATTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTTAATGAAATTTTAAATG
Found at i:34552703 original size:6 final size:6
Alignment explanation
Indices: 34552692--34552744 Score: 70
Period size: 6 Copynumber: 8.8 Consensus size: 6
34552682 TTCTCGTTTT
* * *
34552692 CATTTC CATTTC CATTTT CATTTT CATTTC CATTTC CATTTT CATTTC
1 CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC CATTTC
*
34552740 TATTT
1 CATTT
34552745 TCGTTTTCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (6 bp):
CATTTC
Found at i:34552711 original size:18 final size:18
Alignment explanation
Indices: 34552677--34552755 Score: 104
Period size: 18 Copynumber: 4.3 Consensus size: 18
34552667 TGTAAATGAA
*
34552677 TTCATTTCTCGTTTTCATT
1 TTCATTTC-CATTTTCATT
*
34552696 TCCATTTCCATTTTCATT
1 TTCATTTCCATTTTCATT
*
34552714 TTCATTTCCATTTCCATT
1 TTCATTTCCATTTTCATT
* *
34552732 TTCATTTCTATTTTCGTT
1 TTCATTTCCATTTTCATT
34552750 TTCATT
1 TTCATT
34552756 CAACACGTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 46 0.87
19 7 0.13
ACGTcount: A:0.14, C:0.23, G:0.03, T:0.61
Consensus pattern (18 bp):
TTCATTTCCATTTTCATT
Found at i:34552716 original size:24 final size:24
Alignment explanation
Indices: 34552679--34552738 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
34552669 TAAATGAATT
*
34552679 CATTTCTCGTTTTCATTTCCATTTC
1 CATTT-TCATTTTCATTTCCATTTC
34552704 CATTTTCATTTTCATTTCCATTTC
1 CATTTTCATTTTCATTTCCATTTC
34552728 CATTTTCATTT
1 CATTTTCATTT
34552739 CTATTTTCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 29 0.85
25 5 0.15
ACGTcount: A:0.15, C:0.25, G:0.02, T:0.58
Consensus pattern (24 bp):
CATTTTCATTTTCATTTCCATTTC
Found at i:34552744 original size:24 final size:24
Alignment explanation
Indices: 34552689--34552744 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
34552679 CATTTCTCGT
34552689 TTTC-ATTTCCATTTCCATTTTCA
1 TTTCTATTTCCATTTCCATTTTCA
34552712 TTT-TCATTTCCATTTCCATTTTCA
1 TTTCT-ATTTCCATTTCCATTTTCA
34552736 TTTCTATTT
1 TTTCTATTT
34552745 TCGTTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 3 0.10
24 26 0.87
25 1 0.03
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTCTATTTCCATTTCCATTTTCA
Found at i:34559591 original size:21 final size:21
Alignment explanation
Indices: 34559549--34559591 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
34559539 AATTAGTGAC
*
34559549 AAATATTCTATATTATGCTTA
1 AAATATTCTATATTATACTTA
34559570 AAATATT-TATATTATACATTA
1 AAATATTCTATATTATAC-TTA
34559591 A
1 A
34559592 TGCATCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (21 bp):
AAATATTCTATATTATACTTA
Found at i:34567294 original size:68 final size:68
Alignment explanation
Indices: 34567214--34567351 Score: 276
Period size: 68 Copynumber: 2.0 Consensus size: 68
34567204 AGGAGTGTGG
34567214 AAAAGCTCATGCATGTTTGTTTGTGAGGAACTTGAAAAGACAATAATTGCTAGAAATATAAATAA
1 AAAAGCTCATGCATGTTTGTTTGTGAGGAACTTGAAAAGACAATAATTGCTAGAAATATAAATAA
34567279 GTA
66 GTA
34567282 AAAAGCTCATGCATGTTTGTTTGTGAGGAACTTGAAAAGACAATAATTGCTAGAAATATAAATAA
1 AAAAGCTCATGCATGTTTGTTTGTGAGGAACTTGAAAAGACAATAATTGCTAGAAATATAAATAA
34567347 GTA
66 GTA
34567350 AA
1 AA
34567352 TACAGTTATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (68 bp):
AAAAGCTCATGCATGTTTGTTTGTGAGGAACTTGAAAAGACAATAATTGCTAGAAATATAAATAA
GTA
Found at i:34571116 original size:22 final size:22
Alignment explanation
Indices: 34571073--34571117 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
34571063 CTTCAATCTT
**
34571073 TCAATATTCTCTCAAATTTCTC
1 TCAATATTCTCTCAAAGCTCTC
34571095 TCAAT-TTCCTCTCAAAGCTCTC
1 TCAATATT-CTCTCAAAGCTCTC
34571117 T
1 T
34571118 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 18 0.90
ACGTcount: A:0.24, C:0.31, G:0.02, T:0.42
Consensus pattern (22 bp):
TCAATATTCTCTCAAAGCTCTC
Found at i:34571519 original size:17 final size:17
Alignment explanation
Indices: 34571497--34571529 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
34571487 GTGCGTTGAT
34571497 AGAGAGGTGGAGACCCA
1 AGAGAGGTGGAGACCCA
34571514 AGAGAGGTGGAGACCC
1 AGAGAGGTGGAGACCC
34571530 GAGACACACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.42, T:0.06
Consensus pattern (17 bp):
AGAGAGGTGGAGACCCA
Found at i:34571533 original size:15 final size:16
Alignment explanation
Indices: 34571497--34571533 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
34571487 GTGCGTTGAT
34571497 AGAGAGGTGGAGACCC
1 AGAGAGGTGGAGACCC
34571513 AAGAGAGGTGGAGACCC
1 -AGAGAGGTGGAGACCC
34571530 -GAGA
1 AGAGA
34571534 CACACACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
17 16 0.80
ACGTcount: A:0.35, C:0.16, G:0.43, T:0.05
Consensus pattern (16 bp):
AGAGAGGTGGAGACCC
Found at i:34573269 original size:18 final size:18
Alignment explanation
Indices: 34573239--34573332 Score: 109
Period size: 18 Copynumber: 5.2 Consensus size: 18
34573229 TTTGGTTAAA
*
34573239 AATTAACCT-AATTAACCT
1 AATT-ACCTGAATTAACCG
34573257 AATTACCTGAATTAACCG
1 AATTACCTGAATTAACCG
*
34573275 AATTACTTGAATTAACCG
1 AATTACCTGAATTAACCG
** *
34573293 AATTACCCAAATTAACTG
1 AATTACCTGAATTAACCG
* *
34573311 AATTACCCGAATTAATCG
1 AATTACCTGAATTAACCG
34573329 AATT
1 AATT
34573333 GAATCACTAC
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
17 4 0.06
18 62 0.94
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (18 bp):
AATTACCTGAATTAACCG
Found at i:34573278 original size:27 final size:27
Alignment explanation
Indices: 34573239--34573332 Score: 95
Period size: 27 Copynumber: 3.5 Consensus size: 27
34573229 TTTGGTTAAA
*
34573239 AATTAACCTAATTAACCT-AATTACCTG
1 AATTAACCGAATTAACCTGAATTACC-G
*
34573266 AATTAACCGAATT-ACTTGAATTAACCG
1 AATTAACCGAATTAACCTGAATT-ACCG
* *
34573293 AATTACCCAAATTAA-CTGAATTACCCG
1 AATTAACCGAATTAACCTGAATTA-CCG
*
34573320 AATTAATCGAATT
1 AATTAACCGAATT
34573333 GAATCACTAC
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
26 4 0.07
27 47 0.85
28 4 0.07
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AATTAACCGAATTAACCTGAATTACCG
Found at i:34573330 original size:9 final size:9
Alignment explanation
Indices: 34573239--34573332 Score: 84
Period size: 9 Copynumber: 10.4 Consensus size: 9
34573229 TTTGGTTAAA
*
34573239 AATTAACCT
1 AATTAACCG
*
34573248 AATTAACCT
1 AATTAACCG
34573257 AATT-ACCTG
1 AATTAACC-G
34573266 AATTAACCG
1 AATTAACCG
*
34573275 AATT-ACTTG
1 AATTAAC-CG
34573284 AATTAACCG
1 AATTAACCG
* *
34573293 AATTACCCA
1 AATTAACCG
*
34573302 AATTAACTG
1 AATTAACCG
*
34573311 AATTACCCG
1 AATTAACCG
*
34573320 AATTAATCG
1 AATTAACCG
34573329 AATT
1 AATT
34573333 GAATCACTAC
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
8 5 0.07
9 59 0.86
10 5 0.07
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.31
Consensus pattern (9 bp):
AATTAACCG
Found at i:34574235 original size:116 final size:118
Alignment explanation
Indices: 34573983--34574258 Score: 441
Period size: 116 Copynumber: 2.3 Consensus size: 118
34573973 TTGTACAAAC
* * *
34573983 ATTTTGAATATTTTTATATTATTTCATGTAATGAAATAGAAGGTTGTTTTGAATAAAGTAATTGT
1 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGT
*
34574048 AATTGTAATTTACTTTTATTTTTTTAATAAAATAGAAATTCTTTTAAATAATGCAAT
66 AATTGTAATTTA---TTA-TTTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
34574105 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGT
1 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGT
34574170 AATT-TACATTTA-TA-TTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
66 AATTGTA-ATTTATTATTTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
*
34574221 ATTTTGAATATTTCTATATTATTTGATGTAATAAAATA
1 ATTTTGAATATTTCTATATTATTTCATGTAATAAAATA
34574259 TAAATAATAC
Statistics
Matches: 148, Mismatches: 5, Indels: 8
0.92 0.03 0.05
Matches are distributed among these distances:
116 73 0.49
118 2 0.01
121 2 0.01
122 71 0.48
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.47
Consensus pattern (118 bp):
ATTTTGAATATTTCTATATTATTTCATGTAATAAAATAAAAGGTTGTTTTGAATAAAGTAATTGT
AATTGTAATTTATTATTTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAAT
Found at i:34574239 original size:55 final size:55
Alignment explanation
Indices: 34574068--34574240 Score: 149
Period size: 55 Copynumber: 3.0 Consensus size: 55
34574058 TACTTTTATT
*
34574068 TTTTTAATAAAATAGAAATTCTTTTAAATAATGCAATATTTTGAATATTTCTATATTA
1 TTTTTAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTC--TA-TA
* * * * *
34574126 TTTCATGTAATAAAATA-AAAGGTTGTTTTGAATAAAG-TA-ATTGT-AAT-TTACATTTATA
1 TTT--T-TAATAAAATAGAAA--TTCTTTTAAATAAAGCAATATTTTGAATATT---TCTATA
*
34574184 TTTTTAATAAAATAGAAATTCTTTTAAATAAGGCAATATTTTGAATATTTCTATA
1 TTTTTAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTCTATA
34574239 TT
1 TT
34574241 ATTTGATGTA
Statistics
Matches: 90, Mismatches: 12, Indels: 29
0.69 0.09 0.22
Matches are distributed among these distances:
54 12 0.13
55 18 0.20
56 8 0.09
57 3 0.03
58 12 0.13
59 5 0.06
60 8 0.09
61 12 0.13
62 12 0.13
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (55 bp):
TTTTTAATAAAATAGAAATTCTTTTAAATAAAGCAATATTTTGAATATTTCTATA
Found at i:34577211 original size:24 final size:24
Alignment explanation
Indices: 34577179--34577227 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
34577169 CACTATTTGC
34577179 TTAGAAACGTCTTCTCAAAATTAT
1 TTAGAAACGTCTTCTCAAAATTAT
34577203 TTAGAAACGTCTTCTCAAAATTAT
1 TTAGAAACGTCTTCTCAAAATTAT
34577227 T
1 T
34577228 CTTTCAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (24 bp):
TTAGAAACGTCTTCTCAAAATTAT
Found at i:34577354 original size:150 final size:150
Alignment explanation
Indices: 34577083--34577354 Score: 454
Period size: 150 Copynumber: 1.8 Consensus size: 150
34577073 TAGGCCAAAT
* * * *
34577083 AGGAACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTCTTTTAGTACTTTTGCTGACAAAGCA
1 AGGAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTCAATAATTTTGCTGACAAAGCA
* *
34577148 TCTTGCTTAAAGCGTTTTCGACACTATTTGCTTAGAAACGTCTTCTCAAAATTATTTAGAAACGT
66 TCTTGCTTAAAGCGTTTTCGACACTATTTACTCAGAAACGTCTTCTCAAAATTATTTAGAAACGT
34577213 CTTCTCAAAATTATTCTTTC
131 CTTCTCAAAATTATTCTTTC
* *
34577233 AGGAACTACTGTAGCAAAAAAGCGTTCACGTGGGAGCTTCTTTCAATAATTTTGCTGACAAAGCG
1 AGGAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTCAATAATTTTGCTGACAAAGCA
* *
34577298 TCTTGCTTAAAGCGTTTTTGACACTATTTACTCAGAAACGTCTTTTCAAAATTATTT
66 TCTTGCTTAAAGCGTTTTCGACACTATTTACTCAGAAACGTCTTCTCAAAATTATTT
34577355 TTCAGGAACT
Statistics
Matches: 112, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
150 112 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (150 bp):
AGGAACTACTGTAGCAAAAAAGCGTCCACGTGGGAGCTTCTTTCAATAATTTTGCTGACAAAGCA
TCTTGCTTAAAGCGTTTTCGACACTATTTACTCAGAAACGTCTTCTCAAAATTATTTAGAAACGT
CTTCTCAAAATTATTCTTTC
Found at i:34577530 original size:104 final size:104
Alignment explanation
Indices: 34577412--34577781 Score: 393
Period size: 104 Copynumber: 3.7 Consensus size: 104
34577402 AATTAAACAA
* * * *
34577412 TAATTTAATTAAGTAACCCTAAACCCCAAACCCTGATTTATTTAATTTTTTTCTTAAAAACCCTA
1 TAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAATTTTTTCCTTAAAAACCCTA
* * *
34577477 AACCCTAAACTCTAATCTAATTTTTTTAAAATTTATAAT
66 AACACTAAACCCTAATCTAATTTTTTAAAAATTTATAAT
* * * * *
34577516 TAATGTACTGAAGTAACCCTAAACCCCAAGCCCTAATTTATTTGATTTTTTCCTTAAAAATCCTA
1 TAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAATTTTTTCCTTAAAAACCCTA
34577581 AACACTAAACCCTAATCTAATTTTTTAAAAATTTATAAT
66 AACACTAAACCCTAATCTAATTTTTTAAAAATTTATAAT
** * * *
34577620 TAATTTACTCAAG-----C--AACCTTAAGCTCTAATTTATTTAATTTTTTCCTTAAAAACCATA
1 TAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAATTTTTTCCTTAAAAACCCTA
* * * **
34577678 AAAACGAAACCCTAATCTAA--TTTAAAAAAAATATAAT
66 AACACTAAACCCTAATCTAATTTTTTAAAAATTTATAAT
* * * * * * *
34577715 TAATTTAATTAAGAAACCCTAAACCCTAAACTC-ATATTTATTT-ATTTTTTTCTTTAAAACCCT
1 TAATTTACTCAAGTAACCCTAAACCCCAAACCCTA-ATTTATTTAATTTTTTCCTTAAAAACCCT
34577778 AAAC
65 AAAC
34577782 CCCAAAACCC
Statistics
Matches: 226, Mismatches: 32, Indels: 19
0.82 0.12 0.07
Matches are distributed among these distances:
95 25 0.11
97 56 0.25
99 1 0.00
100 1 0.00
101 21 0.09
102 18 0.08
104 104 0.46
ACGTcount: A:0.40, C:0.19, G:0.03, T:0.38
Consensus pattern (104 bp):
TAATTTACTCAAGTAACCCTAAACCCCAAACCCTAATTTATTTAATTTTTTCCTTAAAAACCCTA
AACACTAAACCCTAATCTAATTTTTTAAAAATTTATAAT
Found at i:34581794 original size:33 final size:33
Alignment explanation
Indices: 34581723--34581804 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
34581713 CATCATGAGG
**
34581723 TAGTCCACTGGGACAGTAAGCATTGAACAGAGA
1 TAGTCCACTGGGACAGTAAGCACAGAACAGAGA
* *
34581756 TAGTCCACTGGGATAGTAAGCACAG-ACATAGA
1 TAGTCCACTGGGACAGTAAGCACAGAACAGAGA
* *
34581788 TAAGTCCGCTAGGACAG
1 T-AGTCCACTGGGACAG
34581805 CAAACACAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
32 7 0.17
33 34 0.83
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (33 bp):
TAGTCCACTGGGACAGTAAGCACAGAACAGAGA
Found at i:34581838 original size:29 final size:28
Alignment explanation
Indices: 34581785--34581844 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 28
34581775 GCACAGACAT
*
34581785 AGATAAGTCCGCTAGGACAGCAAACACA
1 AGATAAGTCCGCTAGGACAACAAACACA
* *
34581813 AGATAACGTCCGCTAGGACAATAAACATA
1 AGATAA-GTCCGCTAGGACAACAAACACA
34581842 AGA
1 AGA
34581845 ACTGTTCGCC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (28 bp):
AGATAAGTCCGCTAGGACAACAAACACA
Found at i:34596846 original size:21 final size:21
Alignment explanation
Indices: 34596822--34596879 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 21
34596812 AATACTATTA
34596822 TTTAAAATAACTTTATACAAT
1 TTTAAAATAACTTTATACAAT
* *
34596843 TTTAACCA-AAC-ATA-ACAAT
1 TTTAA-AATAACTTTATACAAT
34596862 TTTATAAATAACTTTATA
1 TTTA-AAATAACTTTATA
34596880 TTAAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
19 10 0.36
20 6 0.21
21 10 0.36
22 2 0.07
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.40
Consensus pattern (21 bp):
TTTAAAATAACTTTATACAAT
Found at i:34597368 original size:14 final size:14
Alignment explanation
Indices: 34597349--34597393 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
34597339 ATAAGGAAAT
34597349 ATAAATGAAATATA
1 ATAAATGAAATATA
* *
34597363 ATAAAT---ATTTT
1 ATAAATGAAATATA
34597374 ATAAATGAAATATA
1 ATAAATGAAATATA
34597388 ATAAAT
1 ATAAAT
34597394 ATTCAAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
11 9 0.38
14 15 0.62
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
ATAAATGAAATATA
Found at i:34597376 original size:25 final size:25
Alignment explanation
Indices: 34597348--34597396 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
34597338 TATAAGGAAA
34597348 TATAAATGAAATATAATAAATATTT
1 TATAAATGAAATATAATAAATATTT
34597373 TATAAATGAAATATAATAAATATT
1 TATAAATGAAATATAATAAATATT
34597397 CAAAAAGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (25 bp):
TATAAATGAAATATAATAAATATTT
Found at i:34599103 original size:14 final size:14
Alignment explanation
Indices: 34599084--34599125 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
34599074 TATTTTACCC
* *
34599084 TGAACCTCGAACTT
1 TGAACCTCAAACCT
*
34599098 TGAACCTTAAACCT
1 TGAACCTCAAACCT
34599112 TGAACCTCAAACCT
1 TGAACCTCAAACCT
34599126 CGAGGTTCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.33, C:0.31, G:0.10, T:0.26
Consensus pattern (14 bp):
TGAACCTCAAACCT
Found at i:34600413 original size:4 final size:4
Alignment explanation
Indices: 34600404--34600452 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
34600394 AAAGAAAAAA
* * * *
34600404 ATGT ATGT ATGT ATGT ATGT ATGT AAGC AAGT ATGT ATGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
34600452 A
1 A
34600453 ACATGTTAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (4 bp):
ATGT
Found at i:34603515 original size:30 final size:31
Alignment explanation
Indices: 34603459--34603545 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 31
34603449 TGGGTAACCT
* * * *
34603459 TGATATAATATCAACTTG-AGTGAGCAACCC
1 TGATATAATGTCAACTTGTAGTAAGCAAACA
*
34603489 TGTTATAATGTCAACTTGTA-TAAGCAAACA
1 TGATATAATGTCAACTTGTAGTAAGCAAACA
* *
34603519 TGATATAATGTCATCTTGT-GTATGCAA
1 TGATATAATGTCAACTTGTAGTAAGCAA
34603546 TTTAATCACC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
30 46 0.98
31 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (31 bp):
TGATATAATGTCAACTTGTAGTAAGCAAACA
Found at i:34606183 original size:30 final size:30
Alignment explanation
Indices: 34606147--34606205 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
34606137 AATCAAGCAT
* *
34606147 TGAAAATCCCAATCTGTAATTTTGCTTCAG
1 TGAAAATCCCAATATCTAATTTTGCTTCAG
34606177 TGAAAATCCCAATATCTAATTTTGCTTCA
1 TGAAAATCCCAATATCTAATTTTGCTTCA
34606206 AACTATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.37
Consensus pattern (30 bp):
TGAAAATCCCAATATCTAATTTTGCTTCAG
Found at i:34608891 original size:27 final size:27
Alignment explanation
Indices: 34608855--34609039 Score: 155
Period size: 27 Copynumber: 6.9 Consensus size: 27
34608845 TAAAAGTTAA
*
34608855 AACATTATATTAAAACATTATATTTAT
1 AACAATATATTAAAACATTATATTTAT
34608882 AACAATATATTAAAACAATT-TA-TTA-
1 AACAATATATTAAAAC-ATTATATTTAT
* * * * *
34608907 AAAAAGTATATTTATAATAGTATA-TTAA
1 AACAA-TATA-TTAAAACATTATATTTAT
* * * *
34608935 AACAATATATTTATA-ATAATATATTAA
1 AACAATATATTAAAACATTATAT-TTAT
* *
34608962 AACAATATATTAAAAAAGTATATTTAT
1 AACAATATATTAAAACATTATATTTAT
* * *
34608989 AATAGTATATTAAAACAATATATTTAT
1 AACAATATATTAAAACATTATATTTAT
*
34609016 AACAATATATTAAAACAATATATT
1 AACAATATATTAAAACATTATATT
34609040 AAAAAAGTAT
Statistics
Matches: 128, Mismatches: 22, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
25 8 0.06
26 12 0.09
27 96 0.75
28 12 0.09
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (27 bp):
AACAATATATTAAAACATTATATTTAT
Found at i:34608895 original size:40 final size:40
Alignment explanation
Indices: 34608851--34609052 Score: 189
Period size: 40 Copynumber: 5.0 Consensus size: 40
34608841 ATATTAAAAG
* * *
34608851 TTAAAACATTATATTAAAACATTATATTTATAACAATATA
1 TTAAAACAATATATTAAAACAGTATATTTAAAACAATATA
* * * * *
34608891 TTAAAACAATTTATTAAAAAAGTATATTTATAATAGTATA
1 TTAAAACAATATATTAAAACAGTATATTTAAAACAATATA
* * *
34608931 TTAAAACAATATATTTATAATAATATA-TTAAAACAATATA
1 TTAAAACAATATA-TTAAAACAGTATATTTAAAACAATATA
* *
34608971 TTAAAA-AAGTATATTTATAATAGTATA-TTAAAACAATATA
1 TTAAAACAA-TATA-TTAAAACAGTATATTTAAAACAATATA
* *
34609011 TTTATAACAATATATTAAAACAATATA-TTAAAA-AAGTATA
1 -TTAAAACAATATATTAAAACAGTATATTTAAAACAA-TATA
34609051 TT
1 TT
34609053 TATAATAGTA
Statistics
Matches: 139, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
39 6 0.04
40 112 0.81
41 19 0.14
42 2 0.01
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (40 bp):
TTAAAACAATATATTAAAACAGTATATTTAAAACAATATA
Found at i:34608932 original size:67 final size:67
Alignment explanation
Indices: 34608860--34609069 Score: 393
Period size: 67 Copynumber: 3.1 Consensus size: 67
34608850 GTTAAAACAT
* *
34608860 TATATTAAAACATTATATTTATAACAATATATTAAAACAATTTATTAAAAAAGTATATTTATAAT
1 TATATTAAAACAATATATTTATAACAATATATTAAAACAATATATTAAAAAAGTATATTTATAAT
34608925 AG
66 AG
*
34608927 TATATTAAAACAATATATTTATAATAATATATTAAAACAATATATTAAAAAAGTATATTTATAAT
1 TATATTAAAACAATATATTTATAACAATATATTAAAACAATATATTAAAAAAGTATATTTATAAT
34608992 AG
66 AG
34608994 TATATTAAAACAATATATTTATAACAATATATTAAAACAATATATTAAAAAAGTATATTTATAAT
1 TATATTAAAACAATATATTTATAACAATATATTAAAACAATATATTAAAAAAGTATATTTATAAT
34609059 AG
66 AG
34609061 TATATTAAA
1 TATATTAAA
34609070 TGTTAAAATA
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 139 1.00
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (67 bp):
TATATTAAAACAATATATTTATAACAATATATTAAAACAATATATTAAAAAAGTATATTTATAAT
AG
Found at i:34609064 original size:27 final size:25
Alignment explanation
Indices: 34608851--34609069 Score: 152
Period size: 27 Copynumber: 8.2 Consensus size: 25
34608841 ATATTAAAAG
* * *
34608851 TTAAAACATTATATTAAAACATTATA
1 TTAAAA-AATATATTAAAATAATATA
* * *
34608877 TTTATAACAATATATTAAAACAATTTA
1 -TTA-AAAAATATATTAAAATAATATA
* *
34608904 TTAAAAAAGTATATTTATAATAGTATA
1 TTAAAAAA-TATA-TTAAAATAATATA
*
34608931 TTAAAACAATATATTTATAATAATATA
1 TTAAAA-AATATA-TTAAAATAATATA
34608958 TTAAAACAATATATTAAAA-AAGTATA
1 TTAAAA-AATATATTAAAATAA-TATA
* * *
34608984 TTTATAATAGTATATTAAAACAATATA
1 -TTA-AAAAATATATTAAAATAATATA
* *
34609011 TTTATAACAATATATTAAAACAATATA
1 -TTA-AAAAATATATTAAAATAATATA
* *
34609038 TTAAAAAAGTATATTTATAATAGTATA
1 TTAAAAAA-TATA-TTAAAATAATATA
34609065 TTAAA
1 TTAAA
34609070 TGTTAAAATA
Statistics
Matches: 163, Mismatches: 19, Indels: 20
0.81 0.09 0.10
Matches are distributed among these distances:
25 10 0.06
26 23 0.14
27 122 0.75
28 8 0.05
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (25 bp):
TTAAAAAATATATTAAAATAATATA
Found at i:34609104 original size:22 final size:20
Alignment explanation
Indices: 34609051--34609129 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
34609041 AAAAAGTATA
34609051 TTTATAATAGTATATTAAAT
1 TTTATAATAGTATATTAAAT
* *
34609071 GTTAAAATAGTATATTACAAAT
1 TTTATAATAGTATATT--AAAT
* *
34609093 TTTATAACAGTA-ATCAATAT
1 TTTATAATAGTATATTAA-AT
* *
34609113 ATTAAAATAGTATATTA
1 TTTATAATAGTATATTA
34609130 CATTAAAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
19 2 0.04
20 25 0.56
21 5 0.11
22 13 0.29
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (20 bp):
TTTATAATAGTATATTAAAT
Found at i:34612201 original size:22 final size:22
Alignment explanation
Indices: 34612143--34612190 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
34612133 GCGACTTATC
* *
34612143 ACAATTTACTAGCAGCTTGTTT
1 ACAACTTACTAGCAGCTTGTCT
*
34612165 GCAACTTACTAGCAGCTTGTCT
1 ACAACTTACTAGCAGCTTGTCT
34612187 ACAA
1 ACAA
34612191 ACTATTAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (22 bp):
ACAACTTACTAGCAGCTTGTCT
Found at i:34614789 original size:19 final size:19
Alignment explanation
Indices: 34614765--34614845 Score: 96
Period size: 19 Copynumber: 4.4 Consensus size: 19
34614755 AATCTTCAAG
34614765 GATATGAAATCTTAGATAT
1 GATATGAAATCTTAGATAT
*
34614784 GATATGCAATCTTAGATAT
1 GATATGAAATCTTAGATAT
*
34614803 AATAT-ATAATCTTAGATAT
1 GATATGA-AATCTTAGATAT
* *
34614822 GGTATGCAATCTTAGA-A-
1 GATATGAAATCTTAGATAT
34614839 GATATGA
1 GATATGA
34614846 TTTTGTAATC
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
17 5 0.10
18 1 0.02
19 46 0.88
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGAAATCTTAGATAT
Found at i:34615507 original size:22 final size:22
Alignment explanation
Indices: 34615467--34615539 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
34615457 ATACGCATAT
* *
34615467 TTATTTTTTGTAGTATAATATAA
1 TTATTTTTTATA-TGTAATATAA
34615490 TTATTTTTTATATGTAAT-T-A
1 TTATTTTTTATATGTAATATAA
* *
34615510 TTTTTTTATCTATATGT-ATATAT
1 TTATTTT-T-TATATGTAATATAA
34615533 TTATTTT
1 TTATTTT
34615540 AGTATACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
20 7 0.17
21 4 0.10
22 13 0.32
23 17 0.41
ACGTcount: A:0.29, C:0.01, G:0.05, T:0.64
Consensus pattern (22 bp):
TTATTTTTTATATGTAATATAA
Found at i:34615545 original size:22 final size:22
Alignment explanation
Indices: 34615484--34615545 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 22
34615474 TTGTAGTATA
* *
34615484 ATATAATTATTTT-TTATATGT
1 ATATATTTATTTTACTATATGT
34615505 A-ATTATTT-TTTTATCTATATGT
1 ATA-TATTTATTTTA-CTATATGT
*
34615527 ATATATTTATTTTAGTATA
1 ATATATTTATTTTACTATA
34615546 CATATGTATG
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 5 0.15
21 5 0.15
22 17 0.52
23 6 0.18
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (22 bp):
ATATATTTATTTTACTATATGT
Found at i:34619960 original size:24 final size:24
Alignment explanation
Indices: 34619933--34619978 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
34619923 ACAGAATTTT
34619933 TTAAAAATTAGTTTTTAAATTACA
1 TTAAAAATTAGTTTTTAAATTACA
*
34619957 TTAAAAATTATTTTTTAAATTA
1 TTAAAAATTAGTTTTTAAATTA
34619979 TTTTATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (24 bp):
TTAAAAATTAGTTTTTAAATTACA
Found at i:34625021 original size:23 final size:24
Alignment explanation
Indices: 34624963--34625023 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 24
34624953 ATATATATAT
* *
34624963 ATATATATTAAGTTTTTACTTTCA
1 ATATATATTAAGTTTTGACTATCA
*
34624987 ATA-A-ATTAAGTTTTGA-TATGA
1 ATATATATTAAGTTTTGACTATCA
34625008 ATATATATTAAGTTTT
1 ATATATATTAAGTTTT
34625024 AATTCTAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
21 6 0.19
22 12 0.38
23 11 0.34
24 3 0.09
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.51
Consensus pattern (24 bp):
ATATATATTAAGTTTTGACTATCA
Found at i:34626319 original size:17 final size:17
Alignment explanation
Indices: 34626299--34626332 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
34626289 AAACCCAAAT
34626299 AAAGAAA-ATACAAAAAA
1 AAAGAAACA-ACAAAAAA
34626316 AAAGAAACAACAAAAAA
1 AAAGAAACAACAAAAAA
34626333 CAGAAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.94
18 1 0.06
ACGTcount: A:0.82, C:0.09, G:0.06, T:0.03
Consensus pattern (17 bp):
AAAGAAACAACAAAAAA
Found at i:34627267 original size:11 final size:11
Alignment explanation
Indices: 34627247--34627284 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
34627237 AGCTCGGCCC
34627247 ATATTAAATAT
1 ATATTAAATAT
*
34627258 ATATTTAATAT
1 ATATTAAATAT
*
34627269 ATATAAAATAT
1 ATATTAAATAT
34627280 ATATT
1 ATATT
34627285 TGATTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:34630977 original size:13 final size:13
Alignment explanation
Indices: 34630961--34630998 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
34630951 TTTAAACCAA
34630961 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
34630974 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
34630987 ACTTTTCAAAAG
1 ACTTTTCAAAAG
34630999 AAATGAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 4 0.19
13 13 0.62
14 4 0.19
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:34636021 original size:28 final size:28
Alignment explanation
Indices: 34635985--34636084 Score: 191
Period size: 28 Copynumber: 3.6 Consensus size: 28
34635975 TAATGAGATT
34635985 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTGATTATTA
34636013 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTGATTATTA
*
34636041 AGCACTAAGTGTGCGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGATTGATTATTA
34636069 AGCACTAAGTGTGCGA
1 AGCACTAAGTGTGCGA
34636085 ACTTATTAAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTGATTATTA
Found at i:34637015 original size:141 final size:142
Alignment explanation
Indices: 34636808--34637324 Score: 815
Period size: 141 Copynumber: 3.7 Consensus size: 142
34636798 TAATGCTTAA
* * *
34636808 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGATGTAAAAATGCTGCTCAATTTGGT
34636873 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
66 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
*
34636938 TTTATTGTATTT
131 TTTGTTGTATTT
*
34636950 ATGCTGCCCAAATTGTTGTATATATGCTATCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGATGTAAAAATGCTGCTCAATTTGGT
*
34637014 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCTAATTTTTGGTGTAAAAATGCTGCTCAA
66 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
34637079 TTTGTTGTATTT
131 TTTGTTGTATTT
* *
34637091 ATGCTGCCCAAATTGTTGTATATATGCTGGCC-AGTTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGATGTAAAAATGCTGCTCAATTTGGT
* * **
34637155 ATATATATGCTGCCTAATTTGCTGTATATATGCTGTCCAATTTTTGGTGTAAAAATATTGCTCAA
66 ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
* *
34637220 ATTGTTGTATAT
131 TTTGTTGTATTT
* * *
34637232 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGCTG-TCTAGTTTGG
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGATGTAAAAATGCTGCTC-AATTTGG
* * * *
34637296 TATATAAATGCTGTCCAAATTGATGTATA
65 TATATATATGCTGCCCAATTTGTTGTATA
34637325 AGAGCAGTCC
Statistics
Matches: 347, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
141 269 0.78
142 78 0.22
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (142 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGATGTAAAAATGCTGCTCAATTTGGT
ATATATATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAA
TTTGTTGTATTT
Found at i:34637325 original size:23 final size:23
Alignment explanation
Indices: 34636808--34637324 Score: 294
Period size: 23 Copynumber: 22.0 Consensus size: 23
34636798 TAATGCTTAA
* * * *
34636808 ATGCTGCCCAAATTGTTATATAT
1 ATGCTGTCCAATTTGGTGTATAT
* *
34636831 ATGCTGTCCAAATTTTGGTGTAAAA
1 ATGCTGTCC-AA-TTTGGTGTATAT
* *
34636856 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* *
34636879 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* *
34636902 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
** *
34636927 ATGCTG-CTCAATTTATTGTATTT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
34636950 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * * *
34636973 ATGCTATCCAATTTTGATGTAAAA
1 ATGCTGTCCAA-TTTGGTGTATAT
*
34636997 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* *
34637020 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * *
34637043 ATGCTGTCTAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
* *
34637068 ATGCTG-CTCAATTTGTTGTATTT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
34637091 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
* * * * *
34637114 ATGCTGGCCAGTTTTGATGTAAAA
1 ATGCTGTCCA-ATTTGGTGTATAT
*
34637138 ATGCTG-CTCAATTTGGTATATAT
1 ATGCTGTC-CAATTTGGTGTATAT
*
34637161 ATGCTG-CCTAATTTGCTGTATAT
1 ATGCTGTCC-AATTTGGTGTATAT
* *
34637184 ATGCTGTCCAATTTTTGGTGTAAAA
1 ATGCTGTCCAA--TTTGGTGTATAT
** * *
34637209 ATATTG-CTCAAATTGTTGTATAT
1 ATGCTGTC-CAATTTGGTGTATAT
* * *
34637232 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGTCCAATTTGGTGTATAT
*
34637255 ATGCTGTCCAAATTTTGGTGTGA-AA
1 ATGCTGTCC-AA-TTTGGTGT-ATAT
* * * *
34637280 ATGCTGTCTAGTTTGGTATATAA
1 ATGCTGTCCAATTTGGTGTATAT
* *
34637303 ATGCTGTCCAAATTGATGTATA
1 ATGCTGTCCAATTTGGTGTATA
34637325 AGAGCAGTCC
Statistics
Matches: 381, Mismatches: 86, Indels: 54
0.73 0.17 0.10
Matches are distributed among these distances:
22 2 0.01
23 249 0.65
24 50 0.13
25 79 0.21
26 1 0.00
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (23 bp):
ATGCTGTCCAATTTGGTGTATAT
Found at i:34637337 original size:71 final size:71
Alignment explanation
Indices: 34636808--34637324 Score: 707
Period size: 71 Copynumber: 7.3 Consensus size: 71
34636798 TAATGCTTAA
* *
34636808 ATGCTGCCCAAATTGTTATATATATGCTGTCCAAATTTTGGTGTAAAAATGTTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
34636873 ATATAT
66 ATATAT
* * **
34636879 ATGCTGCCCAATTTGTTGTATATATGCTGTCCAATTTTTGGTGTAAAAATGCTGCTCAATTTATT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
34636944 GTATTT
66 ATATAT
* *
34636950 ATGCTGCCCAAATTGTTGTATATATGCTATCC-AATTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
34637014 ATATAT
66 ATATAT
* * * *
34637020 ATGCTGCCCAATTTGTTGTATATATGCTGTCTAATTTTTGGTGTAAAAATGCTGCTCAATTTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
* *
34637085 GTATTT
66 ATATAT
* * *
34637091 ATGCTGCCCAAATTGTTGTATATATGCTGGCC-AGTTTTGATGTAAAAATGCTGCTCAATTTGGT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
34637155 ATATAT
66 ATATAT
* * * * ** * *
34637161 ATGCTGCCTAATTTGCTGTATATATGCTGTCCAATTTTTGGTGTAAAAATATTGCTCAAATTGTT
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
*
34637226 GTATAT
66 ATATAT
* *
34637232 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGCTG-TCTAGTTTGG
1 ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTC-AATTTGG
*
34637296 TATATAA
65 TATATAT
* *
34637303 ATGCTGTCCAAATTGATGTATA
1 ATGCTGCCCAAATTGTTGTATA
34637325 AGAGCAGTCC
Statistics
Matches: 386, Mismatches: 57, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
70 124 0.32
71 262 0.68
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (71 bp):
ATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTAAAAATGCTGCTCAATTTGGT
ATATAT
Found at i:34637947 original size:40 final size:40
Alignment explanation
Indices: 34637903--34637997 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
34637893 CATGGCTATG
* **
34637903 TCTCGTGCACGGCCACACCTACAACAGTCACACGGTCGTA
1 TCTCGTACACGGCCACACCTACAACAGTCACACGACCGTA
* * * *
34637943 TCTCGTACACGGCCACATCTACGACAGTCACATGACCGTG
1 TCTCGTACACGGCCACACCTACAACAGTCACACGACCGTA
34637983 TCTCGTACACGGCCA
1 TCTCGTACACGGCCA
34637998 TGCACACGTC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.24, C:0.37, G:0.20, T:0.19
Consensus pattern (40 bp):
TCTCGTACACGGCCACACCTACAACAGTCACACGACCGTA
Found at i:34640111 original size:30 final size:30
Alignment explanation
Indices: 34640075--34640158 Score: 141
Period size: 30 Copynumber: 2.8 Consensus size: 30
34640065 GTAATCTCGA
*
34640075 TATAATGTCAGCTTATGTGAGCAATCCGGT
1 TATAATGTCAGCTTGTGTGAGCAATCCGGT
*
34640105 TATAATGTCAACTTGTGTGAGCAATCCGGT
1 TATAATGTCAGCTTGTGTGAGCAATCCGGT
*
34640135 TATAATTTCAGCTTGTGTGAGCAA
1 TATAATGTCAGCTTGTGTGAGCAA
34640159 CTCTAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (30 bp):
TATAATGTCAGCTTGTGTGAGCAATCCGGT
Found at i:34645512 original size:265 final size:262
Alignment explanation
Indices: 34644998--34645514 Score: 698
Period size: 265 Copynumber: 2.0 Consensus size: 262
34644988 TATATATTTC
*
34644998 ATACAAATATATAATTTTTATATGATATAAATTAGATAATATATATATAAGAACAAACAAAAGAA
1 ATACAAATATATAATTTTTATATGATATAAATTACATAATATATATATAAGAACAAACAAAAGAA
* * * * * *
34645063 TAATGCATTATAGAATTAAAAAGGTTGAGCTGGCTTGGGTCTTAAATATTGGAGCTCAAACTTAC
66 TAACGCATTATAAAATTAAAAAGGTTAAACTGGCTTGGGTCTTAAATATGGGAGCTCAAACCTAC
* * * * ** *
34645128 CCATTTGTAGACGAGCCTATTTTTGCCCAAGCCATTTTTTGGACTTAATATTTTTTTTAAATCTT
131 ACATTTCTAGACGAGACTATTTTTGCCAAAGCCATTTTTTGGACTTAATATTTTCATGAAATCTT
* * ** **
34645193 CTCAAATCAAATGAGCCTTTGAGTTTGAACATATAATTTCATGTTTGGATATGTCTAGTTTCAAG
196 CTCAAATCAAATGAGCCTTTGAGTTTGAACAGATAATTTAACCTTTAAATATGTCTAGTTTCAAG
34645258 TA
261 TA
* **
34645260 ATACAAATATATAATTTTTATATGATATAAATTACATAATCTATA-A-AAGAACAAATGAAAGAA
1 ATACAAATATATAATTTTTATATGATATAAATTACATAATATATATATAAGAACAAACAAAAGAA
* *
34645323 TAACGCATTATAAAATTAAAAAGGTTAAACTGGGCTTGGGTCTTAAATATGGGAGCTTAAGCCTA
66 TAACGCATTATAAAATTAAAAAGGTTAAACT-GGCTTGGGTCTTAAATATGGGAGCTCAAACCTA
* *
34645388 CACATTTCTAGACGAGACTAGATTTTTGTCAAAGCCCATTTTTTGGGCTTAATAATTTTCATGAA
130 CACATTTCTAGACGAGACT--ATTTTTGCCAAAG-CCATTTTTTGGACTTAAT-ATTTTCATGAA
* *
34645453 A-CATTTTCAAATCAAATGAGTCTTTGAGTTTGAACAGATAATTTAACCTTTAAATATGTCTA
191 ATC-TTCTCAAATCAAATGAGCCTTTGAGTTTGAACAGATAATTTAACCTTTAAATATGTCTA
34645515 ATTGATTTTT
Statistics
Matches: 220, Mismatches: 29, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
260 42 0.19
261 46 0.21
262 43 0.20
263 11 0.05
264 18 0.08
265 60 0.27
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (262 bp):
ATACAAATATATAATTTTTATATGATATAAATTACATAATATATATATAAGAACAAACAAAAGAA
TAACGCATTATAAAATTAAAAAGGTTAAACTGGCTTGGGTCTTAAATATGGGAGCTCAAACCTAC
ACATTTCTAGACGAGACTATTTTTGCCAAAGCCATTTTTTGGACTTAATATTTTCATGAAATCTT
CTCAAATCAAATGAGCCTTTGAGTTTGAACAGATAATTTAACCTTTAAATATGTCTAGTTTCAAG
TA
Found at i:34648728 original size:16 final size:16
Alignment explanation
Indices: 34648707--34648756 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
34648697 GGTTGAATAT
34648707 TTTAAATTTTTTTGAA
1 TTTAAATTTTTTTGAA
* *
34648723 TTTAAATATTTTTAAA
1 TTTAAATTTTTTTGAA
* *
34648739 TTCAAATTATTTTCGAA
1 TTTAAATT-TTTTTGAA
34648756 T
1 T
34648757 AATTGAATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (16 bp):
TTTAAATTTTTTTGAA
Found at i:34648876 original size:6 final size:6
Alignment explanation
Indices: 34648865--34648893 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
34648855 TGCGTTGGTT
34648865 CCATAG CCATAG CCATAG CCATAG CCATA
1 CCATAG CCATAG CCATAG CCATAG CCATA
34648894 TGTCATCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.34, G:0.14, T:0.17
Consensus pattern (6 bp):
CCATAG
Found at i:34650765 original size:14 final size:14
Alignment explanation
Indices: 34650748--34650777 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34650738 CGGGTGTTTG
*
34650748 TTGTTTTTTGTTCT
1 TTGTTCTTTGTTCT
34650762 TTGTTCTTTGTTCT
1 TTGTTCTTTGTTCT
34650776 TT
1 TT
34650778 TCCTTGAATG
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:0.00, C:0.10, G:0.13, T:0.77
Consensus pattern (14 bp):
TTGTTCTTTGTTCT
Found at i:34650839 original size:15 final size:15
Alignment explanation
Indices: 34650808--34650849 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
34650798 TTTTCCATTT
34650808 TTAAAAA-AATA-AA
1 TTAAAAATAATATAA
34650821 TTAAAAATAATATAA
1 TTAAAAATAATATAA
* *
34650836 TTAATAATTATATA
1 TTAAAAATAATATA
34650850 TGTTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 7 0.28
14 4 0.16
15 14 0.56
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAAAAATAATATAA
Found at i:34654482 original size:29 final size:27
Alignment explanation
Indices: 34654423--34654485 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
34654413 TGCATCGACC
34654423 GTGTGTGTCCCACGGCCTAGCACACTG
1 GTGTGTGTCCCACGGCCTAGCACACTG
34654450 GTGTGTGTCCCACGGCCTAGCACACTG
1 GTGTGTGTCCCACGGCCTAGCACACTG
34654477 GTGTGTGTC
1 GTGTGTGTC
34654486 TTGGTCGTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.13, C:0.30, G:0.32, T:0.25
Consensus pattern (27 bp):
GTGTGTGTCCCACGGCCTAGCACACTG
Found at i:34654699 original size:43 final size:43
Alignment explanation
Indices: 34654651--34654748 Score: 187
Period size: 43 Copynumber: 2.3 Consensus size: 43
34654641 GCAGCATGGA
*
34654651 ACACGGGCGTGTCACTTGGCCGTGTGAGCCACATGGTCTGGCC
1 ACACGGGCGTGTCACTTGGCCGTGTGAGCCACACGGTCTGGCC
34654694 ACACGGGCGTGTCACTTGGCCGTGTGAGCCACACGGTCTGGCC
1 ACACGGGCGTGTCACTTGGCCGTGTGAGCCACACGGTCTGGCC
34654737 ACACGGGCGTGT
1 ACACGGGCGTGT
34654749 GTCCCCTGCA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.14, C:0.31, G:0.36, T:0.19
Consensus pattern (43 bp):
ACACGGGCGTGTCACTTGGCCGTGTGAGCCACACGGTCTGGCC
Found at i:34657864 original size:28 final size:28
Alignment explanation
Indices: 34657832--34657900 Score: 102
Period size: 28 Copynumber: 2.5 Consensus size: 28
34657822 TAATGAGATT
* *
34657832 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGATTAATTATAA
* *
34657860 AGCACTAAGTGTGCGAGATTGATTATTA
1 AGCACTAAGTGTGCGAGATTAATTATAA
34657888 AGCACTAAGTGTG
1 AGCACTAAGTGTG
34657901 TGAACTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGATTAATTATAA
Found at i:34658657 original size:23 final size:23
Alignment explanation
Indices: 34658627--34658991 Score: 169
Period size: 23 Copynumber: 15.6 Consensus size: 23
34658617 TGATGCTTAA
* *
34658627 ATGCTGCC-CAATTCGTTGTATTT
1 ATGCTGCCTAAATT-GTTGTATAT
34658650 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
34658673 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * * *
34658696 ATGTTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * * *
34658720 ATGTTG-CTCAATTTGGTATATAT
1 ATGCTGCCT-AAATTGTTGTATAT
*
34658743 ATGCCGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * *
34658766 ATGCTGTCC-AATTTTGATGTA-AA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * *
34658789 AGTGTTG-CTCAATTTGTTATATAT
1 A-TGCTGCCT-AAATTGTTGTATAT
34658813 ATGCTGCCTAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * * *
34658836 ATTCTGTCC-AATTTTGATGTAAAA
1 ATGCTG-CCTAA-ATTGTTGTATAT
* * *
34658860 ATGTTG-CTCAATT-TGGTATAAAT
1 ATGCTGCCTAAATTGTTGTAT--AT
* *
34658883 ATGCTGCCCAATTTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
* * * * *
34658906 ATGCTG-TTCAATTTTTGGTGTAAAA
1 ATGCTGCCT-AA--ATTGTTGTATAT
*
34658931 ATGCTG-CTCAATTTTGTTGTATAT
1 ATGCTGCCT-AA-ATTGTTGTATAT
*
34658955 ATGCTGCCCAAATTGTTGTATAT
1 ATGCTGCCTAAATTGTTGTATAT
34658978 ATGCTGTCC-AAATT
1 ATGCTG-CCTAAATT
34658992 TTGGTGTGAA
Statistics
Matches: 261, Mismatches: 56, Indels: 50
0.71 0.15 0.14
Matches are distributed among these distances:
21 3 0.01
22 5 0.02
23 147 0.56
24 81 0.31
25 25 0.10
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (23 bp):
ATGCTGCCTAAATTGTTGTATAT
Found at i:34658745 original size:70 final size:70
Alignment explanation
Indices: 34658668--34659047 Score: 521
Period size: 70 Copynumber: 5.4 Consensus size: 70
34658658 TAAATTGTTG
*
34658668 TATATATGCTGCCTAAATTGTTGTATATATGTTGTCCAATTTTGATGTAAAAATGTTGCTCAATT
1 TATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATT
34658733 TGGTA
66 TGGTA
* *
34658738 TATATATGCCGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAGTGTTGCTCAATT
1 TATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATT
*
34658803 TGTTA
66 TGGTA
*
34658808 TATATATGCTGCCTAAATTGTTGTATATATTCTGTCCAATTTTGATGTAAAAATGTTGCTCAATT
1 TATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATT
34658873 TGGTA
66 TGGTA
* * * * * *
34658878 TAAATATGCTGCCCAATTTGTTGTATATATGCTGTTCAATTTTTGGTGTAAAAATGCTGCTCAAT
1 TATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAA-TTTTGATGTAAAAATGTTGCTCAA-
* *
34658943 TTTGTTG
64 TTTGGTA
* * * *
34658950 TATATATGCTGCCCAAATTGTTGTATATATGCTGTCCAAATTTTGGTGTGAAAATGTTG-TCTAG
1 TATATATGCTGCCTAAATTGTTGTATATATGCTGTCC-AATTTTGATGTAAAAATGTTGCTC-AA
34659014 TTTGGTA
64 TTTGGTA
* * *
34659021 TATAAATGCTATCC-AAATTGATGTATA
1 TATATATGCT-GCCTAAATTGTTGTATA
34659048 AGGGCTGTCC
Statistics
Matches: 277, Mismatches: 28, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
70 166 0.60
71 50 0.18
72 59 0.21
73 2 0.01
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (70 bp):
TATATATGCTGCCTAAATTGTTGTATATATGCTGTCCAATTTTGATGTAAAAATGTTGCTCAATT
TGGTA
Found at i:34658835 original size:93 final size:93
Alignment explanation
Indices: 34658625--34658837 Score: 204
Period size: 93 Copynumber: 2.3 Consensus size: 93
34658615 TTTGATGCTT
* * * *
34658625 AAATGCTGCC-CAATTCGTTGTATTTATGCTGCCTAAATTGTTGTATATATGCTGCCTAAATTGT
1 AAATGCTGCCTAAATT-GTTGTATATATGCCGCCTAAATTGTTGTATATATGCTGCCTAAATTGA
* *
34658689 TGTATATATGTTGTCCAATTTTGATGTAA
65 TGTATAAATGTTGTCCAATTTTGATATAA
* * * * *
34658718 AAATGTTG-CTCAATTTGGTATATATATGCCGCCTAAATTGTTGTATATATGCTGTCC-AATTTT
1 AAATGCTGCCT-AAATTGTTGTATATATGCCGCCTAAATTGTTGTATATATGCTG-CCTAA-ATT
* *
34658781 GATGTA-AAAGTGTTG-CTCAA-TTTGTTATAT
63 GATGTATAAA-TGTTGTC-CAATTTTGATATAA
*
34658811 ATATGCTGCCTAAATTGTTGTATATAT
1 AAATGCTGCCTAAATTGTTGTATATAT
34658838 TCTGTCCAAT
Statistics
Matches: 95, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
92 1 0.01
93 72 0.76
94 22 0.23
ACGTcount: A:0.27, C:0.13, G:0.17, T:0.43
Consensus pattern (93 bp):
AAATGCTGCCTAAATTGTTGTATATATGCCGCCTAAATTGTTGTATATATGCTGCCTAAATTGAT
GTATAAATGTTGTCCAATTTTGATATAA
Found at i:34659331 original size:12 final size:12
Alignment explanation
Indices: 34659314--34659343 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
34659304 ATGTGATTAA
34659314 ACATATATATAT
1 ACATATATATAT
34659326 ACATATATATAT
1 ACATATATATAT
*
34659338 ATATAT
1 ACATAT
34659344 GGAATGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (12 bp):
ACATATATATAT
Found at i:34661674 original size:16 final size:16
Alignment explanation
Indices: 34661637--34661679 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
34661627 TAATTTATTA
*
34661637 AATAAAA-ATAATCTT
1 AATAAAATATTATCTT
*
34661652 AATTAAAATATTATTTT
1 AA-TAAAATATTATCTT
34661669 AATAAAATATT
1 AATAAAATATT
34661680 TAAATTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 14 0.58
17 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAAAATATTATCTT
Found at i:34664042 original size:10 final size:10
Alignment explanation
Indices: 34664027--34664053 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34664017 TATATTTATT
34664027 TTTTATAATA
1 TTTTATAATA
34664037 TTTTATAATA
1 TTTTATAATA
34664047 TTTTATA
1 TTTTATA
34664054 GGACACTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (10 bp):
TTTTATAATA
Found at i:34673158 original size:31 final size:31
Alignment explanation
Indices: 34673122--34673182 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
34673112 TTGGTCACTA
** *
34673122 AACTATTTGAAAGTTTTCATTTAAGTCATTT
1 AACTATTCAAAAGTTTTCATTTAACTCATTT
*
34673153 AACTATTCAAAAGTTTTTATTTAACTCATT
1 AACTATTCAAAAGTTTTCATTTAACTCATT
34673183 GGGCTATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAACTCATTT
Found at i:34676736 original size:61 final size:67
Alignment explanation
Indices: 34676667--34676811 Score: 162
Period size: 69 Copynumber: 2.2 Consensus size: 67
34676657 GTTACCTTAC
* *
34676667 CCTTTTGTATTAG-TT-T-CT-TT-C-TTTTCATAATATGTAATAG-TTTCTTGTGTTGTTGAGT
1 CCTTTTGTATTAGCTTCTACTATTGCATTTTCATAATATGTAATAGATGT-TTGTGTTGTTAAGT
34676725 TGT
65 TGT
* *
34676728 CCTTTTGTATGAGCTTCTATTATTGGGCATTTTCATAATATGTAATAGATGTTTGTGTTGTTAAG
1 CCTTTTGTATTAGCTTCTACTATT--GCATTTTCATAATATGTAATAGATGTTTGTGTTGTTAAG
34676793 TTGT
64 TTGT
*
34676797 -CTTTCGTATTAGCTT
1 CCTTTTGTATTAGCTT
34676812 TGATTTATTG
Statistics
Matches: 69, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
61 12 0.17
62 2 0.03
63 1 0.01
64 1 0.01
65 2 0.03
68 14 0.20
69 35 0.51
70 2 0.03
ACGTcount: A:0.19, C:0.10, G:0.18, T:0.53
Consensus pattern (67 bp):
CCTTTTGTATTAGCTTCTACTATTGCATTTTCATAATATGTAATAGATGTTTGTGTTGTTAAGTT
GT
Found at i:34681058 original size:150 final size:150
Alignment explanation
Indices: 34680888--34681160 Score: 476
Period size: 150 Copynumber: 1.8 Consensus size: 150
34680878 ATTCATATTG
* * * * *
34680888 TAATATATAAAGCAAGAAAGTAA-AAATAAATTTAAATTTTGCTGGCTGTGAGGTTCGAACTCAC
1 TAATATATAAAGAAAAAAAGTAATAAA-AAAATTAAAATATGCTGGCTGTGAGGTTCGAACTCAC
34680952 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGT
65 GCGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGT
34681017 TTCACAGTTATCTTTTCATTA
130 TTCACAGTTATCTTTTCATTA
34681038 TAATATATAAAGAAAAAAAGTAATAAAAAAATTAAAATATGCTGGCTGTGAGGTTCGAACTCACG
1 TAATATATAAAGAAAAAAAGTAATAAAAAAATTAAAATATGCTGGCTGTGAGGTTCGAACTCACG
*
34681103 CGCACTTCTGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCT
66 CGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCT
34681161 AACTGTTCAC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
150 113 0.97
151 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.28
Consensus pattern (150 bp):
TAATATATAAAGAAAAAAAGTAATAAAAAAATTAAAATATGCTGGCTGTGAGGTTCGAACTCACG
CGCACTTATGTGCAGCAGATCTTAAGTCTGCCCCCTTAACCTCTCGGGCAAACCAGCTGTTCGTT
TCACAGTTATCTTTTCATTA
Found at i:34682909 original size:18 final size:17
Alignment explanation
Indices: 34682855--34682915 Score: 68
Period size: 18 Copynumber: 3.4 Consensus size: 17
34682845 ACCTCTTCGT
34682855 CTTCATCCTCGGAATCA
1 CTTCATCCTCGGAATCA
* * *
34682872 TCTTCATCATCAGAACCA
1 -CTTCATCCTCGGAATCA
34682890 CTTCCATCCTCGGAATCA
1 CTT-CATCCTCGGAATCA
34682908 CTATCATC
1 CT-TCATC
34682916 ATCATCGTCC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 3 0.09
18 31 0.89
19 1 0.03
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.30
Consensus pattern (17 bp):
CTTCATCCTCGGAATCA
Found at i:34688020 original size:19 final size:19
Alignment explanation
Indices: 34687995--34688043 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
34687985 TTAAATGCAT
34687995 TTTTTTATTTTTTA-TTTA
1 TTTTTTATTTTTTACTTTA
*
34688013 TCTTTTTATCTTTTACTTTA
1 T-TTTTTATTTTTTACTTTA
34688033 TTTCTTTATTT
1 TTT-TTTATTT
34688044 CCTTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 11 0.42
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTATTTTTTACTTTA
Found at i:34688078 original size:15 final size:15
Alignment explanation
Indices: 34688055--34688090 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
34688045 CTTTCTTTTT
*
34688055 TTATTTATTCATATA
1 TTATATATTCATATA
34688070 TTATATATTCATATA
1 TTATATATTCATATA
34688085 TT-TATA
1 TTATATA
34688091 AATTCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTCATATA
Found at i:34688446 original size:30 final size:31
Alignment explanation
Indices: 34688412--34688513 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
34688402 TAAAAAATAA
*
34688412 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
34688442 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
34688472 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
34688502 AAATTTCATTTT
1 AAATTTCATTTT
34688514 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:34688796 original size:10 final size:10
Alignment explanation
Indices: 34688777--34688825 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
34688767 TTTTTCGAAG
*
34688777 GAAAACAGAA
1 GAAAAGAGAA
34688787 GAAAAGAGAA
1 GAAAAGAGAA
34688797 GAAAAGAG-A
1 GAAAAGAGAA
*
34688806 -AAGAGAGAA
1 GAAAAGAGAA
34688815 GAAAAGA-AA
1 GAAAAGAGAA
34688824 GA
1 GA
34688826 GTACCGGCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
8 6 0.18
9 6 0.18
10 22 0.65
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:34688810 original size:16 final size:16
Alignment explanation
Indices: 34688783--34688826 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
34688773 GAAGGAAAAC
34688783 AGAAGA-AAAGAGAAGA
1 AGAAGAGAAAGAG-AGA
34688799 A-AAGAGAAAGAGAGA
1 AGAAGAGAAAGAGAGA
*
34688814 AGAAAAGAAAGAG
1 AGAAGAGAAAGAG
34688827 TACCGGCATC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (16 bp):
AGAAGAGAAAGAGAGA
Found at i:34688814 original size:18 final size:17
Alignment explanation
Indices: 34688786--34688821 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
34688776 GGAAAACAGA
34688786 AGAAAAGAGAAGAAAAG
1 AGAAAAGAGAAGAAAAG
34688803 AGAAAGAGAGAAGAAAAG
1 AGAAA-AGAGAAGAAAAG
34688821 A
1 A
34688822 AAGAGTACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AGAAAAGAGAAGAAAAG
Found at i:34688897 original size:3 final size:3
Alignment explanation
Indices: 34688891--34688915 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34688881 GTGTAGGAGG
34688891 AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA A
34688916 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:34689062 original size:31 final size:30
Alignment explanation
Indices: 34689026--34689131 Score: 97
Period size: 35 Copynumber: 3.3 Consensus size: 30
34689016 AAATTAATTA
*
34689026 AAAAAAACAACACAAA-AAAAATAAATCAGCCC
1 AAAAAAA-AAC-CAAACAAAAA-AAAACAGCCC
34689058 AAAAAAAAACCAAAGCAAAAAAAAACAGCCC
1 AAAAAAAAACCAAA-CAAAAAAAAACAGCCC
*
34689089 AAAAAGAAAAGGCCCAAAAAAAAGAAAAACAGCCC
1 AAAAA-AAAA---CCAAACAAAA-AAAAACAGCCC
*
34689124 AGAAAAAA
1 AAAAAAAA
34689132 GAAGCAGGCC
Statistics
Matches: 64, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
30 4 0.06
31 17 0.27
32 16 0.25
34 7 0.11
35 20 0.31
ACGTcount: A:0.70, C:0.20, G:0.08, T:0.02
Consensus pattern (30 bp):
AAAAAAAAACCAAACAAAAAAAAACAGCCC
Found at i:34689091 original size:15 final size:16
Alignment explanation
Indices: 34689041--34689111 Score: 58
Period size: 16 Copynumber: 4.5 Consensus size: 16
34689031 AACAACACAA
*
34689041 AAAAAATAAATCAGCCC
1 AAAAAA-AAACCAGCCC
***
34689058 AAAAAAAAACCAAAGC
1 AAAAAAAAACCAGCCC
34689074 AAAAAAAAA-CAGCCC
1 AAAAAAAAACCAGCCC
*
34689089 AAAAAGAAAA--GGCCC
1 AAAAA-AAAACCAGCCC
34689104 AAAAAAAA
1 AAAAAAAA
34689112 GAAAAACAGC
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
14 3 0.07
15 17 0.38
16 19 0.42
17 6 0.13
ACGTcount: A:0.69, C:0.20, G:0.08, T:0.03
Consensus pattern (16 bp):
AAAAAAAAACCAGCCC
Found at i:34689092 original size:14 final size:14
Alignment explanation
Indices: 34689073--34689111 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 14
34689063 AAAACCAAAG
*
34689073 CAAAAAAAAACAGCC
1 CAAAAAAAAA-GGCC
34689088 CAAAAAGAAAAGGCC
1 CAAAAA-AAAAGGCC
34689103 CAAAAAAAA
1 CAAAAAAAA
34689112 GAAAAACAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 3 0.14
15 15 0.68
16 4 0.18
ACGTcount: A:0.69, C:0.21, G:0.10, T:0.00
Consensus pattern (14 bp):
CAAAAAAAAAGGCC
Found at i:34689106 original size:35 final size:30
Alignment explanation
Indices: 34689026--34689131 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 30
34689016 AAATTAATTA
* *
34689026 AAAAAAACAACACAAAAAAAATAAATCAGCCC
1 AAAAAAA-AAC-CAAAAAAAAAAAAACAGCCC
*
34689058 AAAAAAAAACCAAAGCAAAAAAAAACAGCCC
1 AAAAAAAAACCAAA-AAAAAAAAAACAGCCC
34689089 AAAAAGAAAAGGCCCAAAAAAAAGAAAAACAGCCC
1 AAAAA-AAAA---CCAAAAAAAA-AAAAACAGCCC
*
34689124 AGAAAAAA
1 AAAAAAAA
34689132 GAAGCAGGCC
Statistics
Matches: 63, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
30 4 0.06
31 21 0.33
32 11 0.17
34 7 0.11
35 20 0.32
ACGTcount: A:0.70, C:0.20, G:0.08, T:0.02
Consensus pattern (30 bp):
AAAAAAAAACCAAAAAAAAAAAAACAGCCC
Found at i:34689129 original size:20 final size:19
Alignment explanation
Indices: 34689074--34689134 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 19
34689064 AAACCAAAGC
34689074 AAAA-AAAAACAGCCC--A
1 AAAAGAAAAACAGCCCAAA
*
34689090 AAAAG-AAAA-GGCCCAAAA
1 AAAAGAAAAACAGCCC-AAA
34689108 AAAAGAAAAACAGCCCAGAA
1 AAAAGAAAAACAGCCCA-AA
34689128 AAAAGAA
1 AAAAGAA
34689135 GCAGGCCACA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
15 4 0.11
16 8 0.22
18 6 0.17
19 5 0.14
20 13 0.36
ACGTcount: A:0.69, C:0.18, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAGAAAAACAGCCCAAA
Found at i:34689252 original size:8 final size:8
Alignment explanation
Indices: 34689224--34689316 Score: 80
Period size: 8 Copynumber: 11.0 Consensus size: 8
34689214 AGCAGGCCAG
34689224 GAAAAAAA
1 GAAAAAAA
* *
34689232 GAGAGAAA
1 GAAAAAAA
34689240 GAAAAAGAA
1 GAAAAA-AA
*
34689249 AAAAAGAAA
1 GAAAA-AAA
34689258 GAAGAAAAA
1 GAA-AAAAA
34689267 -AAAAAAGA
1 GAAAAAA-A
*
34689275 GAAAAAAG
1 GAAAAAAA
*
34689283 GAAAAAAG
1 GAAAAAAA
34689291 GAAAAAAGAA
1 G-AAAAA-AA
34689301 GAAAAAAA
1 GAAAAAAA
34689309 GAAAAAAA
1 GAAAAAAA
34689317 AAGAGTTTCA
Statistics
Matches: 70, Mismatches: 8, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
7 4 0.06
8 32 0.46
9 29 0.41
10 5 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:34689262 original size:15 final size:15
Alignment explanation
Indices: 34689237--34689308 Score: 80
Period size: 14 Copynumber: 5.1 Consensus size: 15
34689227 AAAAAGAGAG
34689237 AAAGAAA-AAGAAAA
1 AAAGAAAGAAGAAAA
34689251 AAAGAAAGAAGAAAA
1 AAAGAAAGAAGAAAA
*
34689266 AAAAAAAG-AGAAAA
1 AAAGAAAGAAGAAAA
* * *
34689280 AAGGAAAAAAGGAAA
1 AAAGAAAGAAGAAAA
34689295 AAAG-AAGAA-AAAA
1 AAAGAAAGAAGAAAA
34689308 A
1 A
34689309 GAAAAAAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
13 4 0.08
14 22 0.46
15 22 0.46
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAGAAGAAAA
Found at i:34689287 original size:37 final size:36
Alignment explanation
Indices: 34689225--34689320 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
34689215 GCAGGCCAGG
* *
34689225 AAAAAAAGAGAGAAAGAAAAAGAAAAAAAGAAAGAAGAA
1 AAAAAAAAAGAG-AA-AAAAAGAAAAAAAGAAAAAAG-A
* *
34689264 AAAAAAAAAGAGAAAAAAGGAAAAAAGGAAAAAAGA
1 AAAAAAAAAGAGAAAAAAAGAAAAAAAGAAAAAAGA
* *
34689300 AGAAAAAAAGAAAAAAAAAGA
1 AAAAAAAAAGAGAAAAAAAGA
34689321 GTTTCAATTC
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
36 19 0.38
37 18 0.36
38 2 0.04
39 11 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (36 bp):
AAAAAAAAAGAGAAAAAAAGAAAAAAAGAAAAAAGA
Found at i:34689320 original size:18 final size:18
Alignment explanation
Indices: 34689235--34689320 Score: 102
Period size: 18 Copynumber: 4.7 Consensus size: 18
34689225 AAAAAAAGAG
*
34689235 AGAAAGAAAAAGAAAAAA
1 AGAAAAAAAAAGAAAAAA
34689253 AGAAAGAAGAAAA-AAAAAA
1 AGAAA-AA-AAAAGAAAAAA
* *
34689272 AGAGAAAAAAGGAAAAAA
1 AGAAAAAAAAAGAAAAAA
* *
34689290 GGAAAAAAGAAGAAAAAA
1 AGAAAAAAAAAGAAAAAA
34689308 AGAAAAAAAAAGA
1 AGAAAAAAAAAGA
34689321 GTTTCAATTC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 3 0.05
18 38 0.68
19 11 0.20
20 4 0.07
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (18 bp):
AGAAAAAAAAAGAAAAAA
Found at i:34689902 original size:20 final size:22
Alignment explanation
Indices: 34689861--34689903 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34689851 AATTTTGTGT
*
34689861 AAAAAAATCCAGTGTTTTCAAA
1 AAAAAAATCCAGTGTTTCCAAA
34689883 AAAAAAATCCA-T-TTTCCAAA
1 AAAAAAATCCAGTGTTTCCAAA
34689903 A
1 A
34689904 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAAATCCAGTGTTTCCAAA
Found at i:34689973 original size:18 final size:17
Alignment explanation
Indices: 34689899--34690061 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
34689889 ATCCATTTTC
* *
34689899 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
34689917 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
34689935 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
34689951 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
34689968 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
34689986 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
34690003 CAAAAATCCTCTTGTTTT
1 CAAAAATTTTCGTG-TTT
34690021 CAAAAA-TTTCGGTGTTT
1 CAAAAATTTTC-GTGTTT
**
34690038 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
34690056 CAAAAA
1 CAAAAA
34690062 AAAATCTCGT
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 51 0.43
18 41 0.34
19 12 0.10
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:34690061 original size:35 final size:34
Alignment explanation
Indices: 34689899--34690061 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
34689889 ATCCATTTTC
* * * *
34689899 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
34689935 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
34689968 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
34690003 CAAAAATCCTCTTGTTTTCAAAAATTTCGGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTC-GTGTTT
**
34690038 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
34690062 AAAATCTCGT
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 9 0.08
35 60 0.57
36 12 0.11
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:34702166 original size:193 final size:191
Alignment explanation
Indices: 34701840--34702260 Score: 763
Period size: 193 Copynumber: 2.2 Consensus size: 191
34701830 GTTTCCAAGG
34701840 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTAAATTTTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTAAATTTTTT
* *
34701905 AAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTAGTT
66 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACACCGAGGTATTTTTAGTT
34701970 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTC-
131 TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
34702030 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTTAAATTTT
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTA--TTTAAA-TTT
34702095 TTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACACCGAGGTATTTTTA
63 TTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACACCGAGGTATTTTTA
34702160 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
128 GTTTATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
* **
34702224 AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC
1 AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
34702261 GGCTCACATG
Statistics
Matches: 222, Mismatches: 5, Indels: 4
0.96 0.02 0.02
Matches are distributed among these distances:
190 53 0.24
192 6 0.03
193 129 0.58
194 34 0.15
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (191 bp):
AAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTAAATTTTTT
AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACACCGAGGTATTTTTAGTT
TATGTTTTAAATTGACTCATATTGCGAGAGGTGAGTTAAGCCTTTTAATTTTTGTTTTTCA
Found at i:34702300 original size:16 final size:17
Alignment explanation
Indices: 34702279--34702312 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
34702269 TGCTGAGGTA
*
34702279 TTTTCAATTTATG-TTT
1 TTTTCAATCTATGCTTT
34702295 TTTTCAATCTATGCTTT
1 TTTTCAATCTATGCTTT
34702312 T
1 T
34702313 CAAAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.65
Consensus pattern (17 bp):
TTTTCAATCTATGCTTT
Found at i:34702423 original size:85 final size:87
Alignment explanation
Indices: 34702218--34702463 Score: 295
Period size: 91 Copynumber: 2.8 Consensus size: 87
34702208 TAATTTTTGT
34702218 TTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-GGCTCACATGCTGAGGTATTT
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGC-CAC--GCTGAGGTATTT
* **
34702282 TCAATTTATGTTTTTTTCAATCTATGC
62 TCAATTTATGCTTTACTCAATCTA-GC
* *
34702309 TTTTCAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGCTGAGGTATTTTC
1 TTTTC-AAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTC-AGGCCACGCTGAGGTATTTTC
*
34702373 AATTTCTGCTTTACT-AATTCTA-C
64 AATTTATGCTTTACTCAA-TCTAGC
* *
34702396 TTTTC-AAATCAACTCATATTGCAAGAGGTGAGTTGAGTCTCAGGCCACACGCTGAGGTCTTTTC
1 TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGG-C-CACGCTGAGGTATTTTC
34702460 AATT
64 AATT
34702464 CTGTTTTTAA
Statistics
Matches: 139, Mismatches: 10, Indels: 16
0.84 0.06 0.10
Matches are distributed among these distances:
84 3 0.02
85 33 0.24
87 26 0.19
88 2 0.01
89 29 0.21
91 44 0.32
93 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (87 bp):
TTTTCAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGCCACGCTGAGGTATTTTCAA
TTTATGCTTTACTCAATCTAGC
Found at i:34702478 original size:13 final size:13
Alignment explanation
Indices: 34702462--34702495 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
34702452 GTCTTTTCAA
34702462 TTCTGTTTTTAAT
1 TTCTGTTTTTAAT
34702475 TTCTGTTTTTTTAAT
1 TTCTG--TTTTTAAT
34702490 TTCTGT
1 TTCTGT
34702496 GTTTCAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.32
15 13 0.68
ACGTcount: A:0.12, C:0.09, G:0.09, T:0.71
Consensus pattern (13 bp):
TTCTGTTTTTAAT
Found at i:34702487 original size:15 final size:15
Alignment explanation
Indices: 34702467--34702495 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34702457 TTCAATTCTG
34702467 TTTTTAATTTCTGTT
1 TTTTTAATTTCTGTT
34702482 TTTTTAATTTCTGT
1 TTTTTAATTTCTGT
34702496 GTTTCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.07, G:0.07, T:0.72
Consensus pattern (15 bp):
TTTTTAATTTCTGTT
Found at i:34702655 original size:54 final size:55
Alignment explanation
Indices: 34702571--34702787 Score: 306
Period size: 54 Copynumber: 4.1 Consensus size: 55
34702561 TCAATTTCTA
* *
34702571 CTTTTCAATTTCTGTTTTTCAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
*
34702626 CTTTT-AATTTCTATTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
34702680 C---T---TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 CTTTTCAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
* * *
34702730 CTTTTGCAAATTCT-GTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGC
1 CTTTT-CAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
34702785 CTT
1 CTT
34702788 GGCTCACGTG
Statistics
Matches: 147, Mismatches: 7, Indels: 16
0.86 0.04 0.09
Matches are distributed among these distances:
49 12 0.08
50 35 0.24
51 1 0.01
53 1 0.01
54 47 0.32
55 42 0.29
56 5 0.03
57 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.37
Consensus pattern (55 bp):
CTTTTCAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
Found at i:34703093 original size:30 final size:30
Alignment explanation
Indices: 34703058--34703129 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
34703048 TAAAAAATAA
* *
34703058 AAATTTCATTTTGACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
34703088 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
34703118 AAATTTCATTTT
1 AAATTTCATTTT
34703130 AATCCTAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:34703410 original size:10 final size:10
Alignment explanation
Indices: 34703391--34703440 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
34703381 TTTTTCGAAG
*
34703391 GAAAAAAGAA
1 GAAAAGAGAA
34703401 GAAAAGAGAA
1 GAAAAGAGAA
34703411 GAAAAGAGAA
1 GAAAAGAGAA
* *
34703421 -AGAGGAGAA
1 GAAAAGAGAA
34703430 GAAAAGA-AA
1 GAAAAGAGAA
34703439 GA
1 GA
34703441 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:34703441 original size:17 final size:19
Alignment explanation
Indices: 34703394--34703436 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
34703384 TTCGAAGGAA
34703394 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
34703412 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
34703431 AAAAGA
1 AAAAGA
34703437 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:34703650 original size:20 final size:20
Alignment explanation
Indices: 34703627--34703669 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
34703617 AAAATTAATT
34703627 AAAAAAAAACAACACAAAAA
1 AAAAAAAAACAACACAAAAA
* * * *
34703647 AAAACAAATCAGCCCAAAAA
1 AAAAAAAAACAACACAAAAA
34703667 AAA
1 AAA
34703670 CCAAAGCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.77, C:0.19, G:0.02, T:0.02
Consensus pattern (20 bp):
AAAAAAAAACAACACAAAAA
Found at i:34703694 original size:15 final size:14
Alignment explanation
Indices: 34703646--34703714 Score: 50
Period size: 15 Copynumber: 4.6 Consensus size: 14
34703636 CAACACAAAA
34703646 AAAAACAAATCAGCCC
1 AAAAA-AAA-CAGCCC
***
34703662 AAAAAAAACCAAAGC
1 AAAAAAAA-CAGCCC
34703677 AAAAAAAAGCAGCCC
1 AAAAAAAA-CAGCCC
34703692 AAAAAGAAA-AGGCCC
1 AAAAA-AAACA-GCCC
34703707 AAAAAAAA
1 AAAAAAAA
34703715 AGAAAAAACA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
14 4 0.09
15 31 0.72
16 8 0.19
ACGTcount: A:0.67, C:0.22, G:0.10, T:0.01
Consensus pattern (14 bp):
AAAAAAAACAGCCC
Found at i:34703716 original size:14 final size:15
Alignment explanation
Indices: 34703677--34703717 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
34703667 AAACCAAAGC
34703677 AAAAAAAAGCAGCCCA
1 AAAAAAAAG-AGCCCA
34703693 AAAAGAAAAG-GCCCA
1 AAAA-AAAAGAGCCCA
34703708 AAAAAAAAGA
1 AAAAAAAAGA
34703718 AAAAACAGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 5 0.22
15 9 0.39
16 4 0.17
17 5 0.22
ACGTcount: A:0.68, C:0.17, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGCCCA
Found at i:34703849 original size:15 final size:15
Alignment explanation
Indices: 34703829--34703927 Score: 112
Period size: 15 Copynumber: 6.6 Consensus size: 15
34703819 AGCAGGCCAG
* *
34703829 GAAAAAAGAGAGAAA
1 GAAAAAAGAAAAAAA
34703844 GAAAAAAGAAAAAAA
1 GAAAAAAGAAAAAAA
*
34703859 GAAAGAAGAAAAAAA
1 GAAAAAAGAAAAAAA
*
34703874 GAAAAGAGAAAAAAA
1 GAAAAAAGAAAAAAA
*
34703889 GGAAAAAAGGAAAAAA
1 -GAAAAAAGAAAAAAA
*
34703905 GAAGAAAA-AAAGAAA
1 GAA-AAAAGAAAAAAA
34703920 -AAAAAAGA
1 GAAAAAAGA
34703928 GTTTCAATTC
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
13 4 0.06
14 3 0.04
15 48 0.67
16 17 0.24
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
GAAAAAAGAAAAAAA
Found at i:34703856 original size:8 final size:8
Alignment explanation
Indices: 34703830--34703923 Score: 95
Period size: 8 Copynumber: 11.8 Consensus size: 8
34703820 GCAGGCCAGG
34703830 AAAAAAGA
1 AAAAAAGA
* *
34703838 GAGAAAG-
1 AAAAAAGA
34703845 AAAAAAGA
1 AAAAAAGA
34703853 AAAAAAG-
1 AAAAAAGA
*
34703860 AAAGAAGA
1 AAAAAAGA
34703868 AAAAAAG-
1 AAAAAAGA
*
34703875 AAAAGAGA
1 AAAAAAGA
34703883 AAAAAAGGA
1 AAAAAA-GA
*
34703892 AAAAAGGAA
1 AAAAAAG-A
34703901 AAAAGAAGA
1 AAAA-AAGA
34703910 AAAAAAGA
1 AAAAAAGA
34703918 AAAAAA
1 AAAAAA
34703924 AAGAGTTTCA
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
7 17 0.24
8 34 0.49
9 17 0.24
10 2 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:34703859 original size:23 final size:22
Alignment explanation
Indices: 34703831--34703927 Score: 92
Period size: 22 Copynumber: 4.3 Consensus size: 22
34703821 CAGGCCAGGA
*
34703831 AAAAAGAGAGAAAGAAAAAAGAA
1 AAAAAGAAAGAAAGAAAAAA-AA
34703854 AAAAAGAAAG-AAGAAAAAAAGA
1 AAAAAGAAAGAAAGAAAAAAA-A
* * *
34703876 AAAGAGAAAAAAAGGAAAAAAGGA
1 AAAAAGAAAGAAA-GAAAAAA-AA
34703900 AAAAAG-AAGAAA-AAAAGAAAA
1 AAAAAGAAAGAAAGAAAA-AAAA
34703921 AAAAAGA
1 AAAAAGA
34703928 GTTTCAATTC
Statistics
Matches: 61, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
21 12 0.20
22 20 0.33
23 16 0.26
24 13 0.21
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAGAAAGAAAAAAAA
Found at i:34703885 original size:27 final size:26
Alignment explanation
Indices: 34703830--34703923 Score: 90
Period size: 26 Copynumber: 3.7 Consensus size: 26
34703820 GCAGGCCAGG
34703830 AAAAAAGAGAGAAAGAAAA-AAGAAAA-A
1 AAAAAAGA-AGAAA-AAAAGAA-AAAAGA
* *
34703857 AAGAAAGAAGAAAAAAAGAAAAGAGA
1 AAAAAAGAAGAAAAAAAGAAAAAAGA
*
34703883 AAAAAAG--GAAAAAAGGAAAAAAGA
1 AAAAAAGAAGAAAAAAAGAAAAAAGA
34703907 AGAAAAA-AAGAAAAAAA
1 A-AAAAAGAAGAAAAAAA
34703924 AAGAGTTTCA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
24 16 0.29
25 12 0.21
26 21 0.38
27 7 0.12
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAGAAAAAAAGAAAAAAGA
Found at i:34704508 original size:20 final size:22
Alignment explanation
Indices: 34704467--34704509 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34704457 ATTTTTGTGT
*
34704467 AAAAAAATCCAGTGTTTTCAAA
1 AAAAAAATCCAGTGTTTCCAAA
34704489 AAAAAAATCCA-T-TTTCCAAA
1 AAAAAAATCCAGTGTTTCCAAA
34704509 A
1 A
34704510 TGTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
21 1 0.05
22 11 0.55
ACGTcount: A:0.53, C:0.16, G:0.05, T:0.26
Consensus pattern (22 bp):
AAAAAAATCCAGTGTTTCCAAA
Found at i:34704551 original size:18 final size:17
Alignment explanation
Indices: 34704501--34704667 Score: 142
Period size: 17 Copynumber: 9.5 Consensus size: 17
34704491 AAAAATCCAT
* *
34704501 TTTCCAAAATGTTTAGTG
1 TTTCAAAAAT-TTTTGTG
34704519 TCTTCTAAAAATTTTTGTG
1 T-TTC-AAAAATTTTTGTG
34704538 TTTCAAAAATTTTTGT-
1 TTTCAAAAATTTTTGTG
**
34704554 TTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTTGTG
34704571 TTTCAAAAATTTTTGTG
1 TTTCAAAAATTTTTGTG
*
34704588 TTTTC-AAAATTTTTCGTA
1 -TTTCAAAAATTTTT-GTG
*
34704606 TTTCAAAAATCCTCTTGT-
1 TTTCAAAAAT--TTTTGTG
**
34704624 TTTCAAAAATTTCGGTG
1 TTTCAAAAATTTTTGTG
** *
34704641 TTTTGAAAATTTTCGTG
1 TTTCAAAAATTTTTGTG
34704658 TTTTCAAAAA
1 -TTTCAAAAA
34704668 AAAAATCTCG
Statistics
Matches: 122, Mismatches: 17, Indels: 20
0.77 0.11 0.13
Matches are distributed among these distances:
16 17 0.14
17 53 0.43
18 32 0.26
19 12 0.10
20 8 0.07
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
TTTCAAAAATTTTTGTG
Found at i:34704667 original size:35 final size:34
Alignment explanation
Indices: 34704501--34704667 Score: 158
Period size: 35 Copynumber: 4.8 Consensus size: 34
34704491 AAAAATCCAT
* * * *
34704501 TTTCCAAAATGTTTAGTGTCTTCTAAAAATTTTTGTG
1 TTTCAAAAAT-TTTCGTGTTTTC-AAAAA-TTTCGTG
34704538 TTTCAAAAATTTT--TGTTTTCAAAAATTTCCGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTT-CGTG
* * *
34704571 TTTCAAAAATTTTTGTGTTTTCAAAATTTTTCGTA
1 TTTCAAAAATTTTCGTGTTTTCAAAA-ATTTCGTG
** *
34704606 TTTCAAAAATCCTCTTGTTTTCAAAAATTTCGGTG
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTTC-GTG
**
34704641 TTTTGAAAATTTTCGTGTTTTCAAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAA
34704668 AAAAATCTCG
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
32 3 0.03
33 21 0.19
34 10 0.09
35 60 0.55
36 6 0.06
37 9 0.08
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (34 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAATTTCGTG
Found at i:34704682 original size:39 final size:38
Alignment explanation
Indices: 34704628--34704756 Score: 115
Period size: 36 Copynumber: 3.4 Consensus size: 38
34704618 TCTTGTTTTC
*
34704628 AAAAATTTCGGTGTTTTGAAAATTTTCGTGTTTTCAAAAA
1 AAAAATCTC-GTGTTTT-AAAATTTTCGTGTTTTCAAAAA
*
34704668 AAAAATCTCGTGTTTCATAAATTTT-G-GTTTT-AAAAA
1 AAAAATCTCGTGTTTTA-AAATTTTCGTGTTTTCAAAAA
* * * *
34704704 AAATAT-T-ATGTCTTAAAATTCTCGTGTTTTCAAAACA
1 AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAA-A
*
34704741 AGAAATTCTCGTGTTT
1 A-AAAATCTCGTGTTT
34704757 CAATCGGATC
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
33 6 0.09
34 6 0.09
35 6 0.09
36 14 0.20
37 7 0.10
38 5 0.07
39 14 0.20
40 12 0.17
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (38 bp):
AAAAATCTCGTGTTTTAAAATTTTCGTGTTTTCAAAAA
Found at i:34708028 original size:21 final size:20
Alignment explanation
Indices: 34707983--34708030 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
34707973 ATTTATAATA
34707983 TATAACATTTTAAAAAAAAT
1 TATAACATTTTAAAAAAAAT
*
34708003 TATAA-ATTGTTAAAAAAATT
1 TATAACATT-TTAAAAAAAAT
34708023 TCATAACA
1 T-ATAACA
34708031 CTTCTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 3 0.12
20 16 0.67
21 4 0.17
22 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.35
Consensus pattern (20 bp):
TATAACATTTTAAAAAAAAT
Found at i:34727474 original size:17 final size:16
Alignment explanation
Indices: 34727437--34727470 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
34727427 GGGAATAATC
34727437 AATTTTTATATAAATT
1 AATTTTTATATAAATT
* *
34727453 AATTTTTTTGTAAATT
1 AATTTTTATATAAATT
34727469 AA
1 AA
34727471 ATTTATTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (16 bp):
AATTTTTATATAAATT
Found at i:34728427 original size:26 final size:26
Alignment explanation
Indices: 34728379--34728428 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
34728369 ATAGCAAAAA
**
34728379 AATTGTAAAAAGGGGGGGGGGATTTC
1 AATTGTAAAAAGGGGGAAGGGATTTC
* *
34728405 AATTGTATAAAGGGGGAATGGATT
1 AATTGTAAAAAGGGGGAAGGGATT
34728429 GATGTAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.38, T:0.26
Consensus pattern (26 bp):
AATTGTAAAAAGGGGGAAGGGATTTC
Found at i:34729974 original size:15 final size:15
Alignment explanation
Indices: 34729930--34729962 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
34729920 TTAAATATAT
34729930 TATTAATT-TTATTA
1 TATTAATTATTATTA
34729944 TATTAATTATTATTA
1 TATTAATTATTATTA
34729959 TATT
1 TATT
34729963 GTATATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTAATTATTATTA
Found at i:34730102 original size:38 final size:37
Alignment explanation
Indices: 34730059--34730146 Score: 103
Period size: 38 Copynumber: 2.4 Consensus size: 37
34730049 ATGTAGTACG
34730059 TATATATTTTAT-TATCATATCATATTATTTT-T-ATAGTT
1 TATATATTTTATGTA-CAT-TCATATT-TTTTATGATA-TT
34730097 TATATATTTTATGTACATTCATATTTTTTATGATATT
1 TATATATTTTATGTACATTCATATTTTTTATGATATT
*
34730134 TATAT-TTTCATGT
1 TATATATTTTATGT
34730147 TTTATAATTC
Statistics
Matches: 46, Mismatches: 1, Indels: 8
0.84 0.02 0.15
Matches are distributed among these distances:
36 11 0.24
37 15 0.33
38 18 0.39
39 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.05, T:0.60
Consensus pattern (37 bp):
TATATATTTTATGTACATTCATATTTTTTATGATATT
Found at i:34730138 original size:18 final size:18
Alignment explanation
Indices: 34730061--34730141 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
34730051 GTAGTACGTA
*
34730061 TATATTTTATTATCATA-T
1 TATATTTT-TTATGATATT
*
34730079 CATATTATTTT-T-ATAGTT
1 TATATT-TTTTATGATA-TT
* *
34730097 TATATATTTTATGTACATT
1 TATATTTTTTATG-ATATT
*
34730116 CATATTTTTTATGATATT
1 TATATTTTTTATGATATT
34730134 TATATTTT
1 TATATTTT
34730142 CATGTTTTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
16 3 0.06
17 5 0.10
18 24 0.49
19 15 0.31
20 2 0.04
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.62
Consensus pattern (18 bp):
TATATTTTTTATGATATT
Found at i:34733702 original size:24 final size:24
Alignment explanation
Indices: 34733675--34733724 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
34733665 CAAATGCATT
*
34733675 TTCAAGATAAAATCTTGATGACCC
1 TTCAAGATAAAATCTAGATGACCC
* *
34733699 TTCAAGATAAAGTCTAGGTGACCC
1 TTCAAGATAAAATCTAGATGACCC
34733723 TT
1 TT
34733725 AGATCGAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (24 bp):
TTCAAGATAAAATCTAGATGACCC
Found at i:34733856 original size:53 final size:53
Alignment explanation
Indices: 34733760--34733962 Score: 325
Period size: 53 Copynumber: 3.8 Consensus size: 53
34733750 CATCAAAGGG
* * *
34733760 TTTCCTTGCATTCAACAAACTTCCAAAGATTGTAGCTCAAATTTATTAATAAGA
1 TTTCTTTGCATTCAACAAACTT-CAGAGATTGTAGCTCAAATTTATAAATAAGA
* *
34733814 TTTCTTTGCATTCAACAAACTTTAGAGATTGTAGCTTAAATTTATAAATAAGA
1 TTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTTATAAATAAGA
*
34733867 TTTCTTTGCATTCAATAAACTTCAGAGATTGTAGCTCAAATTTATAAATAAGA
1 TTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTTATAAATAAGA
* *
34733920 TTTCTTTGCACTCAACAAACTTTAGAGATTGTAGCTCAAATTT
1 TTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTT
34733963 CTATCATTCC
Statistics
Matches: 138, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 117 0.85
54 21 0.15
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (53 bp):
TTTCTTTGCATTCAACAAACTTCAGAGATTGTAGCTCAAATTTATAAATAAGA
Found at i:34735265 original size:23 final size:23
Alignment explanation
Indices: 34735239--34735289 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
34735229 CCCTTATACG
* *
34735239 TGTAATATCTCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
34735262 TGTAATACCCCGAAAATTACTAC
1 TGTAATACCCCGAAAATTACTAC
*
34735285 AGTAA
1 TGTAA
34735290 GAAAATAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATACCCCGAAAATTACTAC
Found at i:34741994 original size:26 final size:25
Alignment explanation
Indices: 34741965--34742018 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 25
34741955 TAGAAGGACC
34741965 AAAATGGAAATTATCCCCTCCATGCG
1 AAAATGGAAATTATCCCCTCCATG-G
34741991 AAAATGGAAATTATCCCCTCCATGG
1 AAAATGGAAATTATCCCCTCCATGG
34742016 AAA
1 AAA
34742019 TCTTAGGGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 4 0.14
26 24 0.86
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (25 bp):
AAAATGGAAATTATCCCCTCCATGG
Found at i:34744044 original size:9 final size:9
Alignment explanation
Indices: 34744030--34744060 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34744020 GTTAAACGAA
34744030 TCGAGTTAT
1 TCGAGTTAT
*
34744039 TCGAGTTAA
1 TCGAGTTAT
34744048 TCGAGTTAT
1 TCGAGTTAT
34744057 TCGA
1 TCGA
34744061 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:34744118 original size:9 final size:9
Alignment explanation
Indices: 34744100--34744130 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
34744090 GAGTTCGAAT
*
34744100 AATAACTCG
1 AATAATTCG
34744109 AATAATTCG
1 AATAATTCG
34744118 AATAATTCG
1 AATAATTCG
34744127 AATA
1 AATA
34744131 TCAAACTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.29
Consensus pattern (9 bp):
AATAATTCG
Found at i:34744403 original size:30 final size:29
Alignment explanation
Indices: 34744347--34744403 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
34744337 AACCTTTTAT
*
34744347 TTTTCCCCAAAATTTTTACTCCCTTCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCAC
* *
34744376 TTTTCCCCTAAAACTTTTATTCTCTTCC
1 TTTTCCCC-AAAACTTTTACTCCCTTCC
34744404 CATTCCACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.19, C:0.35, G:0.00, T:0.46
Consensus pattern (29 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCAC
Done.