Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007816.1 Hibiscus syriacus cultivar Beakdansim tig00110151_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: 3994936
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 14
Found at i:2824906 original size:21 final size:23
Alignment explanation
Indices: 2824880--2824931 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
2824870 AGGGAATTGA
2824880 TCCCCCCATG-A-GGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
**
2824901 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCATGAAGGGGAACCGAT
2824924 TCCCCCCA
1 TCCCCCCA
2824932 CAGGGGAATC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 1 0.04
23 16 0.64
ACGTcount: A:0.21, C:0.40, G:0.21, T:0.17
Consensus pattern (23 bp):
TCCCCCCATGAAGGGGAACCGAT
Found at i:2824938 original size:21 final size:21
Alignment explanation
Indices: 2824912--2824951 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2824902 CCCCCTTTGA
*
2824912 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
2824933 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
2824952 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:2833612 original size:22 final size:21
Alignment explanation
Indices: 2833568--2833639 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 21
2833558 ATTATTTTAA
*
2833568 AATATATATTAATT-TTTAAAAT
1 AATAT-TATT-ATTATTTGAAAT
2833590 AATATTA-T-TTATTTGAAAT
1 AATATTATTATTATTTGAAAT
*
2833609 AATATTAATTATTATTTTAAAT
1 AATATT-ATTATTATTTGAAAT
2833631 AATATTATT
1 AATATTATT
2833640 TTAAATTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
18 2 0.05
19 13 0.30
20 2 0.05
21 6 0.14
22 21 0.48
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (21 bp):
AATATTATTATTATTTGAAAT
Found at i:2833620 original size:19 final size:19
Alignment explanation
Indices: 2833557--2833621 Score: 87
Period size: 19 Copynumber: 3.4 Consensus size: 19
2833547 AATATTATGA
2833557 AATTATTTTAAAATATATATT
1 AATTA-TTTAAAATA-ATATT
2833578 AATT-TTTAAAATAATATT
1 AATTATTTAAAATAATATT
* *
2833596 ATTTATTTGAAATAATATT
1 AATTATTTAAAATAATATT
2833615 AATTATT
1 AATTATT
2833622 ATTTTAAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
18 8 0.20
19 28 0.70
21 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
AATTATTTAAAATAATATT
Found at i:2854548 original size:12 final size:12
Alignment explanation
Indices: 2854531--2854555 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2854521 ACAATGGGCT
2854531 AAATTAAAAAAA
1 AAATTAAAAAAA
2854543 AAATTAAAAAAA
1 AAATTAAAAAAA
2854555 A
1 A
2854556 TTAAAAATTT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAATTAAAAAAA
Found at i:2854553 original size:10 final size:10
Alignment explanation
Indices: 2854538--2854562 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2854528 GCTAAATTAA
2854538 AAAAAAAATT
1 AAAAAAAATT
2854548 AAAAAAAATT
1 AAAAAAAATT
2854558 AAAAA
1 AAAAA
2854563 TTTAATGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAAAATT
Found at i:2856207 original size:91 final size:91
Alignment explanation
Indices: 2856043--2856216 Score: 226
Period size: 91 Copynumber: 1.9 Consensus size: 91
2856033 TGAGCTAAGG
* * *
2856043 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTCTTTTCATTATGATC
1 TTGAACAAGCTCTTCTCATTATGAAATTATTCTCCCTCGTTGGATGAGTTCTTTTCATTATGAAC
*
2856108 CCTCCACTGGAAATGTTGTGCCAAGT
66 CCTCCACTGAAAATGTTGTGCCAAGT
* * **
2856134 TTGAACAAGTTCTTCTCTTTAT-AATATTATTCTCCCTCGTTGGATTTGTT-TTTGTCATTATGA
1 TTGAACAAGCTCTTCTCATTATGAA-ATTATTCTCCCTCGTTGGATGAGTTCTTT-TCATTATGA
* *
2856197 ACTCTGCACTGAAAATGTTG
64 ACCCTCCACTGAAAATGTTG
2856217 AGTGCTTTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
90 5 0.07
91 66 0.93
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.42
Consensus pattern (91 bp):
TTGAACAAGCTCTTCTCATTATGAAATTATTCTCCCTCGTTGGATGAGTTCTTTTCATTATGAAC
CCTCCACTGAAAATGTTGTGCCAAGT
Found at i:2861581 original size:23 final size:23
Alignment explanation
Indices: 2861533--2861614 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
2861523 ATGTTTCCCA
* **
2861533 AAGGACCATATAGGGTTGTCCAG
1 AAGGACCACATAGTTTTGTCCAG
* *
2861556 AAGGACCATATAGTTTTATGCC-G
1 AAGGACCACATAGTTTTGT-CCAG
* *
2861579 AAGGAACACATAGTTTTGTCCTG
1 AAGGACCACATAGTTTTGTCCAG
2861602 AAGGACCACATAG
1 AAGGACCACATAG
2861615 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.04
23 46 0.92
24 2 0.04
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.24
Consensus pattern (23 bp):
AAGGACCACATAGTTTTGTCCAG
Found at i:2863803 original size:46 final size:46
Alignment explanation
Indices: 2863635--2863983 Score: 466
Period size: 46 Copynumber: 7.5 Consensus size: 46
2863625 TTATTCATTA
* * * *
2863635 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCCGTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
2863681 ATATTTAGTTATGGCATTCTTTCATGCCTTAATGCATCCGTTCATGC
1 AT-TTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
2863728 ATATTTAGTTATGACATCATTTCATGCCTTAATGCATCCTTTCATGC
1 AT-TTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
2863775 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGG
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
2863821 ATTTCAGTTATGGCATCCTTTCATGACTTAATGCATCCGTTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* * *
2863867 ATTTTTAGTTATGGCATCCTTTCATGCATTAATGCATCTTTTCATGC
1 A-TTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
* *
2863914 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCAT-CTATTCATGC
1 ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCT-TTCATGC
*
2863960 ATTTCAGTTATGACATCCTTTCAT
1 ATTTCAGTTATGGCATCCTTTCAT
2863984 ACAAATAATG
Statistics
Matches: 271, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
45 1 0.00
46 145 0.54
47 125 0.46
ACGTcount: A:0.22, C:0.22, G:0.12, T:0.44
Consensus pattern (46 bp):
ATTTCAGTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGC
Found at i:2863879 original size:139 final size:139
Alignment explanation
Indices: 2863635--2864085 Score: 558
Period size: 139 Copynumber: 3.3 Consensus size: 139
2863625 TTATTCATTA
* * * * *
2863635 ATTTCATTTATGACATCCTTTCATGCTTTAATGCATCCGTTCATGCATATTTAGTTATGGCATTC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCAT-TTCAGTTATGGCATCC
* * *
2863700 TTTCATGCCTTAATGCATCCGTTCATGCATATTTAGTTATGACATCATTTCATGCCTTAATGCAT
65 TTTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGCAT
2863765 CCTTTCATGC
130 CCTTTCATGC
* *
2863775 ATTTCATTTATGGCATCATTTCATGCCTTAATGCATCCTTTCATGGATTTCAGTTATGGCATCCT
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
* *
2863840 TTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCCTTTCATGCATTAATGCATC
66 TTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGCATC
*
2863905 TTTTCATGC
131 CTTTCATGC
* *
2863914 ATTTCATTTATGGCATCCTTTCATGCTTTAATGCAT-CTATTCATGCATTTCAGTTATGACATCC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCT-TTCATGCATTTCAGTTATGGCATCC
* ** * * *
2863978 TTTCAT-ACAAATAATGCA-CCCAT-ATGCATTATTA-TTTTGGCATCATTTCATGCCAATAATG
65 TTTCATGAC--TTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCC-TTAATG
**
2864039 CA-CCCAT-ATGC
127 CATCCTTTCATGC
* *
2864050 ATTATTATTT-TGGCATCCTTTCATGCCGATAATGCA
1 ATT-TCATTTATGGCATCCTTTCATGCC-TTAATGCA
2864086 CCCATATGCA
Statistics
Matches: 274, Mismatches: 31, Indels: 15
0.86 0.10 0.05
Matches are distributed among these distances:
136 23 0.08
137 31 0.11
138 21 0.08
139 149 0.54
140 50 0.18
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.42
Consensus pattern (139 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTCAGTTATGGCATCCT
TTCATGACTTAATGCATCCGTTCATGCATTTTTAGTTATGGCATCATTTCATGCCTTAATGCATC
CTTTCATGC
Found at i:2864027 original size:45 final size:45
Alignment explanation
Indices: 2863831--2864103 Score: 232
Period size: 45 Copynumber: 6.0 Consensus size: 45
2863821 ATTTCAGTTA
* * ** * *
2863831 TGGCATCCTTTCATGAC-TTAATGCATCCGTTCATGCATTTTTAGTTA
1 TGGCATCCTTTCATGCCAATAATGCA-CCCAT-ATGCATTATTA-TTT
* *** *
2863878 TGGCATCCTTTCATG-CATTAATGCATCTTTTCATGCATT-TCATTT
1 TGGCATCCTTTCATGCCAATAATGCA-CCCAT-ATGCATTATTATTT
** * * * *
2863923 ATGGCATCCTTTCATG-CTTTAATGCATCTATTCATGCATT-TCAGTTA
1 -TGGCATCCTTTCATGCCAATAATGCACCCA-T-ATGCATTATTA-TTT
* * *
2863970 TGACATCCTTTCATACAAATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
*
2864015 TGGCATCATTTCATGCCAATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
*
2864060 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATT
1 TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATT
2864104 CTGTTCATTC
Statistics
Matches: 196, Mismatches: 24, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
45 95 0.48
46 55 0.28
47 46 0.23
ACGTcount: A:0.25, C:0.22, G:0.12, T:0.41
Consensus pattern (45 bp):
TGGCATCCTTTCATGCCAATAATGCACCCATATGCATTATTATTT
Found at i:2864727 original size:22 final size:22
Alignment explanation
Indices: 2864702--2864755 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
2864692 TAGATCCATG
2864702 GTATCGATACATCCCTTTGTTA
1 GTATCGATACATCCCTTTGTTA
*
2864724 GTATCGATACTTCCCTTTGTTA
1 GTATCGATACATCCCTTTGTTA
2864746 GTATCGATAC
1 GTATCGATAC
2864756 CCCTTCAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.15, T:0.41
Consensus pattern (22 bp):
GTATCGATACATCCCTTTGTTA
Found at i:2867219 original size:4 final size:4
Alignment explanation
Indices: 2867210--2867258 Score: 71
Period size: 4 Copynumber: 12.2 Consensus size: 4
2867200 TCCATGAAAG
* * *
2867210 GTAT GTAT GTAT GCAT GCAT GTAT GCAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
2867258 G
1 G
2867259 AAATGGATGG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 41 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (4 bp):
GTAT
Found at i:2867233 original size:12 final size:12
Alignment explanation
Indices: 2867216--2867277 Score: 61
Period size: 12 Copynumber: 5.1 Consensus size: 12
2867206 AAAGGTATGT
2867216 ATGTATGCATGC
1 ATGTATGCATGC
*
2867228 ATGTATGCATGT
1 ATGTATGCATGC
* *
2867240 ATGTATGTATGT
1 ATGTATGCATGC
* *
2867252 ATGTATGAAATGG
1 ATGTATG-CATGC
*
2867265 ATGGATGCATGC
1 ATGTATGCATGC
2867277 A
1 A
2867278 GAGCTGGACT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
12 33 0.79
13 9 0.21
ACGTcount: A:0.29, C:0.08, G:0.27, T:0.35
Consensus pattern (12 bp):
ATGTATGCATGC
Found at i:2867295 original size:15 final size:15
Alignment explanation
Indices: 2867275--2867308 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
2867265 ATGGATGCAT
*
2867275 GCAGAGCTGGACTTC
1 GCAGAGCTGGACTTA
2867290 GCAGAGCTGGACTTA
1 GCAGAGCTGGACTTA
2867305 GCAG
1 GCAG
2867309 GACAGGTGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.35, T:0.18
Consensus pattern (15 bp):
GCAGAGCTGGACTTA
Found at i:2875557 original size:49 final size:47
Alignment explanation
Indices: 2875432--2875574 Score: 198
Period size: 48 Copynumber: 3.0 Consensus size: 47
2875422 GTGCATAGAA
* * *
2875432 GGTGTG-AAAAAGCTGAGTTAGTGTTGAATTAGGAAAAGTGTGACTTC
1 GGTGTGAAAAAAGATGACTTAGTGTTGAATT-GGGAAAGTGTGACTTC
*
2875479 TGTGTGAAAAAAGATGACTTAGTGTTGAATTGGGAAACGTGTGACTTC
1 GGTGTGAAAAAAGATGACTTAGTGTTGAATTGGGAAA-GTGTGACTTC
* *
2875527 GGTGTATAAAAAAGATGACTTAGTGTTGAATTGGGAAAGTTTGACTTC
1 GGTGT-GAAAAAAGATGACTTAGTGTTGAATTGGGAAAGTGTGACTTC
2875575 TTGGTGACTA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
47 10 0.12
48 45 0.52
49 31 0.36
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.31
Consensus pattern (47 bp):
GGTGTGAAAAAAGATGACTTAGTGTTGAATTGGGAAAGTGTGACTTC
Found at i:2880045 original size:25 final size:25
Alignment explanation
Indices: 2880017--2880071 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
2880007 AATGAAAGGC
*
2880017 TGAATTTAATGGATATTTTGAACAG
1 TGAATTTAATGGACATTTTGAACAG
* *
2880042 TGAATTTAATTGACATTTTGAATAG
1 TGAATTTAATGGACATTTTGAACAG
2880067 TGAAT
1 TGAAT
2880072 AAATGTTGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (25 bp):
TGAATTTAATGGACATTTTGAACAG
Found at i:2883267 original size:174 final size:172
Alignment explanation
Indices: 2882784--2883268 Score: 437
Period size: 178 Copynumber: 2.8 Consensus size: 172
2882774 GGAGGTTGTC
* * * * * * *
2882784 GATCTCCAAATATTATAATTTTTTTGATGTCCCACAGTGGATTTAGTTTCAATATAGAAAA--TT
1 GATCTCCAAAAATTCTATTTTTTTTAATATCCCTCAGTGGATGTAGTTTCAATATAGAAAATTTT
* * * * * * *
2882847 CAGCACAAAATTCCTTATGTACAATTCTCTGGAAATCCATCAATTACAAGTCCCAAAATTTCTAA
66 CAGCACAAAATTCCTTCTGTAAAATTCTCTGAAAATTCGTCAA-CACAAGTCCC-AAATTTC-GA
* *
2882912 TCAAACATAAGATCAACTTCAACAATGTTTTTAAGGGGGTTTTTT
128 TCAAACATAAGATCAACTTCAACAATATTTTTAAGGGGGTTTTAT
* ** * * *
2882957 GATCTCCAAAAATTCTAAATTGTTTTTGAA-AGTCCCTCAGTGGGCGTAGTCTAAATATGGAAAA
1 GATCTCCAAAAATTCT--ATT-TTTTTTAATA-TCCCTCAGTGGATGTAGTTTCAATATAGAAAA
* * * *
2883021 TATTT-AGCACAAAATTTCTTCTTTAGAATTCTCT-AGAAATTTGTCAATCACAAGTCCCAAATA
62 T-TTTCAGCACAAAATTCCTTCTGTAAAATTCTCTGA-AAATTCGTCAA-CACAAGTCCCAAAT-
* ** * * *
2883084 TGCCGATCAAACATGTGATCAACTTGAGA-ATTATTTTTGAGGGGG-TTTAT
123 T-TCGATCAAACATAAGATCAACTTCA-ACAATATTTTTAAGGGGGTTTTAT
* *
2883134 GATCTCCAAAGATTCTGATTTTTTTTAATATCCCTCAATGGATGTAGTTTCAATAT-GAAAATTT
1 GATCTCCAAAAATTCT-ATTTTTTTTAATATCCCTCAGTGGATGTAGTTTCAATATAGAAAATTT
* *
2883198 TCAACACAAAATTCCTTCCGTAAAATTCTCTGAAAATTCGTCAACGACAAGTCCCAAATCTATCG
65 TCAGCACAAAATTCCTTCTGTAAAATTCTCTGAAAATTCGTCAAC-ACAAGTCCCAAAT-T-TCG
2883263 ATCAAA
127 ATCAAA
2883269 ATTGAATGAT
Statistics
Matches: 249, Mismatches: 48, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
173 18 0.07
174 62 0.25
175 31 0.12
176 35 0.14
177 23 0.09
178 76 0.31
179 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (172 bp):
GATCTCCAAAAATTCTATTTTTTTTAATATCCCTCAGTGGATGTAGTTTCAATATAGAAAATTTT
CAGCACAAAATTCCTTCTGTAAAATTCTCTGAAAATTCGTCAACACAAGTCCCAAATTTCGATCA
AACATAAGATCAACTTCAACAATATTTTTAAGGGGGTTTTAT
Found at i:2883445 original size:16 final size:17
Alignment explanation
Indices: 2883399--2883445 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2883389 TTGTGGATTT
*
2883399 TTTTTTACTTTTTTGGCG
1 TTTTTTA-TTTTTTGGCA
*
2883417 TTTTATATTTTTT-GCA
1 TTTTTTATTTTTTGGCA
2883433 TTTTTTATTTTTT
1 TTTTTTATTTTTT
2883446 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 14 0.54
17 6 0.23
18 6 0.23
ACGTcount: A:0.11, C:0.06, G:0.09, T:0.74
Consensus pattern (17 bp):
TTTTTTATTTTTTGGCA
Found at i:2883457 original size:17 final size:18
Alignment explanation
Indices: 2883417--2883455 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2883407 TTTTTTGGCG
2883417 TTTTATATTTTTTGCATT
1 TTTTATATTTTTTGCATT
* *
2883435 TTTTATTTTTTTTTCATT
1 TTTTATATTTTTTGCATT
2883453 TTT
1 TTT
2883456 ATGAAAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.13, C:0.05, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTATATTTTTTGCATT
Found at i:2883598 original size:16 final size:16
Alignment explanation
Indices: 2883577--2883610 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2883567 TAATTTCACC
2883577 TTATGCATGTACCACT
1 TTATGCATGTACCACT
2883593 TTATGCATGTACCACT
1 TTATGCATGTACCACT
2883609 TT
1 TT
2883611 TCAATTTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.12, T:0.41
Consensus pattern (16 bp):
TTATGCATGTACCACT
Found at i:2894296 original size:46 final size:45
Alignment explanation
Indices: 2894204--2894389 Score: 302
Period size: 46 Copynumber: 4.1 Consensus size: 45
2894194 GTAACCATGC
* *
2894204 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTAGTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTACATTGGTA
2894249 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTACATTGGTA
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTACATTGGTA
* **
2894295 AAATAAGCTTACGAGATTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGGA-TAAATGGTAAGTACATTGGTA
2894341 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTACATT-GTA
1 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTACATTGGTA
2894385 AAATA
1 AAATA
2894390 TTGGATATGC
Statistics
Matches: 132, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
44 8 0.06
45 39 0.30
46 85 0.64
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTACATTGGTA
Found at i:2895476 original size:22 final size:22
Alignment explanation
Indices: 2895451--2895517 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
2895441 CAAAAATGCA
2895451 AATGGGTACCGATACCCCTATG
1 AATGGGTACCGATACCCCTATG
* *
2895473 AATGGGTATCAATACCCCCTATG
1 AATGGGTACCGATA-CCCCTATG
* *
2895496 AATGTGTACCGATACCCTTATG
1 AATGGGTACCGATACCCCTATG
2895518 GTATCAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
22 19 0.50
23 19 0.50
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.27
Consensus pattern (22 bp):
AATGGGTACCGATACCCCTATG
Found at i:2895542 original size:32 final size:32
Alignment explanation
Indices: 2895501--2895621 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 32
2895491 CTATGAATGT
2895501 GTACCGATACCCTTATGGTATCAATACCTTGG
1 GTACCGATACCCTTATGGTATCAATACCTTGG
2895533 GTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATG
1 GTACCGATA-CCCT-T-A-T-GGTATCAATA---CCT-TG---G
* *
2895577 TGTACCGATTCCCCTATGGTATCAATACCTTGG
1 -GTACCGATACCCTTATGGTATCAATACCTTGG
2895610 GTACCGATACCC
1 GTACCGATACCC
2895622 CTCTGACTGG
Statistics
Matches: 73, Mismatches: 3, Indels: 26
0.72 0.03 0.25
Matches are distributed among these distances:
32 20 0.27
33 5 0.07
34 1 0.01
35 1 0.01
36 3 0.04
37 13 0.18
40 13 0.18
41 3 0.04
42 1 0.01
43 1 0.01
44 4 0.05
45 8 0.11
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (32 bp):
GTACCGATACCCTTATGGTATCAATACCTTGG
Found at i:2895565 original size:37 final size:37
Alignment explanation
Indices: 2895517--2895642 Score: 136
Period size: 37 Copynumber: 3.3 Consensus size: 37
2895507 ATACCCTTAT
2895517 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
1 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
*
2895554 GGTATCAATACCCCCTATGAATGTGTACCGAT-TCCC-CT-A-T-
1 GGTATCAATA---CCT-TG---G-GTACCGATACCCCTCTGACTG
2895594 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
1 GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
2895631 GGTATCAATACC
1 GGTATCAATACC
2895643 CCAATAAAGG
Statistics
Matches: 74, Mismatches: 2, Indels: 26
0.73 0.02 0.25
Matches are distributed among these distances:
32 8 0.11
33 4 0.05
34 2 0.03
35 1 0.01
36 3 0.04
37 25 0.34
40 13 0.18
41 3 0.04
42 1 0.01
43 2 0.03
44 4 0.05
45 8 0.11
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (37 bp):
GGTATCAATACCTTGGGTACCGATACCCCTCTGACTG
Found at i:2895580 original size:77 final size:77
Alignment explanation
Indices: 2895453--2895644 Score: 348
Period size: 77 Copynumber: 2.5 Consensus size: 77
2895443 AAAATGCAAA
* * *
2895453 TGGGTACCGATACCCCTATGAATGGGTATCAATACCCCCTATGAATGTGTACCGATACCCTTATG
1 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATACCCCTATG
2895518 GTATCAATACCT
66 GTATCAATACCT
*
2895530 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATTCCCCTATG
1 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATACCCCTATG
2895595 GTATCAATACCT
66 GTATCAATACCT
2895607 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCC
1 TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCC
2895645 AATAAAGGCT
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 111 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (77 bp):
TGGGTACCGATACCCCTCTGACTGGGTATCAATACCCCCTATGAATGTGTACCGATACCCCTATG
GTATCAATACCT
Found at i:2895719 original size:33 final size:33
Alignment explanation
Indices: 2895674--2895739 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
2895664 AATGAAAAAA
*
2895674 AGGTACCGATACCC-CTATAGGTATCAATACCCT
1 AGGTACCAATACCCTC-ATAGGTATCAATACCCT
*
2895707 AGGTACCAATACCCTGCATGGGTATCAATACCC
1 AGGTACCAATACCCT-CATAGGTATCAATACCC
2895740 CTAGCTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 13 0.45
34 15 0.52
35 1 0.03
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (33 bp):
AGGTACCAATACCCTCATAGGTATCAATACCCT
Found at i:2895739 original size:19 final size:15
Alignment explanation
Indices: 2895691--2895721 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2895681 GATACCCCTA
2895691 TAGGTATCAATACCC
1 TAGGTATCAATACCC
*
2895706 TAGGTACCAATACCC
1 TAGGTATCAATACCC
2895721 T
1 T
2895722 GCATGGGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.26
Consensus pattern (15 bp):
TAGGTATCAATACCC
Found at i:2897634 original size:17 final size:17
Alignment explanation
Indices: 2897609--2897650 Score: 66
Period size: 17 Copynumber: 2.4 Consensus size: 17
2897599 ATTATGGTTA
2897609 AAATAAAAAATAAGAATT
1 AAAT-AAAAATAAGAATT
*
2897627 AAATAAAAATAATAATT
1 AAATAAAAATAAGAATT
2897644 AAATAAA
1 AAATAAA
2897651 CAAATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 19 0.83
18 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (17 bp):
AAATAAAAATAAGAATT
Found at i:2898906 original size:3 final size:3
Alignment explanation
Indices: 2898850--2898893 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
2898840 CTTTCAGTTG
2898850 ATT ATT ATT -TT -TT ATT ATT AATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
2898893 A
1 A
2898894 ATAAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.16
3 29 0.76
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:2899937 original size:64 final size:65
Alignment explanation
Indices: 2899842--2899962 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 65
2899832 TATTTTTATA
* *
2899842 AATAATTAAGGTAAAATATGTATTTAGTCC-TTACACTTTTAATAATATTTATTTTAACCCGACT
1 AATAATTAAGGTAAAATATGTATTTAATCCTTTACACTTTTAATAAAATTTATTTTAACCCGACT
* * * *
2899906 AATAATTTAGGT-AAATAT-TATAATTAATCCTTTATAGTTTTATTAAAATTTATTTTA
1 AATAATTAAGGTAAAATATGTAT--TTAATCCTTTACACTTTTAATAAAATTTATTTTA
2899963 GTCCCATATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
62 3 0.06
63 6 0.12
64 17 0.35
65 22 0.46
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (65 bp):
AATAATTAAGGTAAAATATGTATTTAATCCTTTACACTTTTAATAAAATTTATTTTAACCCGACT
Found at i:2900160 original size:14 final size:14
Alignment explanation
Indices: 2900141--2900170 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2900131 TTAATTTCTT
2900141 TTATATTTTAGTTA
1 TTATATTTTAGTTA
2900155 TTATATTTTAGTTA
1 TTATATTTTAGTTA
2900169 TT
1 TT
2900171 TGCAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (14 bp):
TTATATTTTAGTTA
Found at i:2900254 original size:2 final size:2
Alignment explanation
Indices: 2900247--2900272 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2900237 TTACTTAGTC
2900247 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2900273 TATTTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2908225 original size:17 final size:19
Alignment explanation
Indices: 2908198--2908233 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
2908188 AAATGGAAAT
2908198 CATTATTTACATTC-TTTA
1 CATTATTTACATTCATTTA
2908216 CATT-TTTACATTCATTTA
1 CATTATTTACATTCATTTA
2908234 TTTCATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.56
Consensus pattern (19 bp):
CATTATTTACATTCATTTA
Found at i:2913397 original size:112 final size:111
Alignment explanation
Indices: 2913264--2913649 Score: 400
Period size: 112 Copynumber: 3.4 Consensus size: 111
2913254 TATGAAAAAT
* * * *
2913264 AAGAAGAAGTTTATAATGAGAAGAATTTGTTCAATCGTTTGCTCGAATTCATCACTCGATGGATC
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCT-GAATTCATCACTCGATGGATC
* * *
2913329 AACTTTTCCAGATAAAGTTTGTAATGAGAAGAACATATCTGAAGAGG
65 AACTTTTCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAGAGG
* * *
2913376 AAGAAGAAGTTCATAACGAGAAGAGCTTGTTCAACCTTTTGCATG-ACTCTATCACAGAAGGAGA
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TGAATTC-ATCAC---------
* ** * **
2913440 TAGATCAACATCAACTTTTCCAGAGAAAATTCATAATGAGAAGAACGCATCTGAAGAAGG
55 TCGAT--GGATCAACTTTTCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAG-AGG
* *
2913500 AAGGAA-AAGTTCAT-ATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATTACTCAATGGAT
1 AA-GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGC-TGAATTCATCACTCGATGGAT
**
2913563 CAACTTTTCCAGAGAAAATTCGTAATGAGAAGAATTTATCTGAAGAGG
64 CAACTTTTCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAGAGG
* *
2913611 AAGAAGAAGTTCATAATAAGAAGAACTTGTTTAACCTTT
1 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
2913650 GTTTGATTCT
Statistics
Matches: 225, Mismatches: 31, Indels: 36
0.77 0.11 0.12
Matches are distributed among these distances:
110 3 0.01
111 16 0.07
112 107 0.48
113 1 0.00
114 3 0.01
121 4 0.02
123 72 0.32
124 16 0.07
125 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (111 bp):
AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTGAATTCATCACTCGATGGATCA
ACTTTTCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAGAGG
Found at i:2913649 original size:235 final size:235
Alignment explanation
Indices: 2913270--2913734 Score: 646
Period size: 235 Copynumber: 2.0 Consensus size: 235
2913260 AAATAAGAAG
* * * *
2913270 AAGTTTATAATGAGAAGAATTTGTTCAATCGTTTGCTCGAATTCATCACTCGATGGATCAACTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCGTTTGCTCGAATTCATCACTCAATGGATCAACTTT
* * * *
2913335 TCCAGATAAAGTTTGTAATGAGAAGAACATATCTGAAGAGGAAGAAGAAGTTCATAACGAGAAGA
66 TCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAGAGGAAGAAGAAGTTCATAACAAGAAGA
* * *
2913400 GCTTGTTCAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCAACATCAACTTTTCCAG-A
131 ACTTGTTCAACC-TTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAA
2913464 GAAAATTCATAATGAGAAGAACGCATCTGAAGAAGGAAGGAA
195 G-AAATTCATAATGAGAAGAACGCATCTGAAGAAGGAAGGAA
* * *
2913506 AAGTTCAT-ATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATTACTCAATGGATCAACTTT
1 AAGTTCATAATGAGAAGAACTTGTTCAACCGTTTGCTCGAATTCATCACTCAATGGATCAACTTT
** *
2913570 TCCAGAGAAAATTCGTAATGAGAAGAATTTATCTGAAGAGGAAGAAGAAGTTCATAATAAGAAGA
66 TCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAGAGGAAGAAGAAGTTCATAACAAGAAGA
* ** * **
2913635 ACTTGTTTAACCTTTGTTTGATTCTATCACAGAAAGAGATAGATCAGTATCAACATTTCCAGAAG
131 ACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAG
* * * * *
2913700 GAGTTCATAATTAGAATAACTCATCTGAAGAAGGA
196 AAATTCATAATGAGAAGAACGCATCTGAAGAAGGA
2913735 GAAGAATTTG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
234 73 0.37
235 120 0.60
236 7 0.04
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.28
Consensus pattern (235 bp):
AAGTTCATAATGAGAAGAACTTGTTCAACCGTTTGCTCGAATTCATCACTCAATGGATCAACTTT
TCCAGAGAAAATTCGTAATGAGAAGAACATATCTGAAGAGGAAGAAGAAGTTCATAACAAGAAGA
ACTTGTTCAACCTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACATTTCCAGAAG
AAATTCATAATGAGAAGAACGCATCTGAAGAAGGAAGGAA
Found at i:2914034 original size:3 final size:3
Alignment explanation
Indices: 2913974--2914024 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
2913964 CTTTCGGTTG
2913974 ATT ATT ATT -TT ATT ATT ATT AATT -TT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT
2914018 ATT ATT A
1 ATT ATT A
2914025 AAATATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2922266 original size:6 final size:6
Alignment explanation
Indices: 2922255--2922345 Score: 64
Period size: 6 Copynumber: 14.5 Consensus size: 6
2922245 TCGCCTGAAG
*
2922255 AAAGAA AAAGAAA AAAGAA AAA-AA AATA-AA ATGAGAGAA AATGAA AAAG-A
1 AAAGAA AAAG-AA AAAGAA AAAGAA AA-AGAA A--A-AGAA AAAGAA AAAGAA
*
2922305 AAAGAA AAATGAA AAAGAGA AAA-AG AAAGAAA AAAGAA AAA
1 AAAGAA AAA-GAA AAAGA-A AAAGAA AAAG-AA AAAGAA AAA
2922346 AGAATAAATA
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
5 12 0.17
6 31 0.44
7 22 0.31
8 2 0.03
9 3 0.04
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:2922271 original size:7 final size:7
Alignment explanation
Indices: 2922255--2922349 Score: 63
Period size: 7 Copynumber: 12.9 Consensus size: 7
2922245 TCGCCTGAAG
2922255 AAAG-AA
1 AAAGAAA
2922261 AAAGAAA
1 AAAGAAA
2922268 AAAGAAA
1 AAAGAAA
*
2922275 AAAAAATA
1 AAAGAA-A
2922283 AAATGAGAGA
1 AAA-GA-A-A
2922293 AAATG-AA
1 AAA-GAAA
2922300 AAAG--A
1 AAAGAAA
2922305 AAAGAAA
1 AAAGAAA
*
2922312 AATGAAA
1 AAAGAAA
2922319 AAGAGAAAAA
1 AA-AG--AAA
2922329 GAAAGAAA
1 -AAAGAAA
2922337 AAAGAAA
1 AAAGAAA
2922344 AAAGAA
1 AAAGAA
2922350 TAAATAAAAG
Statistics
Matches: 74, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
5 5 0.07
6 5 0.07
7 40 0.54
8 9 0.12
9 1 0.01
10 12 0.16
11 2 0.03
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (7 bp):
AAAGAAA
Found at i:2922307 original size:32 final size:34
Alignment explanation
Indices: 2922252--2922353 Score: 120
Period size: 33 Copynumber: 3.0 Consensus size: 34
2922242 ACTTCGCCTG
2922252 AAGA-AAGAAAAAGAAAAAAGAAAAAAAAATAAA
1 AAGAGAAGAAAAAGAAAAAAGAAAAAAAAATAAA
* *
2922285 ATGAG-AGAAAATG-AAAAAGAAAAGAAAAATGAAA
1 AAGAGAAGAAAAAGAAAAAAGAAAA-AAAAAT-AAA
* *
2922319 AAGAGAAAAAGAAAGAAAAAAGAAAAAAGAATAAA
1 AAGAGAAGAA-AAAGAAAAAAGAAAAAAAAATAAA
2922354 TAAAAGGGGG
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
32 10 0.18
33 16 0.28
34 7 0.12
35 6 0.11
36 8 0.14
37 10 0.18
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (34 bp):
AAGAGAAGAAAAAGAAAAAAGAAAAAAAAATAAA
Found at i:2922345 original size:18 final size:18
Alignment explanation
Indices: 2922252--2922349 Score: 80
Period size: 18 Copynumber: 5.3 Consensus size: 18
2922242 ACTTCGCCTG
2922252 AAGAAAG-AAAAAGAAAA
1 AAGAAAGAAAAAAGAAAA
*
2922269 AAGAAA-AAAAAATAAAA
1 AAGAAAGAAAAAAGAAAA
2922286 TGAGAGAAA-ATGAAAAAGAAAA
1 --A-AGAAAGA--AAAAAGAAAA
2922308 GAA-AAATG-AAAAAGAGAAA
1 -AAGAAA-GAAAAAAGA-AAA
2922327 AAGAAAGAAAAAAGAAAA
1 AAGAAAGAAAAAAGAAAA
2922345 AAGAA
1 AAGAA
2922350 TAAATAAAAG
Statistics
Matches: 68, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
17 15 0.22
18 18 0.26
19 17 0.25
20 7 0.10
21 2 0.03
22 9 0.13
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.04
Consensus pattern (18 bp):
AAGAAAGAAAAAAGAAAA
Found at i:2923860 original size:133 final size:133
Alignment explanation
Indices: 2923610--2924033 Score: 494
Period size: 133 Copynumber: 3.1 Consensus size: 133
2923600 CTTCCCCGAG
* * ** * * *
2923610 GAACAGTGGAATGAACCAATGTCTCCAGATCTGATTTTTCCCTTAAGAAGCCACGAAATAGATCC
1 GAACAGTGGAATGAATCAAT-TTTCCAGATCTGA-TTTTCCCTTAAGAAGCCGTGGAACATAT-C
* *
2923675 CTCTTTTTTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCAATTCAATTTT
63 C-CATTTTTTCCATATTTGATCTTCCCTGAGGAATAGTGGAACAAGTCTGCCTCAATTCAATTTT
2923740 CCTTGAA
127 CCTTGAA
*
2923747 GAACAGTGGAATGAATCAATATTTCTAGATCTGATTTTCCCTTAAGAAGCCGTGGAACATATCCC
1 GAACAGTGGAATGAATCAAT-TTTCCAGATCTGATTTTCCCTTAAGAAGCCGTGGAACATATCCC
** * * * *
2923812 -TTTTTTCCATATTTGATAATCCCTGAGGAATAATGGAATAAGTATGCCTCAATTCAATCTTCCT
65 ATTTTTTCCATATTTGATCTTCCCTGAGGAATAGTGGAACAAGTCTGCCTCAATTCAATTTTCCT
2923876 TGAA
130 TGAA
* * * *
2923880 GAACAGTGGAATGAATAAACTTTTCCAGATCTGATTTT-CGTTGAAGAAACAGTGGAACATATCC
1 GAACAGTGGAATGAATCAA-TTTTCCAGATCTGATTTTCCCTT-AAGAAGCCGTGGAACATATCC
* * * **
2923944 CATTTCTTTCCAGATTTGATCTTCCCTGAGTAGTAGTGGAACAAGTCTGCCTGGATTCAATCTTT
64 CATTT-TTTCCATATTTGATCTTCCCTGAGGAATAGTGGAACAAGTCTGCCTCAATTCAAT-TTT
*
2924009 TC-TGAA
127 CCTTGAA
* *
2924015 GAATAATGGAATGAATCAA
1 GAACAGTGGAATGAATCAA
2924034 CGACCCCAAA
Statistics
Matches: 246, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
132 3 0.01
133 115 0.47
134 5 0.02
135 67 0.27
136 26 0.11
137 30 0.12
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (133 bp):
GAACAGTGGAATGAATCAATTTTCCAGATCTGATTTTCCCTTAAGAAGCCGTGGAACATATCCCA
TTTTTTCCATATTTGATCTTCCCTGAGGAATAGTGGAACAAGTCTGCCTCAATTCAATTTTCCTT
GAA
Found at i:2924028 original size:135 final size:133
Alignment explanation
Indices: 2923677--2924165 Score: 466
Period size: 133 Copynumber: 3.7 Consensus size: 133
2923667 ATAGATCCCT
* * * *
2923677 CTTTTTTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCAATTCAATTTTCC
1 CTTTCTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTATGCCTCAATTCAATCTTCC
* * * * *
2923742 TTGAAGAACAGTGGAATGAATCAA-TATTTCTAGATCTGATTTTCCCTTAAGAAGCCGTGGAACA
66 TTGAAGAACAATGGAATGAATAAACT-TTTCCAGATCTGATTTT-CCTTAAGAAACAGTGGAACA
2923806 TATCC
129 TATCC
* ** * * *
2923811 CTTT-TTTCCATATTTGATAATCCCTGAGGAATAATGGAATAAGTATGCCTCAATTCAATCTTCC
1 CTTTCTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTATGCCTCAATTCAATCTTCC
* *
2923875 TTGAAGAACAGTGGAATGAATAAACTTTTCCAGATCTGATTTTCGTTGAAGAAACAGTGGAACAT
66 TTGAAGAACAATGGAATGAATAAACTTTTCCAGATCTGATTTTCCTT-AAGAAACAGTGGAACAT
2923940 ATCC
130 ATCC
* ** * **
2923944 CATTTCTTTCCAGATTTGATCTTCCCTGAGTAGTAGTGGAACAAGTCTGCCTGGATTCAATCTT-
1 C-TTTCTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTATGCCTCAATTCAATCTTC
* * * **** * * * ****
2924008 TTCTGAAGAATAATGGAATGAATCAACGACCCCAAATCTGATTTTCCCTAAATAAACAACAAAAC
65 CT-TGAAGAACAATGGAATGAATAAACTTTTCCAGATCTGATTTT-CCTTAAGAAACAGTGGAAC
* *
2924073 AAATTC
128 ATATCC
* * * * * *
2924079 C-TTCTTTCAAGATTTGATCTTCCCTAAGCAGCAGTGAAACAAGTATGCCTCGATTCAATCTTCC
1 CTTTCTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTATGCCTCAATTCAATCTTCC
*
2924143 -CGAAAGAACAATGGAATGAATAA
66 TTG-AAGAACAATGGAATGAATAA
2924166 CAGTTGTCGA
Statistics
Matches: 296, Mismatches: 51, Indels: 17
0.81 0.14 0.05
Matches are distributed among these distances:
132 4 0.01
133 184 0.62
134 9 0.03
135 97 0.33
136 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (133 bp):
CTTTCTTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTATGCCTCAATTCAATCTTCC
TTGAAGAACAATGGAATGAATAAACTTTTCCAGATCTGATTTTCCTTAAGAAACAGTGGAACATA
TCC
Found at i:2924096 original size:268 final size:268
Alignment explanation
Indices: 2923682--2924165 Score: 569
Period size: 268 Copynumber: 1.8 Consensus size: 268
2923672 TCCCTCTTTT
*
2923682 TTTCCATATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCAATTCAATTTTCCTTGAA
1 TTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCAATTCAATTTTCCTTGAA
* * ** * * * * ***** *
2923747 GAACAGTGGAATGAATCAATATTTCTAGATCTGATTTTCCCTTAAGAAGCCGTGGAACATATCCC
66 GAACAATGGAATGAATCAAGATCCCCAAATCTGATTTTCCCTAAAGAAACAACAAAACAAATCCC
* * * * * * * * *
2923812 TTTTTTCCATATTTGATAATCCCTGAGGAATAATGGAATAAGTATGCCTCAATTCAATCTTCCTT
131 TTCTTTCAAGATTTGATAATCCCTAAGCAACAATGAAACAAGTATGCCTCAATTCAATCTTCC-C
*
2923877 G-AAGAACAGTGGAATGAATAAACTTTTCCAGATCTGATTTTCGTTGAAGAAACAGTGGAACATA
195 GAAAGAACAATGGAATGAATAAACTTTTCCAGATCTGATTTTCGTTGAAGAAACAGTGGAACATA
2923941 TCCCATTTC
260 TCCCATTTC
* ** ** *
2923950 TTTCCAGATTTGATCTTCCCTGAGTAGTAGTGGAACAAGTCTGCCTGGATTCAATCTTTTC-TGA
1 TTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCAATTCAAT-TTTCCTTGA
* * *
2924014 AGAATAATGGAATGAATCAACGA-CCCCAAATCTGATTTTCCCTAAATAAACAACAAAACAAATT
65 AGAACAATGGAATGAATCAA-GATCCCCAAATCTGATTTTCCCTAAAGAAACAACAAAACAAATC
** * * *
2924078 CCTTCTTTCAAGATTTGATCTTCCCTAAGCAGCAGTGAAACAAGTATGCCTCGATTCAATCTTCC
129 CCTTCTTTCAAGATTTGATAATCCCTAAGCAACAATGAAACAAGTATGCCTCAATTCAATCTTCC
2924143 CGAAAGAACAATGGAATGAATAA
194 CGAAAGAACAATGGAATGAATAA
2924166 CAGTTGTCGA
Statistics
Matches: 174, Mismatches: 39, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
267 1 0.01
268 168 0.97
269 5 0.03
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.31
Consensus pattern (268 bp):
TTTCCAGATTTGATCTTCCCTGAGGAACAGTGGAACAAGTCTGCCTCAATTCAATTTTCCTTGAA
GAACAATGGAATGAATCAAGATCCCCAAATCTGATTTTCCCTAAAGAAACAACAAAACAAATCCC
TTCTTTCAAGATTTGATAATCCCTAAGCAACAATGAAACAAGTATGCCTCAATTCAATCTTCCCG
AAAGAACAATGGAATGAATAAACTTTTCCAGATCTGATTTTCGTTGAAGAAACAGTGGAACATAT
CCCATTTC
Found at i:2924202 original size:3 final size:3
Alignment explanation
Indices: 2924194--2924249 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
2924184 TTCGTCCCGC
2924194 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
2924241 TAT T-T TAT T
1 TAT TAT TAT T
2924250 TATTTTATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:2924914 original size:22 final size:22
Alignment explanation
Indices: 2924872--2924915 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2924862 CCGAAAAGTC
*
2924872 AAGGCTTTTGGGCGGTGTTTAG
1 AAGGCTTTTAGGCGGTGTTTAG
*
2924894 AAGGCTTTCTAGGTGGT-TTTAG
1 AAGGCTTT-TAGGCGGTGTTTAG
2924916 CCTCGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.16, C:0.09, G:0.36, T:0.39
Consensus pattern (22 bp):
AAGGCTTTTAGGCGGTGTTTAG
Found at i:2926417 original size:132 final size:132
Alignment explanation
Indices: 2926142--2926485 Score: 435
Period size: 132 Copynumber: 2.6 Consensus size: 132
2926132 GTAATATCTT
* * * * * *
2926142 TTCATTTCTG-TTGTAGTAATGAATGAATTCATTAAGGCATGAGAGGTCATTTATTCTCGATTGG
1 TTCATTTC-GATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCATTTATTCTCAATTGG
* * *
2926206 AAATAATTAGATATTA-CTATTTTCTCTCAAATCAATATTGATTTTTAAGACGAAATAGTGATAT
65 AAATAATTAGATATTATCTATTTTCACTCAAATCAATATTGAATTTTAAGACAAAATAGTGATAT
*
2926270 CTC
130 ATC
* * * * *
2926273 TTCATTTCGATTGGAGTAATAAATTACA-GTTTTAAGGCATAAGATGTCATTTATTCCCAATTGG
1 TTCATTTCGATTGGAGTAATAAATGA-ATGCTTTAAGGCATGAGAAGTCATTTATTCTCAATTGG
* * *
2926337 AAATCATTAGATATTATC-ATTTTTCACTCAAATCAATGTTGAATTTTAAGATAAAATAGTGATA
65 AAATAATTAGATATTATCTA-TTTTCACTCAAATCAATATTGAATTTTAAGACAAAATAGTGATA
2926401 TATC
129 TATC
* * * *
2926405 TTCATTTCGATTGGAGTAATTAATGAATGCTTTCAGGCATGAGAAGTCGTTTATTCTCAATCGGA
1 TTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCATTTATTCTCAATTGGA
2926470 AATAATTAGATATTAT
66 AATAATTAGATATTAT
2926486 TGTTTTCTCT
Statistics
Matches: 181, Mismatches: 27, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
130 1 0.01
131 67 0.37
132 113 0.62
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (132 bp):
TTCATTTCGATTGGAGTAATAAATGAATGCTTTAAGGCATGAGAAGTCATTTATTCTCAATTGGA
AATAATTAGATATTATCTATTTTCACTCAAATCAATATTGAATTTTAAGACAAAATAGTGATATA
TC
Found at i:2931202 original size:122 final size:121
Alignment explanation
Indices: 2931076--2931348 Score: 388
Period size: 122 Copynumber: 2.2 Consensus size: 121
2931066 GTCGCTAATG
*
2931076 TTACCATTTTGTGGCATTTGTATTTAAAAA-CACACTAATACACTGATTTATTGCAACATTTATT
1 TTACCATTTTGTGGCATTTGTATTTAAAAAGC-CACTAATACAATGATTTATTGCAACATTTATT
* * *
2931140 TTAAAAACGCCATAA-AAGATGAGGCTATAGTGGCATTTTTAGAGAAACACCACAAATA
65 TT-AAAACGCCACAATAA-ATGAGGCTATAGTGGCATTTTTAGAAAAACACAACAAATA
* ** *
2931198 TTACCATTTTGTGGCATTTGTATTTAAAAATGCCACTAATGCAATGATTTATTGCGGCATTTGTT
1 TTACCATTTTGTGGCATTTGTATTTAAAAA-GCCACTAATACAATGATTTATTGCAACATTTATT
* *
2931263 TTAAAACGCCACAATAAATGAGTCTATAGTGGCATTTTTAGAAAAACACAACTAATA
65 TTAAAACGCCACAATAAATGAGGCTATAGTGGCATTTTTAGAAAAACACAACAAATA
*
2931320 TTACCATTTTGTGGCGTTTGATATTTAAA
1 TTACCATTTTGTGGCATTTG-TATTTAAA
2931349 TGCCGATATA
Statistics
Matches: 136, Mismatches: 11, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
122 96 0.71
123 39 0.29
124 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.36
Consensus pattern (121 bp):
TTACCATTTTGTGGCATTTGTATTTAAAAAGCCACTAATACAATGATTTATTGCAACATTTATTT
TAAAACGCCACAATAAATGAGGCTATAGTGGCATTTTTAGAAAAACACAACAAATA
Found at i:2938819 original size:2 final size:2
Alignment explanation
Indices: 2938812--2938839 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2938802 CTTTTAATTG
2938812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2938840 TTTAGAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2951829 original size:23 final size:23
Alignment explanation
Indices: 2951802--2951872 Score: 115
Period size: 23 Copynumber: 3.1 Consensus size: 23
2951792 GGTTCTGTGC
*
2951802 GGTCCTTTGGGACATATCTATGT
1 GGTCCTTCGGGACATATCTATGT
2951825 GGTCCTTCGGGACATATCTATGT
1 GGTCCTTCGGGACATATCTATGT
* *
2951848 GGTCCTTCGGGACATTTCTACGT
1 GGTCCTTCGGGACATATCTATGT
2951871 GG
1 GG
2951873 CACTTTGGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.15, C:0.21, G:0.28, T:0.35
Consensus pattern (23 bp):
GGTCCTTCGGGACATATCTATGT
Found at i:2951898 original size:24 final size:24
Alignment explanation
Indices: 2951862--2951908 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
2951852 CTTCGGGACA
** *
2951862 TTTCTACGTGGCACTTTGGTGCAT
1 TTTCTACACGGCACTTCGGTGCAT
2951886 TTTCTACACGGCACTTCGGTGCA
1 TTTCTACACGGCACTTCGGTGCA
2951909 ATTTATACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (24 bp):
TTTCTACACGGCACTTCGGTGCAT
Found at i:2979028 original size:2 final size:2
Alignment explanation
Indices: 2979021--2979061 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2979011 AGTTATATGA
*
2979021 AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2979062 ATAACTTATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2979033 original size:10 final size:10
Alignment explanation
Indices: 2979014--2979064 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
2979004 TAATACTAGT
*
2979014 TATATGAATA
1 TATATAAATA
2979024 TATATAAATA
1 TATATAAATA
*
2979034 TATATATATA
1 TATATAAATA
*
2979044 TATATATATA
1 TATATAAATA
2979054 TATATATAATA
1 TATATA-AATA
2979065 ACTTATAAAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
10 34 0.92
11 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (10 bp):
TATATAAATA
Found at i:2979194 original size:2 final size:2
Alignment explanation
Indices: 2979187--2979227 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2979177 AATCACAGTA
2979187 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2979228 AAATAAAGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2988527 original size:21 final size:21
Alignment explanation
Indices: 2988479--2988528 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
2988469 GGTCGACCAA
*
2988479 GGACTCCTGTTTGTTCTTGAT
1 GGACTCTTGTTTGTTCTTGAT
2988500 GGACTCTTGGTTT-TTCTTGAT
1 GGACTCTT-GTTTGTTCTTGAT
2988521 GGACTCTT
1 GGACTCTT
2988529 CAGTGCTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.10, C:0.18, G:0.24, T:0.48
Consensus pattern (21 bp):
GGACTCTTGTTTGTTCTTGAT
Found at i:2991647 original size:13 final size:15
Alignment explanation
Indices: 2991629--2991660 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2991619 AATGAGATAA
2991629 AAAATAAG-AAAA-T
1 AAAATAAGTAAAAGT
2991642 AAAATAAGTAAAAGT
1 AAAATAAGTAAAAGT
2991657 AAAA
1 AAAA
2991661 ATAAACAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.75, C:0.00, G:0.09, T:0.16
Consensus pattern (15 bp):
AAAATAAGTAAAAGT
Found at i:2991674 original size:20 final size:21
Alignment explanation
Indices: 2991637--2991675 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
2991627 AAAAAATAAG
* *
2991637 AAAATAAAATAAGTAAAAGTA
1 AAAATAAAACAAGAAAAAGTA
2991658 AAAAT-AAACAAGAAAAAG
1 AAAATAAAACAAGAAAAAG
2991676 GAATGAAGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAATAAAACAAGAAAAAGTA
Found at i:2991977 original size:23 final size:23
Alignment explanation
Indices: 2991941--2991984 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2991931 AAAATAATAG
*
2991941 TAATAAGTATTAAAATAAAAAAAA
1 TAATAAGTAAT-AAATAAAAAAAA
2991965 TAAT-AGTAATAAATAAAAAA
1 TAATAAGTAATAAATAAAAAA
2991985 CAGAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 5 0.26
24 4 0.21
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (23 bp):
TAATAAGTAATAAATAAAAAAAA
Found at i:2997349 original size:100 final size:99
Alignment explanation
Indices: 2997194--2997388 Score: 365
Period size: 100 Copynumber: 2.0 Consensus size: 99
2997184 AATTTTCGAA
2997194 ATATGAATTGCCAATACCACTAAGATAATAATTTAGCATTCTAAGTGTTTAAAACAGAATTTTGA
1 ATATGAATTGCCAATACCACTAAGATAATAATTTAGCATTCTAAGTGTTTAAAACAGAATTTTGA
2997259 CATTTCTGTAC-AAGTGTATCGATACCTATGTAT
66 CATTTCTGTACAAAGTGTATCGATACCTATGTAT
2997292 ATATGAATTGCCAATACCACTAGAGATAATTAATTTAGCATTCTAAGTGTTTAAAACAGAATTTT
1 ATATGAATTGCCAATACCACTA-AGATAA-TAATTTAGCATTCTAAGTGTTTAAAACAGAATTTT
2997357 GACATTTCTGTACAAAGTGTATCGATACCTAT
64 GACATTTCTGTACAAAGTGTATCGATACCTAT
2997389 TTATCGATAC
Statistics
Matches: 94, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
98 22 0.23
99 6 0.06
100 48 0.51
101 18 0.19
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.35
Consensus pattern (99 bp):
ATATGAATTGCCAATACCACTAAGATAATAATTTAGCATTCTAAGTGTTTAAAACAGAATTTTGA
CATTTCTGTACAAAGTGTATCGATACCTATGTAT
Found at i:2997433 original size:21 final size:23
Alignment explanation
Indices: 2997409--2997467 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2997399 ACCGTTGCTA
2997409 TGTATCGATACACT-ATT-AATG
1 TGTATCGATACACTCATTGAATG
* * *
2997430 TGTACCGATACATTCCTTGAATG
1 TGTATCGATACACTCATTGAATG
2997453 TGTATCGATACACTC
1 TGTATCGATACACTC
2997468 CTCGAGTGTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 12 0.39
22 2 0.06
23 17 0.55
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (23 bp):
TGTATCGATACACTCATTGAATG
Found at i:2997482 original size:21 final size:23
Alignment explanation
Indices: 2997426--2997485 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
2997416 ATACACTATT
* *
2997426 AATGTGTACCGATACATTCCTTG
1 AATGTGTACCGATACACTCCTCG
*
2997449 AATGTGTATCGATACACTCCTCG
1 AATGTGTACCGATACACTCCTCG
2997472 -A-GTGTACCGATACA
1 AATGTGTACCGATACA
2997486 GTCGTAGGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.36
22 1 0.03
23 20 0.61
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (23 bp):
AATGTGTACCGATACACTCCTCG
Found at i:2998969 original size:13 final size:13
Alignment explanation
Indices: 2998947--2998980 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
2998937 AGGGGGAGTA
*
2998947 ATTTTCAAAATTG
1 ATTTTCAAAAATG
2998960 A-TTTCAAAAATG
1 ATTTTCAAAAATG
2998972 ATTTTCAAA
1 ATTTTCAAA
2998981 TAAAGTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (13 bp):
ATTTTCAAAAATG
Found at i:2999422 original size:18 final size:19
Alignment explanation
Indices: 2999399--2999448 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
2999389 ATGTAATTAG
2999399 TGTACCGATACACCT-GGA
1 TGTACCGATACACCTAGGA
2999417 TGTACCGATACACCTAGGA
1 TGTACCGATACACCTAGGA
2999436 TGTACCGATACAC
1 TGTACCGATACAC
2999449 TAAGTCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (19 bp):
TGTACCGATACACCTAGGA
Found at i:3006510 original size:18 final size:18
Alignment explanation
Indices: 3006487--3006531 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3006477 GTATTTCTGG
3006487 AAGATTTCTCACCGCTAC
1 AAGATTTCTCACCGCTAC
*
3006505 AAGATTTCCCACCGCTAC
1 AAGATTTCTCACCGCTAC
3006523 AAGATTTCT
1 AAGATTTCT
3006532 TTTCTCGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.11, T:0.29
Consensus pattern (18 bp):
AAGATTTCTCACCGCTAC
Found at i:3019046 original size:35 final size:35
Alignment explanation
Indices: 3018985--3019131 Score: 186
Period size: 35 Copynumber: 4.1 Consensus size: 35
3018975 CAAATTCTTT
*
3018985 CAATTCAATTCAACCTTCACAAAAGAGTAGTGAAG
1 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAG
* * **
3019020 CAATGCAATTCAGCCTCCACGGAAGAGTAGTTGAAACAAG
1 CAATGCAATTCAACCTTCACAAAAGAGTAG-TG----AAG
3019060 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAG
1 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAG
* *
3019095 CAATGCAATTTATCCTTCACAAAAGAGTAGTGAAG
1 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAG
3019130 CA
1 CA
3019132 GGAAAAGATC
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
35 63 0.66
36 2 0.02
39 2 0.02
40 29 0.30
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.21
Consensus pattern (35 bp):
CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAG
Found at i:3019121 original size:75 final size:75
Alignment explanation
Indices: 3018985--3019125 Score: 228
Period size: 75 Copynumber: 1.9 Consensus size: 75
3018975 CAAATTCTTT
* **
3018985 CAATTCAATTCAACCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAGCCTCCACGGAAGAGTAG
1 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAGCCTCCACAAAAGAGTAG
3019050 TTGAAACAAG
66 TTGAAACAAG
* * *
3019060 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAGCAATGCAATTTATCCTTCACAAAAGAGTAG
1 CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAGCCTCCACAAAAGAGTAG
3019125 T
66 T
3019126 GAAGCAGGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
75 60 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.22
Consensus pattern (75 bp):
CAATGCAATTCAACCTTCACAAAAGAGTAGTGAAGCAATGCAATTCAGCCTCCACAAAAGAGTAG
TTGAAACAAG
Found at i:3020711 original size:14 final size:14
Alignment explanation
Indices: 3020686--3020732 Score: 76
Period size: 14 Copynumber: 3.2 Consensus size: 14
3020676 TTATAATAGG
3020686 ATTAATAATATTTAT
1 ATTAA-AATATTTAT
3020701 ATTAAAATATTTAT
1 ATTAAAATATTTAT
3020715 ATTAAAATATTTAGT
1 ATTAAAATATTTA-T
3020730 ATT
1 ATT
3020733 TATCTATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 22 0.71
15 9 0.29
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATTAAAATATTTAT
Found at i:3025223 original size:45 final size:45
Alignment explanation
Indices: 3025133--3025437 Score: 497
Period size: 45 Copynumber: 6.8 Consensus size: 45
3025123 GGTAAACATG
* *
3025133 AAAATAAGCTTACGAGCTTATTGAAT-AATGGCAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
3025177 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
3025222 AAAATAAGCTTACGAGCTTATGGAATAAATTGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* * * *
3025267 AAAATAATCTTACGAGCTTATAGATTAAATGGTAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
*
3025312 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGAT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
3025357 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
* *
3025402 AGAATAAGCTTACGAGCTTATAGG-ATAAATGATAAG
1 AAAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAG
3025438 AAAGTTTATA
Statistics
Matches: 245, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
44 25 0.10
45 218 0.89
46 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (45 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGT
Found at i:3032008 original size:59 final size:59
Alignment explanation
Indices: 3031902--3032029 Score: 139
Period size: 59 Copynumber: 2.2 Consensus size: 59
3031892 GTAGTGTTAA
* * * ** *
3031902 CCCGATTATGACACATAAGGTCATGTCCACTATCTGTACTAGGTATACTTAAGTGCAGT
1 CCCGAATATGACACATAAGGTCATGTCCACCATATACACTAAGTATACTTAAGTGCAGT
* ** * * * *
3031961 CTCGAATATGACACATAAGGTTGTGTCCACCATATACACTAATTATACTTTAGTGTATT
1 CCCGAATATGACACATAAGGTCATGTCCACCATATACACTAAGTATACTTAAGTGCAGT
3032020 CCCGAATATG
1 CCCGAATATG
3032030 CGGCCTGCTG
Statistics
Matches: 55, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
59 55 1.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.32
Consensus pattern (59 bp):
CCCGAATATGACACATAAGGTCATGTCCACCATATACACTAAGTATACTTAAGTGCAGT
Found at i:3039033 original size:24 final size:24
Alignment explanation
Indices: 3039001--3039049 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3038991 AGTCTTCCCG
*
3039001 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATATATGTAC
*
3039025 ATGATGTATTAAACATATATGTAC
1 ATGATGTATAAAACATATATGTAC
3039049 A
1 A
3039050 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (24 bp):
ATGATGTATAAAACATATATGTAC
Found at i:3039945 original size:30 final size:31
Alignment explanation
Indices: 3039905--3039962 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
3039895 AATCAACATT
3039905 AAACCAAGACACCT-AAACTTATCATCTTCC
1 AAACCAAGACACCTCAAACTTATCATCTTCC
* *
3039935 AAACTAAGACACCTCAACCTTATCATCT
1 AAACCAAGACACCTCAAACTTATCATCT
3039963 CCCATAAGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.40, C:0.33, G:0.03, T:0.24
Consensus pattern (31 bp):
AAACCAAGACACCTCAAACTTATCATCTTCC
Found at i:3042454 original size:85 final size:85
Alignment explanation
Indices: 3042311--3042481 Score: 342
Period size: 85 Copynumber: 2.0 Consensus size: 85
3042301 AGCATATGGT
3042311 ACTATATCCTATCATACATTTTGATATAGCTTTAGTCGATAAGAGCTAAATGTAGATCAAAGCTT
1 ACTATATCCTATCATACATTTTGATATAGCTTTAGTCGATAAGAGCTAAATGTAGATCAAAGCTT
3042376 TCAAGTTCGATTCTACTCAA
66 TCAAGTTCGATTCTACTCAA
3042396 ACTATATCCTATCATACATTTTGATATAGCTTTAGTCGATAAGAGCTAAATGTAGATCAAAGCTT
1 ACTATATCCTATCATACATTTTGATATAGCTTTAGTCGATAAGAGCTAAATGTAGATCAAAGCTT
3042461 TCAAGTTCGATTCTACTCAA
66 TCAAGTTCGATTCTACTCAA
3042481 A
1 A
3042482 TCGAGAGCAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 86 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (85 bp):
ACTATATCCTATCATACATTTTGATATAGCTTTAGTCGATAAGAGCTAAATGTAGATCAAAGCTT
TCAAGTTCGATTCTACTCAA
Found at i:3050094 original size:27 final size:27
Alignment explanation
Indices: 3050064--3050117 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
3050054 GCTTCCCGTA
3050064 TAGTTGATGGACTTTTGATTGTTCGGG
1 TAGTTGATGGACTTTTGATTGTTCGGG
3050091 TAGTTGATGGACTTTTGATTGTTCGGG
1 TAGTTGATGGACTTTTGATTGTTCGGG
3050118 CATTCACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.15, C:0.07, G:0.33, T:0.44
Consensus pattern (27 bp):
TAGTTGATGGACTTTTGATTGTTCGGG
Found at i:3053529 original size:68 final size:67
Alignment explanation
Indices: 3053418--3053545 Score: 166
Period size: 68 Copynumber: 1.9 Consensus size: 67
3053408 TGTATATCTG
* * * * *
3053418 GTTTAGAACTATAATGTATAGAAATGACACTTAGTGCAGATGGTGGGCACGACCTTATGTGCTAT
1 GTTTAGAACTATAATGTATAGAAACGAAACCTAATGCAGATGGTGGACA-GACCTTATGTGCTAT
3053483 TCA
65 TCA
* * * *
3053486 GTTTAGCACTATAGTGTATATAAACGAAACCTAATGCATATGGTGGACAGACCTTATGTG
1 GTTTAGAACTATAATGTATAGAAACGAAACCTAATGCAGATGGTGGACAGACCTTATGTG
3053546 GATTGAAAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
67 11 0.22
68 40 0.78
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (67 bp):
GTTTAGAACTATAATGTATAGAAACGAAACCTAATGCAGATGGTGGACAGACCTTATGTGCTATT
CA
Found at i:3057585 original size:19 final size:19
Alignment explanation
Indices: 3057561--3057597 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
3057551 AATTTTTTGG
3057561 TTTATGAACATGTT-ATGGC
1 TTTATGAA-ATGTTGATGGC
3057580 TTTATGAAATGTTGATGG
1 TTTATGAAATGTTGATGG
3057598 ATTTCGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.43
Consensus pattern (19 bp):
TTTATGAAATGTTGATGGC
Found at i:3059332 original size:26 final size:26
Alignment explanation
Indices: 3059313--3059404 Score: 125
Period size: 26 Copynumber: 3.6 Consensus size: 26
3059303 TTCAAGTGTT
3059313 AGTGATAAATAGCACTTTCAAGTACG
1 AGTGATAAATAGCACTTTCAAGTACG
3059339 AGTG--AAATAGCACTTTCAAGTACG
1 AGTGATAAATAGCACTTTCAAGTACG
* * * *
3059363 AGTGATAAATAGCATTTTCGAGTGCA
1 AGTGATAAATAGCACTTTCAAGTACG
*
3059389 AGTGATAAATGGCACT
1 AGTGATAAATAGCACT
3059405 ATGTGTGCAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
24 24 0.41
26 34 0.59
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (26 bp):
AGTGATAAATAGCACTTTCAAGTACG
Found at i:3069223 original size:13 final size:13
Alignment explanation
Indices: 3069205--3069229 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3069195 CAAATTGAGG
3069205 AAGATGAATTAGA
1 AAGATGAATTAGA
3069218 AAGATGAATTAG
1 AAGATGAATTAG
3069230 GTAGAATATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.24, T:0.24
Consensus pattern (13 bp):
AAGATGAATTAGA
Found at i:3106622 original size:90 final size:89
Alignment explanation
Indices: 3106470--3106642 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
3106460 ACACACCCTT
3106470 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
* *
3106535 ATTAATTGGAATTTAATAATCCAC
66 ATTAATTGAAATTAAATAATCCAC
* *
3106559 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
3106624 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
3106643 TTCTGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCAC
Found at i:3113438 original size:13 final size:13
Alignment explanation
Indices: 3113422--3113447 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3113412 TTAGAAACTC
3113422 AATAATTAAAATA
1 AATAATTAAAATA
3113435 AATAATTAAAATA
1 AATAATTAAAATA
3113448 TTATAAGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
AATAATTAAAATA
Found at i:3114591 original size:54 final size:54
Alignment explanation
Indices: 3114519--3114912 Score: 442
Period size: 54 Copynumber: 7.3 Consensus size: 54
3114509 ATTAAGATGG
* * * *
3114519 ACACGTAGTGCTTATACGGTAGTTCATCAACTCATGATGAATTATGTGGGTTGC
1 ACACATAGTGCCTGTACGGTAGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* **
3114573 ACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCCGTGAATTGC
1 ACACATAGTGCCTGTACGG-TAGTTCATCAACTCATGATGAATTCTGTGGGTTGC
** * * * **
3114627 ACACATAAAGCCTGTATGGTTA-TTCATCAACTCATCATGAATTCCGTGAATTGC
1 ACACATAGTGCCTGTACGG-TAGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* * *
3114681 ACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATT-TCGTGGGTTAC
1 ACACATAGTGCCTGTACGGTAGTTCATCAACTCATGATGAATTCT-GTGGGTTGC
* **
3114735 ACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTCTGTGAATTGC
1 ACACATAGTGCCTGTACGG-TAGTTCATCAACTCATGATGAATTCTGTGGGTTGC
* ** *
3114789 ACACATTGTGCCTGTACAATTGTTCATCAACTCATGAT-ATATT-TCGTGGGTTGC
1 ACACATAGTGCCTGTACGGTAGTTCATCAACTCATGATGA-ATTCT-GTGGGTTGC
* *
3114843 ACACATAGTGCCAGTACGGTTGTTCATCAACTCATGATGAATTAC-GTGGGTTGC
1 ACACATAGTGCCTGTACGGTAGTTCATCAACTCATGATGAATT-CTGTGGGTTGC
3114897 ACACATAGTGCCTGTA
1 ACACATAGTGCCTGTA
3114913 GTACACATAG
Statistics
Matches: 290, Mismatches: 39, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
53 4 0.01
54 281 0.97
55 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (54 bp):
ACACATAGTGCCTGTACGGTAGTTCATCAACTCATGATGAATTCTGTGGGTTGC
Found at i:3114667 original size:108 final size:108
Alignment explanation
Indices: 3114519--3114912 Score: 515
Period size: 108 Copynumber: 3.6 Consensus size: 108
3114509 ATTAAGATGG
* * * * **
3114519 ACACGTAGTGCTTATACGG-TAGTTCATCAACTCATGATGAATTATGTGGGTTGCACACATAGTG
1 ACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTACGTGAATTGCACACATAGTG
* * **
3114583 CCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGC
65 CCTGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTGC
** * * *
3114627 ACACATAAAGCCTGTATGGTTATTCATCAACTCATCATGAATTCCGTGAATTGCACACATAGTGC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTACGTGAATTGCACACATAGTGC
* *
3114692 ATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTAC
66 CTGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTGC
* *
3114735 ACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATT-CTGTGAATTGCACACATTGTG
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTAC-GTGAATTGCACACATAGTG
**
3114799 CCTGTACAATTGTTCATCAACTCATGAT-ATATTTCGTGGGTTGC
65 CCTGTACGGTTGTTCATCAACTCATGATGA-ATTTCGTGGGTTGC
* * **
3114843 ACACATAGTGCCAGTACGGTTGTTCATCAACTCATGATGAATTACGTGGGTTGCACACATAGTGC
1 ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTACGTGAATTGCACACATAGTGC
3114908 CTGTA
66 CTGTA
3114913 GTACACATAG
Statistics
Matches: 249, Mismatches: 33, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
107 2 0.01
108 244 0.98
109 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (108 bp):
ACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTACGTGAATTGCACACATAGTGC
CTGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTGC
Found at i:3114817 original size:162 final size:162
Alignment explanation
Indices: 3114519--3114909 Score: 563
Period size: 162 Copynumber: 2.4 Consensus size: 162
3114509 ATTAAGATGG
* * * *
3114519 ACACGTAGTGCTTATACGGTAGTTCATCAACTCATGATGAATTAT-GTGGGTTGCACACATAGTG
1 ACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATT-TCGTGGGTTGCACACATAGTG
* ***
3114583 CCTGTACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACATAAAGCCTGTATGGTT
65 CCTATACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACATAAAGCCTGTACAATT
3114648 ATTCATCAACTCATCATGA-ATTCCGTGAATTGC
130 ATTCATCAACTCATCAT-ATATTCCGTGAATTGC
*
3114681 ACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTACACACATAGTGC
1 ACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTGC
* *** *
3114746 CTATACGGTTATTCATCAACTCATGATGAATTCTGTGAATTGCACACATTGTGCCTGTACAATTG
66 CTATACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACATAAAGCCTGTACAATTA
* * **
3114811 TTCATCAACTCATGATATATTTCGTGGGTTGC
131 TTCATCAACTCATCATATATTCCGTGAATTGC
*
3114843 ACACATAGTGCCA-GTACGGTTGTTCATCAACTCATGATGAATTACGTGGGTTGCACACATAGTG
1 ACACATAGTG-CATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTG
3114907 CCT
65 CCT
3114910 GTAGTACACA
Statistics
Matches: 206, Mismatches: 20, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
161 2 0.01
162 202 0.98
163 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (162 bp):
ACACATAGTGCATGTACGGTTGTTCATCAACTCATGATGAATTTCGTGGGTTGCACACATAGTGC
CTATACGGTTATTCATCAACTCATGATGAATTCCGTGAATTGCACACATAAAGCCTGTACAATTA
TTCATCAACTCATCATATATTCCGTGAATTGC
Found at i:3115265 original size:20 final size:20
Alignment explanation
Indices: 3115240--3115289 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
3115230 TGACTCTATA
3115240 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
3115260 GTATCGATACCCCTACCATG
1 GTATCGATACCCCTACCATG
3115280 GTATCGATAC
1 GTATCGATAC
3115290 TACTATACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.26
Consensus pattern (20 bp):
GTATCGATACCCCTACCATG
Found at i:3115305 original size:22 final size:19
Alignment explanation
Indices: 3115235--3115330 Score: 84
Period size: 20 Copynumber: 4.8 Consensus size: 19
3115225 GTTTTTGACT
* *
3115235 CTATAGTATCGATACCCCTA
1 CTATGGTATCGATA-CTCTA
* *
3115255 CCATGGTATCGATACCCCTA
1 CTATGGTATCGATA-CTCTA
*
3115275 CCATGGTATCGATACTACTATA
1 CTATGGTATCGATACT-C--TA
*
3115297 CTATGGTATTGATACTCTA
1 CTATGGTATCGATACTCTA
*
3115316 CTACGGTATCGATAC
1 CTATGGTATCGATAC
3115331 CATTTTTGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
19 16 0.24
20 33 0.50
21 1 0.02
22 16 0.24
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (19 bp):
CTATGGTATCGATACTCTA
Found at i:3119597 original size:28 final size:30
Alignment explanation
Indices: 3119543--3119603 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 30
3119533 TATATATTGA
3119543 AAATTACACTTTTCATCCCTAAACTTTTAT
1 AAATTACACTTTTCATCCCTAAACTTTTAT
* * *
3119573 AAATTACA-TTTTTAT-CTTAAACTTTTCT
1 AAATTACACTTTTCATCCCTAAACTTTTAT
3119601 AAA
1 AAA
3119604 CTTTATACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.50
29 6 0.21
30 8 0.29
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (30 bp):
AAATTACACTTTTCATCCCTAAACTTTTAT
Found at i:3122050 original size:162 final size:162
Alignment explanation
Indices: 3121783--3122074 Score: 568
Period size: 162 Copynumber: 1.8 Consensus size: 162
3121773 AAACGATCCA
3121783 AAAGATGCCAGATTCAAGTGAGAGCGATGGCTGCAGACGAAGGGAAGGTGAAAATTGAGAAGTTC
1 AAAGATGCCAGATTCAAGTGAGAGCGATGGCTGCAGACGAAGGGAAGGTGAAAATTGAGAAGTTC
3121848 GTTGGTGCGGACTTTGGCTTTTGAAAGATGCAGATTGAAGATTTTTTG-ACCATAAAAAATCTAT
66 GTTGGTGCGGACTTTGGCTTTTGAAAGATGCAGATTGAAGATTTTTTGTACCAT-AAAAATCTAT
3121912 ACCTCTTATCAACCTATCTCTGGAAAGCAACCC
130 ACCTCTTATCAACCTATCTCTGGAAAGCAACCC
3121945 AAAGATGCCAGATTCAAGTGAGAGCGATGGCTGCAGACGAAGGGAAGGTGAAAATTGAGAAGTTC
1 AAAGATGCCAGATTCAAGTGAGAGCGATGGCTGCAGACGAAGGGAAGGTGAAAATTGAGAAGTTC
3122010 GTTGGTGCGGACTTTGGCTTTTGAAAGATGCAGATTGAAGATTTTTTGTACCATAAAAATCTATA
66 GTTGGTGCGGACTTTGGCTTTTGAAAGATGCAGATTGAAGATTTTTTGTACCATAAAAATCTATA
3122075 TCAACCTCTC
Statistics
Matches: 129, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
162 124 0.96
163 5 0.04
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.26
Consensus pattern (162 bp):
AAAGATGCCAGATTCAAGTGAGAGCGATGGCTGCAGACGAAGGGAAGGTGAAAATTGAGAAGTTC
GTTGGTGCGGACTTTGGCTTTTGAAAGATGCAGATTGAAGATTTTTTGTACCATAAAAATCTATA
CCTCTTATCAACCTATCTCTGGAAAGCAACCC
Found at i:3122640 original size:15 final size:15
Alignment explanation
Indices: 3122616--3122647 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
3122606 TGGTAGATCG
*
3122616 AAATCTAGAACGGGA
1 AAATCAAGAACGGGA
3122631 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
3122646 AA
1 AA
3122648 GAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.25, T:0.09
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:3128542 original size:307 final size:307
Alignment explanation
Indices: 3127981--3128594 Score: 1201
Period size: 307 Copynumber: 2.0 Consensus size: 307
3127971 TTATTATTAT
3127981 TTATAATTGGGACTTCAGACATTATAATTTAATTTTGGGAATTGTTATACATGTTTTGAATATTT
1 TTATAATTGGGACTTCAGACATTATAATTTAATTTTGGGAATTGTTATACATGTTTTGAATATTT
3128046 ATTTATATTTGGTTTCTAGAACATTTGTTTTAATAAAATTGTGAAGTTTGAATTTAAAAATTTAT
66 ATTTATATTTGGTTTCTAGAACATTTGTTTTAATAAAATTGTGAAGTTTGAATTTAAAAATTTAT
3128111 TTCATTAAATTATAGTGTAAAATTTAGGATTTGAATCAAAAATGATTTGCCCGAGGGAAAAGATT
131 TTCATTAAATTATAGTGTAAAATTTAGGATTTGAATCAAAAATGATTTGCCCGAGGGAAAAGATT
*
3128176 TCAATTAAACTTTCTAGATTTGACCTAATTCTTTCAGGTAAGGTTTAGGGTCCTACATTTAGTGG
196 TCAATTAAACTTTCTAGATTTGACCTAATTCTTTCAGGTAAGGTTTAGGGTCATACATTTAGTGG
*
3128241 TATCAGAGCCCGGTTCAACCCTTAGATGGTAGAGCTCGATCACAAAA
261 TATCAGAGCCCGATTCAACCCTTAGATGGTAGAGCTCGATCACAAAA
3128288 TTATAATTGGGACTTCAGACATTATAATTTAATTTTGGGAATTGTTATACATGTTTTGAATATTT
1 TTATAATTGGGACTTCAGACATTATAATTTAATTTTGGGAATTGTTATACATGTTTTGAATATTT
3128353 ATTTATATTTGGTTTCTAGAACATTTGTTTTAATAAAATTGTGAAGTTTGAATTTAAAAATTTAT
66 ATTTATATTTGGTTTCTAGAACATTTGTTTTAATAAAATTGTGAAGTTTGAATTTAAAAATTTAT
3128418 TTCATTAAATTATAGTGTAAAATTTAGGATTTGAATCAAAAATGATTTGCCCGAGGGAAAAGATT
131 TTCATTAAATTATAGTGTAAAATTTAGGATTTGAATCAAAAATGATTTGCCCGAGGGAAAAGATT
*
3128483 TCAATTAAACTTTTTAGATTTGACCTAATTCTTTCAGGTAAGGTTTAGGGTCATACATTTAGTGG
196 TCAATTAAACTTTCTAGATTTGACCTAATTCTTTCAGGTAAGGTTTAGGGTCATACATTTAGTGG
3128548 TATCAGAGCCCGATTCAACCCTTAGATGGTAGAGCTCGATCACAAAA
261 TATCAGAGCCCGATTCAACCCTTAGATGGTAGAGCTCGATCACAAAA
3128595 CTTTTAAACC
Statistics
Matches: 304, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
307 304 1.00
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (307 bp):
TTATAATTGGGACTTCAGACATTATAATTTAATTTTGGGAATTGTTATACATGTTTTGAATATTT
ATTTATATTTGGTTTCTAGAACATTTGTTTTAATAAAATTGTGAAGTTTGAATTTAAAAATTTAT
TTCATTAAATTATAGTGTAAAATTTAGGATTTGAATCAAAAATGATTTGCCCGAGGGAAAAGATT
TCAATTAAACTTTCTAGATTTGACCTAATTCTTTCAGGTAAGGTTTAGGGTCATACATTTAGTGG
TATCAGAGCCCGATTCAACCCTTAGATGGTAGAGCTCGATCACAAAA
Found at i:3129803 original size:12 final size:12
Alignment explanation
Indices: 3129785--3129818 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3129775 CTTAATTGCG
3129785 AAAATTTAAATT
1 AAAATTTAAATT
*
3129797 TAAATTTAAATT
1 AAAATTTAAATT
*
3129809 AAAACTTAAA
1 AAAATTTAAA
3129819 ATTCAATTCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:3129966 original size:22 final size:21
Alignment explanation
Indices: 3129941--3130011 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
3129931 ACACTAAAAT
3129941 TAAAAGAAAAAAAATGAATAAC
1 TAAAA-AAAAAAAATGAATAAC
* *
3129963 TAAAATAAAAAATACT-AA-AAT
1 TAAAA-AAAAAA-AATGAATAAC
*
3129984 TAAAAAGGAAAAAATGAATAAC
1 TAAAAA-AAAAAAATGAATAAC
3130006 TAAAAA
1 TAAAAA
3130012 TTTAAAGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 3 0.08
21 13 0.33
22 21 0.54
23 2 0.05
ACGTcount: A:0.72, C:0.04, G:0.07, T:0.17
Consensus pattern (21 bp):
TAAAAAAAAAAAATGAATAAC
Found at i:3129996 original size:43 final size:44
Alignment explanation
Indices: 3129920--3130010 Score: 141
Period size: 43 Copynumber: 2.1 Consensus size: 44
3129910 AAAAACAAAT
3129920 AAATAAAAAATACACTAAAATTAAAAGAAAAAAAATGAATAACTA
1 AAATAAAAAATA-ACTAAAATTAAAAGAAAAAAAATGAATAACTA
*
3129965 AAATAAAAAAT-ACTAAAATTAAAA-AGGAAAAAATGAATAACTA
1 AAATAAAAAATAACTAAAATTAAAAGA-AAAAAAATGAATAACTA
3130008 AAA
1 AAA
3130011 ATTTAAAGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
42 1 0.02
43 32 0.73
45 11 0.25
ACGTcount: A:0.71, C:0.05, G:0.05, T:0.18
Consensus pattern (44 bp):
AAATAAAAAATAACTAAAATTAAAAGAAAAAAAATGAATAACTA
Found at i:3131310 original size:3 final size:3
Alignment explanation
Indices: 3131291--3131346 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
3131281 AAAAATTATT
*
3131291 ATA ATA TATA A-A TTA ATA ATA ATA ATA ATA ATA AT- ATA AT- ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3131334 AT- ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA
3131347 TTTTTGTAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
2 9 0.20
3 33 0.73
4 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:3131331 original size:5 final size:5
Alignment explanation
Indices: 3131290--3131347 Score: 68
Period size: 5 Copynumber: 11.6 Consensus size: 5
3131280 CAAAAATTAT
3131290 TATAA TAT-A TA-AA T-TAA TAATAA TAATAA TAATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA T-ATAA T-ATAA T-ATAA TATAA TATAA
3131335 TATAA TATAA TAT
1 TATAA TATAA TAT
3131348 TTTTGTAGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
4 8 0.16
5 25 0.51
6 16 0.33
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:3135282 original size:22 final size:22
Alignment explanation
Indices: 3135254--3135295 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3135244 CACGGCTCAA
* *
3135254 TCCAAAATCCAAAGGAAATTGC
1 TCCAAAATCAAAAAGAAATTGC
3135276 TCCAAAATCAAAAAGAAATT
1 TCCAAAATCAAAAAGAAATT
3135296 TTCTCTTACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.19, G:0.10, T:0.19
Consensus pattern (22 bp):
TCCAAAATCAAAAAGAAATTGC
Found at i:3138629 original size:34 final size:34
Alignment explanation
Indices: 3138591--3138655 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
3138581 CCAATGTTTA
* *
3138591 TACTATGCGCCTTTGGTAGACACTCTAGTACATG
1 TACTATGCGCCTTCGCTAGACACTCTAGTACATG
*
3138625 TACTATGTGCCTTCGCTAGACACTCTAGTAC
1 TACTATGCGCCTTCGCTAGACACTCTAGTAC
3138656 TACCAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.32
Consensus pattern (34 bp):
TACTATGCGCCTTCGCTAGACACTCTAGTACATG
Found at i:3140086 original size:19 final size:20
Alignment explanation
Indices: 3140062--3140106 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
3140052 CAAAATGGCC
3140062 CAATTTC-ACA-TCCTAACAT
1 CAATTTCAACACT-CTAACAT
3140081 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
*
3140101 TAATTT
1 CAATTT
3140107 ACAGCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.38, C:0.27, G:0.00, T:0.36
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:3144724 original size:42 final size:42
Alignment explanation
Indices: 3144648--3144729 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
3144638 ATAACAACTA
**
3144648 TTCATATTCTTTTTCATTTTTATACATTTCATAACTTTCATT
1 TTCATATTCTTTTTCATTTAGATACATTTCATAACTTTCATT
* *
3144690 TTCATATTCTTTTTC-TTTGAGATACTTTTTATAACTTTCA
1 TTCATATTCTTTTTCATTT-AGATACATTTCATAACTTTCA
3144730 GATTTACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 3 0.09
42 32 0.91
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.59
Consensus pattern (42 bp):
TTCATATTCTTTTTCATTTAGATACATTTCATAACTTTCATT
Found at i:3151336 original size:272 final size:272
Alignment explanation
Indices: 3150850--3151344 Score: 769
Period size: 272 Copynumber: 1.8 Consensus size: 272
3150840 TATTATTGAA
** * * *
3150850 ACAACATAATTCGAGTTAGTCTTTTATGAGCTTAAACATTTTTTTATCTACAACATTATTGTTGA
1 ACAACATAATTCGAGACAGTCTTTTACGAGCTTAAACATTTTTTAATCTACAACATTAGTGTTGA
* * * * *
3150915 TTAGATCCATTCCAAAATCGATATGAAAGGTTGCACTTGGGTATTCAGTATATAAAGCATAGTTA
66 TTAGATCCATTCCAAAATCGATATAAAAGATTGCACTTGGGTACTCAGTATACAAAGCATAGTCA
* *
3150980 CAAGGATTGGTCCCTGTAGACAAGTAACCGATGTGAATCCCAAAGTAAATACCTCTTTCAATGAT
131 CAAGGATTGATCCCTGTAGACAAGTAACCGACGTGAATCCCAAAGTAAATACCTCTTTCAATGAT
3151045 ACGAGGAAACTAAGTCAAAGAAAAAGCCACTCTTAACAAAATTGTTTGCCAAGCGAAAACTGAGA
196 ACGAGGAAACTAAGTCAAAGAAAAAGCCACTCTTAACAAAATTGTTTGCCAAGCGAAAACTGAGA
3151110 TCAAAATTAGTT
261 TCAAAATTAGTT
*
3151122 ACAACATAA-TCTGAGACAGTCTTTTACGAGCTTAAACA-TTTTTAATCTACAACATTGGTGTTG
1 ACAACATAATTC-GAGACAGTCTTTTACGAGCTTAAACATTTTTTAATCTACAACATTAGTGTTG
* * *
3151185 ATTAGATCTATTTCCAAAATCGATATAAAATATTGCACTTGGGTACTCGGTATACAAAGCATAGT
65 ATTAGATCCA-TTCCAAAATCGATATAAAAGATTGCACTTGGGTACTCAGTATACAAAGCATAGT
* * *
3151250 CACAAGGATTGATCCTTGTAGACAAGTAACCGACGTGAATGCCAAAGTAAATACCTCTTTCGATG
129 CACAAGGATTGATCCCTGTAGACAAGTAACCGACGTGAATCCCAAAGTAAATACCTCTTTCAATG
* *
3151315 ATACGAGGAAACTGAGTCAAAGCAAAAGCC
194 ATACGAGGAAACTAAGTCAAAGAAAAAGCC
3151345 TAAGGTTGAT
Statistics
Matches: 200, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
271 33 0.17
272 167 0.83
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (272 bp):
ACAACATAATTCGAGACAGTCTTTTACGAGCTTAAACATTTTTTAATCTACAACATTAGTGTTGA
TTAGATCCATTCCAAAATCGATATAAAAGATTGCACTTGGGTACTCAGTATACAAAGCATAGTCA
CAAGGATTGATCCCTGTAGACAAGTAACCGACGTGAATCCCAAAGTAAATACCTCTTTCAATGAT
ACGAGGAAACTAAGTCAAAGAAAAAGCCACTCTTAACAAAATTGTTTGCCAAGCGAAAACTGAGA
TCAAAATTAGTT
Found at i:3152148 original size:272 final size:271
Alignment explanation
Indices: 3151663--3152206 Score: 1027
Period size: 272 Copynumber: 2.0 Consensus size: 271
3151653 GTATTATGAT
* *
3151663 ATTTTGATATATGTATATCTATGCATATTTTTGATAAATGAATAATTTATAATTTTGATATAAAT
1 ATTTTGATATATCTATAGCTATGCATATTTTTGATAAATGAATAATTTATAATTTTGATATAAAT
3151728 ATCAATGTTGATATTTTTTATATATTTTCATATTGTTTTGCTAAATGATGTTTGAATGATTTTGG
66 ATCAATGTTGATATTTTTTATATATTTTCATATTGTTTTGCTAAATGATGTTTGAATGATTTTGG
3151793 TATTAACTATTCAATGCAGTTTTATATTATATTTTGATATGTTAGTATCTATGGATACTTTTGAT
131 TATTAACTATTCAATGCAGTTTTATATTATATTTTGATATGTTAGTATCTATGGATACTTTTGAT
*
3151858 AAATGAATGGTATATGATTTTGATATAAAAGGCCTTGTATGTGCATTTAGAGTTATTAGTACAAT
196 AAATGAATGGTATATGATTTTGATATAAAAGCCCTTGTATGTGCATTTAGAGTTATTAGTACAAT
3151923 GGCATGCCATG
261 GGCATGCCATG
3151934 ATTTTGATATATCTAT-GCATATGCATATTTTTGATAAATGAATAATTTATAATTTTGATATAAA
1 ATTTTGATATATCTATAGC-TATGCATATTTTTGATAAATGAATAATTTATAATTTTGATATAAA
3151998 TATCAATGTTGATATTTTTTTATATATTTTCATATTGTTTTGCTAAATGATGTTTGAATGATTTT
65 TATCAATGTTGATA-TTTTTTATATATTTTCATATTGTTTTGCTAAATGATGTTTGAATGATTTT
3152063 GGTATTAACTATTCAATGCAGTTTTATATTATATTTTGATATGTTAGTATCTATGGATACTTTTG
129 GGTATTAACTATTCAATGCAGTTTTATATTATATTTTGATATGTTAGTATCTATGGATACTTTTG
*
3152128 ATAAATGAATGGTATATGATTTTGATATAAATGCCCTTGTATGTGCATTTAGAGTTATTAGTACA
194 ATAAATGAATGGTATATGATTTTGATATAAAAGCCCTTGTATGTGCATTTAGAGTTATTAGTACA
3152193 ATGGCATGCCATG
259 ATGGCATGCCATG
3152206 A
1 A
3152207 GGTGGAGTGA
Statistics
Matches: 267, Mismatches: 4, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
270 1 0.00
271 74 0.28
272 192 0.72
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (271 bp):
ATTTTGATATATCTATAGCTATGCATATTTTTGATAAATGAATAATTTATAATTTTGATATAAAT
ATCAATGTTGATATTTTTTATATATTTTCATATTGTTTTGCTAAATGATGTTTGAATGATTTTGG
TATTAACTATTCAATGCAGTTTTATATTATATTTTGATATGTTAGTATCTATGGATACTTTTGAT
AAATGAATGGTATATGATTTTGATATAAAAGCCCTTGTATGTGCATTTAGAGTTATTAGTACAAT
GGCATGCCATG
Found at i:3158488 original size:3 final size:3
Alignment explanation
Indices: 3158480--3158534 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
3158470 AATTATTTAA
* **
3158480 ATT ATT ATT TTT AAA ATT ATT ATT ATT ATT ATT A-T ATAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT
*
3158525 AAT ATT ATT A
1 ATT ATT ATT A
3158535 AATTAAATAT
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 2 0.05
3 37 0.88
4 3 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:3158506 original size:21 final size:24
Alignment explanation
Indices: 3158480--3158534 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3158470 AATTATTTAA
3158480 ATTATTATT-TT-TA-AAATTATT
1 ATTATTATTATTATATAAATTATT
*
3158501 ATTATTATTATTATATATATTATT
1 ATTATTATTATTATATAAATTATT
*
3158525 AATATTATTA
1 ATTATTATTA
3158535 AATTAAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 2 0.07
24 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATTATTATTATATAAATTATT
Found at i:3159827 original size:6 final size:6
Alignment explanation
Indices: 3159816--3159858 Score: 50
Period size: 6 Copynumber: 6.5 Consensus size: 6
3159806 AATTAGTATA
3159816 TTTAAT TTTAAT ATTTATAT TCTGTAAT TTTAAT TTTAAT TTT
1 TTTAAT TTTAAT -TTTA-AT T-T-TAAT TTTAAT TTTAAT TTT
3159859 GATCATTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
6 19 0.58
7 6 0.18
8 6 0.18
9 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (6 bp):
TTTAAT
Found at i:3159953 original size:26 final size:25
Alignment explanation
Indices: 3159889--3159959 Score: 65
Period size: 26 Copynumber: 2.8 Consensus size: 25
3159879 TATATATCTA
**
3159889 ATTTATT-AT-TTTAATTATTATTT
1 ATTTATTAATATTTAATTATTAAAT
* *
3159912 ATTTATCATTATTTTAATTATATAAAT
1 ATTTATTAATA-TTTAATTAT-TAAAT
*
3159939 ATTTATTAATATTTATTTATT
1 ATTTATTAATATTTAATTATT
3159960 TTCAATATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
23 6 0.16
24 1 0.03
25 1 0.03
26 17 0.46
27 12 0.32
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTATTAATATTTAATTATTAAAT
Found at i:3165835 original size:8 final size:8
Alignment explanation
Indices: 3165822--3165875 Score: 99
Period size: 8 Copynumber: 6.8 Consensus size: 8
3165812 ATACTTGAAA
*
3165822 AAAAAAAG
1 AAAAAAGG
3165830 AAAAAAGG
1 AAAAAAGG
3165838 AAAAAAGG
1 AAAAAAGG
3165846 AAAAAAGG
1 AAAAAAGG
3165854 AAAAAAGG
1 AAAAAAGG
3165862 AAAAAAGG
1 AAAAAAGG
3165870 AAAAAA
1 AAAAAA
3165876 TTGAACCAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:3168408 original size:46 final size:45
Alignment explanation
Indices: 3168220--3169433 Score: 1870
Period size: 45 Copynumber: 26.8 Consensus size: 45
3168210 CTATTTCCAA
* *
3168220 CATCTGTAAGCCCTTTAGTGCATGATGTTTTAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3168265 CATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAACCTTCAGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
3168310 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
3168355 CATCTGTAATCCCTTTAGTGCATAATGTTTTCAAAAACCTTCGAGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
3168401 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
3168446 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * * *
3168492 CGTCTATAAGCCCTTCAATGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3168537 CATCTATAAGCCCTTCAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
3168582 CATCTATAAGTCCTTTAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
3168627 CATCTGTAAGCCATTCAGTGCTTGATGTTTTCAAAACCATCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
3168672 CATCTGTAAGTCCTTCAGTGCTTGATGTTCTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
3168717 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3168762 CATCTGTAAGCCCTTGAGTACATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
3168807 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
3168852 CATCTGTAAGCCCTTGAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
3168898 CATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
** *
3168944 CATCTGTAAGCCCTTCAGTGTTTGATGTTTTCAAAAACCTTAGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* *
3168990 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
3169036 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
3169082 CATCAGTAAGCCCTTTAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
3169128 CATCTGTAAGCCCTTCAGTGCTTGATGTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
3169174 CATCTGTAAGTCCTTTAGTGCTTGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3169219 CATCTCTAAGCCCTTCATTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3169264 AATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
3169309 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
3169354 AATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAGCCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3169399 CATCTGTAAGACCTTCAGTACATGATGTTTTCAAA
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
3169434 CATTTTTATC
Statistics
Matches: 1086, Mismatches: 80, Indels: 6
0.93 0.07 0.01
Matches are distributed among these distances:
45 702 0.65
46 384 0.35
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:3169574 original size:15 final size:15
Alignment explanation
Indices: 3169554--3169582 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3169544 ACTTAAATTA
3169554 TTTAAATTATTATTT
1 TTTAAATTATTATTT
3169569 TTTAAATTATTATT
1 TTTAAATTATTATT
3169583 ATTATTATAA
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTAAATTATTATTT
Found at i:3169586 original size:24 final size:24
Alignment explanation
Indices: 3169546--3169625 Score: 69
Period size: 24 Copynumber: 3.5 Consensus size: 24
3169536 TTCATTTTAC
* **
3169546 TTAAATTATT-TAAATTATTATTTT
1 TTAAATTATTAT-TATTATTATAAT
3169570 TTAAATTATTATTATTATTATAAT
1 TTAAATTATTATTATTATTATAAT
* * *
3169594 ATATATTATTAATATTATTA-AA-
1 TTAAATTATTATTATTATTATAAT
3169616 TTAAA-TATTA
1 TTAAATTATTA
3169626 CAAAACCCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
21 5 0.11
22 3 0.06
23 2 0.04
24 36 0.77
25 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAATTATTATTATTATTATAAT
Found at i:3169600 original size:21 final size:19
Alignment explanation
Indices: 3169559--3169618 Score: 68
Period size: 21 Copynumber: 3.1 Consensus size: 19
3169549 AATTATTTAA
*
3169559 ATTATTATT-TTTTAAATT
1 ATTATTATTATTATAAATT
3169577 ATTATTATTATTATAATATAT
1 ATTATTATTATTATAA-AT-T
*
3169598 ATTATTAATATTATTAAATT
1 ATTATTATTATTA-TAAATT
3169618 A
1 A
3169619 AATATTACAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
18 9 0.25
19 5 0.14
20 4 0.11
21 15 0.42
22 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTATTATTATAAATT
Found at i:3176879 original size:21 final size:21
Alignment explanation
Indices: 3176853--3176892 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3176843 CCCCCTTTGA
*
3176853 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
3176874 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
3176893 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:3186800 original size:21 final size:22
Alignment explanation
Indices: 3186771--3186817 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3186761 TAATGATGAT
3186771 TTATAACAAAAGGCATAAATAA
1 TTATAACAAAAGGCATAAATAA
*
3186793 TTAT-ACAAAAGGCGTAAATAA
1 TTATAACAAAAGGCATAAATAA
3186814 TTAT
1 TTAT
3186818 CTAAATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (22 bp):
TTATAACAAAAGGCATAAATAA
Found at i:3189088 original size:30 final size:29
Alignment explanation
Indices: 3189008--3189079 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
3188998 AGGGATAATG
*
3189008 GTTTCAAGAGAAAC-CAACTCAAAGATGAT
1 GTTTCAAAAGAAACAC-ACTCAAAGATGAT
3189037 GTTTCAAAAGAAACACACTCAAAGATGAT
1 GTTTCAAAAGAAACACACTCAAAGATGAT
*
3189066 TTTCTCAAAAGAAA
1 GTT-TCAAAAGAAA
3189080 TTGTCTCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
29 28 0.72
30 11 0.28
ACGTcount: A:0.47, C:0.17, G:0.14, T:0.22
Consensus pattern (29 bp):
GTTTCAAAAGAAACACACTCAAAGATGAT
Found at i:3189160 original size:35 final size:35
Alignment explanation
Indices: 3189114--3189202 Score: 124
Period size: 35 Copynumber: 2.5 Consensus size: 35
3189104 GTTACCAAAA
* * *
3189114 GAAACATACTCAAAGATTTTTATTTTGTCTCAAGT
1 GAAACAGACTCAAATATTTTTATTTCGTCTCAAGT
* * *
3189149 GAAACAGACTCAGATTTTTTTATTTCGTTTCAAGT
1 GAAACAGACTCAAATATTTTTATTTCGTCTCAAGT
3189184 GAAACAGACTCAAATATTT
1 GAAACAGACTCAAATATTT
3189203 CTCAAGAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (35 bp):
GAAACAGACTCAAATATTTTTATTTCGTCTCAAGT
Found at i:3189244 original size:62 final size:63
Alignment explanation
Indices: 3189175--3189384 Score: 227
Period size: 65 Copynumber: 3.4 Consensus size: 63
3189165 TTTTTATTTC
* *
3189175 GTTTCAAGTGAAACAGACTCAAATATTTCTCAAGA-AAACTGTCTCAAGAGAGACAAAACTTT
1 GTTTCAAGTGAAACAGACTCAAATATTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTT
* * * * *
3189237 GTTTCAAGGGAAACAGACTAAAAGTTTTTTTTCAAAAGAAATTGTCTCAAGAGAGAAAAAACTTT
1 GTTTCAAGTGAAACAGACTCAAA--TATTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTT
* * *
3189302 GTTTCCTAA-T-AAACATACTCAAAGATTTTTTAAAAAGAAACTGTCTC--GAGAGACAAAA-TT
1 GTTT-C-AAGTGAAACAGACTCAAATA-TTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
3189362 T
63 T
*
3189363 GTTTCAAGAGAAACA-ACTCAAA
1 GTTTCAAGTGAAACAGACTCAAA
3189385 AGATACTGAT
Statistics
Matches: 124, Mismatches: 16, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
59 2 0.02
60 8 0.06
61 12 0.10
62 31 0.25
64 28 0.23
65 40 0.32
66 1 0.01
67 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (63 bp):
GTTTCAAGTGAAACAGACTCAAATATTTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTT
Found at i:3194992 original size:21 final size:22
Alignment explanation
Indices: 3194963--3195009 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
3194953 TAATGATGAT
3194963 TTATAACAAAAGGCATAAATAA
1 TTATAACAAAAGGCATAAATAA
*
3194985 TTAT-ACAAAAGGCGTAAATAA
1 TTATAACAAAAGGCATAAATAA
3195006 TTAT
1 TTAT
3195010 CTAAATATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (22 bp):
TTATAACAAAAGGCATAAATAA
Found at i:3196788 original size:3 final size:3
Alignment explanation
Indices: 3196780--3196814 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
3196770 ATAAATATAG
3196780 TAA TAA TAA TAA TAA TAA TAA TAA GT-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TA
3196815 TTTTTGGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:3198971 original size:46 final size:48
Alignment explanation
Indices: 3198864--3198975 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 48
3198854 TTATCCCTTT
3198864 AGCTCATAAGCTTA-TTTTTACCAAAATACTTACCATTTAAATTCCATA
1 AGCTCATAAGCTTATTTTTTACCAAAATACTTACCATTT-AATTCCATA
* ** * * *
3198912 AGCTCGTAAGCTTATTTTTTTTCAATATACTTGCCA-TT-ATTCCGTA
1 AGCTCATAAGCTTATTTTTTACCAAAATACTTACCATTTAATTCCATA
*
3198958 ATCTCATAAGCTTATTTT
1 AGCTCATAAGCTTATTTT
3198976 CATGGTTACC
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
46 23 0.42
48 15 0.27
49 17 0.31
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (48 bp):
AGCTCATAAGCTTATTTTTTACCAAAATACTTACCATTTAATTCCATA
Found at i:3199137 original size:40 final size:40
Alignment explanation
Indices: 3199079--3199199 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
3199069 ACCGTAGTGC
3199079 TACACATAA-GTCGTGCCCACCATATACACCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
3199118 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
*
3199158 TACACATAAGGTCGTGCCCACCATATACGCCAAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
3199198 TA
1 TA
3199200 TAAACCTGCA
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 9 0.12
40 69 0.88
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCAAAGTGTAT
Found at i:3201876 original size:18 final size:19
Alignment explanation
Indices: 3201835--3201882 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
3201825 AGTAAATGAT
*
3201835 ATTATAAAAATATCATATC
1 ATTATAAAATTATCATATC
*
3201854 A-TATAAAATTA-CATTTC
1 ATTATAAAATTATCATATC
3201871 ATTATAATAATT
1 ATTATAA-AATT
3201883 TAATTCAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 6 0.24
18 14 0.56
19 5 0.20
ACGTcount: A:0.50, C:0.08, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTATAAAATTATCATATC
Found at i:3202538 original size:47 final size:49
Alignment explanation
Indices: 3202415--3202545 Score: 146
Period size: 47 Copynumber: 2.8 Consensus size: 49
3202405 ATATAAATTT
* *
3202415 CTTACC-TTTTATCCCATAAGCTCATAAGCTTA--TTTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* ** *
3202461 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTTTTTCAATATA
1 CTTACCATTT-AATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
* *
3202511 CTTGCCA-TT-ATTCCGTAAGCTCATAAGCTTATTTT
1 CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTT
3202546 CATGGTTACC
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
46 6 0.08
47 27 0.38
48 20 0.28
49 2 0.03
50 17 0.24
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (49 bp):
CTTACCATTTAATTCCATAAGCTCATAAGCTTATTTTTTTACCAAAATA
Found at i:3202693 original size:40 final size:40
Alignment explanation
Indices: 3202649--3202770 Score: 235
Period size: 40 Copynumber: 3.0 Consensus size: 40
3202639 ACCGTAGTGC
3202649 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
3202689 TACACATAAGGTTGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3202729 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
3202769 TA
1 TA
3202771 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Done.