Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001466.1 Hibiscus syriacus cultivar Beakdansim tig00002841_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: 1236886
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 5
Found at i:1036423 original size:20 final size:20
Alignment explanation
Indices: 1036398--1036591 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1036388 CTTTAAATAT
1036398 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1036418 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1036440 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1036459 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1036479 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1036499 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1036519 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1036539 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1036559 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1036579 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1036592 TGGAAACTGA
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1036563 original size:60 final size:60
Alignment explanation
Indices: 1036400--1036571 Score: 245
Period size: 60 Copynumber: 2.9 Consensus size: 60
1036390 TTAAATATCG
** *
1036400 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
1036461 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
1036521 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
1036572 TCATATTCGC
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 69 0.73
61 26 0.27
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:1040660 original size:24 final size:24
Alignment explanation
Indices: 1040633--1040739 Score: 106
Period size: 24 Copynumber: 4.5 Consensus size: 24
1040623 AAACGGAGAT
*
1040633 ATCAGAAATCAAAACATAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1040657 ATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * * *
1040681 GTTAGGAATCAGAACAGATTTCAG
1 ATCAGAAATCAAAACAGAATTCAG
** *
1040705 ATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAG
1040729 ATCAGAAATCA
1 ATCAGAAATCA
1040740 GATAAAATAT
Statistics
Matches: 63, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.21
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1040739 original size:48 final size:48
Alignment explanation
Indices: 1040633--1040741 Score: 128
Period size: 48 Copynumber: 2.3 Consensus size: 48
1040623 AAACGGAGAT
* * * *
1040633 ATCAGAAATCAAAACATAATTCAGATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * *
1040681 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
1040729 ATCAGAAATCAGA
1 ATCAGAAATCAGA
1040742 TAAAATATTC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.48, C:0.17, G:0.16, T:0.20
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:1043226 original size:15 final size:15
Alignment explanation
Indices: 1043203--1043235 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1043193 GTCAACTCCA
*
1043203 GTCATCGGTCAACGG
1 GTCAACGGTCAACGG
1043218 GTCAACGGTCAACGG
1 GTCAACGGTCAACGG
1043233 GTC
1 GTC
1043236 GGGTCAACGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.27, G:0.33, T:0.18
Consensus pattern (15 bp):
GTCAACGGTCAACGG
Found at i:1043253 original size:18 final size:19
Alignment explanation
Indices: 1043215--1043264 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
1043205 CATCGGTCAA
*
1043215 CGGGTCAACGGTCAACGGGT
1 CGGGTCAACGGGC-ACGGGT
1043235 CGGGTCAACGGGC-CGGGT
1 CGGGTCAACGGGCACGGGT
1043253 CGGGTCAACGGG
1 CGGGTCAACGGG
1043265 TTGGTAAACG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.26, G:0.46, T:0.12
Consensus pattern (19 bp):
CGGGTCAACGGGCACGGGT
Found at i:1043265 original size:13 final size:13
Alignment explanation
Indices: 1043209--1043253 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
1043199 TCCAGTCATC
*
1043209 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
1043224 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
1043237 GGTCAACGGGCCG
1 GGTCAACGGGTCG
1043250 GGTC
1 GGTC
1043254 GGGTCAACGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 16 0.57
15 12 0.43
ACGTcount: A:0.18, C:0.27, G:0.42, T:0.13
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:1043282 original size:30 final size:31
Alignment explanation
Indices: 1043224--1043300 Score: 111
Period size: 30 Copynumber: 2.5 Consensus size: 31
1043214 ACGGGTCAAC
*
1043224 GGTCAACGGGTCGGGTCAACGGGCCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGCCGGGTCG
* *
1043255 GGTCAACGGGT-TGGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTAAACGGGCCGGGTCG
*
1043285 GGTCAATGGGTCGGGT
1 GGTCAACGGGTCGGGT
1043301 CGGGTTGTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 26 0.65
31 14 0.35
ACGTcount: A:0.14, C:0.19, G:0.48, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGCCGGGTCG
Found at i:1043297 original size:18 final size:18
Alignment explanation
Indices: 1043230--1043305 Score: 83
Period size: 18 Copynumber: 4.6 Consensus size: 18
1043220 CAACGGTCAA
*
1043230 CGGGTCGGGTCAACGGGC
1 CGGGTCGGGTCAACGGGT
1043248 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1043266 ----T--GGTAAACGGGT
1 CGGGTCGGGTCAACGGGT
*
1043278 CGGGTCGGGTCAATGGGT
1 CGGGTCGGGTCAACGGGT
1043296 CGGGTCGGGT
1 CGGGTCGGGT
1043306 TGTGACCGGT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
12 10 0.21
14 1 0.02
16 1 0.02
18 36 0.75
ACGTcount: A:0.12, C:0.20, G:0.50, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:1044831 original size:136 final size:137
Alignment explanation
Indices: 1044680--1044952 Score: 521
Period size: 137 Copynumber: 2.0 Consensus size: 137
1044670 GTATAAATAA
*
1044680 TTATTTTATTCTTTTTTTTAATATTCAAACCTCTAACATTTAA-TTTTTTTATCAAAATAACTCT
1 TTATTTTATTCTTTTTTTAAATATTCAAACCTCTAACATTTAATTTTTTTTATCAAAATAACTCT
1044744 CATTGGATAGAAATCATTACAAGTGTTTTAATTAATGATGTGGCATGTACATCATCAAAGTGATG
66 CATTGGATAGAAATCATTACAAGTGTTTTAATTAATGATGTGGCATGTACATCATCAAAGTGATG
1044809 ACATGAC
131 ACATGAC
*
1044816 TTATTTTATTCTTTTTTTAAATATTTAAACCTCTAACATTTAATTTTTTTTATCAAAATAACTCT
1 TTATTTTATTCTTTTTTTAAATATTCAAACCTCTAACATTTAATTTTTTTTATCAAAATAACTCT
1044881 CATTGGATAGAAATCATTACAAGTGTTTTAATTAATGATGTGGCATGTACATCATCAAAGTGATG
66 CATTGGATAGAAATCATTACAAGTGTTTTAATTAATGATGTGGCATGTACATCATCAAAGTGATG
1044946 ACATGAC
131 ACATGAC
1044953 ATGTATCACA
Statistics
Matches: 134, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
136 41 0.31
137 93 0.69
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (137 bp):
TTATTTTATTCTTTTTTTAAATATTCAAACCTCTAACATTTAATTTTTTTTATCAAAATAACTCT
CATTGGATAGAAATCATTACAAGTGTTTTAATTAATGATGTGGCATGTACATCATCAAAGTGATG
ACATGAC
Found at i:1046688 original size:23 final size:23
Alignment explanation
Indices: 1046661--1046706 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1046651 AAGGGATTGC
1046661 GTTAAGATGGTCACCTGACTATT
1 GTTAAGATGGTCACCTGACTATT
1046684 GTTAAGATGGTCACCTGACTATT
1 GTTAAGATGGTCACCTGACTATT
1046707 AATATGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (23 bp):
GTTAAGATGGTCACCTGACTATT
Found at i:1051745 original size:31 final size:31
Alignment explanation
Indices: 1051707--1051784 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1051697 ATATGAGGAT
** *
1051707 GACTTTGACAAAGTCGTCGGCACATGAAGAC
1 GACTTTGACAAAGTCAACGGCAAATGAAGAC
* * *
1051738 GATTTTGATAAAGCCAACGGCAAATGAAGAC
1 GACTTTGACAAAGTCAACGGCAAATGAAGAC
*
1051769 GACTCTGACAAAGTCA
1 GACTTTGACAAAGTCA
1051785 TCGACAAGTG
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.23, T:0.19
Consensus pattern (31 bp):
GACTTTGACAAAGTCAACGGCAAATGAAGAC
Found at i:1053035 original size:69 final size:70
Alignment explanation
Indices: 1052952--1053091 Score: 264
Period size: 69 Copynumber: 2.0 Consensus size: 70
1052942 AAAGATAGAT
1052952 ATGAACAGATTTGACTGCACCGACTAACCAACCACAATAAGAGATCAAATTACGGAAAGATCA-C
1 ATGAACAGATTTGACTGCACCGACTAACCAACCACAATAAGAGATCAAATTACGGAAAGATCATC
1053016 AAAAA
66 AAAAA
*
1053021 ATGAACAGATTTGACTGCACCGACTAACCAACCACAATAAGAGATCAAATTACTGAAAGATCATC
1 ATGAACAGATTTGACTGCACCGACTAACCAACCACAATAAGAGATCAAATTACGGAAAGATCATC
1053086 AAAAA
66 AAAAA
1053091 A
1 A
1053092 ATGCAAATCA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 62 0.90
70 7 0.10
ACGTcount: A:0.48, C:0.21, G:0.14, T:0.17
Consensus pattern (70 bp):
ATGAACAGATTTGACTGCACCGACTAACCAACCACAATAAGAGATCAAATTACGGAAAGATCATC
AAAAA
Found at i:1053317 original size:20 final size:22
Alignment explanation
Indices: 1053280--1053319 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1053270 GGAGGAAAAT
1053280 ATATCAAAATGTAGAGAAAAGA
1 ATATCAAAATGTAGAGAAAAGA
1053302 ATATCAAAA-G-AGAGAAAA
1 ATATCAAAATGTAGAGAAAA
1053320 ATATGCAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.62, C:0.05, G:0.17, T:0.15
Consensus pattern (22 bp):
ATATCAAAATGTAGAGAAAAGA
Found at i:1063609 original size:2 final size:2
Alignment explanation
Indices: 1063567--1063599 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1063557 TCTATTTTAA
1063567 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 A
1063600 ATTTTATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1063925 original size:59 final size:59
Alignment explanation
Indices: 1063859--1064012 Score: 191
Period size: 60 Copynumber: 2.6 Consensus size: 59
1063849 AAATTGAATT
* *
1063859 TTAAACTTTTGAATATTTTAATTTCATCCCAAATTATGACTCTCATTCTAAATTAGTCC
1 TTAAACTTTTGAATATTCTAATTTCATCCCAAATTATGACCCTCATTCTAAATTAGTCC
* * * *
1063918 TTAAACTTTTGAACATTCTAATTTCATCCTTAAACTATGACCCTCATTCTAAATTGGTCC
1 TTAAACTTTTGAATATTCTAATTTCATCC-CAAATTATGACCCTCATTCTAAATTAGTCC
** * * * *
1063978 CCAAGCGTTTGAATCTTCCAATTTCATCCCAAATT
1 TTAAACTTTTGAATATTCTAATTTCATCCCAAATT
1064013 TCATCCAAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
59 31 0.39
60 48 0.61
ACGTcount: A:0.31, C:0.23, G:0.06, T:0.40
Consensus pattern (59 bp):
TTAAACTTTTGAATATTCTAATTTCATCCCAAATTATGACCCTCATTCTAAATTAGTCC
Found at i:1063947 original size:29 final size:29
Alignment explanation
Indices: 1063859--1063953 Score: 79
Period size: 29 Copynumber: 3.2 Consensus size: 29
1063849 AAATTGAATT
* *
1063859 TTAAACTTTTGAATATTTTAATTTCATCC
1 TTAAACTTTTGAACATTCTAATTTCATCC
* * * *
1063888 -CAAA-TTATGACTCTCATTCTAAATT-AGTCC
1 TTAAACTTTTGA---ACATTCTAATTTCA-TCC
1063918 TTAAACTTTTGAACATTCTAATTTCATCC
1 TTAAACTTTTGAACATTCTAATTTCATCC
1063947 TTAAACT
1 TTAAACT
1063954 ATGACCCTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 14
0.67 0.14 0.19
Matches are distributed among these distances:
27 5 0.10
28 3 0.06
29 21 0.43
30 12 0.24
31 3 0.06
32 5 0.10
ACGTcount: A:0.33, C:0.19, G:0.04, T:0.44
Consensus pattern (29 bp):
TTAAACTTTTGAACATTCTAATTTCATCC
Found at i:1065753 original size:60 final size:60
Alignment explanation
Indices: 1065680--1065804 Score: 205
Period size: 60 Copynumber: 2.1 Consensus size: 60
1065670 AACATGCTAA
* * *
1065680 ATAGTCGAGTGACCATTTTGTAACTTTTAATAGTTGAGGGACTCAACAAAGCAACACCCT
1 ATAGTCAAATGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCT
* *
1065740 ATAGTCAAATGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGTATCACCCT
1 ATAGTCAAATGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCT
1065800 ATAGT
1 ATAGT
1065805 TGAGAGATTA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (60 bp):
ATAGTCAAATGACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACCCT
Found at i:1074137 original size:60 final size:60
Alignment explanation
Indices: 1074027--1074140 Score: 138
Period size: 60 Copynumber: 1.9 Consensus size: 60
1074017 GTCGAATGAC
* * * * * *
1074027 TATTTTATAACTTTTAATAGTCGGAGAACTCAACAAAACGACGTCCTATAATAGAATAAT
1 TATTTTATAACGTTTAATAGTCGAAAAACTCAACAAAACAACATCATATAATAGAATAAT
* * * *
1074087 TATTTTATAGCGTTTAATAGTCGAAAAACTCAATAAAATAATATCATATAATAG
1 TATTTTATAACGTTTAATAGTCGAAAAACTCAACAAAACAACATCATATAATAG
1074141 GGAATCATTT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 44 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (60 bp):
TATTTTATAACGTTTAATAGTCGAAAAACTCAACAAAACAACATCATATAATAGAATAAT
Found at i:1079094 original size:13 final size:13
Alignment explanation
Indices: 1079076--1079104 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1079066 ACACTTTAAA
1079076 ATTTTATAATTTT
1 ATTTTATAATTTT
1079089 ATTTTATAATTTT
1 ATTTTATAATTTT
1079102 ATT
1 ATT
1079105 ATATCCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTATAATTTT
Found at i:1080435 original size:60 final size:60
Alignment explanation
Indices: 1080308--1080444 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 60
1080298 ACACCTGAGT
* * * * * *
1080308 GACCATTTTATAACTTTTAATGGTCAAGGGACTCAACAAAGCAACGTCCTATAGTCGATG
1 GACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACGTCCCATAATCGAAG
* * *
1080368 AATCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAG-TA-GTACCCATTAATCGAAG
1 GACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACGT-CCCA-TAATCGAAG
1080428 GACCATTTATGT-ACTTT
1 GACCATTT-TGTAACTTT
1080445 ACCATAATTT
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
58 2 0.03
59 4 0.06
60 54 0.86
61 3 0.05
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.31
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAACGTCCCATAATCGAAG
Found at i:1101337 original size:16 final size:15
Alignment explanation
Indices: 1101316--1101358 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
1101306 TGTTATCATC
*
1101316 TCAAATTCCTAAATTT
1 TCAAATTCCTAAA-CT
*
1101332 TCAAATTCTTAAACT
1 TCAAATTCCTAAACT
1101347 T-AAATTCCTAAA
1 TCAAATTCCTAAA
1101359 ATATCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.42
15 2 0.08
16 12 0.50
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (15 bp):
TCAAATTCCTAAACT
Found at i:1101571 original size:16 final size:16
Alignment explanation
Indices: 1101552--1101582 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1101542 AAAATTAGAG
*
1101552 TTTTTTAAAATAATTT
1 TTTTTTAAAAAAATTT
1101568 TTTTTTAAAAAAATT
1 TTTTTTAAAAAAATT
1101583 CAAAATTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTTAAAAAAATTT
Found at i:1106606 original size:103 final size:103
Alignment explanation
Indices: 1106484--1106680 Score: 385
Period size: 103 Copynumber: 1.9 Consensus size: 103
1106474 AAAAGATGAA
*
1106484 ATGGATGAAAATAAAAATGTCTTGAACCAAGAAGAAGCGGGAGCTTCCGCAAGGCTTTACTGCTG
1 ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCGGGAGCTTCCGCAAGGCTTTACTGCTG
1106549 TGAAAGTTCGCACCTTCGTCGGAGAAAAATATGAAATG
66 TGAAAGTTCGCACCTTCGTCGGAGAAAAATATGAAATG
1106587 ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCGGGAGCTTCCGCAAGGCTTTACTGCTG
1 ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCGGGAGCTTCCGCAAGGCTTTACTGCTG
1106652 TGAAAGTTCGCACCTTCGTCGGAGAAAAA
66 TGAAAGTTCGCACCTTCGTCGGAGAAAAA
1106681 GATGCGTCGC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (103 bp):
ATGGATGAAAACAAAAATGTCTTGAACCAAGAAGAAGCGGGAGCTTCCGCAAGGCTTTACTGCTG
TGAAAGTTCGCACCTTCGTCGGAGAAAAATATGAAATG
Found at i:1117596 original size:12 final size:12
Alignment explanation
Indices: 1117576--1117607 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1117566 GAAACTGAAG
*
1117576 ACATACATTGAT
1 ACATCCATTGAT
1117588 ACATCCATTGAT
1 ACATCCATTGAT
1117600 ACATCCAT
1 ACATCCAT
1117608 GACCTCCACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (12 bp):
ACATCCATTGAT
Found at i:1121776 original size:25 final size:25
Alignment explanation
Indices: 1121748--1121797 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1121738 CGGGGACAAG
1121748 TTCCAAATTGTATAAAACTAAGGAC
1 TTCCAAATTGTATAAAACTAAGGAC
1121773 TTCCAAATTGTATAAAACTAAGGAC
1 TTCCAAATTGTATAAAACTAAGGAC
1121798 AATATGAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (25 bp):
TTCCAAATTGTATAAAACTAAGGAC
Found at i:1124188 original size:164 final size:164
Alignment explanation
Indices: 1123961--1124285 Score: 562
Period size: 164 Copynumber: 2.0 Consensus size: 164
1123951 TCTTATCTTA
*
1123961 CCAAAATGAGACCTACTGGACCACAACTATTGAACATTCGAGCAAGTGTAAAATACTGTATGCCC
1 CCAAAATGAGACCTACTGGACCACAACTATTGAACATTCGAGCAAATGTAAAATACTGTATGCCC
* * * * * *
1124026 CCTGGGTCAGAATTCAGTTACTGATATGTTATTGGTGTGCCACCATGAAATTGTTTTTAGTCAGA
66 CCTGGATCAGAATTCAGTTACCGA-ATGTTATTGGTGTACCACCATGAAATCGTCTTTAATCAGA
1124091 -TTTGAATAGCTTCTGTTCTGCTTTGTTTGGTGTG
130 TTTTGAATAGCTTCTGTTCTGCTTTGTTTGGTGTG
1124125 CCAAAATGAGACCTACTGGACCACAACTATTGAACATTCGAGCAAATGTAAAATACTGTATGCCC
1 CCAAAATGAGACCTACTGGACCACAACTATTGAACATTCGAGCAAATGTAAAATACTGTATGCCC
*
1124190 CCTGGATCAGAATTCAGTTACCGACTGTTATTGGTGTACCACCATGAAATCGTCTTTAATCAGAT
66 CCTGGATCAGAATTCAGTTACCGAATGTTATTGGTGTACCACCATGAAATCGTCTTTAATCAGAT
1124255 TTTGAATAGCTTCTGTTCTGCTTTGTTTGGT
131 TTTGAATAGCTTCTGTTCTGCTTTGTTTGGT
1124286 CCCATGTTTA
Statistics
Matches: 152, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
163 35 0.23
164 117 0.77
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (164 bp):
CCAAAATGAGACCTACTGGACCACAACTATTGAACATTCGAGCAAATGTAAAATACTGTATGCCC
CCTGGATCAGAATTCAGTTACCGAATGTTATTGGTGTACCACCATGAAATCGTCTTTAATCAGAT
TTTGAATAGCTTCTGTTCTGCTTTGTTTGGTGTG
Found at i:1130328 original size:40 final size:40
Alignment explanation
Indices: 1130267--1130374 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 40
1130257 TGTTAATCCA
* *
1130267 ACTTGAGGTAATAAATTTTTTGAAAATTAAACTACCCCTC
1 ACTTGAGGCAATAAATCTTTTGAAAATTAAACTACCCCTC
* *
1130307 ACTTGAGGCAATGAAA-CTTTTGAAAATTAAATTACTCCTC
1 ACTTGAGGCAAT-AAATCTTTTGAAAATTAAACTACCCCTC
* * * *
1130347 TATCTTAAGACAAAAAAGCTTTTGAAAA
1 -A-CTTGAGGCAATAAATCTTTTGAAAA
1130375 AAACACTGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 32 0.56
41 7 0.12
42 18 0.32
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (40 bp):
ACTTGAGGCAATAAATCTTTTGAAAATTAAACTACCCCTC
Found at i:1139201 original size:37 final size:37
Alignment explanation
Indices: 1139125--1139201 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1139115 TTTTTATATT
*
1139125 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* * *
1139162 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
1139199 TTT
1 TTT
1139202 GTAATATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:1139383 original size:20 final size:20
Alignment explanation
Indices: 1139347--1139384 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1139337 ATCCTATTTC
**
1139347 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
1139367 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
1139385 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:1146712 original size:26 final size:27
Alignment explanation
Indices: 1146680--1146731 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1146670 ACTTGGAAAC
1146680 TTTTCTCAAC-GTGGTCCCTGAACTTT
1 TTTTCTCAACAGTGGTCCCTGAACTTT
* * *
1146706 TTTTCTCCACATTGGTCCTTGAACTT
1 TTTTCTCAACAGTGGTCCCTGAACTT
1146732 GAATTATTGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.15, C:0.27, G:0.13, T:0.44
Consensus pattern (27 bp):
TTTTCTCAACAGTGGTCCCTGAACTTT
Found at i:1146858 original size:29 final size:29
Alignment explanation
Indices: 1146826--1146919 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
1146816 CAAGTCCACA
1146826 GACTAATGTGGACCAAAATAAAGTTCAGG
1 GACTAATGTGGACCAAAATAAAGTTCAGG
* **
1146855 GACTAA-GTTGGA--AAAATTGTCAAGTTCAAA
1 GACTAATG-TGGACCAAAA---TAAAGTTCAGG
*
1146885 GACTAATGTGGACCAAGATAAAGTTCAGG
1 GACTAATGTGGACCAAAATAAAGTTCAGG
1146914 GACTAA
1 GACTAA
1146920 GCTGGGAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
27 4 0.08
28 1 0.02
29 24 0.47
30 18 0.35
31 1 0.02
32 3 0.06
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.22
Consensus pattern (29 bp):
GACTAATGTGGACCAAAATAAAGTTCAGG
Found at i:1146892 original size:59 final size:59
Alignment explanation
Indices: 1146813--1146949 Score: 193
Period size: 59 Copynumber: 2.3 Consensus size: 59
1146803 CGGATAAAGT
* * * *
1146813 TGCCAAGTCCACAGACTAATGTGGACCAAAATAAAGTTCAGGGACTAAGTTGGAAAAAT
1 TGCCAAGTTCAAAGACTAATGTGGACCAAAATAAAGTTCAGGGACTAAGCTGGAAAAAC
* * *
1146872 TGTCAAGTTCAAAGACTAATGTGGACCAAGATAAAGTTCAGGGACTAAGCTGGGAAAAC
1 TGCCAAGTTCAAAGACTAATGTGGACCAAAATAAAGTTCAGGGACTAAGCTGGAAAAAC
* *
1146931 TGCCAAGTTCGAGGACTAA
1 TGCCAAGTTCAAAGACTAA
1146950 AAGTTGCTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (59 bp):
TGCCAAGTTCAAAGACTAATGTGGACCAAAATAAAGTTCAGGGACTAAGCTGGAAAAAC
Found at i:1151148 original size:22 final size:22
Alignment explanation
Indices: 1151107--1151187 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1151097 CTCGTATAAA
1151107 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1151130 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1151152 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1151174 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1151188 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1151183 original size:13 final size:13
Alignment explanation
Indices: 1151121--1151183 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
1151111 CCGAAGTGCC
1151121 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1151134 CC---GAAGTGC-
1 CCGTAGAATTGCA
1151143 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1151156 CC---GAAGTGC-
1 CCGTAGAATTGCA
1151165 CCGTAGAATTGCA
1 CCGTAGAATTGCA
1151178 CCGTAG
1 CCGTAG
1151184 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:1152891 original size:21 final size:21
Alignment explanation
Indices: 1152867--1152911 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1152857 TCTTGTTCGT
* *
1152867 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1152888 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1152909 TTG
1 TTG
1152912 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1156121 original size:22 final size:22
Alignment explanation
Indices: 1156080--1156160 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
1156070 CTCGTATAAA
1156080 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
1156103 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
1156125 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
1156147 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
1156161 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:1156156 original size:13 final size:13
Alignment explanation
Indices: 1156094--1156156 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
1156084 CCGAAGTGCC
1156094 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1156107 CC---GAAGTGC-
1 CCGTAGAATTGCA
1156116 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
1156129 CC---GAAGTGC-
1 CCGTAGAATTGCA
1156138 CCGTAGAATTGCA
1 CCGTAGAATTGCA
1156151 CCGTAG
1 CCGTAG
1156157 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:1156815 original size:2 final size:2
Alignment explanation
Indices: 1156808--1156886 Score: 151
Period size: 2 Copynumber: 40.0 Consensus size: 2
1156798 TCTCTTAAAC
1156808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1156849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1156887 CACATGTTCA
Statistics
Matches: 76, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 75 0.99
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1157920 original size:21 final size:21
Alignment explanation
Indices: 1157896--1157940 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1157886 TCTTGTTCGT
* *
1157896 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1157917 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1157938 TTG
1 TTG
1157941 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1165396 original size:36 final size:36
Alignment explanation
Indices: 1165349--1165422 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
1165339 TCAAATATTC
1165349 TGATCTGATCTTTTGGTAAGGAAAACTGACCTGTCT
1 TGATCTGATCTTTTGGTAAGGAAAACTGACCTGTCT
1165385 TGATCTGATCTTTTGGTAAGGAAAACTGACCTGTCT
1 TGATCTGATCTTTTGGTAAGGAAAACTGACCTGTCT
1165421 TG
1 TG
1165423 CTTCGCATCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.16, G:0.23, T:0.36
Consensus pattern (36 bp):
TGATCTGATCTTTTGGTAAGGAAAACTGACCTGTCT
Found at i:1166071 original size:145 final size:148
Alignment explanation
Indices: 1165840--1166139 Score: 570
Period size: 145 Copynumber: 2.0 Consensus size: 148
1165830 CCGAAGTGCC
1165840 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAA-GATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1165905 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
65 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1165970 CATATGTCCCGAAGAACCG
130 CATATGTCCCGAAGAACCG
1165989 CGTAGAATTGCACCGTAGTG-CATAT-A-ATGTCCATAAGGACCACATAGAATTCTTTAAGAATC
1 CGTAGAATTGCACCGTAGTGCCATATAAGATGTCCATAAGGACCACATAGAATTCTTTAAGAATC
1166051 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
66 ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
1166116 ATATGTCCCGAAGAACCG
131 ATATGTCCCGAAGAACCG
1166134 CGTAGA
1 CGTAGA
1166140 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
145 125 0.83
147 1 0.01
148 5 0.03
149 20 0.13
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (148 bp):
CGTAGAATTGCACCGTAGTGCCATATAAGATGTCCATAAGGACCACATAGAATTCTTTAAGAATC
ATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATAC
ATATGTCCCGAAGAACCG
Found at i:1166412 original size:22 final size:21
Alignment explanation
Indices: 1166387--1166432 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1166377 CAATCACCTT
1166387 TATCATGTACACATACTCATCA
1 TATCATGTACACATA-TCATCA
* * *
1166409 TATCTTGTTCACATATGATCA
1 TATCATGTACACATATCATCA
1166430 TAT
1 TAT
1166433 ACTTCATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.39
Consensus pattern (21 bp):
TATCATGTACACATATCATCA
Found at i:1169905 original size:23 final size:23
Alignment explanation
Indices: 1169879--1169923 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1169869 CACCACAGCT
*
1169879 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
1169902 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
1169924 ATATAATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:1170161 original size:149 final size:149
Alignment explanation
Indices: 1169902--1170205 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
1169892 CGAAGTGCCC
*
1169902 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1169967 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1170032 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
1170051 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1170116 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
1170181 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
1170200 CGTAGA
1 CGTAGA
1170206 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:1175647 original size:15 final size:16
Alignment explanation
Indices: 1175627--1175659 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1175617 TCATTCTATT
1175627 TTTAAA-TATTTTATA
1 TTTAAATTATTTTATA
*
1175642 TTTAAATTATTTTTTA
1 TTTAAATTATTTTATA
1175658 TT
1 TT
1175660 AATTAATAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAAATTATTTTATA
Found at i:1187395 original size:20 final size:20
Alignment explanation
Indices: 1187366--1187428 Score: 108
Period size: 20 Copynumber: 3.1 Consensus size: 20
1187356 TTCCAAATTT
1187366 GCAACGCGAATATGTAAATC
1 GCAACGCGAATATGTAAATC
*
1187386 GCAACTCGAATATGTAAATC
1 GCAACGCGAATATGTAAATC
*
1187406 GCAACGCGAATATATAAATC
1 GCAACGCGAATATGTAAATC
1187426 GCA
1 GCA
1187429 GCACAGAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
GCAACGCGAATATGTAAATC
Found at i:1187646 original size:20 final size:20
Alignment explanation
Indices: 1187600--1187648 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1187590 TTGCAAATTT
1187600 GCGTTGCGATTTACATATTA
1 GCGTTGCGATTTACATATTA
* * *
1187620 TCATTGCGATTTACCTATTA
1 GCGTTGCGATTTACATATTA
1187640 GCGTTGCGA
1 GCGTTGCGA
1187649 ATTTGGAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTA
Found at i:1187850 original size:56 final size:56
Alignment explanation
Indices: 1187727--1187852 Score: 189
Period size: 56 Copynumber: 2.2 Consensus size: 56
1187717 TATATCAGTC
1187727 ATTAGCGTTGCGAAATTCAAGTTGCGAATTTAGAGAATTCGCGTTGCGATTTACAT
1 ATTAGCGTTGCGAAATTCAAGTTGCGAATTTAGAGAATTCGCGTTGCGATTTACAT
* * * * * *
1187783 ATTATCATTGCGAAATTCGAGTTGCGAATTTGGAGAATTCGTGTTGCGATTTACCT
1 ATTAGCGTTGCGAAATTCAAGTTGCGAATTTAGAGAATTCGCGTTGCGATTTACAT
*
1187839 ATTCGCGTTGCGAA
1 ATTAGCGTTGCGAA
1187853 TTTAGAAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
56 61 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (56 bp):
ATTAGCGTTGCGAAATTCAAGTTGCGAATTTAGAGAATTCGCGTTGCGATTTACAT
Found at i:1187970 original size:20 final size:20
Alignment explanation
Indices: 1187941--1188005 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1187931 TGCGAATTTG
*
1187941 CGTTGTGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* * **
1187961 CGTTTCGATTTACCTATTCG
1 CGTTGCGATTTACATATTAT
* *
1187981 CATTGCGAATTACATATTAT
1 CGTTGCGATTTACATATTAT
1188001 CGTTG
1 CGTTG
1188006 TAATTTAACT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Found at i:1187994 original size:40 final size:40
Alignment explanation
Indices: 1187950--1188031 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
1187940 GCGTTGTGAT
* *
1187950 TTACATATTATCGTT-TCGATTTACCTATTCGCATTGCGAA
1 TTACATATTATCGTTGT-AATTTAACTATTCGCATTGCGAA
*
1187990 TTACATATTATCGTTGTAATTTAACTATTCGCGTTGCGAA
1 TTACATATTATCGTTGTAATTTAACTATTCGCATTGCGAA
1188030 TT
1 TT
1188032 TGACTTTGGC
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 37 0.97
41 1 0.03
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (40 bp):
TTACATATTATCGTTGTAATTTAACTATTCGCATTGCGAA
Found at i:1188049 original size:20 final size:20
Alignment explanation
Indices: 1188007--1188073 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
1187997 TTATCGTTGT
* *
1188007 AATTTAACTATTCGCGTTGCG
1 AATTTGACT-TTCGCGATGCG
*
1188028 AATTTGACTTTGGCGATGCG
1 AATTTGACTTTCGCGATGCG
* *
1188048 AATTCGACTTTCGCGTTGCG
1 AATTTGACTTTCGCGATGCG
*
1188068 ATTTTG
1 AATTTG
1188074 GAACTTGTGT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 30 0.79
21 8 0.21
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
AATTTGACTTTCGCGATGCG
Found at i:1200460 original size:80 final size:80
Alignment explanation
Indices: 1200327--1200486 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
1200317 CCGTTTGGAA
1200327 GTCTTGATAAATTAGAATACATACATTGATCAAGCTTTAAAATGTTTATATTAATTCGTGTATGC
1 GTCTTGATAAATTAGAATACATACATTGATCAAGCTTTAAAATGTTTATATTAATTCGTGTATGC
1200392 TTATTTAATATCGAT
66 TTATTTAATATCGAT
* *
1200407 GTCTTGATAAATTATAATACATACATTGATCAAGCTTTAAAATGTTTATATTAATTCTTGTATGC
1 GTCTTGATAAATTAGAATACATACATTGATCAAGCTTTAAAATGTTTATATTAATTCGTGTATGC
1200472 TTATTTAATATCGAT
66 TTATTTAATATCGAT
1200487 ATTCTCCCTC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (80 bp):
GTCTTGATAAATTAGAATACATACATTGATCAAGCTTTAAAATGTTTATATTAATTCGTGTATGC
TTATTTAATATCGAT
Found at i:1201607 original size:2 final size:2
Alignment explanation
Indices: 1201600--1201651 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1201590 CCACAATAGC
1201600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1201642 AT AT AT AT AT
1 AT AT AT AT AT
1201652 TGTGAACTCA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1207222 original size:20 final size:19
Alignment explanation
Indices: 1207189--1207227 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1207179 ATTATTATTA
*
1207189 GTATTTTATTTCTTTTTTC
1 GTATTTTATTTCTTATTTC
*
1207208 GTATTTTTTTCTCTTATTTC
1 GTATTTTATT-TCTTATTTC
1207228 AGGCCCATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.10, C:0.13, G:0.05, T:0.72
Consensus pattern (19 bp):
GTATTTTATTTCTTATTTC
Found at i:1207545 original size:42 final size:41
Alignment explanation
Indices: 1207516--1207738 Score: 338
Period size: 42 Copynumber: 5.3 Consensus size: 41
1207506 TCCAAGTTCG
*
1207516 CGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
1207558 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
*
1207600 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* * *
1207642 AGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
1207684 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
1207726 CGTTGCGATAGTC
1 CGTTGCGATAGTC
1207739 CAAAATCGCA
Statistics
Matches: 170, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 170 1.00
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:1207632 original size:84 final size:84
Alignment explanation
Indices: 1207506--1207741 Score: 409
Period size: 84 Copynumber: 2.8 Consensus size: 84
1207496 ATTGCGATAG
*
1207506 TCCAAGTTCGCGTTGCGATAGTCGAAGTTTGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTC
1207571 CAAGTTCGCGTTGCGATTTAT
64 CAAGTTCGCGTTGCGATTTAT
* * * *
1207592 TCCAAGTTCGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTAGTTGTGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1207657 AGTTCGCGTTGCGATTTAT
66 AGTTCGCGTTGCGATTTAT
1207676 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
1207741 A
66 A
1207742 AATCGCAACG
Statistics
Matches: 141, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
84 133 0.94
86 8 0.06
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (84 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCCA
AGTTCGCGTTGCGATTTAT
Found at i:1208486 original size:21 final size:21
Alignment explanation
Indices: 1208460--1208632 Score: 123
Period size: 21 Copynumber: 8.4 Consensus size: 21
1208450 ATTTTGGACT
1208460 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1208481 ATCGCAACACGAACTTCGACT--
1 ATCGC-A-ACGAATTTGGAATAA
*
1208502 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
*
1208523 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
* * *
1208544 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
1208565 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
* * *
1208584 ATCGCAACGCGAACTTCGACT--
1 ATCGCAA--CGAATTTGGAATAA
1208605 ATCGCAACGAATTTGG-A-AA
1 ATCGCAACGAATTTGGAATAA
1208624 ATCGCAACG
1 ATCGCAACG
1208633 CGAACTTAGA
Statistics
Matches: 118, Mismatches: 20, Indels: 30
0.70 0.12 0.18
Matches are distributed among these distances:
19 39 0.33
20 1 0.01
21 59 0.50
22 1 0.01
23 18 0.15
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:1208559 original size:63 final size:61
Alignment explanation
Indices: 1208460--1208592 Score: 221
Period size: 63 Copynumber: 2.1 Consensus size: 61
1208450 ATTTTGGACT
*
1208460 ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAATTTGG-A-AA
* *
1208523 ATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAAA
1 ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAATTTGGAAA
1208584 ATCGCAACG
1 ATCGCAACG
1208593 CGAACTTCGA
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
61 10 0.15
62 1 0.02
63 55 0.83
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (61 bp):
ATCGCAACGAATTTGGAATAAATCGCAACACGAACTTCGACTATCGCAACGAATTTGGAAA
Found at i:1208597 original size:40 final size:40
Alignment explanation
Indices: 1208523--1208651 Score: 222
Period size: 40 Copynumber: 3.2 Consensus size: 40
1208513 TTTGGAATAA
*
1208523 ATCGCAATGAATTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACT
1208565 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
*
1208605 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTAGACT
1 ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
1208645 ATCGCAA
1 ATCGCAA
1208652 TGCGAATATG
Statistics
Matches: 85, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 69 0.81
41 1 0.01
42 15 0.18
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (40 bp):
ATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACT
Found at i:1208648 original size:21 final size:21
Alignment explanation
Indices: 1208544--1208657 Score: 110
Period size: 21 Copynumber: 5.6 Consensus size: 21
1208534 TTTGGAATAA
1208544 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1208565 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
1208584 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1208605 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
1208624 ATCGCAACGCGAACTTAGACT
1 ATCGCAACGCGAACTTCGACT
*
1208645 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1208658 TATGTAAATC
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
19 30 0.42
21 42 0.58
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1208697 original size:21 final size:21
Alignment explanation
Indices: 1208671--1208718 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1208661 GTAAATCGAA
*
1208671 TTGCGATAGTCCAAGTTCGTG
1 TTGCGATAGTCCAAGTTCGCG
*
1208692 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTCGCG
1208713 TTGCGA
1 TTGCGA
1208719 ATCTGGAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (21 bp):
TTGCGATAGTCCAAGTTCGCG
Found at i:1210285 original size:22 final size:22
Alignment explanation
Indices: 1210265--1210311 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1210255 AACATATATT
1210265 TATTAATATTTATAATAATATAA
1 TATT-ATATTTATAATAATATAA
* *
1210288 TATTATATTTTTAATATTATAA
1 TATTATATTTATAATAATATAA
1210310 TA
1 TA
1210312 AAATAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTATATTTATAATAATATAA
Found at i:1210413 original size:28 final size:28
Alignment explanation
Indices: 1210279--1210427 Score: 110
Period size: 28 Copynumber: 5.1 Consensus size: 28
1210269 AATATTTATA
* *
1210279 ATAATATAATATTATATTTTTAAT-AT-T
1 ATAATA-AATATTTTATATTTAATAATAT
1210306 ATAATAAAATAATTAATTATATTATAATAATAAT
1 ATAAT-AAAT-ATT--TTATATT-TAATAAT-AT
* *
1210340 ATAAGATATATATTT-TATTTAATAAATAT
1 ATAATAAATAT-TTTATATTTAAT-AATAT
1210369 ATAATAAATATTTTATATTTAATAATGA-
1 ATAATAAATATTTTATATTTAATAAT-AT
* *
1210397 ATAAT-ATTATTTATATATTTAATATTAT
1 ATAATAAATATTT-TATATTTAATAATAT
1210425 ATA
1 ATA
1210428 TAATCTAATA
Statistics
Matches: 100, Mismatches: 8, Indels: 27
0.74 0.06 0.20
Matches are distributed among these distances:
27 15 0.15
28 30 0.30
29 24 0.24
30 12 0.12
31 6 0.06
32 4 0.04
33 4 0.04
34 5 0.05
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
ATAATAAATATTTTATATTTAATAATAT
Found at i:1210421 original size:18 final size:17
Alignment explanation
Indices: 1210398--1210447 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
1210388 TAATAATGAA
*
1210398 TAATATTATTTATATATT
1 TAATATTATTTATA-ATC
*
1210416 TAATATTATATATAATC
1 TAATATTATTTATAATC
*
1210433 TAATAATATTT-TAAT
1 TAATATTATTTATAAT
1210448 AAAGATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 4 0.14
17 11 0.39
18 13 0.46
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TAATATTATTTATAATC
Found at i:1210428 original size:58 final size:59
Alignment explanation
Indices: 1210278--1210431 Score: 165
Period size: 58 Copynumber: 2.6 Consensus size: 59
1210268 TAATATTTAT
* * * *
1210278 AATAATATAATATTATATTTTTAATATTATAATAAAATAATTAATTATATTATAATAATA
1 AATAATATTATATTATATATTTAATATTAT-ATATAATAAATAATTATATTATAATAATA
* * * *
1210338 ATATAAGATATATATT-T-TATTTAATA-AATATATAATAAATATTTTATATT-TAATAATG
1 A-ATAATAT-TATATTATATATTTAATATTATATATAATAAATA-ATTATATTATAATAATA
1210396 AATAATATTAT-TTATATATTTAATATTATATATAAT
1 AATAATATTATATTATATATTTAATATTATATATAAT
1210432 CTAATAATAT
Statistics
Matches: 78, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
55 2 0.03
56 4 0.05
57 15 0.19
58 27 0.35
59 9 0.12
60 9 0.12
61 7 0.09
62 5 0.06
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (59 bp):
AATAATATTATATTATATATTTAATATTATATATAATAAATAATTATATTATAATAATA
Found at i:1210441 original size:62 final size:58
Alignment explanation
Indices: 1210276--1210445 Score: 154
Period size: 62 Copynumber: 2.9 Consensus size: 58
1210266 ATTAATATTT
* *
1210276 ATAATAATATAATATTATATTTTTAATATTATA-ATAA--AATAAT-TAATTATATTATA
1 ATAATAATATAAT-TTATATATTTAATATTATATATAATTAATAATAT-TTTATATTATA
** * *
1210332 ATAATAATATAAGATATATATTTTAT-TTA-ATAAATATATAATAAATATTTTATATTTAATA
1 ATAATAATATAATTTATATATTTAATATTATATATA-AT-TAAT-AATATTTTATA-TT-ATA
*
1210393 ATGAATAATATTATTTATATATTTAATATTATATATAATCTAATAATATTTTA
1 AT-AATAATATAATTTATATATTTAATATTATATATAAT-TAATAATATTTTA
1210446 ATAAAGATAT
Statistics
Matches: 90, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
53 1 0.01
54 5 0.06
55 11 0.12
56 12 0.13
58 3 0.03
59 8 0.09
60 3 0.03
61 5 0.06
62 29 0.32
63 9 0.10
64 4 0.04
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (58 bp):
ATAATAATATAATTTATATATTTAATATTATATATAATTAATAATATTTTATATTATA
Found at i:1210613 original size:21 final size:20
Alignment explanation
Indices: 1210584--1210623 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1210574 TTAATAAAAT
1210584 TATAAAAATAATATTTAATAA
1 TATAAAAATAAT-TTTAATAA
* *
1210605 TATATAAATTATTTTAATA
1 TATAAAAATAATTTTAATA
1210624 TTTTAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATAAAAATAATTTTAATAA
Found at i:1210875 original size:29 final size:30
Alignment explanation
Indices: 1210833--1210920 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 30
1210823 TTCCTGAAAT
*
1210833 GTAATTCATTTTCCA-AAATTTAAATTACA
1 GTAATTCATTTTCCAGAAATTCAAATTACA
* *
1210862 GTAATTCATTTTCCAGTAATTCAAATTATA
1 GTAATTCATTTTCCAGAAATTCAAATTACA
* * *
1210892 ATAATTCATTTTCTAGAAAATC-AATTACA
1 GTAATTCATTTTCCAGAAATTCAAATTACA
1210921 ACCAATGTAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
29 21 0.42
30 29 0.58
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (30 bp):
GTAATTCATTTTCCAGAAATTCAAATTACA
Found at i:1210878 original size:15 final size:15
Alignment explanation
Indices: 1210833--1210884 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1210823 TTCCTGAAAT
1210833 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
* * ** *
1210848 -AAATTTAAATTACA
1 GTAATTCATTTTCCA
1210862 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
1210877 GTAATTCA
1 GTAATTCA
1210885 AATTATAATA
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
14 9 0.35
15 17 0.65
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:1211664 original size:21 final size:21
Alignment explanation
Indices: 1211623--1211666 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1211613 ATTCTGGGCT
* *
1211623 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
1211644 AGGGGAACCGATATCCC-TTCA
1 AGGGGAACCGATA-CCCATTCA
1211665 AG
1 AG
1211667 CGAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:1211738 original size:23 final size:22
Alignment explanation
Indices: 1211695--1211738 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1211685 ATGTCATGGG
*
1211695 GGAACCGATACCCCCACAGGAT
1 GGAACCGATACCCCCAAAGGAT
* *
1211717 GGAACTGATTCCCCCTAAAGGA
1 GGAACCGATACCCCC-AAAGGA
1211739 AAATTATAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (22 bp):
GGAACCGATACCCCCAAAGGAT
Found at i:1221743 original size:20 final size:20
Alignment explanation
Indices: 1221703--1221745 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1221693 ATATAAATTT
**
1221703 ATAAAATTTTAAAGATGAAA
1 ATAAAATTTTAAAGAAAAAA
*
1221723 ATAAAATTTTCAAGAAAAAA
1 ATAAAATTTTAAAGAAAAAA
1221743 ATA
1 ATA
1221746 TCTAAAATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (20 bp):
ATAAAATTTTAAAGAAAAAA
Found at i:1229473 original size:29 final size:30
Alignment explanation
Indices: 1229401--1229478 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
1229391 AAAATTGAAT
*
1229401 ACTTTAGGTACCTATTTTGACCAAGAAGATA
1 ACTTTAGGTACTTA-TTTGACCAAGAAGATA
*
1229432 ACTTTCGGTACTTACTTTGACCAA-AA-A-A
1 ACTTTAGGTACTTA-TTTGACCAAGAAGATA
1229460 CACTTTAGGTACTTATTTG
1 -ACTTTAGGTACTTATTTG
1229479 TGCTATAAGC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 5 0.12
29 14 0.33
30 2 0.05
31 21 0.50
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (30 bp):
ACTTTAGGTACTTATTTGACCAAGAAGATA
Found at i:1233080 original size:2 final size:2
Alignment explanation
Indices: 1233073--1233124 Score: 59
Period size: 2 Copynumber: 26.0 Consensus size: 2
1233063 CATCTACATA
* * * * *
1233073 TG TG TG TG TG CG CG TG TG TG TG TG CG TG TG TG CG TG TG CG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1233115 TG TG TG TG TG
1 TG TG TG TG TG
1233125 CAAGCAGACA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.10, G:0.50, T:0.40
Consensus pattern (2 bp):
TG
Found at i:1233091 original size:12 final size:12
Alignment explanation
Indices: 1233074--1233122 Score: 71
Period size: 12 Copynumber: 3.9 Consensus size: 12
1233064 ATCTACATAT
*
1233074 GTGTGTGTGCGC
1 GTGTGTGTGTGC
1233086 GTGTGTGTGTGC
1 GTGTGTGTGTGC
1233098 GTGTGTGCGTGTGC
1 GTGTGT--GTGTGC
1233112 GTGTGTGTGTG
1 GTGTGTGTGTG
1233123 TGCAAGCAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
12 22 0.65
14 12 0.35
ACGTcount: A:0.00, C:0.10, G:0.51, T:0.39
Consensus pattern (12 bp):
GTGTGTGTGTGC
Found at i:1233092 original size:14 final size:14
Alignment explanation
Indices: 1233073--1233125 Score: 88
Period size: 14 Copynumber: 3.8 Consensus size: 14
1233063 CATCTACATA
*
1233073 TGTGTGTGTGCGCG
1 TGTGTGTGTGCGTG
1233087 TGTGTGTGTGCGTG
1 TGTGTGTGTGCGTG
*
1233101 TGTGCGTGTGCGTG
1 TGTGTGTGTGCGTG
1233115 TGTGTGTGTGC
1 TGTGTGTGTGC
1233126 AAGCAGACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 36 1.00
ACGTcount: A:0.00, C:0.11, G:0.49, T:0.40
Consensus pattern (14 bp):
TGTGTGTGTGCGTG
Found at i:1236462 original size:18 final size:17
Alignment explanation
Indices: 1236431--1236465 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
1236421 TTGTTCATGT
1236431 ATTTTTATAGAATATTA
1 ATTTTTATAGAATATTA
*
1236448 ATTTTTGATATAATATTA
1 ATTTTT-ATAGAATATTA
1236466 GTTTAAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
ATTTTTATAGAATATTA
Done.