Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008087.1 Hibiscus syriacus cultivar Beakdansim tig00110597_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: 8279816
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 37
Found at i:2435170 original size:10 final size:9
Alignment explanation
Indices: 2435152--2435178 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
2435142 TTAGCTTTAT
2435152 AATAAAAAA
1 AATAAAAAA
2435161 AATAAAAAA
1 AATAAAAAA
2435170 AATAAAAAA
1 AATAAAAAA
2435179 TATATAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AATAAAAAA
Found at i:2435381 original size:28 final size:28
Alignment explanation
Indices: 2435346--2435435 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 28
2435336 TATTTATGTC
2435346 AATATTATTATTAAAATATTAT-ATCTAT
1 AATATTATTATTAAAATATTATGAT-TAT
* * * *
2435374 AATTTTATAAATAAAAAATTATGATTAT
1 AATATTATTATTAAAATATTATGATTAT
* ** *
2435402 TATATT-TTATTAAAATAAAATTATTAT
1 AATATTATTATTAAAATATTATGATTAT
2435429 AA-ATTAT
1 AATATTAT
2435436 ATTTATTATT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 3 0.06
27 17 0.36
28 25 0.53
29 2 0.04
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (28 bp):
AATATTATTATTAAAATATTATGATTAT
Found at i:2435438 original size:31 final size:31
Alignment explanation
Indices: 2435375--2435443 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
2435365 TATATCTATA
*
2435375 ATTTTA-TAAATAAAAAATTATGATTATTAT
1 ATTTTATTAAATAAAAAATTATGATAATTAT
* *
2435405 ATTTTATTAAA-ATAAAATTATTATAAATTAT
1 ATTTTATTAAATAAAAAATTATGAT-AATTAT
2435436 A-TTTATTA
1 ATTTTATTA
2435444 TTTATTATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (31 bp):
ATTTTATTAAATAAAAAATTATGATAATTAT
Found at i:2436514 original size:21 final size:21
Alignment explanation
Indices: 2436490--2436542 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
2436480 GTGCACGCAT
*
2436490 AAAGTGTCGATACATTTATTA
1 AAAGTATCGATACATTTATTA
2436511 AAAGTATCGATACATTTATTA
1 AAAGTATCGATACATTTATTA
2436532 AAAGTATCGAT
1 AAAGTATCGAT
2436543 CCCAAAAACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (21 bp):
AAAGTATCGATACATTTATTA
Found at i:2436943 original size:87 final size:87
Alignment explanation
Indices: 2436847--2437253 Score: 615
Period size: 87 Copynumber: 4.7 Consensus size: 87
2436837 AGACGCTATA
*
2436847 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACAT
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACCT
*
2436912 ATTTTATTATATAAGCGTTACC
66 ATTTTATTATATAAGCGCTACC
* **
2436934 TATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGATAATATTTCCAGTTAAATACCT
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACCT
2436999 ATTTTATTATATAAGCGCTACC
66 ATTTTATTATATAAGCGCTACC
*
2437021 TATTACATTATATAAGCGCTACCTAATATGTTATTGT--TTGATAATATTTCCGGTTAAATACCT
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACCT
2437084 ATTTTATTATATAAGCGCTACC
66 ATTTTATTATATAAGCGCTACC
* * * * *
2437106 TAATATATTATATAAGCGTTATCTAATATGTTATTGTACTTGATAATATTT-TCGATTAAATACC
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCT-GGTTAAATACC
* **
2437170 TAATACATTATATAAGCGCTACC
65 TATTTTATTATATAAGCGCTACC
* * *
2437193 TAATACATTATATAAGCGTTATCTAATATGTTATTGTACTTGATAATATTT-TCGGTTAAAT
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCT-GGTTAAAT
2437254 GATATAACAT
Statistics
Matches: 299, Mismatches: 18, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
85 80 0.27
87 219 0.73
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (87 bp):
TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACCT
ATTTTATTATATAAGCGCTACC
Found at i:2436967 original size:23 final size:23
Alignment explanation
Indices: 2436917--2436961 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
2436907 TACATATTTT
* * *
2436917 ATTATATAAGCGTTACCTATTAC
1 ATTATATAAACGCTACCTAATAC
2436940 ATTATATAAACGCTACCTAATA
1 ATTATATAAACGCTACCTAATA
2436962 TGTTATTGTA
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:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAACGCTACCTAATAC
Found at i:2437020 original size:23 final size:23
Alignment explanation
Indices: 2436994--2437045 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
2436984 TCCAGTTAAA
**
2436994 TACCTATTTTATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
2437017 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
2437040 TACCTA
1 TACCTA
2437046 ATATGTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:2437134 original size:21 final size:23
Alignment explanation
Indices: 2437079--2437139 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
2437069 TCCGGTTAAA
* *
2437079 TACCTATTTTATTATATAAGCGC
1 TACCTAATATATTATATAAGCGC
*
2437102 TACCTAATATATTATATAAGCGT
1 TACCTAATATATTATATAAGCGC
* *
2437125 TATCTAATATGTTAT
1 TACCTAATATATTAT
2437140 TGTACTTGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.13, G:0.08, T:0.44
Consensus pattern (23 bp):
TACCTAATATATTATATAAGCGC
Found at i:2437135 original size:172 final size:173
Alignment explanation
Indices: 2436847--2437253 Score: 629
Period size: 172 Copynumber: 2.3 Consensus size: 173
2436837 AGACGCTATA
*
2436847 TATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGGTTAAATACAT
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTA-TTGATAATATTTCCGGTTAAATACAT
* *
2436912 ATTTTATTATATAAGCGTTACCTATTACATTATATAAACGCTACCTAATATGTTATTGTACTTGA
65 ATTTTATTATATAAGCGCTACCTAATACATTATATAAACGCTACCTAATATGTTATTGTACTTGA
* **
2436977 TAATATTTCC-AGTTAAATACCTATTTTATTATATAAGCGCTACC
130 TAATATTTCCGA-TTAAATACCTAATACATTATATAAGCGCTACC
*
2437021 TATTACATTATATAAGCGCTACCTAATATGTTATTGT-TTGATAATATTTCCGGTTAAATACCTA
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTATTGATAATATTTCCGGTTAAATACATA
* * * *
2437085 TTTTATTATATAAGCGCTACCTAATATATTATATAAGCGTTATCTAATATGTTATTGTACTTGAT
66 TTTTATTATATAAGCGCTACCTAATACATTATATAAACGCTACCTAATATGTTATTGTACTTGAT
*
2437150 AATATTTTCGATTAAATACCTAATACATTATATAAGCGCTACC
131 AATATTTCCGATTAAATACCTAATACATTATATAAGCGCTACC
* * * *
2437193 TAATACATTATATAAGCGTTATCTAATATGTTATTGTACTTGATAATATTTTCGGTTAAAT
1 TATTACATTATATAAGCGCTACCTAATATGTTATTGTA-TTGATAATATTTCCGGTTAAAT
2437254 GATATAACAT
Statistics
Matches: 214, Mismatches: 16, Indels: 6
0.91 0.07 0.03
Matches are distributed among these distances:
172 155 0.72
173 1 0.00
174 58 0.27
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (173 bp):
TATTACATTATATAAGCGCTACCTAATATGTTATTGTATTGATAATATTTCCGGTTAAATACATA
TTTTATTATATAAGCGCTACCTAATACATTATATAAACGCTACCTAATATGTTATTGTACTTGAT
AATATTTCCGATTAAATACCTAATACATTATATAAGCGCTACC
Found at i:2437226 original size:23 final size:23
Alignment explanation
Indices: 2437166--2437220 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
2437156 TTCGATTAAA
2437166 TACCTAATACATTATATAAGCGC
1 TACCTAATACATTATATAAGCGC
*
2437189 TACCTAATACATTATATAAGCGT
1 TACCTAATACATTATATAAGCGC
*
2437212 TATCTAATA
1 TACCTAATA
2437221 TGTTATTGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (23 bp):
TACCTAATACATTATATAAGCGC
Found at i:2438913 original size:163 final size:162
Alignment explanation
Indices: 2438634--2438973 Score: 529
Period size: 163 Copynumber: 2.1 Consensus size: 162
2438624 TATAGCCATA
* *
2438634 TAAACATCCAA-ATTTATCATATATTGAAGAAAAGAGGTAATGACTGAAAAGAAATCATGTTAAA
1 TAAACAT-CAATATTTATCACATATTGAAGAAAAGAGCTAATGACTGAAAAGAAATCATGTTAAA
* * * * *
2438698 CATCAAACATTGGGTATTTCAGCTAGTGGTATAATTCCACTAGCAATCAACTTGCAAACAAGTTA
65 CATCAAACATTGGGCATTTCAGCTACTAGTACAATTCCACAAGCAATCAACTTGCAAACAAGTTA
2438763 GCGAAGAGAATCCAATCCAAATTTACAGTGTAT
130 GCGAAGAGAATCCAATCCAAATTTACAGTGTAT
* * *
2438796 TAAACATCAATATTTATCACATTCTTGAAGAAAAGAGCTAATGACTGACAAGAAATCATGTTAGA
1 TAAACATCAATATTTATCACA-TATTGAAGAAAAGAGCTAATGACTGAAAAGAAATCATGTTAAA
* *
2438861 CATCAAACATTGGGCATTTCAGCTACTAGTACCATTCCACAAGCATTCAACTTGCAAACAAGTTA
65 CATCAAACATTGGGCATTTCAGCTACTAGTACAATTCCACAAGCAATCAACTTGCAAACAAGTTA
* *
2438926 GCGGATAGAATCCAATCCAAATTTACAGTGTAT
130 GCGAAGAGAATCCAATCCAAATTTACAGTGTAT
2438959 TAAACATCAATATTT
1 TAAACATCAATATTT
2438974 GAACATGTAA
Statistics
Matches: 162, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
161 3 0.02
162 16 0.10
163 143 0.88
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (162 bp):
TAAACATCAATATTTATCACATATTGAAGAAAAGAGCTAATGACTGAAAAGAAATCATGTTAAAC
ATCAAACATTGGGCATTTCAGCTACTAGTACAATTCCACAAGCAATCAACTTGCAAACAAGTTAG
CGAAGAGAATCCAATCCAAATTTACAGTGTAT
Found at i:2445258 original size:22 final size:22
Alignment explanation
Indices: 2445231--2445274 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2445221 TTCATCAATT
2445231 AAAAATATTATTGATTAATAAA
1 AAAAATATTATTGATTAATAAA
2445253 AAAAATATTATTGATTAATAAA
1 AAAAATATTATTGATTAATAAA
2445275 TTAGAAACCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAAATATTATTGATTAATAAA
Found at i:2445952 original size:27 final size:27
Alignment explanation
Indices: 2445921--2445973 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2445911 CTCTGATTAT
* *
2445921 ATTATGTTATCGAGTCAGTGCTTGAAC
1 ATTATGTCATCGAGCCAGTGCTTGAAC
*
2445948 ATTATGTCGTCGAGCCAGTGCTTGAA
1 ATTATGTCATCGAGCCAGTGCTTGAA
2445974 AGCAATGACG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (27 bp):
ATTATGTCATCGAGCCAGTGCTTGAAC
Found at i:2446142 original size:21 final size:20
Alignment explanation
Indices: 2446097--2446142 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
2446087 GACTCAACAA
2446097 AATAA-CATTTTATAATTAT
1 AATAATCATTTTATAATTAT
*
2446116 -ATAATCATTTTATAAATTTT
1 AATAATCATTTTAT-AATTAT
2446136 AATAATC
1 AATAATC
2446143 GAAATATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 5 0.22
21 6 0.26
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATCATTTTATAATTAT
Found at i:2450798 original size:29 final size:29
Alignment explanation
Indices: 2450756--2450813 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
2450746 CAGTACCGGG
2450756 GGTAGGTCGCCATGCACGCCCAGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
* *
2450785 GGTAGGTCGCCATGCATGCCCTGCGACCT
1 GGTAGGTCGCCATGCACGCCCAGCGACCT
2450814 ACCAGCCAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.16, C:0.36, G:0.31, T:0.17
Consensus pattern (29 bp):
GGTAGGTCGCCATGCACGCCCAGCGACCT
Found at i:2451096 original size:29 final size:29
Alignment explanation
Indices: 2451035--2451118 Score: 96
Period size: 29 Copynumber: 2.9 Consensus size: 29
2451025 ATGAATCCTT
** * **
2451035 GGTCGCCCCGAGTGCATGGCGACCTCCTT
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
* *
2451064 GGTCGCCGGGCGTGCATGGCGACCTAGGA
1 GGTCGCCGGGAGTGCATGGCGACCTACGA
*
2451093 GGTCGCTGGGAGTGCATGGCGACCTA
1 GGTCGCCGGGAGTGCATGGCGACCTA
2451119 TGGTTGGGTT
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.13, C:0.30, G:0.39, T:0.18
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCATGGCGACCTACGA
Found at i:2452245 original size:26 final size:24
Alignment explanation
Indices: 2452189--2452245 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
2452179 TGATAATTTT
* *
2452189 AAAAATTTTATATAAAATTTAAAA
1 AAAAATATTATATAAAATTAAAAA
* *
2452213 AATAATATTATATATATATTAAAAA
1 AAAAATATTATATA-AAATTAAAAA
2452238 AGAAAATA
1 A-AAAATA
2452246 CATAAATTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 12 0.46
25 9 0.35
26 5 0.19
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAATATTATATAAAATTAAAAA
Found at i:2456031 original size:105 final size:105
Alignment explanation
Indices: 2455847--2456054 Score: 281
Period size: 105 Copynumber: 2.0 Consensus size: 105
2455837 GACCACATAT
* * *
2455847 AAATTCCTTAAGAACCATATACATATACCAATGATCAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAAAGACCTCATACAT
2455912 GCTCCAAAGAATACATATACGTCCCAAATGACCACGTAAA
66 GCTCCAAAGAATACATATACGTCCCAAATGACCACGTAAA
* * * * * *
2455952 AAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATATGTGTCTCAAAGGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAAAGACCTCATACAT
* * * * * *
2456017 GTTCCATAGGATACATATATGTCCCGAATGACCGCGTA
66 GCTCCAAAGAATACATATACGTCCCAAATGACCACGTA
2456055 GACCCTCGAC
Statistics
Matches: 88, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
105 88 1.00
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.25
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCTCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCAAATGACCACGTAAA
Found at i:2456253 original size:53 final size:53
Alignment explanation
Indices: 2456196--2456359 Score: 122
Period size: 53 Copynumber: 3.1 Consensus size: 53
2456186 ACACATTCAT
2456196 GTAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
1 GTAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
* ** * * * * * ** *
2456249 GTAATTCACTTA-CACATAGCACATTTTC--ATGAAATTCACA--GATATCCCTTAGC
1 GTAA-TCACATAGTTCATATCA-ATTCTCATATG-ATTTCATATTCATAT-AATCA-C
* * *
2456302 TTAATCACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATAATCAC
1 GTAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
2456355 GTAAT
1 GTAAT
2456360 TCACTTACAC
Statistics
Matches: 76, Mismatches: 25, Indels: 20
0.63 0.21 0.17
Matches are distributed among these distances:
51 4 0.05
52 16 0.21
53 36 0.47
54 16 0.21
55 4 0.05
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (53 bp):
GTAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCAC
Found at i:2456331 original size:106 final size:106
Alignment explanation
Indices: 2456197--2456410 Score: 392
Period size: 106 Copynumber: 2.0 Consensus size: 106
2456187 CACATTCATG
2456197 TAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
2456262 ACATAGCACATTTTCATGAAATTCACAGATATCCCTTAGCT
66 ACATAGCACATTTTCATGAAATTCACAGATATCCCTTAGCT
* *
2456303 TAATCACGTAGTTCATGTCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
1 TAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
* *
2456368 ACATAGCATATTTTCATGTAATTCACAGATATCCCTTAGCT
66 ACATAGCACATTTTCATGAAATTCACAGATATCCCTTAGCT
2456409 TA
1 TA
2456411 TATCTCTTGA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 104 1.00
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (106 bp):
TAATCACATAGTTCATATCAATTCTCATATGATTTCATATTCATATAATCACGTAATTCACTTAC
ACATAGCACATTTTCATGAAATTCACAGATATCCCTTAGCT
Found at i:2463489 original size:20 final size:21
Alignment explanation
Indices: 2463466--2463548 Score: 87
Period size: 21 Copynumber: 3.9 Consensus size: 21
2463456 TTGGTGCAGA
*
2463466 GGGAATCGATTCCCCCCTGA-
1 GGGAACCGATTCCCCCCTGAG
*
2463486 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-CTG-AG
**
2463509 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCTGAG
* *
2463530 GGGAATCGATACCCCCCTG
1 GGGAACCGATTCCCCCCTG
2463549 GGGTTCTGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
20 15 0.29
21 19 0.37
22 1 0.02
23 16 0.31
ACGTcount: A:0.22, C:0.36, G:0.25, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCTGAG
Found at i:2467330 original size:21 final size:22
Alignment explanation
Indices: 2467266--2467345 Score: 126
Period size: 22 Copynumber: 3.7 Consensus size: 22
2467256 TCGATTGAGG
*
2467266 GGGTATCGATTCCCCCTTGAAT
1 GGGTACCGATTCCCCCTTGAAT
2467288 GGGTACCGATTCCCCCTTGAAT
1 GGGTACCGATTCCCCCTTGAAT
*
2467310 GGGTACCGATT-CCCATTGAAT
1 GGGTACCGATTCCCCCTTGAAT
*
2467331 GGGTACTGATTCCCC
1 GGGTACCGATTCCCC
2467346 TAGCCCAGAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 19 0.35
22 35 0.65
ACGTcount: A:0.19, C:0.29, G:0.24, T:0.29
Consensus pattern (22 bp):
GGGTACCGATTCCCCCTTGAAT
Found at i:2468181 original size:64 final size:63
Alignment explanation
Indices: 2468108--2468250 Score: 182
Period size: 64 Copynumber: 2.2 Consensus size: 63
2468098 ATGCACTGGA
*
2468108 AGTGCATCGATGCACCCCTTAAAAAT-AGAAACATCGAATGCAATTGGTGCATCGATGCATAAAG
1 AGTGCATCGATGCACCCCTT-AAAATGA-AAACATCGAAGGCAATTGGTGCATCGATGCAT-AAG
2468172 -
63 T
* * * **
2468172 AGTGCATCGATGCATCCCCTTAAAATGAAAACATCGAAGGTAATTTGTGTATCGATGCATGGGT
1 AGTGCATCGATGCA-CCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAAGT
2468236 AGTGCATCGATGCAC
1 AGTGCATCGATGCAC
2468251 ATGTTAAAGA
Statistics
Matches: 70, Mismatches: 6, Indels: 7
0.84 0.07 0.08
Matches are distributed among these distances:
63 2 0.03
64 61 0.87
65 7 0.10
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (63 bp):
AGTGCATCGATGCACCCCTTAAAATGAAAACATCGAAGGCAATTGGTGCATCGATGCATAAGT
Found at i:2468779 original size:13 final size:14
Alignment explanation
Indices: 2468750--2468780 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2468740 AACCATGCAA
2468750 GTGATATGAACTAT
1 GTGATATGAACTAT
2468764 GTGATATGAA-TAT
1 GTGATATGAACTAT
2468777 GTGA
1 GTGA
2468781 AATATGATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.35
Consensus pattern (14 bp):
GTGATATGAACTAT
Found at i:2473722 original size:25 final size:27
Alignment explanation
Indices: 2473663--2473722 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
2473653 TTTAAAATAA
* *
2473663 AAAT-AAATTTAATATTTTTATGTTTT
1 AAATGAAATTTAATATTTCTATGCTTT
*
2473689 AAATTAAATTTAATATTTCT-T-CTTT
1 AAATGAAATTTAATATTTCTATGCTTT
*
2473714 ATATGAAAT
1 AAATGAAAT
2473723 GCATATCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 10 0.34
26 5 0.17
27 14 0.48
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (27 bp):
AAATGAAATTTAATATTTCTATGCTTT
Found at i:2474751 original size:35 final size:35
Alignment explanation
Indices: 2474705--2474826 Score: 97
Period size: 35 Copynumber: 3.3 Consensus size: 35
2474695 ATTGTTATTG
*
2474705 ACTATCGAAATAATTAATTAATAATATAAAAATCA
1 ACTATCAAAATAATTAATTAATAATATAAAAATCA
* * *
2474740 ACTATCAAAATATATGATTCTCAACT-TTATTAAAAATCA
1 ACTATCAAAATA-ATTAAT-T-AA-TAATA-TAAAAATCA
* *
2474779 TA-TAAAT-AAAATAACTAATTAATAATATAAAAAGCA
1 -ACT--ATCAAAATAATTAATTAATAATATAAAAATCA
2474815 ACTATCAAAATA
1 ACTATCAAAATA
2474827 TCATTTAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 22
0.68 0.09 0.22
Matches are distributed among these distances:
34 2 0.03
35 18 0.27
36 14 0.21
37 5 0.07
38 5 0.07
39 14 0.21
40 7 0.10
41 2 0.03
ACGTcount: A:0.56, C:0.11, G:0.02, T:0.31
Consensus pattern (35 bp):
ACTATCAAAATAATTAATTAATAATATAAAAATCA
Found at i:2474993 original size:30 final size:30
Alignment explanation
Indices: 2474957--2475020 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
2474947 ATCTCATGGT
2474957 GAAAGTATTACAAACTAAGAGAAACCCGAC
1 GAAAGTATTACAAACTAAGAGAAACCCGAC
* *
2474987 GAAAGTATTACAAGCTAAGAGAAACCCGAT
1 GAAAGTATTACAAACTAAGAGAAACCCGAC
2475017 GAAA
1 GAAA
2475021 AGAAGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.50, C:0.17, G:0.19, T:0.14
Consensus pattern (30 bp):
GAAAGTATTACAAACTAAGAGAAACCCGAC
Found at i:2479161 original size:2 final size:2
Alignment explanation
Indices: 2479154--2479193 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2479144 TCCAGCTACA
2479154 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2479194 ACAGATAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2479495 original size:2 final size:2
Alignment explanation
Indices: 2479488--2479514 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2479478 ATCATATCTC
2479488 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2479515 ATTGTAGTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2484854 original size:2 final size:2
Alignment explanation
Indices: 2484849--2484910 Score: 88
Period size: 2 Copynumber: 30.5 Consensus size: 2
2484839 TAACTAACTC
*
2484849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* *
2484892 AG AG AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2484911 GTGTAATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 56 0.98
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:2494779 original size:42 final size:43
Alignment explanation
Indices: 2494732--2494824 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 43
2494722 TCGAGGGTTC
* *
2494732 TATGTGGTCA-TTCGGAACATATATGT-AATCCTTTGGAATATA
1 TATGTGGTCACTTCGGAACACATAT-TCAATCCATTGGAATATA
* * * *
2494774 TATGTGGT-ACTTCGGTACACCTATTCGATCCATTGGAATATG
1 TATGTGGTCACTTCGGAACACATATTCAATCCATTGGAATATA
2494816 TATGTGGTC
1 TATGTGGTC
2494825 CTTAAGGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
41 2 0.05
42 40 0.95
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.38
Consensus pattern (43 bp):
TATGTGGTCACTTCGGAACACATATTCAATCCATTGGAATATA
Found at i:2495979 original size:23 final size:23
Alignment explanation
Indices: 2495948--2495992 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
2495938 CACTACAGCT
*
2495948 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
2495971 CGTAGAAATGCACCGAAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
2495993 ATATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:2498224 original size:41 final size:41
Alignment explanation
Indices: 2498155--2498435 Score: 323
Period size: 41 Copynumber: 6.8 Consensus size: 41
2498145 TTTGTAGAGA
* *
2498155 CGTTTTTAGAACAAACACCGCTAAAGACTCGTGATTTAGTGG
1 CGTTTTTA-TACAAACGCCGCTAAAGACTCGTGATTTAGTGG
** * * * *
2498197 AATTTTTATACAAACGCTGCTATAGACTCATGATTTTGTGG
1 CGTTTTTATACAAACGCCGCTAAAGACTCGTGATTTAGTGG
*
2498238 CGTTTTTATACAAATGCCGCTAAAGACTCGTGATTTAGTGG
1 CGTTTTTATACAAACGCCGCTAAAGACTCGTGATTTAGTGG
* * * * * *
2498279 CCTTTTTTTACAAACACCGCTAAATAATCATGATTTAGTGG
1 CGTTTTTATACAAACGCCGCTAAAGACTCGTGATTTAGTGG
* *
2498320 CGTTTTTATACAAACCCCGCTATAGACTCGT-ACTTTAGTGG
1 CGTTTTTATACAAACGCCGCTAAAGACTCGTGA-TTTAGTGG
*
2498361 CGTTTTTATACAAACGCCGCTAAAGACTCAT-ACTTTAGTGG
1 CGTTTTTATACAAACGCCGCTAAAGACTCGTGA-TTTAGTGG
* *
2498402 CGTTTGTGTTTACAAACGCCGCTATAGACTCGTG
1 CGTTT-T-TATACAAACGCCGCTAAAGACTCGTG
2498436 TTGCAATTGC
Statistics
Matches: 200, Mismatches: 35, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
40 1 0.00
41 170 0.85
42 7 0.04
43 22 0.11
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.34
Consensus pattern (41 bp):
CGTTTTTATACAAACGCCGCTAAAGACTCGTGATTTAGTGG
Found at i:2498316 original size:123 final size:125
Alignment explanation
Indices: 2498165--2498425 Score: 359
Period size: 123 Copynumber: 2.1 Consensus size: 125
2498155 CGTTTTTAGA
* * * *
2498165 ACAAACACCGCTAAAGACTCGTGATTTAGTGGAATTTTTATACAAACGCTGCTATAGACTCATGA
1 ACAAACACCGCTAAAGAATCATGATTTAGTGGAATTTTTATACAAACCCCGCTATAGACTCAT-A
* * *
2498230 -TTTTGTGGCGTTTTTATACAAATGCCGCTAAAGACTCGTGA-TTTAGTGGCCTTT-T-TTT
65 CTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCAT-ACTTTAGTGGCCTTTGTGTTT
* ** *
2498288 ACAAACACCGCTAAATAATCATGATTTAGTGGCGTTTTTATACAAACCCCGCTATAGACTCGTAC
1 ACAAACACCGCTAAAGAATCATGATTTAGTGGAATTTTTATACAAACCCCGCTATAGACTCATAC
*
2498353 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCGTTTGTGTTT
66 TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCCTTTGTGTTT
*
2498413 ACAAACGCCGCTA
1 ACAAACACCGCTA
2498426 TAGACTCGTG
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
122 2 0.02
123 103 0.85
124 1 0.01
125 15 0.12
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.33
Consensus pattern (125 bp):
ACAAACACCGCTAAAGAATCATGATTTAGTGGAATTTTTATACAAACCCCGCTATAGACTCATAC
TTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATACTTTAGTGGCCTTTGTGTTT
Found at i:2500358 original size:66 final size:66
Alignment explanation
Indices: 2500286--2500416 Score: 199
Period size: 66 Copynumber: 2.0 Consensus size: 66
2500276 GGATAGAAAA
* * *
2500286 TTTGATTCAATGTGAAGTTCCCTGCAAGTCTAGGTGAGGATGGTTTGCTGTTTCTGATTGATGCA
1 TTTGATTCAATGTGAAGATCCCTGCAAGTCTAGATGAGGATGGTTTACTGTTTCTGATTGATGCA
2500351 C
66 C
* * * *
2500352 TTTGATTCAATGTGAAGATCCTTTCAAGTCTAGATGAGGATGGTTTATTGTTTCTGATTGTTGCA
1 TTTGATTCAATGTGAAGATCCCTGCAAGTCTAGATGAGGATGGTTTACTGTTTCTGATTGATGCA
2500417 TTTAGCTTGG
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.21, C:0.13, G:0.25, T:0.40
Consensus pattern (66 bp):
TTTGATTCAATGTGAAGATCCCTGCAAGTCTAGATGAGGATGGTTTACTGTTTCTGATTGATGCA
C
Found at i:2505265 original size:21 final size:21
Alignment explanation
Indices: 2505239--2505283 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2505229 TAATAAAAAA
*
2505239 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATTAATATTT
2505260 TTATTTAAAATATTAATATTT
1 TTATTTAAAATATTAATATTT
2505281 TTA
1 TTA
2505284 ACATTTATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TTATTTAAAATATTAATATTT
Found at i:2509327 original size:12 final size:12
Alignment explanation
Indices: 2509310--2509336 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2509300 TCCAACCACC
2509310 AAAAAAATATAT
1 AAAAAAATATAT
2509322 AAAAAAATATAT
1 AAAAAAATATAT
2509334 AAA
1 AAA
2509337 TCTAAGACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAAAATATAT
Found at i:2510090 original size:2 final size:2
Alignment explanation
Indices: 2510083--2510110 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2510073 CATGTGTCAA
2510083 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
2510111 TAAAAATTAT
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:2512385 original size:13 final size:13
Alignment explanation
Indices: 2512367--2512392 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2512357 TAAATATATT
2512367 TTTATTTTTTTAA
1 TTTATTTTTTTAA
2512380 TTTATTTTTTTAA
1 TTTATTTTTTTAA
2512393 AATATCACAT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTATTTTTTTAA
Found at i:2512730 original size:2 final size:2
Alignment explanation
Indices: 2512723--2512758 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2512713 ATTTAAACTA
2512723 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
2512759 TAAAACTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2514841 original size:18 final size:19
Alignment explanation
Indices: 2514799--2514842 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2514789 TTTGGTTCAC
*
2514799 GGAATATAAGATTACCAGT
1 GGAATAAAAGATTACCAGT
*
2514818 GAGAATAAAAGATTACTAG-
1 G-GAATAAAAGATTACCAGT
2514837 GGAATA
1 GGAATA
2514843 GGATTACTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 2 0.09
20 15 0.68
ACGTcount: A:0.48, C:0.07, G:0.23, T:0.23
Consensus pattern (19 bp):
GGAATAAAAGATTACCAGT
Found at i:2515024 original size:38 final size:37
Alignment explanation
Indices: 2514989--2515059 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2514979 TACAAATTGT
2514989 AAAATATTTATAT-ATTTTCTTTAAAAAAATTAAATTC
1 AAAATATTTATATAATTTT-TTTAAAAAAATTAAATTC
* * *
2515026 ATAATATTTATATAATTTTTTTTACAAAATTAAA
1 AAAATATTTATATAATTTTTTTAAAAAAATTAAA
2515060 AATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
37 25 0.83
38 5 0.17
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (37 bp):
AAAATATTTATATAATTTTTTTAAAAAAATTAAATTC
Found at i:2516799 original size:2 final size:2
Alignment explanation
Indices: 2516792--2516818 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2516782 ACAAACGAGT
2516792 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2516819 GATCCTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2543629 original size:6 final size:6
Alignment explanation
Indices: 2543618--2543650 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
2543608 TGCCCATAAC
2543618 TTCAAA TTCAAA TTCAAA TTCAAA TTCAAA TTC
1 TTCAAA TTCAAA TTCAAA TTCAAA TTCAAA TTC
2543651 GGTGTCTCGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (6 bp):
TTCAAA
Found at i:2548544 original size:18 final size:18
Alignment explanation
Indices: 2548521--2548555 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2548511 TTTTGCAGCC
2548521 AAATGAAA-TGGGAAAAAT
1 AAATGAAACT-GGAAAAAT
2548539 AAATGAAACTGGAAAAA
1 AAATGAAACTGGAAAAA
2548556 GCAACCTACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.63, C:0.03, G:0.20, T:0.14
Consensus pattern (18 bp):
AAATGAAACTGGAAAAAT
Found at i:2550995 original size:181 final size:182
Alignment explanation
Indices: 2550649--2551121 Score: 675
Period size: 181 Copynumber: 2.6 Consensus size: 182
2550639 GATCCAAATT
* * * * *
2550649 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAATCGGTATCA-AAATGAT
* * * * *
2550713 AAAACCGGTAAAGC-TCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAATGATCGACACT
65 AAAACCGGTAAAACGT-TACCGGATATATTAAAAGTGTCGATACTTTAATACAATGATCGACACT
* * *
2550777 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
129 TCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
2550831 AAAAATGTATCGATCCAAAACGATATACCATGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAATCGGTATCAAAATGATA
*
2550896 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATACAATGATCGACACTTT
66 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTTAATACAATGATCGACACTTC
** *
2550960 GTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
2551012 AAAAATATATCGATCCACAACGATATAACATGTAAAAATATGAT-AAATCCGGTATCAAAATGGT
1 AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAAT-CGGTATCAAAATGAT
* * *
2551076 AAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
65 AAAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT
2551122 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 25, Indels: 7
0.89 0.08 0.02
Matches are distributed among these distances:
180 4 0.02
181 161 0.61
182 96 0.37
183 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACATGTAAAAATATGATAAAATCGGTATCAAAATGATA
AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTTAATACAATGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:2553334 original size:21 final size:21
Alignment explanation
Indices: 2553308--2553372 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
2553298 AAGACAATCA
*
2553308 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
2553329 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
2553350 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
2553371 AG
1 AG
2553373 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.42, C:0.11, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:2553448 original size:33 final size:33
Alignment explanation
Indices: 2553406--2553471 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
2553396 AAATAGATGG
*
2553406 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
2553439 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
2553472 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:2555438 original size:23 final size:23
Alignment explanation
Indices: 2555407--2555479 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2555397 ATAGGTAAAA
* *
2555407 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGTTT
*
2555430 ATATAATGTAATACGTAGCGTTT
1 ATATAATGTAATAGGTAGCGTTT
*
2555453 ATATAATGTAATAGGTAGTGTTT
1 ATATAATGTAATAGGTAGCGTTT
2555476 ATAT
1 ATAT
2555480 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGTTT
Found at i:2561659 original size:2 final size:2
Alignment explanation
Indices: 2561652--2561685 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2561642 TTTCATATTC
2561652 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
2561686 TACAGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2570446 original size:2 final size:2
Alignment explanation
Indices: 2570441--2570508 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
2570431 AAAAATAATA
2570441 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
2570483 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
2570509 CGATAAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2575300 original size:23 final size:22
Alignment explanation
Indices: 2575256--2575300 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2575246 AATCTCATAG
*
2575256 GGGAACCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
*
2575278 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
2575301 AAAATGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:2576145 original size:31 final size:31
Alignment explanation
Indices: 2576103--2576227 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
2576093 AGGGTCGAGG
*
2576103 GTTTACATATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2576134 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
2576165 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
2576196 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
2576227 G
1 G
2576228 GTCATTTGGG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 88 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:2576721 original size:21 final size:21
Alignment explanation
Indices: 2576696--2576738 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
2576686 AAAGAATATA
2576696 TTGTATAA-GCTCTGAATAATT
1 TTGTA-AATGCTCTGAATAATT
* *
2576717 TTGTAAATGTTTTGAATAATT
1 TTGTAAATGCTCTGAATAATT
2576738 T
1 T
2576739 AAATGTTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.49
Consensus pattern (21 bp):
TTGTAAATGCTCTGAATAATT
Found at i:2578346 original size:2 final size:2
Alignment explanation
Indices: 2578339--2578368 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2578329 GTTGCAATGA
2578339 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
2578369 GTGTGTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2578908 original size:30 final size:32
Alignment explanation
Indices: 2578851--2578910 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
2578841 CTCCTCCGCC
*
2578851 TAGCTCTCCTCCTCCAGCAACTCCCCCACCCGT
1 TAGCTCTCCTCCTCCAGC-ACTACCCCACCCGT
*
2578884 TAGCTCTCCTCCTCCTGC-C-ACCCCACC
1 TAGCTCTCCTCCTCCAGCACTACCCCACC
2578911 TCCCGCCACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 7 0.28
31 1 0.04
33 17 0.68
ACGTcount: A:0.13, C:0.57, G:0.08, T:0.22
Consensus pattern (32 bp):
TAGCTCTCCTCCTCCAGCACTACCCCACCCGT
Found at i:2578940 original size:30 final size:30
Alignment explanation
Indices: 2578906--2579048 Score: 115
Period size: 30 Copynumber: 4.8 Consensus size: 30
2578896 TCCTGCCACC
* * *
2578906 CCACCTCCCGCCACTCCTCCCCCGGCTTCT
1 CCACCTCCCGCCACCCCACCACCGGCTTCT
* *
2578936 CCACCTCCCGCAACCCCACCACCTGCTTCT
1 CCACCTCCCGCCACCCCACCACCGGCTTCT
* * * * *
2578966 TCTCCTCCCGCCACTCCACCACCCGCCTCT
1 CCACCTCCCGCCACCCCACCACCGGCTTCT
* * * **
2578996 CCGCCTCCCGCTACCCCTCCACCGGCAACT
1 CCACCTCCCGCCACCCCACCACCGGCTTCT
* * * *
2579026 CCTCCTCCTGCAACCACACCACC
1 CCACCTCCCGCCACCCCACCACC
2579049 TGCTCCTTTG
Statistics
Matches: 89, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 89 1.00
ACGTcount: A:0.13, C:0.62, G:0.08, T:0.17
Consensus pattern (30 bp):
CCACCTCCCGCCACCCCACCACCGGCTTCT
Found at i:2578992 original size:15 final size:15
Alignment explanation
Indices: 2578889--2579006 Score: 67
Period size: 15 Copynumber: 7.9 Consensus size: 15
2578879 CCCGTTAGCT
* *
2578889 CTCCTCCTCCTGCCA
1 CTCCACCTCCCGCCA
*
2578904 CCCCACCTCCCGCCA
1 CTCCACCTCCCGCCA
* **
2578919 CTCCTCC-CCCGGCTT
1 CTCCACCTCCC-GCCA
*
2578934 CTCCACCTCCCGCAA
1 CTCCACCTCCCGCCA
* * * **
2578949 CCCCACCACCTGCTT
1 CTCCACCTCCCGCCA
* *
2578964 CTTCTCCTCCCGCCA
1 CTCCACCTCCCGCCA
* *
2578979 CTCCACCACCCGCCT
1 CTCCACCTCCCGCCA
*
2578994 CTCCGCCTCCCGC
1 CTCCACCTCCCGC
2579007 TACCCCTCCA
Statistics
Matches: 73, Mismatches: 28, Indels: 4
0.70 0.27 0.04
Matches are distributed among these distances:
14 3 0.04
15 67 0.92
16 3 0.04
ACGTcount: A:0.09, C:0.64, G:0.08, T:0.19
Consensus pattern (15 bp):
CTCCACCTCCCGCCA
Found at i:2579031 original size:60 final size:60
Alignment explanation
Indices: 2578909--2579033 Score: 153
Period size: 60 Copynumber: 2.1 Consensus size: 60
2578899 TGCCACCCCA
* * * ** *
2578909 CCTCCCGCCACTCCTCCCCCGGCTTCTCCACCTCCCGCAACCCCACCACCTGCTTCTTCT
1 CCTCCCGCCACTCCACCCCCGGCCTCTCCACCTCCCGCAACCCCACCACCGGCAACTCCT
* * *
2578969 CCTCCCGCCACTCCACCACCC-GCCTCTCCGCCTCCCGCTACCCCTCCACCGGCAACTCCT
1 CCTCCCGCCACTCCACC-CCCGGCCTCTCCACCTCCCGCAACCCCACCACCGGCAACTCCT
2579029 CCTCC
1 CCTCC
2579034 TGCAACCACA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 52 0.95
61 3 0.05
ACGTcount: A:0.10, C:0.62, G:0.09, T:0.18
Consensus pattern (60 bp):
CCTCCCGCCACTCCACCCCCGGCCTCTCCACCTCCCGCAACCCCACCACCGGCAACTCCT
Found at i:2579046 original size:60 final size:60
Alignment explanation
Indices: 2578909--2579048 Score: 140
Period size: 60 Copynumber: 2.3 Consensus size: 60
2578899 TGCCACCCCA
* * * * ** *
2578909 CCTCCCGCCACTCCTCC-CCCGGCTTCTCCACCTCCCGCAACCCCACCACCTGCTTCTTCT
1 CCTCCCGCAACTCCACCACCC-GCCTCTCCACCTCCCGCAACCCCACCACCGGCAACTCCT
* * * *
2578969 CCTCCCGCCACTCCACCACCCGCCTCTCCGCCTCCCGCTACCCCTCCACCGGCAACTCCT
1 CCTCCCGCAACTCCACCACCCGCCTCTCCACCTCCCGCAACCCCACCACCGGCAACTCCT
*
2579029 CCTCCTGCAAC-CACACCACC
1 CCTCCCGCAACTC-CACCACC
2579049 TGCTCCTTTG
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
59 1 0.01
60 63 0.94
61 3 0.04
ACGTcount: A:0.13, C:0.61, G:0.09, T:0.17
Consensus pattern (60 bp):
CCTCCCGCAACTCCACCACCCGCCTCTCCACCTCCCGCAACCCCACCACCGGCAACTCCT
Found at i:2585804 original size:12 final size:12
Alignment explanation
Indices: 2585765--2585794 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
2585755 GTAGCATTTG
*
2585765 ATATTTTTATAA
1 ATATATTTATAA
2585777 ATATATTTATAA
1 ATATATTTATAA
2585789 ATATAT
1 ATATAT
2585795 ATATTTATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATTTATAA
Found at i:2587348 original size:33 final size:33
Alignment explanation
Indices: 2587309--2587372 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
2587299 CACCTATAAC
*
2587309 GTGAGTCTATCCCTACTGTAGATATAACTATGA
1 GTGAGTCTATCCCTACTATAGATATAACTATGA
*
2587342 GTGAGTCTATCTCTACTATAGATATAACTAT
1 GTGAGTCTATCCCTACTATAGATATAACTAT
2587373 TCAAATACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (33 bp):
GTGAGTCTATCCCTACTATAGATATAACTATGA
Found at i:2597838 original size:23 final size:23
Alignment explanation
Indices: 2597812--2597860 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
2597802 GTACCAAAAG
*
2597812 GCAGAAGAAAACATGTCATACAA
1 GCAGAAGAAAACATATCATACAA
* *
2597835 GCAGAGGAAAACATATCATATAA
1 GCAGAAGAAAACATATCATACAA
2597858 GCA
1 GCA
2597861 AACTTATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.51, C:0.16, G:0.18, T:0.14
Consensus pattern (23 bp):
GCAGAAGAAAACATATCATACAA
Found at i:2598669 original size:6 final size:6
Alignment explanation
Indices: 2598660--2598722 Score: 58
Period size: 6 Copynumber: 10.5 Consensus size: 6
2598650 GTACAATTGG
* * *
2598660 AATTAT AATTAT TA-TA- AATATAT TATTAA AATTAT AATTAT AATTAT
1 AATTAT AATTAT AATTAT AAT-TAT AATTAT AATTAT AATTAT AATTAT
*
2598707 AATTAAT CATTAT AAT
1 AATT-AT AATTAT AAT
2598723 AAAAAATATG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
4 1 0.02
5 2 0.04
6 35 0.78
7 7 0.16
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (6 bp):
AATTAT
Found at i:2598686 original size:14 final size:14
Alignment explanation
Indices: 2598667--2598707 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
2598657 TGGAATTATA
2598667 ATTATTATAAATAT
1 ATTATTATAAATAT
2598681 ATTATTA-AAAT-T
1 ATTATTATAAATAT
* *
2598693 ATAATTATAATTAT
1 ATTATTATAAATAT
2598707 A
1 A
2598708 ATTAATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 7 0.30
13 7 0.30
14 9 0.39
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATTATAAATAT
Found at i:2604512 original size:228 final size:224
Alignment explanation
Indices: 2604117--2604568 Score: 690
Period size: 228 Copynumber: 2.0 Consensus size: 224
2604107 GTATGATTTG
* * *
2604117 CGATTTGTCGGTGGTATTTTAGTAGCTTGATCCCATTTTATGGTTCATTTGCCGATACGATCAGA
1 CGATTTGTCGGTGGTATTTCAGTAGCTTGATCCCATTTTATGGTTCATTTACCGATACGATAAGA
*
2604182 TATGTTTGAACATATATCTTTGTTCGAATTTTCTTGGTTAGATTTTAAACTTTCCTTGTACGGTC
66 TATGTTTGAACATATATATTTGTTCGAATTTTCTTGGTTAGATTTTAAACTTTCCTTGTACGGTC
* *
2604247 CTTAAGTGATCTTAAGTTGGTAGTTTTGTTTCAATTATTATAGGAAATTGTCCTAATTATGTGGT
131 CTTAAGTGATCTTAAGTTGGTAGTTTTGTTCCAATTATTATAGGAAATTGTCCTAATTATGTGCT
2604312 TAATTTACAATTATAATTATAAATTTTTA
196 TAATTTACAATTATAATTATAAATTTTTA
* *** * *
2604341 CGATTTGTCGGTGGTCTTTCAGTAGCTTGATCTTTTTTTATGGTTCGTTTACCGATGCGATAAGA
1 CGATTTGTCGGTGGTATTTCAGTAGCTTGATCCCATTTTATGGTTCATTTACCGATACGATAAGA
* * *
2604406 TATGTTTGTATATATATATATATTTGTTCGAGTTTTCTTGGTTAGATTTTAATCTTT-CTCTGTA
66 TATGTTTG---A-ACATATATATTTGTTCGAATTTTCTTGGTTAGATTTTAAACTTTCCT-TGTA
* *
2604470 CGTTCCTTAAGTGATCTTAAGTTGGTAGTTTTGTTCCAATTATTATAGGAAATTGTCTTAATTAT
126 CGGTCCTTAAGTGATCTTAAGTTGGTAGTTTTGTTCCAATTATTATAGGAAATTGTCCTAATTAT
*
2604535 GTGCTTAATTTACGATTATAATTATAAATTTTTA
191 GTGCTTAATTTACAATTATAATTATAAATTTTTA
2604569 TCAATTTAAA
Statistics
Matches: 205, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
224 64 0.31
227 3 0.01
228 138 0.67
ACGTcount: A:0.25, C:0.11, G:0.17, T:0.47
Consensus pattern (224 bp):
CGATTTGTCGGTGGTATTTCAGTAGCTTGATCCCATTTTATGGTTCATTTACCGATACGATAAGA
TATGTTTGAACATATATATTTGTTCGAATTTTCTTGGTTAGATTTTAAACTTTCCTTGTACGGTC
CTTAAGTGATCTTAAGTTGGTAGTTTTGTTCCAATTATTATAGGAAATTGTCCTAATTATGTGCT
TAATTTACAATTATAATTATAAATTTTTA
Found at i:2608301 original size:21 final size:21
Alignment explanation
Indices: 2608277--2608316 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2608267 TTATTTGGGG
* *
2608277 TTTATGGTTTTAATATTATAA
1 TTTATGATTTTAAGATTATAA
2608298 TTTATGATTTTAAGATTAT
1 TTTATGATTTTAAGATTAT
2608317 TAAGATTTAA
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:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (21 bp):
TTTATGATTTTAAGATTATAA
Found at i:2609539 original size:21 final size:21
Alignment explanation
Indices: 2609513--2609553 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2609503 TAACAGACGG
2609513 AGCAATGGCGGCAGCCTCCGA
1 AGCAATGGCGGCAGCCTCCGA
2609534 AGCAATGGCGGCAGCCTCCG
1 AGCAATGGCGGCAGCCTCCG
2609554 GATGCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.22, C:0.34, G:0.34, T:0.10
Consensus pattern (21 bp):
AGCAATGGCGGCAGCCTCCGA
Found at i:2612228 original size:32 final size:34
Alignment explanation
Indices: 2612187--2612266 Score: 101
Period size: 35 Copynumber: 2.4 Consensus size: 34
2612177 TTTAAATAGT
*
2612187 TATTATTTTTTATATT-AAT-ATATTTATGTAAA
1 TATTATTTTTTATATTAAATAATATTTATATAAA
* *
2612219 TATTATTTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTATATT-AAATAATATTTATATAAA
2612254 TATTATTTATTTA
1 TATTATTT-TTTA
2612267 GAATTATTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 15 0.38
34 3 0.08
35 19 0.47
36 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (34 bp):
TATTATTTTTTATATTAAATAATATTTATATAAA
Found at i:2612230 original size:34 final size:33
Alignment explanation
Indices: 2612154--2612261 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 33
2612144 GTGGTAAGAA
* *
2612154 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
2612188 ATTATTTTTTATATTAATATATTTATGTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
2612223 ATTTTTTTTATTAAAATAATATTTATATAATTATT
1 ATTTTTTTTATT-TAAT-ATATTTATATAAATATT
2612258 ATTT
1 ATTT
2612262 ATTTAGAATT
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
33 1 0.02
34 27 0.43
35 28 0.44
36 7 0.11
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:2614031 original size:21 final size:21
Alignment explanation
Indices: 2614001--2614048 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2613991 GCAGGGGTAC
* *
2614001 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2614022 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2614043 ATGCCA
1 ATGCCA
2614049 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2614076 original size:21 final size:21
Alignment explanation
Indices: 2614052--2614145 Score: 93
Period size: 21 Copynumber: 4.5 Consensus size: 21
2614042 TATGCCATCT
* *
2614052 CCGCAGGGTTATATTTCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
2614073 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* *
2614094 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
* *
2614115 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCGAGC
2614136 CCGCAGGGTT
1 CCGCAGGGTT
2614146 TTATACCATA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
20 2 0.03
21 63 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:2614727 original size:33 final size:34
Alignment explanation
Indices: 2614668--2614754 Score: 113
Period size: 33 Copynumber: 2.6 Consensus size: 34
2614658 AAATGTTTTT
*
2614668 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
2614702 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
2614735 AAAATATAAATTATAGTATT
1 AAAATAAAAATTATATTATT
2614755 GATATGAGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 27 0.59
34 19 0.41
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:2618495 original size:28 final size:28
Alignment explanation
Indices: 2618435--2618497 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
2618425 TTGATTAATA
2618435 AAATATATTAAAATTATTTTATATTGAAT
1 AAATA-ATTAAAATTATTTTATATTGAAT
*
2618464 -AATAATTAAAAGTCTA-TTTATATT-ACT
1 AAATAATTAAAA-T-TATTTTATATTGAAT
2618491 AAATAAT
1 AAATAAT
2618498 ATATATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
27 9 0.30
28 19 0.63
29 2 0.07
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (28 bp):
AAATAATTAAAATTATTTTATATTGAAT
Found at i:2625021 original size:18 final size:17
Alignment explanation
Indices: 2624988--2625033 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
2624978 AACTTAAAGT
*
2624988 ATTTTTTTAATATTTTA
1 ATTTTTTAAATATTTTA
*
2625005 ATATTTTTAAATCTTTTA
1 AT-TTTTTAAATATTTTA
2625023 ATTCTTTTAAA
1 ATT-TTTTAAA
2625034 AAAAATTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (17 bp):
ATTTTTTAAATATTTTA
Found at i:2625495 original size:20 final size:20
Alignment explanation
Indices: 2625472--2625542 Score: 133
Period size: 20 Copynumber: 3.5 Consensus size: 20
2625462 CACGGAATGT
*
2625472 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTTGGAATAA
2625492 AAGATTACCAGTTGGAATAA
1 AAGATTACCAGTTGGAATAA
2625512 AAGATTACCAGTTGGAATAA
1 AAGATTACCAGTTGGAATAA
2625532 AAGATTACCAG
1 AAGATTACCAG
2625543 GGAATATGAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (20 bp):
AAGATTACCAGTTGGAATAA
Found at i:2629862 original size:2 final size:2
Alignment explanation
Indices: 2629857--2629883 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2629847 TCGTCTTTGT
2629857 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2629884 TTATGTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2631272 original size:34 final size:36
Alignment explanation
Indices: 2631196--2631272 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 36
2631186 AATGATAATA
*
2631196 AACAAAA-TTAACCAAAATATATTAACAAAAAGTCC
1 AACAAAATTTAACCAAAATAAATTAACAAAAAGTCC
*
2631231 AAC-AAATTTAA-CAAGATAAATTAA-AATAAA-TCC
1 AACAAAATTTAACCAAAATAAATTAACAA-AAAGTCC
2631264 AACAAAATT
1 AACAAAATT
2631273 ATTGAAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
33 8 0.22
34 22 0.59
35 7 0.19
ACGTcount: A:0.61, C:0.14, G:0.03, T:0.22
Consensus pattern (36 bp):
AACAAAATTTAACCAAAATAAATTAACAAAAAGTCC
Found at i:2633840 original size:31 final size:31
Alignment explanation
Indices: 2633656--2633827 Score: 317
Period size: 31 Copynumber: 5.5 Consensus size: 31
2633646 GGGTCGAGGG
2633656 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2633687 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2633718 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
2633749 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
2633780 TTACCTATGTTCTTCGGAACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
2633811 TTACCTAGGTTCTTCGG
1 TTACCTATGTTCTTCGG
2633828 AATCTATAGA
Statistics
Matches: 138, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 138 1.00
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:2636043 original size:17 final size:18
Alignment explanation
Indices: 2636014--2636061 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
2636004 TGCAAAAAAA
*
2636014 TTAATTAAA-TAAAATA-
1 TTAAATAAATTAAAATAC
*
2636030 TTAAA-AAATTTAAATAC
1 TTAAATAAATTAAAATAC
2636047 TTAAATAAATTAAAA
1 TTAAATAAATTAAAA
2636062 ACAAAATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 5 0.19
18 8 0.31
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
TTAAATAAATTAAAATAC
Found at i:2641220 original size:23 final size:23
Alignment explanation
Indices: 2641188--2641232 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2641178 CATATACAAA
* *
2641188 TTTTTGAAAACGTTTTCAAAATG
1 TTTTTAAAAACATTTTCAAAATG
2641211 TTTTTAAAAACATTTTCAAAAT
1 TTTTTAAAAACATTTTCAAAAT
2641233 ATTATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (23 bp):
TTTTTAAAAACATTTTCAAAATG
Found at i:2641341 original size:38 final size:38
Alignment explanation
Indices: 2641231--2641430 Score: 248
Period size: 38 Copynumber: 5.2 Consensus size: 38
2641221 CATTTTCAAA
* *
2641231 ATATTATATATTTATTTTCAAAAATATTTTCAAAAGCTAT
1 ATATTATATA--TATTTTCAAAAATGTTTTCAAAAACTAT
2641271 ATATTATATATATATTTTC-AAAATGTTTTCAAAAACTAT
1 ATA-T-TATATATATTTTCAAAAATGTTTTCAAAAACTAT
2641310 ATATTATATATATTTTCAAAAATGTTTTCAAAAACTAT
1 ATATTATATATATTTTCAAAAATGTTTTCAAAAACTAT
2641348 ATATTATATATACGTTTTCAAAAA--TTTTC-AAAACTAT
1 ATATTATATATA--TTTTCAAAAATGTTTTCAAAAACTAT
* **
2641385 ATAATATATATATTTTCGAAAACCGTTTTC-AAAACTAT
1 ATATTATATATATTTTC-AAAAATGTTTTCAAAAACTAT
*
2641423 ACATTATA
1 ATATTATA
2641431 AAAAAACTCC
Statistics
Matches: 146, Mismatches: 6, Indels: 18
0.86 0.04 0.11
Matches are distributed among these distances:
35 5 0.03
36 4 0.03
37 32 0.22
38 57 0.39
39 21 0.14
40 20 0.14
41 1 0.01
42 6 0.04
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (38 bp):
ATATTATATATATTTTCAAAAATGTTTTCAAAAACTAT
Found at i:2641393 original size:75 final size:76
Alignment explanation
Indices: 2641212--2641430 Score: 277
Period size: 77 Copynumber: 2.9 Consensus size: 76
2641202 TTCAAAATGT
* * * *
2641212 TTTTAAAAACATTTTCAAAA-TAT-T-ATATATTTATTTTCAAAAATATTTTCAAAAGCTATATA
1 TTTTCAAAACATTTTCAAAACTATATAATATATATATTTTCAAAAATGTTTTCAAAAACTATATA
*
2641274 TTATATATATA
66 TTATATATACA
** *
2641285 TTTTCAAAATGTTTTCAAAAACTATATATTATATATATTTTCAAAAATGTTTTCAAAAACTATAT
1 TTTTCAAAACATTTTC-AAAACTATATAATATATATATTTTCAAAAATGTTTTCAAAAACTATAT
*
2641350 ATTATATATACG
65 ATTATATATACA
** *
2641362 TTTTCAAAA-ATTTTCAAAACTATATAATATATATATTTTCGAAAACCGTTTTC-AAAACTATAC
1 TTTTCAAAACATTTTCAAAACTATATAATATATATATTTTC-AAAAATGTTTTCAAAAACTATAT
2641425 ATTATA
65 ATTATA
2641431 AAAAAACTCC
Statistics
Matches: 127, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
73 13 0.10
74 4 0.03
75 42 0.33
76 16 0.13
77 52 0.41
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.44
Consensus pattern (76 bp):
TTTTCAAAACATTTTCAAAACTATATAATATATATATTTTCAAAAATGTTTTCAAAAACTATATA
TTATATATACA
Found at i:2643484 original size:25 final size:25
Alignment explanation
Indices: 2643455--2643512 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
2643445 AGAAGCATAG
2643455 CAAAATGGTTGATAAATTATTGAAC
1 CAAAATGGTTGATAAATTATTGAAC
2643480 CAAAATGGTTGATAAATTATTGAAC
1 CAAAATGGTTGATAAATTATTGAAC
2643505 CAAAATGG
1 CAAAATGG
2643513 CAGAAATAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (25 bp):
CAAAATGGTTGATAAATTATTGAAC
Found at i:2657493 original size:2 final size:2
Alignment explanation
Indices: 2657486--2657524 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
2657476 GTCACAACTC
*
2657486 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CA CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2657525 GTTATCTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.03, C:0.51, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:2660363 original size:20 final size:20
Alignment explanation
Indices: 2660340--2660403 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 20
2660330 TTCTAAATCA
*
2660340 CAACACGAATTTTGTTTTCG
1 CAACACGAATTTTATTTTCG
*
2660360 CAACACGAATTTTAATTTCG
1 CAACACGAATTTTATTTTCG
* *
2660380 TAACA--ACTTTTATTTTCG
1 CAACACGAATTTTATTTTCG
2660398 CAACAC
1 CAACAC
2660404 AAATGTTTTG
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
18 15 0.41
20 22 0.59
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (20 bp):
CAACACGAATTTTATTTTCG
Found at i:2660536 original size:14 final size:15
Alignment explanation
Indices: 2660517--2660555 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
2660507 TCCCAATCTC
2660517 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
2660531 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
2660547 TAATTTTTT
1 TAATTTTTT
2660556 CGATGATTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 5 0.23
16 10 0.45
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:2661169 original size:12 final size:12
Alignment explanation
Indices: 2661148--2661181 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2661138 ACCATATTTC
*
2661148 CAATACCAAACA
1 CAATATCAAACA
2661160 CAATATCAAACA
1 CAATATCAAACA
*
2661172 CAATCTCAAA
1 CAATATCAAA
2661182 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:2661338 original size:24 final size:24
Alignment explanation
Indices: 2661311--2661360 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
2661301 TTGAAATTTA
*
2661311 ATCTTGGTCAATACTCGGACTTTG
1 ATCTTGGTCAATACTCAGACTTTG
*
2661335 ATCTTGGTCAATACTCAGATTTTG
1 ATCTTGGTCAATACTCAGACTTTG
2661359 AT
1 AT
2661361 GATGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (24 bp):
ATCTTGGTCAATACTCAGACTTTG
Found at i:2661543 original size:3 final size:3
Alignment explanation
Indices: 2661535--2661568 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2661525 ATATAACCCT
2661535 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2661569 TCTACGGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:2663660 original size:18 final size:18
Alignment explanation
Indices: 2663637--2663672 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2663627 AAGCAAAAGG
*
2663637 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
2663655 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
2663673 CATCCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:2663959 original size:20 final size:20
Alignment explanation
Indices: 2663921--2663961 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2663911 TTGCGAAAGA
* *
2663921 CAAATTCGCAACGCGAAAAT
1 CAAATTCACAACGCAAAAAT
*
2663941 CAAATTCACAAGGCAAAAAT
1 CAAATTCACAACGCAAAAAT
2663961 C
1 C
2663962 GCAACGCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.24, G:0.12, T:0.15
Consensus pattern (20 bp):
CAAATTCACAACGCAAAAAT
Found at i:2664216 original size:20 final size:20
Alignment explanation
Indices: 2664177--2664218 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2664167 ATTGCGAAAG
*
2664177 TCAAATTCGCAACGCGAAAA
1 TCAAATTCGCAACGCAAAAA
* *
2664197 TCAAATTCGTAAGGCAAAAA
1 TCAAATTCGCAACGCAAAAA
2664217 TC
1 TC
2664219 GCAACGCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.21, G:0.14, T:0.19
Consensus pattern (20 bp):
TCAAATTCGCAACGCAAAAA
Found at i:2664298 original size:257 final size:258
Alignment explanation
Indices: 2663837--2664343 Score: 872
Period size: 257 Copynumber: 2.0 Consensus size: 258
2663827 CAATTATCAT
* *
2663837 ATTGTTGTCTGTTATCTTTTTGAAGGTGTTTTCCTTGAATTCGCAACTCGAAAGTCAAATTCACG
1 ATTGTTGTCTGTTATCTTTTTGAAGGTGTTTTCCTTGAATTCGCAACGCGAAAGTCAAATTCACA
*
2663902 TTGCGATTGTTGCGAAAGACAAATTCGCAACGCGAAAATCAAATTCACAAGGCAAAAATCGCAAC
66 TTGCGATTATTGCGAAAGACAAATTCGCAACGCGAAAATCAAATTCACAAGGCAAAAATCGCAAC
* * *
2663967 GCAAATTTGACTTTCGCGTTGCGAAAGTGTACCTTTAATATGTCTTTTTTGTCTTCAACATAATG
131 GCAAATTTGACTTTCGCGTTGCGAAAGTGTACCTTCAACATGTCTTTTTTGCCTTCAACATAATG
* *
2664032 CATATTGAAATTAAACAACAAATCAATTAAAC-AAAAAAATAATTCTTATTTACACTTATTAG
196 CAGATTGAAATTAAACAACAAATCAATTAAACAAAAAAAACAATTCTTATTTACACTTATTAG
*
2664094 ATTGTTGTCTGTTATCTTTTTGAAGGTGTTTTTCTTGAATTCGCAACGCGAAAGTCAAATTCACA
1 ATTGTTGTCTGTTATCTTTTTGAAGGTGTTTTCCTTGAATTCGCAACGCGAAAGTCAAATTCACA
* **
2664159 TTGCGATTATTGCGAAAGTCAAATTCGCAACGCGAAAATCAAATTCGTAAGGCAAAAATCGCAAC
66 TTGCGATTATTGCGAAAGACAAATTCGCAACGCGAAAATCAAATTCACAAGGCAAAAATCGCAAC
* * *
2664224 GCAAATTTGATTTTCGCGTTTCGAAAGTGTACCTTCAACATGTCTTTTTTGCCTTCAATATAATG
131 GCAAATTTGACTTTCGCGTTGCGAAAGTGTACCTTCAACATGTCTTTTTTGCCTTCAACATAATG
2664289 CAGATTGAAATTAAACAACAAATCAATTAAACAAAAAAAACAATTCTTATTTACA
196 CAGATTGAAATTAAACAACAAATCAATTAAACAAAAAAAACAATTCTTATTTACA
2664344 TTTGACAACA
Statistics
Matches: 234, Mismatches: 15, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
257 213 0.91
258 21 0.09
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (258 bp):
ATTGTTGTCTGTTATCTTTTTGAAGGTGTTTTCCTTGAATTCGCAACGCGAAAGTCAAATTCACA
TTGCGATTATTGCGAAAGACAAATTCGCAACGCGAAAATCAAATTCACAAGGCAAAAATCGCAAC
GCAAATTTGACTTTCGCGTTGCGAAAGTGTACCTTCAACATGTCTTTTTTGCCTTCAACATAATG
CAGATTGAAATTAAACAACAAATCAATTAAACAAAAAAAACAATTCTTATTTACACTTATTAG
Found at i:2665775 original size:21 final size:21
Alignment explanation
Indices: 2665752--2665848 Score: 131
Period size: 21 Copynumber: 4.6 Consensus size: 21
2665742 GTGAATCGGG
* *
2665752 CTCTTGAACGGTGGGAGGGGG
1 CTCTTGAACGATGGGAGGGGC
* *
2665773 CTCTTGAATGGTGGGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
*
2665794 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGGGAGGGGC
* *
2665815 CTCTTGAACGATAGAAGGGGC
1 CTCTTGAACGATGGGAGGGGC
2665836 CTCTTGAACGATG
1 CTCTTGAACGATG
2665849 ACATGTGAAT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 67 1.00
ACGTcount: A:0.21, C:0.18, G:0.40, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGGGAGGGGC
Found at i:2666023 original size:4 final size:4
Alignment explanation
Indices: 2665993--2666034 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
2665983 AGGCCGCTAA
* * *
2665993 AAAT AAAT TAAT ACAT AAAT CAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2666035 TGCCGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:2666169 original size:21 final size:21
Alignment explanation
Indices: 2666145--2666184 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2666135 GTAGAGCGGC
*
2666145 TACCTCATCACGTAAAGTAGA
1 TACCTCACCACGTAAAGTAGA
2666166 TACCTCACCACGTAAAGTA
1 TACCTCACCACGTAAAGTA
2666185 CCATTGTCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.23
Consensus pattern (21 bp):
TACCTCACCACGTAAAGTAGA
Found at i:2666281 original size:21 final size:21
Alignment explanation
Indices: 2666257--2666299 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
2666247 ACCATTGTCG
*
2666257 TCACGAAAAGTACCGACCTCA
1 TCACGAAAAGAACCGACCTCA
* *
2666278 TCACGCAAAGAACTGACCTCA
1 TCACGAAAAGAACCGACCTCA
2666299 T
1 T
2666300 TACGTAACTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.33, G:0.14, T:0.16
Consensus pattern (21 bp):
TCACGAAAAGAACCGACCTCA
Found at i:2666468 original size:42 final size:42
Alignment explanation
Indices: 2666421--2666519 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
2666411 GTGATGGAAT
* * * * *
2666421 AGGTGATGGCTCTCGTTGT-AGAGGTGTATAATTGGCTCGATC
1 AGGTGATGGCTCTCGGTGTCA-AGCTGTAGAATCGACTCGATC
* *
2666463 AGGTGATGTCTCTGGGTGTCAAGCTGTAGAATCGACTCGATC
1 AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
2666505 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
2666520 AAGTGGGGGG
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
42 46 0.98
43 1 0.02
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.30
Consensus pattern (42 bp):
AGGTGATGGCTCTCGGTGTCAAGCTGTAGAATCGACTCGATC
Found at i:2671098 original size:20 final size:19
Alignment explanation
Indices: 2671075--2671114 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2671065 CTTAAATTCT
2671075 CAACACGAAAATGAAAATCG
1 CAACACGAAAAT-AAAATCG
* *
2671095 CAACGCGAAACTAAAATCG
1 CAACACGAAAATAAAATCG
2671114 C
1 C
2671115 GTTGCGATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
CAACACGAAAATAAAATCG
Found at i:2672121 original size:18 final size:18
Alignment explanation
Indices: 2672073--2672126 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
2672063 AAATTCCAAT
*
2672073 TATTTGTTTAATTTATAAA
1 TATTTTTTTAATTT-TAAA
*
2672092 T-TTTATTATAATTTTAAA
1 TATTT-TTTTAATTTTAAA
2672110 TATTTTTTTAATTTTAA
1 TATTTTTTTAATTTTAA
2672127 TAAAATTAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 19 0.63
19 11 0.37
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TATTTTTTTAATTTTAAA
Found at i:2679073 original size:21 final size:21
Alignment explanation
Indices: 2679048--2679087 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
2679038 GTATTAAATT
*
2679048 ATAATTATAATAAAATATAAA
1 ATAATTAAAATAAAATATAAA
*
2679069 ATAATTAAAATCAAATATA
1 ATAATTAAAATAAAATATA
2679088 TAATTATATA
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:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATTAAAATAAAATATAAA
Found at i:2679077 original size:16 final size:17
Alignment explanation
Indices: 2679040--2679093 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 17
2679030 AATTTATAGT
* *
2679040 ATTAAATTATAATTATA
1 ATTAAAATATAATAATA
2679057 A-TAAAATATAA-AATA
1 ATTAAAATATAATAATA
2679072 ATTAAAATCA-AATATATA
1 ATTAAAAT-ATAATA-ATA
2679090 ATTA
1 ATTA
2679094 TATAAATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
15 4 0.13
16 17 0.55
17 3 0.10
18 7 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (17 bp):
ATTAAAATATAATAATA
Found at i:2681348 original size:13 final size:13
Alignment explanation
Indices: 2681330--2681366 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2681320 TAAGTATATA
2681330 ATTTTTCTTTAAT
1 ATTTTTCTTTAAT
2681343 ATTTTTCTTTAAT
1 ATTTTTCTTTAAT
2681356 ATTTTTCTTTA
1 ATTTTTCTTTA
2681367 CACATTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTTTCTTTAAT
Found at i:2681480 original size:2 final size:2
Alignment explanation
Indices: 2681464--2681512 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
2681454 TACTCATTGC
2681464 AT AT A- AT AT -T AT AT AT AT -T AT AT AT AT A- 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
2681502 -T AT AT AT AT AT
1 AT AT AT AT AT AT
2681513 TAAATGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
1 5 0.12
2 37 0.88
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2681483 original size:9 final size:9
Alignment explanation
Indices: 2681464--2681510 Score: 67
Period size: 9 Copynumber: 4.9 Consensus size: 9
2681454 TACTCATTGC
2681464 ATATAATATT
1 ATAT-ATATT
2681474 ATATATATT
1 ATATATATT
2681483 ATATATATAAT
1 ATATATAT--T
2681494 ATATATATT
1 ATATATATT
2681503 ATATATAT
1 ATATATAT
2681511 ATTAAATGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
9 22 0.63
10 4 0.11
11 9 0.26
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATATATATT
Found at i:2681489 original size:11 final size:11
Alignment explanation
Indices: 2681473--2681514 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
2681463 CATATAATAT
2681473 TATATATATTA
1 TATATATATTA
2681484 TATATATA--A
1 TATATATATTA
2681493 TATATATATTA
1 TATATATATTA
2681504 TATATATATTA
1 TATATATATTA
2681515 AATGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.31
11 20 0.69
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATATTA
Found at i:2681731 original size:2 final size:2
Alignment explanation
Indices: 2681719--2681767 Score: 89
Period size: 2 Copynumber: 24.0 Consensus size: 2
2681709 ATTGTTAATA
2681719 AT AT GAT 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
2681762 AT AT AT
1 AT AT AT
2681768 TAAAAACTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 44 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2683986 original size:23 final size:23
Alignment explanation
Indices: 2683943--2683987 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2683933 TGTTAGGAGG
* *
2683943 AATAAATTGTTAAATTTAAAAAA
1 AATAAATTGTTAAAATGAAAAAA
2683966 AATAAATT-TATAAAATGAAAAA
1 AATAAATTGT-TAAAATGAAAAA
2683988 TGAAAAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 1 0.05
23 18 0.95
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (23 bp):
AATAAATTGTTAAAATGAAAAAA
Found at i:2688839 original size:15 final size:15
Alignment explanation
Indices: 2688819--2688848 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2688809 TTTAGGAGTG
*
2688819 TAAATGAATACAGTT
1 TAAATGAATAAAGTT
2688834 TAAATGAATAAAGTT
1 TAAATGAATAAAGTT
2688849 ATGTTTGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.13, T:0.33
Consensus pattern (15 bp):
TAAATGAATAAAGTT
Found at i:2689187 original size:10 final size:10
Alignment explanation
Indices: 2689172--2689211 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
2689162 TTTATCACAC
2689172 CAAATTCTCT
1 CAAATTCTCT
2689182 CAAATTCTCT
1 CAAATTCTCT
2689192 -AAATTTCTCT
1 CAAA-TTCTCT
*
2689202 CAAATACTCT
1 CAAATTCTCT
2689212 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:2691509 original size:12 final size:12
Alignment explanation
Indices: 2691492--2691528 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2691482 ATTTATAAGA
2691492 GAGGAGAGATGC
1 GAGGAGAGATGC
*
2691504 GA-G-GAGATGT
1 GAGGAGAGATGC
2691514 GAGGAGAGATGC
1 GAGGAGAGATGC
2691526 GAG
1 GAG
2691529 AACCGATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:2692484 original size:26 final size:26
Alignment explanation
Indices: 2692432--2692489 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
2692422 TTGATAATTT
* *
2692432 TATTTAAATTAATATATATATATATA
1 TATTAAAATTAATATATATATAAATA
*
2692458 TATTAAAATTTAATATTTATA-AAATA
1 TATTAAAA-TTAATATATATATAAATA
*
2692484 TTTTAA
1 TATTAA
2692490 CAACCAAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 16 0.59
27 11 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
TATTAAAATTAATATATATATAAATA
Found at i:2693239 original size:3 final size:3
Alignment explanation
Indices: 2693231--2693262 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2693221 TTCATTCTAA
2693231 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2693263 AAGATAAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2701555 original size:21 final size:21
Alignment explanation
Indices: 2701530--2701587 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
2701520 CCTTAACTAC
2701530 TGATATTGAATGT-TAATTTT
1 TGATATTGAATGTATAATTTT
*
2701550 GTGATATTCAATGTTATAATTTT
1 -TGATATTGAATG-TATAATTTT
*
2701573 TGACATTGAATGTAT
1 TGATATTGAATGTAT
2701588 TATATTGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 14 0.44
22 11 0.34
23 7 0.22
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.50
Consensus pattern (21 bp):
TGATATTGAATGTATAATTTT
Found at i:2702390 original size:11 final size:11
Alignment explanation
Indices: 2702376--2702408 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
2702366 AAATATTTTT
2702376 AAAAATATATA
1 AAAAATATATA
2702387 AAAAATAT-TA
1 AAAAATATATA
2702397 AAAAATA-ATA
1 AAAAATATATA
2702407 AA
1 AA
2702409 TTTAGAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (11 bp):
AAAAATATATA
Found at i:2703066 original size:15 final size:15
Alignment explanation
Indices: 2703046--2703086 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
2703036 GCGGTAGCTA
* *
2703046 CGGTGACGAGGACAG
1 CGGTGACAACGACAG
2703061 CGGTGACAACGACAG
1 CGGTGACAACGACAG
*
2703076 CGATGACAACG
1 CGGTGACAACG
2703087 GCGAGAGCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.32, C:0.24, G:0.37, T:0.07
Consensus pattern (15 bp):
CGGTGACAACGACAG
Found at i:2703204 original size:16 final size:17
Alignment explanation
Indices: 2703171--2703206 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2703161 TAAAATAAAA
2703171 TTATAAAAATTAATATT
1 TTATAAAAATTAATATT
*
2703188 TTATAAATATT-ATATT
1 TTATAAAAATTAATATT
2703204 TTA
1 TTA
2703207 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATAAAAATTAATATT
Found at i:2703252 original size:23 final size:23
Alignment explanation
Indices: 2703203--2703254 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
2703193 AATATTATAT
**
2703203 TTTAATTAAATTAAAATTAAATT
1 TTTAATTAAATTAAAATTAAACG
* * *
2703226 TTTAATTAATTTATAATTATACG
1 TTTAATTAAATTAAAATTAAACG
2703249 TTTAAT
1 TTTAAT
2703255 ACTTAATAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTTAATTAAATTAAAATTAAACG
Found at i:2703913 original size:25 final size:25
Alignment explanation
Indices: 2703885--2703935 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
2703875 GAGAAAGGTC
2703885 GAGTCATCGAGTCTTACGTTGACAT
1 GAGTCATCGAGTCTTACGTTGACAT
2703910 GAGTCATCGAGTCTTACGTTGACAT
1 GAGTCATCGAGTCTTACGTTGACAT
2703935 G
1 G
2703936 TTTATTGGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (25 bp):
GAGTCATCGAGTCTTACGTTGACAT
Done.