Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008319.1 Hibiscus syriacus cultivar Beakdansim tig00111022_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: 4819703
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 15 of 21
Found at i:3186723 original size:20 final size:20
Alignment explanation
Indices: 3186698--3186747 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
3186688 TGAAAAGATT
* *
3186698 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAAGAGAAAA
*
3186718 TAAT-AAATAAAAGGGAAAA
1 TAATAAAATAAAAGAGAAAA
3186737 TAATAAAATAA
1 TAATAAAATAA
3186748 TAAATCATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAAGAGAAAA
Found at i:3186834 original size:17 final size:18
Alignment explanation
Indices: 3186798--3186839 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
3186788 GTTGTTTTTA
3186798 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
3186816 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
3186833 AAATAAA
1 AAATAAA
3186840 TTATTGAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:3187623 original size:76 final size:75
Alignment explanation
Indices: 3187455--3187670 Score: 274
Period size: 76 Copynumber: 2.9 Consensus size: 75
3187445 TAAAACATCT
* * * * *
3187455 TAAATCCTAATTAAAACACTTAAAACTATTTAAAGTAAAATACCTAAAACGAAA-ATAATAT-TT
1 TAAAACCTAATTAAAATAC-TAAAACTATTTAAACTAAAATACCTAAAAC-AAAGATAAAATATA
*
3187518 AAAATAATATTC
64 AAAATAATATCC
* * *
3187530 TAAATCCTAATTAAAATACTAAAACTTATTTAAACAAAAATACTTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAAC-TATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
3187595 AAATAATATCC
65 AAATAATATCC
* * *
3187606 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTTAAACACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
3187671 TGTTTAAAAT
Statistics
Matches: 124, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
74 9 0.07
75 45 0.36
76 69 0.56
77 1 0.01
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.28
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
AATAATATCC
Found at i:3191048 original size:2 final size:2
Alignment explanation
Indices: 3191041--3191070 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3191031 GGTTCTACTT
3191041 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3191071 AAAGGAAATA
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):
TA
Found at i:3197235 original size:33 final size:32
Alignment explanation
Indices: 3197193--3197276 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 32
3197183 ATTTATTAGA
*
3197193 GGATTTCTCGGCGTCTTCTTCACATTGGG-GGG
1 GGATTTCTCGGCGTCTTCTTCACA-TGGGAAGG
*
3197225 TGGATTTCTCGGCGTCTTATTCACATGGGAAGG
1 -GGATTTCTCGGCGTCTTCTTCACATGGGAAGG
* *
3197258 GGATGTCTCGACGTCTTCT
1 GGATTTCTCGGCGTCTTCT
3197277 ATAGTATAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 20 0.44
33 25 0.56
ACGTcount: A:0.13, C:0.21, G:0.31, T:0.35
Consensus pattern (32 bp):
GGATTTCTCGGCGTCTTCTTCACATGGGAAGG
Found at i:3197414 original size:35 final size:32
Alignment explanation
Indices: 3197364--3197429 Score: 96
Period size: 35 Copynumber: 2.0 Consensus size: 32
3197354 TTGTGAATCA
*
3197364 ATTACAGAAGCAAAGAGAGTGAGGGAGGATATCG
1 ATTACAGAAGCAAAGAGAATGA--GAGGATATCG
3197398 ATTATCAGAAGCAAAGAGAATGAGAGGATATC
1 ATTA-CAGAAGCAAAGAGAATGAGAGGATATC
3197430 CATCATTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 9 0.30
34 4 0.13
35 17 0.57
ACGTcount: A:0.44, C:0.09, G:0.30, T:0.17
Consensus pattern (32 bp):
ATTACAGAAGCAAAGAGAATGAGAGGATATCG
Found at i:3200394 original size:29 final size:30
Alignment explanation
Indices: 3200361--3200422 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3200351 CACTTTATCA
* *
3200361 TTTCACATGT-CATATAAGCTCATAGCTTC
1 TTTCACATATACATATAAGCACATAGCTTC
* *
3200390 TTTCACATATACATGTAATCACATAGCTTC
1 TTTCACATATACATATAAGCACATAGCTTC
3200420 TTT
1 TTT
3200423 TCATATTCTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (30 bp):
TTTCACATATACATATAAGCACATAGCTTC
Found at i:3201035 original size:64 final size:64
Alignment explanation
Indices: 3200936--3201080 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 64
3200926 TTCCCTTGAA
* * * * * *
3200936 GTGCATCGATGCATTCAACAGTGCATCGATGCACCAATCACCTTCGATGTTTTCATT-TTAAGGG
1 GTGCATCGATGCACTCCACAGTGAATCGATGCACCAATCACATTCGATGTTTCCATTAAT-AGGG
* * *
3201000 GATGCATCGATGCACTCCTCA-TGAATCGATGCACCAATTACATTCGATGTTTCCATTAATATGG
1 G-TGCATCGATGCACTCCACAGTGAATCGATGCACCAATCACATTCGATGTTTCCATTAATAGGG
3201064 GTGCATCGATGCACTCC
1 GTGCATCGATGCACTCC
3201081 CTGTGCATTG
Statistics
Matches: 70, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
63 16 0.23
64 37 0.53
65 17 0.24
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCACTCCACAGTGAATCGATGCACCAATCACATTCGATGTTTCCATTAATAGGG
Found at i:3204242 original size:29 final size:30
Alignment explanation
Indices: 3204209--3204270 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
3204199 CACTTTATCA
*
3204209 TTTCACATGT-CATATAAGCTCATAGATTC
1 TTTCACATGTACATATAAGCACATAGATTC
* * *
3204238 TTTCACATGTACATGTAATCACATAGCTTC
1 TTTCACATGTACATATAAGCACATAGATTC
3204268 TTT
1 TTT
3204271 TTTATATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 10 0.36
30 18 0.64
ACGTcount: A:0.29, C:0.21, G:0.10, T:0.40
Consensus pattern (30 bp):
TTTCACATGTACATATAAGCACATAGATTC
Found at i:3204873 original size:19 final size:19
Alignment explanation
Indices: 3204849--3204900 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
3204839 TTTTAAGGGG
*
3204849 ATGCATCGATGCACTCCTT
1 ATGCATCGATGCACTCCTC
*
3204868 ATGCATTGATGCACTCCTC
1 ATGCATCGATGCACTCCTC
*
3204887 ATGAATCGATGCAC
1 ATGCATCGATGCAC
3204901 CAATTACATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.17, T:0.29
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTC
Found at i:3204965 original size:82 final size:83
Alignment explanation
Indices: 3204808--3204965 Score: 212
Period size: 83 Copynumber: 1.9 Consensus size: 83
3204798 TCAACAGTGC
* * * *
3204808 ATCGATGCACCAATCACCTTCGATGTTTTCATTTTAAGGGGATGCATCGATGCACTCCTTATGCA
1 ATCGATGCACCAATCACATTCGATGTTTCCATTATAAGGGGATGCATCGATGCACTCCCTATGCA
* *
3204873 TTGATGCACTCCTCATGA
66 TCGATACACTCCTCATGA
* * *
3204891 ATCGATGCACCAATTACATTCGATGTTTCCATTA-ATATGGG-TGCATCGATGCACTCCCTGTGC
1 ATCGATGCACCAATCACATTCGATGTTTCCATTATA-AGGGGATGCATCGATGCACTCCCTATGC
3204954 ATCGATACACTC
65 ATCGATACACTC
3204966 TGTACAAATT
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
82 31 0.48
83 34 0.52
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (83 bp):
ATCGATGCACCAATCACATTCGATGTTTCCATTATAAGGGGATGCATCGATGCACTCCCTATGCA
TCGATACACTCCTCATGA
Found at i:3206313 original size:14 final size:14
Alignment explanation
Indices: 3206296--3206352 Score: 71
Period size: 14 Copynumber: 4.1 Consensus size: 14
3206286 ATCCTTATTA
3206296 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
3206310 TTAAATTATCATTA-
1 TTAAATCATTA-AAG
3206324 TTAAATCATTAAAG
1 TTAAATCATTAAAG
3206338 TTAAATCATTAAAG
1 TTAAATCATTAAAG
3206352 T
1 T
3206353 ATGTCTCTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 1 0.03
14 33 0.94
15 1 0.03
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.40
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:3208831 original size:15 final size:15
Alignment explanation
Indices: 3208787--3208834 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
3208777 ATATTTAGCT
**
3208787 GGGCGGGCGGATGTA
1 GGGCGGGCGGATGCG
3208802 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
3208817 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
3208832 GGG
1 GGG
3208835 TGGGTAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.08, C:0.17, G:0.67, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:3210141 original size:18 final size:18
Alignment explanation
Indices: 3210118--3210158 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
3210108 TTATCTTTTT
3210118 CTTTTAAAACCA-TACTCA
1 CTTTTAAAA-CATTACTCA
3210136 CTTTTAAAACATTACTCA
1 CTTTTAAAACATTACTCA
3210154 CTTTT
1 CTTTT
3210159 GAAATCGAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.34, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CTTTTAAAACATTACTCA
Found at i:3212518 original size:24 final size:23
Alignment explanation
Indices: 3212486--3212567 Score: 116
Period size: 24 Copynumber: 3.6 Consensus size: 23
3212476 GCATGGGTAT
3212486 TGCATCGATGCACATATTAAAGAA
1 TGCATCGATGCAC-TATTAAAGAA
3212510 TGCATCGATGCACTTATTAAAGAA
1 TGCATCGATGCAC-TATTAAAGAA
*
3212534 TGCATCGATGCACT-GT--AGAA
1 TGCATCGATGCACTATTAAAGAA
3212554 TGCATCGATGCACT
1 TGCATCGATGCACT
3212568 TCAAGGAGAA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
20 18 0.32
22 1 0.02
23 1 0.02
24 36 0.64
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (23 bp):
TGCATCGATGCACTATTAAAGAA
Found at i:3213453 original size:18 final size:18
Alignment explanation
Indices: 3213363--3213445 Score: 123
Period size: 18 Copynumber: 4.6 Consensus size: 18
3213353 CCTTCCAAAT
3213363 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
*
3213381 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCCTTCGGGAC
*
3213399 ATAATGGTCCTT-GGGTAC
1 ATAGTGGTCCTTCGGG-AC
*
3213417 ACAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
3213435 ATAGTGGTCCT
1 ATAGTGGTCCT
3213446 ATGGGACAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
17 3 0.05
18 51 0.89
19 3 0.05
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:3214523 original size:23 final size:23
Alignment explanation
Indices: 3214497--3214541 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3214487 CACCACAGCT
*
3214497 CGTATAAATGCACCGA-AGTGCCC
1 CGTAGAAATGCACC-ATAGTGCCC
*
3214520 CGTAGAATTGCACCATAGTGCC
1 CGTAGAAATGCACCATAGTGCC
3214542 ATATAATGAT
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:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCATAGTGCCC
Found at i:3214790 original size:149 final size:149
Alignment explanation
Indices: 3214520--3214823 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
3214510 CGAAGTGCCC
3214520 CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
3214585 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
3214650 CATATGTCCTAAAGAACCA
131 CATATGTCCCAAAGAACCA
*
3214669 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
3214734 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
3214799 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCA
3214818 CGTAGA
1 CGTAGA
3214824 CCCTCTACCC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCATAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCA
Found at i:3215416 original size:67 final size:68
Alignment explanation
Indices: 3215302--3215453 Score: 216
Period size: 67 Copynumber: 2.2 Consensus size: 68
3215292 TTTTTCTCAT
* * * * *
3215302 GGGGGAATCGGTTCCCCCCTTGGGGGTATCGGTTCCCCTCTAACATTCTGGAATTTCATGTCCGT
1 GGGGGTATCGGTTCCCCCCTTGGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCAT
*
3215367 TGA
66 TAA
* *
3215370 GGGGGTATCGGTTCCCCCCTT-GGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCAT
1 GGGGGTATCGGTTCCCCCCTTGGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCAT
3215434 TAA
66 TAA
*
3215437 GAGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
3215454 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
67 55 0.73
68 20 0.27
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.31
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCCCTTGGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCAT
TAA
Found at i:3215980 original size:19 final size:20
Alignment explanation
Indices: 3215934--3215970 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
3215924 CCACGTTTGG
*
3215934 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
3215954 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
3215971 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:3221540 original size:23 final size:23
Alignment explanation
Indices: 3221514--3221558 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3221504 CACCACAGCT
*
3221514 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
3221537 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
3221559 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:3221807 original size:149 final size:149
Alignment explanation
Indices: 3221537--3221840 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
3221527 CGAAGTGCCC
3221537 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
* *
3221602 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGGATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
*
3221667 CATATGTCCTAAAGAACCG
131 CATATGTCCCAAAGAACCG
3221686 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
3221751 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
3221816 CATATGTCCCAAAGAACCG
131 CATATGTCCCAAAGAACCG
3221835 CGTAGA
1 CGTAGA
3221841 CCCTCTACCC
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCAAAGAACCG
Found at i:3222354 original size:19 final size:20
Alignment explanation
Indices: 3222317--3222354 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3222307 TTTTTTCTCA
3222317 TGGGGGAATCGGTTCCCCCC
1 TGGGGGAATCGGTTCCCCCC
*
3222337 TGGGGGTATCGGTTCCCC
1 TGGGGGAATCGGTTCCCC
3222355 TCTAACATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.32, G:0.37, T:0.24
Consensus pattern (20 bp):
TGGGGGAATCGGTTCCCCCC
Found at i:3222431 original size:67 final size:67
Alignment explanation
Indices: 3222318--3222490 Score: 224
Period size: 67 Copynumber: 2.6 Consensus size: 67
3222308 TTTTTCTCAT
* * * * * *
3222318 GGGGGAATCGGTTCCCCCCTGGGGGTATCGGTTCCCCTCTAACATTCTGGAATTTCATGTCCGTT
1 GGGGGTATCGGTTCCCCCCTTGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCATT
3222383 GA
66 GA
* *
3222385 GGGGGTATCGGTTCCCCCCTTGGGGTATCGATTCCCCTCTAGCATTCTGGAAATTCATATTCATT
1 GGGGGTATCGGTTCCCCCCTTGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCATT
3222450 GA
66 GA
*
3222452 GAGGGTATCGGTT--CCCCTTGAATGGGTATCGATTCCCCT
1 GGGGGTATCGGTTCCCCCCTTG---GGGTATCGATTCCCCT
3222491 AACCCAGAAA
Statistics
Matches: 94, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
65 7 0.07
67 71 0.76
68 16 0.17
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.31
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTTGGGGTATCGATTCCCCTCTAACATTCTGGAAATTCATATCCATT
GA
Found at i:3222995 original size:19 final size:20
Alignment explanation
Indices: 3222949--3222985 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
3222939 CCACGTTTGG
*
3222949 AGAAGGAAGAGAAGAAGATA
1 AGAAAGAAGAGAAGAAGATA
3222969 AGAAAGAAG-GAAGAAGA
1 AGAAAGAAGAGAAGAAGA
3222986 AATGAGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.03
Consensus pattern (20 bp):
AGAAAGAAGAGAAGAAGATA
Found at i:3226218 original size:64 final size:63
Alignment explanation
Indices: 3226102--3226242 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 63
3226092 TACATTCAAT
* * * *
3226102 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCCTTAAAGAAGAAACATCAAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * * *
3226165 GTGCATCGATGCATCCCCTTAAA-ATGAAAACATCAAAGGTAATTTGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA-CCCCTTAAAGAAG-AAACATCAAAGGCAATTGGTGCATCGATGCATAGGTA
*
3226229 GTGCATCAATGCAC
1 GTGCATCGATGCAC
3226243 ATGTTAAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
63 18 0.28
64 47 0.72
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (63 bp):
GTGCATCGATGCACCCCTTAAAGAAGAAACATCAAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:3226275 original size:20 final size:20
Alignment explanation
Indices: 3226250--3226287 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3226240 CACATGTTAA
3226250 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
3226270 AGAATGCATTGATGCACT
1 AGAATGCATCGATGCACT
3226288 TCAAGGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:3226648 original size:2 final size:2
Alignment explanation
Indices: 3226636--3226712 Score: 145
Period size: 2 Copynumber: 38.5 Consensus size: 2
3226626 TATTTATGAG
*
3226636 TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3226678 TA TA TA TA 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 TA TA TA TA T
3226713 GCATTTAAAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3227145 original size:18 final size:18
Alignment explanation
Indices: 3227119--3227242 Score: 140
Period size: 18 Copynumber: 6.9 Consensus size: 18
3227109 GAGGGTCTAT
*
3227119 GTGGTCCTTCAGGACATA
1 GTGGTCCTTCGGGACATA
*
3227137 GTAGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * * *
3227155 GTAGTCATTCAGGACACA
1 GTGGTCCTTCGGGACATA
*
3227173 GTGGTCATTCGGGACATA
1 GTGGTCCTTCGGGACATA
* * *
3227191 ATGGTCCTTTGGGACACA
1 GTGGTCCTTCGGGACATA
3227209 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
3227227 GTGGTCATACGGGACA
1 GTGGTCCTTCGGGACA
3227243 AATTTTACGC
Statistics
Matches: 89, Mismatches: 17, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 89 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:3227505 original size:2 final size:2
Alignment explanation
Indices: 3227500--3227529 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3227490 ATATATGTTA
3227500 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
3227530 GAATGAATAT
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:3232033 original size:26 final size:25
Alignment explanation
Indices: 3231975--3232025 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3231965 TTAGGGGCCG
*
3231975 AACTTATAAAATTTTAAAAGAGAAGA
1 AACTTATAAAATTTT-AAAGAGAAAA
*
3232001 AACTTATAAAATTTT-AAGATAAAA
1 AACTTATAAAATTTTAAAGAGAAAA
3232025 A
1 A
3232026 TACATTATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
AACTTATAAAATTTTAAAGAGAAAA
Found at i:3232973 original size:30 final size:30
Alignment explanation
Indices: 3232932--3233034 Score: 170
Period size: 30 Copynumber: 3.4 Consensus size: 30
3232922 ATAATTTTTA
*
3232932 ATAGATGAATGACTCAACGAAAAATACTTT
1 ATAGTTGAATGACTCAACGAAAAATACTTT
*
3232962 ACAGTTGAATGACTCAACGAAAAATACTTT
1 ATAGTTGAATGACTCAACGAAAAATACTTT
* *
3232992 ATAGTTGAATGACTAAACGAAAAATATTTT
1 ATAGTTGAATGACTCAACGAAAAATACTTT
3233022 ATAGTTGAATGAC
1 ATAGTTGAATGAC
3233035 CATTTATGTA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 68 1.00
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.29
Consensus pattern (30 bp):
ATAGTTGAATGACTCAACGAAAAATACTTT
Found at i:3234808 original size:15 final size:14
Alignment explanation
Indices: 3234786--3234818 Score: 57
Period size: 15 Copynumber: 2.3 Consensus size: 14
3234776 TTTTTTCTTA
3234786 AAATCTTAAACCCT
1 AAATCTTAAACCCT
3234800 AAATCCTTAAACCCT
1 AAAT-CTTAAACCCT
3234815 AAAT
1 AAAT
3234819 ATTTTATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (14 bp):
AAATCTTAAACCCT
Found at i:3240310 original size:50 final size:50
Alignment explanation
Indices: 3240229--3240323 Score: 145
Period size: 50 Copynumber: 1.9 Consensus size: 50
3240219 AAACTGGTAT
* *
3240229 ATTATTTTGTAACTTTTAATAGTTGAAAGAGATATCATCAATATCGATAG
1 ATTATTTTGTAACTTTTAATAATTGAAAGAGATAACATCAATATCGATAG
* * *
3240279 ATTATTTTGTAACTTTTCATAATTGAGAGAGATAACATCGATATC
1 ATTATTTTGTAACTTTTAATAATTGAAAGAGATAACATCAATATC
3240324 AAAATGTTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (50 bp):
ATTATTTTGTAACTTTTAATAATTGAAAGAGATAACATCAATATCGATAG
Found at i:3246889 original size:2 final size:2
Alignment explanation
Indices: 3246884--3246909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3246874 ATCTAGATTG
3246884 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
3246910 GTATGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3249382 original size:23 final size:23
Alignment explanation
Indices: 3249356--3249411 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
3249346 TCAAGAGTCT
3249356 AACATTTTAGAGTAATTTGAGTA
1 AACATTTTAGAGTAATTTGAGTA
*
3249379 AACATTTTAGAGTAGTTTGAGTA
1 AACATTTTAGAGTAATTTGAGTA
3249402 AACATTTTAG
1 AACATTTTAG
3249412 GTTGAAATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.38, C:0.05, G:0.18, T:0.39
Consensus pattern (23 bp):
AACATTTTAGAGTAATTTGAGTA
Found at i:3251252 original size:19 final size:19
Alignment explanation
Indices: 3251228--3251332 Score: 120
Period size: 19 Copynumber: 5.2 Consensus size: 19
3251218 GCGATTTTGA
3251228 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
3251247 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTT
*
3251266 AAAATGTGTTGCGAGAGTTT
1 AAAATGTGTTGCGATAG-TT
*
3251286 GAAAAACGTGTTGTTGCGATAGTG
1 --AAAA--TG-TGTTGCGATAGTT
* *
3251310 AAAAAGTGTTGCGATAGTG
1 AAAATGTGTTGCGATAGTT
3251329 AAAA
1 AAAA
3251333 ATCCAAAATA
Statistics
Matches: 76, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
19 52 0.68
20 3 0.04
22 8 0.11
24 3 0.04
25 10 0.13
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTT
Found at i:3251685 original size:19 final size:19
Alignment explanation
Indices: 3251649--3251687 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3251639 GTGGTAATAC
* *
3251649 TAGAGATCTCTTTACGATT
1 TAGAGATCGCATTACGATT
*
3251668 TAGAGATCGCATTGCGATT
1 TAGAGATCGCATTACGATT
3251687 T
1 T
3251688 TCGGTCACTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (19 bp):
TAGAGATCGCATTACGATT
Found at i:3252023 original size:29 final size:29
Alignment explanation
Indices: 3251963--3252024 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
3251953 TGTTGAGTCA
* *
3251963 TCGACAATTAAAAATTACAAAATAGTTCC
1 TCGACAATCAAAAATTACAAAATAGCTCC
* *
3251992 TCGACTATCAAAAGTTACAAAATA-CTCAC
1 TCGACAATCAAAAATTACAAAATAGCTC-C
3252021 TCGA
1 TCGA
3252025 GTATTCATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (29 bp):
TCGACAATCAAAAATTACAAAATAGCTCC
Found at i:3262710 original size:15 final size:16
Alignment explanation
Indices: 3262675--3262712 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
3262665 AAAGAGCCAA
3262675 AAAAATTATTAAATGTT
1 AAAAATTATTAAA-GTT
*
3262692 AAAAATTATTTAA-TT
1 AAAAATTATTAAAGTT
3262707 AAAAAT
1 AAAAAT
3262713 ATAACATATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
17 12 0.60
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAAATTATTAAAGTT
Found at i:3263434 original size:22 final size:25
Alignment explanation
Indices: 3263409--3263454 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
3263399 ATATATATTT
3263409 TTAAAATT-TTA-T-TTTAAAAAAC
1 TTAAAATTGTTATTATTTAAAAAAC
3263431 TTAAAATTGTTATTATTTAAAAAA
1 TTAAAATTGTTATTATTTAAAAAA
3263455 ACCAAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.38
23 3 0.14
24 1 0.05
25 9 0.43
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TTAAAATTGTTATTATTTAAAAAAC
Found at i:3268711 original size:74 final size:74
Alignment explanation
Indices: 3268609--3268817 Score: 373
Period size: 74 Copynumber: 2.8 Consensus size: 74
3268599 GCTTCCGTAG
* * * *
3268609 AAAGTTTTTAAACCAATTTTATAGTAGATTAAATTGTAGTTTGGGTTAAAACAAGTTTTCCCCTA
1 AAAGTTTATAAACCGATTTTATAGTAGATTAAATTGGAGTCTGGGTTAAAACAAGTTTTCCCCTA
3268674 CTTTTCTAA
66 CTTTTCTAA
*
3268683 AAAGTTTATAAATCGATTTTATAGTAGATTAAATTGGAGTCTGGGTTAAAACAAGTTTTCCCCTA
1 AAAGTTTATAAACCGATTTTATAGTAGATTAAATTGGAGTCTGGGTTAAAACAAGTTTTCCCCTA
3268748 CTTTTCTAA
66 CTTTTCTAA
3268757 AAAGTTTATAAACCGATTTTATAGTAGATTAAATTGGAGTCTGGGTTAAAACAAGTTTTCC
1 AAAGTTTATAAACCGATTTTATAGTAGATTAAATTGGAGTCTGGGTTAAAACAAGTTTTCC
3268818 TGGAAAATCT
Statistics
Matches: 129, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 129 1.00
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.39
Consensus pattern (74 bp):
AAAGTTTATAAACCGATTTTATAGTAGATTAAATTGGAGTCTGGGTTAAAACAAGTTTTCCCCTA
CTTTTCTAA
Found at i:3272269 original size:21 final size:21
Alignment explanation
Indices: 3272243--3272298 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
3272233 GCGAATAAGT
3272243 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
3272264 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
3272285 AAATCGCAATGCGA
1 AAATCGCAACGCGA
3272299 TACTGACTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.20, G:0.27, T:0.14
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:3272312 original size:20 final size:20
Alignment explanation
Indices: 3272287--3272400 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
3272277 AATTGGGAAA
*
3272287 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3272307 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
3272327 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
3272348 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
3272368 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
3272388 TTCGCAACGCGAT
1 ATCGCAACGCGAT
3272401 TTACATAGCG
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.02
20 64 0.79
21 13 0.16
22 2 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:3272362 original size:61 final size:61
Alignment explanation
Indices: 3272284--3272400 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
3272274 GCGAATTGGG
* * * * *
3272284 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
3272345 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
3272401 TTACATAGCG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:3272943 original size:20 final size:19
Alignment explanation
Indices: 3272914--3272961 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
3272904 TTCGAGAATG
3272914 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
3272933 AAAATTCGCAACGCGAAACC
1 AAAA-TCGCAACGCGAAATA
3272953 AAAATCGCA
1 AAAATCGCA
3272962 TTGCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.50, C:0.25, G:0.15, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:3272979 original size:19 final size:19
Alignment explanation
Indices: 3272957--3273065 Score: 155
Period size: 19 Copynumber: 5.7 Consensus size: 19
3272947 GAAACCAAAA
3272957 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
3272976 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* **
3272995 TCGCGTTATGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
3273014 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
3273033 TCGCAGTTGCGATTTTCATT
1 TCGCA-TTGCGATTTTCATT
3273053 TCGCATTGCGATT
1 TCGCATTGCGATT
3273066 GTCTGGTCGC
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 63 0.78
20 18 0.22
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:3273076 original size:77 final size:71
Alignment explanation
Indices: 3272957--3273098 Score: 178
Period size: 77 Copynumber: 1.9 Consensus size: 71
3272947 GAAACCAAAA
* * * *
3272957 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCGTTATGATTTTCATTTCGCGTTG
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTGTCATGTCGCG--AT-A--GTCATTTCGCGTTG
3273022 CGATTTTTATT
61 CGATTTTTATT
3273033 TCGCAGTTGCGATTTTCATTTCGCATTGCGATTGTC-TGGTCGCGATAGTCATTTCGCGTTGCGA
1 TCGCA-TTGCGATTTTCATTTCGCATTGCGATTGTCAT-GTCGCGATAGTCATTTCGCGTTGCGA
3273097 TT
64 TT
3273099 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
72 18 0.30
74 1 0.02
75 2 0.03
76 6 0.10
77 33 0.55
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTGTCATGTCGCGATAGTCATTTCGCGTTGCGATT
TTTATT
Found at i:3273085 original size:33 final size:33
Alignment explanation
Indices: 3273048--3273135 Score: 131
Period size: 33 Copynumber: 2.6 Consensus size: 33
3273038 GTTGCGATTT
* * *
3273048 TCATTTCGCATTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
3273081 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
3273114 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
3273136 ATTATCTCGT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 35 0.70
34 15 0.30
ACGTcount: A:0.12, C:0.25, G:0.24, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:3273137 original size:20 final size:20
Alignment explanation
Indices: 3273103--3273160 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
3273093 GCGATTCTCT
**
3273103 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
3273123 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
3273143 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
3273161 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:3275222 original size:42 final size:42
Alignment explanation
Indices: 3275162--3275284 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
3275152 GCCCGACTCG
* * *
3275162 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
3275204 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
3275246 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
3275285 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:3275242 original size:21 final size:21
Alignment explanation
Indices: 3275218--3275284 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3275208 TCATTCCTCG
3275218 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3275239 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3275260 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3275281 AGAG
1 AGAG
3275285 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3276665 original size:14 final size:14
Alignment explanation
Indices: 3276646--3276681 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3276636 TTTGTTTAAT
3276646 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
3276660 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
3276674 TGATTTGT
1 TGATTTGT
3276682 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:3276832 original size:19 final size:19
Alignment explanation
Indices: 3276808--3276866 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3276798 GAAATTAGCG
3276808 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3276827 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3276841 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3276860 TTGCGAT
1 TTGCGAT
3276867 AGTAATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
16 7 0.21
17 7 0.21
19 13 0.39
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3276832 original size:33 final size:34
Alignment explanation
Indices: 3276789--3276865 Score: 104
Period size: 33 Copynumber: 2.3 Consensus size: 34
3276779 AAAAGTACTA
*
3276789 TCGCAATGCGAAAT-TAGCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
* **
3276822 TCGCATTGCG-ATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
3276855 TCGCATTGCGA
1 TCGCATTGCGA
3276866 TAGTAATTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 2 0.05
33 36 0.95
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (34 bp):
TCGCATTGCGAAATCTAGCGTTGCGATTTTCATT
Found at i:3279159 original size:12 final size:12
Alignment explanation
Indices: 3279142--3279166 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3279132 TCTTCGGGGA
3279142 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3279154 CTTTTTCTTCTT
1 CTTTTTCTTCTT
3279166 C
1 C
3279167 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3279408 original size:24 final size:24
Alignment explanation
Indices: 3279357--3279408 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
3279347 ATTCGTGTAT
** *
3279357 TGACCAATATCAAAGTCCGGGTAT
1 TGACCAATATCAAAGTCCGAATAC
* *
3279381 TGACCAATATCAAATTTCGAATAC
1 TGACCAATATCAAAGTCCGAATAC
3279405 TGAC
1 TGAC
3279409 TAGTACTCAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TGACCAATATCAAAGTCCGAATAC
Found at i:3280481 original size:20 final size:20
Alignment explanation
Indices: 3280456--3280513 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
3280446 ATTCATTTGA
3280456 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
3280476 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
3280496 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
3280514 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:3280556 original size:14 final size:15
Alignment explanation
Indices: 3280536--3280608 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 15
3280526 TGAAAATCGT
3280536 ATTGCGATTTTCTCG
1 ATTGCGATTTTCTCG
3280551 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC---TCG
*
3280568 CATTGCGATTTCATTTCG
1 -ATTGCGATTT--TCTCG
3280586 CATTGCGATTTTCTCG
1 -ATTGCGATTTTCTCG
3280602 -TTGCGAT
1 ATTGCGAT
3280609 AGCCATTTCG
Statistics
Matches: 49, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.37
16 4 0.08
17 3 0.06
18 14 0.29
19 9 0.18
21 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.19, T:0.47
Consensus pattern (15 bp):
ATTGCGATTTTCTCG
Found at i:3280573 original size:19 final size:19
Alignment explanation
Indices: 3280551--3280598 Score: 89
Period size: 18 Copynumber: 2.6 Consensus size: 19
3280541 GATTTTCTCG
3280551 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3280570 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
3280588 TTGCGATTTTC
1 TTGCGATTTTC
3280599 TCGTTGCGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 18 0.64
19 10 0.36
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3280734 original size:14 final size:14
Alignment explanation
Indices: 3280715--3280751 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3280705 CATCAATTAA
3280715 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3280729 ACAAATCATCTTTT
1 ACAAATCAACATTT
3280743 ACAAATCAA
1 ACAAATCAA
3280752 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3282653 original size:20 final size:19
Alignment explanation
Indices: 3282619--3282684 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
3282609 AAACTTAAAT
*
3282619 TCGCAATGCGAAATGACTA
1 TCGCAACGCGAAATGACTA
*
3282638 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGACTA
* **
3282658 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGACTA
3282677 TCGCAACG
1 TCGCAACG
3282685 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 22 0.56
20 17 0.44
ACGTcount: A:0.36, C:0.23, G:0.24, T:0.17
Consensus pattern (19 bp):
TCGCAACGCGAAATGACTA
Found at i:3282682 original size:19 final size:19
Alignment explanation
Indices: 3282619--3282673 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
3282609 AAACTTAAAT
3282619 TCGCAATGCGAAATGACTA
1 TCGCAATGCGAAATGACTA
* *
3282638 TCGCAACGCGGAAATGGCTA
1 TCGCAATGC-GAAATGACTA
3282658 TCGCAATGCGAAATGA
1 TCGCAATGCGAAATGA
3282674 AAATCGCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (19 bp):
TCGCAATGCGAAATGACTA
Found at i:3282732 original size:19 final size:17
Alignment explanation
Indices: 3282710--3282805 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
3282700 GAAACACAAA
3282710 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
3282729 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
3282745 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
3282761 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
3282777 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
3282794 TCGCATTGCGAT
1 TCGC-TTGCGAT
3282806 AGCTATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:3282751 original size:14 final size:14
Alignment explanation
Indices: 3282732--3282789 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
3282722 TTTCATTTCG
3282732 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
3282746 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
3282762 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
3282778 CGTTGCGATTTT
1 CGTTGCGATTTT
3282790 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:3282796 original size:33 final size:33
Alignment explanation
Indices: 3282715--3282805 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
3282705 ACAAATCGCA
3282715 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
3282748 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
3282780 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
3282806 AGCTATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:3282833 original size:20 final size:19
Alignment explanation
Indices: 3282778--3282833 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
3282768 GCGATTTTGT
**
3282778 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
3282797 CATTGCGATAG-CTATTTCCG
1 CGTTGCGATAGTC-ATTT-CG
3282817 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
3282834 TCGTGTTACG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 16 0.53
21 1 0.03
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:3283352 original size:18 final size:18
Alignment explanation
Indices: 3283326--3283370 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3283316 GTCGATCAGA
3283326 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
3283344 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
3283362 TGATGGCTC
1 TGATGGCTC
3283371 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:3284715 original size:20 final size:20
Alignment explanation
Indices: 3284690--3284727 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3284680 AATAGTTTCT
3284690 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
3284710 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
3284728 GAGAGAATCG
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:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:3285018 original size:22 final size:22
Alignment explanation
Indices: 3284991--3285034 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
3284981 GATGGAGATA
3284991 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
3285013 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
3285035 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:3285247 original size:20 final size:20
Alignment explanation
Indices: 3285222--3285315 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
3285212 GATTATGTAT
3285222 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3285242 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
3285262 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
3285283 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
3285303 TATCGCATTGCGA
1 TATCGCGTTGCGA
3285316 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:3285316 original size:20 final size:20
Alignment explanation
Indices: 3285202--3285316 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
3285192 CGCTTTGAAA
*
3285202 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
3285223 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
3285243 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
3285263 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
3285284 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
3285304 ATCGCATTGCGAT
1 ATCGCATTGCGAT
3285317 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:3285334 original size:21 final size:21
Alignment explanation
Indices: 3285305--3285397 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
3285295 ATAGTCAGTA
3285305 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3285326 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3285346 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
3285367 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
3285387 TCGCATTGCGA
1 TCGCATTGCGA
3285398 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:3285335 original size:41 final size:41
Alignment explanation
Indices: 3285244--3285378 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
3285234 AAAGTCAGTA
* * * ** *
3285244 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
3285284 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
3285326 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
3285367 TCGCGTTGCGAT
1 TCGCGTTGCGAT
3285379 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:3285379 original size:41 final size:41
Alignment explanation
Indices: 3285305--3285397 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3285295 ATAGTCAGTA
3285305 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3285346 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
3285387 TCGCATTGCGA
1 TCGCATTGCGA
3285398 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:3286372 original size:26 final size:26
Alignment explanation
Indices: 3286341--3286401 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
3286331 TTATTATTTT
*
3286341 GGGTCGGGTTTCTAATTCAT-ATATTC
1 GGGTCGGGTTTCTAAGT-ATGATATTC
* * *
3286367 GGGTCGGTTTTTTAAGTGTGATATTC
1 GGGTCGGGTTTCTAAGTATGATATTC
3286393 GGGTCGGGT
1 GGGTCGGGT
3286402 CGAGTTCGAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 1 0.03
26 28 0.97
ACGTcount: A:0.15, C:0.11, G:0.33, T:0.41
Consensus pattern (26 bp):
GGGTCGGGTTTCTAAGTATGATATTC
Found at i:3286743 original size:21 final size:18
Alignment explanation
Indices: 3286719--3286766 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 18
3286709 TCTATATATA
3286719 ATTTTTTTCAATTAAATCAAT
1 ATTTTTTTCAA-TAAA--AAT
*
3286740 ATTTTTATTGAATAAAAAT
1 ATTTTT-TTCAATAAAAAT
3286759 ATTTTTTT
1 ATTTTTTT
3286767 TATTATTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 9 0.36
21 10 0.40
22 4 0.16
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTTTTTCAATAAAAAT
Found at i:3287194 original size:18 final size:18
Alignment explanation
Indices: 3287156--3287219 Score: 85
Period size: 18 Copynumber: 3.6 Consensus size: 18
3287146 ATATGAAATT
* *
3287156 AGATTTCAATTCC-TGAC
1 AGATTCCAATTCCTTCAC
*
3287173 AGATTTCAATTCCTTCAC
1 AGATTCCAATTCCTTCAC
*
3287191 AGATTCCAATTCATTCAC
1 AGATTCCAATTCCTTCAC
3287209 AGATTCCAATT
1 AGATTCCAATT
3287220 TCCTCATAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
17 13 0.30
18 30 0.70
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAC
Found at i:3289314 original size:29 final size:29
Alignment explanation
Indices: 3289282--3289377 Score: 72
Period size: 29 Copynumber: 3.2 Consensus size: 29
3289272 AAATTATTTA
3289282 TTAAACTTTTGAATATTTTAATTTCATTC
1 TTAAACTTTTGAATATTTTAATTTCATTC
* *
3289311 TTAAACTATCATT--CTCATTTTAAATT-AGTTC
1 TTAAACT-T--TTGAAT-ATTTTAATTTCA-TTC
* * *
3289342 TTAAACTTTTGAACATTCTAATTTCATCC
1 TTAAACTTTTGAATATTTTAATTTCATTC
*
3289371 CTAAACT
1 TTAAACT
3289378 ATGAACCTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
28 2 0.04
29 23 0.45
30 5 0.10
31 19 0.37
32 2 0.04
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (29 bp):
TTAAACTTTTGAATATTTTAATTTCATTC
Found at i:3289331 original size:60 final size:60
Alignment explanation
Indices: 3289253--3289379 Score: 175
Period size: 60 Copynumber: 2.1 Consensus size: 60
3289243 ATATATCCAA
* * * * *
3289253 AAACTATAATTCCTATTTTAAATTATTTATTAAACTTTTGAATATTTTAATTTCATTCTT
1 AAACTATAATTCCTATTTTAAATTAGTTATTAAACTTTTGAACATTCTAATTTCATCCCT
* *
3289313 AAACTATCATT-CTCATTTTAAATTAGTTCTTAAACTTTTGAACATTCTAATTTCATCCCT
1 AAACTATAATTCCT-ATTTTAAATTAGTTATTAAACTTTTGAACATTCTAATTTCATCCCT
3289373 AAACTAT
1 AAACTAT
3289380 GAACCTCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
59 2 0.03
60 57 0.97
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (60 bp):
AAACTATAATTCCTATTTTAAATTAGTTATTAAACTTTTGAACATTCTAATTTCATCCCT
Found at i:3289392 original size:60 final size:60
Alignment explanation
Indices: 3289267--3289396 Score: 170
Period size: 60 Copynumber: 2.2 Consensus size: 60
3289257 TATAATTCCT
* * * * * **
3289267 ATTTTAAATTATTTATTAAACTTTTGAATATTTTAATTTCATTCTTAAACTATCATTCTC
1 ATTTTAAATTAGTTATTAAACTTTTGAACATTCTAATTTCATCCCTAAACTATCAACCTC
* *
3289327 ATTTTAAATTAGTTCTTAAACTTTTGAACATTCTAATTTCATCCCTAAACTATGAACCTC
1 ATTTTAAATTAGTTATTAAACTTTTGAACATTCTAATTTCATCCCTAAACTATCAACCTC
*
3289387 TTTTTAAATT
1 ATTTTAAATT
3289397 GGTCCCAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.49
Consensus pattern (60 bp):
ATTTTAAATTAGTTATTAAACTTTTGAACATTCTAATTTCATCCCTAAACTATCAACCTC
Found at i:3289408 original size:60 final size:60
Alignment explanation
Indices: 3289284--3289411 Score: 148
Period size: 60 Copynumber: 2.1 Consensus size: 60
3289274 ATTATTTATT
* * * * ** * **
3289284 AAACTTTTGAATATTTTAATTTCATTCTTAAACTATCATTCTCATTTTAAATTAGTTCTT
1 AAACTTTTGAACATTCTAATTTCATCCCTAAACTATCAACCTCATTTTAAATTAGTCCCA
* * *
3289344 AAACTTTTGAACATTCTAATTTCATCCCTAAACTATGAACCTCTTTTTAAATTGGTCCCA
1 AAACTTTTGAACATTCTAATTTCATCCCTAAACTATCAACCTCATTTTAAATTAGTCCCA
3289404 AAACTTTT
1 AAACTTTT
3289412 TTTATTTGGG
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (60 bp):
AAACTTTTGAACATTCTAATTTCATCCCTAAACTATCAACCTCATTTTAAATTAGTCCCA
Found at i:3298522 original size:2 final size:2
Alignment explanation
Indices: 3298517--3298549 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3298507 TTTATGTATG
*
3298517 TA TA TA CA 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 TA TA TA T
3298550 TCATTTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:3298678 original size:23 final size:23
Alignment explanation
Indices: 3298652--3298715 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
3298642 ATTTTCCCCT
3298652 TTTATTTTTTACTATTATTATTA
1 TTTATTTTTTACTATTATTATTA
3298675 TTTATTTATTTATGCTATTA-TATTA
1 TTTATTT-TTTA--CTATTATTATTA
*
3298700 --TATTTTTTATTATTAT
1 TTTATTTTTTACTATTAT
3298716 ATACGTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.14
22 4 0.11
23 12 0.33
24 4 0.11
25 5 0.14
26 6 0.17
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTTTTACTATTATTATTA
Found at i:3298718 original size:17 final size:18
Alignment explanation
Indices: 3298666--3298718 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
3298656 TTTTTTACTA
*
3298666 TTATTATTATTTATTTAT
1 TTATTATTATATATTTAT
*
3298684 TTATGCTATTATATTATATTTT
1 TTAT--TATTATA-TAT-TTAT
3298706 TTATTATTATATA
1 TTATTATTATATA
3298719 CGTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 13 0.45
21 3 0.10
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATATATTTAT
Found at i:3298962 original size:19 final size:18
Alignment explanation
Indices: 3298917--3298965 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3298907 TTTTCATTGT
*
3298917 TTTATATTTTATTTTATTA
1 TTTATATTTT-TTTTATCA
* *
3298936 TGTGTATTTTTTTTATCCA
1 TTTATATTTTTTTTAT-CA
3298955 TTTATATTTTT
1 TTTATATTTTT
3298966 CTTCTTTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.71
Consensus pattern (18 bp):
TTTATATTTTTTTTATCA
Found at i:3309526 original size:50 final size:50
Alignment explanation
Indices: 3309447--3309543 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
3309437 AATACTTCGC
* ** *
3309447 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAACGT
* *
3309497 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAA
3309544 GAGGGAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.48, C:0.14, G:0.23, T:0.14
Consensus pattern (50 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAAAAAAAACGT
Found at i:3310854 original size:314 final size:315
Alignment explanation
Indices: 3310284--3310952 Score: 1277
Period size: 314 Copynumber: 2.1 Consensus size: 315
3310274 AGGTTTTACC
*
3310284 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310349 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
*
3310414 AAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
3310479 AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGT
196 AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
3310544 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
261 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3310599 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
3310664 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTCTCAATTTCAGAGCCAATTTCAACTTCATAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
3310728 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
* *
3310793 AACATTTCTCAATTTCAGAGCCAATTTCGACTTCACAACGAGGGATATTGGACTCCAGACAACGC
196 AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
3310858 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
261 AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3310913 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3310953 GAAACAACAC
Statistics
Matches: 348, Mismatches: 6, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
314 255 0.73
315 93 0.27
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (315 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGC
AAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:3310960 original size:105 final size:105
Alignment explanation
Indices: 3310284--3310952 Score: 1277
Period size: 105 Copynumber: 6.4 Consensus size: 105
3310274 AGGTTTTACC
*
3310284 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310349 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3310389 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310454 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3310494 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310559 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3310599 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310664 ACGAAGGGACCGCTGGTTGTCAACAAACA-TTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
3310703 CAGAGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310768 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
3310808 CAGAGCCAATTTCGACTTCACAACGAGGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
3310873 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
3310913 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTC
3310953 GAAACAACAC
Statistics
Matches: 553, Mismatches: 10, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 0.19
105 450 0.81
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:3312683 original size:2 final size:2
Alignment explanation
Indices: 3312671--3312711 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3312661 TATGTATGTG
*
3312671 TA TA CA TA TA TA TA 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 TA TA TA TA TA TA TA T
3312712 TCATTTTACC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3312840 original size:23 final size:23
Alignment explanation
Indices: 3312814--3312877 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 23
3312804 ATTTTCCCCT
3312814 TTTATTTTTTACTATTATTATTA
1 TTTATTTTTTACTATTATTATTA
3312837 TTTATTTATTTATGCTATTA-TATTA
1 TTTATTT-TTTA--CTATTATTATTA
*
3312862 --TATTTTTTATTATTAT
1 TTTATTTTTTACTATTAT
3312878 ATACGTATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
20 5 0.14
22 4 0.11
23 12 0.33
24 4 0.11
25 5 0.14
26 6 0.17
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTATTTTTTACTATTATTATTA
Found at i:3312880 original size:17 final size:18
Alignment explanation
Indices: 3312828--3312880 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
3312818 TTTTTTACTA
*
3312828 TTATTATTATTTATTTAT
1 TTATTATTATATATTTAT
*
3312846 TTATGCTATTATATTATATTTT
1 TTAT--TATTATA-TAT-TTAT
3312868 TTATTATTATATA
1 TTATTATTATATA
3312881 CGTATATGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
20 13 0.45
21 3 0.10
22 7 0.24
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (18 bp):
TTATTATTATATATTTAT
Found at i:3312955 original size:2 final size:2
Alignment explanation
Indices: 3312950--3312983 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3312940 TATACTCTAC
3312950 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
3312984 TATTTATTAT
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:3317175 original size:22 final size:18
Alignment explanation
Indices: 3317158--3317206 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
3317148 AATATTTTTC
3317158 CCGAAGGACCACTATATT
1 CCGAAGGACCACTATATT
*
3317176 CCGAAGGACCACTAT-GT
1 CCGAAGGACCACTATATT
3317193 CTCGAAGGACCACT
1 C-CGAAGGACCACT
3317207 GATAATCCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (18 bp):
CCGAAGGACCACTATATT
Found at i:3317817 original size:64 final size:65
Alignment explanation
Indices: 3317745--3317907 Score: 208
Period size: 64 Copynumber: 2.6 Consensus size: 65
3317735 ATCCCTTGAC
* * * *
3317745 GGGTGCATCGATGCACTATC-TATGCATCGGTACA-TAAATCTCATTCGATGTTTTTATTTTAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT-AATCGCATTCGATGTTTTTATTTTAAA
3317808 G
65 G
* * *
3317809 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCGCATTCGATGTTTTTATTTTAAAG
* *
3317873 GAGTGCATCGATACACT-TCATGTGCATCGATACAC
1 GGGTGCATCGATGCACTATCATGTGCATCGATACAC
3317908 CTTGAACAAT
Statistics
Matches: 87, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 1 0.01
64 85 0.98
65 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCGCATTCGATGTTTTTATTTTAAAG
Found at i:3323838 original size:18 final size:18
Alignment explanation
Indices: 3323814--3323877 Score: 110
Period size: 18 Copynumber: 3.6 Consensus size: 18
3323804 ATTTGTCCTA
3323814 AAGGACCACTATGTCCCG
1 AAGGACCACTATGTCCCG
*
3323832 AAAGACCACTATGTCCCG
1 AAGGACCACTATGTCCCG
*
3323850 AAGGACTACTATGTCCCG
1 AAGGACCACTATGTCCCG
3323868 AAGGACCACT
1 AAGGACCACT
3323878 GATAATCCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.17
Consensus pattern (18 bp):
AAGGACCACTATGTCCCG
Found at i:3324528 original size:64 final size:65
Alignment explanation
Indices: 3324451--3324614 Score: 192
Period size: 64 Copynumber: 2.6 Consensus size: 65
3324441 ATCCCTTGAC
* * *
3324451 GGGTGCATCGATGCACTATC-TATGCATCGGTACA-TAAATCCCATTCGATGTTTGTATTTTAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT-AATCCCATTCGATGTTTGTATTTTAAA
3324514 G
65 G
* * * ** *
3324515 GGGTGCATTGATGCACTA-CTTGTGCATCGATACACTGATGGCATTCGATGTTTTTATTTTAAAG
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
* *
3324579 GAGTGCATCGATACACT-TCATGTGCATCGATACACT
1 GGGTGCATCGATGCACTATCATGTGCATCGATACACT
3324615 TTGAACAATT
Statistics
Matches: 85, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
63 1 0.01
64 83 0.98
65 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (65 bp):
GGGTGCATCGATGCACTATCATGTGCATCGATACACTAATCCCATTCGATGTTTGTATTTTAAAG
Found at i:3326407 original size:18 final size:18
Alignment explanation
Indices: 3326384--3326419 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3326374 TGAATTCTTA
3326384 ATGAAAGGAGAGAAAAAC
1 ATGAAAGGAGAGAAAAAC
3326402 ATGAAAGGAGAGAAAAAC
1 ATGAAAGGAGAGAAAAAC
3326420 CTAAGCGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.06, G:0.28, T:0.06
Consensus pattern (18 bp):
ATGAAAGGAGAGAAAAAC
Found at i:3327374 original size:18 final size:18
Alignment explanation
Indices: 3327338--3327437 Score: 78
Period size: 18 Copynumber: 5.6 Consensus size: 18
3327328 GAGCCCAACA
*
3327338 TGAACTTGGAGA-ACTATG
1 TGAACTTGGA-ACACAATG
* *
3327356 TGGAGTTGGAACACAATG
1 TGAACTTGGAACACAATG
3327374 TGAACTTGGAACACAATG
1 TGAACTTGGAACACAATG
* * **
3327392 TAAACTTTGTTCACAATG
1 TGAACTTGGAACACAATG
* * *
3327410 TGAATTTGGAGCAGAACT-
1 TGAACTTGGAACACAA-TG
3327428 TGAACTTGGA
1 TGAACTTGGA
3327438 GGAAGATCCA
Statistics
Matches: 64, Mismatches: 16, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
17 1 0.02
18 62 0.97
19 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.28
Consensus pattern (18 bp):
TGAACTTGGAACACAATG
Found at i:3332309 original size:2 final size:2
Alignment explanation
Indices: 3332302--3332339 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3332292 ATCCAATTTA
3332302 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
3332340 CGTACTTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3332546 original size:20 final size:20
Alignment explanation
Indices: 3332521--3332558 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3332511 TTTGATTTTA
3332521 ATTTTAAGAATCA-ATTAAAC
1 ATTTTAA-AATCACATTAAAC
3332541 ATTTTAAAATCACATTAA
1 ATTTTAAAATCACATTAA
3332559 TGTAATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.37
Consensus pattern (20 bp):
ATTTTAAAATCACATTAAAC
Found at i:3333407 original size:31 final size:31
Alignment explanation
Indices: 3333372--3333468 Score: 176
Period size: 31 Copynumber: 3.1 Consensus size: 31
3333362 TAATATGTTA
3333372 TCACTTTCATTTTTACTTAATTAAGATTTGG
1 TCACTTTCATTTTTACTTAATTAAGATTTGG
3333403 TCACTTTCATTTTTACTTAATTAAGATTTGG
1 TCACTTTCATTTTTACTTAATTAAGATTTGG
* *
3333434 TCACTTTCATTTTTATTTAATTAAGATGTGG
1 TCACTTTCATTTTTACTTAATTAAGATTTGG
3333465 TCAC
1 TCAC
3333469 CGAAGGTTAC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 64 1.00
ACGTcount: A:0.26, C:0.13, G:0.10, T:0.51
Consensus pattern (31 bp):
TCACTTTCATTTTTACTTAATTAAGATTTGG
Found at i:3333989 original size:31 final size:31
Alignment explanation
Indices: 3333944--3334005 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
3333934 ATAACATTCA
* *
3333944 ATCATTTTCGTTTTTATTTTATTAAGATGTG
1 ATCATATTCATTTTTATTTTATTAAGATGTG
3333975 ATCATATTCATTTTTATTTTATTAAGATGTG
1 ATCATATTCATTTTTATTTTATTAAGATGTG
3334006 GTCACTTACC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.06, G:0.11, T:0.56
Consensus pattern (31 bp):
ATCATATTCATTTTTATTTTATTAAGATGTG
Found at i:3334521 original size:14 final size:14
Alignment explanation
Indices: 3334485--3334538 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
3334475 AAACTATTTT
*
3334485 AATATCAATAAATA
1 AATATTAATAAATA
* *
3334499 TATTTTAATAAATA
1 AATATTAATAAATA
3334513 AA-ATCTAATAAA-A
1 AATAT-TAATAAATA
3334526 AATATTAATAAAT
1 AATATTAATAAAT
3334539 TTAATGGTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 11 0.34
14 21 0.66
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (14 bp):
AATATTAATAAATA
Found at i:3335126 original size:28 final size:27
Alignment explanation
Indices: 3335086--3335147 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
3335076 GTTTAAGGGC
*
3335086 ATTTTCATAATTTTACCCA-CTTGAAGTT
1 ATTTTAATAA-TTTA-CCATCTTGAAGTT
*
3335114 ATTTTAATAATTTACCATTCTTGATGTT
1 ATTTTAATAATTTACCA-TCTTGAAGTT
3335142 ATTTTA
1 ATTTTA
3335148 TTCACATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 4 0.13
28 23 0.77
ACGTcount: A:0.29, C:0.13, G:0.06, T:0.52
Consensus pattern (27 bp):
ATTTTAATAATTTACCATCTTGAAGTT
Found at i:3345961 original size:35 final size:35
Alignment explanation
Indices: 3345914--3345999 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
3345904 AAAACAGTCA
* * *
3345914 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
3345949 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
3345984 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
3346000 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:3345993 original size:21 final size:21
Alignment explanation
Indices: 3345968--3346010 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
3345958 TTCTAAACCC
3345968 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
3345989 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
3346010 T
1 T
3346011 TAAGGTCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:3346165 original size:16 final size:18
Alignment explanation
Indices: 3346133--3346166 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
3346123 TATTAATGTA
3346133 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
3346151 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
3346167 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:3346844 original size:130 final size:130
Alignment explanation
Indices: 3346641--3346888 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
3346631 AATTTTCTTC
* * *
3346641 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
3346706 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
3346771 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
3346836 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
3346889 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:3352152 original size:90 final size:90
Alignment explanation
Indices: 3351999--3352400 Score: 432
Period size: 90 Copynumber: 4.5 Consensus size: 90
3351989 GCTCGAAAGA
* *
3351999 CTTACTGATGGCCCGAATGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCA
1 CTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCA
* * *
3352064 TTTGAAAAAATCCTACACTGAAGGT
66 TTTGAAAACATCATGCACTGAAGGT
* *
3352089 CTTACGGATGGCCCGAAGGACTTAGAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAGAATCTCA
1 CTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCA
*
3352154 TTTGAAAACATCCTGCACTGAAGGT
66 TTTGAAAACATCATGCACTGAAGGT
* ** ** * * **
3352179 CTTATGGATGGCCCGAAGGACTTATC--ATCTTG-----CTTGAAAGACTTATAGATTACCCAAA
1 CTTACGGATGGCCCGAAGGACTTA-CAAATCAAGAAACCCCCG-AAGGC-T-TAG-TTTCTAAAA
** ** * * *
3352237 --GGATTT--ACGCATCATGCTC-GAAAGA
61 TCTCATTTGAAAACATCATGCACTGAAGGT
* * *
3352262 CTTACTGATGGCCCAAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTAAAATCTCA
1 CTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCA
3352327 TTTGAAAACATCATGCACTGAAGGT
66 TTTGAAAACATCATGCACTGAAGGT
3352352 CTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTT
1 CTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTT
3352401 GAATTCTTGA
Statistics
Matches: 250, Mismatches: 45, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
82 1 0.00
83 25 0.10
84 15 0.06
85 10 0.04
86 8 0.03
87 8 0.03
88 9 0.04
89 17 0.07
90 157 0.63
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (90 bp):
CTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCA
TTTGAAAACATCATGCACTGAAGGT
Found at i:3352277 original size:42 final size:42
Alignment explanation
Indices: 3352179--3352286 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
3352169 CACTGAAGGT
* * * * *
3352179 CTTATGGATGGCCCGAAGGACTTA-TCATCTTGCTTGAAAGA
1 CTTATAGATGGCCCAAAGGACTTACGCATCATGCTCGAAAGA
** *
3352220 CTTATAGATTACCCAAAGGATTTACGCATCATGCTCGAAAGA
1 CTTATAGATGGCCCAAAGGACTTACGCATCATGCTCGAAAGA
3352262 CTTACT-GATGGCCCAAAGGACTTAC
1 CTTA-TAGATGGCCCAAAGGACTTAC
3352287 AAATCAAGAA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
41 19 0.35
42 34 0.63
43 1 0.02
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (42 bp):
CTTATAGATGGCCCAAAGGACTTACGCATCATGCTCGAAAGA
Found at i:3352287 original size:263 final size:262
Alignment explanation
Indices: 3351804--3352400 Score: 973
Period size: 263 Copynumber: 2.3 Consensus size: 262
3351794 ATCAAAAATG
* * * * * * *
3351804 TTGAAAACATCATGC-CCGAAGGTCATATGGATGGCCTGAATGACTTAAAAATCAAGAAACCCCC
1 TTGAAAAAATCATACACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCC
* *
3351868 GAAGGTTTAGTTTCTAAATCTCATTTGAAAATATCCTGCACTGAAGGTCTTATGGATGGCCCAAA
66 GAAGGCTTAGTTTCTAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCAAA
* *
3351933 GGACTTATCATCTTTCTATAAAGACTTATAGATGACCCGAAGGATTTACGCATCATGCTCGAAAG
131 GGACTTATCATCTTGCTATAAAGACTTATAGATGACCCAAAGGATTTACGCATCATGCTCGAAAG
* *
3351998 ACTTACTGATGGCCCGAATGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
196 ACTTACTGATGGCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
3352063 AT
261 AT
* *
3352065 TTGAAAAAATCCTACACTGAAGGTCTTACGGATGGCCCGAAGGACTTAGAAATCAAGAAACCCCC
1 TTGAAAAAATCATACACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCC
*
3352130 GAAGGCTTAGTTTCTAGAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGA
66 GAAGGCTTAGTTTCTA-AATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCAA
*
3352195 AGGACTTATCATCTTGCT-TGAAAGACTTATAGATTACCCAAAGGATTTACGCATCATGCTCGAA
130 AGGACTTATCATCTTGCTAT-AAAGACTTATAGATGACCCAAAGGATTTACGCATCATGCTCGAA
*
3352259 AGACTTACTGATGGCCCAAAGGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTAAAATC
194 AGACTTACTGATGGCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATC
3352324 TCAT
259 TCAT
* * *
3352328 TTGAAAACATCATGCACTGAAGGTCTTACGGATGGCCCGAAGGACTTACAAATCAAGAAACCCCC
1 TTGAAAAAATCATACACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCC
3352393 GAAGGCTT
66 GAAGGCTT
3352401 GAATTCTTGA
Statistics
Matches: 311, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
261 12 0.04
262 59 0.19
263 240 0.77
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (262 bp):
TTGAAAAAATCATACACTGAAGGTCTTACGGATGGCCCGAAGGACTTAAAAATCAAGAAACCCCC
GAAGGCTTAGTTTCTAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCAAA
GGACTTATCATCTTGCTATAAAGACTTATAGATGACCCAAAGGATTTACGCATCATGCTCGAAAG
ACTTACTGATGGCCCAAAGGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTC
AT
Found at i:3353610 original size:28 final size:28
Alignment explanation
Indices: 3353569--3353631 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
3353559 GATAAAAGGC
*
3353569 TCAGGTTGACTTGGGAAGGTAATGTGTT
1 TCAGGTTAACTTGGGAAGGTAATGTGTT
* *
3353597 TCAGGTTAATTTGGGGAGGTAATGTGTT
1 TCAGGTTAACTTGGGAAGGTAATGTGTT
3353625 TCAGGTT
1 TCAGGTT
3353632 GGCTTCTTGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.21, C:0.06, G:0.35, T:0.38
Consensus pattern (28 bp):
TCAGGTTAACTTGGGAAGGTAATGTGTT
Found at i:3357483 original size:20 final size:20
Alignment explanation
Indices: 3357458--3357496 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3357448 GTGTAAAGGT
*
3357458 AAATGCAAATGCGAAAATGC
1 AAATGCAAATGCAAAAATGC
*
3357478 AAATGCATATGCAAAAATG
1 AAATGCAAATGCAAAAATG
3357497 TTGATTCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATGCAAATGCAAAAATGC
Found at i:3360704 original size:31 final size:32
Alignment explanation
Indices: 3360666--3360735 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
3360656 AAGAAAACAA
* *
3360666 TATATAATATATGTTATATTCGAAA-AAATAG
1 TATATAATATATCTTATATTCGAAATAAAAAG
*
3360697 TATATAATATATCTTATATTTGAAATAAAAAG
1 TATATAATATATCTTATATTCGAAATAAAAAG
*
3360729 TAAATAA
1 TATATAA
3360736 AATACATTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 23 0.68
32 11 0.32
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (32 bp):
TATATAATATATCTTATATTCGAAATAAAAAG
Found at i:3361951 original size:31 final size:31
Alignment explanation
Indices: 3361888--3361962 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 31
3361878 AAGTTTAATC
*
3361888 TAAATTTTTAAAAATTTAGAGGAGGCTAAAT
1 TAAATTTTTAAAAATTTAGAGGAGACTAAAT
*
3361919 TAAAGTTTTTAAAAATTTTA-A-GATACTAAAT
1 TAAA-TTTTTAAAAA-TTTAGAGGAGACTAAAT
3361950 TATAATTTTTAAA
1 TA-AATTTTTAAA
3361963 TTTTGAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 22 0.56
32 13 0.33
33 4 0.10
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (31 bp):
TAAATTTTTAAAAATTTAGAGGAGACTAAAT
Found at i:3362494 original size:27 final size:28
Alignment explanation
Indices: 3362442--3362494 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
3362432 ATAATAATAT
**
3362442 ATTTTCTTTAAAAAATTAAATTTATACA
1 ATTTTCTTTAAAAAATTAAAAATATACA
*
3362470 ATTTT-TTTACAAAATTAAAAATATA
1 ATTTTCTTTAAAAAATTAAAAATATA
3362495 AAAAGGTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 17 0.77
28 5 0.23
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTTTCTTTAAAAAATTAAAAATATACA
Found at i:3363576 original size:16 final size:16
Alignment explanation
Indices: 3363557--3363587 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3363547 GATTTTAATA
3363557 ATTTAAATTTTTGGAT
1 ATTTAAATTTTTGGAT
3363573 ATTTAAATTTTTGGA
1 ATTTAAATTTTTGGA
3363588 GCGGATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (16 bp):
ATTTAAATTTTTGGAT
Found at i:3368498 original size:13 final size:13
Alignment explanation
Indices: 3368482--3368506 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3368472 TATTATTTAT
3368482 TTTAATTTTAAAG
1 TTTAATTTTAAAG
3368495 TTTAATTTTAAA
1 TTTAATTTTAAA
3368507 AAATGTTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (13 bp):
TTTAATTTTAAAG
Found at i:3376008 original size:35 final size:35
Alignment explanation
Indices: 3375968--3376081 Score: 87
Period size: 29 Copynumber: 3.3 Consensus size: 35
3375958 GTTGTATTTT
3375968 GTATTTGGTTGGTTTAGTAGGAATGTAAGATTATC
1 GTATTTGGTTGGTTTAGTAGGAATGTAAGATTATC
* * ** *
3376003 GTA--T--TT-GATTA-AAGGAATAAAAGATTATTGGAAT
1 GTATTTGGTTGGTTTAGTAGGAATGTAAGATTA-T----C
3376037 GTATTTGGTTGGTTTAGTAGGAATGTAAGATTATC
1 GTATTTGGTTGGTTTAGTAGGAATGTAAGATTATC
*
3376072 GTGTTTGGTT
1 GTATTTGGTT
3376082 AAAGAAATAA
Statistics
Matches: 57, Mismatches: 11, Indels: 22
0.63 0.12 0.24
Matches are distributed among these distances:
29 13 0.23
30 5 0.09
31 2 0.04
33 1 0.02
34 3 0.05
35 12 0.21
36 1 0.02
38 2 0.04
39 5 0.09
40 13 0.23
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.42
Consensus pattern (35 bp):
GTATTTGGTTGGTTTAGTAGGAATGTAAGATTATC
Done.