Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009259.1 Hibiscus syriacus cultivar Beakdansim tig00112910_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: 1149570
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:383857 original size:16 final size:15
Alignment explanation
Indices: 383795--383857 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 15
383785 ACAAAAAGGG
383795 CAAAAAAGAAA-AGAA
1 CAAAAAA-AAAGAGAA
* *
383810 GCAAAAAAGAAGAAAA
1 -CAAAAAAAAAGAGAA
*
383826 CAAAAAAAAGAAAGAA
1 CAAAAAAAA-AGAGAA
383842 CAAAAAGAAAAGAGAA
1 CAAAAA-AAAAGAGAA
383858 AAAGGGATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
15 10 0.26
16 25 0.66
17 3 0.08
ACGTcount: A:0.78, C:0.06, G:0.16, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAGAGAA
Found at i:386289 original size:106 final size:106
Alignment explanation
Indices: 385242--386288 Score: 1655
Period size: 106 Copynumber: 9.9 Consensus size: 106
385232 GAGAGTGGAT
* * *
385242 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
**
385307 CAACTTCACGGCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
385348 TTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
385413 CAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
385454 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCTAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
385519 CAACTTCACAACGAAGCATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
385560 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* * *
385625 CAACTTCATAGCGAAGGATATTGGACTCGAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
385666 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
385731 CAACTTCACAGCGAAAGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * *
385772 TTCAACTTCACGACGAAGGGACCGTTGATTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
385837 CAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* **
385878 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTTTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
385943 TAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
385984 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
386049 CAACTTCACAGCGAAGGATAATGGAC-CCGAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAG
* * * *
386090 TTCAACTTCACGACAAAGGGACCGCTGGTTTTCAACAAACAATTTCCCAATTTCGGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* * *
386155 CAACTTCACAACAAAGGATATTGGACTCGAGACAACACAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * * *
386196 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* *
386261 CAACTTCACGACGGAGGATATTGGACTC
66 CAACTTCACAACGAAGGATATTGGACTC
386289 GGAACAATGC
Statistics
Matches: 873, Mismatches: 66, Indels: 4
0.93 0.07 0.00
Matches are distributed among these distances:
105 2 0.00
106 870 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:387113 original size:37 final size:37
Alignment explanation
Indices: 387024--387127 Score: 136
Period size: 37 Copynumber: 2.8 Consensus size: 37
387014 CTTTTCGTCC
* *
387024 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
* *
387061 TGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTA
1 TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
** * *
387098 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAAAATAGGAT
387128 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.32
Consensus pattern (37 bp):
TACTAGGATTCAAACTCCTAAAAATAGGATAGAATTA
Found at i:387585 original size:2 final size:2
Alignment explanation
Indices: 387572--387602 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
387562 CCTTATTATT
*
387572 TA TA TG 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 T
387603 TTAATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:387939 original size:14 final size:14
Alignment explanation
Indices: 387902--387951 Score: 57
Period size: 14 Copynumber: 3.5 Consensus size: 14
387892 ATACATTTTA
*
387902 TATTTATATATATATA
1 TATTTATAT-TAT-TT
*
387918 TATATATATTATTT
1 TATTTATATTATTT
387932 TATTTATATTA-TT
1 TATTTATATTATTT
387945 TATTTAT
1 TATTTAT
387952 TTTCATTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 9 0.29
14 11 0.35
15 3 0.10
16 8 0.26
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTATATTATTT
Found at i:387939 original size:22 final size:22
Alignment explanation
Indices: 387912--387963 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
387902 TATTTATATA
387912 TATATATATATATATTATTTT-ATT
1 TATAT-TATATAT-TTATTTTCA-T
*
387936 TATATTATTTATTTATTTTCAT
1 TATATTATATATTTATTTTCAT
387958 TATATT
1 TATATT
387964 TTTAGTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
22 14 0.54
23 7 0.27
24 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TATATTATATATTTATTTTCAT
Found at i:387960 original size:13 final size:13
Alignment explanation
Indices: 387902--387951 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
387892 ATACATTTTA
*
387902 TATTTATATATA-
1 TATTTATTTATAT
* *
387914 TATATATATATAT
1 TATTTATTTATAT
387927 TATTTTATTTATAT
1 TA-TTTATTTATAT
387941 TATTTATTTAT
1 TATTTATTTAT
387952 TTTCATTATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 11 0.33
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATTTATTTATAT
Found at i:389220 original size:45 final size:45
Alignment explanation
Indices: 389168--389297 Score: 206
Period size: 45 Copynumber: 2.9 Consensus size: 45
389158 TATATGATAT
389168 TTGACCTATGTGATTACATGAAAATGTGATATAAGCTATGTGACA
1 TTGACCTATGTGATTACATGAAAATGTGATATAAGCTATGTGACA
389213 TTGACCTATGTGATTACATGAAAATGTGATATAAGCTATGTGACA
1 TTGACCTATGTGATTACATGAAAATGTGATATAAGCTATGTGACA
* * * ***
389258 ATGATCTATGTGATTATATGTCTATGTGATATAAGCTATG
1 TTGACCTATGTGATTACATGAAAATGTGATATAAGCTATG
389298 GAAATGTATA
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.36
Consensus pattern (45 bp):
TTGACCTATGTGATTACATGAAAATGTGATATAAGCTATGTGACA
Found at i:389433 original size:23 final size:23
Alignment explanation
Indices: 389375--389448 Score: 103
Period size: 23 Copynumber: 3.2 Consensus size: 23
389365 GAGTCGAGGG
* *
389375 TTCTACGCGGTCATTCGGGACAA
1 TTCTACGCGGTCCTTCGGGACAT
*
389398 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGCGGTCCTTCGGGACAT
**
389421 TTCTACGCGGTCCTTCAAGACAT
1 TTCTACGCGGTCCTTCGGGACAT
389444 TTCTA
1 TTCTA
389449 TGTGGCACTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.32
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGACAT
Found at i:400157 original size:31 final size:30
Alignment explanation
Indices: 400095--400160 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
400085 TGTTCTCAGA
* *
400095 TGCTACATAACGGCTCTTTAACGCATCCCC
1 TGCTACATAACCGCTCTTTAACGAATCCCC
400125 TGCTACATAACCGCTC-TTAGTACGAATCCCC
1 TGCTACATAACCGCTCTTTA--ACGAATCCCC
400156 TGCTA
1 TGCTA
400161 GTATGCCTCC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 15 0.47
31 14 0.44
ACGTcount: A:0.24, C:0.35, G:0.14, T:0.27
Consensus pattern (30 bp):
TGCTACATAACCGCTCTTTAACGAATCCCC
Found at i:404132 original size:40 final size:41
Alignment explanation
Indices: 404077--404157 Score: 137
Period size: 41 Copynumber: 2.0 Consensus size: 41
404067 TTAAGTTACA
*
404077 ATTAACAAAAGCACATTGA-GGGGGAAGTTTTTATTTTCTT
1 ATTAACAAAAGCACATTGAGGGGGGAAGTTTGTATTTTCTT
*
404117 ATTAACATAAGCACATTGAGGGGGGAAGTTTGTATTTTCTT
1 ATTAACAAAAGCACATTGAGGGGGGAAGTTTGTATTTTCTT
404158 GTTTACATCC
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 18 0.47
41 20 0.53
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.37
Consensus pattern (41 bp):
ATTAACAAAAGCACATTGAGGGGGGAAGTTTGTATTTTCTT
Found at i:405228 original size:19 final size:20
Alignment explanation
Indices: 405168--405235 Score: 93
Period size: 20 Copynumber: 3.4 Consensus size: 20
405158 GGTAACGAAT
*
405168 TTGACAAAATCGATTAGAAA
1 TTGACAAAACCGATTAGAAA
*
405188 TTGACAAAACCGATTGGAAA
1 TTGACAAAACCGATTAGAAA
*
405208 TTGACAAAACCGGTT-GAAA
1 TTGACAAAACCGATTAGAAA
405227 TTTGACAAA
1 -TTGACAAA
405236 TCCAGTTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
19 4 0.09
20 40 0.91
ACGTcount: A:0.46, C:0.13, G:0.18, T:0.24
Consensus pattern (20 bp):
TTGACAAAACCGATTAGAAA
Found at i:405780 original size:197 final size:197
Alignment explanation
Indices: 405300--405796 Score: 557
Period size: 197 Copynumber: 2.5 Consensus size: 197
405290 TATCAATATG
* *
405300 TTTATAAATATATGTACCAAAGTATCGGTACTGTAGGAATTTAAAAGAAATGAAAAAAAAAGGAA
1 TTTATAAATATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAAATG----AAAAATGAA
* * **
405365 AATGTCTCGAAAGTATCGATACCTT-ACACATGTATCGATACATGACAATATAACAGGTTGAGGT
62 AATGTCTTGAAAGTATCGATACCTTAACACATGTATCGATACATGACAATATAACAGGTTAAAAT
* * *
405429 TTGAAAAAACCAGTTTCAATTTAACAAAACCGGTAAAGAGATACCATAATGGTTAACGTATGTAT
127 TTGAAAAAACCAATATCAATATAACAAAACCGGTAAAGAGATACCATAATGGTTAACG-ATGTAT
405494 CGATACT
191 CGATACT
* * * *
405501 TTTATAAATATATGCACCAAAGTATCGGTACTTTAGGAATTTAAAAGAATTG--TAAT-AATA-G
1 TTTATAAATATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAAATGAAAAATGAAAATG
* * * *
405562 CTCGTAT-AAAGTATTGATACCTTAGAGACATGTATCGATACATGACAGTATAACATGTTAAAAT
66 -TC-T-TGAAAGTATCGATACCTTA-ACACATGTATCGATACATGACAATATAACAGGTTAAAAT
* * *
405626 TTGACAAAACCAATATCAATATAACAAAACCGGTAAAGTGATACCCGAT-AT-GTTGAC-A-GTA
127 TTGAAAAAACCAATATCAATATAACAAAACCGGTAAAGAGATA-CC-ATAATGGTTAACGATGTA
405687 TCGATACT
190 TCGATACT
* * *
405695 TTTATAAGTATATGTATCATAGTATCGGTACTTTAGGAA-TTAAAATGAAATGACAAAATGAAAA
1 TTTATAAATATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAA-GAAATGA-AAAATGAAAA
* * *
405759 TGTCTTGAAAGAATCGATACCTTACACAAAAGTATCGA
64 TGTCTTGAAAGTATCGATACCTTA-ACACATGTATCGA
405797 GACTTAGGTA
Statistics
Matches: 249, Mismatches: 33, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
193 7 0.03
194 56 0.22
195 19 0.08
196 1 0.00
197 105 0.42
198 9 0.04
199 3 0.01
201 49 0.20
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (197 bp):
TTTATAAATATATGTACCAAAGTATCGGTACTTTAGGAATTTAAAAGAAATGAAAAATGAAAATG
TCTTGAAAGTATCGATACCTTAACACATGTATCGATACATGACAATATAACAGGTTAAAATTTGA
AAAAACCAATATCAATATAACAAAACCGGTAAAGAGATACCATAATGGTTAACGATGTATCGATA
CT
Found at i:406197 original size:3 final size:3
Alignment explanation
Indices: 406184--406257 Score: 116
Period size: 3 Copynumber: 24.7 Consensus size: 3
406174 GCAAAGTATG
406184 TAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
406230 TAA -AGA TAA TAA TAA T-A TAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TA
406258 TTTTTTCGAG
Statistics
Matches: 67, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
2 3 0.04
3 60 0.90
4 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:406742 original size:83 final size:83
Alignment explanation
Indices: 406552--406742 Score: 247
Period size: 83 Copynumber: 2.3 Consensus size: 83
406542 GGGTGATAAT
* ** * *
406552 ACGGTTCCTACGCGATGAGGATGGTTCATTATCTAGGGGTGACACGGCTTCTACGTGATAAGGAG
1 ACGGTTCCTACGCGATGAGGACGACTCATTATCTAAGGGTGACACGGCTCCTACGTGATAAGGAG
* *
406617 ATCTAGTCGGTGGATGAC
66 ATCTAGCCGGGGGATGAC
* * * ** *
406635 ACGGTTCCTACGTGATAAGAACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAGGAG
1 ACGGTTCCTACGCGATGAGGACGACTCATTATCTAAGGGTGACACGGCTCCTACGTGATAAGGAG
* *
406700 ATCTGGCCGGGGGATGTC
66 ATCTAGCCGGGGGATGAC
406718 ACGGTTCCTACGCGATGAGGACGAC
1 ACGGTTCCTACGCGATGAGGACGAC
406743 ATGCCATCTT
Statistics
Matches: 90, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
83 90 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.24
Consensus pattern (83 bp):
ACGGTTCCTACGCGATGAGGACGACTCATTATCTAAGGGTGACACGGCTCCTACGTGATAAGGAG
ATCTAGCCGGGGGATGAC
Found at i:406874 original size:65 final size:65
Alignment explanation
Indices: 406759--406975 Score: 215
Period size: 67 Copynumber: 3.3 Consensus size: 65
406749 TCTTTAGGGA
* * * * * *
406759 TTTGTTTCAAGGGAAACATACTCAAAGATAATGT-ATTAAAGGAAACTGTCTCAAGAGAGACAAA
1 TTTGTTTCAAGAGAAACAAACTCAAAGAT-TTTTCTTTAAA-GAAATTGTCTCAAGAGAGACAAA
406823 A-
64 AC
*
406824 TTTGTTTCAAGAGAAACAAACTCAAAGATTTTTCTTTGAAAGAAATTGTCTCAAGAAAGACAAAA
1 TTTGTTTCAAGAGAAACAAACTCAAAGATTTTTCTTT-AAAGAAATTGTCTCAAGAGAGACAAAA
406889 C
65 C
* * ** * * *
406890 GTTTTTTTCGAGAGAAACGGACTCAACA-AGTTTTCTTCAAAAGAAATTGTCTCAAGAGAGATAA
1 -TTTGTTTCAAGAGAAACAAACTCAA-AGATTTTTCTT-TAAAGAAATTGTCTCAAGAGAGACAA
*
406954 AAT
63 AAC
*
406957 TTTATTTCAAGAGAAACAA
1 TTTGTTTCAAGAGAAACAA
406976 TTTCAAAGTC
Statistics
Matches: 126, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
64 2 0.02
65 51 0.40
66 18 0.14
67 54 0.43
68 1 0.01
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (65 bp):
TTTGTTTCAAGAGAAACAAACTCAAAGATTTTTCTTTAAAGAAATTGTCTCAAGAGAGACAAAAC
Found at i:406924 original size:67 final size:65
Alignment explanation
Indices: 406800--406975 Score: 219
Period size: 67 Copynumber: 2.7 Consensus size: 65
406790 TGTATTAAAG
* * * **
406800 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAACTCAAAGATTTTTCTTTGAAA
1 GAAATTGTCTCAAGAGAGACAAAATTTTTTTCAAGAGAAACAAACTCAAAGAGTTTTCTTCAAAA
* * **
406865 GAAATTGTCTCAAGAAAGACAAAACGTTTTTTTCGAGAGAAACGGACTCAACA-AGTTTTCTTCA
1 GAAATTGTCTCAAGAGAGACAAAA--TTTTTTTCAAGAGAAACAAACTCAA-AGAGTTTTCTTCA
406929 AAA
63 AAA
*
406932 GAAATTGTCTCAAGAGAGATAAAATTTTATTTCAAGAGAAACAA
1 GAAATTGTCTCAAGAGAGACAAAATTTT-TTTCAAGAGAAACAA
406976 TTTCAAAGTC
Statistics
Matches: 93, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
65 26 0.28
66 12 0.13
67 54 0.58
68 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (65 bp):
GAAATTGTCTCAAGAGAGACAAAATTTTTTTCAAGAGAAACAAACTCAAAGAGTTTTCTTCAAAA
Found at i:406996 original size:67 final size:63
Alignment explanation
Indices: 406800--407001 Score: 192
Period size: 67 Copynumber: 3.0 Consensus size: 63
406790 TGTATTAAAG
* * *
406800 GAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACAAACTCAAAGATTTTTCTTT-GAA
1 GAAATTGTCTCAAGAGAGACAAAATTTTTTTCAAGAGAAAC-AACTCAAAG-TTTTT-TTTCAAA
406864 A
63 A
* * * *
406865 GAAATTGTCTCAAGAAAGACAAAACGTTTTTTTCGAGAGAAACGGACTCAACAAG-TTTTCTTCA
1 GAAATTGTCTCAAGAGAGACAAAA--TTTTTTTCAAGAGAAAC-AACTC-A-AAGTTTTTTTTCA
406929 AAA
61 AAA
* *
406932 GAAATTGTCTCAAGAGAGATAAAATTTTATTTCAAGAGAAACAATTTCAAAGTCTTTTGTTTCAA
1 GAAATTGTCTCAAGAGAGACAAAATTTT-TTTCAAGAGAAACAA-CTCAAAGT-TTTT-TTTCAA
*
406997 GA
62 AA
406999 GAA
1 GAA
407002 GCAATTTCAA
Statistics
Matches: 112, Mismatches: 15, Indels: 18
0.77 0.10 0.12
Matches are distributed among these distances:
64 3 0.03
65 28 0.25
66 20 0.18
67 57 0.51
68 1 0.01
69 3 0.03
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (63 bp):
GAAATTGTCTCAAGAGAGACAAAATTTTTTTCAAGAGAAACAACTCAAAGTTTTTTTTCAAAA
Found at i:406997 original size:30 final size:30
Alignment explanation
Indices: 406956--407014 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
406946 AGAGATAAAA
406956 TTTTATTTCAAGAGAAACAATTTCAAAGTC
1 TTTTATTTCAAGAGAAACAATTTCAAAGTC
* *
406986 TTTTGTTTCAAGAGAAGCAATTTCAAAGT
1 TTTTATTTCAAGAGAAACAATTTCAAAGT
407015 TTGTCTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (30 bp):
TTTTATTTCAAGAGAAACAATTTCAAAGTC
Found at i:407050 original size:36 final size:36
Alignment explanation
Indices: 407010--407090 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 36
407000 AAGCAATTTC
* **
407010 AAAGTTTGTCTTAAGAAAGACTGTCTCAAGTGAGAT
1 AAAGTTTGTCTTAAGAAAAACAATCTCAAGTGAGAT
* *
407046 AAAGTTTGTTTTGAGAAAAACAATCTCAAGTGAGAT
1 AAAGTTTGTCTTAAGAAAAACAATCTCAAGTGAGAT
*
407082 AAACTTTGT
1 AAAGTTTGT
407091 TTCAAGTGAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (36 bp):
AAAGTTTGTCTTAAGAAAAACAATCTCAAGTGAGAT
Found at i:407212 original size:37 final size:36
Alignment explanation
Indices: 407135--407213 Score: 88
Period size: 37 Copynumber: 2.2 Consensus size: 36
407125 AGGAAAAATG
* **
407135 TCTCAAGCGAGACGAAATTTGTTTTGAGAAAACTTG
1 TCTCAAGCGAGACGAAATTTGTTTTAAGAAAACTAA
**
407171 TCTCAAGCGAGACGACCCTTTGTTTTAAGAGAAAC-AA
1 TCTCAAGCGAGACGA-AATTTGTTTTAAGA-AAACTAA
407208 TCTCAA
1 TCTCAA
407214 AGGAGATCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
36 15 0.42
37 17 0.47
38 4 0.11
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (36 bp):
TCTCAAGCGAGACGAAATTTGTTTTAAGAAAACTAA
Found at i:408351 original size:15 final size:15
Alignment explanation
Indices: 408331--408393 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
408321 CTCTTTTTAC
408331 TTTTTTTT-TCTTTG
1 TTTTTTTTGTCTTTG
*
408345 TTTTTTTCG-CTTCT-
1 TTTTTTTTGTCTT-TG
408359 TTTACTTTTTGTCTTTG
1 TTT--TTTTTGTCTTTG
*
408376 TTTCTTTTGTCTTTG
1 TTTTTTTTGTCTTTG
408391 TTT
1 TTT
408394 GATTGGATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 13 0.32
15 15 0.38
16 6 0.15
17 6 0.15
ACGTcount: A:0.02, C:0.13, G:0.10, T:0.76
Consensus pattern (15 bp):
TTTTTTTTGTCTTTG
Found at i:410256 original size:30 final size:31
Alignment explanation
Indices: 410222--410284 Score: 119
Period size: 30 Copynumber: 2.1 Consensus size: 31
410212 TGATGAAAAA
410222 TAACACAAACAAAAGA-GAAAAATGAGTTAG
1 TAACACAAACAAAAGAGGAAAAATGAGTTAG
410252 TAACACAAACAAAAGAGGAAAAATGAGTTAG
1 TAACACAAACAAAAGAGGAAAAATGAGTTAG
410283 TA
1 TA
410285 CAAGCAAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (31 bp):
TAACACAAACAAAAGAGGAAAAATGAGTTAG
Found at i:411528 original size:3 final size:3
Alignment explanation
Indices: 411520--411566 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
411510 AACAATTAAA
* *
411520 AAT AAT AAT AAT AAT AA- AAT AAC GAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
411566 A
1 A
411567 TTTTTTTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:411540 original size:17 final size:17
Alignment explanation
Indices: 411518--411566 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
411508 GTAACAATTA
411518 AAAATAATAATAATAAT
1 AAAATAATAATAATAAT
**
411535 AAAATAACGATAATAAT
1 AAAATAATAATAATAAT
*
411552 AATATAATAATAATA
1 AAAATAATAATAATA
411567 TTTTTTTGAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAATAATAATAATAAT
Found at i:411549 original size:20 final size:20
Alignment explanation
Indices: 411524--411561 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
411514 ATTAAAAATA
411524 ATAATAATAATAAAATAACG
1 ATAATAATAATAAAATAACG
*
411544 ATAATAATAATATAATAA
1 ATAATAATAATAAAATAA
411562 TAATATTTTT
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:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
ATAATAATAATAAAATAACG
Found at i:412866 original size:13 final size:13
Alignment explanation
Indices: 412848--412872 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
412838 ATGTCTATCG
412848 TTGATGGAGGAAT
1 TTGATGGAGGAAT
412861 TTGATGGAGGAA
1 TTGATGGAGGAA
412873 AATGTAGAGT
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:0.32, C:0.00, G:0.40, T:0.28
Consensus pattern (13 bp):
TTGATGGAGGAAT
Found at i:412954 original size:39 final size:39
Alignment explanation
Indices: 412897--412976 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
412887 TATGGTGATT
*
412897 ATTCATTTCTTCTATGGGTCCCATGTGTTGTAGTAGAAG
1 ATTCATTTCCTCTATGGGTCCCATGTGTTGTAGTAGAAG
* *
412936 ATTCATTTCCTCTGTGGGTCTCATGTGTTGTAGTAGAAG
1 ATTCATTTCCTCTATGGGTCCCATGTGTTGTAGTAGAAG
412975 AT
1 AT
412977 AAAGGTAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (39 bp):
ATTCATTTCCTCTATGGGTCCCATGTGTTGTAGTAGAAG
Found at i:415532 original size:18 final size:18
Alignment explanation
Indices: 415511--415550 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
415501 GATGTAAGCC
415511 AAATTTTGTATGTGAATG
1 AAATTTTGTATGTGAATG
415529 AAATTTTGTATGTGAATG
1 AAATTTTGTATGTGAATG
415547 AAAT
1 AAAT
415551 AATGTATATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (18 bp):
AAATTTTGTATGTGAATG
Found at i:415556 original size:18 final size:18
Alignment explanation
Indices: 415517--415557 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
415507 AGCCAAATTT
**
415517 TGTATGTGAATGAAATTT
1 TGTATGTGAATGAAATAA
415535 TGTATGTGAATGAAATAA
1 TGTATGTGAATGAAATAA
415553 TGTAT
1 TGTAT
415558 ATGTTGAGCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (18 bp):
TGTATGTGAATGAAATAA
Found at i:417150 original size:17 final size:17
Alignment explanation
Indices: 417128--417166 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
417118 TGAATCAAAT
417128 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
417145 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
417162 -AATTA
1 TAATTA
417167 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:419271 original size:200 final size:199
Alignment explanation
Indices: 418909--419387 Score: 602
Period size: 200 Copynumber: 2.4 Consensus size: 199
418899 TTTTATATTT
* *
418909 GTATCAATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCTCGCAATAAAGTATTGATACACG
1 GTATC-ATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACGCAA-AAAGTATCGATACACG
* * * ***
418974 TATATCAAGTATCGATACTTATAATTTCAAAACTTATTACTTTACAGTAATAGGTAAATATATGT
64 TATAACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATATACAA
* *
419039 TCATAACGGTAAAAATCTACAGGTTGAATGATAATAGGTGTAAAAATAAAGTATCGATACGTACT
129 TCAAAACGGTAAAAATCTACAGGTTAAATGATAATAGGTGTAAAAATAAAGTATCGATACGTACT
419104 AAATACA
194 AAATA-A
* *
419111 -TATCGATACTTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATAAACGT
1 GTATC-ATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATACACGT
** ** * * *
419175 ATAACAAGTATCGATACTTATAATTTTGAAACCTATTTTTTTAAATTAATAGGTAATTTTACAAT
65 ATAACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATATACAAT
* * * * * *
419240 GAAAACGGTAAAAATCTATC-GGTTAAATGATAATAGGTGTAAACATAAAGTTTTGATACTTATT
130 CAAAACGGTAAAAATCTA-CAGGTTAAATGATAATAGGTGTAAAAATAAAGTATCGATACGTACT
*
419304 ATATAA
194 AAATAA
* * * *
419310 GTATCACTACTTTTATTCCAGTGTGCATCTGAAACAATTTGCACGCAAAAAAGTATCGATACACA
1 GTATCA-TACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACGC-AAAAAGTATCGATACACG
*
419375 TATAAAAAGTATC
64 TATAACAAGTATC
419388 AATATAATTA
Statistics
Matches: 239, Mismatches: 34, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
199 2 0.01
200 164 0.69
201 73 0.31
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (199 bp):
GTATCATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATACACGTA
TAACAAGTATCGATACTTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATATACAATC
AAAACGGTAAAAATCTACAGGTTAAATGATAATAGGTGTAAAAATAAAGTATCGATACGTACTAA
ATAA
Found at i:419708 original size:21 final size:19
Alignment explanation
Indices: 419684--419722 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
419674 TGCACGCACA
419684 AAGTATCGATACATGTATAAC
1 AAGTATCGATA-AT-TATAAC
419705 AAGTATCGATAATTATAA
1 AAGTATCGATAATTATAA
419723 TTTTGAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 2 0.11
21 11 0.61
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
AAGTATCGATAATTATAAC
Found at i:419777 original size:525 final size:527
Alignment explanation
Indices: 418909--419911 Score: 1216
Period size: 525 Copynumber: 1.9 Consensus size: 527
418899 TTTTATATTT
* * * * *
418909 GTATCAATACTTTTAGTCCAGTATGCATCTCAAACAATTTGCTCGCAATAAAGTATTGATACACG
1 GTATCAATACTATTAGTCCAGTATGCATCTCAAACAATTTACACGCAATAAAGTATCGATACACA
* * * * *
418974 TATATCAAGTATCGATACTTATAATTTCAAAACTTATTACTTTACAGTAATAGGTAAATATATGT
66 TATATAAAGTATCGATACCTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATAAATGT
* *
419039 TCATAACGGTAAAAATCTACAGGTTGAATGATAATAGGTGTAAAAATAAAGTATCGATACGTACT
131 TCA-AACGGTAAAAATCTACAGGTTGAATGATAATAGGCGTAAAAATAAAGTATAGATACGTACT
419104 AAATACATATCGATACTTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAAAAGTATCGAT
195 AAATACATATCGATACTTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAAAAGTATCGAT
* ** *
419169 AAACGTATAACAAGTATCGATACTTATAATTTTGAAACCTATTTTTTTAAATTAATAGGTAATTT
260 AAACGTATAACAAGTATCGATAATTATAATTTTGAAACCTATTACTTTAAATTAATAGGTAAATT
* ** * *
419234 TACAATGAAAACGGTAAAAATCTATCGGTTAAATGATAATAGGTGTAAACATAAAGTTTTGATAC
325 CACAATGAAAACGGTAAAAATCTATCGGTTAAATGATAATAGGCATAAACATAAAGTATTAATAC
* * * * *
419299 TTATTATATAAGTATC-ACTACTTTTATTCCAGTGTGCATCTGAAACAATTTGCACGCAAAAAAG
390 TTATTATATAAGTATCGA-TAATTTTAGTCCAATATGCATCTCAAACAATTTGCACGC-AAAAAG
419363 TATCGATACACATATAAAAAGTATCAATATAATTATAATAGGTGTAAACATAGAGTGTCAAAACT
453 TATCGATACACATATAAAAAGTATCAATATAATTATAATAGGTGTAAACATAGAGTGTCAAAACT
419428 TTTTGTATAG
518 TTTTGTATAG
* ** * *
419438 GTATCGATACTATTAGTCCAGTATGTTTCTC-AACAATTTACACGTAA-AATGTATCGATACACA
1 GTATCAATACTATTAGTCCAGTATGCATCTCAAACAATTTACACGCAATAAAGTATCGATACACA
* * *
419501 TGTATAAAGTATC-AGTACCTATAATTTCGAAACCTATTACTTTAAAGTTATAGGTAAATTAAAA
66 TATATAAAGTATCGA-TACCTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAA-T-AAA
* * * * * * * *
419565 TG-TC-AATGGTAAAAGTCTACCA-GTTTAGTGATAATAGGCGTAAACATAAATTATATATACTT
128 TGTTCAAACGGTAAAAATCTA-CAGGTTGAATGATAATAGGCGTAAAAATAAAGTATAGATACGT
** ** ** * * * * *
419627 TTTGTATAGGTATCGATACTTTTCGTCCAGTATGCTTCT-TAACAATTTGCACGCACAAAGTATC
192 ACTAAATACATATCGATACTTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAAAAGTATC
* * *
419691 GATACATGTATAACAAGTATCGATAATTATAATTTTGAAACC-ACTTACTTTAAAGTT-TTAGGT
257 GATAAACGTATAACAAGTATCGATAATTATAATTTTGAAACCTA-TTACTTTAAA-TTAATAGGT
** * * * * * *
419754 AAATTCACAATGTCAATGGTAAAAGTCTATCGGTTTAATGATAGTAGGCATAAATATATAGTATT
320 AAATTCACAATGAAAACGGTAAAAATCTATCGGTTAAATGATAATAGGCATAAACATAAAGTATT
* * * * *
419819 AATAGTTTTTGTATAGGTATCGATAATTTTAGTCCAATATGCTTCTCAAACAATTTGCACGCAAA
385 AATACTTATTATATAAGTATCGATAATTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAA
* *
419884 ATGTATCGATACACATATATAAAGTATC
450 AAGTATCGATACACATATAAAAAGTATC
419912 GATACTTATA
Statistics
Matches: 396, Mismatches: 71, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
524 30 0.08
525 176 0.44
526 79 0.20
527 64 0.16
528 16 0.04
529 31 0.08
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (527 bp):
GTATCAATACTATTAGTCCAGTATGCATCTCAAACAATTTACACGCAATAAAGTATCGATACACA
TATATAAAGTATCGATACCTATAATTTCAAAACCTATTACTTTAAAGTAATAGGTAAATAAATGT
TCAAACGGTAAAAATCTACAGGTTGAATGATAATAGGCGTAAAAATAAAGTATAGATACGTACTA
AATACATATCGATACTTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAAAAGTATCGATA
AACGTATAACAAGTATCGATAATTATAATTTTGAAACCTATTACTTTAAATTAATAGGTAAATTC
ACAATGAAAACGGTAAAAATCTATCGGTTAAATGATAATAGGCATAAACATAAAGTATTAATACT
TATTATATAAGTATCGATAATTTTAGTCCAATATGCATCTCAAACAATTTGCACGCAAAAAGTAT
CGATACACATATAAAAAGTATCAATATAATTATAATAGGTGTAAACATAGAGTGTCAAAACTTTT
TGTATAG
Found at i:419984 original size:200 final size:199
Alignment explanation
Indices: 419392--420010 Score: 748
Period size: 198 Copynumber: 3.1 Consensus size: 199
419382 AGTATCAATA
* * * * * *
419392 TAATTATAATAGGTGTAAACATAGAGTGTCA-AAACTTTTTGTATAGGTATCGATACTATTAGTC
1 TAATGATAATAGGCGTAAACATAAAGTAT-ATATACTTTTTGTATAGGTATCGATACTTTTAGTC
* * * * *
419456 CAGTATGTTTCTCAACAATTTACACGTAAAATGTATCGATACACATGTATAAAGTATC-AGTACC
65 CAGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCGA-TACT
* * *
419520 TATAATTTCGAAACCTATTACTTTAAAGTTATAGG-TAAATTAAAATGTCAATGGTAAAAGTCTA
129 TATAATTTTGAAACCTATTACTTTAAAGTTATAGGTTAATTTACAATGTCAATGGTAAAAGTCTA
* *
419584 CCAGTT
194 TCGGTT
* * *
419590 TAGTGATAATAGGCGTAAACATAAATTATATATACTTTTTGTATAGGTATCGATACTTTTCGTCC
1 TAATGATAATAGGCGTAAACATAAAGTATATATACTTTTTGTATAGGTATCGATACTTTTAGTCC
* ** *
419655 AGTATGCTTCTTAACAATTTGCACGCACAAA-GTATCGATACATGTATA-ACAAGTATCGATAAT
66 AGTATGCTTCTCAACAATTTGCACGCA-AAATGTATCGATACACATATATA-AAGTATCGATACT
* * *
419718 TATAATTTTGAAACC-ACTTACTTTAAAGTTTTAGGTAAATTCACAATGTCAATGGTAAAAGTCT
129 TATAATTTTGAAACCTA-TTACTTTAAAGTTATAGGTTAATTTACAATGTCAATGGTAAAAGTCT
419782 ATCGGTT
193 ATCGGTT
* * * * * *
419789 TAATGATAGTAGGCATAAATATATAGTAT-TAATAGTTTTTGTATAGGTATCGATAATTTTAGTC
1 TAATGATAATAGGCGTAAACATAAAGTATAT-ATACTTTTTGTATAGGTATCGATACTTTTAGTC
*
419853 CAATATGCTTCTCAAACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCGATACT
65 CAGTATGCTTCTC-AACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCGATACT
* * * * ** * *
419918 TATAATTTTTAAACCTATTACTATAAGGTAATAGGTTAATTTACAATGAAAACGGTAAATGTCTA
129 TATAATTTTGAAACCTATTACTTTAAAGTTATAGGTTAATTTACAATGTCAATGGTAAAAGTCTA
*
419983 TCGGTA
194 TCGGTT
419989 TAATGATAATAGGCGTAAACAT
1 TAATGATAATAGGCGTAAACAT
420011 CAACTATCGA
Statistics
Matches: 355, Mismatches: 55, Indels: 20
0.83 0.13 0.05
Matches are distributed among these distances:
197 3 0.01
198 132 0.37
199 100 0.28
200 118 0.33
201 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.35
Consensus pattern (199 bp):
TAATGATAATAGGCGTAAACATAAAGTATATATACTTTTTGTATAGGTATCGATACTTTTAGTCC
AGTATGCTTCTCAACAATTTGCACGCAAAATGTATCGATACACATATATAAAGTATCGATACTTA
TAATTTTGAAACCTATTACTTTAAAGTTATAGGTTAATTTACAATGTCAATGGTAAAAGTCTATC
GGTT
Found at i:420064 original size:128 final size:129
Alignment explanation
Indices: 419887--420233 Score: 315
Period size: 130 Copynumber: 2.7 Consensus size: 129
419877 ACGCAAAATG
* * * ** **
419887 TATCGATACACATATATAAAGTATCGATACTTATAATTTTTAAACCTATTACTATAAGGTAATAG
1 TATCGATACACATATATAAAATATCGATACGTACAATTTCAAAACCTATTACTATAAAATAATAG
* * * *
419952 GTTAATTTACAATGAAAACGGTAAA-TGTCTATCGGTATAATGATAATAGGCGTAAACATCAAC
66 GTAAATTAACAATGAAAACGGTAAACTGTCTACCGGTATAATGAAAATAGGCGTAAACATCAAC
* * * *
420015 TATCGATACACATGTATAAAATATCGATACGTGCAATTTCAAAACCTATTGCTTTAAAATAATAG
1 TATCGATACACATATATAAAATATCGATACGTACAATTTCAAAACCTATTACTATAAAATAATAG
* * * * *
420080 GTAAATTAACAATGTACATGGTAAACGTTTCTACCGGTATAATGAAAATAGGCGTAAATGTAT-A
66 GTAAATTAACAATGAAAACGGTAAAC-TGTCTACCGGTATAATGAAAATAGGCGTAAA--CATCA
*
420144 AG
128 AC
*** * * * * * * * * *
420146 TATCGATA-TTTTCATAT-AAGTATCAATTCTTATAATTTCGAAACATATTACTTTAAAGTAATA
1 TATCGATACACAT-ATATAAAATATCGATACGTACAATTTCAAAACCTATTACTATAAAATAATA
* *
420209 GGTAAATTAACAATGTACACGGTAA
65 GGTAAATTAACAATGAAAACGGTAA
420234 TATGTTGATA
Statistics
Matches: 178, Mismatches: 36, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
128 74 0.42
130 89 0.50
131 13 0.07
132 2 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.33
Consensus pattern (129 bp):
TATCGATACACATATATAAAATATCGATACGTACAATTTCAAAACCTATTACTATAAAATAATAG
GTAAATTAACAATGAAAACGGTAAACTGTCTACCGGTATAATGAAAATAGGCGTAAACATCAAC
Found at i:422272 original size:19 final size:19
Alignment explanation
Indices: 422248--422294 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
422238 TTTATTTACA
422248 TTTTATATTAAAT-ATATAT
1 TTTTATATTAAATAATAT-T
* *
422267 TTTTATACT-ATTAATATT
1 TTTTATATTAAATAATATT
422285 TTTTATATTA
1 TTTTATATTA
422295 TGTTTAAACA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATATTAAATAATATT
Found at i:422337 original size:2 final size:2
Alignment explanation
Indices: 422304--422350 Score: 51
Period size: 2 Copynumber: 24.0 Consensus size: 2
422294 ATGTTTAAAC
* * * *
422304 AT AT AT A- AT AT TT AT AA AT CT AT AT CT 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
422345 AT AT AT
1 AT AT AT
422351 TACATTTTTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:422447 original size:3 final size:3
Alignment explanation
Indices: 422439--422466 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
422429 TGTTTACCTA
422439 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
422467 TCCTTTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:423064 original size:16 final size:16
Alignment explanation
Indices: 423040--423094 Score: 83
Period size: 16 Copynumber: 3.4 Consensus size: 16
423030 TTCGATGAGT
*
423040 TTAACGAGCAACGCGC
1 TTAACGAGCAACGAGC
*
423056 TTAATGAGCAACGAGC
1 TTAACGAGCAACGAGC
*
423072 TTAACAAGCAACGAGC
1 TTAACGAGCAACGAGC
423088 TTAACGA
1 TTAACGA
423095 ACAATTAGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (16 bp):
TTAACGAGCAACGAGC
Found at i:425816 original size:17 final size:16
Alignment explanation
Indices: 425767--425817 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
425757 CCGTGGGTTA
425767 TTTTTT-TTTTA-ATT
1 TTTTTTATTTTAGATT
* *
425781 TTTTTTAATTTTGGTTT
1 TTTTTT-ATTTTAGATT
425798 TTTTTTATTATTAGATT
1 TTTTTTATT-TTAGATT
425815 TTT
1 TTT
425818 CATATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
14 6 0.21
16 7 0.24
17 16 0.55
ACGTcount: A:0.16, C:0.00, G:0.06, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTTAGATT
Found at i:426059 original size:20 final size:20
Alignment explanation
Indices: 426022--426060 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
426012 TTTGAAACTT
*
426022 AAATTCGCAATACAAAAATG
1 AAATTCGCAACACAAAAATG
*
426042 AAATTCGCAACACGAAAAT
1 AAATTCGCAACACAAAAAT
426061 CGCAACGCGA
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:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (20 bp):
AAATTCGCAACACAAAAATG
Found at i:426146 original size:20 final size:20
Alignment explanation
Indices: 426084--426149 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
426074 TAGTTTTGCA
*
426084 TTGCAATTTTCATTTTCGCG
1 TTGCGATTTTCATTTTCGCG
**
426104 TTAAGATTTTCATTTTCGCG
1 TTGCGATTTTCATTTTCGCG
*
426124 TTGCGATTTTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
426144 TTGCGA
1 TTGCGA
426150 ATTTAAGTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.15, C:0.17, G:0.18, T:0.50
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCG
Found at i:426160 original size:20 final size:20
Alignment explanation
Indices: 426117--426160 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
426107 AGATTTTCAT
* * *
426117 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGAATTTAAG
*
426137 TTTCGTGTTGCGAATTTAAG
1 TTTCGCGTTGCGAATTTAAG
426157 TTTC
1 TTTC
426161 AAAAACTACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGAATTTAAG
Found at i:427850 original size:21 final size:21
Alignment explanation
Indices: 427803--427852 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
427793 GTTAGGCGAG
* *
427803 TTACGAGATGAGGTCAGTGCT
1 TTACGTGATGAGGTCAGTACT
*
427824 TTACGTGATGAGGTCGGTACT
1 TTACGTGATGAGGTCAGTACT
427845 TTACGTGA
1 TTACGTGA
427853 CGACAATGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.32, T:0.32
Consensus pattern (21 bp):
TTACGTGATGAGGTCAGTACT
Found at i:428118 original size:12 final size:11
Alignment explanation
Indices: 428092--428132 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
428082 TTTTTCGGCA
428092 TTATTTATTAT
1 TTATTTATTAT
428103 TTATTTATTGAT
1 TTATTTATT-AT
*
428115 TTATGTATTAAT
1 TTATTTATT-AT
428127 TTATTT
1 TTATTT
428133 TTAGCAGCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (11 bp):
TTATTTATTAT
Found at i:428302 original size:21 final size:21
Alignment explanation
Indices: 428277--428372 Score: 131
Period size: 21 Copynumber: 4.6 Consensus size: 21
428267 ATTCACCTAA
*
428277 CATCGTTCAAGAGGCTCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* *
428298 TATCGTTCAATAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
428319 CATCGTTCAAGAGGCCCCTCT
1 CATCGTTCAAGAGGCCCCTCC
*
428340 TATCGTTCAA-AGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
*
428360 CACCGTTCAAGAG
1 CATCGTTCAAGAG
428373 CCCGATTCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 17 0.27
21 47 0.73
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:428324 original size:42 final size:41
Alignment explanation
Indices: 428277--428372 Score: 156
Period size: 42 Copynumber: 2.3 Consensus size: 41
428267 ATTCACCTAA
*
428277 CATCGTTCAAGAGGCTCCTCCTATCGTTCAATAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCCTATCGTTCAA-AGGCCCCTCC
*
428319 CATCGTTCAAGAGGCCCCTCTTATCGTTCAAAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCCTATCGTTCAAAGGCCCCTCC
*
428360 CACCGTTCAAGAG
1 CATCGTTCAAGAG
428373 CCCGATTCAT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 22 0.43
42 29 0.57
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.24
Consensus pattern (41 bp):
CATCGTTCAAGAGGCCCCTCCTATCGTTCAAAGGCCCCTCC
Found at i:429331 original size:19 final size:19
Alignment explanation
Indices: 429309--429350 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
429299 CAGAGGGGAT
429309 TGTGGTCCTCTTGTATGCA
1 TGTGGTCCTCTTGTATGCA
429328 TGTGGTCCTCTTGTATGCA
1 TGTGGTCCTCTTGTATGCA
429347 TGTG
1 TGTG
429351 CTTGGAACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.10, C:0.19, G:0.29, T:0.43
Consensus pattern (19 bp):
TGTGGTCCTCTTGTATGCA
Found at i:429813 original size:16 final size:16
Alignment explanation
Indices: 429784--429818 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
429774 TGTAAATAAG
* *
429784 AATTGTTTTTTTGTTT
1 AATTGATTTGTTGTTT
429800 AATTGATTTGTTGTTT
1 AATTGATTTGTTGTTT
429816 AAT
1 AAT
429819 CGACAATCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.20, C:0.00, G:0.14, T:0.66
Consensus pattern (16 bp):
AATTGATTTGTTGTTT
Found at i:429932 original size:20 final size:20
Alignment explanation
Indices: 429909--429973 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
429899 GAAAGTCAAA
*
429909 TTCGCGTTGCG-ATTTTGATT
1 TTCGCGTTGCGAATTTT-ACT
*
429929 TTCGCATTGCGAATTTTACT
1 TTCGCGTTGCGAATTTTACT
** *
429949 TTCGCGTTTTGAATTTGACT
1 TTCGCGTTGCGAATTTTACT
429969 TTCGC
1 TTCGC
429974 AACAATCGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 33 0.87
21 5 0.13
ACGTcount: A:0.14, C:0.18, G:0.20, T:0.48
Consensus pattern (20 bp):
TTCGCGTTGCGAATTTTACT
Found at i:432547 original size:24 final size:24
Alignment explanation
Indices: 432513--432566 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
432503 CTGAAACATC
432513 ATCAAAATCTGAGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
* *
432537 ATCAAAGTCTGGGTATTGACCAAG
1 ATCAAAATCTGAGTATTGACCAAG
432561 ATCAAA
1 ATCAAA
432567 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.24
Consensus pattern (24 bp):
ATCAAAATCTGAGTATTGACCAAG
Found at i:433527 original size:20 final size:19
Alignment explanation
Indices: 433481--433589 Score: 80
Period size: 20 Copynumber: 5.6 Consensus size: 19
433471 CAAAACATTT
* *
433481 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAATTAAAATC
*
433500 -TATTGCGAAATTAAAATTC
1 GTGTTGCGAAATTAAAA-TC
433519 GTGTTGCG-AATTCGAAAATC
1 GTGTTGCGAAATT--AAAATC
* *
433539 GAGTTGCGAAAATAAAATTC
1 GTGTTGCGAAATTAAAA-TC
*
433559 GTGTTGCG-ATTTAAAAAATC
1 GTGTTGCGAAATT--AAAATC
*
433579 TTGTTGCGAAA
1 GTGTTGCGAAA
433590 AGGAAACTTG
Statistics
Matches: 70, Mismatches: 11, Indels: 16
0.72 0.11 0.16
Matches are distributed among these distances:
18 14 0.20
19 11 0.16
20 33 0.47
21 12 0.17
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (19 bp):
GTGTTGCGAAATTAAAATC
Found at i:433555 original size:40 final size:40
Alignment explanation
Indices: 433502--433608 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 40
433492 ATAAAAGCTA
* **
433502 TTGCGAAATTAAAATTCGTGTTGCGAATTCGAAAATCGAG
1 TTGCGAAAATAAAATTCGTGTTGCGAATTAAAAAATCGAG
* **
433542 TTGCGAAAATAAAATTCGTGTTGCGATTTAAAAAATCTTG
1 TTGCGAAAATAAAATTCGTGTTGCGAATTAAAAAATCGAG
* *
433582 TTGCGAAAAGGAAACTT-GTGTTGCGAA
1 TTGCGAAAA-TAAAATTCGTGTTGCGAA
433609 AAAGAAATTC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
40 52 0.91
41 5 0.09
ACGTcount: A:0.36, C:0.11, G:0.22, T:0.31
Consensus pattern (40 bp):
TTGCGAAAATAAAATTCGTGTTGCGAATTAAAAAATCGAG
Found at i:433624 original size:20 final size:20
Alignment explanation
Indices: 433581--433627 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
433571 AAAAAATCTT
* *
433581 GTTGCGAAAAGGAAACTTGT
1 GTTGCGAAAAAGAAACTTGC
433601 GTTGCGAAAAAGAAA-TTCGC
1 GTTGCGAAAAAGAAACTT-GC
433621 GTTGCGA
1 GTTGCGA
433628 TTGCAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.34, C:0.13, G:0.30, T:0.23
Consensus pattern (20 bp):
GTTGCGAAAAAGAAACTTGC
Found at i:433659 original size:20 final size:20
Alignment explanation
Indices: 433634--433673 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
433624 GCGATTGCAA
*
433634 AAACTGAGTTACGAATTTGG
1 AAACTGAGTTACGAAATTGG
* *
433654 AAACTGTGTTGCGAAATTGG
1 AAACTGAGTTACGAAATTGG
433674 TGTTTGCGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (20 bp):
AAACTGAGTTACGAAATTGG
Found at i:433684 original size:20 final size:20
Alignment explanation
Indices: 433661--433707 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
433651 TGGAAACTGT
* * *
433661 GTTGCGAAATTGGTGTTTGC
1 GTTGCGAAATTCGAGATTGC
433681 GTTGCG-AATTCGAGATTGC
1 GTTGCGAAATTCGAGATTGC
433700 GTTGCGAA
1 GTTGCGAA
433708 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.19, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
GTTGCGAAATTCGAGATTGC
Found at i:438387 original size:13 final size:13
Alignment explanation
Indices: 438371--438406 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
438361 CGTTGACTTG
438371 ACCCGACCCGTTA
1 ACCCGACCCGTTA
* *
438384 ACCCAACCCGTTG
1 ACCCGACCCGTTA
438397 ACCCGACCCG
1 ACCCGACCCG
438407 ATCTGTTGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.22, C:0.50, G:0.17, T:0.11
Consensus pattern (13 bp):
ACCCGACCCGTTA
Found at i:438405 original size:18 final size:18
Alignment explanation
Indices: 438352--438421 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 18
438342 GTCACAACCT
**
438352 GACCCAACCCGTTGACTT
1 GACCCAACCCGTTGACCC
*
438370 GACCCGACCCGTT-A---
1 GACCCAACCCGTTGACCC
438384 -ACCCAACCCGTTGACCC
1 GACCCAACCCGTTGACCC
* * *
438401 GACCCGATCTGTTGACCC
1 GACCCAACCCGTTGACCC
438419 GAC
1 GAC
438422 TCGTTGACCG
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
17 1 0.02
18 29 0.69
ACGTcount: A:0.21, C:0.43, G:0.19, T:0.17
Consensus pattern (18 bp):
GACCCAACCCGTTGACCC
Found at i:438427 original size:31 final size:31
Alignment explanation
Indices: 438351--438430 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
438341 GGTCACAACC
**
438351 TGACCCAACCCGTTGACTTGACCCGACCCGT
1 TGACCCAACCCGTTGACCCGACCCGACCCGT
* * *
438382 TAACCCAACCCGTTGACCCGACCCGATCTGT
1 TGACCCAACCCGTTGACCCGACCCGACCCGT
* *
438413 TGACCCGACTCGTTGACC
1 TGACCCAACCCGTTGACC
438431 GTTGATTGGC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.20, C:0.41, G:0.19, T:0.20
Consensus pattern (31 bp):
TGACCCAACCCGTTGACCCGACCCGACCCGT
Found at i:439674 original size:13 final size:13
Alignment explanation
Indices: 439627--439663 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
439617 GACCGGTCAC
439627 AACCCGACCCGTT
1 AACCCGACCCGTT
*
439640 AACCCAACCCGTT
1 AACCCGACCCGTT
*
439653 GACCCGACCCG
1 AACCCGACCCG
439664 ACCCGTTGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.24, C:0.49, G:0.16, T:0.11
Consensus pattern (13 bp):
AACCCGACCCGTT
Found at i:442184 original size:24 final size:24
Alignment explanation
Indices: 442157--442220 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
442147 TTATATTATA
*
442157 ATACCTGACCTGGATTCTGATCGG
1 ATACATGACCTGGATTCTGATCGG
442181 ATACATGACCTGGATTCTGATCGG
1 ATACATGACCTGGATTCTGATCGG
*
442205 ATACTTGACCTGGATT
1 ATACATGACCTGGATT
442221 ATGTTATGAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.31
Consensus pattern (24 bp):
ATACATGACCTGGATTCTGATCGG
Found at i:444585 original size:29 final size:29
Alignment explanation
Indices: 444543--444606 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
444533 TATTTGTTTG
* *
444543 TTTAGTAGTTGAAATTTTTATACTATAGA
1 TTTATTAGTTGAAATTTTTATACTATAAA
444572 TTTATTAGTTGAAATTTTTATACTATAAA
1 TTTATTAGTTGAAATTTTTATACTATAAA
444601 TTTATT
1 TTTATT
444607 TGGTGTATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.53
Consensus pattern (29 bp):
TTTATTAGTTGAAATTTTTATACTATAAA
Found at i:444603 original size:15 final size:15
Alignment explanation
Indices: 444554--444603 Score: 50
Period size: 15 Copynumber: 3.4 Consensus size: 15
444544 TTAGTAGTTG
444554 AAATTTTTATACTAT
1 AAATTTTTATACTAT
* * *
444569 AGATTTAT-TAGT-T
1 AAATTTTTATACTAT
444582 GAAATTTTTATACTAT
1 -AAATTTTTATACTAT
444598 AAATTT
1 AAATTT
444604 ATTTGGTGTA
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 1 0.04
14 9 0.35
15 15 0.58
16 1 0.04
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (15 bp):
AAATTTTTATACTAT
Found at i:448445 original size:62 final size:62
Alignment explanation
Indices: 448348--448475 Score: 256
Period size: 62 Copynumber: 2.1 Consensus size: 62
448338 CTATCCACAC
448348 TTGAAGTCAAGAAAAATGAGTTTCCATTTTTTATTCGTGCATTTTCTCTTTTATATAATGTA
1 TTGAAGTCAAGAAAAATGAGTTTCCATTTTTTATTCGTGCATTTTCTCTTTTATATAATGTA
448410 TTGAAGTCAAGAAAAATGAGTTTCCATTTTTTATTCGTGCATTTTCTCTTTTATATAATGTA
1 TTGAAGTCAAGAAAAATGAGTTTCCATTTTTTATTCGTGCATTTTCTCTTTTATATAATGTA
448472 TTGA
1 TTGA
448476 GTTTTATTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (62 bp):
TTGAAGTCAAGAAAAATGAGTTTCCATTTTTTATTCGTGCATTTTCTCTTTTATATAATGTA
Found at i:456165 original size:10 final size:9
Alignment explanation
Indices: 456136--456191 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
456126 TTCAACTAGT
456136 TTTGACCGG
1 TTTGACCGG
456145 TTTGACCGG
1 TTTGACCGG
*
456154 TTTCGACTGG
1 TTT-GACCGG
* *
456164 TTCGAACCGT
1 TTTG-ACCGG
456174 TTTGACCGG
1 TTTGACCGG
*
456183 TCTGACCGG
1 TTTGACCGG
456192 ACCTGACCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
9 25 0.66
10 13 0.34
ACGTcount: A:0.12, C:0.25, G:0.30, T:0.32
Consensus pattern (9 bp):
TTTGACCGG
Found at i:456227 original size:17 final size:17
Alignment explanation
Indices: 456205--456242 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
456195 TGACCCGACC
456205 GACCCGAACCGACCGTT
1 GACCCGAACCGACCGTT
*
456222 GACCCGACCCGACCGTT
1 GACCCGAACCGACCGTT
456239 GACC
1 GACC
456243 GTTGACCGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.21, C:0.45, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGAACCGACCGTT
Found at i:470758 original size:2 final size:2
Alignment explanation
Indices: 470751--470784 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
470741 ATCTTTTATG
470751 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
470785 GTTTAAATTG
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:472371 original size:13 final size:13
Alignment explanation
Indices: 472353--472378 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
472343 AAATATATGG
472353 ATTTTCAAAATTT
1 ATTTTCAAAATTT
472366 ATTTTCAAAATTT
1 ATTTTCAAAATTT
472379 TAAATATATT
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:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
ATTTTCAAAATTT
Found at i:472388 original size:20 final size:20
Alignment explanation
Indices: 472360--472397 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
472350 TGGATTTTCA
*
472360 AAATTTATTTTCAAAATTTT
1 AAATATATTTTCAAAATTTT
*
472380 AAATATATTTTTAAAATT
1 AAATATATTTTCAAAATT
472398 ATATTTAAAA
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:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATATATTTTCAAAATTTT
Found at i:472677 original size:2 final size:2
Alignment explanation
Indices: 472670--472707 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
472660 ATCATAAATT
472670 TA TA 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
472708 ATTTATTTTT
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):
TA
Found at i:473763 original size:4 final size:4
Alignment explanation
Indices: 473754--473781 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
473744 TTTTCTCAGA
473754 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT
473782 TGTAAAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:476880 original size:2 final size:2
Alignment explanation
Indices: 476873--476916 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
476863 ATTTAAGTTG
476873 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
476915 AT
1 AT
476917 CTTCGTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:477609 original size:30 final size:31
Alignment explanation
Indices: 477575--477651 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
477565 ATCAATAATT
*
477575 ATTAAAGTTTATCCAA-T-TTATAAAAT-ATTA
1 ATTAAA-TTTATCAAAGTGTTATAAAATGA-TA
*
477605 ATTAAAATTTATCAAAGTGTTCTAAAATGATA
1 ATT-AAATTTATCAAAGTGTTATAAAATGATA
477637 ATTAAATTTATCAAA
1 ATTAAATTTATCAAA
477652 ATTCTATAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 11 0.27
31 16 0.39
32 13 0.32
33 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.40
Consensus pattern (31 bp):
ATTAAATTTATCAAAGTGTTATAAAATGATA
Found at i:478361 original size:2 final size:2
Alignment explanation
Indices: 478354--478401 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
478344 CAATGGTAAT
478354 TA TA TA TA 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
478396 TA TA TA
1 TA TA TA
478402 AACCTACAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:478957 original size:41 final size:39
Alignment explanation
Indices: 478844--479059 Score: 155
Period size: 41 Copynumber: 5.3 Consensus size: 39
478834 TATAAAAACA
* * * * *
478844 CCGCCAAAAACTATACTTTATTGGTTTTTTTAGAATAAATG
1 CCGCTAAAGACTATACTTTAGTGG-TTTTTTA-TACAAATG
* * * **
478885 CTGCTAAATACTTGTACTTTAGTAGCATTTTTATACAAATG
1 CCGCTAAAGAC-TATACTTTAGT-GGTTTTTTATACAAATG
478926 CCGCTAAAGACTATACTTTAGTGGCATTTTTT-TACAAATG
1 CCGCTAAAGACTATACTTTAGTGG--TTTTTTATACAAATG
* * * * **
478966 CCGTTATAGACTCGTGCTTTAGTGGTGTTTTTATACAAACA
1 CCGCTAAAGACT-ATACTTTAGTGGT-TTTTTATACAAATG
* * *
479007 CCGCTATAGACTCATGCTTTAGTGGTGTTTTTATACAAACG
1 CCGCTAAAGACT-ATACTTTAGTGGT-TTTTTATACAAATG
*
479048 CCACTAAAGACT
1 CCGCTAAAGACT
479060 CGTGGGGCTT
Statistics
Matches: 143, Mismatches: 25, Indels: 14
0.79 0.14 0.08
Matches are distributed among these distances:
39 2 0.01
40 33 0.23
41 92 0.64
42 15 0.10
43 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.38
Consensus pattern (39 bp):
CCGCTAAAGACTATACTTTAGTGGTTTTTTATACAAATG
Found at i:479060 original size:41 final size:41
Alignment explanation
Indices: 478912--479060 Score: 183
Period size: 41 Copynumber: 3.7 Consensus size: 41
478902 TTTAGTAGCA
* * **
478912 TTTTTATACAAATGCCGCTAAAGACT-ATACTTTAGTGGCA
1 TTTTTATACAAACGCCGCTAAAGACTCATGCTTTAGTGGTG
* * * * *
478952 TTTTTTTACAAATGCCGTTATAGACTCGTGCTTTAGTGGTG
1 TTTTTATACAAACGCCGCTAAAGACTCATGCTTTAGTGGTG
* *
478993 TTTTTATACAAACACCGCTATAGACTCATGCTTTAGTGGTG
1 TTTTTATACAAACGCCGCTAAAGACTCATGCTTTAGTGGTG
*
479034 TTTTTATACAAACGCCACTAAAGACTC
1 TTTTTATACAAACGCCGCTAAAGACTC
479061 GTGGGGCTTG
Statistics
Matches: 93, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 23 0.25
41 70 0.75
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (41 bp):
TTTTTATACAAACGCCGCTAAAGACTCATGCTTTAGTGGTG
Found at i:482129 original size:13 final size:13
Alignment explanation
Indices: 482111--482139 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
482101 CCACCGTACT
482111 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
482124 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
482137 CCG
1 CCG
482140 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:483356 original size:229 final size:228
Alignment explanation
Indices: 482943--483739 Score: 1472
Period size: 229 Copynumber: 3.5 Consensus size: 228
482933 GATGGAAATG
* * *
482943 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
483008 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
*
483073 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
483138 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
195 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
*
483172 TTTGGAAACATAATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGC
*
483237 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
483302 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
130 CATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAA
483367 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
195 GGCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
483401 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
483465 CCCGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTG-AAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
*
483529 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCGAAG
131 ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
483594 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
196 GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
483627 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483692 CCCGAAGGCTTTTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
66 CCCGAAGGC--TTTTTGGAAACATCATGCACTGAAGGACTTACAGATG
483740 TGAGAAATAG
Statistics
Matches: 553, Mismatches: 11, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
226 158 0.29
227 81 0.15
228 12 0.02
229 302 0.55
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (228 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAG
GCTTTGAAAACATCAAAAAGCTCCCGAAGGCTT
Found at i:483450 original size:152 final size:152
Alignment explanation
Indices: 482943--483739 Score: 1472
Period size: 153 Copynumber: 5.2 Consensus size: 152
482933 GATGGAAATG
* * *
482943 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
483008 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
65 TCCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAA
483073 CATCAAAAAGCTCCCGAAGGCTT
130 CATCAAAAAGCTCCCGAAGGCTT
*
483096 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
483161 CCCGAAGGCTTTTTGGAAACATAATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTGAAAA
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAA
483226 CATCAAAAAGCTCCCGAAGGCTT
130 CATCAAAAAGCTCCCGAAGGCTT
*
483249 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483314 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
483379 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
483401 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
483465 CCCGAAGGCTTTTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTG-AAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
483529 ATCAAAAAGCTCCCGAAGGCTT
131 ATCAAAAAGCTCCCGAAGGCTT
*
483551 TTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483616 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
66 CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
483681 ATCAAAAAGCTCCCGAAGGCTTTT
131 ATCAAAAAGCTCCCGAAGGC--TT
483705 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
483740 TGAGAAATAG
Statistics
Matches: 626, Mismatches: 13, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
150 82 0.13
151 132 0.21
152 186 0.30
153 190 0.30
154 36 0.06
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (152 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTTTTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAAC
ATCAAAAAGCTCCCGAAGGCTT
Found at i:483764 original size:76 final size:76
Alignment explanation
Indices: 482943--483739 Score: 1472
Period size: 76 Copynumber: 10.5 Consensus size: 76
482933 GATGGAAATG
* * *
482943 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGC
483008 TCCCGAAGGCTT
65 TCCCGAAGGCTT
483020 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483085 CCCGAAGGCTT
66 CCCGAAGGCTT
*
483096 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483161 CCCGAAGGCTT
66 CCCGAAGGCTT
*
483172 TTTGGAAACATAATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGC-TTTGAAAACATCAAAAAGC
483237 TCCCGAAGGCTT
65 TCCCGAAGGCTT
*
483249 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGATTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483314 CCCGAAGGCTT
66 CCCGAAGGCTT
483325 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483390 CCCGAAGGCTT
66 CCCGAAGGCTT
483401 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483465 CCCGAAGGCTT
66 CCCGAAGGCTT
*
483476 TTTGGAAACATCATGCACTGGAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483540 CCCGAAGGCTT
66 CCCGAAGGCTT
*
483551 TTTGGAAACATCATGCACTGAAGGACTTATAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483616 CCCGAAGGCTT
66 CCCGAAGGCTT
483627 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
483692 CCCGAAGGCTTTT
66 CCCGAAGGC--TT
483705 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
483740 TGAGAAATAG
Statistics
Matches: 702, Mismatches: 13, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
74 7 0.01
75 131 0.19
76 411 0.59
77 116 0.17
78 37 0.05
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:484439 original size:22 final size:22
Alignment explanation
Indices: 484414--484468 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
484404 CATAAAGTTT
*
484414 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
*
484436 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
484458 TCATCTTTGAA
1 TCATCTTTGAA
484469 GAGTGTAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:484914 original size:54 final size:54
Alignment explanation
Indices: 484832--484987 Score: 240
Period size: 54 Copynumber: 2.9 Consensus size: 54
484822 AGAATAGCAG
* ***
484832 GTTCGTAAAACATTTGATAGTGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* **
484886 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTATTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
484940 GTTCGTAAAACATTTGACAACACATTCATCCTTTACTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
484988 CAAGATTTCT
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:487320 original size:83 final size:83
Alignment explanation
Indices: 487179--487443 Score: 433
Period size: 83 Copynumber: 3.2 Consensus size: 83
487169 TCTACTATGA
* * *
487179 GCAAATTCATCTTCCAAATTTAATGATTGGTTTTGTCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACAC
*
487244 TTCTAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
* *
487262 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAATTCAAAGAACAC
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACAC
*
487327 TTCCAGAAGATGATATTG
66 TTCCAGAAGATGCTATTG
* *
487345 GCAAATTTATCTTCTGAATTCAATGATTGGTTCTGTTC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCTAAATTCAATGATTGGTTCTG-TCAAACCAGATCAGATAACTCAAAGAACA
487409 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
487428 GCAAATTCATCTTCTA
1 GCAAATTCATCTTCTA
487444 GTTAATGTTT
Statistics
Matches: 167, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
83 166 0.99
84 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.31
Consensus pattern (83 bp):
GCAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:489711 original size:17 final size:17
Alignment explanation
Indices: 489685--489717 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
489675 TCAATTTTCC
489685 TTTTTCTTC-TTCTTTT
1 TTTTTCTTCTTTCTTTT
489701 TTTTGTCTTCTTTCTTT
1 TTTT-TCTTCTTTCTTT
489718 GTTGGATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTCTTCTTTCTTTT
Found at i:494315 original size:9 final size:9
Alignment explanation
Indices: 494295--494337 Score: 54
Period size: 9 Copynumber: 4.9 Consensus size: 9
494285 AATACTTGAA
494295 AATAAA-AT
1 AATAAATAT
494303 AATAAATAT
1 AATAAATAT
494312 AATAAATAT
1 AATAAATAT
*
494321 TATGAAA-AT
1 AAT-AAATAT
494330 AATAAATA
1 AATAAATA
494338 ATAAAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 9 0.30
9 18 0.60
10 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AATAAATAT
Found at i:494346 original size:18 final size:18
Alignment explanation
Indices: 494300--494347 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
494290 TTGAAAATAA
*
494300 AATAATAAATATAATAAAT
1 AATAA-AAAAATAATAAAT
* **
494319 ATTATGAAAATAATAAAT
1 AATAAAAAAATAATAAAT
494337 AATAAAAAAAT
1 AATAAAAAAAT
494348 TGAAATAAAA
Statistics
Matches: 22, Mismatches: 7, Indels: 1
0.73 0.23 0.03
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AATAAAAAAATAATAAAT
Found at i:494353 original size:17 final size:17
Alignment explanation
Indices: 494332--494373 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
494322 ATGAAAATAA
*
494332 TAAATAATA-AAAAAAT
1 TAAATAAAAGAAAAAAT
494348 TGAAATAAAAGAAAAAAT
1 T-AAATAAAAGAAAAAAT
494366 TAAATAAA
1 TAAATAAA
494374 TGATTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 14 0.61
18 8 0.35
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAATAAAAGAAAAAAT
Found at i:495872 original size:13 final size:13
Alignment explanation
Indices: 495854--495882 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
495844 CCACCGTACT
495854 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
495867 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
495880 CCG
1 CCG
495883 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:496639 original size:3 final size:3
Alignment explanation
Indices: 496631--496700 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
496621 ATATATATAT
* *
496631 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TATT TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
*
496677 TAA TAA -ATT TAA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA
496701 AATTTAAATG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
2 1 0.02
3 55 0.93
4 3 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:496681 original size:34 final size:34
Alignment explanation
Indices: 496640--496706 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
496630 TTAATAATAA
*
496640 TAATAAT-AATAATAATAATAATAATAATATTTAG
1 TAATAATAAAT-ATAATAATAATAATAAAATTTAG
*
496674 TAATAATAAATTTAATAATAATAATAAAATTTA
1 TAATAATAAATATAATAATAATAATAAAATTTA
496707 AATGAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.90
35 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (34 bp):
TAATAATAAATATAATAATAATAATAAAATTTAG
Found at i:498571 original size:85 final size:84
Alignment explanation
Indices: 498412--498602 Score: 233
Period size: 85 Copynumber: 2.2 Consensus size: 84
498402 GGCGTTCGTA
* * * *
498412 TCCAAAAACGCCGCTATAGATATGACCTTTTACGACATTTGTCCGAAAAACGTTGCTATAGTTCT
1 TCCAAAAACGCCGCTATAGATATGACCTTTTACGACATTTGTCC-AAAAACGTCGCTAAAGATCC
*
498477 CGACATTTTGCCGCATTTGT
65 CGACATTTTGCCGCATCTGT
* *
498497 TCCAAAAACGCCGCTATAGATATGACCTTTTGCTG-CGTTTGTTCC-AAAACTGTCGCTAAAGAT
1 TCCAAAAACGCCGCTATAGATATGACCTTTTAC-GACATTTG-TCCAAAAAC-GTCGCTAAAGAT
* * * *
498560 CCCGTCCTTTTGCGGCGTCTGT
63 CCCGACATTTTGCCGCATCTGT
498582 TCCAAAAACGCCGCTATAGAT
1 TCCAAAAACGCCGCTATAGAT
498603 CTCGATAATT
Statistics
Matches: 92, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
84 5 0.05
85 83 0.90
86 4 0.04
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (84 bp):
TCCAAAAACGCCGCTATAGATATGACCTTTTACGACATTTGTCCAAAAACGTCGCTAAAGATCCC
GACATTTTGCCGCATCTGT
Found at i:498615 original size:43 final size:43
Alignment explanation
Indices: 498400--498622 Score: 193
Period size: 43 Copynumber: 5.2 Consensus size: 43
498390 AAGGTAATTA
* * *
498400 GCGGCGTTCGTATCCAAAAACGCCGCTATAGATAT-GACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTCGACATTTT
* * * ** *
498443 ACGACATTTG-TCCGAAAAACGTTGCTATAGTTCTCGACATTTT
1 GCGGCGTTTGTTCC-AAAAACGCCGCTATAGATCTCGACATTTT
* * * *
498486 GCCGCATTTGTTCCAAAAACGCCGCTATAGATAT-GACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACATTTT
* * * * * *
498528 GCTGCGTTTGTTCC-AAAACTGTCGCTAAAGATCCCGTCCTTTT
1 GCGGCGTTTGTTCCAAAAAC-GCCGCTATAGATCTCGACATTTT
* * *
498571 GCGGCGTCTGTTCCAAAAACGCCGCTATAGATCTCGATAATTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACATTTT
498614 GCGGCGTTT
1 GCGGCGTTT
498623 TTTGTTCTCT
Statistics
Matches: 140, Mismatches: 34, Indels: 12
0.75 0.18 0.06
Matches are distributed among these distances:
41 8 0.06
42 45 0.32
43 79 0.56
44 8 0.06
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (43 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTCGACATTTT
Found at i:505193 original size:29 final size:31
Alignment explanation
Indices: 505160--505232 Score: 102
Period size: 29 Copynumber: 2.5 Consensus size: 31
505150 GTAAAAAAAT
505160 TAATTAAATAAAATATTAA-AAAAT-TTAAA
1 TAATTAAATAAAATATTAACAAAATATTAAA
*
505189 TAATTAAATAAAATACTAACAAAATATTAAA
1 TAATTAAATAAAATATTAACAAAATATTAAA
505220 T-A-T-AATAAAATAT
1 TAATTAAATAAAATAT
505233 ACCTTAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 9 0.22
29 19 0.47
30 6 0.15
31 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (31 bp):
TAATTAAATAAAATATTAACAAAATATTAAA
Found at i:505231 original size:17 final size:18
Alignment explanation
Indices: 505199--505232 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
505189 TAATTAAATA
505199 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
505217 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
505233 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:506002 original size:19 final size:20
Alignment explanation
Indices: 505975--506013 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
505965 TGGTTGGGAG
* *
505975 CTTTTTTTGTGTTTT-GTTT
1 CTTTCTTTGAGTTTTCGTTT
505994 CTTTCTTTGAGTTTTCGTTT
1 CTTTCTTTGAGTTTTCGTTT
506014 TAGAGTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.03, C:0.10, G:0.15, T:0.72
Consensus pattern (20 bp):
CTTTCTTTGAGTTTTCGTTT
Found at i:509892 original size:17 final size:17
Alignment explanation
Indices: 509839--509893 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
509829 TTCATGCATT
*
509839 TAGTTCATTAATAAAGT
1 TAGTTCATTAATAAAGC
*
509856 TAGTTCATTAATCAAGC
1 TAGTTCATTAATAAAGC
* *
509873 TAGTTCATTTATAAAAC
1 TAGTTCATTAATAAAGC
509890 TAGT
1 TAGT
509894 GTATCAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATAAAGC
Found at i:509903 original size:34 final size:34
Alignment explanation
Indices: 509839--509904 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
509829 TTCATGCATT
** *
509839 TAGTTCATTAATAAAGTTAGTTCATTAATCAAGC
1 TAGTTCATTAATAAAACTAGTTCATCAATCAAGC
*
509873 TAGTTCATTTATAAAACTAGTGT-ATCAATCAA
1 TAGTTCATTAATAAAACTAGT-TCATCAATCAA
509905 ACTAACTCTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 26 0.96
35 1 0.04
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.38
Consensus pattern (34 bp):
TAGTTCATTAATAAAACTAGTTCATCAATCAAGC
Found at i:511575 original size:21 final size:22
Alignment explanation
Indices: 511549--511589 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
511539 GGAGTGTTTG
*
511549 GTGAGGTT-TTTCTTTTTATCT
1 GTGAGGTTATATCTTTTTATCT
511570 GTGAGGTTATATCTTTTTAT
1 GTGAGGTTATATCTTTTTAT
511590 TACTAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.15, C:0.07, G:0.20, T:0.59
Consensus pattern (22 bp):
GTGAGGTTATATCTTTTTATCT
Found at i:514001 original size:34 final size:34
Alignment explanation
Indices: 513963--514032 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 34
513953 TTCATGCATT
*
513963 TAGTTCA-TTAATAAAGTTAGT-TCATTAATCAAAC
1 TAGTTCATTTAATAAA-CTAGTGT-ATTAATCAAAC
*
513997 TAGTTCATTTATTAAACTAGTGTATTAATCAAAC
1 TAGTTCATTTAATAAACTAGTGTATTAATCAAAC
514031 TA
1 TA
514033 ACTCTTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
34 24 0.75
35 8 0.25
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (34 bp):
TAGTTCATTTAATAAACTAGTGTATTAATCAAAC
Found at i:514030 original size:17 final size:17
Alignment explanation
Indices: 513963--514032 Score: 81
Period size: 17 Copynumber: 4.1 Consensus size: 17
513953 TTCATGCATT
*
513963 TAGTTCATTAAT-AAAGT
1 TAGTTCATTAATCAAA-C
513980 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
* *
513997 TAGTTCATTTATTAAAC
1 TAGTTCATTAATCAAAC
514014 TAGTGT-ATTAATCAAAC
1 TAGT-TCATTAATCAAAC
514031 TA
1 TA
514033 ACTCTTAATT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 42 0.91
18 4 0.09
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:518264 original size:7 final size:7
Alignment explanation
Indices: 518252--518304 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
518242 CCTAAGGAGG
518252 GAAAAAT
1 GAAAAAT
518259 GAAAAATT
1 GAAAAA-T
518267 AAGAAAAAT
1 --GAAAAAT
518276 GAAAAA-
1 GAAAAAT
518282 G-AAAA-
1 GAAAAAT
518287 GAAAAAT
1 GAAAAAT
518294 GAAAAA-
1 GAAAAAT
518300 GAAAA
1 GAAAA
518305 GAAAAATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
5 5 0.12
6 10 0.24
7 18 0.44
8 1 0.02
9 1 0.02
10 6 0.15
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.09
Consensus pattern (7 bp):
GAAAAAT
Found at i:518281 original size:18 final size:18
Alignment explanation
Indices: 518252--518311 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
518242 CCTAAGGAGG
**
518252 GAAAAATGAAAAA-TTAA
1 GAAAAATGAAAAAGAAAA
518269 GAAAAATGAAAAAGAAAA
1 GAAAAATGAAAAAGAAAA
518287 GAAAAATGAAAAAGAAAA
1 GAAAAATGAAAAAGAAAA
518305 GAAAAAT
1 GAAAAAT
518312 TAAATAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
17 13 0.32
18 27 0.68
ACGTcount: A:0.75, C:0.00, G:0.15, T:0.10
Consensus pattern (18 bp):
GAAAAATGAAAAAGAAAA
Found at i:518285 original size:13 final size:12
Alignment explanation
Indices: 518267--518310 Score: 56
Period size: 11 Copynumber: 3.7 Consensus size: 12
518257 ATGAAAAATT
518267 AAGAAAAATGAAA
1 AAGAAAAA-GAAA
518280 AAG-AAAAGAAA
1 AAGAAAAAGAAA
518291 AATGAAAAAG-AA
1 AA-GAAAAAGAAA
518303 AAGAAAAA
1 AAGAAAAA
518311 TTAAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 12 0.41
12 9 0.31
13 8 0.28
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:518310 original size:6 final size:6
Alignment explanation
Indices: 518267--518310 Score: 56
Period size: 6 Copynumber: 7.3 Consensus size: 6
518257 ATGAAAAATT
518267 AAGAAA AATGAAA AAG-AA AAGAAA AATGAAA AAG-AA AAGAAA AA
1 AAGAAA AA-GAAA AAGAAA AAGAAA AA-GAAA AAGAAA AAGAAA AA
518311 TTAAATAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
5 10 0.29
6 12 0.35
7 12 0.35
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:518801 original size:21 final size:23
Alignment explanation
Indices: 518777--518819 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
518767 TATAAAAATT
*
518777 CCAATTTTCTT-ATTT-CAAGCC
1 CCAACTTTCTTCATTTACAAGCC
*
518798 CCAACTTTGTTCATTTACAAGC
1 CCAACTTTCTTCATTTACAAGC
518820 ATCTTATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 4 0.22
23 5 0.28
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.40
Consensus pattern (23 bp):
CCAACTTTCTTCATTTACAAGCC
Found at i:521119 original size:119 final size:119
Alignment explanation
Indices: 520886--521141 Score: 295
Period size: 119 Copynumber: 2.2 Consensus size: 119
520876 TAAAACTATT
* * *
520886 ACAGAAGGAGGTGGATCATCATTTCCAAAGGAGGAATTCATAATGAGAAGAACTCATCCGATAAG
1 ACAGAAGGAGGTGGATCACCATTTCCAAAGCAGGAATTCATAATGAGAAGAACTCATCCGAGAAG
* *
520951 GAAAAATAAGTTCATAATGAGAATAACTTTTTCGACCTTTTACTCAAATCCATC
66 GAAAAAGAAGTTCATAATGAGAAGAACTTTTTCGACCTTTTACTCAAATCCATC
* * * * *
521005 ATAGAAGGAGGTGGATCACCATTTCCAATA-CATGG-GTTCATAATGAGAAGAACTCGTCTGAGG
1 ACAGAAGGAGGTGGATCACCATTTCCAA-AGCA-GGAATTCATAATGAGAAGAACTCATCCGAGA
* * ** *
521068 AGG-AAAAGAAGTTCATAATGAGAAGAA-TTTGTTTGACATTTTTGTTTAAATCCATC
64 AGGAAAAAGAAGTTCATAATGAGAAGAACTTT-TTCGAC-CTTTTACTCAAATCCATC
* *
521124 ACATAAGGAGTTGGATCA
1 ACAGAAGGAGGTGGATCA
521142 ACATCAACAT
Statistics
Matches: 115, Mismatches: 18, Indels: 8
0.82 0.13 0.06
Matches are distributed among these distances:
117 3 0.03
118 27 0.23
119 82 0.71
120 3 0.03
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (119 bp):
ACAGAAGGAGGTGGATCACCATTTCCAAAGCAGGAATTCATAATGAGAAGAACTCATCCGAGAAG
GAAAAAGAAGTTCATAATGAGAAGAACTTTTTCGACCTTTTACTCAAATCCATC
Found at i:529091 original size:44 final size:44
Alignment explanation
Indices: 529023--529147 Score: 117
Period size: 44 Copynumber: 2.8 Consensus size: 44
529013 TTCGACCTTT
* * * * *
529023 TTGCTTAAATCCATTACATAAGGAGGTTGATCAGCATCACCATG
1 TTGCTTGATTCCATCACAGAAGGAGGTTGATCAGCATCAACATG
* * * * ** *
529067 TTGCTTGATTCTATCATAGAAGGAGATAGATCAATATCAACATT
1 TTGCTTGATTCCATCACAGAAGGAGGTTGATCAGCATCAACATG
*
529111 TTGTTTGATTCCATCACAGAAGGAGG-TGAATCAGCAT
1 TTGCTTGATTCCATCACAGAAGGAGGTTG-ATCAGCAT
529148 AATCGAATGA
Statistics
Matches: 61, Mismatches: 19, Indels: 2
0.74 0.23 0.02
Matches are distributed among these distances:
43 1 0.02
44 60 0.98
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (44 bp):
TTGCTTGATTCCATCACAGAAGGAGGTTGATCAGCATCAACATG
Found at i:531149 original size:18 final size:18
Alignment explanation
Indices: 531112--531154 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
531102 TGTTTATGTG
* * *
531112 TTAATTGTTTTTTTTTAT
1 TTAATTGTTATCTTTAAT
531130 TTAATTGTTATCTTTAAT
1 TTAATTGTTATCTTTAAT
531148 TTCAATT
1 TT-AATT
531155 TCGTTAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.67
Consensus pattern (18 bp):
TTAATTGTTATCTTTAAT
Found at i:532717 original size:33 final size:32
Alignment explanation
Indices: 532675--532757 Score: 123
Period size: 33 Copynumber: 2.6 Consensus size: 32
532665 CCTCCCCGAT
532675 TATATATATATATATATTTATTTTTTATATTAA
1 TATATATATA-ATATATTTATTTTTTATATTAA
*
532708 TATATATATAATATTTTATATTTTTTATATTAA
1 TATATATATAATATATT-TATTTTTTATATTAA
*
532741 T-TATATATAAAATATTT
1 TATATATATAATATATTT
532758 TCAGGTTCGA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
31 1 0.02
32 19 0.41
33 26 0.57
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (32 bp):
TATATATATAATATATTTATTTTTTATATTAA
Found at i:541766 original size:19 final size:19
Alignment explanation
Indices: 541742--541818 Score: 84
Period size: 19 Copynumber: 4.1 Consensus size: 19
541732 GACCGGTCCC
*
541742 ACTCGACCCAAATTGTTTG
1 ACTCGACCCAAACTGTTTG
541761 ACTCGACCCAAACTGTTTG
1 ACTCGACCCAAACTGTTTG
* ** *
541780 AC-CCACCTGAACTATTTG
1 ACTCGACCCAAACTGTTTG
* *
541798 ACTCAACCCGAACTGTTTG
1 ACTCGACCCAAACTGTTTG
541817 AC
1 AC
541819 CCAACCCGTT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.29
19 35 0.71
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.27
Consensus pattern (19 bp):
ACTCGACCCAAACTGTTTG
Found at i:541823 original size:19 final size:19
Alignment explanation
Indices: 541755--541826 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
541745 CGACCCAAAT
* * *
541755 TGTTTGACTCGACCCAAAC
1 TGTTTGACCCAACCCGAAC
*
541774 TGTTTGACCC-ACCTGAAC
1 TGTTTGACCCAACCCGAAC
* *
541792 TATTTGACTCAACCCGAAC
1 TGTTTGACCCAACCCGAAC
541811 TGTTTGACCCAACCCG
1 TGTTTGACCCAACCCG
541827 TTGACTTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.32
19 30 0.68
ACGTcount: A:0.25, C:0.33, G:0.15, T:0.26
Consensus pattern (19 bp):
TGTTTGACCCAACCCGAAC
Found at i:541867 original size:16 final size:16
Alignment explanation
Indices: 541826--541870 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
541816 GACCCAACCC
* *
541826 GTTGACTTTAACTAGA
1 GTTGACTTTGACCAGA
*
541842 GTTGACTTTGACCAGT
1 GTTGACTTTGACCAGA
541858 GTTGACTTTGACC
1 GTTGACTTTGACC
541871 CAAAAAGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (16 bp):
GTTGACTTTGACCAGA
Found at i:546214 original size:19 final size:18
Alignment explanation
Indices: 546153--546215 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 18
546143 CGGTCCTACT
546153 CGACCCAAACTGTTTGACC
1 CGACCCAAACTGTTTGA-C
*
546172 CAACCCAAACTGTTTGAC
1 CGACCCAAACTGTTTGAC
546190 CTGACCCAAACTGTTTGAC
1 C-GACCCAAACTGTTTGAC
546209 ACGACCC
1 -CGACCC
546216 GTTGACTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.05
19 37 0.93
20 1 0.03
ACGTcount: A:0.29, C:0.37, G:0.14, T:0.21
Consensus pattern (18 bp):
CGACCCAAACTGTTTGAC
Found at i:546237 original size:16 final size:16
Alignment explanation
Indices: 546216--546260 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
546206 GACACGACCC
546216 GTTGACTTTAACCAGA
1 GTTGACTTTAACCAGA
*
546232 GTTGACTTTGACCAGA
1 GTTGACTTTAACCAGA
546248 GTTGACTTTAACC
1 GTTGACTTTAACC
546261 CCAAAAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (16 bp):
GTTGACTTTAACCAGA
Found at i:555880 original size:22 final size:22
Alignment explanation
Indices: 555855--555901 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
555845 AAGTCAAACG
*
555855 CCGGTGACCACCACGTCAGTTT
1 CCGGTGACCACCACATCAGTTT
*
555877 CCGGTGACTACCACATCAGTTT
1 CCGGTGACCACCACATCAGTTT
555899 CCG
1 CCG
555902 TTCCCGTTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.36, G:0.21, T:0.23
Consensus pattern (22 bp):
CCGGTGACCACCACATCAGTTT
Found at i:558046 original size:23 final size:23
Alignment explanation
Indices: 558012--558055 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
558002 TTTTTATTAC
558012 TTTTTAACTCTTAAATTATTGTT
1 TTTTTAACTCTTAAATTATTGTT
*
558035 TTTTTAATTCTTAAATTATTG
1 TTTTTAACTCTTAAATTATTG
558056 ATAATTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.27, C:0.07, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTTTAACTCTTAAATTATTGTT
Found at i:558063 original size:23 final size:23
Alignment explanation
Indices: 558014--558066 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
558004 TTTATTACTT
* * **
558014 TTTAACTCTTAAATTATTGTTTT
1 TTTAATTCTTAAATTATTGATAA
558037 TTTAATTCTTAAATTATTGATAA
1 TTTAATTCTTAAATTATTGATAA
558060 TTTAATT
1 TTTAATT
558067 AATTTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (23 bp):
TTTAATTCTTAAATTATTGATAA
Found at i:558354 original size:10 final size:10
Alignment explanation
Indices: 558254--558354 Score: 66
Period size: 10 Copynumber: 10.4 Consensus size: 10
558244 CGAACCCCGT
*
558254 TTTATATTTA
1 TTTATAATTA
* *
558264 TTTTAAAATTG
1 -TTTATAATTA
*
558275 TTTATATTTA
1 TTTATAATTA
*
558285 TTTATGATTA
1 TTTATAATTA
*
558295 TTTGTAATTA
1 TTTATAATTA
*
558305 TTTATATTTA
1 TTTATAATTA
558315 -TT-TAATTA
1 TTTATAATTA
* *
558323 TTAAAAATTA
1 TTTATAATTA
**
558333 AATAT-A-TA
1 TTTATAATTA
558341 TTTATAATTA
1 TTTATAATTA
558351 TTTA
1 TTTA
558355 CAAAAAAAAT
Statistics
Matches: 65, Mismatches: 21, Indels: 9
0.68 0.22 0.09
Matches are distributed among these distances:
8 10 0.15
9 5 0.08
10 43 0.66
11 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (10 bp):
TTTATAATTA
Found at i:558583 original size:18 final size:18
Alignment explanation
Indices: 558524--558586 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 18
558514 ATTTATTTTC
*
558524 ATAAATAATTATA-AATT
1 ATAAATAATTATATAAAT
* *
558541 ATAAAT-GTATATTTAAAT
1 ATAAATAAT-TATATAAAT
* *
558559 TTTAATAATTATATAAAT
1 ATAAATAATTATATAAAT
558577 ATAAATAATT
1 ATAAATAATT
558587 TTAAACTGTA
Statistics
Matches: 34, Mismatches: 9, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
16 1 0.03
17 9 0.26
18 23 0.68
19 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATAAATAATTATATAAAT
Done.