Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007724.1 Hibiscus syriacus cultivar Beakdansim tig00109971_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: 1221931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:366781 original size:9 final size:9
Alignment explanation
Indices: 366769--366846 Score: 66
Period size: 9 Copynumber: 8.3 Consensus size: 9
366759 ACCTGCTCAG
*
366769 GACGACGAC
1 GACGACGAT
366778 GACGACGAT
1 GACGACGAT
*
366787 GACGATGAT
1 GACGACGAT
* *
366796 GACGATGGT
1 GACGACGAT
366805 GACGACGAT
1 GACGACGAT
* *
366814 GATGATGGTGAT
1 GACGA---CGAT
*
366826 GACGACGAC
1 GACGACGAT
366835 GACGACGAT
1 GACGACGAT
366844 GAC
1 GAC
366847 AGCGAGGAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
9 48 0.87
12 7 0.13
ACGTcount: A:0.31, C:0.19, G:0.36, T:0.14
Consensus pattern (9 bp):
GACGACGAT
Found at i:367099 original size:35 final size:33
Alignment explanation
Indices: 367060--367144 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
367050 ATATTTCAGT
367060 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
367095 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
367130 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
367145 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:370574 original size:12 final size:12
Alignment explanation
Indices: 370557--370589 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
370547 ATTTATAAGA
370557 GAGGAGAGATGT
1 GAGGAGAGATGT
370569 GA-G-GAGATGT
1 GAGGAGAGATGT
370579 GAGGAGAGATG
1 GAGGAGAGATG
370590 CGAGAACCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (12 bp):
GAGGAGAGATGT
Found at i:373630 original size:108 final size:107
Alignment explanation
Indices: 373477--373861 Score: 310
Period size: 108 Copynumber: 3.5 Consensus size: 107
373467 CGTTTTTTTA
* * *
373477 AAGCTGATGGGGCCTTTAGAAATCCGACGATAACAAAATAAGTTAATTACTTAATTTGTCATGAG
1 AAGCTGATGGAGCC-TTAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTCAT-AG
* *
373542 TATTATCAACATAATAGGTAACGCCCAAAATGTTACCAAAGTTT
64 TATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTT
* * * * *
373586 ACGCTGATGGAGCCTTAGAAATCCAACGATAACATAATCGGTTAATTACTGTAAACATTATCA-A
1 AAGCTGATGGAGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTACT-T-AA-TTTGTCATA
* * * * * ***
373650 GCATAAT-AACATATTAGGTAGCGCTTATGTAACGTAATAGGTAGCGC-CTTTTT
63 GTATTATCAACATATTAGGTAACGC----CTAA---AAT-GTTA-C-CAAAGTTT
* * * * * *
373703 AAAGCTGATGGGGCTTTAGAAATCCGATGATAACAAAATAGGTTAATTATTTAATTTGTGATAAG
1 -AAGCTGATGGAGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTCAT-AG
* *
373768 TATTATCAATATATTAGGTGACGCCTAAAATGTTACCAAAGTTT
64 TATTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTT
* * * *
373812 AAGCTGATGGAGCCTTAGAAATTCGAA-GATAATATAATCGGTTAATTACT
1 AAGCTGATGGAGCCTTAGAAA-TCCAACGATAACAAAATAGGTTAATTACT
373862 GAAAATATTA
Statistics
Matches: 210, Mismatches: 47, Indels: 39
0.71 0.16 0.13
Matches are distributed among these distances:
108 86 0.41
109 26 0.12
110 5 0.02
111 8 0.04
112 2 0.01
114 3 0.01
115 7 0.03
116 5 0.02
117 11 0.05
118 57 0.27
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (107 bp):
AAGCTGATGGAGCCTTAGAAATCCAACGATAACAAAATAGGTTAATTACTTAATTTGTCATAGTA
TTATCAACATATTAGGTAACGCCTAAAATGTTACCAAAGTTT
Found at i:373831 original size:226 final size:226
Alignment explanation
Indices: 373158--373919 Score: 1148
Period size: 226 Copynumber: 3.4 Consensus size: 226
373148 AAAAATATTG
* *
373158 ACGATAACATAACCGGTTAATTACTGGAAACATTATCAAGCATAATAACATATTAGATAGCGCTT
1 ACGATAACATAACCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
* * * *
373223 ATATAACATAATAGGTAGCGTATTTTTAAAGCTGATGGAGCATTAGAAATCCGACGATAACAAAA
66 ATGTAACGTAATAGGTAGCGTATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAAAA
* * * * * *
373288 TATGTTAATTACTTAATTTGTTATTAGTATTATCAACATATTAGATAAAGCCTAAAATATTACCA
131 TAAGTTAATTACTTAATTTGTCATAAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCA
* *
373353 AAGTTTAAGCTGATGGAGCCTTAGGAATCCG
196 AAGTTTAAGCTGATGGAGCCTTAGAAATCCA
* * *
373384 ACGATAACATAACCGGTTAATTACTATAAATATTATAAAGCATAATAACATATTAGGTAGCGCTT
1 ACGATAACATAACCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
*
373449 ATGTAACGTAATAGGTAGCGTTTTTTTAAAGCTGATGGGGCCTTTAGAAATCCGACGATAACAAA
66 ATGTAACGTAATAGGTAGCGTATTTTTAAAGCTGATGGGG-CTTTAGAAATCCGACGATAACAAA
* * *
373514 ATAAGTTAATTACTTAATTTGTCATGAGTATTATCAACATAATAGGTAACGCCCAAAATGTTACC
130 ATAAGTTAATTACTTAATTTGTCATAAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACC
*
373579 AAAGTTTACGCTGATGGAGCCTTAGAAATCCA
195 AAAGTTTAAGCTGATGGAGCCTTAGAAATCCA
*
373611 ACGATAACATAATCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
1 ACGATAACATAACCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
** *
373676 ATGTAACGTAATAGGTAGCGCCTTTTTAAAGCTGATGGGGCTTTAGAAATCCGATGATAACAAAA
66 ATGTAACGTAATAGGTAGCGTATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAAAA
* * * * *
373741 TAGGTTAATTATTTAATTTGTGATAAGTATTATCAATATATTAGGTGACGCCTAAAATGTTACCA
131 TAAGTTAATTACTTAATTTGTCATAAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCA
*
373806 AAGTTTAAGCTGATGGAGCCTTAGAAATTCGA
196 AAGTTTAAGCTGATGGAGCCTTAGAAA-TCCA
* * * * * * *
373838 A-GATAATATAATCGGTTAATTACTGAAAATATTATGAAACATAATAACATATTAGGTAGTGCTT
1 ACGATAACATAACCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
373902 ATGTAACGTAATAGGTAG
66 ATGTAACGTAATAGGTAG
373920 TGCTTATGTA
Statistics
Matches: 490, Mismatches: 44, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
226 278 0.57
227 212 0.43
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (226 bp):
ACGATAACATAACCGGTTAATTACTGTAAACATTATCAAGCATAATAACATATTAGGTAGCGCTT
ATGTAACGTAATAGGTAGCGTATTTTTAAAGCTGATGGGGCTTTAGAAATCCGACGATAACAAAA
TAAGTTAATTACTTAATTTGTCATAAGTATTATCAACATATTAGGTAACGCCTAAAATGTTACCA
AAGTTTAAGCTGATGGAGCCTTAGAAATCCA
Found at i:373916 original size:23 final size:23
Alignment explanation
Indices: 373890--373942 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
373880 AATAACATAT
373890 TAGGTAGTGCTTATGTAACGTAA
1 TAGGTAGTGCTTATGTAACGTAA
*
373913 TAGGTAGTGCTTATGTAATGTAA
1 TAGGTAGTGCTTATGTAACGTAA
373936 TAGGTAG
1 TAGGTAG
373943 AACATTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.30, C:0.06, G:0.28, T:0.36
Consensus pattern (23 bp):
TAGGTAGTGCTTATGTAACGTAA
Found at i:376146 original size:199 final size:198
Alignment explanation
Indices: 375806--376214 Score: 597
Period size: 199 Copynumber: 2.1 Consensus size: 198
375796 TGTGTCTGGG
* * *
375806 TATCGATACATTCTGCGTGCATCTAGTTGGGAATCATACTGGACAAAAAGTATTGATACAAATAC
1 TATCGATACTTTCTGCGTGCATCTAGTTGGGAAGCATACTGGACAAAAAGTATGGATACAAATAC
* * *
375871 AAAAAGTAAGCATACTTTATGTTAACTTATTTTGTCATTAAACCGGTATATTTTTACCGCTTACA
66 AAAAAGTAAGCATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCGCTTAAA
* *
375936 TTATAAATTTACTTATTACTTTAAAGTAATTGGTTTCAACGATTTAAGAATCGATACTTTTCATA
131 TTATAAATTTACCTATTACTTTAAAGTAATCGGTTTCAA-GATTTAAGAATCGATACTTTTCATA
**
376001 TGTA
195 CATA
* *
376005 TATCGATACTTTCTGCGTGTATCTAGTTTGGGAAGCATACTGGACAAAAAGTATGGATACACATA
1 TATCGATACTTTCTGCGTGCATCTAG-TTGGGAAGCATACTGGACAAAAAGTATGGATACAAATA
* *
376070 CAAAAAGT-ATCGATACTTTATGTTTACATATTTT-TCATTAAACCGATATATTTTTACCGCTTA
65 CAAAAAGTAAGC-ATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCGCTTA
* * * * *
376133 AATTGTAAATTTACCTATTTCTTTAAAGTAATCGTTTTGAAGTTTTAAGAATCGATACTTTTCAT
129 AATTATAAATTTACCTATTACTTTAAAGTAATCGGTTTCAAGATTTAAGAATCGATACTTTTCAT
*
376198 ACATG
194 ACATA
376203 TATCGATACTTT
1 TATCGATACTTT
376215 ATAGGCATAA
Statistics
Matches: 188, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
198 37 0.20
199 88 0.47
200 63 0.34
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (198 bp):
TATCGATACTTTCTGCGTGCATCTAGTTGGGAAGCATACTGGACAAAAAGTATGGATACAAATAC
AAAAAGTAAGCATACTTTATGTTAACATATTTTGTCATTAAACCGATATATTTTTACCGCTTAAA
TTATAAATTTACCTATTACTTTAAAGTAATCGGTTTCAAGATTTAAGAATCGATACTTTTCATAC
ATA
Found at i:378097 original size:24 final size:24
Alignment explanation
Indices: 378064--378126 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
378054 AGTGGAGCCG
378064 AAATTGAAATTGAAATTCAAACTC
1 AAATTGAAATTGAAATTCAAACTC
* **
378088 AAATTAAAATTGAAATTCAGTCTC
1 AAATTGAAATTGAAATTCAAACTC
378112 AAATTGAAATTGAAA
1 AAATTGAAATTGAAA
378127 ACTGTATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.30
Consensus pattern (24 bp):
AAATTGAAATTGAAATTCAAACTC
Found at i:381238 original size:199 final size:200
Alignment explanation
Indices: 380896--382222 Score: 1464
Period size: 200 Copynumber: 6.6 Consensus size: 200
380886 TCGTTGTTTT
* * * * * * *
380896 CATATTGGACCAAAAGTATCAATACAT-ATACAAAAAGTATTGATACTTTATGTTAACATATTTT
1 CATACTGGACAAAAAGTATCGATAC-TCATACAAAAAGTATCGATACTTTATGTTTACGTATCTT
* * *
380960 GTCATTAAACCGGTA-ATTTTTACCG-AATACATTGTAAATTTACCTATTACTTTAAAGTAATCG
65 GTCATTAAACCGGTATCTTTTTACCGCTA-ACATTGTAAATTTACCTATTACTTTAAATTAATCG
* * * *
381023 GTTTCGAATTTTTAAGAATCGATA-TTTCTCATAAGTGTATCGATACTTTCTGCGTGCATCTAGT
129 ATTTCAAAGTTTTAAGAATCGATACTTT-TCATACGTGTATCGATACTTTCTGCGTGCATCTAGT
*
381087 TTGTGAAG
193 TTGGGAAG
* * * *
381095 -AGTATTGGACAAAAAGTATCTATACACATA-AAAAAGTATAC-ATACTTTATGTTTATGTATCT
1 CA-TACTGGACAAAAAGTATCGATACTCATACAAAAAGTAT-CGATACTTTATGTTTACGTATCT
* * *
381157 TGTCATTAAATCGGTATCTTTTTACCGTTAACATTGTAAATTTACGTATTACTTTAAATTAATCG
64 TGTCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATCG
* * * *
381222 ATTTCAAAGATTTAAGAATCGATA-TTTTTATGCGTGTATCGATACTTTCTGCGTTCATCTAGTT
129 ATTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTT
381286 TGGGAAG
194 TGGGAAG
* * * * * *
381293 CATACTAGATAAAAAGTTTCAATACTCATACAAAAAGTATCGATACTTTATGTTTATGTATTTTG
1 CATACTGGACAAAAAGTATCGATACTCATACAAAAAGTATCGATACTTTATGTTTACGTATCTTG
* * * *
381358 CCATTAAA-CTGTATCTTTTTACCGCTAACATTGT-AA---A--T-TTACTTTAAATTAATTGGT
66 TCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATCGAT
* * * *
381415 TTCAAAGTTTGAAGAATCGATACTTTGCATACGTGTATCGATACTTTATGCGTGCATCTCGTTTG
131 TTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTG
381480 GGAAG
196 GGAAG
* * *
381485 CATACTAGAAAAAAAGTATCGATACTCATACAAAATTATTGATACTTAAAAAGTATCAATACTTT
1 CATACTGGACAAAAAGTATCGATA--C-T-C----------ATAC--AAAAAGTATCGATACTTT
*
381550 ATGTTTACGTATCTTGTCATTAAACCGGTATATTTTTACCGCTAACATTGT-AATTTACCTATTA
50 ATGTTTACGTATCTTGTCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTA
* * *
381614 CTTTAAATTAATC-AGTTTCAAAGTTTTAAGAATCGATATTTTTCATATGTGTATCGATACTTTT
115 CTTTAAATTAATCGA-TTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTC
381678 TGCGTGCATCTAGTTTGGGAAG
179 TGCGTGCATCTAGTTTGGGAAG
* *
381700 CATACTGGACAAAAAGTTTCGATACTCATACAAAAAGTATCGATACTTTATGTTTACGTATTTTG
1 CATACTGGACAAAAAGTATCGATACTCATACAAAAAGTATCGATACTTTATGTTTACGTATCTTG
* * * * * *
381765 TCATTAAATCGATATCGTTTAACCGTTAACATTGTAAATTTACTTATTACTTTAAATTAATC-AG
66 TCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATCGA-
* * * * * * * * *
381829 TTTCGAAGTTTGAAGAATCGATACTTTGCATATGTGTGTCAATACTTTATGTGTGCATCTCGTTT
130 TTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTT
381894 GGGAAG
195 GGGAAG
* * * *
381900 CATACTGGACAAAAAGTATCGATACTCATACAAAACGTATCGATATTTTATGTTTACATAACTTG
1 CATACTGGACAAAAAGTATCGATACTCATACAAAAAGTATCGATACTTTATGTTTACGTATCTTG
*
381965 TCATTAAACCGGTATCTTTTTACCGCTAACATTTTAAATTTACCTATTACTTTAAATTAATCTG-
66 TCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATC-GA
* * *
382029 TTTCGAAGTTTTAAGAATCAATACTTTTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTT
130 TTTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTT
382094 GGGAAG
195 GGGAAG
* * ** *
382100 CATACTGGATAAAAAGCT-TTGATACTCATACAAAAA-TGATAAAAACTTTATG-TTA--TAT-T
1 CATACTGGACAAAAAG-TATCGATACTCATACAAAAAGT-ATCGATACTTTATGTTTACGTATCT
** * ** * * *
382159 ATGTCATTAAACCAATATATTTTTACTTCTTACATTGTAAATTTAACTATTACTTTAAAGTAAT
64 -TGTCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAAT
382223 AAATGTTGAA
Statistics
Matches: 971, Mismatches: 118, Indels: 80
0.83 0.10 0.07
Matches are distributed among these distances:
191 37 0.04
192 63 0.06
194 2 0.00
195 1 0.00
196 2 0.00
197 58 0.06
198 128 0.13
199 193 0.20
200 308 0.32
201 5 0.01
206 4 0.00
208 38 0.04
209 26 0.03
211 1 0.00
212 2 0.00
213 1 0.00
214 1 0.00
215 101 0.10
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.39
Consensus pattern (200 bp):
CATACTGGACAAAAAGTATCGATACTCATACAAAAAGTATCGATACTTTATGTTTACGTATCTTG
TCATTAAACCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATCGAT
TTCAAAGTTTTAAGAATCGATACTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTG
GGAAG
Found at i:381519 original size:20 final size:17
Alignment explanation
Indices: 381495--381548 Score: 54
Period size: 17 Copynumber: 3.0 Consensus size: 17
381485 CATACTAGAA
381495 AAAAAGTATCGATACTCAT
1 AAAAAGTATCGATACT--T
* *
381514 ACAAAATTATTGATACTT
1 A-AAAAGTATCGATACTT
*
381532 AAAAAGTATCAATACTT
1 AAAAAGTATCGATACTT
381549 TATGTTTACG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
17 13 0.45
18 2 0.07
19 1 0.03
20 13 0.45
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.31
Consensus pattern (17 bp):
AAAAAGTATCGATACTT
Found at i:381674 original size:407 final size:401
Alignment explanation
Indices: 380923--382135 Score: 1461
Period size: 407 Copynumber: 3.0 Consensus size: 401
380913 ATCAATACAT
* * * * * * *
380923 ATACAAAAAGTATTGATACTTTATGTTAACATATTTTGTCATTAAACCGGTAAT--TTTTACCG-
1 ATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGCCATTAAATCGAT-ATCGTTTAACCGC
* * * * * *
380985 AATACATTGTAAATTTACCTATTACTTTAAAGTAATCGGTTTCGAATTTTTAAGAATCGATA-TT
65 TA-ACATTGTAAA--TA-CTATTACTTTAAATTAATCAGTTTCAAAGTTTGAAGAATCGATACTT
* * * * * * * * *
381049 TCTCATAAGTGTATCGATACTTTCTGCGTGCATCTAGTTTGTGAAG-AGTATTGGACAAAAAGTA
126 T-GCATACGTGTATCAATACTTTATGCGTGCATCTCGTTTGGGAAGCA-TACTAGAAAAAAAGTA
* * * *
381113 TC--TA-T-ACAC-ATA-AAAAAGTAT-ACATACTTTATGTTTATGTATCTTGTCATTAAATCGG
189 TCGATACTCATACAAAACAAAAAGTATCA-ATACTTTATGTTTACGTATCTTGTCATTAAACCGG
* * *
381171 TATCTTTTTACCGTTAACATTGTAAATTTACGTATTACTTTAAATTAATCGATTTCAAAGATTTA
253 TATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATCG-TTTCAAAGTTTTA
* * *
381236 AGAATCGATATTTTT-ATGCGTGTATCGATACTTTCTGCGTTCATCTAGTTTGGGAAGCATACTA
317 AGAATCGATATTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTG
*
381300 GATAAAAAGTTTCAATACTC
382 GATAAAAAGTTTCGATACTC
* * *
381320 ATACAAAAAGTATCGATACTTTATGTTTATGTATTTTGCCATTAAA-CTG-TATCTTTTTACCGC
1 ATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGCCATTAAATC-GATATCGTTTAACCGC
**
381383 TAACATTGT-AA-A-T-TTACTTTAAATTAATTGGTTTCAAAGTTTGAAGAATCGATACTTTGCA
65 TAACATTGTAAATACTATTACTTTAAATTAATCAGTTTCAAAGTTTGAAGAATCGATACTTTGCA
*
381444 TACGTGTATCGATACTTTATGCGTGCATCTCGTTTGGGAAGCATACTAGAAAAAAAGTATCGATA
130 TACGTGTATCAATACTTTATGCGTGCATCTCGTTTGGGAAGCATACTAGAAAAAAAGTATCGATA
381509 CTCATACAAAATTATTGATACTTAAAAAGTATCAATACTTTATGTTTACGTATCTTGTCATTAAA
195 CTCATAC---A--A---A-AC--AAAAAGTATCAATACTTTATGTTTACGTATCTTGTCATTAAA
*
381574 CCGGTATATTTTTACCGCTAACATTGT-AATTTACCTATTACTTTAAATTAATCAGTTTCAAAGT
249 CCGGTATCTTTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATC-GTTTCAAAGT
* *
381638 TTTAAGAATCGATATTTTTCATATGTGTATCGATACTTTTTGCGTGCATCTAGTTTGGGAAGCAT
313 TTTAAGAATCGATATTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCAT
*
381703 ACTGGACAAAAAGTTTCGATACTC
378 ACTGGATAAAAAGTTTCGATACTC
* *
381727 ATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGTCATTAAATCGATATCGTTTAACCGTT
1 ATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGCCATTAAATCGATATCGTTTAACCGCT
*
381792 AACATTGTAAATTTACTTATTACTTTAAATTAATCAGTTTCGAAGTTTGAAGAATCGATACTTTG
66 AACATTGTAAA--TAC-TATTACTTTAAATTAATCAGTTTCAAAGTTTGAAGAATCGATACTTTG
* * * * *
381857 CATATGTGTGTCAATACTTTATGTGTGCATCTCGTTTGGGAAGCATACTGGACAAAAAGTATCGA
128 CATACGTGTATCAATACTTTATGCGTGCATCTCGTTTGGGAAGCATACTAGAAAAAAAGTATCGA
* * * *
381922 TACTCATACAAAAC-----GTATCGATATTTTATGTTTACATAACTTGTCATTAAACCGGTATCT
193 TACTCATACAAAACAAAAAGTATCAATACTTTATGTTTACGTATCTTGTCATTAAACCGGTATCT
* *
381982 TTTTACCGCTAACATTTTAAATTTACCTATTACTTTAAATTAATCTGTTTCGAAGTTTTAAGAAT
258 TTTTACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATC-GTTTCAAAGTTTTAAGAAT
* * *
382047 CAATACTTTTCATACGTGTATCGATACTTTCTGTGTGCATCTAGTTTGGGAAGCATACTGGATAA
322 CGATATTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGATAA
382112 AAAGCTTT-GATACTC
387 AAAG-TTTCGATACTC
382127 ATACAAAAA
1 ATACAAAAA
382136 TGATAAAAAC
Statistics
Matches: 717, Mismatches: 62, Indels: 71
0.84 0.07 0.08
Matches are distributed among these distances:
390 90 0.13
391 5 0.01
392 2 0.00
393 2 0.00
394 3 0.00
395 2 0.00
396 4 0.01
397 57 0.08
398 1 0.00
399 58 0.08
400 124 0.17
401 3 0.00
404 1 0.00
406 54 0.08
407 172 0.24
408 22 0.03
409 2 0.00
410 1 0.00
412 2 0.00
414 1 0.00
415 111 0.15
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (401 bp):
ATACAAAAAGTATCGATACTTTATGTTTACGTATTTTGCCATTAAATCGATATCGTTTAACCGCT
AACATTGTAAATACTATTACTTTAAATTAATCAGTTTCAAAGTTTGAAGAATCGATACTTTGCAT
ACGTGTATCAATACTTTATGCGTGCATCTCGTTTGGGAAGCATACTAGAAAAAAAGTATCGATAC
TCATACAAAACAAAAAGTATCAATACTTTATGTTTACGTATCTTGTCATTAAACCGGTATCTTTT
TACCGCTAACATTGTAAATTTACCTATTACTTTAAATTAATCGTTTCAAAGTTTTAAGAATCGAT
ATTTTTCATACGTGTATCGATACTTTCTGCGTGCATCTAGTTTGGGAAGCATACTGGATAAAAAG
TTTCGATACTC
Found at i:389434 original size:3 final size:3
Alignment explanation
Indices: 389426--389457 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
389416 GATTTTAGTT
389426 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
389458 TAGGAAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:391155 original size:11 final size:11
Alignment explanation
Indices: 391139--391163 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
391129 TGAGTTTAAC
391139 CAAAGATTACA
1 CAAAGATTACA
391150 CAAAGATTACA
1 CAAAGATTACA
391161 CAA
1 CAA
391164 CTTGGGTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.20, G:0.08, T:0.16
Consensus pattern (11 bp):
CAAAGATTACA
Found at i:391258 original size:21 final size:21
Alignment explanation
Indices: 391221--391260 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
391211 ATTAACATCA
*
391221 AACACTAACAAATTTTTAACT
1 AACACTAACAAACTTTTAACT
*
391242 AACACTAACAACCTTTTAA
1 AACACTAACAAACTTTTAA
391261 TTAATTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (21 bp):
AACACTAACAAACTTTTAACT
Found at i:396686 original size:13 final size:13
Alignment explanation
Indices: 396668--396695 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
396658 TATTAGTTGG
396668 GCTTAAATAATCT
1 GCTTAAATAATCT
396681 GCTTAAATAATCT
1 GCTTAAATAATCT
396694 GC
1 GC
396696 GATGCAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (13 bp):
GCTTAAATAATCT
Found at i:399640 original size:127 final size:127
Alignment explanation
Indices: 399368--399876 Score: 833
Period size: 127 Copynumber: 4.0 Consensus size: 127
399358 GTACTATTCA
* * * * * * *
399368 CGTGAAGGCACGTTCCCGAGGGCGCGCCTTCAATTATTTTGTCAAAGAATATGTTATTATTGCCC
1 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
399433 TATTATGTCACTTATGTCCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGT-CCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
399496 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTTCATTATTTTGTCAGAGAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
* *
399561 TATTATGTCACTTATGTCTCCCGGGAACTATTCATGCCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
*
399623 TGTGAAGGCGCGTTCCC-GGGG-ACGTACCTTCCATTATTTTGTCAGAGAATATGTTATCATTAC
1 CGTGAAGGCGCGTTCCCGGGGGCACG--CCTTCCATTATTTTGTCAGAGAATATGTTATCATTAC
* *
399686 TCTATTATGTCACTTATGTCCCCCGAGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
64 CCTATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
* *
399750 CGTGAAGGCGCGTTCCTGGGGGCACGCCTTCCATTATTTTGTCAGAAAATATGTTATCATTACCC
1 CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
*
399815 TATTATGTCACTTATGTCCCCCGGGAACTATTCATATCAATACCTATTATTCCTTAGGGGAC
66 TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
399877 TTTAAAGCGC
Statistics
Matches: 355, Mismatches: 22, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
125 3 0.01
126 4 0.01
127 267 0.75
128 78 0.22
129 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.33
Consensus pattern (127 bp):
CGTGAAGGCGCGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTACCC
TATTATGTCACTTATGTCCCCCGGGAACTATTCATGTCAATACCTATTATTCCTTAGGGGAC
Found at i:400344 original size:34 final size:34
Alignment explanation
Indices: 400306--400406 Score: 123
Period size: 34 Copynumber: 3.0 Consensus size: 34
400296 GAATTTAATG
*
400306 TTAAATTTCGAATATTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
** * *
400340 TTAAATTTTAAATAATACTATTTTA-ATTTTAATT
1 TTAAATTTCGAATAATA-TAATTTATATTTTAAAT
* *
400374 TTAAATTTCGAATACTATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
400407 AACATTTATT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
33 5 0.09
34 43 0.80
35 6 0.11
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:405825 original size:2 final size:2
Alignment explanation
Indices: 405818--405908 Score: 168
Period size: 2 Copynumber: 46.5 Consensus size: 2
405808 TTGCCCCGAT
405818 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
405860 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA T- 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
405900 TA TA TA TA T
1 TA TA TA TA T
405909 GTTTTATGAA
Statistics
Matches: 87, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
1 2 0.02
2 85 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:406366 original size:30 final size:30
Alignment explanation
Indices: 406332--406463 Score: 212
Period size: 30 Copynumber: 4.4 Consensus size: 30
406322 GAAAAATTAC
*
406332 AAATTGGTCACTAACT-TTATCATTTGTTAT
1 AAATTGGTCACTAA-TGTTATCGTTTGTTAT
406362 AAATTGGTCACTAATGTTATCGTTTGTTAT
1 AAATTGGTCACTAATGTTATCGTTTGTTAT
* * *
406392 AAATTGATCTCTAATTTTATCGTTTGTTAT
1 AAATTGGTCACTAATGTTATCGTTTGTTAT
406422 AAATTGGTCACTAATGTTATCGTTTGTTAT
1 AAATTGGTCACTAATGTTATCGTTTGTTAT
406452 AAATTGGTCACT
1 AAATTGGTCACT
406464 CGCATTAACA
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
29 1 0.01
30 93 0.99
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (30 bp):
AAATTGGTCACTAATGTTATCGTTTGTTAT
Found at i:407851 original size:30 final size:30
Alignment explanation
Indices: 407817--407917 Score: 157
Period size: 30 Copynumber: 3.4 Consensus size: 30
407807 AATAGCGAGT
*
407817 GACCAATTTGTAACAAATGATAACGTTAGC
1 GACCAATTTATAACAAATGATAACGTTAGC
*
407847 GACCACTTTATAACAAATGATAACGTTAGC
1 GACCAATTTATAACAAATGATAACGTTAGC
* *
407877 GACCAATTTATAACAAATGATAATGTTAGT
1 GACCAATTTATAACAAATGATAACGTTAGC
*
407907 GACCGATTTAT
1 GACCAATTTAT
407918 GATTTTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.30
Consensus pattern (30 bp):
GACCAATTTATAACAAATGATAACGTTAGC
Found at i:411725 original size:2 final size:2
Alignment explanation
Indices: 411718--411758 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
411708 TATTTATGTT
411718 TA TA TA 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
411759 TGAAAATTGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:412118 original size:4 final size:4
Alignment explanation
Indices: 412073--412102 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
412063 TAAATGTCCA
412073 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
412103 TCATGCGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:412778 original size:16 final size:17
Alignment explanation
Indices: 412750--412783 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
412740 AATAAATTCA
412750 TAATTATTTTTAAAATT
1 TAATTATTTTTAAAATT
412767 TAATTA-TTTTAAAATT
1 TAATTATTTTTAAAATT
412783 T
1 T
412784 TCAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TAATTATTTTTAAAATT
Found at i:416993 original size:3 final size:3
Alignment explanation
Indices: 416987--417013 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
416977 ATAAAAAAAA
416987 GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT
417014 AATACATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:421859 original size:15 final size:15
Alignment explanation
Indices: 421841--421870 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
421831 GGGGAGAAAG
421841 AGGAAGGTGAGGGTT
1 AGGAAGGTGAGGGTT
*
421856 AGGAGGGTGAGGGTT
1 AGGAAGGTGAGGGTT
421871 CTTCCAATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.57, T:0.20
Consensus pattern (15 bp):
AGGAAGGTGAGGGTT
Found at i:423713 original size:27 final size:27
Alignment explanation
Indices: 423682--423737 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
423672 AGCCCTAATA
423682 AATAATGTAAAACATCATATCTAATCC
1 AATAATGTAAAACATCATATCTAATCC
* *
423709 AATAATGTAAAACGTCGTATCTAATCC
1 AATAATGTAAAACATCATATCTAATCC
423736 AA
1 AA
423738 ATTTTACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.46, C:0.18, G:0.07, T:0.29
Consensus pattern (27 bp):
AATAATGTAAAACATCATATCTAATCC
Found at i:424083 original size:14 final size:14
Alignment explanation
Indices: 424064--424101 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
424054 TTTAGATTTT
424064 TTAAAATTACATTA
1 TTAAAATTACATTA
*
424078 TTAAAAATACATTA
1 TTAAAATTACATTA
424092 TTAATAATTA
1 TTAA-AATTA
424102 TAAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (14 bp):
TTAAAATTACATTA
Found at i:424195 original size:21 final size:21
Alignment explanation
Indices: 424171--424228 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
424161 AATTATGTGA
* *
424171 TAGGGTTTATGATTTAAGTTT
1 TAGGGTTTATGGTTTAAGATT
424192 TAGGGTTTATGGTTTAAGATT
1 TAGGGTTTATGGTTTAAGATT
424213 TAGGGTTTATGGTTTA
1 TAGGGTTTATGGTTTA
424229 GGGTTCATGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
TAGGGTTTATGGTTTAAGATT
Found at i:424200 original size:7 final size:7
Alignment explanation
Indices: 424171--424244 Score: 58
Period size: 7 Copynumber: 10.6 Consensus size: 7
424161 AATTATGTGA
424171 TAGGGTT
1 TAGGGTT
* *
424178 TATGATT
1 TAGGGTT
* *
424185 TAAGTTT
1 TAGGGTT
424192 TAGGGTT
1 TAGGGTT
*
424199 TATGGTT
1 TAGGGTT
* *
424206 TAAGATT
1 TAGGGTT
424213 TAGGGTT
1 TAGGGTT
*
424220 TATGGTT
1 TAGGGTT
424227 TAGGGTT
1 TAGGGTT
* *
424234 CATGGTT
1 TAGGGTT
424241 TAGG
1 TAGG
424245 ATTCATGGTT
Statistics
Matches: 50, Mismatches: 17, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.20, C:0.01, G:0.31, T:0.47
Consensus pattern (7 bp):
TAGGGTT
Found at i:424238 original size:14 final size:14
Alignment explanation
Indices: 424211--424256 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
424201 TGGTTTAAGA
*
424211 TTTAGGGTTTATGG
1 TTTAGGGTTCATGG
424225 TTTAGGGTTCATGG
1 TTTAGGGTTCATGG
*
424239 TTTAGGATTCATGG
1 TTTAGGGTTCATGG
424253 TTTA
1 TTTA
424257 ATTTATACAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.17, C:0.04, G:0.30, T:0.48
Consensus pattern (14 bp):
TTTAGGGTTCATGG
Found at i:424240 original size:21 final size:21
Alignment explanation
Indices: 424172--424242 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
424162 ATTATGTGAT
* * *
424172 AGGGTTTATGATTTAAGTTTT
1 AGGGTTTATGGTTTAAGATTC
*
424193 AGGGTTTATGGTTTAAGATTT
1 AGGGTTTATGGTTTAAGATTC
* *
424214 AGGGTTTATGGTTTAGGGTTC
1 AGGGTTTATGGTTTAAGATTC
*
424235 ATGGTTTA
1 AGGGTTTA
424243 GGATTCATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (21 bp):
AGGGTTTATGGTTTAAGATTC
Found at i:424576 original size:17 final size:18
Alignment explanation
Indices: 424537--424573 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
424527 AATGTCAAAT
424537 AATTAAAATTACAAGACAC
1 AATTAAAA-TACAAGACAC
424556 AATTAAAA-ACAAG-CAC
1 AATTAAAATACAAGACAC
424572 AA
1 AA
424574 ATTGAATGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.28
17 5 0.28
19 8 0.44
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (18 bp):
AATTAAAATACAAGACAC
Found at i:428807 original size:14 final size:14
Alignment explanation
Indices: 428788--428817 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
428778 TTTAGATTTT
*
428788 TTAAAATTACATTA
1 TTAAAAATACATTA
428802 TTAAAAATACATTA
1 TTAAAAATACATTA
428816 TT
1 TT
428818 GATAATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTAAAAATACATTA
Found at i:429380 original size:21 final size:21
Alignment explanation
Indices: 429335--429445 Score: 98
Period size: 21 Copynumber: 5.3 Consensus size: 21
429325 TTGCAATGAG
*
429335 CCCTAAA-CCTTAACCATAAA
1 CCCTAAATCCTAAACCATAAA
* *
429355 TCCTAAATCCTAAACTATAAA
1 CCCTAAATCCTAAACCATAAA
** *
429376 CCCTAAATATTAAATCATAAA
1 CCCTAAATCCTAAACCATAAA
* * *
429397 CACTAAACCCTAAACCCTAAA
1 CCCTAAATCCTAAACCATAAA
** *
429418 CCCTAAATATTAAACCCTAAA
1 CCCTAAATCCTAAACCATAAA
*
429439 CCATAAA
1 CCCTAAA
429446 CAATAAAAAC
Statistics
Matches: 71, Mismatches: 19, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
20 6 0.08
21 65 0.92
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (21 bp):
CCCTAAATCCTAAACCATAAA
Found at i:429438 original size:7 final size:7
Alignment explanation
Indices: 429335--429471 Score: 78
Period size: 7 Copynumber: 19.6 Consensus size: 7
429325 TTGCAATGAG
429335 CCCTAAA
1 CCCTAAA
*
429342 -CCTTAA
1 CCCTAAA
*
429348 CCATAAA
1 CCCTAAA
*
429355 TCCTAAA
1 CCCTAAA
*
429362 TCCTAAA
1 CCCTAAA
**
429369 CTATAAA
1 CCCTAAA
429376 CCCTAAA
1 CCCTAAA
***
429383 TATTAAA
1 CCCTAAA
* *
429390 TCATAAA
1 CCCTAAA
*
429397 CACTAAA
1 CCCTAAA
429404 CCCTAAA
1 CCCTAAA
429411 CCCTAAA
1 CCCTAAA
429418 CCCTAAA
1 CCCTAAA
***
429425 TATTAAA
1 CCCTAAA
429432 CCCTAAA
1 CCCTAAA
*
429439 CCATAAA
1 CCCTAAA
**
429446 CAATAAAA
1 CCCT-AAA
*
429454 ACCTAAA
1 CCCTAAA
*
429461 TCCTAAA
1 CCCTAAA
429468 CCCT
1 CCCT
429472 TAATCCAATT
Statistics
Matches: 96, Mismatches: 32, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
6 5 0.05
7 87 0.91
8 4 0.04
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (7 bp):
CCCTAAA
Found at i:430109 original size:11 final size:11
Alignment explanation
Indices: 430093--430124 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
430083 AAAATAATTT
430093 TGGAATCGAGC
1 TGGAATCGAGC
430104 TGGAATCGAGC
1 TGGAATCGAGC
430115 TGGAATCGAG
1 TGGAATCGAG
430125 TTTCAATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.38, T:0.19
Consensus pattern (11 bp):
TGGAATCGAGC
Found at i:430187 original size:31 final size:33
Alignment explanation
Indices: 430141--430227 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 33
430131 TTGAGAGTAT
* *
430141 TTTTAAGTTCAAGTTGAGTTTTA-ATATTTTA-
1 TTTTGAGTTCGAGTTGAGTTTTATATATTTTAG
*
430172 TTTTGAGTTCGAGTTGAG-TTTATATTTTTTAG
1 TTTTGAGTTCGAGTTGAGTTTTATATATTTTAG
*
430204 TTTTTGAGTTTTTGAGTTGAGTTT
1 -TTTTGAG--TTCGAGTTGAGTTT
430228 ATTTTTTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
30 4 0.09
31 23 0.50
33 7 0.15
35 10 0.22
36 2 0.04
ACGTcount: A:0.21, C:0.02, G:0.20, T:0.57
Consensus pattern (33 bp):
TTTTGAGTTCGAGTTGAGTTTTATATATTTTAG
Found at i:431219 original size:22 final size:20
Alignment explanation
Indices: 431164--431205 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
431154 AGGCATTTAC
* *
431164 AAAAAAATTCAATAAAAATAT
1 AAAAAAATT-ATTTAAAATAT
431185 AAAAAAATTATTTAAAATAT
1 AAAAAAATTATTTAAAATAT
431205 A
1 A
431206 TAATAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAAAATTATTTAAAATAT
Found at i:432087 original size:21 final size:21
Alignment explanation
Indices: 432050--432090 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
432040 TACTCTAGAG
*
432050 TATTTAATTTTTATTTTTAAT
1 TATTTAATTGTTATTTTTAAT
432071 TATTATAATTGTT-TTTTTAA
1 TATT-TAATTGTTATTTTTAA
432091 AATCATAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTTAATTGTTATTTTTAAT
Found at i:437644 original size:17 final size:17
Alignment explanation
Indices: 437622--437659 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
437612 CCCTTAGCGA
437622 AGACTAAGGGAAGCATG
1 AGACTAAGGGAAGCATG
437639 AGACTAAGGGAAGCATG
1 AGACTAAGGGAAGCATG
437656 AGAC
1 AGAC
437660 ATAGACTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.13, G:0.34, T:0.11
Consensus pattern (17 bp):
AGACTAAGGGAAGCATG
Found at i:438358 original size:42 final size:40
Alignment explanation
Indices: 438182--438545 Score: 171
Period size: 42 Copynumber: 8.6 Consensus size: 40
438172 TTAATTTTAG
* * * *
438182 TAATCTCACGTTTTATCTTTATAACTG-GGACCTCTAATTTT
1 TAATCTCAC-TTTTACCTTTATAATTGAGG-CCCCTATTTTT
* ** *
438223 TAATC-CTATTTTTTATATTTATAATTGAGGCTCCTATATTTT
1 TAATCTC-A-CTTTTACCTTTATAATTGAGGCCCCTAT-TTTT
* * ****
438265 CAA-C-CAACCTTTTACCTTTGTAATTGAGGTTTATAATTTTTT
1 TAATCTC-A-CTTTTACCTTTATAATTGAGGCCCCT-A-TTTTT
438307 TAATCTCACTTTCTACCTTTATAATTGAGGCCCCTATTTTT
1 TAATCTCACTTT-TACCTTTATAATTGAGGCCCCTATTTTT
* * **
438348 GTAATCTCACTGTTTATCTTTATAATTGGGGCTCCAAATTTTT
1 -TAATCTCACT-TTTACCTTTATAATTGAGGC-CCCTATTTTT
* ** ***
438391 TAATCTCACCGTTTATTTTTATAATAT-AGGCTAGTAATTTTT
1 TAATCTCA-CTTTTACCTTTATAAT-TGAGGCCCCT-ATTTTT
* * * *
438433 TCAATCTCTCCTTTTACATTTATAATTGAGGCCACTAGTTTT
1 T-AATCTC-ACTTTTACCTTTATAATTGAGGCCCCTATTTTT
* * * *
438475 TAATCTTACTTTTTACCCTTATAATTGATGCCCTTAATTTTTTT
1 TAATCTCAC-TTTTACCTTTATAATTGAGGCCCCT-A--TTTTT
* *
438519 TCAATCTTACTTTTTACTTTTATAATT
1 T-AATCTCAC-TTTTACCTTTATAATT
438546 TAGACTCTTA
Statistics
Matches: 250, Mismatches: 50, Indels: 42
0.73 0.15 0.12
Matches are distributed among these distances:
40 2 0.01
41 77 0.31
42 85 0.34
43 57 0.23
44 6 0.02
45 23 0.09
ACGTcount: A:0.25, C:0.17, G:0.08, T:0.50
Consensus pattern (40 bp):
TAATCTCACTTTTACCTTTATAATTGAGGCCCCTATTTTT
Found at i:445129 original size:18 final size:18
Alignment explanation
Indices: 445106--445145 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
445096 AAAGGCGATG
*
445106 GCGGCATCATATATGGCT
1 GCGGCATCATAAATGGCT
445124 GCGGCATCATAAATGGCT
1 GCGGCATCATAAATGGCT
445142 GCGG
1 GCGG
445146 TGAAGGTCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.33, T:0.23
Consensus pattern (18 bp):
GCGGCATCATAAATGGCT
Found at i:446824 original size:17 final size:18
Alignment explanation
Indices: 446781--446821 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
446771 AAATTATATT
446781 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
446798 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
446816 ATTAAA
1 AGTAAA
446822 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:447505 original size:39 final size:41
Alignment explanation
Indices: 447440--447533 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 41
447430 TATTTTGTCC
447440 TAATATTTTAAATTTATAAAACTTT-AAACTATTTT-A-CT
1 TAATATTTTAAATTTATAAAACTTTAAAACTATTTTAACCT
*** *
447478 ATAATATTTTAAATTCT-TAATTTTTTAAAATTATTTTAACCT
1 -TAATATTTTAAATT-TATAAAACTTTAAAACTATTTTAACCT
447520 TAATATTTTAAATT
1 TAATATTTTAAATT
447534 ATTTTTTAAT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
39 20 0.43
40 10 0.21
41 15 0.32
42 2 0.04
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.53
Consensus pattern (41 bp):
TAATATTTTAAATTTATAAAACTTTAAAACTATTTTAACCT
Found at i:447578 original size:39 final size:41
Alignment explanation
Indices: 447508--447610 Score: 113
Period size: 40 Copynumber: 2.6 Consensus size: 41
447498 TTTTTTAAAA
* *
447508 TTATTTTAACCTTAATAT-TTTAAATTATTTTT-TAATTAT
1 TTATTTTAACTTTAAAATATTTAAATTATTTTTATAATTAT
* * *
447547 TTATTTTAACTTTAAAATATTTAAGTT-TTTTTATATTTCT
1 TTATTTTAACTTTAAAATATTTAAATTATTTTTATAATTAT
**
447587 TTATTTTATTTTTAATAATATTTA
1 TTATTTTAACTTTAA-AATATTTA
447611 TCATTTAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
39 21 0.39
40 25 0.46
41 8 0.15
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (41 bp):
TTATTTTAACTTTAAAATATTTAAATTATTTTTATAATTAT
Found at i:448902 original size:20 final size:21
Alignment explanation
Indices: 448862--448907 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
448852 TGAGTAATAC
*
448862 TGATACTGATTCAATTAGTAT
1 TGATACTGATTCAAGTAGTAT
*
448883 TGATACTGA-TGAAGTAGTAT
1 TGATACTGATTCAAGTAGTAT
*
448903 CGATA
1 TGATA
448908 TCATGATTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (21 bp):
TGATACTGATTCAAGTAGTAT
Found at i:450041 original size:55 final size:55
Alignment explanation
Indices: 449423--450031 Score: 859
Period size: 55 Copynumber: 11.1 Consensus size: 55
449413 GTACTAAAGA
* * * * * *
449423 CACTTCATGTGCATATTTATGGAATTCATCATGAGTTGAAGAATCACCGTACATG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
* * * **
449478 TACTTTGTGTGCATATTCAC-AGAATTCATCATGAGTTGATGAATAACCGTACAAA
1 CACTTCGTGTGCATATTCACGA-AATTCATCATGAGTTGATGAATCACCGTACAGG
* *
449533 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGACGAATCATCGTACAGG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
* *
449588 CACTTCGTGTGCATATTCACGAAATTTATCATGAGTTGATGAATCACCGTATAGG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
449643 CACTTCGTGTGCATATTCAC-AGAATTCATCATGAGTTGATGAATCACCGTACAGG
1 CACTTCGTGTGCATATTCACGA-AATTCATCATGAGTTGATGAATCACCGTACAGG
* *
449698 CACTTCGTGTGCATATTCACGGAATTCATCATGAGTTGATGAATCACTGTACAGG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
* * * *
449753 CACTTCGTGTGAATATTCAC-AGAATTCATCATGAGTTGATGGAGCACCTTACAGG
1 CACTTCGTGTGCATATTCACGA-AATTCATCATGAGTTGATGAATCACCGTACAGG
* * * *
449808 CACTTCGTGTACATATTCAC-ATAATTCATAATGAGTTGATGAATTACTGTACAGG
1 CACTTCGTGTGCATATTCACGA-AATTCATCATGAGTTGATGAATCACCGTACAGG
*
449863 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCATCGTACAGG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
* * * *
449918 CACTTCGTGTGCATATTCACGCAATTCATCATGAGTTGATGAATTACTGAACAGG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
*
449973 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATTC-CCGTATAGG
1 CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAA-TCACCGTACAGG
450028 CACT
1 CACT
450032 AATTATGCAT
Statistics
Matches: 492, Mismatches: 55, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
54 1 0.00
55 488 0.99
56 3 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (55 bp):
CACTTCGTGTGCATATTCACGAAATTCATCATGAGTTGATGAATCACCGTACAGG
Found at i:453140 original size:17 final size:17
Alignment explanation
Indices: 453118--453161 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
453108 ATGTAAAAAT
453118 AAATATTTAAATTTAAA
1 AAATATTTAAATTTAAA
** **
453135 AAATATAAAAATTTATT
1 AAATATTTAAATTTAAA
453152 AAATATTTAA
1 AAATATTTAA
453162 TCAAGTAGGG
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
AAATATTTAAATTTAAA
Found at i:458859 original size:24 final size:24
Alignment explanation
Indices: 458825--458873 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
458815 TAATTCAAAA
*
458825 TACTTCTTTTTTCGAAAAGGATGT
1 TACTTCATTTTTCGAAAAGGATGT
458849 TACTTCATTTTTCGAAAAGGATGT
1 TACTTCATTTTTCGAAAAGGATGT
458873 T
1 T
458874 TTGTACGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (24 bp):
TACTTCATTTTTCGAAAAGGATGT
Found at i:459109 original size:21 final size:21
Alignment explanation
Indices: 459084--459127 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
459074 CCTCTTCTTC
*
459084 TTTTTTCTTTTTCTCTTTTTGA
1 TTTTTT-TTCTTCTCTTTTTGA
*
459106 TTTTTTTTCTTTTCTTTTTGA
1 TTTTTTTTCTTCTCTTTTTGA
459127 T
1 T
459128 ATAAAACAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.05, C:0.11, G:0.05, T:0.80
Consensus pattern (21 bp):
TTTTTTTTCTTCTCTTTTTGA
Found at i:459871 original size:20 final size:20
Alignment explanation
Indices: 459848--459896 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
459838 TGTTCCCAGG
459848 AAGTCGAATGTGCTTTCTAT
1 AAGTCGAATGTGCTTTCTAT
*
459868 AAGTCAAATGTGCTTTCTAT
1 AAGTCGAATGTGCTTTCTAT
*
459888 AAGCCGAAT
1 AAGTCGAAT
459897 CTTCCTCCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (20 bp):
AAGTCGAATGTGCTTTCTAT
Found at i:460177 original size:27 final size:27
Alignment explanation
Indices: 460124--460177 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
460114 ATTTAAAAGC
*
460124 AACTTGAAAATAAAAGTAAAACCGAAA
1 AACTTGAAAATAAAAGTAAAACAGAAA
*
460151 AACTTGAAAAGTAAAA-TAAAAGAGAAA
1 AACTTGAAAA-TAAAAGTAAAACAGAAA
460178 GCTTTAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 19 0.79
28 5 0.21
ACGTcount: A:0.65, C:0.07, G:0.13, T:0.15
Consensus pattern (27 bp):
AACTTGAAAATAAAAGTAAAACAGAAA
Found at i:460975 original size:20 final size:21
Alignment explanation
Indices: 460927--460975 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
460917 ATTTTGGTGG
*
460927 TGATGGACGATAATGGTAATT
1 TGATGGATGATAATGGTAATT
* *
460948 TGA-CGATGATAATGGTGA-T
1 TGATGGATGATAATGGTAATT
460967 TGATGGATG
1 TGATGGATG
460976 TGTATCCTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 4 0.17
20 16 0.70
21 3 0.13
ACGTcount: A:0.31, C:0.04, G:0.33, T:0.33
Consensus pattern (21 bp):
TGATGGATGATAATGGTAATT
Found at i:461907 original size:29 final size:29
Alignment explanation
Indices: 461861--461924 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
461851 TCTTATGTTA
*
461861 AGAGGGTAAATCTAAATTTATAAAATTCT
1 AGAGGGTAAATCTAAATTTAAAAAATTCT
* *
461890 AGAGGGTAAATTTGAATTTAAAAAATTCT
1 AGAGGGTAAATCTAAATTTAAAAAATTCT
*
461919 AAAGGG
1 AGAGGG
461925 GACGAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.05, G:0.19, T:0.31
Consensus pattern (29 bp):
AGAGGGTAAATCTAAATTTAAAAAATTCT
Found at i:465623 original size:13 final size:13
Alignment explanation
Indices: 465605--465629 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
465595 TAATATAATT
465605 TTTTTATTAAATG
1 TTTTTATTAAATG
465618 TTTTTATTAAAT
1 TTTTTATTAAAT
465630 TAAGTGAATA
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:0.04, T:0.64
Consensus pattern (13 bp):
TTTTTATTAAATG
Found at i:467503 original size:21 final size:21
Alignment explanation
Indices: 467465--467508 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
467455 AGTTTTTAGC
* ** *
467465 GTGGTTTCGAAACCCCCTCAG
1 GTGGTTTCAAAAAACCCTAAG
467486 GTGGTTTCAAAAAACCCTAAG
1 GTGGTTTCAAAAAACCCTAAG
467507 GT
1 GT
467509 AGTAGCTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (21 bp):
GTGGTTTCAAAAAACCCTAAG
Found at i:471091 original size:16 final size:16
Alignment explanation
Indices: 471070--471128 Score: 100
Period size: 16 Copynumber: 3.7 Consensus size: 16
471060 ATAAATAAAT
471070 GAACATAAACGAACAC
1 GAACATAAACGAACAC
471086 GAACATAAACGAACAC
1 GAACATAAACGAACAC
*
471102 GAACATAAATGAACAC
1 GAACATAAACGAACAC
*
471118 GAAAATAAACG
1 GAACATAAACG
471129 TTGGAGACCC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.58, C:0.20, G:0.14, T:0.08
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:472237 original size:14 final size:13
Alignment explanation
Indices: 472220--472299 Score: 64
Period size: 14 Copynumber: 6.3 Consensus size: 13
472210 AATTAACATA
472220 AACGAACATAACCG
1 AACGAACATAA-CG
*
472234 AACGAACATAAAG
1 AACGAACATAACG
472247 -A--AACATAATCG
1 AACGAACATAA-CG
*
472258 AACGAACATAAAG
1 AACGAACATAACG
472271 -A--AACATAATCG
1 AACGAACATAA-CG
472282 AACGAACATAACCG
1 AACGAACATAA-CG
472296 AACG
1 AACG
472300 TTCACGAACG
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
10 14 0.26
11 2 0.04
12 4 0.08
13 2 0.04
14 31 0.58
ACGTcount: A:0.55, C:0.21, G:0.14, T:0.10
Consensus pattern (13 bp):
AACGAACATAACG
Found at i:472241 original size:24 final size:24
Alignment explanation
Indices: 472214--472292 Score: 133
Period size: 24 Copynumber: 3.3 Consensus size: 24
472204 TAAATAAATT
*
472214 AACATAAACG-AACATAACCGAACG
1 AACATAAA-GAAACATAATCGAACG
472238 AACATAAAGAAACATAATCGAACG
1 AACATAAAGAAACATAATCGAACG
472262 AACATAAAGAAACATAATCGAACG
1 AACATAAAGAAACATAATCGAACG
472286 AACATAA
1 AACATAA
472293 CCGAACGTTC
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
23 1 0.02
24 52 0.98
ACGTcount: A:0.58, C:0.19, G:0.11, T:0.11
Consensus pattern (24 bp):
AACATAAAGAAACATAATCGAACG
Found at i:486225 original size:41 final size:41
Alignment explanation
Indices: 486168--486245 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
486158 AACTCCCAGG
* *
486168 GAAATAACACGGTTGACGCAGGATCCTAGAGGAAGAAAAGA
1 GAAATAACACGGTTGACACAGGATCCCAGAGGAAGAAAAGA
* *
486209 GAAATAACATGGTTGACACAGTATCCCAGAGGAAGAA
1 GAAATAACACGGTTGACACAGGATCCCAGAGGAAGAA
486246 TAAAGATGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.44, C:0.15, G:0.27, T:0.14
Consensus pattern (41 bp):
GAAATAACACGGTTGACACAGGATCCCAGAGGAAGAAAAGA
Found at i:498642 original size:6 final size:6
Alignment explanation
Indices: 498631--498709 Score: 130
Period size: 6 Copynumber: 13.8 Consensus size: 6
498621 TATTTAGCAT
498631 ATTTTA ATTTTA A-TTTA ATTTTA A-TTTA ATTTTA ATTTTA A-TTTA
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA
498676 ATTTTA ATTTTA A-TTTA ATTTTA ATTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
498710 TACAGGTACC
Statistics
Matches: 69, Mismatches: 0, Indels: 8
0.90 0.00 0.10
Matches are distributed among these distances:
5 20 0.29
6 49 0.71
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
ATTTTA
Found at i:498649 original size:11 final size:12
Alignment explanation
Indices: 498631--498709 Score: 130
Period size: 11 Copynumber: 6.9 Consensus size: 12
498621 TATTTAGCAT
498631 ATTTTAATTTTA
1 ATTTTAATTTTA
498643 A-TTTAATTTTA
1 ATTTTAATTTTA
498654 A-TTTAATTTTA
1 ATTTTAATTTTA
498665 ATTTTAA-TTTA
1 ATTTTAATTTTA
498676 ATTTTAATTTTA
1 ATTTTAATTTTA
498688 A-TTTAATTTTA
1 ATTTTAATTTTA
498699 ATTTTAATTTT
1 ATTTTAATTTT
498710 TACAGGTACC
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
11 44 0.69
12 20 0.31
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTTAATTTTA
Found at i:498653 original size:17 final size:17
Alignment explanation
Indices: 498631--498708 Score: 140
Period size: 17 Copynumber: 4.6 Consensus size: 17
498621 TATTTAGCAT
498631 ATTTTAATTTTAA-TTTA
1 ATTTTAA-TTTAATTTTA
498648 ATTTTAATTTAATTTTA
1 ATTTTAATTTAATTTTA
498665 ATTTTAATTTAATTTTA
1 ATTTTAATTTAATTTTA
498682 ATTTTAATTTAATTTTA
1 ATTTTAATTTAATTTTA
498699 ATTTTAATTT
1 ATTTTAATTT
498709 TTACAGGTAC
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
16 5 0.08
17 55 0.92
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTAATTTAATTTTA
Found at i:508764 original size:15 final size:18
Alignment explanation
Indices: 508727--508781 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
508717 AATGGAGCTT
* * *
508727 ATAAAAAATAAAAAAAAA
1 ATAATAAATAAATAAATA
508745 ATAAT-AAT-AAT-AATA
1 ATAATAAATAAATAAATA
508760 ATAATAAATAAATAAATA
1 ATAATAAATAAATAAATA
508778 ATAA
1 ATAA
508782 AATGATTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 8 0.26
16 5 0.16
17 6 0.19
18 12 0.39
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (18 bp):
ATAATAAATAAATAAATA
Found at i:509491 original size:84 final size:86
Alignment explanation
Indices: 509332--509493 Score: 202
Period size: 84 Copynumber: 1.9 Consensus size: 86
509322 ATATCAACAT
* * * *
509332 AATTTAGTCCTTGAACTTTTAATTAGATATTCATTTAACATAATTAATTAGGGTTATTAATTAGA
1 AATTTAGTCATTGAACTTTT-ATTAGATATTCATTTAACATAATTAACTAGGATTAGTAATTAGA
* *
509397 GCTTTAATCTTAAACTCTACAC
65 GCCTCAATCTTAAACTCTACAC
* * * *
509419 AATTTAGTCATTGAAC-TTT-TTAGGTATTCATTTGATATAATTAACTAGGATTGGTAATTAGAG
1 AATTTAGTCATTGAACTTTTATTAGATATTCATTTAACATAATTAACTAGGATTAGTAATTAGAG
*
509482 CCTCCATCTTAA
66 CCTCAATCTTAA
509494 TTAAATTTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
84 46 0.72
86 3 0.05
87 15 0.23
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (86 bp):
AATTTAGTCATTGAACTTTTATTAGATATTCATTTAACATAATTAACTAGGATTAGTAATTAGAG
CCTCAATCTTAAACTCTACAC
Found at i:522412 original size:17 final size:17
Alignment explanation
Indices: 522399--522433 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
522389 GAGTTATATA
522399 AAATATATTTTTATTAT
1 AAATATATTTTTATTAT
*
522416 AATTATATTTTTATTAT
1 AAATATATTTTTATTAT
522433 A
1 A
522434 GTTTAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATATATTTTTATTAT
Found at i:525151 original size:6 final size:6
Alignment explanation
Indices: 525140--525185 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
525130 GCTTAACCTA
*
525140 AAAAAT AAAAAT AAAAAAGT AAAAA- ATAAAT AAAAAT AAAAAT AAA
1 AAAAAT AAAAAT -AAAAA-T AAAAAT AAAAAT AAAAAT AAAAAT AAA
525186 TGATGTAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 4 0.11
6 20 0.57
7 10 0.29
8 1 0.03
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:529705 original size:21 final size:21
Alignment explanation
Indices: 529676--529718 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
529666 ATGTTCCTTG
529676 GTATCGATACC-CTTCACATAT
1 GTATCGATACCTCTTC-CATAT
*
529697 GTATTGATACCTCTTCCATAT
1 GTATCGATACCTCTTCCATAT
529718 G
1 G
529719 GTAGCTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.37
Consensus pattern (21 bp):
GTATCGATACCTCTTCCATAT
Found at i:539390 original size:20 final size:18
Alignment explanation
Indices: 539344--539392 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
539334 ATTTATTTTA
539344 AAAAGTAAATAAAATAAT
1 AAAAGTAAATAAAATAAT
*
539362 AAAAGGTAAATAAAAATGAT
1 AAAA-GTAAAT-AAAATAAT
539382 AGAAAGTAAAT
1 A-AAAGTAAAT
539393 TGAAACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 4 0.15
19 6 0.22
20 14 0.52
21 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.20
Consensus pattern (18 bp):
AAAAGTAAATAAAATAAT
Found at i:539824 original size:13 final size:13
Alignment explanation
Indices: 539808--539865 Score: 64
Period size: 13 Copynumber: 4.5 Consensus size: 13
539798 TAAAAATATT
539808 AAAAAAAA-AAAA
1 AAAAAAAATAAAA
*
539820 AAAAATAATAAAA
1 AAAAAAAATAAAA
* *
539833 TAAATAAATAAAA
1 AAAAAAAATAAAA
*
539846 AAAACAAATAAAA
1 AAAAAAAATAAAA
*
539859 AATAAAA
1 AAAAAAA
539866 TGCTCCAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
12 7 0.19
13 30 0.81
ACGTcount: A:0.86, C:0.02, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAAAATAAAA
Found at i:539824 original size:21 final size:24
Alignment explanation
Indices: 539799--539848 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 24
539789 TGAATCCCAT
*
539799 AAAAATATTAAAA-AAA-AAA-AA
1 AAAAATAATAAAATAAATAAATAA
539820 AAAAATAATAAAATAAATAAATAA
1 AAAAATAATAAAATAAATAAATAA
539844 AAAAA
1 AAAAA
539849 ACAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 12 0.48
22 3 0.12
23 3 0.12
24 7 0.28
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (24 bp):
AAAAATAATAAAATAAATAAATAA
Found at i:539866 original size:29 final size:26
Alignment explanation
Indices: 539797--539864 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 26
539787 ATTGAATCCC
539797 ATAAAAATATTAAA-AAAAAAAAAAAAA
1 ATAAAAA-A-TAAATAAAAAAAAAAAAA
539824 ATAATAAAATAAATAAATAAAAAAAACAA
1 ATAA-AAAATAAATAAA-AAAAAAAA-AA
539853 ATAAAAAATAAA
1 ATAAAAAATAAA
539865 ATGCTCCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.11
27 8 0.22
28 19 0.51
29 6 0.16
ACGTcount: A:0.82, C:0.01, G:0.00, T:0.16
Consensus pattern (26 bp):
ATAAAAAATAAATAAAAAAAAAAAAA
Found at i:540229 original size:20 final size:20
Alignment explanation
Indices: 540188--540231 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
540178 TGTCACTAAG
*
540188 TATACCTATACATATACCTA
1 TATACCTATACATATACATA
* *
540208 TATACCTATATATATATATA
1 TATACCTATACATATACATA
540228 TATA
1 TATA
540232 AATATTATGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (20 bp):
TATACCTATACATATACATA
Found at i:550280 original size:26 final size:26
Alignment explanation
Indices: 550236--550297 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
550226 TAAAAAACTT
* * *
550236 ATTAAAAATATTTTTAAAATTCAAAAAC
1 ATTAAAAA-ATTTTAAAAAGT-AAAAAA
550264 A-TAAAAAATTTTAAAAAGTAAAAAA
1 ATTAAAAAATTTTAAAAAGTAAAAAA
550289 ATTAAAAAA
1 ATTAAAAAA
550298 ATTACTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.20
26 17 0.57
27 6 0.20
28 1 0.03
ACGTcount: A:0.66, C:0.03, G:0.02, T:0.29
Consensus pattern (26 bp):
ATTAAAAAATTTTAAAAAGTAAAAAA
Found at i:550474 original size:10 final size:9
Alignment explanation
Indices: 550443--550502 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
550433 ATTAATTCAA
*
550443 AAAAAATAA
1 AAAAAATAT
550452 AAAAAAT-T
1 AAAAAATAT
550460 AAAAAATAT
1 AAAAAATAT
* *
550469 ATAAAATTT
1 AAAAAATAT
* *
550478 TAAAATTAT
1 AAAAAATAT
550487 AAAAGGAATAT
1 AAAA--AATAT
550498 AAAAA
1 AAAAA
550503 TTTCAAAAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
8 7 0.18
9 24 0.62
11 8 0.21
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
AAAAAATAT
Found at i:550474 original size:17 final size:17
Alignment explanation
Indices: 550443--550490 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
550433 ATTAATTCAA
* *
550443 AAAAAATAAAAAAAATT
1 AAAAAATATATAAAATT
550460 AAAAAATATATAAAATT
1 AAAAAATATATAAAATT
**
550477 TTAAAAT-TATAAAA
1 AAAAAATATATAAAA
550491 GGAATATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAAAATATATAAAATT
Found at i:562686 original size:19 final size:18
Alignment explanation
Indices: 562653--562702 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
562643 TTATTTTTAA
* *
562653 AATTTTTTTAAAAAATAT
1 AATTTATTTAAAAAAAAT
* *
562671 TATTATATTTATAAAAAAT
1 AATT-TATTTAAAAAAAAT
562690 AATTTATTTAAAA
1 AATTTATTTAAAA
562703 TTATAAAAAG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATTTATTTAAAAAAAAT
Found at i:569822 original size:16 final size:16
Alignment explanation
Indices: 569801--569838 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
569791 CTTAGCCACA
569801 AGTCGAGCCTTGTATC
1 AGTCGAGCCTTGTATC
569817 AGTCGAGCCTTGTATC
1 AGTCGAGCCTTGTATC
569833 AGTCGA
1 AGTCGA
569839 TACTGCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (16 bp):
AGTCGAGCCTTGTATC
Found at i:572725 original size:16 final size:16
Alignment explanation
Indices: 572704--572741 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
572694 CTTAGCCACA
572704 AGTCGAGCCTTGTATC
1 AGTCGAGCCTTGTATC
572720 AGTCGAGCCTTGTATC
1 AGTCGAGCCTTGTATC
572736 AGTCGA
1 AGTCGA
572742 TACTGCCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (16 bp):
AGTCGAGCCTTGTATC
Found at i:576531 original size:67 final size:67
Alignment explanation
Indices: 576408--576536 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 67
576398 TTCCAAAAGA
* * * *
576408 CATGCTTTAGTATTATAGTACGTGCCTTTCTCTACGTGGCATTTGCCAAGATCATTTGAATATGT
1 CATGCTTTAGTATTAGAGTACGTGCCTTTCTCTACGTGGCATCTGCCAAGACCATTTAAATATGT
576473 AG
66 AG
* * * *
576475 CATGTTTTAGTTTTAGAGTACGTGCCTTTCTCTACGTGGCATCTGTCAAGGCCATTTAAATA
1 CATGCTTTAGTATTAGAGTACGTGCCTTTCTCTACGTGGCATCTGCCAAGACCATTTAAATA
576537 GATTGTTACG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (67 bp):
CATGCTTTAGTATTAGAGTACGTGCCTTTCTCTACGTGGCATCTGCCAAGACCATTTAAATATGT
AG
Found at i:577428 original size:36 final size:36
Alignment explanation
Indices: 577388--577598 Score: 111
Period size: 36 Copynumber: 5.8 Consensus size: 36
577378 TAAAATTTCA
* *
577388 TGTTTCGAGTGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCGAGTGAAACTATCTCAAGTGAGACAAAGTT
** * * * *
577424 TGTTTTAAG-AAAAATAATCTCAAGTGAGATAAATTGT
1 TGTTTCGAGTGAAACT-ATCTCAAGTGAGACAAAGT-T
* * * *
577461 TGTTTCGAGGGAAACTTTCTCCAGTGAGA-ACTAGTT
1 TGTTTCGAGTGAAACTATCTCAAGTGAGACA-AAGTT
** ** * * * *
577497 TGTTTTAAGAAAAACAATCTCAAGTGAAATAAATTGT
1 TGTTTCGAGTGAAACTATCTCAAGTGAGACAAAGT-T
* * **
577534 TGTTTCGAGTGAAACTGTCTCAAGCGAGACGCAGTT
1 TGTTTCGAGTGAAACTATCTCAAGTGAGACAAAGTT
** ** *
577570 TGTTTTAAGAAAAACAATCTCAAGTGAGA
1 TGTTTCGAGTGAAACTATCTCAAGTGAGA
577599 TAAATTGCTA
Statistics
Matches: 124, Mismatches: 45, Indels: 12
0.69 0.25 0.07
Matches are distributed among these distances:
35 4 0.03
36 70 0.56
37 46 0.37
38 4 0.03
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
TGTTTCGAGTGAAACTATCTCAAGTGAGACAAAGTT
Found at i:577621 original size:146 final size:147
Alignment explanation
Indices: 577348--577678 Score: 499
Period size: 146 Copynumber: 2.3 Consensus size: 147
577338 CCTTCTGTGG
577348 TTGTTTTAAGAAAAACAATCTCGAA-TGAGATAAAATT-TCATGTTTCGAGTGAAACTGTCTCAA
1 TTGTTTTAAGAAAAACAATCTC-AAGTGAGAT-AAATTGT-ATGTTTCGAGTGAAACTGTCTCAA
* * * *
577411 GAGAGACAAAGTTTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGTTGTTTCGAGGGAAAC
63 GAGAGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGGGAAAC
* *
577476 TTTCTCCAGTGAG-AACTAGT
128 TTTCTCCAGCGAGAAAC-AAT
* *
577496 TTGTTTTAAGAAAAACAATCTCAAGTGAAATAAATTGT-TGTTTCGAGTGAAACTGTCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTATGTTTCGAGTGAAACTGTCTCAAGAG
** *
577560 AGACGCAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTT
66 AGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGGGAAACTTT
577625 CTCCAGCGAGAAACAAT
131 CTCCAGCGAGAAACAAT
577642 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTG
577679 CTATTTGAAA
Statistics
Matches: 168, Mismatches: 12, Indels: 8
0.89 0.06 0.04
Matches are distributed among these distances:
146 130 0.77
147 10 0.06
148 28 0.17
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.31
Consensus pattern (147 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGTATGTTTCGAGTGAAACTGTCTCAAGAG
AGACAAAGTTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGGGAAACTTT
CTCCAGCGAGAAACAAT
Found at i:577684 original size:73 final size:73
Alignment explanation
Indices: 577348--577680 Score: 447
Period size: 73 Copynumber: 4.5 Consensus size: 73
577338 CCTTCTGTGG
*
577348 TTGTTTTAAGAAAAACAATCTCGAA-TGAGATAAAATTTCATGTTTCGAGTGAAACTGTCTCAAG
1 TTGTTTTAAGAAAAACAATCTC-AAGTGAGAT-AAATTGC-TGTTTCGAGTGAAACTGTCTCAAG
*
577412 AGAGACAA-AGT
63 CGAGA-AACAGT
* * * * * *
577423 TTGTTTTAAGAAAAATAATCTCAAGTGAGATAAATTGTTGTTTCGAGGGAAACTTTCTCCAGTGA
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTGTTTCGAGTGAAACTGTCTCAAGCGA
577488 G-AACTAGT
66 GAAAC-AGT
* *
577496 TTGTTTTAAGAAAAACAATCTCAAGTGAAATAAATTGTTGTTTCGAGTGAAACTGTCTCAAGCGA
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTGTTTCGAGTGAAACTGTCTCAAGCGA
**
577561 GACGCAGT
66 GAAACAGT
* * * *
577569 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTATTTCAAGTGAAACTTTCTCCAGCGA
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTGTTTCGAGTGAAACTGTCTCAAGCGA
*
577634 GAAACAAT
66 GAAACAGT
577642 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCT
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCT
577681 ATTTGAAAAC
Statistics
Matches: 230, Mismatches: 24, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
71 2 0.01
73 193 0.84
74 8 0.03
75 27 0.12
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (73 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATTGCTGTTTCGAGTGAAACTGTCTCAAGCGA
GAAACAGT
Found at i:578379 original size:35 final size:35
Alignment explanation
Indices: 578339--578410 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
578329 TTTTATCTTT
578339 AATAACATCGGTTTTCTTCATCTGAACTTTTTTAG
1 AATAACATCGGTTTTCTTCATCTGAACTTTTTTAG
578374 AATAACATCGGTTTTCTTCATCTGAACTTTTTTAG
1 AATAACATCGGTTTTCTTCATCTGAACTTTTTTAG
578409 AA
1 AA
578411 ATCCAATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.44
Consensus pattern (35 bp):
AATAACATCGGTTTTCTTCATCTGAACTTTTTTAG
Found at i:578466 original size:22 final size:22
Alignment explanation
Indices: 578438--578500 Score: 108
Period size: 22 Copynumber: 2.9 Consensus size: 22
578428 TCTAAAAAAA
578438 AGAATCTATCAGCTTTGAAGAG
1 AGAATCTATCAGCTTTGAAGAG
578460 AGAATCTATCAGCTTTGAAGAG
1 AGAATCTATCAGCTTTGAAGAG
* *
578482 AGAATATATCATCTTTGAA
1 AGAATCTATCAGCTTTGAA
578501 TAGTGTAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (22 bp):
AGAATCTATCAGCTTTGAAGAG
Found at i:587059 original size:27 final size:25
Alignment explanation
Indices: 586992--587082 Score: 73
Period size: 26 Copynumber: 3.6 Consensus size: 25
586982 ATGAAATTTA
* *
586992 AATAAAATAAAAATATTAATAAAAAT
1 AATATAATAAAAATATT-ATGAAAAT
*
587018 AATATACATATAAATATTATGAAAAT
1 AATATA-ATAAAAATATTATGAAAAT
587044 AATAAGTAATAAAAAT-TT-TGAAAGA-
1 AAT-A-TAATAAAAATATTATGAAA-AT
587069 AA-ATAATTAAAAAT
1 AATATAA-TAAAAAT
587083 TAAATAAATA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
22 3 0.05
23 8 0.14
25 7 0.12
26 18 0.32
27 18 0.32
28 2 0.04
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (25 bp):
AATATAATAAAAATATTATGAAAAT
Found at i:587253 original size:16 final size:15
Alignment explanation
Indices: 587234--587263 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
587224 GTAATGTGGA
587234 TAAAAATGATTTTGAT
1 TAAAAATG-TTTTGAT
587250 TAAAAATGTTTTGA
1 TAAAAATGTTTTGA
587264 GAGTCGCCAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (15 bp):
TAAAAATGTTTTGAT
Found at i:587599 original size:2 final size:2
Alignment explanation
Indices: 587592--587617 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
587582 AGTAAAGTAA
587592 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
587618 TTAAGTTATT
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:587757 original size:16 final size:16
Alignment explanation
Indices: 587736--587766 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
587726 CATTTTTCTA
587736 ATAATTTAAAAAATAT
1 ATAATTTAAAAAATAT
*
587752 ATAATTTATAAAATA
1 ATAATTTAAAAAATA
587767 AGGATATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATAATTTAAAAAATAT
Found at i:588954 original size:2 final size:2
Alignment explanation
Indices: 588947--589031 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
588937 TTTATTTCGA
588947 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
588989 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
589031 A
1 A
589032 AAGCTGAAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:598579 original size:16 final size:17
Alignment explanation
Indices: 598538--598580 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
598528 ATTTTAAAAG
598538 AAATATCAA-AAAGTTAT
1 AAATAT-AATAAAGTTAT
598555 AAA-ATAATAAA-TTAT
1 AAATATAATAAAGTTAT
598570 AAATATAATAA
1 AAATATAATAA
598581 TTTAAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 9 0.38
16 12 0.50
17 3 0.12
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (17 bp):
AAATATAATAAAGTTAT
Found at i:600958 original size:5 final size:5
Alignment explanation
Indices: 600948--600972 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
600938 TCCTACTCTT
600948 TGTAA TGTAA TGTAA TGTAA TGTAA
1 TGTAA TGTAA TGTAA TGTAA TGTAA
600973 CCCTGTACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
TGTAA
Found at i:605393 original size:17 final size:16
Alignment explanation
Indices: 605339--605394 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 16
605329 AAAAACTGAT
605339 AAACCGAACCGAATCGAA
1 AAACCGAACCGAA-C-AA
605357 AAATCCGAACCGTTAA-AA
1 AAA-CCGAACCG--AACAA
605375 AAACCGAACCGAACCAA
1 AAACCGAACCGAA-CAA
605392 AAA
1 AAA
605395 AACCGGTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.06
17 13 0.39
18 8 0.24
19 8 0.24
21 2 0.06
ACGTcount: A:0.54, C:0.27, G:0.12, T:0.07
Consensus pattern (16 bp):
AAACCGAACCGAACAA
Found at i:605393 original size:19 final size:19
Alignment explanation
Indices: 605339--605399 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
605329 AAAAACTGAT
*
605339 AAACCGAACCGAATCGAAA
1 AAACCGAACCGAATCAAAA
* *
605358 AATCCGAACCG--TTAAAA
1 AAACCGAACCGAATCAAAA
*
605375 AAACCGAACCGAACCAAAA
1 AAACCGAACCGAATCAAAA
605394 AAACCG
1 AAACCG
605400 GTTTCGGTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 14 0.41
19 20 0.59
ACGTcount: A:0.52, C:0.28, G:0.13, T:0.07
Consensus pattern (19 bp):
AAACCGAACCGAATCAAAA
Found at i:611009 original size:11 final size:11
Alignment explanation
Indices: 610993--611018 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
610983 TTACCAGAAA
610993 AATATTAAAAT
1 AATATTAAAAT
611004 AATATTAAAAT
1 AATATTAAAAT
611015 AATA
1 AATA
611019 CAACTCGGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATTAAAAT
Found at i:611203 original size:26 final size:26
Alignment explanation
Indices: 611166--611217 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
611156 TTTAAATAAC
611166 TTAATATAATTACT-AAATAATATTAT
1 TTAATATAATTA-TAAAATAATATTAT
*
611192 TTAATACT-ATTATAAAATTATATTAT
1 TTAATA-TAATTATAAAATAATATTAT
611218 AATTACATAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 1 0.04
26 21 0.91
27 1 0.04
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATATAATTATAAAATAATATTAT
Found at i:612314 original size:19 final size:18
Alignment explanation
Indices: 612290--612332 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
612280 CCTGTGTGCC
*
612290 TTGTAACCAGGCTTCCATT
1 TTGTAAACAGGCTTCCA-T
**
612309 TTGTAAATGGGCTTCCAT
1 TTGTAAACAGGCTTCCAT
612327 TTGTAA
1 TTGTAA
612333 TATTATTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.40
Consensus pattern (18 bp):
TTGTAAACAGGCTTCCAT
Found at i:612367 original size:7 final size:7
Alignment explanation
Indices: 612342--612399 Score: 73
Period size: 7 Copynumber: 8.1 Consensus size: 7
612332 ATATTATTTA
612342 ATAATA-
1 ATAATAT
612348 ATAATATT
1 ATAATA-T
612356 ATAATAT
1 ATAATAT
612363 ATAATAT
1 ATAATAT
612370 ATAATAT
1 ATAATAT
*
612377 ATTATATT
1 ATAATA-T
*
612385 ATTATAT
1 ATAATAT
612392 ATAATAT
1 ATAATAT
612399 A
1 A
612400 AACGTCACTC
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
6 6 0.13
7 28 0.60
8 13 0.28
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
ATAATAT
Found at i:612383 original size:29 final size:28
Alignment explanation
Indices: 612342--612399 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
612332 ATATTATTTA
612342 ATAATAATAATATTATAATATATAATAT
1 ATAATAATAATATTATAATATATAATAT
* *
612370 ATAATATATTATATTATTATATATAATAT
1 ATAATA-ATAATATTATAATATATAATAT
612399 A
1 A
612400 AACGTCACTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
ATAATAATAATATTATAATATATAATAT
Found at i:612399 original size:22 final size:22
Alignment explanation
Indices: 612330--612398 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 22
612320 CTTCCATTTG
612330 TAATATTATT-TA-ATAATA-A
1 TAATATTATTATATATAATATA
*
612349 TAATATTATAATATATAATATA
1 TAATATTATTATATATAATATA
*
612371 TAATA-TATTATATTATTATATA
1 TAATATTATTATA-TATAATATA
612393 TAATAT
1 TAATAT
612399 AAACGTCACT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 9 0.21
20 2 0.05
21 12 0.29
22 19 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TAATATTATTATATATAATATA
Found at i:614566 original size:70 final size:70
Alignment explanation
Indices: 614479--614693 Score: 378
Period size: 70 Copynumber: 3.1 Consensus size: 70
614469 AATTTAATAA
*
614479 ATCCTAATACTTAACTATCCTTAAATTAAATTCATCCATCCTTACTCTCATCTTTTCCTTTAACT
1 ATCCTAATACTTAACTATCCCTAAATTAAATTCATCCATCCTTACTCTCATCTTTTCCTTTAACT
614544 ATTAT
66 ATTAT
*
614549 ATCTTAATACTTAACTATCCCTAAATTAAATTCATCCATCCTTACTCTCATCTTTTCCTTTAACT
1 ATCCTAATACTTAACTATCCCTAAATTAAATTCATCCATCCTTACTCTCATCTTTTCCTTTAACT
614614 ATTAT
66 ATTAT
* *
614619 ATCCTAATACTTAACTATCCCTAAATTAAATTCATCCATCCTTACTCTCACCTTTTTCCTTTAGC
1 ATCCTAATACTTAACTATCCCTAAATTAAATTCATCCATCCTTACTCTCATC-TTTTCCTTTAAC
614684 TATTAT
65 TATTAT
614690 -TCCT
1 ATCCT
614694 TCTTAATTAT
Statistics
Matches: 139, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
70 122 0.88
71 17 0.12
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (70 bp):
ATCCTAATACTTAACTATCCCTAAATTAAATTCATCCATCCTTACTCTCATCTTTTCCTTTAACT
ATTAT
Found at i:620479 original size:15 final size:15
Alignment explanation
Indices: 620455--620520 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
620445 TACAAATTAT
*
620455 CAATATCAACATCTC
1 CAATAACAACATCTC
620470 CAATAACAACATCTC
1 CAATAACAACATCTC
* *
620485 TAATGACAACGA-CTC
1 CAATAACAAC-ATCTC
* * *
620500 CGATAACAATAACTC
1 CAATAACAACATCTC
620515 CAATAA
1 CAATAA
620521 TAGTGACTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 1 0.02
15 39 0.95
16 1 0.02
ACGTcount: A:0.45, C:0.29, G:0.05, T:0.21
Consensus pattern (15 bp):
CAATAACAACATCTC
Found at i:621242 original size:2 final size:2
Alignment explanation
Indices: 621235--621275 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
621225 AATTGAATTC
621235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
621276 GTTATTATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:626049 original size:2 final size:2
Alignment explanation
Indices: 626042--626087 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
626032 TTTGGCTTCA
626042 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
626084 AT AT
1 AT AT
626088 GCTCTTCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:636918 original size:16 final size:16
Alignment explanation
Indices: 636894--636926 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
636884 TATCGTCGAT
*
636894 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
636910 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
636926 C
1 C
636927 ATGAATAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.33
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:638742 original size:3 final size:3
Alignment explanation
Indices: 638724--638760 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
638714 TTGTCCAGTT
*
638724 TTA TT- TTA TT- TTA TTA TTA CTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
638761 AATAATTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 4 0.13
3 26 0.87
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:639345 original size:31 final size:31
Alignment explanation
Indices: 639308--639412 Score: 104
Period size: 31 Copynumber: 3.3 Consensus size: 31
639298 CATGAGAGCG
639308 ACCTGAACCCGAATTGAACCGAAAACATGAT
1 ACCTGAACCCGAATTGAACCGAAAACATGAT
* * **** *
639339 ACCTGAACCCGAACTGCATCCGACCTGA-GAACG
1 ACCTGAACCCGAATTG-AACCGAAAACATG-A-T
*
639372 ACCTGAACCCGAATTGAACCGAAAATATGAT
1 ACCTGAACCCGAATTGAACCGAAAACATGAT
639403 ACCTGAACCC
1 ACCTGAACCC
639413 CAACTGCATC
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
31 26 0.46
32 14 0.25
33 16 0.29
ACGTcount: A:0.37, C:0.30, G:0.17, T:0.15
Consensus pattern (31 bp):
ACCTGAACCCGAATTGAACCGAAAACATGAT
Found at i:639360 original size:64 final size:64
Alignment explanation
Indices: 639289--639426 Score: 240
Period size: 64 Copynumber: 2.2 Consensus size: 64
639279 GAACCTGACT
* *
639289 TGCATCCGACATGAGAGCGACCTGAACCCGAATTGAACCGAAAACATGATACCTGAACCCGAAC
1 TGCATCCGACATGAGAACGACCTGAACCCGAATTGAACCGAAAACATGATACCTGAACCCCAAC
* *
639353 TGCATCCGACCTGAGAACGACCTGAACCCGAATTGAACCGAAAATATGATACCTGAACCCCAAC
1 TGCATCCGACATGAGAACGACCTGAACCCGAATTGAACCGAAAACATGATACCTGAACCCCAAC
639417 TGCATCCGAC
1 TGCATCCGAC
639427 TGATATGAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 70 1.00
ACGTcount: A:0.35, C:0.31, G:0.19, T:0.15
Consensus pattern (64 bp):
TGCATCCGACATGAGAACGACCTGAACCCGAATTGAACCGAAAACATGATACCTGAACCCCAAC
Found at i:639502 original size:16 final size:16
Alignment explanation
Indices: 639479--639531 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
639469 TAGTACCCAG
639479 CCTGTTTTCAACCTGA
1 CCTGTTTTCAACCTGA
*
639495 CTTGTTTTCAACCTGA
1 CCTGTTTTCAACCTGA
*
639511 CCTGTTTTTAACCTGA
1 CCTGTTTTCAACCTGA
639527 CCTGT
1 CCTGT
639532 AAATGATCCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.17, C:0.28, G:0.13, T:0.42
Consensus pattern (16 bp):
CCTGTTTTCAACCTGA
Found at i:639790 original size:14 final size:14
Alignment explanation
Indices: 639768--639814 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
639758 CGCAAAGGAA
*
639768 AATTAATATAGTTT
1 AATTTATATAGTTT
639782 AATTTATATA----
1 AATTTATATAGTTT
639792 AA-TTATATAGTTT
1 AATTTATATAGTTT
639805 AATTTATATA
1 AATTTATATA
639815 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:639801 original size:23 final size:24
Alignment explanation
Indices: 639767--639816 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
639757 ACGCAAAGGA
639767 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
639791 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
639814 AAA
1 AAA
639817 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:640848 original size:20 final size:19
Alignment explanation
Indices: 640825--640929 Score: 88
Period size: 20 Copynumber: 5.1 Consensus size: 19
640815 GGTTACATAT
*
640825 ATAGTTTATATAACATATAA
1 ATAGTTTATAT-ACATATAC
640845 ATAGATTGTATATATACATATAC
1 ATAG--T-T-TATATACATATAC
*
640868 TATAGGTTATAT--ATATAC
1 -ATAGTTTATATACATATAC
640886 ATAGTTTATATACACTATAC
1 ATAGTTTATATACA-TATAC
640906 ATAGTTTATACATACATGATAC
1 ATAGTTTAT--ATACAT-ATAC
640928 AT
1 AT
640930 GTACTATAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.14
18 6 0.08
19 1 0.01
20 23 0.32
21 2 0.03
22 12 0.17
23 8 0.11
24 9 0.13
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (19 bp):
ATAGTTTATATACATATAC
Found at i:640860 original size:24 final size:24
Alignment explanation
Indices: 640831--640888 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
640821 ATATATAGTT
*
640831 TATATA-ACATATA-AATAGATTG
1 TATATATACATATACAATAGATTA
* *
640853 TATATATACATATACTATAGGTTA
1 TATATATACATATACAATAGATTA
640877 TATATATACATA
1 TATATATACATA
640889 GTTTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 18 0.58
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
TATATATACATATACAATAGATTA
Found at i:640966 original size:37 final size:37
Alignment explanation
Indices: 640918--640988 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
640908 AGTTTATACA
*
640918 TACATGATACATGTACTATAAGTTACA-TATATAGTT
1 TACATGATACATATACTATAAGTTACATTATATAGTT
* *
640954 TACATGTATACATATATTATAGGTTACATTATATA
1 TACATG-ATACATATACTATAAGTTACATTATATA
640989 TATTAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 6 0.20
37 18 0.60
38 6 0.20
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (37 bp):
TACATGATACATATACTATAAGTTACATTATATAGTT
Found at i:640980 original size:24 final size:23
Alignment explanation
Indices: 640947--640991 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
640937 AAGTTACATA
*
640947 TATAGTTTACATGTATACATATAT
1 TATAGGTTACAT-TATACATATAT
*
640971 TATAGGTTACATTATATATAT
1 TATAGGTTACATTATACATAT
640992 TAACTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TATAGGTTACATTATACATATAT
Found at i:641016 original size:7 final size:7
Alignment explanation
Indices: 641006--641100 Score: 59
Period size: 7 Copynumber: 13.6 Consensus size: 7
640996 TATTGTTTAT
641006 GTTTAGG
1 GTTTAGG
641013 GTTTAGG
1 GTTTAGG
*
641020 GTTTATG
1 GTTTAGG
* *
641027 ATGTAAGG
1 GT-TTAGG
*
641035 G-TTAAG
1 GTTTAGG
641041 GTTTAGG
1 GTTTAGG
* **
641048 ATTTAAA
1 GTTTAGG
*
641055 GTTTATG
1 GTTTAGG
641062 GTTTAGG
1 GTTTAGG
*
641069 ATTTAGG
1 GTTTAGG
* *
641076 GTCTCA-A
1 GT-TTAGG
641083 GTTTAGG
1 GTTTAGG
641090 GTTTAGG
1 GTTTAGG
641097 GTTT
1 GTTT
641101 TTATATAATA
Statistics
Matches: 63, Mismatches: 21, Indels: 8
0.68 0.23 0.09
Matches are distributed among these distances:
6 6 0.10
7 52 0.83
8 5 0.08
ACGTcount: A:0.22, C:0.02, G:0.33, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:641064 original size:21 final size:21
Alignment explanation
Indices: 641013--641073 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
641003 TATGTTTAGG
* * * *
641013 GTTTAGGGTTTATGATGTAAG
1 GTTTAAGGTTTAGGATTTAAA
*
641034 GGTTAAGGTTTAGGATTTAAA
1 GTTTAAGGTTTAGGATTTAAA
*
641055 GTTTATGGTTTAGGATTTA
1 GTTTAAGGTTTAGGATTTA
641074 GGGTCTCAAG
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (21 bp):
GTTTAAGGTTTAGGATTTAAA
Found at i:641202 original size:38 final size:38
Alignment explanation
Indices: 641160--641233 Score: 148
Period size: 38 Copynumber: 1.9 Consensus size: 38
641150 TATAAACTAT
641160 ATAAGTAATTTACTTTATATGATATATATATATATACA
1 ATAAGTAATTTACTTTATATGATATATATATATATACA
641198 ATAAGTAATTTACTTTATATGATATATATATATATA
1 ATAAGTAATTTACTTTATATGATATATATATATATA
641234 TATACATAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (38 bp):
ATAAGTAATTTACTTTATATGATATATATATATATACA
Found at i:641289 original size:18 final size:18
Alignment explanation
Indices: 641266--641336 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 18
641256 GTACTATAAG
641266 TTACATATATAGTTTACA
1 TTACATATATAGTTTACA
*
641284 TTACATGTATATA-TATACTATAA
1 TTACA--TATATAGT-T--TA-CA
641307 GTTACATATATAGTTTACA
1 -TTACATATATAGTTTACA
*
641326 TTACATGTATA
1 TTACATATATA
641337 CACATACTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
18 15 0.36
19 2 0.05
20 9 0.21
22 9 0.21
23 2 0.05
24 5 0.12
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (18 bp):
TTACATATATAGTTTACA
Found at i:641296 original size:20 final size:20
Alignment explanation
Indices: 641271--641336 Score: 57
Period size: 20 Copynumber: 3.2 Consensus size: 20
641261 ATAAGTTACA
641271 TATATAGTTTACATTACATG
1 TATATAGTTTACATTACATG
*
641291 TATATA-TATACTATAAGTTACA--
1 TATATAGT-T--TA-CA-TTACATG
641313 TATATAGTTTACATTACATG
1 TATATAGTTTACATTACATG
641333 TATA
1 TATA
641337 CACATACTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 16
0.67 0.04 0.30
Matches are distributed among these distances:
18 5 0.14
19 2 0.06
20 13 0.36
22 9 0.25
23 2 0.06
24 5 0.14
ACGTcount: A:0.39, C:0.09, G:0.08, T:0.44
Consensus pattern (20 bp):
TATATAGTTTACATTACATG
Done.