Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007858.1 Hibiscus syriacus cultivar Beakdansim tig00110220_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: 969818
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:209725 original size:20 final size:20
Alignment explanation
Indices: 209700--209893 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
209690 CTTTAAATAT
209700 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
209720 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
209742 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
209761 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
209781 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
209801 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
209821 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
209841 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
209861 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
209881 CGCGTTGCGATTT
1 CGCGTTGCGATTT
209894 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:209887 original size:60 final size:60
Alignment explanation
Indices: 209700--209893 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
209690 CTTTAAATAT
**
209700 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
209761 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
209821 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
209881 CGCGTTGCGATTT
1 CGCGTTGCGATTT
209894 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:209910 original size:21 final size:21
Alignment explanation
Indices: 209880--209962 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
209870 ATTTTCATAT
*
209880 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
209901 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
209922 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
209943 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
209963 CTAATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:209953 original size:42 final size:43
Alignment explanation
Indices: 209860--209958 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
209850 ATTTATGTGT
* *
209860 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
209901 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
209943 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
209959 GAAACTAATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:210271 original size:23 final size:21
Alignment explanation
Indices: 210237--210280 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
210227 TATAAAAAAA
210237 TTATTTTTTATTAAATATTTTT
1 TTATTTTTTATTAAAT-TTTTT
*
210259 TTATATTTTTATTTAATTTTTT
1 TTAT-TTTTTATTAAATTTTTT
210281 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTTTATTAAATTTTTT
Found at i:219143 original size:15 final size:15
Alignment explanation
Indices: 219123--219235 Score: 103
Period size: 14 Copynumber: 7.5 Consensus size: 15
219113 TAATAAGGTT
219123 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
219138 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
219153 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
219167 A---ATTTTAAAATA
1 ATTTATTTTAAAATA
*
219179 ATTTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
219198 TTGATTTATTTT-AAATA
1 ---ATTTATTTTAAAATA
219215 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
219229 ATTTATT
1 ATTTATT
219236 AGTATGGATT
Statistics
Matches: 83, Mismatches: 4, Indels: 23
0.75 0.04 0.21
Matches are distributed among these distances:
11 1 0.01
12 10 0.12
14 30 0.36
15 22 0.27
16 4 0.05
17 3 0.04
19 3 0.04
20 2 0.02
21 1 0.01
22 7 0.08
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:219175 original size:26 final size:27
Alignment explanation
Indices: 219123--219193 Score: 90
Period size: 26 Copynumber: 2.5 Consensus size: 27
219113 TAATAAGGTT
219123 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTA-TTTAAAATAA--TATTATAAAATA
*
219153 ATTTATTTAAAATAA-ATTTTAAAATA
1 ATTTATTTAAAATAATATTATAAAATA
219179 ATTTATTATAAAATA
1 ATTTATT-TAAAATA
219194 TGGATTGATT
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 17 0.44
27 7 0.18
29 10 0.26
30 5 0.13
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTATTTAAAATAATATTATAAAATA
Found at i:219254 original size:22 final size:23
Alignment explanation
Indices: 219229--219302 Score: 71
Period size: 22 Copynumber: 3.2 Consensus size: 23
219219 ATTTTAAATA
219229 ATTTAT-TAGTATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
219251 ATTT-TAAAATATGGATTGATTT
1 ATTTATATAGTATGGATTGATTT
* *
219273 ATTATTGTAGTTGTATGGATTGATTT
1 A-T-TTATA-TAGTATGGATTGATTT
219299 ATTT
1 ATTT
219303 TAAATAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.02
22 19 0.45
23 1 0.02
24 4 0.10
25 3 0.07
26 14 0.33
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (23 bp):
ATTTATATAGTATGGATTGATTT
Found at i:219326 original size:32 final size:32
Alignment explanation
Indices: 219285--219445 Score: 157
Period size: 32 Copynumber: 5.7 Consensus size: 32
219275 TATTGTAGTT
219285 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
219317 GTATGGATTGATTAATTTT--A-AA---A-TA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
219342 -TA--GATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
219371 GTATGTATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
219394 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
219425 GTAT-GATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
219446 ATATAGATTG
Statistics
Matches: 105, Mismatches: 4, Indels: 41
0.70 0.03 0.27
Matches are distributed among these distances:
22 26 0.25
23 4 0.04
24 3 0.03
25 5 0.05
26 4 0.04
28 4 0.04
29 5 0.05
30 3 0.03
31 21 0.20
32 30 0.29
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:219355 original size:54 final size:54
Alignment explanation
Indices: 219290--219462 Score: 312
Period size: 54 Copynumber: 3.2 Consensus size: 54
219280 TAGTTGTATG
*
219290 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTAATTTTAAAATATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA
* *
219344 GATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATG
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA
219398 GATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATA
1 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA
219451 GATTGATTTATT
1 GATTGATTTATT
219463 ATTGTAGTTG
Statistics
Matches: 114, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 32 0.28
54 82 0.72
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (54 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATA
Found at i:219388 original size:22 final size:22
Alignment explanation
Indices: 219372--219414 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
219362 AATTTATTAG
*
219372 TATGTATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
219394 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
219415 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:219489 original size:79 final size:80
Alignment explanation
Indices: 219394--219542 Score: 266
Period size: 79 Copynumber: 1.9 Consensus size: 80
219384 TATTTTAAAA
219394 TATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTTTAAAATAT-AGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGA-ATTGA
219457 TTTATTATTGTAGTTG
65 TTTATTATTGTAGTTG
*
219473 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATCTGAATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTGAT
219538 TTATT
66 TTATT
219543 TTAAAAAATT
Statistics
Matches: 67, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
79 36 0.54
80 30 0.45
81 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.53
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGAATTGAT
TTATTATTGTAGTTG
Found at i:219532 original size:22 final size:22
Alignment explanation
Indices: 219507--219548 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
219497 TTTATTAGTA
219507 TGAATTGATTTATTTTAAAATC
1 TGAATTGATTTATTTTAAAATC
219529 TGAATTGATTTATTTTAAAA
1 TGAATTGATTTATTTTAAAA
219549 AATTTATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.10, T:0.50
Consensus pattern (22 bp):
TGAATTGATTTATTTTAAAATC
Found at i:219538 original size:187 final size:188
Alignment explanation
Indices: 219215--219557 Score: 618
Period size: 187 Copynumber: 1.8 Consensus size: 188
219205 ATTTTAAATA
*
219215 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTG
*
219280 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTAATTTTAAAATATAG
66 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTAATTTTAAAATATAG
*
219345 ATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTG
131 ATTGATTTATTTTAAAAAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTG
219403 ATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAAATATAGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTG
* *
219467 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATCT-G
66 TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTAATTTTAAAATATAG
219531 AATTGATTTATTTTAAAAAATTTATTA
131 -ATTGATTTATTTTAAAAAATTTATTA
219558 TTGTAATTGT
Statistics
Matches: 149, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
186 1 0.01
187 122 0.82
188 26 0.17
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (188 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAGATTGATTTATTATTG
TAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTAATTTTAAAATATAG
ATTGATTTATTTTAAAAAATTTATTAGTATGTATTGATTTATTTTAAAATATGGATTG
Found at i:219629 original size:31 final size:31
Alignment explanation
Indices: 219572--219630 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
219562 AATTGTATGG
* *
219572 ATTATTTAAATTTCAGTATTATAAAACTAAA
1 ATTATTTAAATCTCAGTATTACAAAACTAAA
* *
219603 ATTATTTAAATCTCATTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTACAAAACT
219631 CTTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTACAAAACTAAA
Found at i:220012 original size:28 final size:30
Alignment explanation
Indices: 219972--220028 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
219962 AAAATGATAT
*
219972 ATTATTAA-TTTTT-AAATATTATAAAATG
1 ATTATAAATTTTTTGAAATATTATAAAATG
*
220000 ATTATAAATTTTTTGAATTATTATAAAAT
1 ATTATAAATTTTTTGAAATATTATAAAAT
220029 ATTTAATGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.28
29 5 0.20
30 13 0.52
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
ATTATAAATTTTTTGAAATATTATAAAATG
Found at i:220042 original size:20 final size:20
Alignment explanation
Indices: 219998--220044 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
219988 TATTATAAAA
* *
219998 TGATTATAAATTTTTTGAAT
1 TGATTATAAAATATTTGAAT
220018 T-ATTATAAAATATTT-AAT
1 TGATTATAAAATATTTGAAT
220036 GTGATTATA
1 -TGATTATA
220045 TATAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 13 0.57
20 7 0.30
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (20 bp):
TGATTATAAAATATTTGAAT
Found at i:225511 original size:75 final size:75
Alignment explanation
Indices: 225374--225512 Score: 174
Period size: 75 Copynumber: 1.9 Consensus size: 75
225364 ATGAACATAG
* * * * * *
225374 ATAAAATTTTAGTGTGGAAACCATCAATAAAATGGGTCACTATTCGAAGAAAATTAATATTTCAT
1 ATAAAATTTTAGTGTGGAAACCACCAATAAAATAGATCACTAATCAAAGAAAATCAATATTTCAT
225439 GGTGGGAATA
66 GGTGGGAATA
* *
225449 ATAAAATTTTAAG-GTGGACACCACCAATAAAATAGATGACTAATCAAAGAAAATCCAA-ATTTC
1 ATAAAATTTT-AGTGTGGAAACCACCAATAAAATAGATCACTAATCAAAGAAAAT-CAATATTTC
225512 A
64 A
225513 GTGCTCACCC
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
75 50 0.93
76 4 0.07
ACGTcount: A:0.45, C:0.12, G:0.15, T:0.27
Consensus pattern (75 bp):
ATAAAATTTTAGTGTGGAAACCACCAATAAAATAGATCACTAATCAAAGAAAATCAATATTTCAT
GGTGGGAATA
Found at i:226794 original size:2 final size:2
Alignment explanation
Indices: 226789--226818 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
226779 GGAGTGTGTG
*
226789 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
226819 ATTTCAATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:227767 original size:196 final size:196
Alignment explanation
Indices: 227433--227818 Score: 729
Period size: 196 Copynumber: 2.0 Consensus size: 196
227423 AGTTTTTAAA
* *
227433 AAAATTGAAAGTTTAAGTATTAAAATATATAGTTTACCCTAAAATTTATAACTCATAGATTAATA
1 AAAATTGAAAGTTTAAGTATTAAAACATATAGTTTACCCTAAAATTTATAACACATAGATTAATA
227498 TATTTTTTTAACTCATTGTAATATAATATTTTTAGAATTAGGGCTTAGGTTTAGAGTTAAGAGTT
66 TATTTTTTTAACTCATTGTAATATAATATTTTTAGAATTAGGGCTTAGGTTTAGAGTTAAGAGTT
227563 AAGAGTTTATGAGTTGATGGTTATGTGTTAGTGATTATGGGTTATGGATGAGGGATTTTAATACT
131 AAGAGTTTATGAGTTGATGGTTATGTGTTAGTGATTATGGGTTATGGATGAGGGATTTTAATACT
227628 T
196 T
227629 AAAATTGAAAGTTTAAGTATTAAAACATATAGTTTACCCTAAAATTTATAACACATAGATTAATA
1 AAAATTGAAAGTTTAAGTATTAAAACATATAGTTTACCCTAAAATTTATAACACATAGATTAATA
*
227694 TATTTTTTTAACTCATTGTAATATAATATTTTTAGAATTAGGGCTTAGGTTTAG-GATTTAGAGT
66 TATTTTTTTAACTCATTGTAATATAATATTTTTAGAATTAGGGCTTAGGTTTAGAG-TTAAGAGT
227758 TAAGAGTTTATGAGTTGATGGTTATGTGTTAGTGATTATGGGTTATGGATGAGGGATTTTA
130 TAAGAGTTTATGAGTTGATGGTTATGTGTTAGTGATTATGGGTTATGGATGAGGGATTTTA
227819 GGGTTTGAAA
Statistics
Matches: 186, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
195 1 0.01
196 185 0.99
ACGTcount: A:0.35, C:0.05, G:0.19, T:0.42
Consensus pattern (196 bp):
AAAATTGAAAGTTTAAGTATTAAAACATATAGTTTACCCTAAAATTTATAACACATAGATTAATA
TATTTTTTTAACTCATTGTAATATAATATTTTTAGAATTAGGGCTTAGGTTTAGAGTTAAGAGTT
AAGAGTTTATGAGTTGATGGTTATGTGTTAGTGATTATGGGTTATGGATGAGGGATTTTAATACT
T
Found at i:229408 original size:2 final size:2
Alignment explanation
Indices: 229401--229434 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
229391 AGACTGTTCA
*
229401 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
229435 TGCATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:231439 original size:19 final size:20
Alignment explanation
Indices: 231417--231459 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
231407 GAAAAGATAT
231417 TCTCT-ATTTGAGG-AAAATA
1 TCTCTCATTTG-GGTAAAATA
231436 TCTCTCATTTGGGTTAAAATA
1 TCTCTCATTTGGG-TAAAATA
231457 TCT
1 TCT
231460 GTAAGTCCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (20 bp):
TCTCTCATTTGGGTAAAATA
Found at i:240857 original size:9 final size:9
Alignment explanation
Indices: 240843--240870 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
240833 TGGAAACAGG
240843 TGTTACTTT
1 TGTTACTTT
240852 TGTTACTTT
1 TGTTACTTT
240861 TGTTACTTT
1 TGTTACTTT
240870 T
1 T
240871 ATTGTCCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.11, C:0.11, G:0.11, T:0.68
Consensus pattern (9 bp):
TGTTACTTT
Found at i:245299 original size:20 final size:19
Alignment explanation
Indices: 245274--245327 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
245264 GTGAAATAAA
245274 AATCGCAACGCGATCTCCAG
1 AATCGCAACGCGATC-CCAG
** *
245294 AATCGCAAATCAGTTCCCAG
1 AATCGCAACGC-GATCCCAG
245314 AATCGCAACGCGAT
1 AATCGCAACGCGAT
245328 TATGAAGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.33, C:0.31, G:0.19, T:0.17
Consensus pattern (19 bp):
AATCGCAACGCGATCCCAG
Found at i:245400 original size:20 final size:20
Alignment explanation
Indices: 245376--245708 Score: 300
Period size: 20 Copynumber: 16.6 Consensus size: 20
245366 CAATTTTCCA
* *
245376 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATACGT
* **
245396 AAATCGCAACGCGAACATAT
1 AAATCGCAACGCGAATACGT
*
245416 AAATCGCAACGCG-ATTC-T
1 AAATCGCAACGCGAATACGT
* * * * *
245434 GACTATCGCAACGAGTATCCAT
1 -A-AATCGCAACGCGAATACGT
245456 AAAATCGCAACGAC-AATACGTT
1 -AAATCGCAACG-CGAATACG-T
* *
245478 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGT
*
245498 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGAATACGT
*
245518 AAATCGCAACGCGTAT-CTGT
1 AAATCGCAACGCGAATAC-GT
*
245538 AAATCGCAACGAGAATACGT
1 AAATCGCAACGCGAATACGT
* * *
245558 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATACGT
* * *
245578 AAATCGCAATGCTAATATGT
1 AAATCGCAACGCGAATACGT
*
245598 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
245618 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
245638 AAATCGCAATGCGAATACGT
1 AAATCGCAACGCGAATACGT
*
245658 AAATCGCAATGCGAAT-CTGT
1 AAATCGCAACGCGAATAC-GT
**
245678 AAATCGCAATACGAAT-CTGT
1 AAATCGCAACGCGAATAC-GT
245698 AAATCGCAACG
1 AAATCGCAACG
245709 AGATTCTGAC
Statistics
Matches: 266, Mismatches: 37, Indels: 20
0.82 0.11 0.06
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 227 0.85
21 31 0.12
22 3 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATACGT
Found at i:246597 original size:24 final size:24
Alignment explanation
Indices: 246570--246621 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
246560 ATTCAAAATA
246570 TGATCTTGGTCAATACCCGGACTT
1 TGATCTTGGTCAATACCCGGACTT
* *
246594 TGATCTTGGTCAATACTCGGATTT
1 TGATCTTGGTCAATACCCGGACTT
246618 TGAT
1 TGAT
246622 GATTTTTCAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATCTTGGTCAATACCCGGACTT
Found at i:249058 original size:20 final size:20
Alignment explanation
Indices: 249033--249087 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
249023 AGACATTCAT
*
249033 TTGACTATCACAATGCGGAA
1 TTGACTATCACAACGCGGAA
*
249053 TTGACTATCGCAACGCGGAA
1 TTGACTATCACAACGCGGAA
* *
249073 ATGACTATCGCAACG
1 TTGACTATCACAACG
249088 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.33, C:0.24, G:0.22, T:0.22
Consensus pattern (20 bp):
TTGACTATCACAACGCGGAA
Found at i:249148 original size:33 final size:35
Alignment explanation
Indices: 249106--249196 Score: 114
Period size: 38 Copynumber: 2.5 Consensus size: 35
249096 GCAAAGCGAA
*
249106 TTCATTTTCGCAGTGCGATTCA-CTCG-TTGCGATT
1 TTCA-TTTCGCATTGCGATTCATCTCGATTGCGATT
*
249140 TTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
1 TTCATTTCGCATTGCGA--TTCATCTCG-ATTGCGATT
249178 TTCATTTCGCATTGCGATT
1 TTCATTTCGCATTGCGATT
249197 TTCATCTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 8
0.83 0.03 0.13
Matches are distributed among these distances:
33 12 0.24
34 4 0.08
35 4 0.08
36 5 0.10
38 25 0.50
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (35 bp):
TTCATTTCGCATTGCGATTCATCTCGATTGCGATT
Found at i:249156 original size:19 final size:19
Alignment explanation
Indices: 249132--249201 Score: 140
Period size: 19 Copynumber: 3.7 Consensus size: 19
249122 GATTCACTCG
249132 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
249151 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
249170 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
249189 TTGCGATTTTCAT
1 TTGCGATTTTCAT
249202 CTTTTCCTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 51 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:249432 original size:20 final size:20
Alignment explanation
Indices: 249407--249459 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
249397 AGACATTCAT
*
249407 TTGACTATCGCAATGCGGAA
1 TTGACTATCGCAACGCGGAA
249427 TTGACTATCGCAACGCGGAA
1 TTGACTATCGCAACGCGGAA
* *
249447 ATGACTTTCGCAA
1 TTGACTATCGCAA
249460 AGAGAGAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.25
Consensus pattern (20 bp):
TTGACTATCGCAACGCGGAA
Found at i:249490 original size:19 final size:19
Alignment explanation
Indices: 249466--249545 Score: 98
Period size: 19 Copynumber: 4.4 Consensus size: 19
249456 GCAAAGAGAG
249466 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
249485 AATCGCAATGCGAAATGCA
1 AATCGCAATGCGAAATGAA
*
249504 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
249518 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
249538 AATCGCAA
1 AATCGCAA
249546 CATGAAATTA
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
14 8 0.15
16 5 0.10
17 2 0.04
18 3 0.06
19 26 0.50
20 8 0.15
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:249582 original size:20 final size:19
Alignment explanation
Indices: 249557--249643 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 19
249547 ATGAAATTAG
249557 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
249576 TTTTCGCATTGTGA--TTCA
1 -TTTCGCGTTGCGATTTTCA
*
249594 ---CTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* *
249610 TTTCGCATTGTGATTTTCA
1 TTTCGCGTTGCGATTTTCA
249629 TTTCCGCGTTGCGAT
1 TTT-CGCGTTGCGAT
249644 AGTCTGTTTT
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
14 7 0.14
16 4 0.08
18 4 0.08
19 16 0.31
20 20 0.39
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.47
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:249762 original size:13 final size:14
Alignment explanation
Indices: 249744--249778 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
249734 ATATCATTAA
249744 ACAAATCA-CATTT
1 ACAAATCATCATTT
*
249757 ACAAATCATCTTTT
1 ACAAATCATCATTT
249771 ACAAATCA
1 ACAAATCA
249779 ATTAAACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCATCATTT
Found at i:253225 original size:20 final size:20
Alignment explanation
Indices: 253200--253262 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
253190 TTTTGGTTGA
253200 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
253220 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
253239 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
253260 AAT
1 AAT
253263 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 35 0.95
21 1 0.03
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:253266 original size:14 final size:14
Alignment explanation
Indices: 253247--253335 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
253237 GGAAATGACT
253247 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
253261 ATCGCAACGCGAAATTAAA
1 ATCGCAA--CG--A-GAGA
253280 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
253294 ATCGCAACGCGAAATTAAA
1 ATCGCAA--CG--A-GAGA
253313 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
253327 ATCGCAACG
1 ATCGCAACG
253336 CGAAATGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 20
0.67 0.09 0.24
Matches are distributed among these distances:
14 27 0.47
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 18 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:253284 original size:19 final size:19
Alignment explanation
Indices: 253260--253321 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
253250 GCAACGAGAG
253260 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATTAA
* *
253279 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATTAA
253293 AATCGCAACGCGAAATTAA
1 AATCGCAACGCGAAATTAA
253312 AATCGCAACG
1 AATCGCAACG
253322 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 9 0.26
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 19 0.56
ACGTcount: A:0.45, C:0.23, G:0.19, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATTAA
Found at i:253284 original size:33 final size:33
Alignment explanation
Indices: 253226--253351 Score: 200
Period size: 33 Copynumber: 3.8 Consensus size: 33
253216 AGAGAATGAA
* **
253226 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATTAAAATCGCAACGAGAG
253260 AATCGCAACGCGAAATTAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATTAAAATCGCAACGAGAG
253293 AATCGCAACGCGAAATTAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATTAAAATCGCAACGAGAG
*
253326 AATCGCAACGCGAAA-TGAAATCGCAA
1 AATCGCAACGCGAAATTAAAATCGCAA
253352 TGCGATTTTG
Statistics
Matches: 88, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
32 10 0.11
33 67 0.76
34 11 0.12
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATTAAAATCGCAACGAGAG
Found at i:253402 original size:21 final size:21
Alignment explanation
Indices: 253376--253439 Score: 87
Period size: 21 Copynumber: 3.1 Consensus size: 21
253366 CGCGTTGCGA
253376 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
253397 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
253418 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
253438 TT
1 TT
253440 TCATGTTGTG
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 16 0.42
21 22 0.58
ACGTcount: A:0.11, C:0.20, G:0.17, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:253452 original size:20 final size:19
Alignment explanation
Indices: 253383--253454 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 19
253373 CGATTCTCTC
253383 GTTGCGATTTTCATTTCTCT
1 GTTGCGATTTTCATTT-TCT
**
253403 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTC-T
253424 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTC-T
*
253444 GTTGTGATTTT
1 GTTGCGATTTT
253455 AAGTTTAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
20 29 0.66
21 15 0.34
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.53
Consensus pattern (19 bp):
GTTGCGATTTTCATTTTCT
Found at i:254031 original size:20 final size:20
Alignment explanation
Indices: 254006--254219 Score: 214
Period size: 20 Copynumber: 10.6 Consensus size: 20
253996 CTTTAAAAAT
*
254006 CGCGTTACGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
254026 CGCGTTGTGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* * *
254046 TGTCATTGCGCTTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * *
254067 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
254087 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
254107 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
254127 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
254147 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
**
254168 TTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
254188 CGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
254209 CTCGTTGCGAT
1 CGCGTTGCGAT
254220 AGTCAGAATT
Statistics
Matches: 155, Mismatches: 34, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
20 106 0.68
21 49 0.32
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:254095 original size:40 final size:41
Alignment explanation
Indices: 254008--254219 Score: 320
Period size: 41 Copynumber: 5.2 Consensus size: 41
253998 TTAAAAATCG
* * *
254008 CGTTACGATTTACGGATACGCGTTGTGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * *
254049 CATTGCGCTTTACGGATACGCATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
254089 CGTTGCGATTTACAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
*
254129 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
254170 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
254211 CGTTGCGAT
1 CGTTGCGAT
254220 AGTCAGAATT
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 74 0.48
41 81 0.52
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:254270 original size:20 final size:20
Alignment explanation
Indices: 254233--254276 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
254223 CAGAATTGCG
*
254233 TTGCGATTTATATGTTCGCA
1 TTGCGATTTATATATTCGCA
*
254253 TTGCGATTT-TCATATTCGCG
1 TTGCGATTTAT-ATATTCGCA
254273 TTGC
1 TTGC
254277 AATTATGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.16, C:0.18, G:0.20, T:0.45
Consensus pattern (20 bp):
TTGCGATTTATATATTCGCA
Found at i:254333 original size:21 final size:20
Alignment explanation
Indices: 254248--254339 Score: 51
Period size: 21 Copynumber: 4.5 Consensus size: 20
254238 ATTTATATGT
*
254248 TCGCATTGCGATTTTCATAT
1 TCGCATTGCGATTTTCATAA
* * ** *
254268 TCGCGTTGCAATTATGGAAAA
1 TCGCATTGCGATT-TTCATAA
* * *
254289 CCGCAATGCGAATTTTTACT-A
1 TCGCATTGCG-ATTTTCA-TAA
254310 TCGCATTGCGATTATTCATAA
1 TCGCATTGCGATT-TTCATAA
*
254331 TCGCGTTGC
1 TCGCATTGC
254340 AATTCTGGGA
Statistics
Matches: 50, Mismatches: 17, Indels: 9
0.66 0.22 0.12
Matches are distributed among these distances:
20 15 0.30
21 32 0.64
22 3 0.06
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTTCATAA
Found at i:257190 original size:18 final size:18
Alignment explanation
Indices: 257167--257202 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
257157 ACCGATCAAC
257167 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
257185 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
257203 TGACCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.50, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:258573 original size:19 final size:19
Alignment explanation
Indices: 258487--258613 Score: 103
Period size: 20 Copynumber: 7.1 Consensus size: 19
258477 TCTTTTGGTT
*
258487 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
258506 GAGAATGAAAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
258526 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
258544 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
258560 GAAATTAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
258577 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
258593 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
258612 GA
1 GA
258614 TTTTGGTTTC
Statistics
Matches: 85, Mismatches: 11, Indels: 24
0.71 0.09 0.20
Matches are distributed among these distances:
14 18 0.21
15 2 0.02
16 4 0.05
17 3 0.04
18 3 0.04
19 25 0.29
20 28 0.33
21 2 0.02
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:258573 original size:33 final size:33
Alignment explanation
Indices: 258487--258608 Score: 154
Period size: 33 Copynumber: 3.5 Consensus size: 33
258477 TCTTTTGGTT
258487 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
258526 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
258560 GAAATTAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
258593 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
258609 TGCGATTTTG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
33 45 0.59
34 11 0.14
36 1 0.01
37 1 0.01
38 3 0.04
40 15 0.20
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:258659 original size:21 final size:21
Alignment explanation
Indices: 258633--258694 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 21
258623 CGCGTTGCGA
258633 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
* **
258654 TTCTCTCGTTAC-ATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
258674 TTC-GT-GTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
258693 TT
1 TT
258695 TCATGTTGTG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 4 0.12
19 9 0.27
20 9 0.27
21 11 0.33
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:259280 original size:20 final size:20
Alignment explanation
Indices: 259255--259482 Score: 233
Period size: 20 Copynumber: 11.2 Consensus size: 20
259245 GATTATAATG
259255 GCGATTTACGGATACGCGTT
1 GCGATTTACGGATACGCGTT
259275 GCGATTTACGGATACGCGTT
1 GCGATTTACGGATACGCGTT
* * *
259295 GCGATTTTACGTAT-TGTCATT
1 GCGA-TTTACGGATACG-CGTT
* *
259316 GCGCTTTACGGATACGCATT
1 GCGATTTACGGATACGCGTT
* * * *
259336 ACGATTTACGTATTCTCGTT
1 GCGATTTACGGATACGCGTT
**
259356 GCGATTTATAGATACGCGTT
1 GCGATTTACGGATACGCGTT
* * *
259376 GCGATTTACGTATTCTCGTT
1 GCGATTTACGGATACGCGTT
259396 GCGATTTACGGATACGCGTT
1 GCGATTTACGGATACGCGTT
* * ***
259416 GCGATTTTAAGTATTTTCGTT
1 GCGA-TTTACGGATACGCGTT
259437 GCGATTTACGGATACGCGTT
1 GCGATTTACGGATACGCGTT
*
259457 GCGATTTTACGGATACTCGTT
1 GCGA-TTTACGGATACGCGTT
259478 GCGAT
1 GCGAT
259483 AGTCAGAATT
Statistics
Matches: 166, Mismatches: 37, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
20 117 0.70
21 49 0.30
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GCGATTTACGGATACGCGTT
Found at i:259318 original size:41 final size:41
Alignment explanation
Indices: 259271--259482 Score: 311
Period size: 41 Copynumber: 5.2 Consensus size: 41
259261 TACGGATACG
*
259271 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* * * *
259312 CATTGCGCTTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
**
259352 CGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
259392 CGTTGCGATTTACGGATACGCGTTGCGATTTTAAGTATTTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
* *
259433 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
259474 CGTTGCGAT
1 CGTTGCGAT
259483 AGTCAGAATT
Statistics
Matches: 151, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 71 0.47
41 80 0.53
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCT
Found at i:259519 original size:20 final size:20
Alignment explanation
Indices: 259496--259539 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
259486 CAGAATTGCA
*
259496 TTGCGATTTAT-ATGTTCGCG
1 TTGCGATTT-TCATATTCGCG
259516 TTGCGATTTTCATATTCGCG
1 TTGCGATTTTCATATTCGCG
259536 TTGC
1 TTGC
259540 AATTATGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCATATTCGCG
Found at i:262433 original size:18 final size:18
Alignment explanation
Indices: 262410--262445 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
262400 ACCGATCAAC
262410 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
262428 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTCGGGTCG
262446 TGACCGGTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.19, G:0.50, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:271938 original size:21 final size:21
Alignment explanation
Indices: 271889--271939 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
271879 CCAAATCACC
*
271889 AATTTTTCTAAAATTAAAAAT
1 AATTTTTTTAAAATTAAAAAT
* *
271910 AATATTTTTAAAA-TAATAATT
1 AATTTTTTTAAAATTAA-AAAT
271931 AATTTTTTT
1 AATTTTTTT
271940 TTTGTAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTTTTAAAATTAAAAAT
Found at i:274014 original size:35 final size:36
Alignment explanation
Indices: 273968--274055 Score: 108
Period size: 36 Copynumber: 2.5 Consensus size: 36
273958 TTGTTAAAAG
*
273968 TTTCAAAGTTTGG-CAA-CCAACTTTGAAAAATGTTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATG-TT
****
274003 TTTCAAAGTTTGGTAAATGTTTCTTTGAAAAATGTT
1 TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATGTT
274039 TTTCAAAGTTTGGTAAA
1 TTTCAAAGTTTGGTAAA
274056 ATTTTGGTAG
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
35 13 0.28
36 21 0.46
37 12 0.26
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (36 bp):
TTTCAAAGTTTGGTAAATCCAACTTTGAAAAATGTT
Found at i:280351 original size:87 final size:87
Alignment explanation
Indices: 280205--280369 Score: 330
Period size: 87 Copynumber: 1.9 Consensus size: 87
280195 ACAATCTCCT
280205 TTCTTAAATACATGTCTGGATTAGATTTGTCATGTAACAATCTGATAGGCTTCATTCCTCAGAGT
1 TTCTTAAATACATGTCTGGATTAGATTTGTCATGTAACAATCTGATAGGCTTCATTCCTCAGAGT
280270 CTTGGGAAGCTGAAAGGAGACA
66 CTTGGGAAGCTGAAAGGAGACA
280292 TTCTTAAATACATGTCTGGATTAGATTTGTCATGTAACAATCTGATAGGCTTCATTCCTCAGAGT
1 TTCTTAAATACATGTCTGGATTAGATTTGTCATGTAACAATCTGATAGGCTTCATTCCTCAGAGT
280357 CTTGGGAAGCTGA
66 CTTGGGAAGCTGA
280370 CATCCCTTCA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 78 1.00
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.34
Consensus pattern (87 bp):
TTCTTAAATACATGTCTGGATTAGATTTGTCATGTAACAATCTGATAGGCTTCATTCCTCAGAGT
CTTGGGAAGCTGAAAGGAGACA
Found at i:285316 original size:3 final size:3
Alignment explanation
Indices: 285310--285347 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
285300 TAATAATAAT
*
285310 AAC AAC AAG AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
285348 TAATAATAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.68, C:0.29, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:285352 original size:3 final size:3
Alignment explanation
Indices: 285346--285430 Score: 170
Period size: 3 Copynumber: 28.3 Consensus size: 3
285336 CAACAACAAC
285346 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
285394 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
285431 CATTGTCTAT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:300958 original size:26 final size:26
Alignment explanation
Indices: 300922--300976 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
300912 AAATGTCAGG
300922 GGTTAATCATGGTATTTTGACAATCT
1 GGTTAATCATGGTATTTTGACAATCT
300948 GGTTAATCATGGTATTTTGACAATCT
1 GGTTAATCATGGTATTTTGACAATCT
300974 GGT
1 GGT
300977 AGGAAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (26 bp):
GGTTAATCATGGTATTTTGACAATCT
Found at i:304201 original size:17 final size:17
Alignment explanation
Indices: 304179--304220 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
304169 TTATAGTTTC
304179 TCTCACACCCCTTTTAA
1 TCTCACACCCCTTTTAA
304196 TCTCACACCCCTTTTAA
1 TCTCACACCCCTTTTAA
304213 TCTCACAC
1 TCTCACAC
304221 GTTGATTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.43, G:0.00, T:0.33
Consensus pattern (17 bp):
TCTCACACCCCTTTTAA
Found at i:305218 original size:30 final size:29
Alignment explanation
Indices: 305160--305225 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
305150 TTATCTTATT
* * *
305160 AAATATATTTTATTTTTATTTTTAATATA
1 AAATATATTTCATTATTATTTATAATATA
305189 AAATATATTTCATTATTATCTTATAATATA
1 AAATATATTTCATTATTAT-TTATAATATA
305219 AAATATA
1 AAATATA
305226 AAATTTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 17 0.52
30 16 0.48
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
AAATATATTTCATTATTATTTATAATATA
Found at i:305428 original size:30 final size:30
Alignment explanation
Indices: 305385--305467 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
305375 TATTTTTACT
*
305385 TTAAAATAAAAATAAAATATATTTAATAAG
1 TTAAAACAAAAATAAAATATATTTAATAAG
* *
305415 TTAAGACAAAAATAAAATACATTTAATAAG
1 TTAAAACAAAAATAAAATATATTTAATAAG
* *
305445 TTAAAATAAAAATAAAAGATATT
1 TTAAAACAAAAATAAAATATATT
305468 CTTAAAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (30 bp):
TTAAAACAAAAATAAAATATATTTAATAAG
Found at i:309074 original size:74 final size:74
Alignment explanation
Indices: 308953--309101 Score: 271
Period size: 74 Copynumber: 2.0 Consensus size: 74
308943 GCTGTGATAG
308953 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
1 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
309018 TAATTCCTA
66 TAATTCCTA
* **
309027 ATTACAAAATATTCTTCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGTT
1 ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
309092 TAATTCCTA
66 TAATTCCTA
309101 A
1 A
309102 ATTATAGCCT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 72 1.00
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (74 bp):
ATTACAAAATATTCTCCAAATATTTTGTATTTACTATTGTATATTTAGTTGCCTAAGTTATAGCC
TAATTCCTA
Found at i:313523 original size:19 final size:19
Alignment explanation
Indices: 313501--313537 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
313491 TATTTAGTTG
*
313501 CCTAAGTTATAGCCTAATT
1 CCTAAATTATAGCCTAATT
313520 CCTAAATTATAGCCTAAT
1 CCTAAATTATAGCCTAAT
313538 GATTAGGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (19 bp):
CCTAAATTATAGCCTAATT
Found at i:314235 original size:19 final size:19
Alignment explanation
Indices: 314194--314236 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
314184 ATTCACTGTT
314194 TATAA-TTTTTTTCTTAAA
1 TATAATTTTTTTTCTTAAA
314212 TATAATTTTTATTTCTTAAA
1 TATAATTTTT-TTTCTTAAA
314232 -ATAAT
1 TATAAT
314237 GAAACAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.22
19 9 0.39
20 9 0.39
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (19 bp):
TATAATTTTTTTTCTTAAA
Found at i:314612 original size:21 final size:21
Alignment explanation
Indices: 314583--314649 Score: 107
Period size: 21 Copynumber: 3.2 Consensus size: 21
314573 ATTCTGACTA
* * *
314583 TCGCATTGCGATTTCCCAAAT
1 TCGCGTTGCGATTTTCCTAAT
314604 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTTCCTAAT
314625 TCGCGTTGCGATTTTCCTAAT
1 TCGCGTTGCGATTTTCCTAAT
314646 TCGC
1 TCGC
314650 AATACGAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.16, C:0.27, G:0.18, T:0.39
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCCTAAT
Found at i:314675 original size:20 final size:20
Alignment explanation
Indices: 314646--314858 Score: 345
Period size: 20 Copynumber: 10.7 Consensus size: 20
314636 TTTTCCTAAT
*
314646 TCGCAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
314666 TCGTAATACGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
314686 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
314706 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
314726 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
314746 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
314766 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
314786 TCGTAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
* *
314806 TCACAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
314826 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
314846 TCGCAATGCGAAT
1 TCGCAATGCGAAT
314859 CTGACTATCG
Statistics
Matches: 178, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 178 1.00
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:315083 original size:22 final size:22
Alignment explanation
Indices: 315058--315115 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 22
315048 ACATCCGTCT
315058 CCATCTCCGACGAAATCAGTCC
1 CCATCTCCGACGAAATCAGTCC
*
315080 CCA--T--GACGATAA-CAGTCT
1 CCATCTCCGACGA-AATCAGTCC
*
315098 CCATCTCCGGCGAAATCA
1 CCATCTCCGACGAAATCA
315116 TTCACGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
18 13 0.46
19 2 0.07
20 2 0.07
21 2 0.07
22 9 0.32
ACGTcount: A:0.29, C:0.36, G:0.16, T:0.19
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCC
Found at i:316840 original size:20 final size:20
Alignment explanation
Indices: 316815--316958 Score: 174
Period size: 20 Copynumber: 7.5 Consensus size: 20
316805 AGAATAGTTT
316815 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
316835 ACTATCGTAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
316855 ACTATCGCAA--CG-AGAT-
1 ACTATCGCAATGCGAAAATG
*
316871 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
316889 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
316909 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* * **
316929 ACTATCACAATGTGAATTTG
1 ACTATCGCAATGCGAAAATG
316949 ACTATCGCAA
1 ACTATCGCAA
316959 CGAAAGAATC
Statistics
Matches: 106, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 6 0.06
16 3 0.03
17 6 0.06
18 3 0.03
20 88 0.83
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:317048 original size:20 final size:20
Alignment explanation
Indices: 317005--317123 Score: 90
Period size: 20 Copynumber: 6.3 Consensus size: 20
316995 GATTCTCTCG
** *
317005 TTGCGATAGTCAAATTCACA
1 TTGCGATAGTCATTTTCGCA
*
317025 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
**
317045 TTGCGATTTTCA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
317064 TTGTGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
** *
317078 TTGCGATAGTCAAATTAGCA
1 TTGCGATAGTCATTTTCGCA
317098 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
317118 TTGCGA
1 TTGCGA
317124 CTATCGCAAT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
14 6 0.08
16 6 0.08
17 2 0.03
18 2 0.03
19 12 0.16
20 49 0.64
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:317050 original size:73 final size:73
Alignment explanation
Indices: 316967--317123 Score: 217
Period size: 73 Copynumber: 2.2 Consensus size: 73
316957 AACGAAAGAA
*
316967 TCGCAATGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCA-CATTGCGA
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATT-AGCATTGCGA
317031 TAGTCATTT
65 TAGTCATTT
* ** ** ** *
317040 TCGCGTTGCGATTTTCATTTCGCATTGTGATTCTCTCGTTGCGATAGTCAAATTAGCATTGCGAT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTAGCATTGCGAT
317105 AGTCATTT
66 AGTCATTT
317113 TCGCATTGCGA
1 TCGCATTGCGA
317124 CTATCGCAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
72 1 0.01
73 72 0.99
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (73 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTAGCATTGCGAT
AGTCATTT
Found at i:317713 original size:21 final size:21
Alignment explanation
Indices: 317622--317713 Score: 87
Period size: 21 Copynumber: 4.4 Consensus size: 21
317612 GACTCACCTG
**
317622 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTA
317644 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * *
317664 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
317685 CCACCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGGCCCCTA
317706 TCATCGTT
1 TCATCGTT
317714 GAAAAGGTCC
Statistics
Matches: 54, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.06
21 50 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:319109 original size:13 final size:14
Alignment explanation
Indices: 319078--319113 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
319068 TGATTGTTAA
319078 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
319092 ATGATTTGT-AAAG
1 TTGATTTGTAAAAG
319105 TTGATTTGT
1 TTGATTTGT
319114 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:319122 original size:13 final size:14
Alignment explanation
Indices: 319067--319114 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
319057 CATTATTATT
319067 TTGA-TTGTT-AA-
1 TTGATTTGTTAAAG
*
319078 TTGATTTGTAAAAG
1 TTGATTTGTTAAAG
*
319092 ATGATTTG-TAAAG
1 TTGATTTGTTAAAG
319105 TTGATTTGTT
1 TTGATTTGTT
319115 TAATTGATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.14
12 4 0.14
13 13 0.45
14 8 0.28
ACGTcount: A:0.29, C:0.00, G:0.21, T:0.50
Consensus pattern (14 bp):
TTGATTTGTTAAAG
Found at i:319303 original size:34 final size:33
Alignment explanation
Indices: 319215--319310 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
319205 AAAACAGACT
* ** *
319215 ATCGCAACGCGGAAATGACTATCACAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
319249 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
319282 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
319311 CGAAACTAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:319306 original size:20 final size:19
Alignment explanation
Indices: 319248--319315 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
319238 ACAACGAGAG
319248 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
319267 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
319281 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
319301 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
319316 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.20
16 5 0.12
17 2 0.05
18 3 0.08
19 11 0.28
20 11 0.28
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:319341 original size:19 final size:19
Alignment explanation
Indices: 319319--319425 Score: 143
Period size: 19 Copynumber: 5.8 Consensus size: 19
319309 CGCGAAACTA
* *
319319 ATTTCGCGTTGTGATTTTC
1 ATTTCGCATTGCGATTTTC
319338 ATTTTCGCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
319356 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
319372 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
319391 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
319410 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
319426 CTCTCGTTGC
Statistics
Matches: 78, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 3 0.04
18 4 0.05
19 47 0.60
20 11 0.14
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:319382 original size:33 final size:33
Alignment explanation
Indices: 319325--319447 Score: 147
Period size: 33 Copynumber: 3.5 Consensus size: 33
319315 ACTAATTTCG
*
319325 CGTTGTGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
319359 CGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGTTGCGATTTTCATTTCGCATTGCGA--TTCA-CT
*
319395 CGCATTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CG--TTGCGATTTTCATTTCGCATTGCGATTCACT
**
319430 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
319448 CGTGTTGCGA
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
33 27 0.35
34 13 0.17
35 7 0.09
36 6 0.08
38 25 0.32
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:319456 original size:20 final size:20
Alignment explanation
Indices: 319431--319504 Score: 121
Period size: 20 Copynumber: 3.7 Consensus size: 20
319421 CGATTCTCTC
319431 GTTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTTCCGT
* *
319451 GTTGCGATAGTCAATTCCGC
1 GTTGCGATAGTCATTTCCGT
*
319471 ATTGCGATAGTCATTTCCGT
1 GTTGCGATAGTCATTTCCGT
319491 GTTGCGATAGTCAT
1 GTTGCGATAGTCAT
319505 ATTCACGTTG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTGCGATAGTCATTTCCGT
Found at i:319487 original size:40 final size:41
Alignment explanation
Indices: 319432--319508 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 41
319422 GATTCTCTCG
319432 TTGCGATAGTCATTTCCGTGTTGCGATAGTCA-ATTCCGCA
1 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCCGCA
319472 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC
1 TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC
319509 ACGTTGCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.19, C:0.21, G:0.22, T:0.38
Consensus pattern (41 bp):
TTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTCCGCA
Found at i:319514 original size:20 final size:18
Alignment explanation
Indices: 319430--319518 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 18
319420 GCGATTCTCT
319430 CGTTGCGATAGTCATTTC
1 CGTTGCGATAGTCATTTC
*
319448 CGTGTTGCGATAGTCAATTC
1 C--GTTGCGATAGTCATTTC
319468 CGCATTGCGATAGTCATTTC
1 CG--TTGCGATAGTCATTTC
319488 CGTGTTGCGATAGTCATATTC
1 C--GTTGCGATAGTCAT-TTC
319509 ACGTTGCGAT
1 -CGTTGCGAT
319519 TTCCGCGTTG
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.03
20 54 0.89
21 3 0.05
22 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (18 bp):
CGTTGCGATAGTCATTTC
Found at i:319516 original size:40 final size:38
Alignment explanation
Indices: 319430--319518 Score: 142
Period size: 40 Copynumber: 2.2 Consensus size: 38
319420 GCGATTCTCT
319430 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAATTC
1 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAATTC
319468 CGCATTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC
1 CG--TTGCGATAGTCATTTCCGTGTTGCGATAGTCA-ATTC
319509 ACGTTGCGAT
1 -CGTTGCGAT
319519 TTCCGCGTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
38 2 0.04
40 39 0.83
41 4 0.09
42 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.36
Consensus pattern (38 bp):
CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCAATTC
Found at i:322889 original size:20 final size:20
Alignment explanation
Indices: 322879--322951 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
322869 CGAATTACAC
*
322879 ATTCGCATTGCGATTTACTT
1 ATTCGCATTGCGATTTACGT
322899 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
322919 AATCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
322939 ATTCGCATTGCGA
1 ATTCGCATTGCGA
322952 ATCAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:322910 original size:40 final size:40
Alignment explanation
Indices: 322866--322953 Score: 122
Period size: 40 Copynumber: 2.2 Consensus size: 40
322856 CAGAATCTCG
* *
322866 TTGCGAATTACACATTCGCATTGCGATTTACTTATTCGCA
1 TTGCGAATTACACAATCGCATTGCGATTTACGTATTCGCA
* ** *
322906 TTGCGATTTACGTAATCGCGTTGCGATTTACGTATTCGCA
1 TTGCGAATTACACAATCGCATTGCGATTTACGTATTCGCA
322946 TTGCGAAT
1 TTGCGAAT
322954 CAGGAAAATC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (40 bp):
TTGCGAATTACACAATCGCATTGCGATTTACGTATTCGCA
Found at i:323523 original size:16 final size:16
Alignment explanation
Indices: 323504--323535 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
323494 AATTAAATAG
323504 TTTTTTACACCAATCA
1 TTTTTTACACCAATCA
*
323520 TTTTTTATACCAATCA
1 TTTTTTACACCAATCA
323536 GGTGGTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.22, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTTTTACACCAATCA
Found at i:326913 original size:10 final size:10
Alignment explanation
Indices: 326898--326972 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
326888 CATTTAATAA
326898 ATAAACGAAC
1 ATAAACGAAC
326908 ATAAACG-A-
1 ATAAACGAAC
*
326916 AT--ATGAAC
1 ATAAACGAAC
326924 ATAAACGAAC
1 ATAAACGAAC
** *
326934 ACGAAC-ATAA
1 ATAAACGA-AC
326944 ATAAACACGAAC
1 AT-AA-ACGAAC
326956 ATAAACGAAC
1 ATAAACGAAC
326966 ATAAACG
1 ATAAACG
326973 TTGGATACCC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 2 0.04
7 1 0.02
8 4 0.08
9 2 0.04
10 31 0.63
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.19, G:0.11, T:0.12
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:326925 original size:16 final size:16
Alignment explanation
Indices: 326902--326966 Score: 94
Period size: 16 Copynumber: 4.1 Consensus size: 16
326892 TAATAAATAA
*
326902 ACGAACATAAACGAAT
1 ACGAACATAAACGAAC
*
326918 ATGAACATAAACGAAC
1 ACGAACATAAACGAAC
**
326934 ACGAACATAAATAAAC
1 ACGAACATAAACGAAC
326950 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
326966 A
1 A
326967 TAAACGTTGG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.58, C:0.20, G:0.11, T:0.11
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:328072 original size:14 final size:14
Alignment explanation
Indices: 328055--328087 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
328045 AAACATAAAT
*
328055 GAACGAATATAACC
1 GAACGAACATAACC
328069 GAACGAACATAACC
1 GAACGAACATAACC
328083 GAACG
1 GAACG
328088 TTCACGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (14 bp):
GAACGAACATAACC
Found at i:331220 original size:2 final size:2
Alignment explanation
Indices: 331213--331256 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
331203 AAATTACTAC
331213 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
331255 AT
1 AT
331257 GGATAAGTCA
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:335833 original size:16 final size:17
Alignment explanation
Indices: 335805--335839 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
335795 CGTATCACTG
335805 ACCAAATTTCACTATTC
1 ACCAAATTTCACTATTC
335822 ACCAAA-TTCACTATTC
1 ACCAAATTTCACTATTC
335838 AC
1 AC
335840 GTGAATAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.37, C:0.31, G:0.00, T:0.31
Consensus pattern (17 bp):
ACCAAATTTCACTATTC
Found at i:345707 original size:37 final size:37
Alignment explanation
Indices: 345631--345707 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
345621 TTTTTATATT
*
345631 TTTAATTTTGTAAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
* ** *
345668 TTTAATTTTTTAAAGGAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAAAAAAATTATATAAATATTAT-CAA
345705 TTT
1 TTT
345708 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 13 0.38
37 21 0.62
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAAAAAAATTATATAAATATTATCAA
Found at i:345889 original size:20 final size:20
Alignment explanation
Indices: 345853--345890 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
345843 ATCCTATTAC
**
345853 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
345873 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
345891 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:348794 original size:21 final size:21
Alignment explanation
Indices: 348768--348824 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
348758 CCGAGTTACT
*
348768 CGCGACGGCCGCAATAGCGTC
1 CGCGACGGCCGCAATAGCGCC
* *
348789 CGCGACGACCGTAATAGCGCC
1 CGCGACGGCCGCAATAGCGCC
348810 CGCGACGGCCGCAAT
1 CGCGACGGCCGCAAT
348825 CACGGTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.21, C:0.39, G:0.32, T:0.09
Consensus pattern (21 bp):
CGCGACGGCCGCAATAGCGCC
Found at i:349482 original size:19 final size:18
Alignment explanation
Indices: 349457--349503 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
349447 CTACTTGAAT
*
349457 TTTAAAAAATCAGAAAAA
1 TTTAAAAAAACAGAAAAA
349475 TTTAAAAAAACAGAAAAA
1 TTTAAAAAAACAGAAAAA
*
349493 ATTACAAAAAA
1 TTTA-AAAAAA
349504 AAATTAGTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.19
Consensus pattern (18 bp):
TTTAAAAAAACAGAAAAA
Found at i:349517 original size:115 final size:115
Alignment explanation
Indices: 349386--349599 Score: 376
Period size: 115 Copynumber: 1.9 Consensus size: 115
349376 TTTATGTTTT
*
349386 AAAAAATTAATATGTTTATTTATCTAATTTCAATGTATTTTTATATATCTTGTAATTTAATCTAC
1 AAAAAATTAATATGTTTATTTATCTAATTTCAATGTATTTTTATATATCTTGCAATTTAATCTAC
*
349451 TTGAATTTTAAAAAATCAGAAAAATT-TAAAAAAACAGAAAAAATTACAAA
66 TTGAA-TTTAAAAAATCAGAAAAATTACAAAAAAACAGAAAAAATTACAAA
* *
349501 AAAAAATTAGTATGTTTATTTATCTAATTTCAATGTATTTTTATCTATCTTGCAATTTAATCTAC
1 AAAAAATTAATATGTTTATTTATCTAATTTCAATGTATTTTTATATATCTTGCAATTTAATCTAC
349566 TTGAATTTAAAAAATCAGAAAAATTACAAAAAAA
66 TTGAATTTAAAAAATCAGAAAAATTACAAAAAAA
349600 ATAATATGTT
Statistics
Matches: 94, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
114 20 0.21
115 74 0.79
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (115 bp):
AAAAAATTAATATGTTTATTTATCTAATTTCAATGTATTTTTATATATCTTGCAATTTAATCTAC
TTGAATTTAAAAAATCAGAAAAATTACAAAAAAACAGAAAAAATTACAAA
Found at i:349573 original size:96 final size:97
Alignment explanation
Indices: 349473--349696 Score: 341
Period size: 96 Copynumber: 2.3 Consensus size: 97
349463 AAATCAGAAA
*
349473 AATTTAAAAAAACAGAAAAAATTACAAAAAAAAATTAGTATGTTTATTTATCTAATTTCAATGTA
1 AATTTAAAAAAACAGAAAAAATTACAAAAAAAAA-TAATATGTTTATTTATCTAATTTCAATGTA
*
349538 -TT-TTTATCTATCTTGCAATTTAATCTACTTG
65 TTTATTTATATATCTTGCAATTTAATCTACTTG
*
349569 AATTTAAAAAATCAG-AAAAATTAC-AAAAAAAATAATATGTTTATTTATCTAATTTCAATGTAT
1 AATTTAAAAAAACAGAAAAAATTACAAAAAAAAATAATATGTTTATTTATCTAATTTCAATGTA-
349632 TTTATTTATATATCTTGCAATTTAATCTACTTG
65 TTTATTTATATATCTTGCAATTTAATCTACTTG
*
349665 AATTTAAAAAAAATCA-AAACAATTACAAAAAA
1 AATTT-AAAAAAA-CAGAAAAAATTACAAAAAA
349697 GAAAAAGAAA
Statistics
Matches: 116, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
93 29 0.25
94 8 0.07
95 11 0.09
96 47 0.41
97 6 0.05
98 10 0.09
99 5 0.04
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.38
Consensus pattern (97 bp):
AATTTAAAAAAACAGAAAAAATTACAAAAAAAAATAATATGTTTATTTATCTAATTTCAATGTAT
TTATTTATATATCTTGCAATTTAATCTACTTG
Found at i:349574 original size:15 final size:17
Alignment explanation
Indices: 349543--349575 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
349533 ATGTATTTTT
349543 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
349560 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
349575 A
1 A
349576 AAAATCAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:352367 original size:41 final size:41
Alignment explanation
Indices: 352307--352388 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
352297 TGTTCGGGCC
* *
352307 TGATCCTTTGTATATATCACTAAAAAAGTAAAATAATAATA
1 TGATCCTTTGCATAAATCACTAAAAAAGTAAAATAATAATA
352348 TGATCCTTTGCATAAATCACTAAAAAAGTAAAATAATAATA
1 TGATCCTTTGCATAAATCACTAAAAAAGTAAAATAATAATA
352389 ATTTAATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.32
Consensus pattern (41 bp):
TGATCCTTTGCATAAATCACTAAAAAAGTAAAATAATAATA
Found at i:356675 original size:24 final size:24
Alignment explanation
Indices: 356648--356733 Score: 73
Period size: 24 Copynumber: 3.6 Consensus size: 24
356638 TCCGATTTGA
*
356648 ATTCTGTTATGATACCTGACATGG
1 ATTCTGTTCTGATACCTGACATGG
* * * *
356672 ATTCTATTCTTATACATGACCTGG
1 ATTCTGTTCTGATACCTGACATGG
* * * *
356696 ATTTTGTTCTGATATCTGACTTGA
1 ATTCTGTTCTGATACCTGACATGG
* *
356720 ATTATGTTTTGATA
1 ATTCTGTTCTGATA
356734 TATCCATTTA
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (24 bp):
ATTCTGTTCTGATACCTGACATGG
Found at i:367131 original size:2 final size:2
Alignment explanation
Indices: 367124--367159 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
367114 AACAAAAACA
367124 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
367160 TTTGACTAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:368845 original size:24 final size:25
Alignment explanation
Indices: 368813--368860 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
368803 ACAAAATTAT
368813 TCAAAAAAAATAAATT-TTAAAATA
1 TCAAAAAAAATAAATTATTAAAATA
*
368837 TCAAAAAAATTAAATTATTAAAAT
1 TCAAAAAAAATAAATTATTAAAAT
368861 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
TCAAAAAAAATAAATTATTAAAATA
Found at i:368866 original size:24 final size:23
Alignment explanation
Indices: 368815--368866 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 23
368805 AAAATTATTC
368815 AAAAAAAATAAATTTTAAAATAT
1 AAAAAAAATAAATTTTAAAATAT
*
368838 CAAAAAAATTAAATTATTAAAAT-T
1 -AAAAAAAATAAATT-TTAAAATAT
368862 AAAAA
1 AAAAA
368867 TATATTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 5 0.19
24 14 0.54
25 7 0.27
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAAAAAATAAATTTTAAAATAT
Found at i:369478 original size:22 final size:22
Alignment explanation
Indices: 369423--369492 Score: 63
Period size: 21 Copynumber: 3.2 Consensus size: 22
369413 GTTAAAAATA
* *
369423 TATATATATTTTTTAGTAATTT
1 TATATTTATTTTTTAATAATTT
* *
369445 AAT-TCTTA-TTTTTAATATTTT
1 TATAT-TTATTTTTTAATAATTT
*
369466 TATATTTATTTTTTCTATAATTT
1 TATATTTATTTTTT-AATAATTT
369489 TATA
1 TATA
369493 ATTAAAATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
21 17 0.46
22 10 0.27
23 10 0.27
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (22 bp):
TATATTTATTTTTTAATAATTT
Found at i:370504 original size:18 final size:18
Alignment explanation
Indices: 370481--370547 Score: 82
Period size: 18 Copynumber: 3.8 Consensus size: 18
370471 TTCAATTTGA
*
370481 TTAAATTGTTAATTAACT
1 TTAAATTATTAATTAACT
**
370499 TTAAATTATTAATT-TTT
1 TTAAATTATTAATTAACT
*
370516 TTAAATTATTAAATAACT
1 TTAAATTATTAATTAACT
*
370534 TTGAATTATTAATT
1 TTAAATTATTAATT
370548 TATTTAAGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
17 14 0.35
18 26 0.65
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (18 bp):
TTAAATTATTAATTAACT
Found at i:370520 original size:17 final size:17
Alignment explanation
Indices: 370481--370559 Score: 77
Period size: 18 Copynumber: 4.5 Consensus size: 17
370471 TTCAATTTGA
* *
370481 TTAAATTGTTAATTAACT
1 TTAAATTATTAATTTA-T
*
370499 TTAAATTATTAATTTTT
1 TTAAATTATTAATTTAT
* *
370516 TTAAATTATTAAATAACT
1 TTAAATTATTAATTTA-T
*
370534 TTGAATTATTAATTTAT
1 TTAAATTATTAATTTAT
*
370551 TTAAGTTAT
1 TTAAATTAT
370560 ACTTGAACAA
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
17 22 0.45
18 27 0.55
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTATTAATTTAT
Found at i:370520 original size:35 final size:35
Alignment explanation
Indices: 370481--370559 Score: 113
Period size: 35 Copynumber: 2.3 Consensus size: 35
370471 TTCAATTTGA
* * *
370481 TTAAATTGTTAATTAACTTTAAATTATTAATTTTT
1 TTAAATTATTAAATAACTTTAAATTATTAATTTAT
*
370516 TTAAATTATTAAATAACTTTGAATTATTAATTTAT
1 TTAAATTATTAAATAACTTTAAATTATTAATTTAT
*
370551 TTAAGTTAT
1 TTAAATTAT
370560 ACTTGAACAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (35 bp):
TTAAATTATTAAATAACTTTAAATTATTAATTTAT
Found at i:373006 original size:21 final size:21
Alignment explanation
Indices: 372980--373037 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
372970 AGGGTGTCAA
*
372980 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCACTGC
* *
373001 AGTGCATCCATGTACCACTGT
1 AGTGCATCCATGCACCACTGC
373022 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
373038 TGCCACTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCACTGC
Found at i:374401 original size:19 final size:20
Alignment explanation
Indices: 374377--374424 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
374367 AACGATTTTC
* *
374377 TTTTGAAAGCAAAAATG-GA
1 TTTTGAAAACAAAAATGAAA
*
374396 TTTTGAAAACCAAAATGAAA
1 TTTTGAAAACAAAAATGAAA
374416 TTTTGAAAA
1 TTTTGAAAA
374425 AGGATTTAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (20 bp):
TTTTGAAAACAAAAATGAAA
Found at i:375814 original size:21 final size:21
Alignment explanation
Indices: 375788--375887 Score: 182
Period size: 21 Copynumber: 4.8 Consensus size: 21
375778 ACGGTGTCAA
* *
375788 AGTGCATCCATGCACTCATGC
1 AGTGCATCCATGCACCCCTGC
375809 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
375830 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
375851 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
375872 AGTGCATCCATGCACC
1 AGTGCATCCATGCACC
375888 TGCCACTAGT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 77 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.20
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:377679 original size:34 final size:33
Alignment explanation
Indices: 377641--377707 Score: 91
Period size: 34 Copynumber: 2.0 Consensus size: 33
377631 GGTAATAAAA
377641 AAATTAAGCAAAATAAATTAACAA-AAAGTCCAAC
1 AAATTAAGCAAAATAAATTAA-AATAAA-TCCAAC
* *
377675 AAATTTATCAAAATAAATTAAAATAAATCCAAC
1 AAATTAAGCAAAATAAATTAAAATAAATCCAAC
377708 CATATTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 8 0.27
34 22 0.73
ACGTcount: A:0.61, C:0.13, G:0.03, T:0.22
Consensus pattern (33 bp):
AAATTAAGCAAAATAAATTAAAATAAATCCAAC
Found at i:377773 original size:13 final size:13
Alignment explanation
Indices: 377747--377790 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
377737 TGATAAATAA
377747 AAAAAAGTTACAAT
1 AAAAAAG-TACAAT
*
377761 AAAAAAGTCCAAT
1 AAAAAAGTACAAT
* *
377774 AAACAACTACAAT
1 AAAAAAGTACAAT
377787 AAAA
1 AAAA
377791 GTACTAAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
13 18 0.72
14 7 0.28
ACGTcount: A:0.66, C:0.14, G:0.05, T:0.16
Consensus pattern (13 bp):
AAAAAAGTACAAT
Found at i:378249 original size:33 final size:33
Alignment explanation
Indices: 378211--378277 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
378201 CCTCCAGGAT
*
378211 GGGTCATAAAACTC-TGTGAAGGCGGCGGCGGCG
1 GGGTCATAAAAC-CAGGTGAAGGCGGCGGCGGCG
378244 GGGTCATAAAACCAGGTGAAGGCGGCGGCGGCG
1 GGGTCATAAAACCAGGTGAAGGCGGCGGCGGCG
378277 G
1 G
378278 CGACATCTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.22, C:0.21, G:0.45, T:0.12
Consensus pattern (33 bp):
GGGTCATAAAACCAGGTGAAGGCGGCGGCGGCG
Found at i:380031 original size:12 final size:12
Alignment explanation
Indices: 380014--380041 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
380004 AACTGCAAAA
380014 AAATAATTAAAT
1 AAATAATTAAAT
380026 AAATAATTAAAT
1 AAATAATTAAAT
380038 AAAT
1 AAAT
380042 TAAATACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATAATTAAAT
Found at i:385886 original size:3 final size:3
Alignment explanation
Indices: 385878--385929 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
385868 TTTAAATGCT
385878 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
385924 TTA TTA
1 TTA TTA
385930 AGTTTAGGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 43 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:386074 original size:53 final size:53
Alignment explanation
Indices: 385987--386148 Score: 243
Period size: 53 Copynumber: 3.1 Consensus size: 53
385977 TTTAACAATG
* * * *
385987 AACGCTCAATCACTCTTACTGCAGTCGTTGGTGTTCAAATTTGCAACCGAAAT
1 AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
* *
386040 ACCGCCCAATCACTCCTACTGCAGTCGTTAGTGTTCGAATTTGTAACCGAAAT
1 AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
* * *
386093 AACGCCCAATCACTCCTACTACAATCATTGGTGTTCGAATTTGTAACCGAAAT
1 AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
386146 AAC
1 AAC
386149 ACCATTCTTT
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
53 98 1.00
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (53 bp):
AACGCCCAATCACTCCTACTGCAGTCGTTGGTGTTCGAATTTGTAACCGAAAT
Found at i:386938 original size:2 final size:2
Alignment explanation
Indices: 386925--386959 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
386915 TGGAAAATTT
*
386925 TA TA TC TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
386960 CCCACAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:399529 original size:2 final size:2
Alignment explanation
Indices: 399522--399550 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
399512 AACCATTCAA
399522 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 A
399551 ATTGCATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:400115 original size:230 final size:233
Alignment explanation
Indices: 399712--400175 Score: 907
Period size: 230 Copynumber: 2.0 Consensus size: 233
399702 ATTTAACGTC
399712 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
1 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
399777 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
66 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
399842 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAG-AAATT-AAAAATAAAGAT
131 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
399905 -AAATACAATGCATGTATAAATAAATAAATAAATACAT
196 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
399942 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
1 ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
400007 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
66 ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
400072 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
131 AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
400137 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
196 AAAATACAATGCATGTATAAATAAATAAATAAATACAT
400175 A
1 A
400176 ATTGAACAGT
Statistics
Matches: 231, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
230 176 0.76
231 5 0.02
232 12 0.05
233 38 0.16
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.23
Consensus pattern (233 bp):
ATAAAATGAGGCATACTAATTTAAAGAATAAAATGTAATTAATAATGGAAAATAAGGAAGTAACA
ACAACAATAAAACCCTATTCCTATATGCAATGGGGTAAGGGGAGATAGGGTAGTAGGATGCCCCC
AATGCTAGGTTGATAGTAGCTTCCGTGAAAGACCTCCGGAAGTCAGAAAATTAAAAAATAAAGAT
AAAATACAATGCATGTATAAATAAATAAATAAATACAT
Found at i:410933 original size:84 final size:85
Alignment explanation
Indices: 410845--411022 Score: 308
Period size: 87 Copynumber: 2.1 Consensus size: 85
410835 ATCTAACTCT
410845 AAGATATTATCAGTTTGTTCGTTCAGAAAACATATTATTTTATTA-A-AAAAATATATCCACTTT
1 AAGATATTATCAGTTTGTTCGTTCAG-AAACATATTATTTTATTATATAAAAATATATCCACTTT
410908 AATTTAGTCACTGACGTTGCA
65 AATTTAGTCACTGACGTTGCA
410929 AAGATATTATCAGTTTGTTCGTTCAGAAACATATTATTTTATTATTATTAAAAATATATCCACTT
1 AAGATATTATCAGTTTGTTCGTTCAGAAACATATTATTTTATTA-TA-TAAAAATATATCCACTT
410994 TAATTTAGTCACTGACGTTGCA
64 TAATTTAGTCACTGACGTTGCA
411016 AA-ATATT
1 AAGATATT
411023 GTTCATTTTA
Statistics
Matches: 90, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
83 18 0.20
84 26 0.29
85 1 0.01
86 5 0.06
87 40 0.44
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (85 bp):
AAGATATTATCAGTTTGTTCGTTCAGAAACATATTATTTTATTATATAAAAATATATCCACTTTA
ATTTAGTCACTGACGTTGCA
Found at i:411701 original size:16 final size:19
Alignment explanation
Indices: 411671--411734 Score: 64
Period size: 18 Copynumber: 3.5 Consensus size: 19
411661 ACGGTTAAAT
*
411671 TAATATATTATATAATT-TA
1 TAATATTTTA-ATAATTATA
411690 T-AT-TTTTAATAATTAATA
1 TAATATTTTAATAATT-ATA
411708 TAATATTTTAATAA-TATA
1 TAATATTTTAATAATTATA
*
411726 AAATATTTT
1 TAATATTTT
411735 TTTAAATATT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 6 0.15
17 4 0.10
18 16 0.41
19 4 0.10
20 9 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TAATATTTTAATAATTATA
Found at i:411713 original size:21 final size:19
Alignment explanation
Indices: 411689--411735 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
411679 TATATAATTT
*
411689 ATATTTTTAATAAT-TAAT
1 ATATTTTTAATAATATAAA
411707 ATAATATTTTAATAATATAAA
1 AT-AT-TTTTAATAATATAAA
411728 ATATTTTT
1 ATATTTTT
411736 TTAAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 12 0.48
21 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATATTTTTAATAATATAAA
Found at i:411739 original size:21 final size:20
Alignment explanation
Indices: 411692--411739 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
411682 ATAATTTATA
*
411692 TTTTTAATAATTAATATAAT
1 TTTTTAATAATTAAAATAAT
* *
411712 ATTTTAATAATATAAAATATT
1 TTTTTAATAAT-TAAAATAAT
411733 TTTTTAA
1 TTTTTAA
411740 ATATTAATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTTAATAATTAAAATAAT
Done.