Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008278.1 Hibiscus syriacus cultivar Beakdansim tig00110937_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: 776496
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:263233 original size:30 final size:29
Alignment explanation
Indices: 263194--263268 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 29
263184 TAAAATTATC
*
263194 TTTTGTTTTTGTTTTAACTTATTAAATATA
1 TTTTATTTTT-TTTTAACTTATTAAATATA
263224 TTTTATTTTTTTCTTAACTTATTAAATATA
1 TTTTATTTTTTT-TTAACTTATTAAATATA
263254 -TTTATTTTTATTTTA
1 TTTTATTTTT-TTTTA
263269 GTGTAAAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
29 14 0.33
30 28 0.67
ACGTcount: A:0.27, C:0.04, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTATTTTTTTTTAACTTATTAAATATA
Found at i:263518 original size:29 final size:29
Alignment explanation
Indices: 263486--263576 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
263476 ATATTTTAAT
* * **
263486 ATATTTTTTAAATTTTAGATAATGATAAA
1 ATATTTTTTAAATTTAAAATAAAAATAAA
*
263515 ATATATTTTAAATTTAAAATAAAAATAAA
1 ATATTTTTTAAATTTAAAATAAAAATAAA
* * * *
263544 ATA-TTTTT-AAGTGAAGATAAGAATAAA
1 ATATTTTTTAAATTTAAAATAAAAATAAA
263571 ATATTT
1 ATATTT
263577 AAATATATTT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
27 18 0.35
28 6 0.12
29 27 0.53
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.42
Consensus pattern (29 bp):
ATATTTTTTAAATTTAAAATAAAAATAAA
Found at i:263563 original size:27 final size:28
Alignment explanation
Indices: 263510--263576 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
263500 TTAGATAATG
* *
263510 ATAAAATATATTTTAAATTTAAAATAAAA
1 ATAAAATAT-TTTTAAAGTGAAAATAAAA
* *
263539 ATAAAATATTTTT-AAGTGAAGATAAGA
1 ATAAAATATTTTTAAAGTGAAAATAAAA
263566 ATAAAATATTT
1 ATAAAATATTT
263577 AAATATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 21 0.62
28 4 0.12
29 9 0.26
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (28 bp):
ATAAAATATTTTTAAAGTGAAAATAAAA
Found at i:263601 original size:15 final size:16
Alignment explanation
Indices: 263575--263604 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
263565 AATAAAATAT
263575 TTAAATATATTTTAAG
1 TTAAATATATTTTAAG
263591 TTAAA-ATATTTTAA
1 TTAAATATATTTTAA
263605 AAAATTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATATATTTTAAG
Found at i:263633 original size:188 final size:188
Alignment explanation
Indices: 263417--263990 Score: 738
Period size: 188 Copynumber: 3.0 Consensus size: 188
263407 TTCTTTTTTT
* * *
263417 AAAATATCTTAACTTAAATTATATTTTATTTTTAAATTGAAATACATTTTGAAGTTAGGATATTT
1 AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAGTTAGGATATTT
*
263482 TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTAAATTTAAAATAAAAATAAAATA
66 TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTTAATTTAAAATAAAAATAAAATA
263547 TTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAA
131 TTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAA
*
263605 AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATGCATTTTGAAGTTAGGATATTT
1 AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAGTTAGGATATTT
* * *
263670 TAATATATTTTTAAAAATTTAGATAATGATAAAATATATTTTTAATTTGAAATAAAAATAAAATA
66 TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTTAATTTAAAATAAAAAT-AAA-A
263735 TATTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAAAAA
129 TATTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTT---AA
* ** ** *
263798 ACATAATTTTCAGTGATGATAAATATAAAAAAAAACTTATTTTTAAATTAAAAAACATTTTGAAG
1 A-A-AA-TTTC-----T--TAACT-TAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAG
* *
263863 TTAAGATATTTTAATATA-TTTTTAAATATTTATATAATGATAAAAATATATTTTTAATTTAAAA
55 TTAGGATATTTTAATATATTTTTTAAAT-TTTAGATAATGAT-AAAATATATTTTTAATTTAAAA
* * *
263927 TAAAAAT-AAA-A----TAAGTGAAGATAA-TA-AAAATA-TT-AATATATTTTACGTTAAAACA
118 TAAAAATAAAATATTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATA
263982 TTTTAA
183 TTTTAA
263988 AAA
1 AAA
263991 TATATTTTTA
Statistics
Matches: 345, Mismatches: 23, Indels: 36
0.85 0.06 0.09
Matches are distributed among these distances:
188 117 0.34
189 4 0.01
190 62 0.18
193 26 0.08
194 3 0.01
195 8 0.02
196 5 0.01
197 13 0.04
201 2 0.01
202 1 0.00
203 13 0.04
204 63 0.18
205 28 0.08
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (188 bp):
AAAATTTCTTAACTTAAATTAAATTTTATTTTTAAATTAAAATACATTTTGAAGTTAGGATATTT
TAATATATTTTTTAAATTTTAGATAATGATAAAATATATTTTTAATTTAAAATAAAAATAAAATA
TTTTTAAGTGAAGATAAGAATAAAATATTTAAATATATTTTAAGTTAAAATATTTTAA
Found at i:263709 original size:31 final size:31
Alignment explanation
Indices: 263671--263743 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
263661 AGGATATTTT
* **
263671 AATATATTTTTAAAAATTT-AGATAATGATAA
1 AATATATTTTT-AAAATTTGAAATAAAAATAA
263702 AATATATTTTT--AATTTGAAATAAAAATAA
1 AATATATTTTTAAAATTTGAAATAAAAATAA
263731 AATATATTTTTAA
1 AATATATTTTTAA
263744 GTGAAGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 5 0.14
29 20 0.56
31 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (31 bp):
AATATATTTTTAAAATTTGAAATAAAAATAA
Found at i:263730 original size:29 final size:29
Alignment explanation
Indices: 263698--263764 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
263688 TTAGATAATG
*
263698 ATAAAATATATTTTTAATTTGAA-ATAAAA
1 ATAAAATATATTTTTAA-GTGAAGATAAAA
*
263727 ATAAAATATATTTTTAAGTGAAGATAAGA
1 ATAAAATATATTTTTAAGTGAAGATAAAA
263756 ATAAAATAT
1 ATAAAATAT
263765 TTAAATATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 4 0.11
29 31 0.89
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.37
Consensus pattern (29 bp):
ATAAAATATATTTTTAAGTGAAGATAAAA
Found at i:263791 original size:15 final size:16
Alignment explanation
Indices: 263765--263794 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
263755 AATAAAATAT
263765 TTAAATATATTTTAAG
1 TTAAATATATTTTAAG
263781 TTAAA-ATATTTTAA
1 TTAAATATATTTTAA
263795 AAAACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TTAAATATATTTTAAG
Found at i:264076 original size:26 final size:27
Alignment explanation
Indices: 264040--264091 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
264030 ACATTAAAAT
264040 AAAAAT-AA-ATATTTAATAAGTTAAG
1 AAAAATAAATATATTTAATAAGTTAAG
*
264065 AAAAATTAAATATATTTAATAATTTAA
1 AAAAA-TAAATATATTTAATAAGTTAA
264092 AACAAAAAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 1 0.04
27 2 0.09
28 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (27 bp):
AAAAATAAATATATTTAATAAGTTAAG
Found at i:264192 original size:2 final size:2
Alignment explanation
Indices: 264185--264216 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
264175 CCATAAATAA
*
264185 AT AT AT AT AT AA 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
264217 TAATTATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:264198 original size:12 final size:12
Alignment explanation
Indices: 264181--264216 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
264171 GGTACCATAA
264181 ATAAATATATAT
1 ATAAATATATAT
264193 ATAAATATATAT
1 ATAAATATATAT
*
264205 ATATATATATAT
1 ATAAATATATAT
264217 TAATTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATAAATATATAT
Found at i:264198 original size:16 final size:16
Alignment explanation
Indices: 264177--264211 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
264167 TTAAGGTACC
264177 ATAAATAAATATATAT
1 ATAAATAAATATATAT
*
264193 ATAAATATATATATAT
1 ATAAATAAATATATAT
264209 ATA
1 ATA
264212 TATATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAATAAATATATAT
Found at i:264394 original size:19 final size:19
Alignment explanation
Indices: 264370--264421 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
264360 TGTTTGGTGG
264370 AAAATAAATTTATTAAATT
1 AAAATAAATTTATTAAATT
264389 AAAATAAATTTATTAAATT
1 AAAATAAATTTATTAAATT
264408 AAAATAAATTTATT
1 AAAATAAATTTATT
264422 CATCCAATCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATAAATTTATTAAATT
Found at i:265942 original size:25 final size:24
Alignment explanation
Indices: 265890--265942 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
265880 TATTATCATT
*
265890 ATTTCTAAAATGTTATAAAATTAT
1 ATTTCTAAAATGTTATAAAATTAC
*
265914 ATTTCTTAAAATTTTAT-AAATTCAC
1 ATTTC-TAAAATGTTATAAAATT-AC
265939 ATTT
1 ATTT
265943 TAATATAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 10 0.40
25 15 0.60
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (24 bp):
ATTTCTAAAATGTTATAAAATTAC
Found at i:268828 original size:18 final size:19
Alignment explanation
Indices: 268790--268828 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
268780 AGAGAGAGAT
*
268790 AAAAGAACAAAGAAGATGA
1 AAAAGAACAAAGAAGAGGA
*
268809 AAAAGAA-AAAGAGGAGGA
1 AAAAGAACAAAGAAGAGGA
268827 AA
1 AA
268829 CGAAGGAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.69, C:0.03, G:0.26, T:0.03
Consensus pattern (19 bp):
AAAAGAACAAAGAAGAGGA
Found at i:273814 original size:15 final size:16
Alignment explanation
Indices: 273789--273818 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
273779 TCGAACGATA
273789 AAAATAAAAAATTAAC
1 AAAATAAAAAATTAAC
273805 AAAA-AAAAAATTAA
1 AAAATAAAAAATTAA
273819 TTAATTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAATAAAAAATTAAC
Found at i:291206 original size:3 final size:3
Alignment explanation
Indices: 291198--291223 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
291188 CAAGGGTTTT
291198 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
291224 TGTTCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:292369 original size:3 final size:3
Alignment explanation
Indices: 292361--292386 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
292351 CAAGGGTTTT
292361 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
292387 TGTTCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:301858 original size:2 final size:2
Alignment explanation
Indices: 301851--301882 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
301841 GTCAGTGCAA
301851 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
301883 TCATTGCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314564 original size:15 final size:15
Alignment explanation
Indices: 314544--314574 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
314534 GGTTACCTAC
314544 GTTCTTCGGGACATG
1 GTTCTTCGGGACATG
314559 GTTCTTCGGGACATG
1 GTTCTTCGGGACATG
314574 G
1 G
314575 ACTGTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.19, G:0.35, T:0.32
Consensus pattern (15 bp):
GTTCTTCGGGACATG
Found at i:314623 original size:31 final size:31
Alignment explanation
Indices: 314559--314716 Score: 214
Period size: 31 Copynumber: 5.2 Consensus size: 31
314549 TCGGGACATG
* *
314559 GTTCTTCGGGAC--ATGGACTGTTTACTTAT
1 GTTCTTCGGGACATATGGACTGATTACCTAT
* * * *
314588 GTTCTTCGGGATATATTGCCTGCTTACCTAT
1 GTTCTTCGGGACATATGGACTGATTACCTAT
314619 GTTCTTCGGGACATATGGACT-ATTTACCTAT
1 GTTCTTCGGGACATATGGACTGA-TTACCTAT
314650 GTTCTTCGGGACATATGGACTGATTACCTAT
1 GTTCTTCGGGACATATGGACTGATTACCTAT
* *
314681 ATTCTTCGGGACATATGGACTGATTACCTAG
1 GTTCTTCGGGACATATGGACTGATTACCTAT
314712 GTTCT
1 GTTCT
314717 GATGGATCTA
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
29 11 0.10
31 101 0.89
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.39
Consensus pattern (31 bp):
GTTCTTCGGGACATATGGACTGATTACCTAT
Found at i:315274 original size:21 final size:21
Alignment explanation
Indices: 315248--315346 Score: 180
Period size: 21 Copynumber: 4.7 Consensus size: 21
315238 GGCCGAAATT
*
315248 ACTGTAGCAGGGTATTTGTAC
1 ACTGTAGCAGGGTATTGGTAC
*
315269 ACTGTAGCAGGGTATTGATAC
1 ACTGTAGCAGGGTATTGGTAC
315290 ACTGTAGCAGGGTATTGGTAC
1 ACTGTAGCAGGGTATTGGTAC
315311 ACTGTAGCAGGGTATTGGTAC
1 ACTGTAGCAGGGTATTGGTAC
315332 ACTGTAGCAGGGTAT
1 ACTGTAGCAGGGTAT
315347 CGATACTCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.29
Consensus pattern (21 bp):
ACTGTAGCAGGGTATTGGTAC
Found at i:315421 original size:20 final size:20
Alignment explanation
Indices: 315398--315436 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
315388 CTGTTCACAC
*
315398 AGTATCGATACTTTTTGCAG
1 AGTATCGATACTATTTGCAG
*
315418 AGTATCGGTACTATTTGCA
1 AGTATCGATACTATTTGCA
315437 CATTGTCGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (20 bp):
AGTATCGATACTATTTGCAG
Found at i:315876 original size:20 final size:20
Alignment explanation
Indices: 315835--315877 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
315825 AAGATTTTTT
*
315835 TATATATTCTTTACTAATAA
1 TATATATTCTATACTAATAA
*
315855 TATATATTCATATATTAA-AA
1 TATATATTC-TATACTAATAA
315875 TAT
1 TAT
315878 CATAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (20 bp):
TATATATTCTATACTAATAA
Found at i:322639 original size:39 final size:38
Alignment explanation
Indices: 322561--322703 Score: 154
Period size: 39 Copynumber: 3.8 Consensus size: 38
322551 AGTCCAATTG
*
322561 TATTTTAATAATATAATTAAAAATT-A--TT--ATTAA
1 TATTTTAATAATCTAATTAAAAATTAATTTTAAATTAA
322594 TA-TTTAATAATCTAATTAAAAATTAATTTTACAATTAA
1 TATTTTAATAATCTAATTAAAAATTAATTTTA-AATTAA
* * * *
322632 TATTTTAACAATCTAAATAAAAATTATTTTTATAATTTA
1 TATTTTAATAATCTAATTAAAAATTAATTTTA-AATTAA
* *
322671 TATTTTAATAATCTAACTAAAATTTAAATTTTA
1 TATTTTAATAATCTAATTAAAAATT-AATTTTA
322704 TGAAATTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
32 21 0.23
33 3 0.03
35 2 0.02
38 7 0.08
39 53 0.58
40 6 0.07
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (38 bp):
TATTTTAATAATCTAATTAAAAATTAATTTTAAATTAA
Found at i:326479 original size:17 final size:17
Alignment explanation
Indices: 326452--326490 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
326442 AATTTACAAT
326452 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
*
326468 TAATTATAAATAATATT
1 TAATTATAAATAATATC
326485 TAATTA
1 TAATTA
326491 ATTTGATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:326826 original size:19 final size:19
Alignment explanation
Indices: 326798--326853 Score: 105
Period size: 19 Copynumber: 3.0 Consensus size: 19
326788 GTTTTGCACA
326798 ATAT-ATGATACTTTAATT
1 ATATAATGATACTTTAATT
326816 ATATAATGATACTTTAATT
1 ATATAATGATACTTTAATT
326835 ATATAATGATACTTTAATT
1 ATATAATGATACTTTAATT
326854 GATTTGCATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.11
19 33 0.89
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (19 bp):
ATATAATGATACTTTAATT
Found at i:327646 original size:9 final size:9
Alignment explanation
Indices: 327598--327648 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
327588 TATAAATTTA
327598 TAATT-AAT
1 TAATTAAAT
*
327606 TAATCAAAT
1 TAATTAAAT
*
327615 TAATTAAAA
1 TAATTAAAT
*
327624 TAATTTATATT
1 TAA-TTA-AAT
327635 TAATTAAAT
1 TAATTAAAT
327644 TAATT
1 TAATT
327649 CGACTCATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
8 4 0.12
9 20 0.59
10 6 0.18
11 4 0.12
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (9 bp):
TAATTAAAT
Found at i:337376 original size:14 final size:14
Alignment explanation
Indices: 337357--337389 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
337347 ACTATTGAAG
337357 ACACCCCAATTGCA
1 ACACCCCAATTGCA
337371 ACACCCCAATTGCA
1 ACACCCCAATTGCA
337385 ACACC
1 ACACC
337390 GAGAACAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.45, G:0.06, T:0.12
Consensus pattern (14 bp):
ACACCCCAATTGCA
Found at i:337743 original size:12 final size:12
Alignment explanation
Indices: 337726--337758 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
337716 TGGGGTCTAG
337726 AGCAGAGGGGGA
1 AGCAGAGGGGGA
337738 AGCAGAGGGGGA
1 AGCAGAGGGGGA
*
337750 AGAAGAGGG
1 AGCAGAGGG
337759 AGTTTTTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.58, T:0.00
Consensus pattern (12 bp):
AGCAGAGGGGGA
Found at i:339202 original size:36 final size:36
Alignment explanation
Indices: 339160--339235 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
339150 TATAGCTAAA
*
339160 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
339196 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
339232 AAAA
1 AAAA
339236 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:368340 original size:33 final size:33
Alignment explanation
Indices: 368298--368368 Score: 142
Period size: 33 Copynumber: 2.2 Consensus size: 33
368288 CCTTAACTGT
368298 CAATTGGCTGGGTCACTAGAGTTTTGCTTGCAC
1 CAATTGGCTGGGTCACTAGAGTTTTGCTTGCAC
368331 CAATTGGCTGGGTCACTAGAGTTTTGCTTGCAC
1 CAATTGGCTGGGTCACTAGAGTTTTGCTTGCAC
368364 CAATT
1 CAATT
368369 TCATATGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.20, C:0.21, G:0.25, T:0.34
Consensus pattern (33 bp):
CAATTGGCTGGGTCACTAGAGTTTTGCTTGCAC
Found at i:368454 original size:37 final size:37
Alignment explanation
Indices: 368412--368486 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
368402 TCCAAATATG
*
368412 GAAACTAAATTCAAGGTTGTTCCGTTCATAGAACAAA
1 GAAACTAAATTCAAGGTTGTTCCATTCATAGAACAAA
*
368449 GAAACTAAATTCAAGGTTGTTCCATTTATAGAACAAA
1 GAAACTAAATTCAAGGTTGTTCCATTCATAGAACAAA
368486 G
1 G
368487 TAAAACATTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (37 bp):
GAAACTAAATTCAAGGTTGTTCCATTCATAGAACAAA
Found at i:371818 original size:31 final size:30
Alignment explanation
Indices: 371756--371841 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 30
371746 ACAAAGGGTC
*
371756 AATTCATTATAAATTATTAAT-TTAGTGATT
1 AATTTATTATAAATTA-TAATATTAGTGATT
*
371786 AATTTATTATAAATTGATAATATTAGTTATT
1 AATTTATTATAAATT-ATAATATTAGTGATT
371817 AATTTATTATAAATTAATAATATTA
1 AATTTATTATAAATT-ATAATATTA
371842 ATGACTAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
30 18 0.35
31 33 0.65
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (30 bp):
AATTTATTATAAATTATAATATTAGTGATT
Found at i:382930 original size:13 final size:13
Alignment explanation
Indices: 382912--382938 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
382902 AAAAGTGTAA
382912 TATTTTTTAATAT
1 TATTTTTTAATAT
382925 TATTTTTTAATAT
1 TATTTTTTAATAT
382938 T
1 T
382939 TTTATTTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TATTTTTTAATAT
Found at i:385989 original size:17 final size:15
Alignment explanation
Indices: 385957--385988 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
385947 CATAACTATG
385957 TACTATATAAATATA
1 TACTATATAAATATA
*
385972 TACTATATAAATTTA
1 TACTATATAAATATA
385987 TA
1 TA
385989 TTCCTTCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TACTATATAAATATA
Found at i:387135 original size:16 final size:17
Alignment explanation
Indices: 387102--387135 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
387092 GTATGCTAAA
*
387102 TTTTGAATAAATTCATT
1 TTTTAAATAAATTCATT
387119 TTTTAAATAAATT-ATT
1 TTTTAAATAAATTCATT
387135 T
1 T
387136 GATAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTTAAATAAATTCATT
Found at i:394373 original size:21 final size:21
Alignment explanation
Indices: 394331--394379 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
394321 CAATTATCTC
*
394331 ATAAATCAAGGGAAAATAATAT
1 ATAAAT-AAGGAAAAATAATAT
394353 ATAAATAAGGAAAAGAT-ATAT
1 ATAAATAAGGAAAA-ATAATAT
394374 A-AAATA
1 ATAAATA
394380 TTCTTAAGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 5 0.20
21 12 0.48
22 8 0.32
ACGTcount: A:0.63, C:0.02, G:0.12, T:0.22
Consensus pattern (21 bp):
ATAAATAAGGAAAAATAATAT
Found at i:396355 original size:18 final size:18
Alignment explanation
Indices: 396332--396370 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
396322 ACAAAACCGG
* *
396332 TAAAACATATAATAATAA
1 TAAAACAAATAAAAATAA
396350 TAAAACAAATAAAAATAA
1 TAAAACAAATAAAAATAA
396368 TAA
1 TAA
396371 TATTTCCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAACAAATAAAAATAA
Found at i:397127 original size:17 final size:16
Alignment explanation
Indices: 397107--397148 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 16
397097 ACATATAAAT
397107 ATTAATATAATTAAAAA
1 ATTAATAT-ATTAAAAA
397124 ATT-A-AT-TTAAAAA
1 ATTAATATATTAAAAA
397137 ATTAATATATTA
1 ATTAATATATTA
397149 TTTTCTTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.45
14 1 0.05
15 4 0.18
16 4 0.18
17 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTAATATATTAAAAA
Found at i:397264 original size:16 final size:17
Alignment explanation
Indices: 397233--397275 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
397223 GTATCCATTT
*
397233 AATTTGAATATAAATTC
1 AATTTGAATATAAATTA
*
397250 AATTTTAAT-TAAATTA
1 AATTTGAATATAAATTA
*
397266 AATTTAAATA
1 AATTTGAATA
397276 ACTCGTCTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
AATTTGAATATAAATTA
Found at i:397799 original size:16 final size:15
Alignment explanation
Indices: 397753--397802 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 15
397743 GATTGTAACA
397753 TAAAATATTATAAATT
1 TAAAATATT-TAAATT
397769 TATATAATATTTTAAATT
1 TA-A-AATA-TTTAAATT
397787 TAAAATATCTTAAATT
1 TAAAATAT-TTAAATT
397803 ATAATTAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.03
16 13 0.43
17 2 0.07
18 12 0.40
19 2 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAAATATTTAAATT
Found at i:398671 original size:6 final size:6
Alignment explanation
Indices: 398660--398686 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
398650 TTAATTGCGA
398660 AAATTT AAATTT AAATTT AAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAA
398687 ATATTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (6 bp):
AAATTT
Found at i:400059 original size:23 final size:22
Alignment explanation
Indices: 400032--400086 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
400022 TCCTACAAAA
400032 AATAAAATAAAGAAATTAT--T
1 AATAAAATAAAGAAATTATAAT
*
400052 AATAATAATAAATAAATTATAAT
1 AATAA-AATAAAGAAATTATAAT
400075 AATAAAAATAAA
1 AAT-AAAATAAA
400087 AATATAAAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 5 0.17
21 13 0.43
23 10 0.33
24 2 0.07
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AATAAAATAAAGAAATTATAAT
Found at i:400074 original size:20 final size:21
Alignment explanation
Indices: 400032--400086 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 21
400022 TCCTACAAAA
*
400032 AATAA-AATAAAGAAATTATT
1 AATAATAATAAATAAATTATT
400052 AATAATAATAAATAAATTA-T
1 AATAATAATAAATAAATTATT
400072 AATAATAA-AAATAAA
1 AATAATAATAAATAAA
400087 AATATAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 7 0.21
20 14 0.42
21 12 0.36
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (21 bp):
AATAATAATAAATAAATTATT
Found at i:400092 original size:20 final size:20
Alignment explanation
Indices: 400032--400093 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
400022 TCCTACAAAA
* *
400032 AATAA-AATAAAGAAATTATT
1 AATAATAATAAATAAAATA-T
*
400052 AATAATAATAAATAAATTAT
1 AATAATAATAAATAAAATAT
400072 AATAATAA-AAATAAAAATAT
1 AATAATAATAAAT-AAAATAT
400092 AA
1 AA
400094 AACCCGGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.11
20 22 0.58
21 12 0.32
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (20 bp):
AATAATAATAAATAAAATAT
Found at i:401036 original size:32 final size:31
Alignment explanation
Indices: 401000--401075 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
400990 CGGGGCCGTG
*
401000 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
401032 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
401063 GAGCCTACCTAAG
1 GGGCCTACCTAAG
401076 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:401059 original size:63 final size:63
Alignment explanation
Indices: 400953--401075 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
400943 ACCTAAGGGA
* * ** *
400953 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
401016 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
401076 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:402610 original size:18 final size:18
Alignment explanation
Indices: 402587--402621 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
402577 TTCCATCCGG
*
402587 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
402605 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
402622 GTCATTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:403922 original size:7 final size:7
Alignment explanation
Indices: 403910--403941 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
403900 TGGTCAACTC
403910 CGGTCAA
1 CGGTCAA
403917 CGGTCAA
1 CGGTCAA
403924 CGGGTCAA
1 C-GGTCAA
403932 CGGTCAA
1 CGGTCAA
403939 CGG
1 CGG
403942 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:403931 original size:8 final size:8
Alignment explanation
Indices: 403911--403957 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
403901 GGTCAACTCC
403911 GGTCAAC-
1 GGTCAACG
403918 GGTCAACG
1 GGTCAACG
403926 GGTCAAC-
1 GGTCAACG
403933 GGTCAACG
1 GGTCAACG
403941 GGT---CG
1 GGTCAACG
403946 GGTCAACG
1 GGTCAACG
403954 GGTC
1 GGTC
403958 GGGTCGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:403931 original size:15 final size:15
Alignment explanation
Indices: 403911--403957 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
403901 GGTCAACTCC
403911 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
403926 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
403941 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
403954 GGTC
1 GGTC
403958 GGGTCGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:403951 original size:13 final size:13
Alignment explanation
Indices: 403918--403962 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
403908 TCCGGTCAAC
*
403918 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
403933 GGTCAACGGGTCG
1 GGTCAACGGGTCG
403946 GGTCAACGGGTCG
1 GGTCAACGGGTCG
403959 GGTC
1 GGTC
403963 GGGTAACCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:403962 original size:18 final size:17
Alignment explanation
Indices: 403939--403979 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 17
403929 CAACGGTCAA
403939 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGT-AACGGGT
403957 CGGGTCGGGTAACCGGGT
1 CGGGTCGGGTAA-CGGGT
403975 CGGGT
1 CGGGT
403980 AACCGGGTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (17 bp):
CGGGTCGGGTAACGGGT
Found at i:403973 original size:13 final size:13
Alignment explanation
Indices: 403957--403989 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
403947 GTCAACGGGT
403957 CGGGTCGGGTAAC
1 CGGGTCGGGTAAC
403970 CGGGTCGGGTAAC
1 CGGGTCGGGTAAC
403983 CGGGTCG
1 CGGGTCG
403990 AGACCGTCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.24, G:0.48, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTAAC
Found at i:405967 original size:7 final size:7
Alignment explanation
Indices: 405955--405986 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
405945 TGGTCAACTC
405955 CGGTCAA
1 CGGTCAA
405962 CGGTCAA
1 CGGTCAA
405969 CGGGTCAA
1 C-GGTCAA
405977 CGGTCAA
1 CGGTCAA
405984 CGG
1 CGG
405987 GTCGGGTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.25, C:0.28, G:0.34, T:0.12
Consensus pattern (7 bp):
CGGTCAA
Found at i:405976 original size:8 final size:8
Alignment explanation
Indices: 405956--406002 Score: 59
Period size: 8 Copynumber: 6.5 Consensus size: 8
405946 GGTCAACTCC
405956 GGTCAAC-
1 GGTCAACG
405963 GGTCAACG
1 GGTCAACG
405971 GGTCAAC-
1 GGTCAACG
405978 GGTCAACG
1 GGTCAACG
405986 GGT---CG
1 GGTCAACG
405991 GGTCAACG
1 GGTCAACG
405999 GGTC
1 GGTC
406003 GGGTCGGGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
5 5 0.14
7 14 0.40
8 16 0.46
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:405976 original size:15 final size:15
Alignment explanation
Indices: 405956--406002 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
405946 GGTCAACTCC
405956 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
405971 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
405986 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
405999 GGTC
1 GGTC
406003 GGGTCGGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 12 0.39
15 19 0.61
ACGTcount: A:0.21, C:0.26, G:0.38, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:405996 original size:13 final size:13
Alignment explanation
Indices: 405963--406007 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
405953 TCCGGTCAAC
*
405963 GGTCAACGGGTCAAC
1 GGTCAACGGGTC--G
405978 GGTCAACGGGTCG
1 GGTCAACGGGTCG
405991 GGTCAACGGGTCG
1 GGTCAACGGGTCG
406004 GGTC
1 GGTC
406008 GGGTAATAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 17 0.59
15 12 0.41
ACGTcount: A:0.18, C:0.24, G:0.42, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:415931 original size:31 final size:31
Alignment explanation
Indices: 415889--415995 Score: 137
Period size: 30 Copynumber: 3.5 Consensus size: 31
415879 TTACATATTC
* *
415889 AGTCATCCAATTAT-TATTTTAGTTTCATTTT
1 AGTCATTCAATTATCT-TTTTAGTTTTATTTT
415920 AGTCATTCAATTATCTTTTTA-TTTTATTTT
1 AGTCATTCAATTATCTTTTTAGTTTTATTTT
* *
415950 AGTCATTAAATTATCTTTTTTGATTTTATTTT
1 AGTCATTCAATTATCTTTTTAG-TTTTATTTT
*
415982 AGTCACTCAATTAT
1 AGTCATTCAATTAT
415996 TTTATCTTAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
30 27 0.40
31 18 0.27
32 22 0.33
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (31 bp):
AGTCATTCAATTATCTTTTTAGTTTTATTTT
Found at i:415981 original size:32 final size:30
Alignment explanation
Indices: 415889--415995 Score: 135
Period size: 31 Copynumber: 3.5 Consensus size: 30
415879 TTACATATTC
* *
415889 AGTCATCCAATTAT-TATTTTAGTTTCATTTT
1 AGTCATTCAATTATCT-TTTTA-TTTTATTTT
415920 AGTCATTCAATTATCTTTTTATTTTATTTT
1 AGTCATTCAATTATCTTTTTATTTTATTTT
*
415950 AGTCATTAAATTATCTTTTTTGATTTTATTTT
1 AGTCATTCAATTATC-TTTTT-ATTTTATTTT
*
415982 AGTCACTCAATTAT
1 AGTCATTCAATTAT
415996 TTTATCTTAA
Statistics
Matches: 68, Mismatches: 5, Indels: 5
0.87 0.06 0.06
Matches are distributed among these distances:
30 22 0.32
31 23 0.34
32 23 0.34
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (30 bp):
AGTCATTCAATTATCTTTTTATTTTATTTT
Found at i:416003 original size:37 final size:31
Alignment explanation
Indices: 415889--415995 Score: 114
Period size: 32 Copynumber: 3.5 Consensus size: 31
415879 TTACATATTC
* * *
415889 AGTCATCCAATTAT-TATTTTAGTTTCATTTT
1 AGTCATCAAATTATCTTTTTTA-TTTTATTTT
415920 AGTCATTC-AATTATC-TTTTTATTTTATTTT
1 AGTCA-TCAAATTATCTTTTTTATTTTATTTT
*
415950 AGTCATTAAATTATCTTTTTTGATTTTATTTT
1 AGTCATCAAATTATCTTTTTT-ATTTTATTTT
415982 AGTCACTC-AATTAT
1 AGTCA-TCAAATTAT
415996 TTTATCTTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
29 1 0.02
30 20 0.30
31 21 0.32
32 23 0.35
33 1 0.02
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (31 bp):
AGTCATCAAATTATCTTTTTTATTTTATTTT
Found at i:420899 original size:21 final size:21
Alignment explanation
Indices: 420784--420899 Score: 67
Period size: 21 Copynumber: 5.6 Consensus size: 21
420774 GCGAAATAAA
* *
420784 AATCACAACGCGA-TCTCCAG
1 AATCGCAACGCGATTTTCCAG
** * *
420804 AATCGCAAATC-AGTTCCCAG
1 AATCGCAACGCGATTTTCCAG
* **
420824 AATCGCAACGCGATTATGAAG
1 AATCGCAACGCGATTTTCCAG
* ** *
420845 AATCGCAATGCGATAGTACA-
1 AATCGCAACGCGATTTTCCAG
**
420865 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTTTCCAG
420887 AATCGCAACGCGA
1 AATCGCAACGCGA
420900 ACATATAAAT
Statistics
Matches: 69, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.35
21 42 0.61
22 2 0.03
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (21 bp):
AATCGCAACGCGATTTTCCAG
Found at i:420970 original size:61 final size:60
Alignment explanation
Indices: 420887--421139 Score: 170
Period size: 61 Copynumber: 4.2 Consensus size: 60
420877 GATTTTCCAG
* * ** * **
420887 AATCGCAACGCGAACATATAAATCGCAACGCGATTC-TGACTATCGCAACGAGCATCCGTAA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGATACAT-AAAATCGCAACGAGCATCCGT-A
* * * * * *
420948 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACG-CGATACATAAAATCGCAACGAGCATCCGTA
* * * * *
421009 AATCGCAACGAGAATACGTAAATCGCAACGCG-TATC-TGTAAATCGTAATGAGAATACGTA
1 AATCGCAACGAGAATACGTAAATCGCAACGCGATA-CAT-AAAATCGCAACGAGCATCCGTA
* * * * * ** * * *
421069 AATCGCAATGTGTATTCGTAAATCGTAACGATAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAATCGCAACG-CGATACATAAAATCGCAACGAGCATCCGTA
*
421130 AATCGTAACG
1 AATCGCAACG
421140 CGATCGATAA
Statistics
Matches: 149, Mismatches: 36, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
59 3 0.02
60 43 0.29
61 78 0.52
62 24 0.16
63 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (60 bp):
AATCGCAACGAGAATACGTAAATCGCAACGCGATACATAAAATCGCAACGAGCATCCGTA
Found at i:420972 original size:20 final size:20
Alignment explanation
Indices: 420928--421141 Score: 180
Period size: 20 Copynumber: 10.6 Consensus size: 20
420918 GATTCTGACT
* *
420928 ATCGCAACGAGCATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
420949 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
420969 ATCGCAACGAC-AATACATAAA
1 ATCGCAACG-CGTATCCGT-AA
420990 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
421010 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
421030 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * * * *
421050 ATCGTAATGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
421070 ATCGCAATGTGTATTCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
421090 ATCGTAACG-ATAATACGTAAA
1 ATCGCAACGCGT-ATCCGT-AA
421111 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
421131 ATCGTAACGCG
1 ATCGCAACGCG
421142 ATCGATAATT
Statistics
Matches: 154, Mismatches: 33, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
19 1 0.01
20 105 0.68
21 47 0.31
22 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:421043 original size:40 final size:41
Alignment explanation
Indices: 420928--421139 Score: 293
Period size: 41 Copynumber: 5.2 Consensus size: 41
420918 GATTCTGACT
* *
420928 ATCGCAACGAGCATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
420969 ATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
421010 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* * * * *
421050 ATCGTAATGAGAATACGT-AAATCGCAATGTGTATTCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
421090 ATCGTAACGATAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
421131 ATCGTAACG
1 ATCGCAACG
421140 CGATCGATAA
Statistics
Matches: 152, Mismatches: 18, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
40 71 0.47
41 81 0.53
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:421240 original size:21 final size:21
Alignment explanation
Indices: 421211--421265 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
421201 ATTCTGACTA
421211 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
421232 TCGCGTTGCGGTTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
421253 TCGCAATGCGATT
1 TCGCATTGCGATT
421266 ACGTAAATCG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:421328 original size:20 final size:20
Alignment explanation
Indices: 421253--421318 Score: 98
Period size: 20 Copynumber: 3.3 Consensus size: 20
421243 TTTTCCTAAT
*
421253 TCGCAATGCGATTAC-GTAAA
1 TCGCAATGCGAAT-CTGTAAA
421273 TCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
*
421293 TCGTAATGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
421313 TCGCAA
1 TCGCAA
421319 CGAGATTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATCTGTAAA
Found at i:422208 original size:24 final size:24
Alignment explanation
Indices: 422181--422234 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
422171 TTATTCGAAA
422181 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
422205 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
422229 TTTGAT
1 TTTGAT
422235 GATTTTTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:423043 original size:40 final size:41
Alignment explanation
Indices: 422999--423077 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 41
422989 TCTTTTGGTT
**
422999 GAAATAAAAATCGCAACGAGAG-AATGACTATCGCAACGCG
1 GAAATAAAAATCGCAACGAGAGAAATGAAAATCGCAACGCG
* **
423039 GAAATGACTATCGCAACGAGAGAAATGAAAATCGCAACG
1 GAAATAAAAATCGCAACGAGAGAAATGAAAATCGCAACG
423078 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 19 0.58
41 14 0.42
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (41 bp):
GAAATAAAAATCGCAACGAGAGAAATGAAAATCGCAACGCG
Found at i:423065 original size:21 final size:21
Alignment explanation
Indices: 423008--423083 Score: 111
Period size: 20 Copynumber: 3.7 Consensus size: 21
422998 TGAAATAAAA
423008 ATCGCAACGAGAG-AATGACT
1 ATCGCAACGAGAGAAATGACT
*
423028 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAGAAATGACT
**
423048 ATCGCAACGAGAGAAATGAAA
1 ATCGCAACGAGAGAAATGACT
423069 ATCGCAACGAGAGAA
1 ATCGCAACGAGAGAA
423084 TCGCAACGCG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.02
20 27 0.54
21 22 0.44
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.12
Consensus pattern (21 bp):
ATCGCAACGAGAGAAATGACT
Found at i:423179 original size:21 final size:20
Alignment explanation
Indices: 423153--423229 Score: 79
Period size: 21 Copynumber: 3.9 Consensus size: 20
423143 CGCGTTGCGA
423153 TTCTCTCGTTGCGATTTTCAT
1 TTCTCT-GTTGCGATTTTCAT
**
423174 TTCTCTCGTTGCGATAGTCAT
1 TTCTCT-GTTGCGATTTTCAT
423195 TT-TCGTGTTGCGA-TTTCAT
1 TTCTC-TGTTGCGATTTTCAT
*
423214 TTC-ATGTTGCGATTTT
1 TTCTCTGTTGCGATTTT
423230 AAGTTTAGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 8 0.17
19 9 0.19
20 9 0.19
21 22 0.46
ACGTcount: A:0.12, C:0.19, G:0.18, T:0.51
Consensus pattern (20 bp):
TTCTCTGTTGCGATTTTCAT
Found at i:423206 original size:20 final size:18
Alignment explanation
Indices: 423181--423226 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
423171 CATTTCTCTC
*
423181 GTTGCGATAGTCATTTTCGT
1 GTTGCGAT-GTCA-TTTCAT
*
423201 GTTGCGATTTCATTTCAT
1 GTTGCGATGTCATTTCAT
423219 GTTGCGAT
1 GTTGCGAT
423227 TTTAAGTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 3 0.12
20 8 0.33
ACGTcount: A:0.15, C:0.15, G:0.24, T:0.46
Consensus pattern (18 bp):
GTTGCGATGTCATTTCAT
Found at i:423807 original size:20 final size:20
Alignment explanation
Indices: 423742--423952 Score: 183
Period size: 20 Copynumber: 10.4 Consensus size: 20
423732 TAAAAATCGT
**
423742 GTTGCGATTTATTGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
423762 GTTACGATTTTATGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
423783 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * * *
423803 ATTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
**
423823 GTTGCGATTTACATATACGC
1 GTTGCGATTTACGGATACGC
* * *
423843 GTTGCGATTTACGTATTCTC
1 GTTGCGATTTACGGATACGC
423863 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* * *
423883 GTTGCGATTTTATGTAT-TGTC
1 GTTGCGA-TTTACGGATACG-C
423904 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
423924 GTTGCTATTTTACGGATACTC
1 GTTGCGA-TTTACGGATACGC
423945 GTTGCGAT
1 GTTGCGAT
423953 AGTCAGAATC
Statistics
Matches: 153, Mismatches: 31, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
20 104 0.68
21 49 0.32
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:423947 original size:41 final size:41
Alignment explanation
Indices: 423742--423952 Score: 291
Period size: 41 Copynumber: 5.2 Consensus size: 41
423732 TAAAAATCGT
** * * *
423742 GTTGCGATTTATTGATACGCGTTACGATTTTATGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
423783 GTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
**
423823 GTTGCGATTTACATATACGCGTTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
423863 GTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * *
423904 GTTGCGATTTACGGATACGCGTTGCTATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
423945 GTTGCGAT
1 GTTGCGAT
423953 AGTCAGAATC
Statistics
Matches: 151, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 73 0.48
41 78 0.52
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:424031 original size:21 final size:21
Alignment explanation
Indices: 424001--424079 Score: 65
Period size: 21 Copynumber: 3.8 Consensus size: 21
423991 ATTTTCATAT
*
424001 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGGAAAA
* * **
424022 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGAAAA
424043 TCGCATTGCGATTCT--AATAA
1 TCGCATTGCGATTCTGGAA-AA
*
424063 TCGCGTTGCGATTCTGG
1 TCGCATTGCGATTCTGG
424080 GAACTGATTT
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.41
21 22 0.50
22 3 0.07
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTCTGGAAAA
Found at i:424071 original size:20 final size:20
Alignment explanation
Indices: 423959--424077 Score: 73
Period size: 20 Copynumber: 5.8 Consensus size: 20
423949 CGATAGTCAG
423959 AATCGCGTTGCGATT-TATAT
1 AATCGCGTTGCGATTCTA-AT
** * * *
423979 GTTCGCGTTGTGATTTTCAT
1 AATCGCGTTGCGATTCTAAT
*
423999 ATTCGCGTTGCGATTCTGGAA-
1 AATCGCGTTGCGATTCT--AAT
** * *
424020 AATCGCAATGCGAATTTGTACT
1 AATCGCGTTGCG-A-TTCTAAT
*
424042 -ATCGCATTGCGATTCTAAT
1 AATCGCGTTGCGATTCTAAT
424061 AATCGCGTTGCGATTCT
1 AATCGCGTTGCGATTCT
424078 GGGAACTGAT
Statistics
Matches: 75, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
19 5 0.07
20 44 0.59
21 21 0.28
22 2 0.03
23 3 0.04
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTAAT
Found at i:424111 original size:20 final size:20
Alignment explanation
Indices: 424042--424115 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
424032 AATTTGTACT
* *
424042 ATCGCATTGCGATTCTA-ATA
1 ATCGCGTTGCGATTCTAGA-G
*
424062 ATCGCGTTGCGATTCT-GGG
1 ATCGCGTTGCGATTCTAGAG
* **
424081 AACTGATTTGCGATTCTAGAG
1 ATC-GCGTTGCGATTCTAGAG
424102 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
424116 TTTATTTCGC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 35 0.85
21 4 0.10
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATTCTAGAG
Found at i:424578 original size:18 final size:18
Alignment explanation
Indices: 424548--424582 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
424538 TAATGGTTAA
424548 AAAAATTATTGATATTCAT
1 AAAAATTATTGAT-TTCAT
424567 AAAAATTA-TGATTTCA
1 AAAAATTATTGATTTCA
424583 AACATCAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAAATTATTGATTTCAT
Found at i:425175 original size:18 final size:19
Alignment explanation
Indices: 425140--425176 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
425130 CACGGAATGT
425140 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
425160 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
425177 GGATAACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:425417 original size:36 final size:35
Alignment explanation
Indices: 425345--425415 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 35
425335 ACTATAAGAT
* * *
425345 ATTTATATATTTTTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTTTAAAAAATTGAAAATCATAAA
425380 ATTTATATAATTTTTTAAAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTTTAAAAAATTGAAAATCATAAA
425415 A
1 A
425416 ATGTTTAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
35 14 0.44
36 18 0.56
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (35 bp):
ATTTATATATTTTTTAAAAAATTGAAAATCATAAA
Found at i:425848 original size:18 final size:19
Alignment explanation
Indices: 425814--425850 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
425804 CACTGAATGT
425814 AAGATTACCAGTGAGAATAA
1 AAGATTACCA-TGAGAATAA
425834 AAGATTACC-TGAGAATA
1 AAGATTACCATGAGAATA
425851 GATTACTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
20 9 0.53
ACGTcount: A:0.49, C:0.11, G:0.19, T:0.22
Consensus pattern (19 bp):
AAGATTACCATGAGAATAA
Found at i:426116 original size:678 final size:673
Alignment explanation
Indices: 425111--427111 Score: 2906
Period size: 678 Copynumber: 3.0 Consensus size: 673
425101 TGTAGTACGA
* * * *
425111 CCTTAGGGTGCGTTTGGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCAGGGAAT
1 CCTTAGGGTGTGCTTAGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCTGGGAAT
* * * * *
425176 AGGATAACTGAGAATGTTGTGTTTTGTGTTTTGTTGGTTTAGCAATAATGTAAGATTACTATGTT
66 AGGATTACTGGGAATGTTGTATTTTGTG-TTTGTTGGTTTAGCAAGAATGTAAGATTACTGTGTT
*
425241 TGGTTAAAGGAATAAAAGATTATTGGAATGTATA-TTGACCAAATTGTCCTTA-T-TATATTTGT
130 TGGTTAAAGGAATAAAAGATTATTAGAATGTATATTTGACCAAATTGTCCTTATTATATATTTG-
*
425303 TTTTTTAACAAGTTGAATTATACTATAATATTACTATAAGATATTTATATATTTT-TTTAAAAAT
194 TTTTTTAACAAGTTGAATTATACTATAATATTACTATAAGATATTTATATATTTTCTTTAAAAAA
*
425367 TTAAATTCATAAAATTTATATAATTTTTTAAAAAATTGAAAATATAAAAATGTTTAATGAAAGGG
259 TTAAATTCATAAAATTTATA-AATTTTTTAAAAAATTGAAAATATAAAAAGGTTTAATGAAAGGG
*
425432 TAAAATTTTATTTTAACCCCTGAACTTCATATAAAACTTTAATTATAGATTTTTTTGTAAATCTA
323 TAAAATTTTATTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTGTAAATCTA
* * * * * *
425497 AAATATTTTAAGGATTAATTTATAATTTAACCTTTGTAGAATTTTTATTATTCAATGACAGAATA
388 AAATAGTTTAAGGATAAATTTGTAATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAAGA
*
425562 ATGATATTTTTGAAAAAAAAAATTAAGGGCATTTTAGTCTAAAACGCCGATAATCCAACAATACC
453 ATGATATTTTTGAAAAAAAAAATTAAGGGCATTTTAGTCCAAAACGCCGATAATCCAACAATACC
* * * *
425627 TAAAGGAATGAGACAATGAAATTATCAGTAATATACCCAAAAAAATCTACTGTTGGTAATAAAAC
518 TAAAGGAA-GGGATAATGAAATTCTCAGTAATATACCCAAAAAAATCCACTGTTGGTAATAAAAC
425692 ATTACCGGGAATGAGATTACCGGCCAACCAAACGGAGGAATGTGGATTTCATTCCCCCGGTAAT-
582 ATTACCGGGAATGAGATTACCGGCCAACCAAACGGAGGAAT-TGGATTTCATTCCCCCGGTAATC
425756 CACATTCCCCGAACCAGAACCAAACAACC
646 CACATT-CCCGAACCAGAACCAAACAACC
* * *
425785 CCTTAGGGTGTGCTTAGTTCACTGAATGTAAGATTACCAGTGAGAATAAAAGATTACCTGAGAAT
1 CCTTAGGGTGTGCTTAGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCTGGGAAT
* * *
425850 A-GATTACTGGGAATGTTATATTTTGTGTTTGATTGGTTTAGCAGGAATGTAAGATTACCGTGTT
66 AGGATTACTGGGAATGTTGTATTTTGTGTTTG-TTGGTTTAGCAAGAATGTAAGATTACTGTGTT
* *
425914 TGGTTAAAGGAATAAAATATTATTAGAATGTATATTTGACCAAAATGGTCCTTATTATATATTTG
130 TGGTTAAAGGAATAAAAGATTATTAGAATGTATATTTGACC-AAATTGTCCTTATTATATATTTG
425979 TTTTTTAACAAGTTGAATTATACTATAATATTACTATAAGATATTTATATATTTTCTTTAAAAAA
194 TTTTTTAACAAGTTGAATTATACTATAATATTACTATAAGATATTTATATATTTTCTTT-AAAAA
* * **
426044 ATTAAATTCATAAAATTTATAGAATTTTTTATAGAATTGAAAATATAAAAAGGTTTAATGAAATA
258 ATTAAATTCATAAAATTTATA-AATTTTTTAAAAAATTGAAAATATAAAAAGGTTTAATGAAAGG
*
426109 GTAAAATTTTATTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGATTTTTTTGTAAATCT
322 GTAAAATTTTATTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTGTAAATCT
426174 AAAATAGTTTAAGGATAAATTTGTAATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAAG
387 AAAATAGTTTAAGGATAAATTTGTAATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAAG
426239 AATGATATTTTTG--AAAAAAAATTAAGGGCATTTTAGTCCAAAACGCCGATAATCCAACAATAC
452 AATGATATTTTTGAAAAAAAAAATTAAGGGCATTTTAGTCCAAAACGCCGATAATCCAACAATAC
*
426302 CTAAGGGAAGGGATAATGAAATTCTCAGTAATATACCCAAAAAAATCCACTGTTGGTAATAAAAC
517 CTAAAGGAAGGGATAATGAAATTCTCAGTAATATACCCAAAAAAATCCACTGTTGGTAATAAAAC
**
426367 ATTACCGGGAATGAGATTACCGGCCAACCAAACGG-GGAATATGGATTTCATTCCCAAGGTAATC
582 ATTACCGGGAATGAGATTACCGGCCAACCAAACGGAGGAAT-TGGATTTCATTCCCCCGGTAAT-
426431 CCACATT-CC---CC-GAACCAAACAACC
645 CCACATTCCCGAACCAGAACCAAACAACC
*
426455 CCTTAGGGTGTGCTTAGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACTTGGGAAT
1 CCTTAGGGTGTGCTTAGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCTGGGAAT
* * * *
426520 AGGATTACTGGAAATGTTGTATTTTGTGTTTGGTTGATTTATCAAGAATGTAAGATTATTGTGTT
66 AGGATTACTGGGAATGTTGTATTTTGTGTTT-GTTGGTTTAGCAAGAATGTAAGATTACTGTGTT
* * *
426585 TGGTTAAAGAAATAAAAGATTATTATAATGTATATTTGATCAAATTGTCCTTATTATATATTTGT
130 TGGTTAAAGGAATAAAAGATTATTAGAATGTATATTTGACCAAATTGTCCTTATTATATATTTGT
* * *
426650 TTTTTAACAAGTTGAATTCTACTATAACATTACTATAAAATATTTATATATTTTCTTT---AAA-
195 TTTTTAACAAGTTGAATTATACTATAATATTACTATAAGATATTTATATATTTTCTTTAAAAAAT
* * *
426711 -AAATT--T-AAATATATAATTTTTTTACAAAATTGAAAATATAAAAAGGTTTAATGAAAGGGTA
260 TAAATTCATAAAATTTATAAATTTTTTAAAAAATTGAAAATATAAAAAGGTTTAATGAAAGGGTA
* *
426772 AAATTTTATTTTAACCCATGAACTTCATATACAATTTTAATTATAGATTTTTTTTGTAAATCTAA
325 AAATTTTATTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGA-TTTTTTTGTAAATCTAA
* * *
426837 AATAGTTTAAGGATAAATTTGTAATTTGACATTCGTAAAATTTTTATTATTCAATGACATAAGAA
389 AATAGTTTAAGGATAAATTTGTAATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAAGAA
** **** *
426902 TGCGATTTTTGAAAAGAACTTTTTTTAAGGGCATTTTAGTCCAAAACGCC-AGTAATCTAACAAT
454 TGATATTTTTGAAAA-AA--AAAATTAAGGGCATTTTAGTCCAAAACGCCGA-TAATCCAACAAT
* * * * *
426966 ACCT-AAGGTAAGGGGTAATGACATTCCCGGTAATATA---AAAAAAATCCACTTTTGGTAATAA
515 ACCTAAAGG-AAGGGATAATGAAATTCTCAGTAATATACCCAAAAAAATCCACTGTTGGTAATAA
** ** * *
427027 AACATTACCGGGAATGAGATTACCGATCAACCAAAC-GAGAGAATACGAATTCTATTCTCCCGGT
579 AACATTACCGGGAATGAGATTACCGGCCAACCAAACGGAG-GAATTGGATTTC-ATTCCCCCGGT
427091 AATCCCACATTCACCGAACCA
642 AAT-CCACATTC-CCGAACCA
427112 AACAATCCCT
Statistics
Matches: 1205, Mismatches: 94, Indels: 60
0.89 0.07 0.04
Matches are distributed among these distances:
660 85 0.07
661 96 0.08
662 2 0.00
663 65 0.05
664 30 0.02
665 4 0.00
666 70 0.06
669 2 0.00
670 153 0.13
671 93 0.08
672 5 0.00
673 82 0.07
674 92 0.08
675 98 0.08
676 119 0.10
677 11 0.01
678 198 0.16
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (673 bp):
CCTTAGGGTGTGCTTAGTTCACGGAATGTAAGATTACCAGTGGGAATAAAAGATTACCTGGGAAT
AGGATTACTGGGAATGTTGTATTTTGTGTTTGTTGGTTTAGCAAGAATGTAAGATTACTGTGTTT
GGTTAAAGGAATAAAAGATTATTAGAATGTATATTTGACCAAATTGTCCTTATTATATATTTGTT
TTTTAACAAGTTGAATTATACTATAATATTACTATAAGATATTTATATATTTTCTTTAAAAAATT
AAATTCATAAAATTTATAAATTTTTTAAAAAATTGAAAATATAAAAAGGTTTAATGAAAGGGTAA
AATTTTATTTTAACCCCTGAACTTCATATAAAATTTTAATTATAGATTTTTTTGTAAATCTAAAA
TAGTTTAAGGATAAATTTGTAATTTAACATTCGTAGAATTTTTATTATTCAATGACAGAAGAATG
ATATTTTTGAAAAAAAAAATTAAGGGCATTTTAGTCCAAAACGCCGATAATCCAACAATACCTAA
AGGAAGGGATAATGAAATTCTCAGTAATATACCCAAAAAAATCCACTGTTGGTAATAAAACATTA
CCGGGAATGAGATTACCGGCCAACCAAACGGAGGAATTGGATTTCATTCCCCCGGTAATCCACAT
TCCCGAACCAGAACCAAACAACC
Found at i:426734 original size:26 final size:27
Alignment explanation
Indices: 426694--426751 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 27
426684 ATAAAATATT
*
426694 TATAT-ATTTTCTTTAAAAAATTTAAA
1 TATATAATTTTCTTTAAAAAATTGAAA
*
426720 TATATAATTTT-TTTACAAAATTGAAA
1 TATATAATTTTCTTTAAAAAATTGAAA
426746 -ATATAA
1 TATATAA
426752 AAAGGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 6 0.21
26 18 0.62
27 5 0.17
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (27 bp):
TATATAATTTTCTTTAAAAAATTGAAA
Found at i:434255 original size:2 final size:2
Alignment explanation
Indices: 434248--434277 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
434238 AAACAATTAT
434248 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
434278 AATAAATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:434314 original size:22 final size:22
Alignment explanation
Indices: 434289--434349 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
434279 ATAAATTTAA
*
434289 ATTAAATTAAAAATATTTATAT
1 ATTAATTTAAAAATATTTATAT
* *
434311 ATT-ATTTATATATTATTTATAT
1 ATTAATTTA-AAAATATTTATAT
*
434333 ATTTAATTTAAATATAT
1 A-TTAATTTAAAAATAT
434350 ATACCAGACC
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
21 4 0.13
22 15 0.50
23 6 0.20
24 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTAATTTAAAAATATTTATAT
Found at i:434318 original size:11 final size:11
Alignment explanation
Indices: 434302--434335 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
434292 AAATTAAAAA
434302 TATTTATATAT
1 TATTTATATAT
434313 TATTTATATAT
1 TATTTATATAT
434324 TATTTATATAT
1 TATTTATATAT
434335 T
1 T
434336 TAATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATATAT
Found at i:438052 original size:7 final size:7
Alignment explanation
Indices: 438040--438069 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
438030 TTGGTTATTT
438040 TTTTTCC
1 TTTTTCC
438047 TTTTTCC
1 TTTTTCC
438054 TTTTTCC
1 TTTTTCC
438061 TTTTTCC
1 TTTTTCC
438068 TT
1 TT
438070 ATATGATGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCC
Found at i:438908 original size:24 final size:24
Alignment explanation
Indices: 438855--438930 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 24
438845 AATAATAATA
* *
438855 TATATTTTAAAATTTTTAGTA-TTT
1 TATATTTT-AAATTTTAAATATTTT
* *
438879 TATTATATTTAACTTTTTGAATATTTT
1 TA-TAT-TTTAA-ATTTTAAATATTTT
438906 TATATTTTAAATTTTAAATATTTT
1 TATATTTTAAATTTTAAATATTTT
438930 T
1 T
438931 TTTATAAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
24 15 0.35
25 10 0.23
26 13 0.30
27 5 0.12
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (24 bp):
TATATTTTAAATTTTAAATATTTT
Found at i:438913 original size:17 final size:16
Alignment explanation
Indices: 438855--438920 Score: 55
Period size: 17 Copynumber: 4.0 Consensus size: 16
438845 AATAATAATA
*
438855 TATATTTTAAAATTTT
1 TATATTTTAATATTTT
* *
438871 TAGTATTTTATTATATT
1 TA-TATTTTAATATTTT
438888 TA-ACTTTTTGAATATTTT
1 TATA--TTTT-AATATTTT
438906 TATATTTTAA-ATTTT
1 TATATTTTAATATTTT
438921 AAATATTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
15 6 0.15
16 4 0.10
17 21 0.52
18 8 0.20
19 1 0.03
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.64
Consensus pattern (16 bp):
TATATTTTAATATTTT
Found at i:440305 original size:76 final size:75
Alignment explanation
Indices: 440180--440326 Score: 285
Period size: 76 Copynumber: 1.9 Consensus size: 75
440170 ACCTATACTT
440180 TAAATGGTAAAACATGGGTTGCTTATTGAAATTTAAACACATAATTAATCTCATATTATAAGTTA
1 TAAATGGTAAAACATGGGTTGCTTATTGAAATTTAAACACATAATTAATCTCATATTATAAGTTA
440245 ATTTAAACAC
66 ATTTAAACAC
440255 TAAATGGTAAAAACATGGGTTGCTTATTGAAATTTAAACACATAATTAATCTCATATTATAAGTT
1 TAAATGGT-AAAACATGGGTTGCTTATTGAAATTTAAACACATAATTAATCTCATATTATAAGTT
440320 AATTTAA
65 AATTTAA
440327 CAATTGAATT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
75 8 0.11
76 63 0.89
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (75 bp):
TAAATGGTAAAACATGGGTTGCTTATTGAAATTTAAACACATAATTAATCTCATATTATAAGTTA
ATTTAAACAC
Found at i:442639 original size:3 final size:3
Alignment explanation
Indices: 442631--442682 Score: 88
Period size: 3 Copynumber: 17.3 Consensus size: 3
442621 ATCAATTGGG
442631 TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
442677 -TA TTA T
1 TTA TTA T
442683 GGTAAATATT
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:449099 original size:36 final size:34
Alignment explanation
Indices: 449049--449167 Score: 110
Period size: 36 Copynumber: 3.6 Consensus size: 34
449039 ATTGGACAGT
449049 ACTCGACTCTTGCTCGTTAGAAAAATTGTTGCTCG
1 ACTCGACTCTTGCTCGTTA-AAAAATTGTTGCTCG
* *
449084 ACTCGATTCGTTGCTCGTT--AAAATT-TTGCTTG
1 ACTCGACTC-TTGCTCGTTAAAAAATTGTTGCTCG
*
449116 ACTC-A---TT-CTCGTTAAAAAAACTTGTTGCTCA
1 ACTCGACTCTTGCTCGTT-AAAAAA-TTGTTGCTCG
449147 ACTCGACTCGTTGCTCGTTAA
1 ACTCGACTC-TTGCTCGTTAA
449168 GCTCACATGA
Statistics
Matches: 68, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
26 6 0.09
27 2 0.03
29 4 0.06
30 2 0.03
31 10 0.15
32 11 0.16
33 6 0.09
35 8 0.12
36 13 0.19
37 6 0.09
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.37
Consensus pattern (34 bp):
ACTCGACTCTTGCTCGTTAAAAAATTGTTGCTCG
Found at i:454485 original size:28 final size:29
Alignment explanation
Indices: 454450--454529 Score: 119
Period size: 28 Copynumber: 2.8 Consensus size: 29
454440 AAACTAAATT
*
454450 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
454479 GA-GTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
454507 GATGTCA-TGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
454530 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
28 36 0.77
29 11 0.23
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:456029 original size:177 final size:177
Alignment explanation
Indices: 455733--456076 Score: 688
Period size: 177 Copynumber: 1.9 Consensus size: 177
455723 AGGCAGAGGT
455733 AGGCCATGGACGAGGTGGAAGTCGAGGTCGTGGACGAGGCTGGAATTACAACAATAACAATTCCA
1 AGGCCATGGACGAGGTGGAAGTCGAGGTCGTGGACGAGGCTGGAATTACAACAATAACAATTCCA
455798 ACAACAACTATGAGAAAGGAGAAAGCTCAACACGAGGCCGTGGAAGAATTAATCCAAACTCAAAG
66 ACAACAACTATGAGAAAGGAGAAAGCTCAACACGAGGCCGTGGAAGAATTAATCCAAACTCAAAG
455863 TATGACAAATCTCAAATTCGATGTTATAATTGTCAAATTTGAGGTAG
131 TATGACAAATCTCAAATTCGATGTTATAATTGTCAAATTTGAGGTAG
455910 AGGCCATGGACGAGGTGGAAGTCGAGGTCGTGGACGAGGCTGGAATTACAACAATAACAATTCCA
1 AGGCCATGGACGAGGTGGAAGTCGAGGTCGTGGACGAGGCTGGAATTACAACAATAACAATTCCA
455975 ACAACAACTATGAGAAAGGAGAAAGCTCAACACGAGGCCGTGGAAGAATTAATCCAAACTCAAAG
66 ACAACAACTATGAGAAAGGAGAAAGCTCAACACGAGGCCGTGGAAGAATTAATCCAAACTCAAAG
456040 TATGACAAATCTCAAATTCGATGTTATAATTGTCAAA
131 TATGACAAATCTCAAATTCGATGTTATAATTGTCAAA
456077 AATTTGGGCA
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
177 167 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (177 bp):
AGGCCATGGACGAGGTGGAAGTCGAGGTCGTGGACGAGGCTGGAATTACAACAATAACAATTCCA
ACAACAACTATGAGAAAGGAGAAAGCTCAACACGAGGCCGTGGAAGAATTAATCCAAACTCAAAG
TATGACAAATCTCAAATTCGATGTTATAATTGTCAAATTTGAGGTAG
Found at i:459224 original size:29 final size:29
Alignment explanation
Indices: 459191--459291 Score: 184
Period size: 29 Copynumber: 3.4 Consensus size: 29
459181 AATTGATGTA
*
459191 CTTACATCATTTAATTAAAGATGTCATTG
1 CTTACATCATTTAATTAATGATGTCATTG
459220 CTTACATCATTTAATTAATGATGTCATTG
1 CTTACATCATTTAATTAATGATGTCATTG
459249 CTTACATCATTTAATTAATGATGTCATTG
1 CTTACATCATTTAATTAATGATGTCATTG
459278 CTTACATCAATTTA
1 CTTACATC-ATTTA
459292 GTTAGGTGAG
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
29 65 0.93
30 5 0.07
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.44
Consensus pattern (29 bp):
CTTACATCATTTAATTAATGATGTCATTG
Found at i:467162 original size:16 final size:16
Alignment explanation
Indices: 467138--467169 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
467128 TATCGCCGAC
*
467138 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
467154 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
467170 TGTGAATAGT
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:0.34, C:0.25, G:0.06, T:0.34
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:470840 original size:30 final size:30
Alignment explanation
Indices: 470806--470883 Score: 129
Period size: 30 Copynumber: 2.6 Consensus size: 30
470796 TTACAGTTCG
*
470806 AATGAAGGTCGTCGGGTGGTCTGGGCGACC
1 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
*
470836 AATGAAGGTCGCCGGGTGTTCTGGGCGACC
1 AATGAAGGTCGCCGGGTGGTCTGGGCGACC
*
470866 AATGAAGGTCGCCAGGTG
1 AATGAAGGTCGCCGGGTG
470884 ATCCATGGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.19, C:0.21, G:0.41, T:0.19
Consensus pattern (30 bp):
AATGAAGGTCGCCGGGTGGTCTGGGCGACC
Found at i:471622 original size:30 final size:30
Alignment explanation
Indices: 471581--471658 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
471571 TCCCATGGAT
*
471581 CACCTGGCGACCTTCATTGGCCGCCCAGAA
1 CACCCGGCGACCTTCATTGGCCGCCCAGAA
* * *
471611 CACTCGGCGACCTTCATTGGTCGCCCAGAC
1 CACCCGGCGACCTTCATTGGCCGCCCAGAA
471641 CACCCGGCGACCTTCATT
1 CACCCGGCGACCTTCATT
471659 CGAACTGTAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.19
Consensus pattern (30 bp):
CACCCGGCGACCTTCATTGGCCGCCCAGAA
Found at i:477973 original size:31 final size:31
Alignment explanation
Indices: 477935--477996 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
477925 TTAAAGTCCT
* *
477935 CTGTAAAACCAAAGGCATGGTGCCACATCAG
1 CTGTAAAACCAAAAGCAGGGTGCCACATCAG
477966 CTGTAAAACCAAAAGCAGGGTGCCACATCAG
1 CTGTAAAACCAAAAGCAGGGTGCCACATCAG
477997 TAAAGGTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.37, C:0.26, G:0.23, T:0.15
Consensus pattern (31 bp):
CTGTAAAACCAAAAGCAGGGTGCCACATCAG
Found at i:482948 original size:37 final size:38
Alignment explanation
Indices: 482839--482958 Score: 109
Period size: 39 Copynumber: 3.2 Consensus size: 38
482829 TAAATTTTTT
* * *
482839 ATTTATAATTCTCAAATTATTTTA-CTCTAACATTCTAA
1 ATTTTTAATTCTAAAATTATTTCACCT-TAACATTCTAA
** * * *
482877 ATTTCAAATTTCTTAAATTATTTTATCTTAACATTCTAA
1 ATTTTTAA-TTCTAAAATTATTTCACCTTAACATTCTAA
* *
482916 ATTTTTAA-TCTAAAATTATTTCACCTTCACATTATAA
1 ATTTTTAATTCTAAAATTATTTCACCTTAACATTCTAA
*
482953 TTTTTT
1 ATTTTT
482959 TAAATATTTA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
37 29 0.42
38 6 0.09
39 32 0.46
40 2 0.03
ACGTcount: A:0.35, C:0.14, G:0.00, T:0.51
Consensus pattern (38 bp):
ATTTTTAATTCTAAAATTATTTCACCTTAACATTCTAA
Found at i:483402 original size:3 final size:3
Alignment explanation
Indices: 483394--483423 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
483384 GATAGTTTAC
483394 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
483424 TCTTAGGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:490156 original size:60 final size:60
Alignment explanation
Indices: 490080--490232 Score: 209
Period size: 60 Copynumber: 2.5 Consensus size: 60
490070 ATTGGTCATT
* * * * *
490080 AAACTTTTGAAAATTCTAATTTCATCTCTAAATTATGACTCTCATTCTAAATTAGTCTCC
1 AAACTTTTGAATATTCTAATTTCATCCCTAAATGATGACCCTCATTCTAAATTAGTCCCC
*
490140 AAACTTTT-AGATATTCTAATTTCATCCCTAAATGATGACCCTCTTTCTAAATTAGTCCCC
1 AAACTTTTGA-ATATTCTAATTTCATCCCTAAATGATGACCCTCATTCTAAATTAGTCCCC
* * *
490200 AAACTTTTGAATATTCCAATTCCATCCCCAAAT
1 AAACTTTTGAATATTCTAATTTCATCCCTAAAT
490233 TCATCTAAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
59 1 0.01
60 80 0.98
61 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.39
Consensus pattern (60 bp):
AAACTTTTGAATATTCTAATTTCATCCCTAAATGATGACCCTCATTCTAAATTAGTCCCC
Found at i:493260 original size:21 final size:22
Alignment explanation
Indices: 493236--493287 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
493226 TAAATTATAT
493236 TTCTTAAATATA-AACCCTAAA
1 TTCTTAAATATATAACCCTAAA
* * * *
493257 TTCTAAAATTTATAATCTTAAA
1 TTCTTAAATATATAACCCTAAA
493279 TT-TTAAATA
1 TTCTTAAATA
493288 ATACACATTA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (22 bp):
TTCTTAAATATATAACCCTAAA
Found at i:494525 original size:18 final size:18
Alignment explanation
Indices: 494502--494539 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
494492 GTCGGATGAT
494502 TATTTTATAATTTTTTAA
1 TATTTTATAATTTTTTAA
494520 TATTTTATAATTTTTTAA
1 TATTTTATAATTTTTTAA
494538 TA
1 TA
494540 GTAAAAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTTATAATTTTTTAA
Found at i:494630 original size:60 final size:60
Alignment explanation
Indices: 494518--494631 Score: 158
Period size: 60 Copynumber: 1.9 Consensus size: 60
494508 ATAATTTTTT
* * * *
494518 AATATTTTATAATTTTTTAATAGTAAAAAACTTAACAAAATAGTATCTTATAATAAAAAA
1 AATATTTTATAATTTTTTAATAATAAAAAACTTAACAAAATAATAACATATAATAAAAAA
* *
494578 AATATTTTATAA-TTTTTAATAATAAAAATATTTAATAAAATAATAACATATAAT
1 AATATTTTATAATTTTTTAATAATAAAAA-ACTTAACAAAATAATAACATATAAT
494632 CGCTATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 15 0.32
60 32 0.68
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (60 bp):
AATATTTTATAATTTTTTAATAATAAAAAACTTAACAAAATAATAACATATAATAAAAAA
Found at i:499944 original size:15 final size:15
Alignment explanation
Indices: 499924--499958 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
499914 TTTTATCCAG
499924 ACTATCACAATATAA
1 ACTATCACAATATAA
* *
499939 ACTATCAGAATATGA
1 ACTATCACAATATAA
499954 ACTAT
1 ACTAT
499959 TAAATCATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.49, C:0.17, G:0.06, T:0.29
Consensus pattern (15 bp):
ACTATCACAATATAA
Found at i:501769 original size:31 final size:31
Alignment explanation
Indices: 501734--501798 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
501724 AACAACTTAG
* *
501734 GACTAAAATTAAATGAATCAATAACATTAAA
1 GACTAAAATCAAATGAACCAATAACATTAAA
* * * *
501765 GACTAGAATCGAATGAACCGATAACATTATA
1 GACTAAAATCAAATGAACCAATAACATTAAA
501796 GAC
1 GAC
501799 CATTCTCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (31 bp):
GACTAAAATCAAATGAACCAATAACATTAAA
Found at i:504194 original size:22 final size:22
Alignment explanation
Indices: 504151--504194 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
504141 AAATTTACAT
*
504151 TCACATAAAATAAAATAAATTG
1 TCACATAAAATAAAACAAATTG
* * *
504173 TCACTTAAAATAACACACATTG
1 TCACATAAAATAAAACAAATTG
504195 CATCGTTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.16, G:0.05, T:0.27
Consensus pattern (22 bp):
TCACATAAAATAAAACAAATTG
Found at i:506554 original size:3 final size:3
Alignment explanation
Indices: 506546--506597 Score: 61
Period size: 3 Copynumber: 17.3 Consensus size: 3
506536 TTGTAAGTTA
** *
506546 AAT AAT AAT AAT AAT GCT AAT AAT AAT AATT AA- AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
506591 AAT AAT A
1 AAT AAT A
506598 TATACAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:506813 original size:43 final size:42
Alignment explanation
Indices: 506752--506879 Score: 136
Period size: 43 Copynumber: 3.0 Consensus size: 42
506742 TGTTGGGGAC
*
506752 GACACTGCTCATACGTGATGAAGAGTTTGGGTCGTCTAAAGGT
1 GACACGGCTCATACGTGATGAAGAGTTT-GGTCGTCTAAAGGT
* * ***
506795 GACACGGCTCCTACGTGATGAAGAGCTCTGGTCG-GGGAA--T
1 GACACGGCTCATACGTGATGAAGAG-TTTGGTCGTCTAAAGGT
* *
506835 GACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GACACGGCTCATACGTGATGAAGAGTT-TGGTCGTCTAAAGGT
506878 GA
1 GA
506880 TAACACGGTT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 29 0.43
41 2 0.03
42 2 0.03
43 31 0.46
44 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (42 bp):
GACACGGCTCATACGTGATGAAGAGTTTGGTCGTCTAAAGGT
Found at i:506850 original size:40 final size:40
Alignment explanation
Indices: 506794--507035 Score: 168
Period size: 40 Copynumber: 5.8 Consensus size: 40
506784 CGTCTAAAGG
* *
506794 TGACACGGCTCCTACGTGATGAAGAGCTCTGGTC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGG-A
* *
506834 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TC---AGGGGA
* * * *
506880 TAACACGGTTCCTACGTGATG-AG-GACTACTGGTTATCTAAGGG-
1 TGACACGGCTCATACGTGATGAAGAGA-T-CTGG---TC-AGGGGA
* * * * *
506923 TGACCCGGTTCCTACGTGATGAGGAAATCTGGTCAGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGA
* * *
506963 TGACACAGCTCATACGTGATGAGGAGATCTGGTCTGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGG-A
* *
507004 TGGCACGGCTCATACGTGATGAAGAGTTCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
507036 CCAATCTAAA
Statistics
Matches: 162, Mismatches: 27, Indels: 25
0.76 0.13 0.12
Matches are distributed among these distances:
39 4 0.02
40 65 0.40
41 29 0.18
43 25 0.15
44 6 0.04
45 4 0.02
46 26 0.16
47 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (40 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCAGGGGA
Found at i:506918 original size:46 final size:43
Alignment explanation
Indices: 506836--506947 Score: 116
Period size: 46 Copynumber: 2.5 Consensus size: 43
506826 TCGGGGAATG
* * * * *
506836 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGTTCCTACGTGATGAGGACTACTGGCCATCT-AAGG-G-TA
** *
506882 ACACGGTTCCTACGTGATGAGGACTACTGGTTATCTAAGGGTG
1 ACACGGTTCCTACGTGATGAGGACTACTGGCCATCTAAGGGTA
*
506925 ACCCGGTTCCTACGTGATGAGGA
1 ACACGGTTCCTACGTGATGAGGA
506948 AATCTGGTCA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
43 23 0.40
44 1 0.02
45 4 0.07
46 29 0.51
ACGTcount: A:0.26, C:0.21, G:0.29, T:0.25
Consensus pattern (43 bp):
ACACGGTTCCTACGTGATGAGGACTACTGGCCATCTAAGGGTA
Found at i:507015 original size:41 final size:40
Alignment explanation
Indices: 506935--507035 Score: 139
Period size: 41 Copynumber: 2.5 Consensus size: 40
506925 ACCCGGTTCC
*
506935 TACGTGATGAGGAAATCTGGTCAGGGGATGACACAGCTCA
1 TACGTGATGAGGAGATCTGGTCAGGGGATGACACAGCTCA
* * *
506975 TACGTGATGAGGAGATCTGGTCTGGGGAATGGCACGGCTCA
1 TACGTGATGAGGAGATCTGGTCAGGGG-ATGACACAGCTCA
* *
507016 TACGTGATGAAGAGTTCTGG
1 TACGTGATGAGGAGATCTGG
507036 CCAATCTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
40 25 0.46
41 29 0.54
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.23
Consensus pattern (40 bp):
TACGTGATGAGGAGATCTGGTCAGGGGATGACACAGCTCA
Found at i:507489 original size:35 final size:36
Alignment explanation
Indices: 507438--507517 Score: 92
Period size: 35 Copynumber: 2.2 Consensus size: 36
507428 TGAGACAAAA
* * **
507438 TTTGTTTTTAAGGGAAAC-GTTCTCAAAGAT-GTTTAT
1 TTTG-TTTCAAGGGAAACAGAT-TCAAAGATGGTAAAT
507474 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
1 TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
507510 TTTGTTTC
1 TTTGTTTC
507518 CAAAGAAACA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 20 0.53
36 18 0.47
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACAGATTCAAAGATGGTAAAT
Found at i:508309 original size:66 final size:67
Alignment explanation
Indices: 508221--508418 Score: 249
Period size: 67 Copynumber: 3.0 Consensus size: 67
508211 AAAGATTTAC
** * * * * *
508221 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-ATGTTTCAAAAGAAACAAACTCAAAGATTTT
508284 TGT
65 TGT
* *
508287 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTATGTTTCAAAAGAAACAAACTCAAAGATTTTT
508352 GT
66 GT
* * *
508354 TTCAAAAGAAACTATCTTAAAAGAGA-AAGAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAA-AATTATGTTTCAAAAGAAACAAACTCAAAGATTTT
508418 T
65 T
508419 TTCACAAAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
65 1 0.01
66 33 0.28
67 83 0.71
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.30
Consensus pattern (67 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTATGTTTCAAAAGAAACAAACTCAAAGATTTTT
GT
Found at i:508357 original size:67 final size:67
Alignment explanation
Indices: 508263--508457 Score: 256
Period size: 67 Copynumber: 3.0 Consensus size: 67
508253 TCATTTTAAG
* *
508263 AGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
508328 AA
66 AA
* *
508330 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAAAGAGA-AAGAATTTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAA-AATTTTGTTTC
*
508394 CAA
65 AAA
* * * * *
508397 AGAAACAAACTCAAAGA-TTTT-TTTC-ACA-AAATTGTCTCAAGAGATACAAAACTTTGTTTCA
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
508458 GACTCAAAGA
Statistics
Matches: 113, Mismatches: 13, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
63 23 0.20
64 4 0.04
65 4 0.04
66 6 0.05
67 76 0.67
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCA
AA
Found at i:508485 original size:52 final size:53
Alignment explanation
Indices: 508405--508509 Score: 167
Period size: 52 Copynumber: 2.0 Consensus size: 53
508395 AAAGAAACAA
*
508405 ACTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGATACAAAACTTTGTTTCAG
1 ACTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
* *
508459 ACTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGATAAAACTTTGTTTCA
1 ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
508510 AAATAAATAG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
52 39 0.81
54 9 0.19
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.34
Consensus pattern (53 bp):
ACTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAG
Found at i:508565 original size:28 final size:29
Alignment explanation
Indices: 508506--508585 Score: 92
Period size: 28 Copynumber: 2.8 Consensus size: 29
508496 AAAACTTTGT
* * * *
508506 TTCAAAATAAATAGACTCAAAG-TTTTTT
1 TTCAAAAGAAACAGACTCAAAGATATTTA
508534 TTCAAAAGAAAC-GACTCAAAGATATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
* *
508562 TTCAAAAGGAACAAACTCAAAGAT
1 TTCAAAAGAAACAGACTCAAAGAT
508586 TTTTCAAGAG
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
27 9 0.20
28 25 0.57
29 10 0.23
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.28
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATATTTA
Found at i:509021 original size:36 final size:36
Alignment explanation
Indices: 508937--509041 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
508927 AAAGGAAAAA
* * *
508937 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
508971 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* *
509007 TGTCTCAAGCGAGACAAAGTTTGTTTTTTGAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
509042 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
34 19 0.33
35 4 0.07
36 35 0.60
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Done.