Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008245.1 Hibiscus syriacus cultivar Beakdansim tig00110895_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: 6601124
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 33
Found at i:246801 original size:30 final size:29
Alignment explanation
Indices: 246748--246808 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
246738 AACGACGTTT
**
246748 TTGAAAAATTACTCCTTTTACTTTAACAC
1 TTGAAAAATTACTCCCCTTACTTTAACAC
246777 TTGAAAAATTACTTCCCCTTACTTTAACAC
1 TTGAAAAATTAC-TCCCCTTACTTTAACAC
246807 TT
1 TT
246809 CTCCCATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (29 bp):
TTGAAAAATTACTCCCCTTACTTTAACAC
Found at i:249098 original size:19 final size:20
Alignment explanation
Indices: 249074--249132 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
249064 CCAGAACCCC
*
249074 AGGGGGTATCGATTCCCCT-
1 AGGGGGAATCGATTCCCCTA
*
249093 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGATTCCCC-T--A
249116 AGGGGGAATCGATTCCC
1 AGGGGGAATCGATTCCC
249133 TCATGAGGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 16 0.48
20 1 0.03
23 16 0.48
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.22
Consensus pattern (20 bp):
AGGGGGAATCGATTCCCCTA
Found at i:264530 original size:31 final size:31
Alignment explanation
Indices: 264492--264552 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
264482 TCAAAAAGTA
* *
264492 TAAGTTTTGGTCACTTACGTTATTATTTTAT
1 TAAGTTTTGGTCACTTACATTATCATTTTAT
*
264523 TAAGTTTTTGTCACTTACATTATCATTTTA
1 TAAGTTTTGGTCACTTACATTATCATTTTA
264553 CGTTTTGGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.11, G:0.10, T:0.54
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATCATTTTAT
Found at i:268746 original size:18 final size:19
Alignment explanation
Indices: 268711--268747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
268701 CACGGAATGT
268711 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GGGAATAA
268731 AAGATTATCA-GGGAATA
1 AAGATTATCAGGGGAATA
268748 GGATTACTGG
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:0.05, G:0.24, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGGGAATAA
Found at i:269489 original size:2 final size:2
Alignment explanation
Indices: 269482--269526 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
269472 CGATTTAGTT
269482 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
269524 TA T
1 TA T
269527 TTAATTTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:271535 original size:14 final size:14
Alignment explanation
Indices: 271513--271554 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
271503 TCGATTATAT
*
271513 GTTCGTTTATGTTC
1 GTTCATTTATGTTC
271527 GTTCATTTATGTTC
1 GTTCATTTATGTTC
*
271541 ATTCATTTATGTTC
1 GTTCATTTATGTTC
271555 TAACATATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:271838 original size:14 final size:14
Alignment explanation
Indices: 271810--271849 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
271800 TTTTTTTTGT
271810 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
271823 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
*
271837 GTTCGTGTTCGTT
1 GTTTGTGTTCGTT
271850 TATGCTCGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 8 0.35
14 15 0.65
ACGTcount: A:0.03, C:0.12, G:0.28, T:0.57
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:276644 original size:21 final size:21
Alignment explanation
Indices: 276615--276654 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
276605 TTTTTATTAT
* *
276615 TTTATTAAAAGAATTGGTATG
1 TTTAGTAAAACAATTGGTATG
*
276636 TTTAGTAAAACACTTGGTA
1 TTTAGTAAAACAATTGGTA
276655 CATTTAGACT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGTAAAACAATTGGTATG
Found at i:277294 original size:3 final size:3
Alignment explanation
Indices: 277286--277316 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
277276 GATAGCGGAG
277286 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
277317 AGGATTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:288455 original size:24 final size:24
Alignment explanation
Indices: 288405--288456 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
288395 TATGTTATAG
288405 ATTAATTAAATTTTTTAAATAAGT
1 ATTAATTAAATTTTTTAAATAAGT
288429 ATTATATTAAATTATTTTAAA-AA-T
1 ATTA-ATTAAATT-TTTTAAATAAGT
288453 ATTA
1 ATTA
288457 CTATCATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.35
25 10 0.38
26 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAATTAAATTTTTTAAATAAGT
Found at i:288680 original size:24 final size:24
Alignment explanation
Indices: 288630--288681 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
288620 TATGTTATAG
288630 ATTAATTAAATTTTTTAAATAAGT
1 ATTAATTAAATTTTTTAAATAAGT
288654 ATTATATTAAATTATTTTAAA-AA-T
1 ATTA-ATTAAATT-TTTTAAATAAGT
288678 ATTA
1 ATTA
288682 CTATCATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 9 0.35
25 10 0.38
26 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
ATTAATTAAATTTTTTAAATAAGT
Found at i:288703 original size:225 final size:226
Alignment explanation
Indices: 288311--288759 Score: 848
Period size: 225 Copynumber: 2.0 Consensus size: 226
288301 GATACAATAC
* *
288311 CTAAAGTTTGATTGTATTTAGTGCATTTGACCCCCATATATTATTATTTGAATGATTTAGATTTA
1 CTAAAGTTTGATGGTATTTAGTGCATTTGACACCCATATATTATTATTTGAATGATTTAGATTTA
288376 AATATTTACTTTTGTATAATATGTTATAGATTAATTAAATTTTTTAAATAAGTATTATATTAAAT
66 AATATTTACTTTTGTATAATATGTTATAGATTAATTAAATTTTTTAAATAAGTATTATATTAAAT
288441 TATTTTAAAAATATTACTATCATATTTTAATTTTATTGTTATAGGCAACTTTATCCAAATAATAT
131 TATTTTAAAAATATTACTATCATATTTTAATTTTATTGTTATAGGCAACTTTATCCAAATAATAT
288506 CGTTTCTTTCTTTTCACCAAAATAGCATTAT
196 CGTTTCTTTCTTTTCACCAAAATAGCATTAT
288537 CTAAAGTTTGATGGTATTTAGTGCAGTTT-A-ACCCATATATTATTATTTGAATGATTTAGATTT
1 CTAAAGTTTGATGGTATTTAGTGCA-TTTGACACCCATATATTATTATTTGAATGATTTAGATTT
288600 AAATATTTACTTTTGTATAATATGTTATAGATTAATTAAATTTTTTAAATAAGTATTATATTAAA
65 AAATATTTACTTTTGTATAATATGTTATAGATTAATTAAATTTTTTAAATAAGTATTATATTAAA
*
288665 TTATTTTAAAAATATTACTATCATATTTTATTTTTATTGTTATAGGCAACTTTATCCAAATAATA
130 TTATTTTAAAAATATTACTATCATATTTTAATTTTATTGTTATAGGCAACTTTATCCAAATAATA
288730 TCGTTTCTTTCTTTTCACCAAAATAGCATT
195 TCGTTTCTTTCTTTTCACCAAAATAGCATT
288760 TAAAATACTC
Statistics
Matches: 219, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
225 191 0.87
226 25 0.11
227 3 0.01
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (226 bp):
CTAAAGTTTGATGGTATTTAGTGCATTTGACACCCATATATTATTATTTGAATGATTTAGATTTA
AATATTTACTTTTGTATAATATGTTATAGATTAATTAAATTTTTTAAATAAGTATTATATTAAAT
TATTTTAAAAATATTACTATCATATTTTAATTTTATTGTTATAGGCAACTTTATCCAAATAATAT
CGTTTCTTTCTTTTCACCAAAATAGCATTAT
Found at i:316359 original size:15 final size:15
Alignment explanation
Indices: 316336--316474 Score: 58
Period size: 15 Copynumber: 9.2 Consensus size: 15
316326 ATATTACATG
* *
316336 CTATATGATATTGAC
1 CTATGTGATATTGAA
316351 CTATGTGATTATATGAA
1 CTATGTGA-TAT-TGAA
*
316368 C-ATATGATA-T-AA
1 CTATGTGATATTGAA
* *
316380 GCTATGTGACATTGAC
1 -CTATGTGATATTGAA
316396 CTATGTGATTATATGAA
1 CTATGTGA-TAT-TGAA
316413 C-ATGTGATA-T-AA
1 CTATGTGATATTGAA
* ** *
316425 GCTATGTGACAAGGAT
1 -CTATGTGATATTGAA
* *
316441 CTATGTTATTATATG-T
1 CTATGTGA-TAT-TGAA
316457 CTATGTGATATTGAA
1 CTATGTGATATTGAA
316472 CTA
1 CTA
316475 CATGATTATA
Statistics
Matches: 92, Mismatches: 17, Indels: 30
0.66 0.12 0.22
Matches are distributed among these distances:
12 4 0.04
13 4 0.04
14 15 0.16
15 33 0.36
16 27 0.29
17 9 0.10
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (15 bp):
CTATGTGATATTGAA
Found at i:316394 original size:45 final size:45
Alignment explanation
Indices: 316335--316455 Score: 179
Period size: 45 Copynumber: 2.7 Consensus size: 45
316325 TATATTACAT
* *
316335 GCTATATGATATTGACCTATGTGATTATATGAACATATGATATAA
1 GCTATGTGACATTGACCTATGTGATTATATGAACATATGATATAA
*
316380 GCTATGTGACATTGACCTATGTGATTATATGAACATGTGATATAA
1 GCTATGTGACATTGACCTATGTGATTATATGAACATATGATATAA
** * *
316425 GCTATGTGACAAGGATCTATGTTATTATATG
1 GCTATGTGACATTGACCTATGTGATTATATG
316456 TCTATGTGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 69 1.00
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.37
Consensus pattern (45 bp):
GCTATGTGACATTGACCTATGTGATTATATGAACATATGATATAA
Found at i:316419 original size:16 final size:17
Alignment explanation
Indices: 316351--316495 Score: 70
Period size: 15 Copynumber: 9.5 Consensus size: 17
316341 TGATATTGAC
316351 CTATGTGATTATATGAA
1 CTATGTGATTATATGAA
* *
316368 C-ATATGA-TATA--AG
1 CTATGTGATTATATGAA
* *
316381 CTATGTGA-CAT-TGAC
1 CTATGTGATTATATGAA
316396 CTATGTGATTATATGAA
1 CTATGTGATTATATGAA
*
316413 C-ATGTGA-TATA--AG
1 CTATGTGATTATATGAA
* * *
316426 CTATGTGA-CA-AGGAT
1 CTATGTGATTATATGAA
* *
316441 CTATGTTATTATATG-T
1 CTATGTGATTATATGAA
316457 CTATGTGA-TAT-TGAA
1 CTATGTGATTATATGAA
**
316472 CTACATGATTATATGAA
1 CTATGTGATTATATGAA
316489 -TATGTGA
1 CTATGTGA
316496 ACTATATAAA
Statistics
Matches: 96, Mismatches: 19, Indels: 27
0.68 0.13 0.19
Matches are distributed among these distances:
13 5 0.05
14 16 0.17
15 34 0.35
16 30 0.31
17 11 0.11
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (17 bp):
CTATGTGATTATATGAA
Found at i:316645 original size:23 final size:23
Alignment explanation
Indices: 316589--316648 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
316579 GGTCCTTTGG
* * *
316589 GATAATTCTACGTGGTCATTCGG
1 GATATTTCTATGTGGTCATTCGA
* *
316612 GACATATCTATGTGGTCATTCGA
1 GATATTTCTATGTGGTCATTCGA
316635 GATATTTCTATGTG
1 GATATTTCTATGTG
316649 TCACTTTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.38
Consensus pattern (23 bp):
GATATTTCTATGTGGTCATTCGA
Found at i:318301 original size:13 final size:14
Alignment explanation
Indices: 318278--318306 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
318268 TTATTCCTTT
318278 TTTTCCTTCATTTA
1 TTTTCCTTCATTTA
318292 TTTT-CTTCATTTA
1 TTTTCCTTCATTTA
318305 TT
1 TT
318307 ATTATACTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTCCTTCATTTA
Found at i:319277 original size:28 final size:28
Alignment explanation
Indices: 319245--319311 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
319235 TATCAATAAT
319245 CATATATTTAACTAAACTCAAATCCATA
1 CATATATTTAACTAAACTCAAATCCATA
*
319273 CATATATTTAACTAAACTCAAATTCATA
1 CATATATTTAACTAAACTCAAATCCATA
319301 CATATATTTAA
1 CATATATTTAA
319312 AACATTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (28 bp):
CATATATTTAACTAAACTCAAATCCATA
Found at i:324046 original size:32 final size:35
Alignment explanation
Indices: 323975--324049 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 35
323965 TATAATTTAG
* *
323975 ATTTATAAATTTTATGTTTATTTTATAGATGAATT
1 ATTTTTAAATTTTATGTTTATTTAATAGATGAATT
* *
324010 -TTTTTAAGTTTTATGTTT-TTTAAT-G-TGGATT
1 ATTTTTAAATTTTATGTTTATTTAATAGATGAATT
324041 ATTTTTAAA
1 ATTTTTAAA
324050 AAATAATATA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
31 5 0.15
32 8 0.24
33 5 0.15
34 16 0.47
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.60
Consensus pattern (35 bp):
ATTTTTAAATTTTATGTTTATTTAATAGATGAATT
Found at i:324067 original size:16 final size:16
Alignment explanation
Indices: 324048--324078 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
324038 ATTATTTTTA
*
324048 AAAAATAATATAAATT
1 AAAAATAAAATAAATT
324064 AAAAATAAAATAAAT
1 AAAAATAAAATAAAT
324079 ATTAAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:326888 original size:2 final size:2
Alignment explanation
Indices: 326881--326920 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
326871 ATTATTATTA
326881 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
326921 TATGTGACTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326951 original size:17 final size:17
Alignment explanation
Indices: 326929--326962 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
326919 ATTATGTGAC
326929 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
326946 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
326963 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:326984 original size:16 final size:15
Alignment explanation
Indices: 326959--327007 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
326949 TATAAAAGTA
326959 ATAACAAAATAATATT
1 ATAA-AAAATAATATT
326975 ATAAATAAATAATATT
1 ATAAA-AAATAATATT
326991 -TAAAAGCAATAATATT
1 ATAAAA--AATAATATT
327007 A
1 A
327008 AATTGCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.03
15 5 0.17
16 23 0.79
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
ATAAAAAATAATATT
Found at i:327015 original size:16 final size:15
Alignment explanation
Indices: 326966--327031 Score: 53
Period size: 16 Copynumber: 4.2 Consensus size: 15
326956 GTAATAACAA
**
326966 AATAATATTATAAATA
1 AATAATATTA-AAAGC
326982 AATAATATTTAAAAGC
1 AATAATA-TTAAAAGC
*
326998 AATAATATTAAATTGC
1 AATAATATTAAA-AGC
*
327014 AA-AATATATAAAAAC
1 AATAATAT-TAAAAGC
327029 AAT
1 AAT
327032 CAGGATCAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 13 0.32
16 25 0.61
17 3 0.07
ACGTcount: A:0.61, C:0.05, G:0.03, T:0.32
Consensus pattern (15 bp):
AATAATATTAAAAGC
Found at i:328385 original size:3 final size:3
Alignment explanation
Indices: 328360--328444 Score: 84
Period size: 3 Copynumber: 29.0 Consensus size: 3
328350 GTTGTATCTG
* * * *
328360 TAA TAA -AA TAA T-A TAT TAT TAA TAA TAA TAA TAT TAA TAA TAA AAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
328406 TAA TAG TAA TAA AAA TAA AAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
328445 AAACCTAAAT
Statistics
Matches: 66, Mismatches: 14, Indels: 4
0.79 0.17 0.05
Matches are distributed among these distances:
2 4 0.06
3 62 0.94
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:328396 original size:15 final size:15
Alignment explanation
Indices: 328379--328444 Score: 96
Period size: 15 Copynumber: 4.4 Consensus size: 15
328369 AATATATTAT
* *
328379 TAATAATAATAATAT
1 TAATAATAAAAATAA
328394 TAATAATAAAAATAA
1 TAATAATAAAAATAA
*
328409 TAGTAATAAAAATAA
1 TAATAATAAAAATAA
*
328424 AAATAATAAAAATAA
1 TAATAATAAAAATAA
328439 TAATAA
1 TAATAA
328445 AAACCTAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
TAATAATAAAAATAA
Found at i:328688 original size:79 final size:79
Alignment explanation
Indices: 328598--328777 Score: 233
Period size: 79 Copynumber: 2.3 Consensus size: 79
328588 CTTTGGGATT
* ** * *
328598 AGTTCTTCTCATTATGAACTTTTCCACTGGGGATGATAATTTGTCTCCTTTTGTAAT-GTAAT-T
1 AGTTCTTCTCATTATGAACTTTT-CACTGGGGATGACAATTCATCTCCTTCTGTAATAG-AATCA
328661 TAGCAAAA-AGTT-AACA
64 T-GCAAAAGA-TTAAACA
*
328677 AGTTCTTCTCATTATGAACTCTTTCACTGGGGATGACAATTCATCTCCTTCTGTGATAGAATCAT
1 AGTTCTTCTCATTATGAACT-TTTCACTGGGGATGACAATTCATCTCCTTCTGTAATAGAATCAT
328742 GCAAAAGATTAAACA
65 GCAAAAGATTAAACA
328757 AGTTCTTCTCATTATGAACTT
1 AGTTCTTCTCATTATGAACTT
328778 CTTCTTCCTT
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 60 0.67
80 30 0.33
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.38
Consensus pattern (79 bp):
AGTTCTTCTCATTATGAACTTTTCACTGGGGATGACAATTCATCTCCTTCTGTAATAGAATCATG
CAAAAGATTAAACA
Found at i:328879 original size:73 final size:73
Alignment explanation
Indices: 328797--328962 Score: 251
Period size: 73 Copynumber: 2.3 Consensus size: 73
328787 TCTTCAGATG
* * * * * *
328797 AGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAAAAA
1 AGTTCTTCTCATTATGAACTCGCCCTGGAAAAGCTGATCCATCGAATGATAAATTCAAGCAAAAA
328862 GTTGAACA
66 GTTGAACA
* * *
328870 AGTTCTTCTCATTATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGCCCTGGAAAAGCTGATCCATCGAATGATAAATTCAAGCAAAAA
328935 GTTGAACA
66 GTTGAACA
328943 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
328963 TCTTCTTCCT
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 84 1.00
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCGCCCTGGAAAAGCTGATCCATCGAATGATAAATTCAAGCAAAAA
GTTGAACA
Found at i:328988 original size:113 final size:113
Alignment explanation
Indices: 328870--329597 Score: 1287
Period size: 113 Copynumber: 6.5 Consensus size: 113
328860 AAGTTGAACA
* * *
328870 AGTTCTTCTCATTATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATAAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
328935 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
328983 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGTGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
329048 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
329096 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCAAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
*
329161 GTTGAACAAGTTCTTCTCATTATAAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
329209 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTTAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
329274 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
329322 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
329387 GTTGAACAAGTTCTTCTCATTATGAA----------CTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
329425 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
* * *
329490 GTTGAACAAGTTCTTCTCATTATGAAATTCTTGTTCCTTCTTCAGATT
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
329538 TGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGC
1 AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGC
329598 TTTGCTAAAA
Statistics
Matches: 592, Mismatches: 13, Indels: 20
0.95 0.02 0.03
Matches are distributed among these distances:
103 103 0.17
113 489 0.83
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCGAAAA
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:329489 original size:103 final size:105
Alignment explanation
Indices: 329310--329597 Score: 472
Period size: 103 Copynumber: 2.7 Consensus size: 105
329300 CTTCTTCTTC
329310 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAA
329375 TTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATG-AA-
66 TTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAAT
329413 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAA
1 CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAA
329478 TTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAATTCTTGTT
66 TTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAA-------T
**
329525 CCTTCTTCAGATTTGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGA
1 -CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGA
329590 ATTCAAGC
65 ATTCAAGC
329598 TTTGCTAAAA
Statistics
Matches: 173, Mismatches: 2, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
103 101 0.58
104 2 0.01
113 70 0.40
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (105 bp):
CTTCTTCAGATGAGTTCTTCTCATTATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAA
TTCAAGCGAAAAGTTGAACAAGTTCTTCTCATTATGAAAT
Found at i:330020 original size:22 final size:22
Alignment explanation
Indices: 329995--330049 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
329985 GATAAAGCTT
*
329995 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
330017 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
330039 TCATCTTTGAA
1 TCATCTTTGAA
330050 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:330498 original size:54 final size:54
Alignment explanation
Indices: 330416--330527 Score: 197
Period size: 54 Copynumber: 2.1 Consensus size: 54
330406 AGAATAGCAG
*
330416 GTTCGTAAAACATTTGACAGCACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* *
330470 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTTTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
330524 GTTC
1 GTTC
330528 TCAATCATTG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:331611 original size:12 final size:12
Alignment explanation
Indices: 331594--331618 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
331584 TCAACATTAC
331594 TTCTTGTTGAGA
1 TTCTTGTTGAGA
331606 TTCTTGTTGAGA
1 TTCTTGTTGAGA
331618 T
1 T
331619 GAGCCTCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (12 bp):
TTCTTGTTGAGA
Found at i:334835 original size:8 final size:8
Alignment explanation
Indices: 334822--334893 Score: 67
Period size: 8 Copynumber: 8.8 Consensus size: 8
334812 CTTGATTCAA
334822 TTTTTTCT
1 TTTTTTCT
334830 TTTTTTCCT
1 TTTTTT-CT
334839 TTTTGTT-T
1 TTTT-TTCT
334847 TTTTGTT-T
1 TTTT-TTCT
*
334855 TTTTTTAT
1 TTTTTTCT
*
334863 TTCTTTCCT
1 TT-TTTTCT
*
334872 TTTTTCCT
1 TTTTTTCT
334880 TTTTTTCT
1 TTTTTTCT
334888 TTTTTT
1 TTTTTT
334894 TCCTTTCTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
7 2 0.04
8 41 0.72
9 12 0.21
10 2 0.04
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.83
Consensus pattern (8 bp):
TTTTTTCT
Found at i:340534 original size:2 final size:2
Alignment explanation
Indices: 340527--340554 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
340517 TTATTATTTA
340527 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
340555 TTATGTGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:340584 original size:17 final size:17
Alignment explanation
Indices: 340564--340597 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
340554 TTTATGTGAC
340564 TAATATGAAAA-TAATAA
1 TAATAT-AAAAGTAATAA
340581 TAATATAAAAGTAATAA
1 TAATATAAAAGTAATAA
340598 CAAAATAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
TAATATAAAAGTAATAA
Found at i:340619 original size:16 final size:16
Alignment explanation
Indices: 340600--340635 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
340590 AGTAATAACA
340600 AAATAATA-TTATAAAT
1 AAATAATATTTA-AAAT
340616 AAATAATATTTAAAAT
1 AAATAATATTTAAAAT
340632 AAAT
1 AAAT
340636 TTAAAAGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.84
17 3 0.16
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATAATATTTAAAAT
Found at i:341880 original size:3 final size:3
Alignment explanation
Indices: 341866--341960 Score: 113
Period size: 3 Copynumber: 32.0 Consensus size: 3
341856 GTTGTATCTG
* *
341866 TAA TAA -AA TAA TAA TAT TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
341913 AAA TAA TAA TAA TAG TAA TAA AAA TAA -AA TTAA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA
341958 TAA
1 TAA
341961 AAACCCAAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
2 4 0.05
3 71 0.92
4 2 0.03
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:342591 original size:21 final size:21
Alignment explanation
Indices: 342562--342609 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
342552 CCTAATATTG
*
342562 CAATATCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
342583 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
342604 TAATGT
1 CAATGT
342610 TTGAAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:347230 original size:21 final size:21
Alignment explanation
Indices: 347205--347246 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
347195 CCTAATATTG
347205 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
347226 CAATGTTAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
347247 TAATATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.43, C:0.12, G:0.19, T:0.26
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:359114 original size:14 final size:14
Alignment explanation
Indices: 359095--359122 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
359085 TTAAGCTCGT
359095 GAGTGATTTTAGAA
1 GAGTGATTTTAGAA
359109 GAGTGATTTTAGAA
1 GAGTGATTTTAGAA
359123 ACTGAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.29, T:0.36
Consensus pattern (14 bp):
GAGTGATTTTAGAA
Found at i:359866 original size:21 final size:21
Alignment explanation
Indices: 359842--359908 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
359832 TCATTCCTCG
359842 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
359863 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
359884 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
359905 AGAG
1 AGAG
359909 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:359869 original size:42 final size:42
Alignment explanation
Indices: 359815--359908 Score: 102
Period size: 42 Copynumber: 2.2 Consensus size: 42
359805 CTACTCCTAT
* *
359815 CGTTGAAGAGGCCCCTATCATTCCTCG-AGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCACTATCA-TCCTCGAAGAGGT-CCCTCCCAC
* * *
359857 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
*
359899 CATTCAAGAG
1 CGTTCAAGAG
359909 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
41 4 0.09
42 38 0.86
43 2 0.05
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCTCGAAGAGGTCCCTCCCAC
Found at i:361275 original size:14 final size:14
Alignment explanation
Indices: 361256--361291 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
361246 ATTGTTTAAT
361256 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
361270 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
361284 TGATTTGT
1 TGATTTGT
361292 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:361515 original size:33 final size:32
Alignment explanation
Indices: 361473--361665 Score: 273
Period size: 33 Copynumber: 5.9 Consensus size: 32
361463 AATTAATTCG
*
361473 CGTTGCGATTTTCATTTCGCGTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
*
361506 CGTTGCGATTTTCATTTCGCATTGCGAAATT-CG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
361539 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
361572 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
361605 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
361638 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
361666 AGTAATTTCC
Statistics
Matches: 145, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
31 6 0.04
33 133 0.92
35 6 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:361545 original size:66 final size:66
Alignment explanation
Indices: 361467--361664 Score: 369
Period size: 66 Copynumber: 3.0 Consensus size: 66
361457 ACGCGAAATT
*
361467 AATTCGCGTTGCGATTTTCATTTCGCGTTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
361532 A
66 A
361533 AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
1 AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
361598 A
66 A
* *
361599 AATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCG
1 AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
361664 A
66 A
361665 TAGTAATTTC
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 129 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCG
A
Found at i:363974 original size:12 final size:12
Alignment explanation
Indices: 363957--363981 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
363947 TCTTCGGGGA
363957 CTTTTTCTTCTT
1 CTTTTTCTTCTT
363969 CTTTTTCTTCTT
1 CTTTTTCTTCTT
363981 C
1 C
363982 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:364190 original size:24 final size:24
Alignment explanation
Indices: 364156--364209 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
364146 CTGAAACATC
* *
364156 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
364180 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
364204 ATCAAA
1 ATCAAA
364210 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:365336 original size:19 final size:19
Alignment explanation
Indices: 365312--365359 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
365302 AAAATTGCAA
365312 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
365331 TGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCAT
365350 TGCGATTTTC
1 TGCGATTTTC
365360 TCGTTGCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCAT
Found at i:367413 original size:20 final size:19
Alignment explanation
Indices: 367378--367444 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
367368 GAAACTTAAA
367378 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
367397 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
367417 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
367436 ATCGCAACG
1 ATCGCAACG
367445 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:367452 original size:14 final size:14
Alignment explanation
Indices: 367433--367490 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
367423 ATGCGAAATG
367433 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
367447 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
*
367463 ATGAAATCGCAATGAC
1 A--AAATCGCAACGAC
367479 AAAATCGCAACG
1 AAAATCGCAACG
367491 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 7 0.19
18 9 0.25
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:367480 original size:32 final size:33
Alignment explanation
Indices: 367417--367495 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
367407 GGAAATGGCT
*
367417 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
367450 ATCGCAACGCGAAATG-AAATCGCAATGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
367482 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
367496 CACAAATCGC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 29 0.66
33 15 0.34
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:367524 original size:19 final size:16
Alignment explanation
Indices: 367502--367597 Score: 65
Period size: 19 Copynumber: 5.7 Consensus size: 16
367492 GAAACACAAA
367502 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTT-ATT
*
367521 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
367537 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTT-ATT
*
367553 TCGCGTTGCGATTT-TG
1 TCGC-TTGCGATTTATT
367569 TCG-TTGCGATTTTTATT
1 TCGCTTGCGA--TTTATT
367586 TCGCATTGCGAT
1 TCGC-TTGCGAT
367598 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 15 0.24
16 15 0.24
17 5 0.08
18 12 0.19
19 16 0.25
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (16 bp):
TCGCTTGCGATTTATT
Found at i:367543 original size:14 final size:14
Alignment explanation
Indices: 367524--367581 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
367514 TTTCATTTCG
367524 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
367538 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
367554 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
367570 CGTTGCGATTTT
1 CGTTGCGATTTT
367582 TATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:367554 original size:32 final size:33
Alignment explanation
Indices: 367507--367597 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
367497 ACAAATCGCA
367507 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
367540 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
* *
367572 TTGCGATTTTTATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
367598 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 32 0.58
33 23 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:367605 original size:19 final size:20
Alignment explanation
Indices: 367583--367625 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
367573 TGCGATTTTT
367583 ATTT-CGCATTGCGATAGCC
1 ATTTCCGCATTGCGATAGCC
* *
367602 ATTTCCGCGTTGCGATAGTC
1 ATTTCCGCATTGCGATAGCC
367622 ATTT
1 ATTT
367626 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (20 bp):
ATTTCCGCATTGCGATAGCC
Found at i:367616 original size:20 final size:20
Alignment explanation
Indices: 367591--367636 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
367581 TTATTTCGCA
367591 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTTCCGCG
* * *
367611 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGCCATTTCCGCG
367631 TTGCGA
1 TTGCGA
367637 AAGTAAACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.15, C:0.22, G:0.26, T:0.37
Consensus pattern (20 bp):
TTGCGATAGCCATTTCCGCG
Found at i:368135 original size:18 final size:18
Alignment explanation
Indices: 368109--368153 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
368099 GTCGATCAGA
*
368109 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
368127 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
368145 TGATGGCTC
1 TGATGGCTC
368154 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:369498 original size:20 final size:20
Alignment explanation
Indices: 369473--369510 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
369463 AATAGTTTCT
369473 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
369493 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
369511 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:369799 original size:22 final size:22
Alignment explanation
Indices: 369774--369817 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
369764 GATTTAGATA
*
369774 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
*
369796 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGCCAGAGATGGG
369818 TGAGAGAGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.16, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATGGG
Found at i:370030 original size:20 final size:20
Alignment explanation
Indices: 370005--370098 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
369995 GATTATGTAT
370005 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
370025 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
370045 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
370066 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
370086 TATCGCATTGCGA
1 TATCGCGTTGCGA
370099 TTTTCCCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:370070 original size:41 final size:41
Alignment explanation
Indices: 370025--370102 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
370015 CGAAAGTCAG
* * *
370025 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
370066 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
370103 CCCAATTCAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:370099 original size:20 final size:20
Alignment explanation
Indices: 369985--370099 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
369975 CGCTTTGAAA
*
369985 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
370006 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
370026 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
370046 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
370067 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
370087 ATCGCATTGCGAT
1 ATCGCATTGCGAT
370100 TTTCCCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:370118 original size:41 final size:41
Alignment explanation
Indices: 370088--370183 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 41
370078 ATAGTCAGTA
* * *
370088 TCGCATTGCGATTTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
* *
370129 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
370170 TCGCATTGCGAATT
1 TCGCATTGCGAATT
370184 GGGAAAATCG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCACGTTGCGATTCACGTAT
Found at i:370119 original size:21 final size:21
Alignment explanation
Indices: 370093--370163 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
370083 CAGTATCGCA
370093 TTGCGATTTTCCCAATTCACG
1 TTGCGATTTTCCCAATTCACG
* ** * *
370114 TTGCGA-TTTACTTATTCGCA
1 TTGCGATTTTCCCAATTCACG
*
370134 TTGCGAATTTCCCAATTCACG
1 TTGCGATTTTCCCAATTCACG
370155 TTGCGATTT
1 TTGCGATTT
370164 ACTTATTCGC
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
20 15 0.39
21 23 0.61
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (21 bp):
TTGCGATTTTCCCAATTCACG
Found at i:370137 original size:20 final size:20
Alignment explanation
Indices: 370114--370180 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
370104 CCAATTCACG
370114 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
* ** * *
370134 TTGCGAATTTCCCAATTCACG
1 TTGCG-ATTTACTTATTCGCA
370155 TTGCGATTTACTTATTCGCA
1 TTGCGATTTACTTATTCGCA
370175 TTGCGA
1 TTGCGA
370181 ATTGGGAAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.40
Consensus pattern (20 bp):
TTGCGATTTACTTATTCGCA
Found at i:370293 original size:28 final size:28
Alignment explanation
Indices: 370253--370321 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
370243 AAAATGCAAC
370253 GCGAATTTGCGATAATGGAGATCGCGTT
1 GCGAATTTGCGATAATGGAGATCGCGTT
370281 GCGAATTTGCGATAATGGAGATCGCGTT
1 GCGAATTTGCGATAATGGAGATCGCGTT
*
370309 GCGAATTAGCGAT
1 GCGAATTTGCGAT
370322 CGCATTGCGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.28
Consensus pattern (28 bp):
GCGAATTTGCGATAATGGAGATCGCGTT
Found at i:370669 original size:21 final size:20
Alignment explanation
Indices: 370645--370739 Score: 79
Period size: 19 Copynumber: 4.7 Consensus size: 20
370635 TCGACTATCG
* *
370645 CGTTGCGATTTATTACAAATT
1 CGTTGCGA-TTAGTCCAAATT
*
370666 CGTTGCGA-TAGTCCAAGTT
1 CGTTGCGATTAGTCCAAATT
* *
370685 CGTTGCGA-TAGTCGAAGTT
1 CGTTGCGATTAGTCCAAATT
*
370704 CGCGTTGCGATTTATTCCAAATT
1 --CGTTGCGA-TTAGTCCAAATT
370727 CGTTGCGA-TAGTC
1 CGTTGCGATTAGTC
370740 GAAGTTCGCG
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
19 30 0.48
21 24 0.39
23 8 0.13
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTAGTCCAAATT
Found at i:370733 original size:42 final size:42
Alignment explanation
Indices: 370677--370766 Score: 162
Period size: 42 Copynumber: 2.1 Consensus size: 42
370667 GTTGCGATAG
*
370677 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
370719 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
1 TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
*
370761 TTCAAA
1 TCCAAA
370767 ATCGCAACGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.22, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
TCCAAATTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTAT
Found at i:370756 original size:21 final size:19
Alignment explanation
Indices: 370664--370747 Score: 96
Period size: 19 Copynumber: 4.2 Consensus size: 19
370654 TTATTACAAA
370664 TTCGTTGCGATAGTCCAAG
1 TTCGTTGCGATAGTCCAAG
*
370683 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
* *
370702 TTCGCGTTGCGATTTATTCCAAA
1 TT--CGTTGCGA--TAGTCCAAG
*
370725 TTCGTTGCGATAGTCGAAG
1 TTCGTTGCGATAGTCCAAG
370744 TTCG
1 TTCG
370748 CGTTGCGATT
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 30 0.56
21 16 0.30
23 8 0.15
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (19 bp):
TTCGTTGCGATAGTCCAAG
Found at i:370866 original size:6 final size:6
Alignment explanation
Indices: 370855--370879 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
370845 GACACGTATT
370855 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
370880 GAAGAGACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:373049 original size:21 final size:20
Alignment explanation
Indices: 373016--373062 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
373006 AGCGATGATG
*
373016 TTATTATTATTTAATAAAATA
1 TTATAATTATTT-ATAAAATA
* *
373037 TTATAATTGTTTATTAAATA
1 TTATAATTATTTATAAAATA
373057 TTATAA
1 TTATAA
373063 AATGTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTATAATTATTTATAAAATA
Found at i:373057 original size:20 final size:21
Alignment explanation
Indices: 373032--373072 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
373022 TTATTTAATA
*
373032 AAATATTAT-AATTGTTTATT
1 AAATATTATAAAATGTTTATT
373052 AAATATTATAAAATGTTTATT
1 AAATATTATAAAATGTTTATT
373073 TTATGATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
AAATATTATAAAATGTTTATT
Found at i:374083 original size:14 final size:14
Alignment explanation
Indices: 374056--374109 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
374046 ATTATACTAT
374056 TTAATTTAATTTAAA
1 TTAATTT-ATTTAAA
*
374071 TTAATTTATTTAAC
1 TTAATTTATTTAAA
* *
374085 TTCATTTATTT-AT
1 TTAATTTATTTAAA
374098 TTATATTTATTT
1 TTA-ATTTATTT
374110 CTTTATTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
13 3 0.09
14 24 0.71
15 7 0.21
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (14 bp):
TTAATTTATTTAAA
Found at i:374097 original size:18 final size:18
Alignment explanation
Indices: 374074--374120 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
374064 ATTTAAATTA
374074 ATTTATTTA-ACTTCATTT
1 ATTTATTTATA-TTCATTT
*
374092 ATTTATTTATATTTATTT
1 ATTTATTTATATTCATTT
*
374110 CTTTATTTATA
1 ATTTATTTATA
374121 ATTTTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (18 bp):
ATTTATTTATATTCATTT
Found at i:375544 original size:20 final size:20
Alignment explanation
Indices: 375521--375569 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
375511 ATTTAAAGAT
375521 TTATAAATAACAA-TAAATTA
1 TTATAAA-AACAAGTAAATTA
* *
375541 TTATAAAAGCAAGTGAATTA
1 TTATAAAAACAAGTAAATTA
375561 TTATAAAAA
1 TTATAAAAA
375570 AATTAAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.33
Consensus pattern (20 bp):
TTATAAAAACAAGTAAATTA
Found at i:377539 original size:20 final size:19
Alignment explanation
Indices: 377495--377553 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
377485 AACCGATATT
*
377495 CTCTTCTTCTCTTTTCCTT-
1 CTCTT-TTCTCTTTTTCTTC
*
377514 CGCTTTTCTCTTATTTCTTC
1 CTCTTTTCTCTT-TTTCTTC
377534 CTCTTTTCTCTTCTTTCTTC
1 CTCTTTTCTCTT-TTTCTTC
377554 TCCTCTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.21
19 9 0.26
20 18 0.53
ACGTcount: A:0.02, C:0.34, G:0.02, T:0.63
Consensus pattern (19 bp):
CTCTTTTCTCTTTTTCTTC
Found at i:377562 original size:20 final size:18
Alignment explanation
Indices: 377499--377575 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 18
377489 GATATTCTCT
* *
377499 TCTTCTCTTTTCCTTCGC
1 TCTTCTCTTTTTCTTCCC
*
377517 TTTTCTCTTATTTCTTCCTC
1 TCTTCTCTT-TTTCTTCC-C
*
377537 TTTTCTCTTCTTTCTTCTCC
1 TCTTCTCTT-TTTCTTC-CC
*
377557 TCTTCTTTTTTTCATTCCC
1 TCTTCTCTTTTTC-TTCCC
377576 GGCGTAATCA
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
18 8 0.16
19 12 0.24
20 28 0.57
21 1 0.02
ACGTcount: A:0.03, C:0.34, G:0.01, T:0.62
Consensus pattern (18 bp):
TCTTCTCTTTTTCTTCCC
Found at i:378028 original size:22 final size:20
Alignment explanation
Indices: 377991--378030 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
377981 ATGGAGAATA
*
377991 AAATATTAAATTTAATTTAT
1 AAATATTAAATGTAATTTAT
378011 AAATATATAAATCGTAATTT
1 AAATAT-TAAAT-GTAATTT
378031 TTTAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 5 0.29
22 6 0.35
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (20 bp):
AAATATTAAATGTAATTTAT
Found at i:378982 original size:60 final size:59
Alignment explanation
Indices: 378890--379001 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 59
378880 CGAGTGATAT
**
378890 TTTTATAATTTCAATAGTCGAAATACTCAATAAAGTAACATTCTATAATCGAATGATCA
1 TTTTATAATTTCAATAGTCGAAATACTCAATAAAACAACATTCTATAATCGAATGATCA
* * * * *
378949 TTTTATAATTTTTAATAGTCGGAAA-ATTTAATAAAACAATATTTTATAATCGA
1 TTTTATAA-TTTCAATAGTC-GAAATACTCAATAAAACAACATTCTATAATCGA
379002 TAAATCATTT
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
59 8 0.18
60 32 0.73
61 4 0.09
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.39
Consensus pattern (59 bp):
TTTTATAATTTCAATAGTCGAAATACTCAATAAAACAACATTCTATAATCGAATGATCA
Found at i:380067 original size:14 final size:14
Alignment explanation
Indices: 380048--380097 Score: 54
Period size: 14 Copynumber: 3.9 Consensus size: 14
380038 ATTGGGCTAA
380048 ACATAAATGAACAC
1 ACATAAATGAACAC
*
380062 ACATAAACG---A-
1 ACATAAATGAACAC
*
380072 ACATAAATGAACGC
1 ACATAAATGAACAC
380086 ACATAAATGAAC
1 ACATAAATGAAC
380098 GAACATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
10 8 0.28
11 1 0.03
14 20 0.69
ACGTcount: A:0.56, C:0.20, G:0.10, T:0.14
Consensus pattern (14 bp):
ACATAAATGAACAC
Found at i:380079 original size:24 final size:24
Alignment explanation
Indices: 380047--380097 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
380037 GATTGGGCTA
380047 AACATAAATGAACACACATAAACG
1 AACATAAATGAACACACATAAACG
* *
380071 AACATAAATGAACGCACATAAATG
1 AACATAAATGAACACACATAAACG
380095 AAC
1 AAC
380098 GAACATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.20, G:0.10, T:0.14
Consensus pattern (24 bp):
AACATAAATGAACACACATAAACG
Found at i:380098 original size:14 final size:14
Alignment explanation
Indices: 380067--380104 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
380057 AACACACATA
380067 AACGAACATAAATG
1 AACGAACATAAATG
*
380081 AACGCACATAAATG
1 AACGAACATAAATG
380095 AACGAACATA
1 AACGAACATA
380105 TTACCGAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.55, C:0.18, G:0.13, T:0.13
Consensus pattern (14 bp):
AACGAACATAAATG
Found at i:381015 original size:24 final size:24
Alignment explanation
Indices: 380979--381052 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
380969 TAATCATTCG
380979 ATGCAAAAAATATGATGTCTCTTA
1 ATGCAAAAAATATGATGTCTCTTA
*
381003 ATGCAAAAGATATGATGTCTCTTA
1 ATGCAAAAAATATGATGTCTCTTA
*
381027 ATGCAAAAAATATGATGTCACTTA
1 ATGCAAAAAATATGATGTCTCTTA
381051 AT
1 AT
381053 ACGCCATCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (24 bp):
ATGCAAAAAATATGATGTCTCTTA
Found at i:388142 original size:75 final size:76
Alignment explanation
Indices: 388056--388263 Score: 296
Period size: 75 Copynumber: 2.8 Consensus size: 76
388046 CCGTTGTACA
* * *
388056 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
** *
388120 CAAAACTGTTT
66 CAAAACCATTC
* *
388131 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
*
388195 CCAAACCATTC
66 CAAAACCATTC
*
388206 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCA-ATCTGGAATT
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATA-CTGGAATT
388264 TTTGGCTTTG
Statistics
Matches: 118, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
75 87 0.74
76 31 0.26
ACGTcount: A:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCATACTGGAATTCTCGGAG
CAAAACCATTC
Found at i:388872 original size:17 final size:17
Alignment explanation
Indices: 388852--388895 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
388842 TTCATAAATC
388852 CAAAATCCAACAATCCA
1 CAAAATCCAACAATCCA
*
388869 CAAAATCAAACAATCCA
1 CAAAATCCAACAATCCA
388886 -AAATATCCAA
1 CAAA-ATCCAA
388896 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (17 bp):
CAAAATCCAACAATCCA
Found at i:388887 original size:9 final size:8
Alignment explanation
Indices: 388847--388897 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
388837 AACTATTCAT
388847 AAATCC-A
1 AAATCCAA
388854 AAATCCAA
1 AAATCCAA
*
388862 CAATCCACA
1 AAATCCA-A
388871 AAAT-CAA
1 AAATCCAA
388878 ACAATCCAA
1 A-AATCCAA
388887 AATATCCAA
1 AA-ATCCAA
388896 AA
1 AA
388898 TGTTGAAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.22
8 13 0.35
9 16 0.43
ACGTcount: A:0.59, C:0.27, G:0.00, T:0.14
Consensus pattern (8 bp):
AAATCCAA
Found at i:390842 original size:21 final size:21
Alignment explanation
Indices: 390816--390901 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 21
390806 CAGAACCCCA
*
390816 GGGGGGTATCGATTCCCCTGC
1 GGGGGGAATCGATTCCCCTGC
* *
390837 GGGGGGAATCGGTTCCCCTTC
1 GGGGGGAATCGATTCCCCTGC
* *
390858 AAAGGGGGAATCGGTT-CCCT-C
1 --GGGGGGAATCGATTCCCCTGC
*
390879 AGGGGGGGATCGATTCCCTCTGC
1 -GGGGGGAATCGATTCCC-CTGC
390902 ACCAAAATGC
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
20 12 0.23
21 21 0.40
22 6 0.11
23 14 0.26
ACGTcount: A:0.14, C:0.27, G:0.37, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGC
Found at i:396871 original size:76 final size:76
Alignment explanation
Indices: 396668--396873 Score: 292
Period size: 75 Copynumber: 2.7 Consensus size: 76
396658 CCGTTGTACA
* * * *
396668 AGGGGGGAATCGGTACCCCCT-TGGGGGGGATCGGTTCCCTCCGAGC-ATACTGGAATTCTCGGA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAAT-CTGGAAATCTCGGA
** *
396731 GCAAAACTGTTT
65 GCAAAACCATTC
*
396743 AGGGGGGAATCGGTTCCTCCTAT-GGGGGAATCGGTTCCCTCCGAGCATTCTGGAAATCTCGGAG
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAG
*
396807 CCAAACCATTC
66 CAAAACCATTC
*
396818 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCTGAGCAATCTGGAA
1 AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAA
396874 TTTTTTGGCT
Statistics
Matches: 117, Mismatches: 11, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
75 85 0.73
76 32 0.27
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.23
Consensus pattern (76 bp):
AGGGGGGAATCGGTTCCTCCTATGGGGGGAATCGGTTCCCTCCGAGCAATCTGGAAATCTCGGAG
CAAAACCATTC
Found at i:403772 original size:19 final size:19
Alignment explanation
Indices: 403748--403796 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
403738 AGATTTTATT
403748 ATTATTTTTATAATATAAA
1 ATTATTTTTATAATATAAA
* * * *
403767 ATTATTTATATTATATTAT
1 ATTATTTTTATAATATAAA
*
403786 ATTATATTTAT
1 ATTATTTTTAT
403797 TTTATATTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
ATTATTTTTATAATATAAA
Found at i:403780 original size:5 final size:5
Alignment explanation
Indices: 403767--403804 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
403757 ATAATATAAA
*
403767 ATTAT -TTAT ATTAT ATTAT ATTAT ATTTAT TTTAT ATT
1 ATTAT ATTAT ATTAT ATTAT ATTAT A-TTAT ATTAT ATT
403805 TAATTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (5 bp):
ATTAT
Found at i:403811 original size:10 final size:11
Alignment explanation
Indices: 403769--403811 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
403759 AATATAAAAT
403769 TATTTATATTA
1 TATTTATATTA
403780 TA-TTATATTA
1 TATTTATATTA
*
403790 TATTTATTTTA
1 TATTTATATTA
403801 TATTTA-ATTA
1 TATTTATATTA
403811 T
1 T
403812 TTGAACAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
10 14 0.48
11 15 0.52
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATATTA
Found at i:403941 original size:17 final size:18
Alignment explanation
Indices: 403919--403956 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
403909 ACAATATGAA
403919 ATTGTG-TTATTTAAATT
1 ATTGTGATTATTTAAATT
*
403936 ATTGTGATTTTTTAAATT
1 ATTGTGATTATTTAAATT
403954 ATT
1 ATT
403957 TTAGATTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.29, C:0.00, G:0.11, T:0.61
Consensus pattern (18 bp):
ATTGTGATTATTTAAATT
Found at i:406004 original size:7 final size:7
Alignment explanation
Indices: 405992--406027 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
405982 AAATACTGTA
405992 TGAATAG
1 TGAATAG
405999 TGAATAG
1 TGAATAG
*
406006 TGAATAA
1 TGAATAG
*
406013 TGAACAG
1 TGAATAG
406020 TGAATAG
1 TGAATAG
406027 T
1 T
406028 ACGATGAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (7 bp):
TGAATAG
Found at i:406562 original size:24 final size:23
Alignment explanation
Indices: 406517--406562 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
406507 AAACCATATA
*
406517 ACATTTCATATAATAAAATGCAT
1 ACATTTCATATAACAAAATGCAT
* *
406540 ACATATTCATATACCAAATTGCA
1 ACAT-TTCATATAACAAAATGCA
406563 CTCACCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (23 bp):
ACATTTCATATAACAAAATGCAT
Found at i:419472 original size:22 final size:22
Alignment explanation
Indices: 419447--419488 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
419437 CAATTCATTT
419447 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
419469 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
419489 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:419831 original size:9 final size:9
Alignment explanation
Indices: 419817--419862 Score: 56
Period size: 9 Copynumber: 4.8 Consensus size: 9
419807 TATTTTTTTT
419817 CAAAAAAAA
1 CAAAAAAAA
419826 CAAAAAAAA
1 CAAAAAAAA
*
419835 GGCAAAAAAAGG
1 --CAAAAAAA-A
419847 CAAAAAAAA
1 CAAAAAAAA
419856 CAAAAAA
1 CAAAAAA
419863 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 16 0.50
10 8 0.25
11 8 0.25
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:419852 original size:11 final size:11
Alignment explanation
Indices: 419817--419855 Score: 57
Period size: 10 Copynumber: 3.8 Consensus size: 11
419807 TATTTTTTTT
419817 CAAAAAAAA--
1 CAAAAAAAAGG
419826 CAAAAAAAAGG
1 CAAAAAAAAGG
419837 C-AAAAAAAGG
1 CAAAAAAAAGG
419847 CAAAAAAAA
1 CAAAAAAAA
419856 CAAAAAAGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 9 0.33
10 10 0.37
11 8 0.30
ACGTcount: A:0.79, C:0.10, G:0.10, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGG
Found at i:424191 original size:22 final size:22
Alignment explanation
Indices: 424166--424207 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
424156 CAATTCATTT
424166 ATCTT-TTCTTTATATTGTTTTA
1 ATCTTATT-TTTATATTGTTTTA
*
424188 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATATTGTTT
424208 CCAGTACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATATTGTTTTA
Found at i:425056 original size:35 final size:34
Alignment explanation
Indices: 425015--425085 Score: 88
Period size: 35 Copynumber: 2.1 Consensus size: 34
425005 TAAACTAAAA
* * *
425015 AATAAGTCTATTGATCAAATGACATGACTTATTAT
1 AATAAGTCCATTCACCAAATGACATGACTTA-TAT
* *
425050 AATAAGTCCATTCACCAAGTGACATGGCTTATAT
1 AATAAGTCCATTCACCAAATGACATGACTTATAT
425084 AA
1 AA
425086 ATGGCATCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
34 5 0.16
35 26 0.84
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.32
Consensus pattern (34 bp):
AATAAGTCCATTCACCAAATGACATGACTTATAT
Found at i:427852 original size:16 final size:17
Alignment explanation
Indices: 427831--427863 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
427821 GTAGTTTCAT
427831 TCACATA-TACATGTAA
1 TCACATAGTACATGTAA
*
427847 TCACATAGTTCATGTAA
1 TCACATAGTACATGTAA
427864 ATTCTCATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.18, G:0.09, T:0.33
Consensus pattern (17 bp):
TCACATAGTACATGTAA
Found at i:429977 original size:19 final size:19
Alignment explanation
Indices: 429950--429997 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
429940 GTCATTAGTA
* *
429950 CATCAATGCGTAAGGAGTG
1 CATCGATGCATAAGGAGTG
429969 CATCGATGCATAAGGAGTG
1 CATCGATGCATAAGGAGTG
*
429988 CATTGATGCA
1 CATCGATGCA
429998 CCCGCTTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.29, T:0.23
Consensus pattern (19 bp):
CATCGATGCATAAGGAGTG
Found at i:430681 original size:18 final size:18
Alignment explanation
Indices: 430638--430698 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
430628 AGGGATTATC
430638 AGTGGTCCTTC-AGGACAT
1 AGTGGTCCTTCGA-GACAT
**
430656 AGAAGTCCTTCGAGACAT
1 AGTGGTCCTTCGAGACAT
* *
430674 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGAGACAT
430692 AGTGGTC
1 AGTGGTC
430699 ATCCGGGACA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
18 35 0.97
19 1 0.03
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGAGACAT
Found at i:430706 original size:18 final size:18
Alignment explanation
Indices: 430669--430708 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
430659 AGTCCTTCGA
* **
430669 GACATAGTGGTCCTTTGG
1 GACATAGTGGTCATCCGG
430687 GACATAGTGGTCATCCGG
1 GACATAGTGGTCATCCGG
430705 GACA
1 GACA
430709 AATATTCAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.33, T:0.25
Consensus pattern (18 bp):
GACATAGTGGTCATCCGG
Found at i:436325 original size:42 final size:42
Alignment explanation
Indices: 436253--436339 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 42
436243 CCCTACCAAG
* * *
436253 GACGAGAAGACCATTCATAAAGATGAGAAGACTC-TCAATAAA
1 GACGAGAAAACCATTCATAAAGATCAGAAGACCCTTC-ATAAA
436295 GACGAGAAAACCATTCATAAAGA-CATGAAGACCCTTCATAAA
1 GACGAGAAAACCATTCATAAAGATCA-GAAGACCCTTCATAAA
436337 GAC
1 GAC
436340 ATAAAGACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
41 1 0.03
42 37 0.93
43 2 0.05
ACGTcount: A:0.47, C:0.20, G:0.17, T:0.16
Consensus pattern (42 bp):
GACGAGAAAACCATTCATAAAGATCAGAAGACCCTTCATAAA
Found at i:436341 original size:21 final size:20
Alignment explanation
Indices: 436257--436340 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 20
436247 ACCAAGGACG
* *
436257 AGAAGACCATTCATAAAGATG
1 AGAAGACCCTTCATAAAGA-C
*
436278 AGAAGACTC-TCAATAAAGAC
1 AGAAGACCCTTC-ATAAAGAC
* *
436298 GAGAAAACCATTCATAAAGAC
1 -AGAAGACCCTTCATAAAGAC
436319 ATGAAGACCCTTCATAAAGAC
1 A-GAAGACCCTTCATAAAGAC
436340 A
1 A
436341 TAAAGACCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.06
21 46 0.90
22 2 0.04
ACGTcount: A:0.49, C:0.19, G:0.15, T:0.17
Consensus pattern (20 bp):
AGAAGACCCTTCATAAAGAC
Found at i:436346 original size:21 final size:21
Alignment explanation
Indices: 436290--436353 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
436280 AAGACTCTCA
* *
436290 ATAAAGACGAGAAA-ACCATTC
1 ATAAAGAC-ATAAAGACCCTTC
*
436311 ATAAAGACATGAAGACCCTTC
1 ATAAAGACATAAAGACCCTTC
436332 ATAAAGACATAAAGACCACTTC
1 ATAAAGACATAAAGACC-CTTC
436354 GCATTGGAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
20 3 0.08
21 30 0.81
22 4 0.11
ACGTcount: A:0.48, C:0.22, G:0.12, T:0.17
Consensus pattern (21 bp):
ATAAAGACATAAAGACCCTTC
Found at i:441936 original size:125 final size:125
Alignment explanation
Indices: 441709--441982 Score: 422
Period size: 125 Copynumber: 2.2 Consensus size: 125
441699 AAGTTAGGCT
* * * * *
441709 ATGTTGGGGCACGACTGAACCCACATTATGTTGAGATGACAACTTTCAGACCAAGGAGGCATGAA
1 ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGACAACATTAAGACCAAGGAGACATGAA
* *
441774 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACTAGTATAAGATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAAATA
* * * *
441834 ATGTGGGGGCACGATTGAACCCACATCGTATTGAGATGACAAGATTAAGACCAAGGAGACATGAA
1 ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGACAACATTAAGACCAAGGAGACATGAA
**
441899 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCTTGTACCAGTATAAAATA
66 GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAAATA
*
441959 AGGTTGGGGCACGACTGAACCCAC
1 ATGTTGGGGCACGACTGAACCCAC
441983 GTCAAGATGA
Statistics
Matches: 133, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
125 133 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (125 bp):
ATGTTGGGGCACGACTGAACCCACATCATATTGAGATGACAACATTAAGACCAAGGAGACATGAA
GAATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAAATA
Found at i:442027 original size:125 final size:124
Alignment explanation
Indices: 441711--442013 Score: 419
Period size: 125 Copynumber: 2.4 Consensus size: 124
441701 GTTAGGCTAT
* * ** *
441711 GTTGGGGCACGACTGAACCCACATTATGTTGAGATGACAACTTTCAGACCAAGGAGGCATGAAGA
1 GTTGGGGCACGACTGAACCCACATCA-GATGAGATGACAAGATTCAGACCAAGGAGACATGAAGA
* * *
441776 ATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACTAGTATAAGATAAT
65 ATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAAATAAG
* * *
441836 GTGGGGGCACGATTGAACCCACATC-GTATTGAGATGACAAGATTAAGACCAAGGAGACATGAAG
1 GTTGGGGCACGACTGAACCCACATCAG-A-TGAGATGACAAGATTCAGACCAAGGAGACATGAAG
**
441900 AATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCTTGTACCAGTATAAAATAAG
64 AATGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAAATAAG
* **
441961 GTTGGGGCACGACTGAACCCACGTCAAGATGAGAAAACAAGATTCAGACCAAG
1 GTTGGGGCACGACTGAACCCACATC-AGATGAGATGACAAGATTCAGACCAAG
442014 AAGTCATTGA
Statistics
Matches: 155, Mismatches: 19, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
123 1 0.01
125 152 0.98
126 1 0.01
127 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (124 bp):
GTTGGGGCACGACTGAACCCACATCAGATGAGATGACAAGATTCAGACCAAGGAGACATGAAGAA
TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAAATAAG
Found at i:442773 original size:34 final size:34
Alignment explanation
Indices: 442727--442792 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
442717 GGGCAAGTCA
* *
442727 ATCTTAAGCCTTCACTGAAAAGTAGTAAAGCACC
1 ATCTTAACCCTTCACCGAAAAGTAGTAAAGCACC
* *
442761 ATCTTAACCCTTCACCGAAGAGTAGTGAAGCA
1 ATCTTAACCCTTCACCGAAAAGTAGTAAAGCA
442793 AACTCATCTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (34 bp):
ATCTTAACCCTTCACCGAAAAGTAGTAAAGCACC
Found at i:443170 original size:214 final size:214
Alignment explanation
Indices: 442796--443453 Score: 946
Period size: 214 Copynumber: 3.1 Consensus size: 214
442786 TGAAGCAAAC
*
442796 TCATCTGTAAGCCTTTAGGGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGG
442861 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
* * *
442926 TAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCAT
131 GAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
**
442991 GATGCTTAGTTCCTTCGGG
196 GATGCTTAAATCCTTCGGG
* * * *
443010 TCATATGTAAGCCTTTAGAGCCAGATGATAAGTCCTTTGGGCCATCCGTAAAACCTTCAGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGG
443075 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
* * *
443140 GAATGTGATTTTCAAAATTTCAAAATTTATAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGTAT
131 GAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
443205 GATGCTTAAATCCTTCGGG
196 GATGCTTAAATCCTTCGGG
* * *
443224 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAGAA-CTTCGGGCAA
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAA-AACCTTCGGGTAG
* * * * *
443288 GATGTCTTT-ACATGAATTTGAAGAATGAGAAAGTAATGTTTTAAGAAAATGAAATTTTTGAGAA
65 GATGT-TTTCACATGAATTTGAA-AATGA-AAAATGATGTTTTAAGAAGATGGAATTTTTGAAAA
* * * * * * *
443352 -GTAAGAAGGTGATTTCCAATACTTCGCACTATATAAGTCCTTCGGGCCATCAGTAAGTCTTTCG
127 CG-AAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCG
* * *
443416 AGCATGATGATTAAGTCCTCCGGG
191 AGCATGATGCTTAAATCCTTCGGG
* *
443440 CCATC-CTAAGCCTT
1 TCATCTGTAAGCCTT
443454 CACCGAAGAG
Statistics
Matches: 399, Mismatches: 40, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
214 273 0.68
215 19 0.05
216 107 0.27
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (214 bp):
TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
GAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGCTTAAATCCTTCGGG
Found at i:443487 original size:36 final size:36
Alignment explanation
Indices: 443440--443511 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
443430 GTCCTCCGGG
443440 CCATCCTAAGCCTTCACCGAAGAGTAGTAAAGCAAA
1 CCATCCTAAGCCTTCACCGAAGAGTAGTAAAGCAAA
* *
443476 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAA
1 CCATCCTAAGCCTTCACCGAAGAGTAGTAAAGCAAA
443512 TCGATCTCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (36 bp):
CCATCCTAAGCCTTCACCGAAGAGTAGTAAAGCAAA
Found at i:448638 original size:19 final size:19
Alignment explanation
Indices: 448614--448682 Score: 120
Period size: 19 Copynumber: 3.6 Consensus size: 19
448604 ATGCCATTAT
*
448614 TGCATCGATGCGTAAGGAG
1 TGCATCGATGCATAAGGAG
*
448633 TGCATCAATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
448652 TGCATCGATGCATAAGGAG
1 TGCATCGATGCATAAGGAG
448671 TGCATCGATGCA
1 TGCATCGATGCA
448683 CCCACTTAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.22
Consensus pattern (19 bp):
TGCATCGATGCATAAGGAG
Found at i:452563 original size:18 final size:18
Alignment explanation
Indices: 452540--452581 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
452530 CCACTGAATG
452540 TTAACGATTGTTAAACCT
1 TTAACGATTGTTAAACCT
452558 TTAACGATTGTTAAACCT
1 TTAACGATTGTTAAACCT
452576 TTAACG
1 TTAACG
452582 GTTTGCTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (18 bp):
TTAACGATTGTTAAACCT
Found at i:452736 original size:31 final size:31
Alignment explanation
Indices: 452695--452755 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
452685 AACTTCGGTC
*
452695 ACTTATGTTATCATTTTATTAAGTTTTAGTT
1 ACTTACGTTATCATTTTATTAAGTTTTAGTT
*
452726 ACTTACGTTATCGTTTTATTAAGTTTTAGT
1 ACTTACGTTATCATTTTATTAAGTTTTAGT
452756 CACTAGGACG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (31 bp):
ACTTACGTTATCATTTTATTAAGTTTTAGTT
Found at i:453124 original size:15 final size:15
Alignment explanation
Indices: 453104--453136 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
453094 CATTTAGAGA
453104 TAAAATGAAGCTATG
1 TAAAATGAAGCTATG
453119 TAAAATGAAGCTATG
1 TAAAATGAAGCTATG
453134 TAA
1 TAA
453137 TCTCAATTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (15 bp):
TAAAATGAAGCTATG
Found at i:453956 original size:23 final size:23
Alignment explanation
Indices: 453930--453980 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
453920 AATATTTTAA
*
453930 ATATTATAGTAACATACTCA-ATT
1 ATATTATAATAACATACT-ATATT
*
453953 ATATTATAATAATATACTATATT
1 ATATTATAATAACATACTATATT
453976 ATATT
1 ATATT
453981 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 1 0.04
23 24 0.96
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (23 bp):
ATATTATAATAACATACTATATT
Found at i:454471 original size:2 final size:2
Alignment explanation
Indices: 454464--454498 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
454454 CAATTTTCAT
454464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
454499 GTTTGAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:454565 original size:34 final size:32
Alignment explanation
Indices: 454485--454635 Score: 115
Period size: 36 Copynumber: 4.4 Consensus size: 32
454475 ATATATATAT
* *
454485 ATATATATATTATAG-TTTGAAATCATTTTAAAAA
1 ATATATATA-TATAGTTTTTAAATC-TTTT-GAAA
* *
454519 ATTATATAATATATGGGTTTTTAAATGTTTTGAAA
1 A-TATAT-ATATAT-AGTTTTTAAATCTTTTGAAA
*
454554 ATATATGATATATAGTTTTTAAAAATATTTTTGAAA
1 ATATAT-ATATATAGTTTTT--AAAT-CTTTTGAAA
* * * *
454590 ATATATATTATATCGTTTTGAAAACTTTTAAAA
1 ATATATA-TATATAGTTTTTAAATCTTTTGAAA
454623 ATATATATATATA
1 ATATATATATATA
454636 TAATATAATT
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
32 5 0.05
33 20 0.21
34 15 0.16
35 17 0.18
36 32 0.33
37 7 0.07
ACGTcount: A:0.44, C:0.02, G:0.08, T:0.46
Consensus pattern (32 bp):
ATATATATATATAGTTTTTAAATCTTTTGAAA
Found at i:454698 original size:39 final size:38
Alignment explanation
Indices: 454554--454894 Score: 271
Period size: 39 Copynumber: 9.2 Consensus size: 38
454544 TGTTTTGAAA
* * **
454554 ATATATGA-TATATAGTTTTTAAAAATA-TTTTTGAAA-
1 ATATAT-ATTATATAGTTTTGAAAATTAGTTTTAAAAAC
* * * *
454590 ATATATATTATATCGTTTTGAAAACT--TTTAAAAATAT
1 ATATATATTATATAGTTTTGAAAATTAGTTTTAAAA-AC
* * **
454627 ATATATATATAATATAATTTTTAAAAAAAGTTTTGAAAAAC
1 ATATATAT-T-ATATAGTTTTGAAAATTAGTTTT-AAAAAC
* *
454668 ATATATATTATATGGTTTTGAAAATTAGTTTT--TAA-
1 ATATATATTATATAGTTTTGAAAATTAGTTTTAAAAAC
* * *
454703 A-A-AT-CTATATAGTTTTGAAAA-CATTTTTGAAAAAC
1 ATATATATTATATAGTTTTGAAAATTAGTTTT-AAAAAC
* *
454738 ATATATATTATATAGTTTTGAAAATTAGTTTT-TAAAT
1 ATATATATTATATAGTTTTGAAAATTAGTTTTAAAAAC
* * *
454775 ATACATATTATATAGTTTTAAAAATTAGCTTTTAAAAAT
1 ATATATATTATATAGTTTTGAAAATTAG-TTTTAAAAAC
* *
454814 ATATATATTATATAGTTTTAAAAATTAGTTTT-TAAA-
1 ATATATATTATATAGTTTTGAAAATTAGTTTTAAAAAC
* *
454850 ATATATATTATATGGTTTTGAAAATTATTTTTTAAAAAC
1 ATATATATTATATAGTTTTGAAAATTA-GTTTTAAAAAC
454889 ATATAT
1 ATATAT
454895 TGTGTAATTT
Statistics
Matches: 246, Mismatches: 38, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
31 5 0.02
32 15 0.06
33 2 0.01
34 3 0.01
35 8 0.03
36 50 0.20
37 46 0.19
38 28 0.11
39 72 0.29
40 1 0.00
41 12 0.05
42 4 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (38 bp):
ATATATATTATATAGTTTTGAAAATTAGTTTTAAAAAC
Done.