Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009633.1 Hibiscus syriacus cultivar Beakdansim tig00117032_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: 2608659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 13
Found at i:545873 original size:139 final size:139
Alignment explanation
Indices: 545608--545884 Score: 430
Period size: 139 Copynumber: 2.0 Consensus size: 139
545598 ATGTCCAAAG
*
545608 ATTTGTAAAGCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATATTTTCGCATGAAAATGAGAA
1 ATTTATAAAGCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATATTTTCGCATGAAAATGAGAA
* * * **
545673 AGTAATTTTCAAAGTTTTTCGTTTAATGTTCAAGAAAATTAAATCCTCCGGGTAATTTGTAAAAC
66 AGTAATTTCCAAAGTTTTTCATTTAATGTTCAAGAAAATTAAAACCTCAAGGTAATTTGTAAAAC
545738 CTCTGGGTA
131 CTCTGGGTA
* * *
545747 ATTTATAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTATGA-AGTTTTCGCATGAAAATGAGA
1 ATTTATAAAGCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATA-TTTTCGCATGAAAATGAGA
* * *
545811 AAGTGATTTCCAAAGTTTTTCATTTAATGTTCTAGAAAATTAAAACCTCAAGGTAATTTGTAAAT
65 AAGTAATTTCCAAAGTTTTTCATTTAATGTTCAAGAAAATTAAAACCTCAAGGTAATTTGTAAAA
545876 CCTCTGGGT
130 CCTCTGGGT
545885 CATCTGTAAA
Statistics
Matches: 125, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
138 1 0.01
139 124 0.99
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (139 bp):
ATTTATAAAGCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATATTTTCGCATGAAAATGAGAA
AGTAATTTCCAAAGTTTTTCATTTAATGTTCAAGAAAATTAAAACCTCAAGGTAATTTGTAAAAC
CTCTGGGTA
Found at i:545879 original size:20 final size:20
Alignment explanation
Indices: 545851--545905 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
545841 TCTAGAAAAT
*
545851 TAAAACCTCAAGGTAATTTG
1 TAAAACCTCAAGGTAATCTG
* ** *
545871 TAAATCCTCTGGGTCATCTG
1 TAAAACCTCAAGGTAATCTG
545891 TAAAACCTCAAGGTA
1 TAAAACCTCAAGGTA
545906 GGATGTTTTC
Statistics
Matches: 26, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (20 bp):
TAAAACCTCAAGGTAATCTG
Found at i:545943 original size:119 final size:119
Alignment explanation
Indices: 545732--546627 Score: 1515
Period size: 119 Copynumber: 7.5 Consensus size: 119
545722 GGGTAATTTG
* * * * *
545732 TAAAACCTCTGGGTAATTTATAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTATGAAGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* * *
545797 GCATGAAAATGAGAAAGTGATTTCCAAAGTTTTTCATTTAATGTTCTAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* * *
545851 TAAAACCTCAAGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAAGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
*
545916 GCATGAAAATGAGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* * * * *
545970 TAAATCTTCCGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCATGATAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* *
546035 GCATGAAAATGAGAAAGTGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
546089 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
*
546154 GCATGAAAATGAGAAAGCGATTTCCGAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
546208 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
546273 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
546327 TAAAACCTCAGGGTAA-TTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* *
546391 GCATGAAAATGAGAAAACGATTTCTAAAGTTTCTCATTTAATGTTCAAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
546445 TAAAACCTCAGGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* * *
546510 GGATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAAT
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
* *
546564 TAAAACCTCCGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTT
1 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTT
546628 TACTTTAATT
Statistics
Matches: 736, Mismatches: 40, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
118 116 0.16
119 620 0.84
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (119 bp):
TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
Found at i:545995 original size:20 final size:20
Alignment explanation
Indices: 545970--546018 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
545960 TCAAGAAAAT
* *
545970 TAAATCTTCCGGGTAATTTG
1 TAAATCCTCCGGGTAATCTG
*
545990 TAAATCCTCCGGGTCATCTG
1 TAAATCCTCCGGGTAATCTG
*
546010 TAAAACCTC
1 TAAATCCTC
546019 ATGATAGGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (20 bp):
TAAATCCTCCGGGTAATCTG
Found at i:546117 original size:20 final size:20
Alignment explanation
Indices: 546089--546143 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
546079 TCTAGAAAAT
*
546089 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
546109 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
546129 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
546144 GGATGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:546236 original size:20 final size:20
Alignment explanation
Indices: 546208--546262 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
546198 TCAAGAAAAT
*
546208 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
546228 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
546248 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
546263 TGATGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:546354 original size:19 final size:20
Alignment explanation
Indices: 546327--546380 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
546317 TCAAGAAAAT
546327 TAAAACCTCAGGGTAAT-TG
1 TAAAACCTCAGGGTAATCTG
* * *
546346 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
546366 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
546381 TGATGTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.26
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:546473 original size:20 final size:20
Alignment explanation
Indices: 546445--546499 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
546435 TCAAGAAAAT
*
546445 TAAAACCTCAGGGTAATTTG
1 TAAAACCTCAGGGTAATCTG
* * *
546465 TAAATCCTCTGGGTCATCTG
1 TAAAACCTCAGGGTAATCTG
546485 TAAAACCTCAGGGTA
1 TAAAACCTCAGGGTA
546500 GGATGTTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (20 bp):
TAAAACCTCAGGGTAATCTG
Found at i:546527 original size:356 final size:357
Alignment explanation
Indices: 545732--546627 Score: 1542
Period size: 356 Copynumber: 2.5 Consensus size: 357
545722 GGGTAATTTG
* * * *
545732 TAAAACCTCTGGGTAATTTATAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTATGAAGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* * *
545797 GCATGAAAATGAGAAAGTGATTTCCAAAGTTTTTCATTTAATGTTCTAGAAAATTAAAACCTCAA
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAG
* * *
545862 GGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAAGGTAGGATGTTTTCGCATGAAAATG
131 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATG
* * *
545927 AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAATCTTCCGGGTAATTTGTA
196 AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAGGGTAATTTGTA
* **
545992 AATCCTCCGGGTCATCTGTAAAACCTCATGATAGGATGTTTTCGCATGAAAATGAGAAAGTGATT
261 AATCCTCCGGGTCATCTGTAAAACCTCAGGATAGGATGTTTTCGCATGAAAATGAGAAAACGATT
*
546057 TCCAAAGTTTCTCATTTAATGTTCTAGAAAAT
326 TCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
*
546089 TAAAACCTCAGGGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* *
546154 GCATGAAAATGAGAAAGCGATTTCCGAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAG
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAG
546219 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATG
131 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATG
*
546284 AGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAGGGTAA-TTGTA
196 AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAGGGTAATTTGTA
* *
546348 AATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATGAGAAAACGATT
261 AATCCTCCGGGTCATCTGTAAAACCTCAGGATAGGATGTTTTCGCATGAAAATGAGAAAACGATT
*
546413 TCTAAAGTTTCTCATTTAATGTTCAAGAAAAT
326 TCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
546445 TAAAACCTCAGGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
1 TAAAACCTCAGGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
* * *
546510 GGATGAAAATGAGAAAGCGATTACCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCCG
66 GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAG
546575 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTT
131 GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTT
546628 TACTTTAATT
Statistics
Matches: 509, Mismatches: 30, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
356 272 0.53
357 237 0.47
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (357 bp):
TAAAACCTCAGGGTAATTTGTAAATCCTCTGGGTCATCTGTAAAACCTCAGGGTAGGATGTTTTC
GCATGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAATGTTCTAGAAAATTAAAACCTCAG
GGTAATTTGTAAATCCTCCGGGTCATCTGTAAAACCTCAGGGTATGATGTTTTCGCATGAAAATG
AGAAAGAGATTTCCAAAGTTTCTCATTTAATGTTCAAGAAAATTAAAACCTCAGGGTAATTTGTA
AATCCTCCGGGTCATCTGTAAAACCTCAGGATAGGATGTTTTCGCATGAAAATGAGAAAACGATT
TCCAAAGTTTCTCATTTAATGTTCAAGAAAAT
Found at i:546592 original size:20 final size:20
Alignment explanation
Indices: 546564--546618 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
546554 TCTAGAAAAT
*
546564 TAAAACCTCCGGGTAATTTG
1 TAAAACCTCCGGGTAATCTG
* *
546584 TAAATCCTCCGGGTCATCTG
1 TAAAACCTCCGGGTAATCTG
*
546604 TAAAACCTCAGGGTA
1 TAAAACCTCCGGGTA
546619 TGATGTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
TAAAACCTCCGGGTAATCTG
Found at i:546769 original size:3 final size:3
Alignment explanation
Indices: 546761--546818 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
546751 CGAGACTATA
* * *
546761 TAT TAT TAT TAT TA- TAT TAC AAC TAT TAT TCA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT
546805 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
546819 CAAATATTAC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.92
4 1 0.02
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:548361 original size:60 final size:60
Alignment explanation
Indices: 548264--548417 Score: 224
Period size: 60 Copynumber: 2.6 Consensus size: 60
548254 AAATAATGAC
* * *
548264 TAATTAAAATATAATAAAGCCTATAGTGCTATTATTATTAATAAAAAGGTAGAAGCA-T-
1 TAATTAAAATATAATAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTA
*
548322 TAATTAAAATATTAATAAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGTATTA
1 TAATTAAAATA-TAAT-AAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTA
548384 TAATT-AAATAATAATAAAACCCATAGTGCTATCA
1 TAATTAAAAT-ATAATAAAACCCATAGTGCTATCA
548418 CATATGTATA
Statistics
Matches: 87, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
58 11 0.13
59 4 0.05
60 57 0.66
61 9 0.10
62 6 0.07
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.32
Consensus pattern (60 bp):
TAATTAAAATATAATAAAACCCATAGTGCTATCATTATTAATAAAAAGGTAGAAGCATTA
Found at i:548593 original size:17 final size:18
Alignment explanation
Indices: 548566--548599 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
548556 AATAATTATG
548566 TTAATTAATTTAATTAAT
1 TTAATTAATTTAATTAAT
548584 TTAA-TAATTTAATTAA
1 TTAATTAATTTAATTAA
548600 AGAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAATTAATTTAATTAAT
Found at i:550015 original size:29 final size:29
Alignment explanation
Indices: 549959--550016 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
549949 GGATTTTATG
**
549959 ATATTTTAGAAATTTTATGAGTTGTTTTT
1 ATATTTTAGAAATTTTATGAGTAATTTTT
549988 ATATTTTAGAAATTTT-TAGAGTAATTTTT
1 ATATTTTAGAAATTTTAT-GAGTAATTTTT
550017 TTAAAAAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 25 0.96
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (29 bp):
ATATTTTAGAAATTTTATGAGTAATTTTT
Found at i:550900 original size:16 final size:17
Alignment explanation
Indices: 550875--550907 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
550865 ATACAATTAT
550875 TTTTTAAAATTATTTAA
1 TTTTTAAAATTATTTAA
550892 TTTTT-AAATTATTTAA
1 TTTTTAAAATTATTTAA
550908 AGAACCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTTAAAATTATTTAA
Found at i:560553 original size:23 final size:23
Alignment explanation
Indices: 560522--560590 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
560512 CACCATAACT
* * *
560522 CGTATAAATGCACCGAAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
*
560545 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
560568 CGTAGAATTGTACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
560591 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.30, C:0.22, G:0.26, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:573440 original size:15 final size:15
Alignment explanation
Indices: 573420--573469 Score: 84
Period size: 15 Copynumber: 3.3 Consensus size: 15
573410 GAAAGCGTAT
573420 GAAGTGGACAAGAAG
1 GAAGTGGACAAGAAG
573435 GAAGTGGACAAGAAG
1 GAAGTGGACAAGAAG
573450 GAAGT-GAGCAAGAAG
1 GAAGTGGA-CAAGAAG
573465 GAAGT
1 GAAGT
573470 TGCCATCCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
14 2 0.06
15 32 0.94
ACGTcount: A:0.46, C:0.06, G:0.40, T:0.08
Consensus pattern (15 bp):
GAAGTGGACAAGAAG
Found at i:575295 original size:19 final size:20
Alignment explanation
Indices: 575267--575308 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
575257 TGGAATTATT
*
575267 ATAATATTTTATAATTAATA
1 ATAATATTTTATAATAAATA
575287 ATAAT-TTTTATAATAAATA
1 ATAATATTTTATAATAAATA
575306 ATA
1 ATA
575309 TTAACTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAATATTTTATAATAAATA
Found at i:575307 original size:22 final size:22
Alignment explanation
Indices: 575277--575328 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
575267 ATAATATTTT
* * *
575277 ATAATTAATAATAATTTTTATA
1 ATAAATAATAATAACTATTATA
*
575299 ATAAATAATATTAACTATTATA
1 ATAAATAATAATAACTATTATA
*
575321 TTAAATAA
1 ATAAATAA
575329 CTATCATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAATAATAATAACTATTATA
Found at i:576265 original size:34 final size:34
Alignment explanation
Indices: 576226--576298 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 34
576216 TTAAGTTGAA
* *
576226 TTTAATGTTAAATTTTGAATACCATAATTTGTAT
1 TTTAATGTTAAATTTCGAAAACCATAATTTGTAT
* *
576260 TTTAATTTTAAATTTCGAAAACTATAATTTGTAT
1 TTTAATGTTAAATTTCGAAAACCATAATTTGTAT
*
576294 ATTAA
1 TTTAA
576299 AAACATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.49
Consensus pattern (34 bp):
TTTAATGTTAAATTTCGAAAACCATAATTTGTAT
Found at i:576834 original size:21 final size:21
Alignment explanation
Indices: 576810--576883 Score: 62
Period size: 21 Copynumber: 3.5 Consensus size: 21
576800 AAAACCCTAC
576810 GGGCTAGGCATGTAACCTGGT
1 GGGCTAGGCATGTAACCTGGT
* *
576831 GGGCTATGAATGTAACCT--T
1 GGGCTAGGCATGTAACCTGGT
* * *
576850 GCGGATATGGCATATAAACTGGT
1 G-GGCTA-GGCATGTAACCTGGT
*
576873 GGGCTTGGCAT
1 GGGCTAGGCAT
576884 ATATCCCTGA
Statistics
Matches: 40, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
19 2 0.05
20 4 0.10
21 29 0.73
22 3 0.08
23 2 0.05
ACGTcount: A:0.23, C:0.16, G:0.34, T:0.27
Consensus pattern (21 bp):
GGGCTAGGCATGTAACCTGGT
Found at i:578479 original size:28 final size:30
Alignment explanation
Indices: 578415--578481 Score: 77
Period size: 28 Copynumber: 2.3 Consensus size: 30
578405 TCAGTTTCCT
578415 AAATAATATGCATTATAAAAATTTATAATTA
1 AAATAATATGCATTAT-AAAATTTATAATTA
* *
578446 ATATAA-ATTCATTAT-AAATTTA-AATTAA
1 AAATAATATGCATTATAAAATTTATAATT-A
578474 AAATAATA
1 AAATAATA
578482 ATAAATATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 4 0.13
28 13 0.42
29 1 0.03
30 8 0.26
31 5 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (30 bp):
AAATAATATGCATTATAAAATTTATAATTA
Found at i:578680 original size:17 final size:18
Alignment explanation
Indices: 578638--578685 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 18
578628 TTTAAATAAA
* *
578638 TAATAATTATATAAATAT
1 TAATATTTATATAAAAAT
*
578656 T-ATTTTTATA-AAAAAT
1 TAATATTTATATAAAAAT
578672 TAATATTTATATAA
1 TAATATTTATATAA
578686 TTATATTACT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
16 6 0.25
17 15 0.62
18 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TAATATTTATATAAAAAT
Found at i:582494 original size:39 final size:39
Alignment explanation
Indices: 582463--582593 Score: 208
Period size: 39 Copynumber: 3.4 Consensus size: 39
582453 GTCTTATCCA
* * *
582463 TTGGCTTGAAGATGCCATGCACTCCTGGAGTCTTTACAT
1 TTGGCCTGAAGACGCCATGCACTCCTAGAGTCTTTACAT
*
582502 TTGGCCTGAAAACGCCATGCACTCCTAGAGTCTTTACAT
1 TTGGCCTGAAGACGCCATGCACTCCTAGAGTCTTTACAT
* *
582541 TTGGCCTGAAGACGTCATGCACTCCTAAAGTCTTTACAT
1 TTGGCCTGAAGACGCCATGCACTCCTAGAGTCTTTACAT
582580 TTGGCCTGAAGACG
1 TTGGCCTGAAGACG
582594 GCAATGTAGT
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.30
Consensus pattern (39 bp):
TTGGCCTGAAGACGCCATGCACTCCTAGAGTCTTTACAT
Found at i:584188 original size:24 final size:25
Alignment explanation
Indices: 584138--584185 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
584128 AAAAAATGAT
* *
584138 TTTTTTAAATAATATATATTTTTAA
1 TTTTTTAAATAATATAAATTTTAAA
584163 TTTTTTAAA-AATA-AAATTTTAAA
1 TTTTTTAAATAATATAAATTTTAAA
584186 ATTATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 4 0.19
25 9 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTTAAATAATATAAATTTTAAA
Found at i:600599 original size:47 final size:48
Alignment explanation
Indices: 600545--600661 Score: 121
Period size: 47 Copynumber: 2.5 Consensus size: 48
600535 TAGTCTAGTG
* *
600545 ATATAGAGCTCACAAGTTTCTATTGAAAACTTACAAGTT-TTTTTAGC
1 ATATAGAGCTCACAAGTTTCTATTGAAAACTTACAAGTTCTTTGTAGA
* * * ** * *
600592 ATATAGAGCTTACAGGTTTTTATTGGGAACTTGCACGTTCTTTGTAGA
1 ATATAGAGCTCACAAGTTTCTATTGAAAACTTACAAGTTCTTTGTAGA
*
600640 ATATGGAGCTTC-CAAGTTTCTA
1 ATATAGAGC-TCACAAGTTTCTA
600662 CTATTTTTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 3
0.77 0.18 0.04
Matches are distributed among these distances:
47 32 0.58
48 22 0.40
49 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (48 bp):
ATATAGAGCTCACAAGTTTCTATTGAAAACTTACAAGTTCTTTGTAGA
Found at i:604962 original size:22 final size:21
Alignment explanation
Indices: 604934--605000 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 21
604924 TTCTATCCCT
604934 AACTTAAAACCCTAAACTAATA
1 AACTTAAAACCCTAAA-TAATA
*
604956 AACTT-AAACCCTAAATCATA
1 AACTTAAAACCCTAAATAATA
* *
604976 ATCTTATAACCTCTAAA-ACATA
1 AACTTAAAACC-CTAAATA-ATA
604998 AAC
1 AAC
605001 CCTAAACCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
20 8 0.22
21 14 0.38
22 15 0.41
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.25
Consensus pattern (21 bp):
AACTTAAAACCCTAAATAATA
Found at i:604966 original size:21 final size:20
Alignment explanation
Indices: 604934--604992 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 20
604924 TTCTATCCCT
604934 AACTTAAAACCCTAAACTAATA
1 AACTT-AAACCCTAAA-TAATA
*
604956 AACTTAAACCCTAAATCATA
1 AACTTAAACCCTAAATAATA
*
604976 ATCTTATAACCTCTAAA
1 AACTTA-AACC-CTAAA
604993 ACATAAACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.27
21 14 0.42
22 10 0.30
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (20 bp):
AACTTAAACCCTAAATAATA
Found at i:607660 original size:29 final size:29
Alignment explanation
Indices: 607618--607676 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
607608 ATTCTTCCTC
* * *
607618 AGCTTGTAGGAGCACTTACCTCTGCTAAG
1 AGCTTGTAGAAGCACATACCTCTACTAAG
607647 AGCTTGTAGAAGCACATACCTCTACTAAG
1 AGCTTGTAGAAGCACATACCTCTACTAAG
607676 A
1 A
607677 TCTGGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (29 bp):
AGCTTGTAGAAGCACATACCTCTACTAAG
Found at i:614982 original size:37 final size:39
Alignment explanation
Indices: 614930--615018 Score: 132
Period size: 37 Copynumber: 2.4 Consensus size: 39
614920 TTTTGTTCGG
*
614930 GTCGGG-TCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
*
614967 GTC-GGTT-GGGTTTTTTTAAGTGTGATATTCGGGTTAA
1 GTCGGGTTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
615004 GTCGGGTTCGGGTTT
1 GTCGGGTTCGGGTTT
615019 AGGGTGAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
36 5 0.11
37 31 0.67
38 4 0.09
39 6 0.13
ACGTcount: A:0.12, C:0.09, G:0.37, T:0.42
Consensus pattern (39 bp):
GTCGGGTTCGGGTTTTTTTAAGTGTGATATTCGGGTCAA
Found at i:620059 original size:20 final size:20
Alignment explanation
Indices: 620022--620060 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
620012 ATTGTTAATA
*
620022 CATTGTTTCAAAACAATTCT
1 CATTGTTTCAAAAAAATTCT
620042 CATT-TTTCAAATAAAATTC
1 CATTGTTTCAAA-AAAATTC
620061 ACTTTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.38, C:0.18, G:0.03, T:0.41
Consensus pattern (20 bp):
CATTGTTTCAAAAAAATTCT
Found at i:623384 original size:2 final size:2
Alignment explanation
Indices: 623377--623403 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
623367 TAAAAAGAAA
623377 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
623404 ACCTACATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:626373 original size:31 final size:32
Alignment explanation
Indices: 626266--626375 Score: 123
Period size: 32 Copynumber: 3.5 Consensus size: 32
626256 CTTAAGATGA
* * * *
626266 CCTTTGGTAGGCTCTGAGGCCCCAAAGCATTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAAGTACTT
*
626298 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACTT
1 CCTTGGGTAGGCTCTAAGGCCCCAAAGTACTT
* * * * *
626330 CATTGGGTAGGCTCTTAGGCCCTAATGTACTC
1 CCTTGGGTAGGCTCTAAGGCCCCAAAGTACTT
626362 CCTT-GGTAGGCTCT
1 CCTTGGGTAGGCTCT
626376 CAAGCCCAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
31 10 0.15
32 57 0.85
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (32 bp):
CCTTGGGTAGGCTCTAAGGCCCCAAAGTACTT
Found at i:627684 original size:17 final size:17
Alignment explanation
Indices: 627659--627693 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
627649 AGACCACTGA
*
627659 TTGTTCCGAATAACCAC
1 TTGTCCCGAATAACCAC
*
627676 TTGTCCCGAATGACCAC
1 TTGTCCCGAATAACCAC
627693 T
1 T
627694 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.14, T:0.29
Consensus pattern (17 bp):
TTGTCCCGAATAACCAC
Found at i:628458 original size:19 final size:19
Alignment explanation
Indices: 628434--628485 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
628424 TTTAAGTAGG
628434 TGCATCGATGCACTCCTCA
1 TGCATCGATGCACTCCTCA
* *
628453 TGCATCAATGCACTCCTTA
1 TGCATCGATGCACTCCTCA
628472 TGCATCGATGCACT
1 TGCATCGATGCACT
628486 AATTGCATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.23, C:0.33, G:0.15, T:0.29
Consensus pattern (19 bp):
TGCATCGATGCACTCCTCA
Found at i:634604 original size:2 final size:2
Alignment explanation
Indices: 634597--634623 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
634587 AAACTAAAAT
634597 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
634624 TTGTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:635447 original size:16 final size:16
Alignment explanation
Indices: 635405--635455 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
635395 CATAATTAAT
*
635405 TATAAGGGA-TTAAAA
1 TATAAGGGACTAAAAA
* **
635420 TAAAAGTTACTAAAAA
1 TATAAGGGACTAAAAA
635436 TATAAGGGACTAAATAA
1 TATAAGGGACTAAA-AA
635453 TAT
1 TAT
635456 TTATTCTAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
15 6 0.22
16 16 0.59
17 5 0.19
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (16 bp):
TATAAGGGACTAAAAA
Found at i:637402 original size:3 final size:3
Alignment explanation
Indices: 637394--637489 Score: 113
Period size: 3 Copynumber: 32.3 Consensus size: 3
637384 ATTTGGGCCT
* * * *
637394 ATA ATA ATA ATA ATA ATT ATA TTA ATA ATA ATA ATA TTA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
637442 ATA ATA TTA ATA A-A ATA ATA ATA ATA TTA TTA ATA ACA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
637489 A
1 A
637490 AATTGAGAAT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:637775 original size:124 final size:124
Alignment explanation
Indices: 637619--637949 Score: 491
Period size: 124 Copynumber: 2.7 Consensus size: 124
637609 GATTAAGACA
* *
637619 AAAATGTTGAACAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * *
637684 ACGAACTTCTTCTGGAAAATATTGATGTTGCTCTATCTCCTTCTGCGATAGAGTCGAGC
66 ACGAACTCCTTCTGGAAAATATTGATGATGCTCTATCTCCTTCTGCGATAGAATCGAGC
* * * * * *
637743 AATAGGTTGAATAATTTCTTCAGATTATGAACTTCTTATTCCTCCTCAAATGAGGTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* *
637808 ACGAACTCCTTCTGGAAAATGTTGATGATGCTCTATCTCCTTCTGCGATATAATCGAGC
66 ACGAACTCCTTCTGGAAAATATTGATGATGCTCTATCTCCTTCTGCGATAGAATCGAGC
* * *
637867 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTATTCTTCATCTTCAGACGAGTTCTTCTTATT
1 AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
* * *
637932 ACAAACTCTTTATGGAAA
66 ACGAACTCCTTCTGGAAA
637950 TGTTTTAAGA
Statistics
Matches: 182, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
124 182 1.00
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.38
Consensus pattern (124 bp):
AAAAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATT
ACGAACTCCTTCTGGAAAATATTGATGATGCTCTATCTCCTTCTGCGATAGAATCGAGC
Found at i:638429 original size:26 final size:26
Alignment explanation
Indices: 638392--638442 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
638382 ATGACTCAAG
638392 AATATCACCAA-GTTCAGAAATGAATA
1 AATATCACCAAGGTT-AGAAATGAATA
*
638418 AATATC-CTCAAGGTTTGAAATGAAT
1 AATATCAC-CAAGGTTAGAAATGAAT
638443 GGAAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 1 0.05
26 18 0.82
27 3 0.14
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (26 bp):
AATATCACCAAGGTTAGAAATGAATA
Found at i:640992 original size:15 final size:16
Alignment explanation
Indices: 640960--640993 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
640950 TGTGCAAATC
640960 CGGGTACCCGGATTTT
1 CGGGTACCCGGATTTT
640976 CGGGTACCCGG-TTTT
1 CGGGTACCCGGATTTT
640991 CGG
1 CGG
640994 ATATCCGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.09, C:0.26, G:0.35, T:0.29
Consensus pattern (16 bp):
CGGGTACCCGGATTTT
Found at i:641001 original size:15 final size:16
Alignment explanation
Indices: 640964--641002 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
640954 CAAATCCGGG
*
640964 TACCCGGATTTTCGGG
1 TACCCGGATTTTCGGA
640980 TACCCGG-TTTTCGGA
1 TACCCGGATTTTCGGA
*
640995 TATCCGGA
1 TACCCGGA
641003 ACTTCCGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (16 bp):
TACCCGGATTTTCGGA
Found at i:642160 original size:20 final size:20
Alignment explanation
Indices: 642129--642169 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
642119 TATAAATTTT
* *
642129 TATTTTCTTTTATTTAATAAA
1 TATTTCCTTTAATTT-ATAAA
642150 TATTTCCTTTAATTTATAAA
1 TATTTCCTTTAATTTATAAA
642170 AATGGTGGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTTCCTTTAATTTATAAA
Found at i:642580 original size:29 final size:30
Alignment explanation
Indices: 642517--642574 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
642507 AATTAGTTCT
*
642517 CAAAC-TTTTGAACATTTAAAATTCATCCC
1 CAAACTTTTTGAACATTCAAAATTCATCCC
* *
642546 CAAACTTTTTGAACATTCCAATTTCATCC
1 CAAACTTTTTGAACATTCAAAATTCATCC
642575 TAAACTATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 5 0.20
30 20 0.80
ACGTcount: A:0.34, C:0.26, G:0.03, T:0.36
Consensus pattern (30 bp):
CAAACTTTTTGAACATTCAAAATTCATCCC
Found at i:643097 original size:21 final size:20
Alignment explanation
Indices: 643011--643209 Score: 114
Period size: 21 Copynumber: 9.8 Consensus size: 20
643001 AAATGACCAA
**
643011 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
643030 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
643050 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
643070 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
643091 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
643112 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
643132 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
643153 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
643173 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
643194 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
643210 ACACATAAAT
Statistics
Matches: 134, Mismatches: 39, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
19 16 0.12
20 56 0.42
21 62 0.46
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:643159 original size:20 final size:20
Alignment explanation
Indices: 643011--643228 Score: 113
Period size: 20 Copynumber: 10.8 Consensus size: 20
643001 AAATGACCAA
643011 CAAAATCGCAACGCGAA-AT
1 CAAAATCGCAACGCGAATAT
* **
643030 AAAAATCGCAACGCG-ATCCC
1 CAAAATCGCAACGCGAAT-AT
* ** * *
643050 CAGAATCGCAAATC-AGTTT
1 CAAAATCGCAACGCGAATAT
* *
643069 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGAAT-AT
* *
643091 GAAAATCGCAATGCG-ATAGT
1 CAAAATCGCAACGCGAATA-T
* ** * *
643111 ACAAATTCGCATTGCGATTTT
1 -CAAAATCGCAACGCGAATAT
643132 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* ** * *
643153 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
643173 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
643194 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
643213 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
643229 TATCCGTAAA
Statistics
Matches: 146, Mismatches: 42, Indels: 21
0.70 0.20 0.10
Matches are distributed among these distances:
18 1 0.01
19 15 0.10
20 69 0.47
21 58 0.40
22 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:643171 original size:41 final size:41
Alignment explanation
Indices: 643092--643203 Score: 174
Period size: 41 Copynumber: 2.7 Consensus size: 41
643082 GCGATTCTTG
*
643092 AAAATCGCAATGCG-ATA-GTACAAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATG-A-AAA-TCGCATTGCGATTTTCC
643134 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
1 AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
643175 AAAATCGCAACGCGAATATGAAAATCGCA
1 AAAATCGCAACGCGAATATGAAAATCGCA
643204 ACGCGAACAC
Statistics
Matches: 67, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
41 46 0.69
42 16 0.24
43 4 0.06
44 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGCGAATATGAAAATCGCATTGCGATTTTCC
Found at i:643238 original size:20 final size:20
Alignment explanation
Indices: 643176--643369 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
643166 CGATTTTCCA
* ** *
643176 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
643196 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
643216 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
643236 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
643256 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
643276 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
643296 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
643316 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
643336 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
643357 AAATCGCAACGCG
1 AAATCGCAACGCG
643370 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:643268 original size:60 final size:60
Alignment explanation
Indices: 643176--643369 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
643166 CGATTTTCCA
* ** * *
643176 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
643236 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
643296 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
643357 AAATCGCAACGCG
1 AAATCGCAACGCG
643370 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:643789 original size:33 final size:33
Alignment explanation
Indices: 643750--643820 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
643740 TTCACTTAGA
* *
643750 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
643783 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
643816 TTTCA
1 TTTCA
643821 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:643926 original size:21 final size:20
Alignment explanation
Indices: 643900--644005 Score: 91
Period size: 21 Copynumber: 5.5 Consensus size: 20
643890 TGCAGAAGAG
643900 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
643921 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
643941 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
*
643962 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
643976 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
643995 TCGCAACGAGA
1 TCGCAACGAGA
644006 GAATCGCAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
16 2 0.03
17 2 0.03
19 11 0.17
20 16 0.24
21 25 0.38
ACGTcount: A:0.45, C:0.19, G:0.25, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:643944 original size:20 final size:21
Alignment explanation
Indices: 643898--643976 Score: 92
Period size: 21 Copynumber: 3.8 Consensus size: 21
643888 TTTGCAGAAG
*
643898 AGTCGCAACGAGATAAATGAAA
1 AGTCGCAACGAGA-GAATGAAA
*
643920 A-TCGCAACGAGAGAATG-AC
1 AGTCGCAACGAGAGAATGAAA
*
643939 TGTCGCAACGAGAGAAATGAAA
1 AGTCGCAACGAGAG-AATGAAA
643961 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
643977 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 1 0.02
20 19 0.39
21 26 0.53
22 3 0.06
ACGTcount: A:0.46, C:0.16, G:0.27, T:0.11
Consensus pattern (21 bp):
AGTCGCAACGAGAGAATGAAA
Found at i:643957 original size:41 final size:38
Alignment explanation
Indices: 643893--644009 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
643883 TTCAATTTGC
* *
643893 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
643931 AGAATGACTGTCGCAACGAGAGAAATGAAAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
643972 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
644005 AGAAT
1 AGAAT
644010 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.46, C:0.17, G:0.26, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:643982 original size:14 final size:14
Alignment explanation
Indices: 643963--644016 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
643953 AAATGAAAAG
643963 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
643977 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
643996 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
644010 CGCAACG
1 CGCAACG
644017 CGAAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:643992 original size:33 final size:33
Alignment explanation
Indices: 643952--644021 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
643942 CGCAACGAGA
643952 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
*
643985 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
644018 GAAA
1 GAAA
644022 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.47, C:0.20, G:0.26, T:0.07
Consensus pattern (33 bp):
GAAATGAAAAGCGCAACGAGAGAATCGCAACGC
Found at i:644028 original size:33 final size:33
Alignment explanation
Indices: 643958--644032 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
643948 GAGAGAAATG
* **
643958 AAAAGCGCAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
643991 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
644024 AAAATCGCA
1 AAAATCGCA
644033 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.47, C:0.24, G:0.23, T:0.07
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:644050 original size:19 final size:19
Alignment explanation
Indices: 644028--644130 Score: 100
Period size: 19 Copynumber: 5.9 Consensus size: 19
644018 GAAACCAAAA
* *
644028 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
644047 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
*
644063 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
*
644080 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATC
644099 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
644115 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
644131 TTCAACCAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 18
0.74 0.06 0.19
Matches are distributed among these distances:
14 16 0.23
16 11 0.16
17 8 0.11
19 35 0.50
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATC
Found at i:644111 original size:52 final size:52
Alignment explanation
Indices: 644028--644133 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
644018 GAAACCAAAA
* *
644028 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
*
644080 TCGCGTTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
644132 TC
1 TC
644134 AACCAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTGTCATCTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:646135 original size:93 final size:93
Alignment explanation
Indices: 645830--646208 Score: 726
Period size: 93 Copynumber: 4.1 Consensus size: 93
645820 TAGATTGCTT
*
645830 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
645895 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
645923 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
645986 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
646014 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
646079 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
646107 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
646172 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
646200 AGTAAATTT
1 AGTAAATTT
646209 ATCCATTCAA
Statistics
Matches: 281, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 90 0.32
93 191 0.68
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:646139 original size:184 final size:185
Alignment explanation
Indices: 645830--646210 Score: 728
Period size: 184 Copynumber: 2.1 Consensus size: 185
645820 TAGATTGCTT
*
645830 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
645895 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
645960 GTGTATTCTTTAACAC-TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
646014 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
646079 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
646144 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACAC-GTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
646200 AGTAAATTTAT
1 AGTAAATTTAT
646211 CCATTCAAGT
Statistics
Matches: 192, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
184 144 0.75
186 48 0.25
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (185 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:646372 original size:19 final size:19
Alignment explanation
Indices: 646252--646366 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
646242 TAGTTTACTT
* *
646252 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
646272 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
646291 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
646310 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
646329 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
646343 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
646362 TCGCA
1 TCGCA
646367 TTGCGATTTT
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 53 0.65
20 13 0.16
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:646384 original size:19 final size:19
Alignment explanation
Indices: 646362--646495 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
646352 GAAACCAAAA
*
646362 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
646381 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
646397 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
646414 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
646430 T--CGTTGCGATTTT-ATT
1 TCGCGTTGCGATTTTCATT
**
646446 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
646465 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
646485 TCGTGTTGCGA
1 TCGCGTTGCGA
646496 AAGTAAACTA
Statistics
Matches: 94, Mismatches: 9, Indels: 23
0.75 0.07 0.18
Matches are distributed among these distances:
14 15 0.16
16 12 0.13
17 9 0.10
18 12 0.13
19 34 0.36
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:646403 original size:14 final size:14
Alignment explanation
Indices: 646384--646440 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
646374 TTTCATTTCG
646384 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
646398 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
646415 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
646431 CGTTGCGATT
1 CGTTGCGATT
646441 TTATTTCGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:646455 original size:32 final size:33
Alignment explanation
Indices: 646367--646458 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
646357 CAAAATCGCA
*
646367 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
646400 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
646433 TTGCGATTTT-ATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
646459 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 15 0.27
33 41 0.73
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:648430 original size:14 final size:14
Alignment explanation
Indices: 648411--648446 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
648401 ATTGTTTAAT
648411 TGATTTGTAAAACA
1 TGATTTGTAAAACA
**
648425 TGATTTGTAAAAGT
1 TGATTTGTAAAACA
648439 TGATTTGT
1 TGATTTGT
648447 GTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.03, G:0.19, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAACA
Found at i:648577 original size:19 final size:19
Alignment explanation
Indices: 648553--648652 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
648543 AAAATTGACT
648553 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
648572 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
648591 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
648605 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
648624 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
648644 ATCGCAATG
1 ATCGCAATG
648653 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:648682 original size:53 final size:53
Alignment explanation
Indices: 648553--648669 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
648543 AAAATTGACT
648553 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
648605 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
648658 ATCGCAATGCGA
1 ATCGCAATGCGA
648670 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:648687 original size:19 final size:19
Alignment explanation
Indices: 648659--648826 Score: 177
Period size: 19 Copynumber: 9.6 Consensus size: 19
648649 AATGGGAGAA
* *
648659 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
648678 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
648694 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
648711 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
648730 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
648746 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
648763 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
648782 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
648798 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
648815 TCCGCATTGCGA
1 T-CGCATTGCGA
648827 AATGTAATGG
Statistics
Matches: 125, Mismatches: 8, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 18 0.14
16 21 0.17
17 18 0.14
18 2 0.02
19 60 0.48
20 6 0.05
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:648702 original size:33 final size:33
Alignment explanation
Indices: 648665--648826 Score: 159
Period size: 33 Copynumber: 4.7 Consensus size: 33
648655 AGAATCGCAA
*
648665 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
648698 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
648736 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
648769 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
648802 TGCGATTTTCATTTCCGCATTGCGA
1 TGCGATTTTCATTT-CGCATTGCGA
648827 AATGTAATGG
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
31 9 0.09
32 5 0.05
33 49 0.47
34 10 0.10
35 5 0.05
36 4 0.04
37 2 0.02
38 8 0.08
39 3 0.03
40 9 0.09
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:648722 original size:52 final size:52
Alignment explanation
Indices: 648659--648826 Score: 309
Period size: 52 Copynumber: 3.2 Consensus size: 52
648649 AATGGGAGAA
* *
648659 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
648711 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
648763 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
648815 TCCGCATTGCGA
1 T-CGCATTGCGA
648827 AATGTAATGG
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.91
53 10 0.09
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:648908 original size:19 final size:19
Alignment explanation
Indices: 648884--648981 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
648874 AAAATTGACT
648884 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
648903 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
648922 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
648936 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
648955 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
648975 ATCGCAA
1 ATCGCAA
648982 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:649013 original size:53 final size:53
Alignment explanation
Indices: 648884--649000 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
648874 AAAATTGACT
648884 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
648936 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
648989 ATCGCAATGCGA
1 ATCGCAATGCGA
649001 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:651551 original size:24 final size:24
Alignment explanation
Indices: 651517--651563 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
651507 CTGAAACATC
651517 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
651541 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
651564 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:652274 original size:20 final size:20
Alignment explanation
Indices: 652246--652495 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
652236 AAATTTCAGT
* *
652246 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
652266 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
652286 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
652306 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
652326 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
652346 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
652366 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
652386 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
652406 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
652426 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
652446 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
652466 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
652486 GTTGCGATTT
1 GTTGCGATTT
652496 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:652512 original size:21 final size:21
Alignment explanation
Indices: 652482--652564 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
652472 ATTTTCATAT
*
652482 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
652503 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
652524 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
652545 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
652565 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:652555 original size:42 final size:43
Alignment explanation
Indices: 652462--652560 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
652452 ATTTATGTGT
* *
652462 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
652503 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
652545 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
652561 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:652763 original size:20 final size:20
Alignment explanation
Indices: 652717--652763 Score: 76
Period size: 21 Copynumber: 2.3 Consensus size: 20
652707 AAATAGTAAT
652717 TATTTTTATTTATTTAAAAA
1 TATTTTTATTTATTTAAAAA
*
652737 TACTTTTTATTTTTTTAAAAA
1 TA-TTTTTATTTATTTAAAAA
652758 TATTTT
1 TATTTT
652764 AAAATTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TATTTTTATTTATTTAAAAA
Found at i:677297 original size:2 final size:2
Alignment explanation
Indices: 677290--677315 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
677280 CGCCTCTTCA
677290 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
677316 GATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:682232 original size:213 final size:215
Alignment explanation
Indices: 681733--682283 Score: 858
Period size: 213 Copynumber: 2.5 Consensus size: 215
681723 TATTATTATT
* *
681733 TCGGGTCGGGTCAGATTTCTAATTCATATATTTGGGTCGGGTCGGGTCGGGTGAAACTTTATTTT
1 TCGGGTCGGGTCGGATTTCTAATTCATATA--T---TCGGGTCGGGTCGGATGAAACTTTATTTT
* *
681798 GGTCGGGTCGGATCGGGTTTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTTCGGGTTTAGGG
61 GTTCGGGTCGGGTCGGG---TTTTTTAAGTGTGATA-T----TCGGGTCGGGTTCGGGTTTAGGG
681863 TGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTT
118 TGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTT
*
681928 TTATTAAATAAAATATTTTTTTATTATTTCGGG
183 TTATTAAATAAAATATATTTTTATTATTTCGGG
* * *
681961 TCGGGTCGGTTTGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTTG
1 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
682026 GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTG-AAAAAACCGG
66 GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGG
*
682090 ACCTACCCGAAAATATATATAATTC-GAGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAA
131 ACCGACCCGAAAATATATATAATTCAG-GTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAA
682154 A-ATATTTTTATTATTTCGGG
195 ATATATTTTTATTATTTCGGG
682174 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
1 TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
*
682239 GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTT-GGGT
66 GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGT
682284 CGGGTTTTTT
Statistics
Matches: 309, Mismatches: 13, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
212 4 0.01
213 121 0.39
214 72 0.23
215 25 0.08
219 1 0.00
220 16 0.05
223 42 0.14
226 1 0.00
228 27 0.09
ACGTcount: A:0.21, C:0.13, G:0.29, T:0.37
Consensus pattern (215 bp):
TCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCG
GGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGG
ACCGACCCGAAAATATATATAATTCAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAA
TATATTTTTATTATTTCGGG
Found at i:682302 original size:38 final size:38
Alignment explanation
Indices: 682239--682327 Score: 146
Period size: 38 Copynumber: 2.4 Consensus size: 38
682229 ATTTTGTTCG
682239 GGTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
*
682275 GAGTTGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
682314 GGTCGGGTCGGGTT
1 GGTCGGGTCGGGTT
682328 CGAGTTTAGG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 1 0.02
37 10 0.21
38 36 0.75
39 1 0.02
ACGTcount: A:0.11, C:0.10, G:0.40, T:0.38
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCA
Found at i:682727 original size:17 final size:17
Alignment explanation
Indices: 682705--682737 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
682695 AAAATGAAAA
682705 TTTAATATTTTT-TAATT
1 TTTAAT-TTTTTATAATT
682722 TTTAATTTTTTATAAT
1 TTTAATTTTTTATAAT
682738 ATATTACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAATTTTTTATAATT
Found at i:687169 original size:36 final size:35
Alignment explanation
Indices: 687090--687227 Score: 195
Period size: 36 Copynumber: 3.9 Consensus size: 35
687080 ATGAACAACC
* *
687090 GAATCGAAAGTGCTGACGCTTCCTTCCGTTCACTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTT
* * *
687125 GAATCGAAAGTGCCGGTGCTTCCTTTCGTTCTTCTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTC-ACTT
687161 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTT
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCAC-TT
* *
687197 GAATCGAAAGTGCTGATGCTTCCTTTCGTTC
1 GAATCGAAAGTGCCGATGCTTCCTTCCGTTC
687228 TTCTTATTCA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
35 28 0.31
36 63 0.69
ACGTcount: A:0.18, C:0.26, G:0.21, T:0.35
Consensus pattern (35 bp):
GAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTT
Found at i:687228 original size:72 final size:71
Alignment explanation
Indices: 687090--687232 Score: 241
Period size: 72 Copynumber: 2.0 Consensus size: 71
687080 ATGAACAACC
* *
687090 GAATCGAAAGTGCTGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGGTGCTTCCTTTCGTT
1 GAATCGAAAGTGCCGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCGTT
687155 CTTCTT
66 CTTCTT
* *
687161 GAATCGAAAGTGCCGATGCTTCCTTCCGTTCACTTTGAATCGAAAGTGCTGATGCTTCCTTTCGT
1 GAATCGAAAGTGCCGACGCTTCCTTCCGTTCAC-TTGAATCGAAAGTGCCGATGCTTCCTTTCGT
687226 TCTTCTT
65 TCTTCTT
687233 ATTCACCTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
71 31 0.46
72 36 0.54
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.36
Consensus pattern (71 bp):
GAATCGAAAGTGCCGACGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCGTT
CTTCTT
Found at i:689915 original size:42 final size:41
Alignment explanation
Indices: 689836--689918 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
689826 ATAGCTATTA
689836 TTAAAACTTCAATTTCGCACCAGAATGCCTCTGCATCGGAT
1 TTAAAACTTCAATTTCGCACCAGAATGCCTCTGCATCGGAT
* *
689877 TTAAAACTTCAATTTTGCACTAGAAATGCCTCTGCATCGGAT
1 TTAAAACTTCAATTTCGCACCAG-AATGCCTCTGCATCGGAT
689919 ATCAACCCCC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
41 21 0.54
42 18 0.46
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.31
Consensus pattern (41 bp):
TTAAAACTTCAATTTCGCACCAGAATGCCTCTGCATCGGAT
Found at i:691185 original size:14 final size:14
Alignment explanation
Indices: 691125--691184 Score: 102
Period size: 14 Copynumber: 4.3 Consensus size: 14
691115 CGTTCGTGAA
691125 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
691139 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
691153 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
* *
691167 CGTTTGATTATGTT
1 CGTTCGGTTATGTT
691181 CGTT
1 CGTT
691185 TATGTTCATT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.08, C:0.13, G:0.27, T:0.52
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:691999 original size:16 final size:16
Alignment explanation
Indices: 691974--692030 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
691964 CCAACGTTAA
*
691974 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
691990 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
* *
692006 TGTTCGTTTAAGTTCG
1 TGTTCATTTATGTTCG
692022 T-TT-ATTTAT
1 TGTTCATTTAT
692031 TAAATGAACG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
14 4 0.11
15 2 0.06
16 30 0.83
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:692111 original size:16 final size:16
Alignment explanation
Indices: 692090--692122 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
692080 CAAAAAAAAT
*
692090 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
692106 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
692122 T
1 T
692123 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:695508 original size:3 final size:3
Alignment explanation
Indices: 695500--695538 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
695490 CTGGAAACTC
* *
695500 TCT TCT TCT TTT TCT TCT TCT TCT TCT CCT CTCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT -TCT TCT TC
695539 CCGTGTGCCC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:696497 original size:21 final size:23
Alignment explanation
Indices: 696473--696514 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
696463 ATACATATGG
*
696473 TATGTGA-CAGAAGA-AAATGTA
1 TATGTGATCACAAGAGAAATGTA
696494 TATGTGATCACAAGAGAAATG
1 TATGTGATCACAAGAGAAATG
696515 ACATGAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.45, C:0.07, G:0.24, T:0.24
Consensus pattern (23 bp):
TATGTGATCACAAGAGAAATGTA
Found at i:696645 original size:22 final size:22
Alignment explanation
Indices: 696615--696675 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
696605 GGGTCTACGC
* * *
696615 GGTCTTTCGGTACATATACAGA
1 GGTCATTCGGGACAAATACAGA
* *
696637 GGTCCTTCGGGACAAATACATA
1 GGTCATTCGGGACAAATACAGA
696659 GGTCATTCGGGACAAAT
1 GGTCATTCGGGACAAAT
696676 TTCACATGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (22 bp):
GGTCATTCGGGACAAATACAGA
Found at i:697241 original size:22 final size:23
Alignment explanation
Indices: 697213--697265 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
697203 GAACGAAATT
*
697213 ACTGTAGCAAGGGTATCGGTA-C
1 ACTGTAGCAAGGGTATCGATACC
697235 ACTGTAGC-AGGGTATCGATACC
1 ACTGTAGCAAGGGTATCGATACC
*
697257 CCTGTAGCA
1 ACTGTAGCA
697266 TTCTGGAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (23 bp):
ACTGTAGCAAGGGTATCGATACC
Found at i:698903 original size:21 final size:19
Alignment explanation
Indices: 698861--698902 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
698851 ATGCGAATTG
*
698861 AAAATATATTTTATGTTAA
1 AAAATATATATTATGTTAA
698880 AAAATATATATTAT-TTAA
1 AAAATATATATTATGTTAA
698898 TAAAA
1 -AAAA
698903 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATATATATTATGTTAA
Found at i:699835 original size:176 final size:175
Alignment explanation
Indices: 699535--699898 Score: 595
Period size: 176 Copynumber: 2.1 Consensus size: 175
699525 ATAAAAATTA
*
699535 AATATTTTATAATTCAAAAAACAATTTATAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTT-TAATTCAAAAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
* *
699600 TTTTATATAAATTTTTTAATTAATTAATATTCATATAGGTTTAAAAGTTATTGGATCTTAAATTA
65 TTTTATATAAAATTTTTAATTAATTAATATTCATATAGGTTTAAAAGTTATTAGATCTTAAATTA
* * * *
699665 TTAATTGAGTTTTAAATGGTTTGGGCTGATCCCATATGTTATATGT
130 TTAATTGAATTTTAAATGGTTTGGGCTGAACCCATACGTTATATAT
*
699711 AATATTTTTAATTCAGAAAAACATTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AATATTTTTAATTCA-AAAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
* *
699776 TTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTA
65 TTTTATATAAAATTTTTAATTAATTAATATTCATATAGGTTTAAAAGTTATTAGATCTTAAATTA
*
699841 TTAATTGAATTTTAAATGGTTTGGGTTGAACCCATACGTTATATAT
130 TTAATTGAATTTTAAATGGTTTGGGCTGAACCCATACGTTATATAT
699887 AAT-TTATTTAAT
1 AATATT-TTTAAT
699899 ATTTAAAATT
Statistics
Matches: 175, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
175 9 0.05
176 166 0.95
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (175 bp):
AATATTTTTAATTCAAAAAACAATTTACAATTAATTTAAATAATATATAATTATAAAATAAAAAT
TTTATATAAAATTTTTAATTAATTAATATTCATATAGGTTTAAAAGTTATTAGATCTTAAATTAT
TAATTGAATTTTAAATGGTTTGGGCTGAACCCATACGTTATATAT
Found at i:708202 original size:16 final size:17
Alignment explanation
Indices: 708175--708207 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
708165 TTTTTAATTT
708175 TATTATTTATTTATAAG
1 TATTATTTATTTATAAG
*
708192 TATTA-TTATTTTTAAG
1 TATTATTTATTTATAAG
708208 CCATTTTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
TATTATTTATTTATAAG
Found at i:713190 original size:4 final size:4
Alignment explanation
Indices: 713183--713208 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
713173 TTGTTCTTTC
713183 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
713209 TTATTGTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:718824 original size:13 final size:13
Alignment explanation
Indices: 718806--718830 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
718796 GAGTGCTTCA
718806 TACTATATATTTT
1 TACTATATATTTT
718819 TACTATATATTT
1 TACTATATATTT
718831 GCAGGTTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TACTATATATTTT
Found at i:723349 original size:27 final size:30
Alignment explanation
Indices: 723300--723354 Score: 71
Period size: 27 Copynumber: 1.9 Consensus size: 30
723290 ATTATTTATT
* *
723300 TTTTAGATTGATTTATTATAATA-ATAAAA
1 TTTTAGATTGATTTAATAGAATACATAAAA
723329 TTTTA-ATT-ATTTAATAGAATACATAA
1 TTTTAGATTGATTTAATAGAATACATAA
723355 TTGTTGTGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 7 0.30
29 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (30 bp):
TTTTAGATTGATTTAATAGAATACATAAAA
Found at i:724261 original size:20 final size:21
Alignment explanation
Indices: 724236--724328 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
724226 TTTTCCCAAT
*
724236 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
724256 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
724277 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
724297 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
724318 TCGCAATGCGA
1 TCGCAATGCGA
724329 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:724281 original size:41 final size:41
Alignment explanation
Indices: 724236--724328 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
724226 TTTTCCCAAT
724236 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
724277 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
724318 TCGCAATGCGA
1 TCGCAATGCGA
724329 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:724341 original size:41 final size:41
Alignment explanation
Indices: 724255--724389 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
724245 GAATAAGTAA
** *
724255 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
724296 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
724337 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
* *
724378 TTTGCAACGCGA
1 ATCGCAACGCGA
724390 TACTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:724342 original size:20 final size:20
Alignment explanation
Indices: 724317--724410 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
724307 AATTGGGAAA
*
724317 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * * **
724337 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-TACT
*
724358 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
724378 TTTGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
724398 TTCGCAACGCGAT
1 ATCGCAACGCGAT
724411 TTACATAGCG
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:724981 original size:19 final size:19
Alignment explanation
Indices: 724929--724975 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
724919 TTCGAGAATG
*
724929 AAAATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAACA
* *
724948 AAAATCGCAGCGCGAAACC
1 AAAATCGCAACGCGAAACA
724967 AAAATCGCA
1 AAAATCGCA
724976 TTGCGATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACA
Found at i:725017 original size:20 final size:19
Alignment explanation
Indices: 724971--725103 Score: 141
Period size: 20 Copynumber: 7.1 Consensus size: 19
724961 GAAACCAAAA
*
724971 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
724990 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
725009 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
725029 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
725043 TCTCGTTGCGATAGTCATTT
1 TCGCGTTGCGATTTTCA-TT
*
725063 TCGCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
725082 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
725102 TC
1 TC
725104 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 16
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 3 0.03
19 32 0.33
20 49 0.51
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:725061 original size:33 final size:34
Alignment explanation
Indices: 725014--725078 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
725004 TTATTTCGCG
**
725014 GTTGCGATTTTCA-TTTCGCGTTGCGATTCTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
725047 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
1 GTTGCGATAGTCATTTTCGCGTTGCGATTCTC
725079 ATTATCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (34 bp):
GTTGCGATAGTCATTTTCGCGTTGCGATTCTCTC
Found at i:725063 original size:39 final size:39
Alignment explanation
Indices: 724978--725064 Score: 97
Period size: 39 Copynumber: 2.2 Consensus size: 39
724968 AAATCGCATT
* * * *
724978 GCGATTTTCATTTCGCGTTGCGATTTTTATTTCGCGGTT
1 GCGATTTTCATTTCGCGTTGCGATTTCTAGTTCGCGATA
*
725017 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT-GCGATA
1 GCGATTTTCATTTCGCGTTGCGATT-TCTAGTTCGCGATA
725056 GTC-ATTTTC
1 G-CGATTTTC
725065 GCGTTGCGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 36 0.88
40 5 0.12
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.46
Consensus pattern (39 bp):
GCGATTTTCATTTCGCGTTGCGATTTCTAGTTCGCGATA
Found at i:727165 original size:42 final size:42
Alignment explanation
Indices: 727105--727227 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
727095 GCCCGACTCG
* * *
727105 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
727147 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
727189 ACTGTCATCGTTGAAGAGATCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGAG-TCCACTCCCACCGTTCAAGAG
727228 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 63 0.95
43 3 0.05
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:727185 original size:21 final size:21
Alignment explanation
Indices: 727161--727227 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
727151 TCATTCCTCG
727161 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
727182 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
727203 AGAGAT-CCCTCCCACCATTCA
1 AGAG-TCCCCTCCCACCGTTCA
727224 AGAG
1 AGAG
727228 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.25, C:0.36, G:0.19, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:728606 original size:14 final size:14
Alignment explanation
Indices: 728587--728622 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
728577 ATTGTTTAAT
728587 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
728601 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
728615 TGATTTGT
1 TGATTTGT
728623 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:728930 original size:19 final size:19
Alignment explanation
Indices: 728906--728964 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
728896 GAAATTAGCG
728906 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
728925 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
728939 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
728958 TTGCGAT
1 TTGCGAT
728965 AGTAATTTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 5 0.16
16 7 0.23
17 7 0.23
19 12 0.39
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:728962 original size:33 final size:32
Alignment explanation
Indices: 728804--728964 Score: 187
Period size: 33 Copynumber: 4.9 Consensus size: 32
728794 AATTAAATTC
* **
728804 GCGTTGCGATTTTCATTTCGCATTGCAATTCCC
1 GCGTTGCGATTTTCATTTCGCATTGCGATT-TA
* * *
728837 TCGTTGCGATTTTCATTTCGCATTACGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG-ATTTA
* *
728870 GCGTTGCGATTTTCATTTCGCATTACGAAATTA
1 GCGTTGCGATTTTCATTTCGCATTGCG-ATTTA
*
728903 GCGTTGCGATTTTCATTTCGCATTGCGATTCTC
1 GCGTTGCGATTTTCATTTCGCATTGCGATT-TA
* *
728936 TCGTTGTGATTTTCATTTCGCATTGCGAT
1 GCGTTGCGATTTTCATTTCGCATTGCGAT
728965 AGTAATTTCC
Statistics
Matches: 114, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
32 2 0.02
33 110 0.96
34 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (32 bp):
GCGTTGCGATTTTCATTTCGCATTGCGATTTA
Found at i:730410 original size:23 final size:23
Alignment explanation
Indices: 730384--730430 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
730374 ATTGTTAGCA
730384 TCCATGGCTACTGCTAATAAGTT
1 TCCATGGCTACTGCTAATAAGTT
730407 TCCATGGCTACTGCTAATAAGTT
1 TCCATGGCTACTGCTAATAAGTT
730430 T
1 T
730431 ACTCCAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (23 bp):
TCCATGGCTACTGCTAATAAGTT
Found at i:731293 original size:12 final size:12
Alignment explanation
Indices: 731276--731300 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
731266 TCTTCGGGGA
731276 CTTTTTCTTCTT
1 CTTTTTCTTCTT
731288 CTTTTTCTTCTT
1 CTTTTTCTTCTT
731300 C
1 C
731301 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:732563 original size:20 final size:20
Alignment explanation
Indices: 732508--732565 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
732498 ATTCATTTGA
*
732508 TTATCGCAACGCCAAAATGG
1 TTATCGCAACGCGAAAATGG
*
732528 CTATCGCAACGCGAAAATGG
1 TTATCGCAACGCGAAAATGG
*
732548 TTATCGCAACGAGAAAAT
1 TTATCGCAACGCGAAAAT
732566 CACGATTTTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
TTATCGCAACGCGAAAATGG
Found at i:734607 original size:19 final size:19
Alignment explanation
Indices: 734583--734646 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
734573 GAAACTTAAA
734583 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
734602 ATCGCAACGCGAAATGGCT
1 ATCGCAACGCGAAATGACT
* *
734621 ATCGCAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
734639 ATCGCAAC
1 ATCGCAAC
734647 AACAAAATCG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 7 0.17
19 33 0.82
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:734751 original size:29 final size:30
Alignment explanation
Indices: 734698--734781 Score: 98
Period size: 29 Copynumber: 2.7 Consensus size: 30
734688 AATCACATTA
* *
734698 CGATTTTATTTCGCGTTGCGATTTGTCGTTG
1 CGATTTCATTTCGC-ATGCGATTTGTCGTTG
*
734729 C-ATTTCATTTCGCATGCGTTTTGTCGTTG
1 CGATTTCATTTCGCATGCGATTTGTCGTTG
734758 CGATTTTTCATTTCGCATTGCGAT
1 CGA--TTTCATTTCGCA-TGCGAT
734782 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 15 0.33
30 12 0.27
31 1 0.02
32 12 0.27
33 5 0.11
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (30 bp):
CGATTTCATTTCGCATGCGATTTGTCGTTG
Found at i:734817 original size:20 final size:20
Alignment explanation
Indices: 734766--734809 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
734756 TGCGATTTTT
*
734766 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTGCGATAGC
*
734785 CATTTCCGCGTTGCGATAGT
1 CATTTCCGCGTTGCGATAGC
734805 CATTT
1 CATTT
734810 TCGTGTTGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.36
Consensus pattern (20 bp):
CATTTCCGCGTTGCGATAGC
Found at i:735316 original size:18 final size:18
Alignment explanation
Indices: 735290--735334 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
735280 GTCGATCAGA
*
735290 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
735308 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
735326 TGATGGCTC
1 TGATGGCTC
735335 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:736661 original size:20 final size:20
Alignment explanation
Indices: 736636--736673 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
736626 AATAGTTTCT
736636 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
736656 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
736674 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:737189 original size:20 final size:20
Alignment explanation
Indices: 737164--737257 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
737154 GATTATGTAT
*
737164 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTAAG
737184 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTAAG
* *** * *
737204 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTAAG
* *
737225 TATCGCATTGCGATAGTAAG
1 TATCGCGTTGCGAAAGTAAG
*
737245 TATCGCATTGCGA
1 TATCGCGTTGCGA
737258 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:0.24, C:0.17, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTAAG
Found at i:737258 original size:20 final size:20
Alignment explanation
Indices: 737144--737258 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
737134 CGCTTTGAAA
*
737144 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTAAGT
* * *
737165 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTAAGT
* *
737185 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTAAGT
* * ** * *
737205 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTAAGT
737226 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTAAGT
737246 ATCGCATTGCGAT
1 ATCGCATTGCGAT
737259 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:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTAAGT
Done.