Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008569.1 Hibiscus syriacus cultivar Beakdansim tig00111493_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: 1513883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 8
Found at i:272643 original size:27 final size:29
Alignment explanation
Indices: 272612--272670 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 29
272602 ATGCTTTAAA
*
272612 ATATTATATATAT-TTTTCAAAAAC-TAT
1 ATATTATATATATATATTCAAAAACATAT
*
272639 ATATTATATATATATATTCAAAACCATAT
1 ATATTATATATATATATTCAAAAACATAT
272668 ATA
1 ATA
272671 GGATACTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.46
28 9 0.32
29 6 0.21
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (29 bp):
ATATTATATATATATATTCAAAAACATAT
Found at i:273894 original size:6 final size:6
Alignment explanation
Indices: 273883--273932 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
273873 CTCTTAAAAT
*
273883 TCACTC TCACTC TCACTC TCACTC TCACTC TCACTC TCACCC TCACTC
1 TCACTC TCACTC TCACTC TCACTC TCACTC TCACTC TCACTC TCACTC
273931 TC
1 TC
273933 TCCGTCCTCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
TCACTC
Found at i:285828 original size:13 final size:13
Alignment explanation
Indices: 285810--285834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
285800 TAGTCATTAG
285810 TTCATAATCAATA
1 TTCATAATCAATA
285823 TTCATAATCAAT
1 TTCATAATCAAT
285835 GTGTAATGGT
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:0.44, C:0.16, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCATAATCAATA
Found at i:285943 original size:19 final size:19
Alignment explanation
Indices: 285919--285970 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
285909 AGTTTAAATA
285919 AATCAAACCAAATTCAAAC
1 AATCAAACCAAATTCAAAC
*
285938 AATCAAAACAAATTCAAAC
1 AATCAAACCAAATTCAAAC
*
285957 AATTAAAACCAAAT
1 AA-TCAAACCAAAT
285971 AAACATTCAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.17
Consensus pattern (19 bp):
AATCAAACCAAATTCAAAC
Found at i:287419 original size:12 final size:13
Alignment explanation
Indices: 287397--287434 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
287387 TCCTAATGGG
*
287397 CAATCTTTGAAAA
1 CAATGTTTGAAAA
*
287410 CTAT-TTTGAAAA
1 CAATGTTTGAAAA
287422 CAATGTTTGAAAA
1 CAATGTTTGAAAA
287435 ATCATAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (13 bp):
CAATGTTTGAAAA
Found at i:287487 original size:20 final size:19
Alignment explanation
Indices: 287459--287500 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
287449 AGTTTTCATG
*
287459 AAAATAACATAATTAAATCA
1 AAAACAACA-AATTAAATCA
*
287479 AAAACAACAATTTAAATCA
1 AAAACAACAAATTAAATCA
287498 AAA
1 AAA
287501 CACTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAACAACAAATTAAATCA
Found at i:301132 original size:20 final size:21
Alignment explanation
Indices: 301059--301130 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
301049 ATTAAAAATC
301059 TTACTTATTCCTAAATGCAGT
1 TTACTTATTCCTAAATGCAGT
*
301080 TTACTTATTCCTAAACGCAGT
1 TTACTTATTCCTAAATGCAGT
*
301101 TTACTTATT-C-AATTGCATGT
1 TTACTTATTCCTAAATGCA-GT
301121 TTACTTATTC
1 TTACTTATTC
301131 AAACGGTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 5 0.11
20 12 0.26
21 29 0.63
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.46
Consensus pattern (21 bp):
TTACTTATTCCTAAATGCAGT
Found at i:303259 original size:41 final size:41
Alignment explanation
Indices: 303202--303279 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
303192 TTTACACATC
*
303202 CGTAATCTCTACATTTATAATGGATTATTGTTATTCACAAT
1 CGTAATCTCTACATTTATAATGAATTATTGTTATTCACAAT
*
303243 CGTAATCTCTACATTTATAATGAATTATTGTTCTTCA
1 CGTAATCTCTACATTTATAATGAATTATTGTTATTCA
303280 TATTCATGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (41 bp):
CGTAATCTCTACATTTATAATGAATTATTGTTATTCACAAT
Found at i:309096 original size:37 final size:38
Alignment explanation
Indices: 309046--309118 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 38
309036 TTTATTTTGT
*
309046 TCGGGTCGTG-TTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGGTCGTGTTTTTTTAAGCGTGATATTCGGGTCGAG
309083 TCGGGTCAG-GTTTTTTTAAGCGTGATATTCGGGTCG
1 TCGGGTC-GTGTTTTTTTAAGCGTGATATTCGGGTCG
309119 GGTTCGAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 8 0.24
38 25 0.76
ACGTcount: A:0.14, C:0.12, G:0.34, T:0.40
Consensus pattern (38 bp):
TCGGGTCGTGTTTTTTTAAGCGTGATATTCGGGTCGAG
Found at i:309263 original size:248 final size:248
Alignment explanation
Indices: 308863--309767 Score: 1302
Period size: 248 Copynumber: 3.7 Consensus size: 248
308853 TCGGGTCGGG
* ** * * *
308863 TCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACCTGACCGACCCGAACATATATATAATTCAGGTC
1 TCGGGTCGGGTTCGGGTTTAGGGTAAAAAAACAGGACCGACCAGAAAATATATATAATTCGGGTC
* * *
308928 GGGTCGGAGTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGG
66 GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGGGTCGG
* *
308993 GTTGGATCTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGTGTT
131 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGTGTT
* *
309058 TTTTAAGTGTGATATTCGGGTCGAGTCGGGTCAGGTTTTTTTAAGCGTGATAT
196 TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATAT
* * *
309111 TCGGGTCGGGTTCGAGTTTAGGGTAAAAAAATAGGACCGACCATAAAATATATATAATTCGGGTC
1 TCGGGTCGGGTTCGGGTTTAGGGTAAAAAAACAGGACCGACCAGAAAATATATATAATTCGGGTC
* *
309176 GGGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTTATTATTTTGGGTCGGGTCGG
66 GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGGGTCGG
* * *
309241 GTCGGATTTCTATTTCATATATTTGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTT
131 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGTGTT
* *
309306 TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCGGGTTTTTTTAAGTGTGAAAT
196 TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATAT
* * *
309359 TCGGGTCGGATCGGGTCGGGTTTAGGGTGAAAAAAACCGGACCAACCAGAAAATATATATAA-T-
1 TCGGGTC-G---GGTTCGGGTTTAGGGT-AAAAAAACAGGACCGACCAGAAAATATATATAATTC
*
309422 ---TCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTA-TT----TC-G
61 GGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGG
*
309478 GT----TCGGATTTCTAATTCATATATTCGAGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC
126 GTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC
*
309539 GGGTTGGGTTTTTTAAGTGTGATATTTGGGACGAGTCGGGT-AGGGTTTTTTTAAGTGTGATAT
191 --G-T--GTTTTTTAAGTGTGATATTTGGGTCGAGTCGGGTCA-GGTTTTTTTAAGTGTGATAT
* * * *
309602 TCGGGTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCCGAAAATATATATAATTCGGGTT
1 TCGGGTCGGGTTCGGGTTTAGGGTAAAAAAACAGGACCGACCAGAAAATATATATAATTCGGGTC
309667 GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGGGTCGG
66 GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGGGTCGG
309732 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGG
131 GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGG
309768 GTTTTTTAAG
Statistics
Matches: 584, Mismatches: 47, Indels: 47
0.86 0.07 0.07
Matches are distributed among these distances:
238 84 0.14
239 16 0.03
240 1 0.00
242 4 0.01
243 110 0.19
244 2 0.00
247 2 0.00
248 283 0.48
249 4 0.01
252 15 0.03
253 63 0.11
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (248 bp):
TCGGGTCGGGTTCGGGTTTAGGGTAAAAAAACAGGACCGACCAGAAAATATATATAATTCGGGTC
GGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGGGTCGG
GTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGTGTT
TTTTAAGTGTGATATTTGGGTCGAGTCGGGTCAGGTTTTTTTAAGTGTGATAT
Found at i:309355 original size:38 final size:38
Alignment explanation
Indices: 309294--309381 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
309284 TTTATTTTGT
* *
309294 TCGGGTCGGG-TTTTTTAAGTGTGATATTTGGGTC-GA
1 TCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGA
309330 GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGA
1 -TCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGA
309369 TCGGGTCGGGTTT
1 TCGGGTCGGGTTT
309382 AGGGTGAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
37 10 0.21
38 35 0.74
39 2 0.04
ACGTcount: A:0.12, C:0.10, G:0.39, T:0.39
Consensus pattern (38 bp):
TCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGA
Found at i:309791 original size:32 final size:34
Alignment explanation
Indices: 309750--309832 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 34
309740 TCTAATTCAT
309750 ATATTCGGGTCGGGTC-G-GGTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTCGGCGGTTTTTTAAGTGTG
*
309782 ATATTCGGGTCGAGTCGGGTCGGTTTTTTAAGTGTG
1 ATATTCGGGTCGGGTC-GG-CGGTTTTTTAAGTGTG
*
309818 AAATTCGGGTCGGGT
1 ATATTCGGGTCGGGT
309833 TTAGGGTGAA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 15 0.34
34 1 0.02
36 28 0.64
ACGTcount: A:0.14, C:0.11, G:0.37, T:0.37
Consensus pattern (34 bp):
ATATTCGGGTCGGGTCGGCGGTTTTTTAAGTGTG
Found at i:309814 original size:36 final size:37
Alignment explanation
Indices: 309758--309829 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
309748 ATATATTCGG
*
309758 GTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTAAGTGTGAAATTCGGGTCGA
309795 GTCGGGTC-GGTTTTTTAAGTGTGAAATTCGGGTCG
1 GTCGGGTCGGGTTTTTTAAGTGTGAAATTCGGGTCG
309830 GGTTTAGGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 26 0.76
37 8 0.24
ACGTcount: A:0.14, C:0.11, G:0.38, T:0.38
Consensus pattern (37 bp):
GTCGGGTCGGGTTTTTTAAGTGTGAAATTCGGGTCGA
Found at i:309828 original size:491 final size:482
Alignment explanation
Indices: 308824--310075 Score: 1439
Period size: 491 Copynumber: 2.6 Consensus size: 482
308814 TTTTGGTCGG
* * *
308824 GTCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGA-AAT----TCGGGTCGGATCGGG-TCGGGTTTAGGGTGA
* * * * *
308889 AAAAACCTGACCGACCCGAACATATATATAATTCAGGTCGGGTCGGAGTAAGTCACTGTTTTTAT
60 AAAAACCAGACCAACCAGAAAATATATATAA-T----TCGGGTCGGATTAAGTCACTGTTTTTAT
* *
308954 TAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGGTTGGATCTCTAATTCATATATTCGG
120 TAAATAAAAATAATTTTTTATTATTTC-GGT----TC-----GGATTTCTAATTCATATATTCGG
309019 GTCGGGTCGGATGAAACTTTATTTTGTTCGGGTC--G-T--GTTTTTTAAGTGTGATATTCGGGT
175 GTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGT
* *
309079 CGAGTCGGGTCA-GGTTTTTTTAAGCGTGATATTCGGGTCGGGTTCGAGTTTAGGGTAAAAAAAT
240 CGAGTCGGGT-AGGGTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAAT
* *
309143 AGGACCGACCATAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATA
304 AGGACAGACCAGAAAATATATATAATTCGGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATA
* * *
309208 AAAACAATTTTTTATTATTTTGGGTCGGGTCGGGTCGGATTTCTATTTCATATATTTGGGTCGGG
369 AAAACAATTTTTTATTATTTCGGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGG
* *
309273 TCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTTGGGTCGA
434 TCGGATGAAACTTTATTTCGGTCGGGTCGGGTTTTTTAAGTGTGATA--------GA
309330 GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGATCGGGTCGGGTTTAGGGTGAAAAAAA
1 GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGATCGGGTCGGGTTTAGGGTG-AAAAAA
*
309395 CCGGACCAACCAGAAAATATATATAATTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
65 CCAGACCAACCAGAAAATATATATAATTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAA
*
309460 TAATTTTTTATTATTTCGGTTCGGATTTCTAATTCATATATTCGAGTCGGGTCGGATGAAACTTT
130 TAATTTTTTATTATTTCGGTTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTT
* *
309525 ATTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTTGGGACGAGTCGGGTAGGGTTTTTT
195 ATTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTAGGGTTTTTT
*
309590 TAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCCGAAAATATAT
260 TAAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCAGAAAATATAT
* *
309655 ATAATTCGGGTTGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTC
325 ATAATTCGGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTTATTATTTC
**
309720 GGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGG--G----TTT-TTTAAG
390 GGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTCGG
* * * *
309778 T---GT---G-ATATT-CG-G-G-TCGA
455 TCGGGTCGGGTTTTTTAAGTGTGATAGA
* * ** *
309795 GTCGGGTC-GG-TTTTTTAAGTGTGAAATTCGGGTCGGGTTTAGGGT---G-AAAA----AAATC
1 GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTC-GG-ATCGGGTCGGGTTTAGGGTGAAA--
** * *** * *
309850 GGACC-GACCAGA--A-AATATATATAATTCGGGTCAGGTCGGATTAAGTCACTATTTTTATTAA
62 AAACCAGACCA-ACCAGAAAATATAT-A-T-AATTCGGGTCGGATTAAGTCACTGTTTTTATTAA
***
309911 ATAAAAATAATTTTTTATTATTTCGGGAAGGATTTCTAATTCATATATTCGGGTCGGGTCGGATG
123 ATAAAAATAATTTTTTATTATTTCGGTTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATG
309976 AAACTTTATTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTAGG
188 AAACTTTATTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTAGG
*
310041 GTTTTTTTAAGTGTGATATTCGGGTCAGG-TCGGGT
253 GTTTTTTTAAGTGTGATATTCGGGTCGGGTTCGGGT
310076 CGGGTTCGGG
Statistics
Matches: 681, Mismatches: 50, Indels: 79
0.84 0.06 0.10
Matches are distributed among these distances:
455 8 0.01
456 5 0.01
457 12 0.02
458 185 0.27
461 1 0.00
462 1 0.00
463 24 0.04
464 4 0.01
465 15 0.02
473 1 0.00
474 1 0.00
475 1 0.00
476 1 0.00
477 3 0.00
478 1 0.00
481 2 0.00
484 4 0.01
485 3 0.00
486 55 0.08
488 1 0.00
489 2 0.00
490 1 0.00
491 210 0.31
495 3 0.00
496 53 0.08
500 15 0.02
501 42 0.06
505 2 0.00
506 25 0.04
ACGTcount: A:0.24, C:0.11, G:0.28, T:0.37
Consensus pattern (482 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGAAATTCGGGTCGGATCGGGTCGGGTTTAGGGTGAAAAAAC
CAGACCAACCAGAAAATATATATAATTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAAT
AATTTTTTATTATTTCGGTTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTA
TTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGTAGGGTTTTTTT
AAGTGTGATATTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCAGAAAATATATA
TAATTCGGGTCGGGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTTATTATTTCG
GGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGATGAAACTTTATTTCGGT
CGGGTCGGGTTTTTTAAGTGTGATAGA
Found at i:309916 original size:215 final size:219
Alignment explanation
Indices: 309531--309937 Score: 635
Period size: 215 Copynumber: 1.9 Consensus size: 219
309521 CTTTATTTTG
* * *
309531 TTCGGGTCGGGTTGGGTTTTTTAAGTGTGATATTTGGGACGAGTCGGGTAGGGTTTTTTTAAGTG
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGAGTCGGGTACGGTTTTTTTAAGTG
* *
309596 TGATATTCGGGTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCCGAAAATATATATAATT
66 TGATAAT---GTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCAGAAAATATATATAATT
** *
309661 CGGGTTGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCG
128 CGGGTCAGGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCG
309726 GGTCGGGTCGGATTTCTAATTCATATA
193 GGTCGGGTCGGATTTCTAATTCATATA
*
309753 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTCGGGT-CGG-TTTTTTAAGTG
1 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGAGTCGGGTACGGTTTTTTTAAGTG
* *
309816 TGA-AAT-TCGGG-TCGGGTTTAGGGTGAAAAAAATCGGACCGACCAGAAAATATATATAATTCG
66 TGATAATGTCGGGTTCGGGTTTAGGGT-AAAAAAATAGGACAGACCAGAAAATATATATAATTCG
*
309878 GGTCAGGTCGGATTAAGTCACTATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGG
130 GGTCAGGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTTATTATTTCGGG
309938 AAGGATTTCT
Statistics
Matches: 172, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
214 13 0.08
215 95 0.55
219 2 0.01
220 14 0.08
221 2 0.01
222 46 0.27
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.36
Consensus pattern (219 bp):
TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGACGAGTCGGGTACGGTTTTTTTAAGTG
TGATAATGTCGGGTTCGGGTTTAGGGTAAAAAAATAGGACAGACCAGAAAATATATATAATTCGG
GTCAGGTCGGATTAAGTCACTATTTTTATTAAATAAAAACAATTTTTTATTATTTCGGGTCGGGT
CGGGTCGGATTTCTAATTCATATA
Found at i:310056 original size:38 final size:38
Alignment explanation
Indices: 309993--310081 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
309983 ATTTTGTTCG
*
309993 GGTCGGGTTGGG-TTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTAGGGTTTTTTTAAGTGTGATATTCGGGTCA
310029 GAGTCGGGTAGGGTTTTTTTAAGTGTGATATTCGGGTCA
1 G-GTCGGGTAGGGTTTTTTTAAGTGTGATATTCGGGTCA
*
310068 GGTCGGGTCGGGTT
1 GGTCGGGTAGGGTT
310082 CGGGTTTAGG
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:0.12, C:0.09, G:0.40, T:0.38
Consensus pattern (38 bp):
GGTCGGGTAGGGTTTTTTTAAGTGTGATATTCGGGTCA
Found at i:312125 original size:27 final size:28
Alignment explanation
Indices: 312067--312127 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
312057 ACCCGACTTG
* *
312067 ACCCGAATATCACGCTTAAAAAAACCCG
1 ACCCGAATATCACACTTAAAAAAACCCA
312095 ACCCGAATATCACACTT-AAAAAACCCA
1 ACCCGAATATCACACTTAAAAAAACCCA
312122 ACCCGA
1 ACCCGA
312128 CCCGAACAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 15 0.48
28 16 0.52
ACGTcount: A:0.44, C:0.34, G:0.08, T:0.13
Consensus pattern (28 bp):
ACCCGAATATCACACTTAAAAAAACCCA
Found at i:313593 original size:21 final size:21
Alignment explanation
Indices: 313569--313609 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
313559 AAAAAATTAC
*
313569 TTAAAATATTATTATTTTTAT
1 TTAAAATATTAATATTTTTAT
*
313590 TTAAAATATTAATGTTTTTA
1 TTAAAATATTAATATTTTTA
313610 ATATTTCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTAAAATATTAATATTTTTAT
Found at i:314222 original size:24 final size:24
Alignment explanation
Indices: 314161--314223 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 24
314151 ATGTGGTTTC
* *
314161 TTAAAATTTTAAAATTATTATATA
1 TTAAAATTTTATAATTTTTATATA
*
314185 TTAAAA-TTT-T-ATTTTTATCT-
1 TTAAAATTTTATAATTTTTATATA
314205 TCTAAAATTTTATAATTTT
1 T-TAAAATTTTATAATTTT
314224 AAATTTCTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
20 1 0.03
21 13 0.41
22 3 0.09
23 4 0.12
24 11 0.34
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAAAATTTTATAATTTTTATATA
Found at i:314231 original size:24 final size:23
Alignment explanation
Indices: 314157--314231 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 23
314147 GGAGATGTGG
*
314157 TTTCTTAAAATTTTAAAATTATTATA
1 TTTC-TAAAATTTTATAATT-TTA-A
*
314183 TAT-TAAAATTTTAT--TTTT-A
1 TTTCTAAAATTTTATAATTTTAA
314202 TCTTCTAAAATTTTATAATTTTAAA
1 T-TTCTAAAATTTTATAATTTT-AA
314227 TTTCT
1 TTTCT
314232 CTTCTCTCGA
Statistics
Matches: 40, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
19 2 0.05
20 1 0.03
21 13 0.32
22 2 0.05
23 4 0.10
24 14 0.35
25 2 0.05
26 2 0.05
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTCTAAAATTTTATAATTTTAA
Found at i:321766 original size:32 final size:32
Alignment explanation
Indices: 321671--321771 Score: 109
Period size: 31 Copynumber: 3.2 Consensus size: 32
321661 CCGAATAACC
* *
321671 TAGGTAA-ACTATCCATATGTTCCTTAGAACA
1 TAGGTAATACTGTCCATATGTTCCCTAGAACA
* *
321702 TAGGT-ATACTGTCCATATG-TCCCAAAAGACA
1 TAGGTAATACTGTCCATATGTTCCCTAGA-ACA
** *
321733 TAGGTAATTTTGTCCATATGTTCCGTAGAACA
1 TAGGTAATACTGTCCATATGTTCCCTAGAACA
321765 TAGGTAA
1 TAGGTAA
321772 ACCCTCGACT
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
30 6 0.11
31 24 0.42
32 22 0.39
33 5 0.09
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Consensus pattern (32 bp):
TAGGTAATACTGTCCATATGTTCCCTAGAACA
Found at i:327035 original size:22 final size:20
Alignment explanation
Indices: 326999--327062 Score: 56
Period size: 20 Copynumber: 3.0 Consensus size: 20
326989 AAGTAAATTA
* *
326999 TGCAAATCATAAATTTTCTT
1 TGCAAATCTTTAATTTTCTT
* **
327019 TTCAAACTCATTTAATTTGATT
1 TGCAAA-TC-TTTAATTTTCTT
327041 TGCAAATCTTTAATTTTACTT
1 TGCAAATCTTTAATTTT-CTT
327062 T
1 T
327063 CAAGATCATT
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 13 0.39
21 7 0.21
22 13 0.39
ACGTcount: A:0.31, C:0.14, G:0.05, T:0.50
Consensus pattern (20 bp):
TGCAAATCTTTAATTTTCTT
Found at i:327140 original size:22 final size:21
Alignment explanation
Indices: 327098--327137 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
327088 GAGATTATTT
*
327098 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTAAAATA
327119 TCATTTTTGT-ATTTTAAAA
1 TCATTTTT-TAATTTTAAAA
327138 ATAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 16 0.94
22 1 0.06
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTAAAATA
Found at i:332383 original size:23 final size:22
Alignment explanation
Indices: 332346--332409 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 22
332336 CAGCTCATAT
* *
332346 AAATACACCAAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCA-GTAG
** *
332369 AGTTGCACCGTAGTGCCGAGTAG
1 AAATGCACCGAAGTGCC-AGTAG
332392 AAATGCACCGAAGTGCCA
1 AAATGCACCGAAGTGCCA
332410 TATAAGGTTG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (22 bp):
AAATGCACCGAAGTGCCAGTAG
Found at i:332807 original size:2 final size:2
Alignment explanation
Indices: 332800--332877 Score: 156
Period size: 2 Copynumber: 39.0 Consensus size: 2
332790 ATGTCTTATC
332800 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
332842 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
332878 CACATGTTCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 76 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:332944 original size:2 final size:2
Alignment explanation
Indices: 332937--332973 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
332927 TTCATCTTCC
332937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
332974 CATTTTCCTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:337268 original size:41 final size:42
Alignment explanation
Indices: 337223--337482 Score: 140
Period size: 41 Copynumber: 6.4 Consensus size: 42
337213 GATTATGACT
*
337223 ATCGCAATGCGATTTTCCCAATTCGCAATGCGAATAAGTA-A
1 ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTACA
* * *** * * *
337264 ATCGCAATACGAATTTGGAAAATCGCAATGCG-AT-ACTGACT
1 ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGT-ACA
* * * * *
337305 ATCGCAATGCAATTTTCCTAATTCGCATTGCGATTTA-TATA
1 ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTACA
* ** * *
337346 TTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTA-A
1 ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTACA
* *** * * * * *
337387 ATCGCAACGCGA-TTAAGTAAATCACAATGCGAATTAGGAAA
1 ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTACA
* * * * ** *
337428 ATCGCAATGCGA-ATACGTAAATCGCAATGCGAAT-CTTACT
1 ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTACA
337468 ATCGCAATGCGATTT
1 ATCGCAATGCGATTT
337483 ACATAGCGCC
Statistics
Matches: 162, Mismatches: 50, Indels: 14
0.72 0.22 0.06
Matches are distributed among these distances:
39 2 0.01
40 35 0.22
41 120 0.74
42 4 0.02
43 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (42 bp):
ATCGCAATGCGATTTTCCTAATTCGCAATGCGAATAAGTACA
Found at i:337269 original size:61 final size:60
Alignment explanation
Indices: 337204--337482 Score: 181
Period size: 61 Copynumber: 4.5 Consensus size: 60
337194 GTTTCTAGAT
* * *
337204 TCGCAACGCGATTATGACTATCGCAATGCGATTTTCCCAATTCGCAATGCGAATAAGTAAA
1 TCGCAATGCGATTATGA-TATCGCAATGCGATTTTCACAATTCGCAATGCGAATACGTAAA
* * ** * * * * *
337265 TCGCAATACGAATT-TGGAAAATCGCAATGCGATACTGACTA-TCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCG-ATTAT-G-ATATCGCAATGCGATTTTCACAATTCGCAATGCGAA--TACGTAAA
* ** *
337327 TCGCATTGCGATTTAT-ATATTCGCGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAA
1 TCGCAATGCGA-TTATGATA-TCGCAATGCGATTTTCACAATTCGCAATGCGAATACGTAAA
* * * * *** *
337388 TCGCAACGCGATTAAGTAAATCACAATGCGAATTAGGA-AAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGATTATG-ATATCGCAATGCG-ATTTTCACAATTCGCAATGCGAATACGTAAA
* * *
337449 TCGCAATGCGAATCTTACTATCGCAATGCGATTT
1 TCGCAATGCGATTATGA-TATCGCAATGCGATTT
337483 ACATAGCGCC
Statistics
Matches: 160, Mismatches: 44, Indels: 29
0.69 0.19 0.12
Matches are distributed among these distances:
60 11 0.07
61 96 0.60
62 49 0.31
63 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (60 bp):
TCGCAATGCGATTATGATATCGCAATGCGATTTTCACAATTCGCAATGCGAATACGTAAA
Found at i:337270 original size:20 final size:21
Alignment explanation
Indices: 337245--337296 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
337235 TTTTCCCAAT
*
337245 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
337265 TCGCAATACGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
337286 TCGCAATGCGA
1 TCGCAATGCGA
337297 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:337350 original size:20 final size:21
Alignment explanation
Indices: 337306--337378 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
337296 ATACTGACTA
* * *
337306 TCGCAATGCAATTTTCCTAAT
1 TCGCATTGCGATTTTCATAAT
337327 TCGCATTGCGA-TTT-ATATAT
1 TCGCATTGCGATTTTCATA-AT
*
337347 TCGCGTTGCGATTTTCATAAT
1 TCGCATTGCGATTTTCATAAT
*
337368 TCGCAATGCGA
1 TCGCATTGCGA
337379 ATACGTAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 2 0.05
20 15 0.35
21 23 0.53
22 3 0.07
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCATAAT
Found at i:337393 original size:20 final size:20
Alignment explanation
Indices: 337368--337479 Score: 127
Period size: 20 Copynumber: 5.5 Consensus size: 20
337358 TTTTCATAAT
337368 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
337388 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
337408 TCACAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
337429 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
337449 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
337469 TCGCAATGCGA
1 TCGCAATGCGA
337480 TTTACATAGC
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
19 3 0.04
20 57 0.74
21 17 0.22
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:338052 original size:14 final size:14
Alignment explanation
Indices: 338033--338093 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
338023 GGAAATAACT
*
338033 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
338047 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
338066 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
338080 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
338094 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:338070 original size:19 final size:19
Alignment explanation
Indices: 338006--338074 Score: 60
Period size: 19 Copynumber: 3.8 Consensus size: 19
337996 TAGTTTCGAG
338006 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
*
338026 AAT-AACTATCGCAA--CG-
1 AATGAA-AATCGCAACGCGA
*
338042 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
338059 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
338075 AGATAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 15
0.67 0.07 0.26
Matches are distributed among these distances:
14 7 0.18
15 2 0.05
16 2 0.05
17 1 0.03
18 2 0.05
19 14 0.37
20 10 0.26
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:338070 original size:33 final size:32
Alignment explanation
Indices: 338012--338104 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 32
338002 CGAGAATGAA
*
338012 AATCGCAACGCGGAAATAACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATAA-AATCGCAACGAGAG
*
338046 AATCGCAACGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAACGCGAAAT-AAAATCGCAACGAGAG
*
338079 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAA-TAAAATCGCA
338105 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 41 0.76
34 13 0.24
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (32 bp):
AATCGCAACGCGAAATAAAATCGCAACGAGAG
Found at i:338122 original size:19 final size:19
Alignment explanation
Indices: 338100--338245 Score: 132
Period size: 19 Copynumber: 8.1 Consensus size: 19
338090 GAAACCAAAA
*
338100 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
338119 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
338133 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
338152 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
338171 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
338185 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
338204 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
338224 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
338244 TC
1 TC
338246 AACCAAAAGA
Statistics
Matches: 103, Mismatches: 12, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
14 20 0.19
16 5 0.05
17 5 0.05
19 40 0.39
20 32 0.31
21 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:338183 original size:52 final size:52
Alignment explanation
Indices: 338100--338237 Score: 204
Period size: 52 Copynumber: 2.6 Consensus size: 52
338090 GAAACCAAAA
* **
338100 TCGCATTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
**
338152 TCGCGTTGCGATAGTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
*
338204 TCCGCGTTGCGATTTTCATTATCTCGTTGCGATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATT
338238 TTCATTTCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
52 48 0.63
53 16 0.21
54 12 0.16
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (52 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTCTCTCGTTGCGATAGTCATT
Found at i:340414 original size:21 final size:21
Alignment explanation
Indices: 340345--340414 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
340335 CTGTCATCCC
* *
340345 TCAAGAGTCCACTCCTATCGT
1 TCAAGAGTCCCCTCCCATCGT
* * ** *
340366 TGAAGAGGCCCCTATCATTC-C
1 TCAAGAGTCCCCTCCCA-TCGT
*
340387 TCGAGAGTCCCCTCCCATCGT
1 TCAAGAGTCCCCTCCCATCGT
340408 TCAAGAG
1 TCAAGAG
340415 GCAACTGTCA
Statistics
Matches: 33, Mismatches: 14, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (21 bp):
TCAAGAGTCCCCTCCCATCGT
Found at i:342322 original size:12 final size:12
Alignment explanation
Indices: 342305--342341 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
342295 TCTTCGGGGA
342305 CTTTTTCTTCTT
1 CTTTTTCTTCTT
342317 CTTTTTCTTCTT
1 CTTTTTCTTCTT
342329 CTTTTTCTTCTT
1 CTTTTTCTTCTT
342341 C
1 C
342342 AGGATTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:342583 original size:24 final size:24
Alignment explanation
Indices: 342516--342575 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
342506 CTGAAACATC
* *
342516 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAATTCCGAGTATTGACCAAG
*
342540 ATCAAAGTT-CGGGTATTGACCAAG
1 ATCAAA-TTCCGAGTATTGACCAAG
342564 ATCAAATTCCGA
1 ATCAAATTCCGA
342576 ATACTGACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 27 0.90
25 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (24 bp):
ATCAAATTCCGAGTATTGACCAAG
Found at i:343337 original size:20 final size:20
Alignment explanation
Indices: 343316--343423 Score: 162
Period size: 20 Copynumber: 5.4 Consensus size: 20
343306 TGTATTATCT
* *
343316 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
343336 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
343356 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
343376 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
* * *
343396 CGTTACGAAAGTTAGTATCG
1 CGTTGCGAAAGTCAGAATCG
343416 CGTTGCGA
1 CGTTGCGA
343424 TTTTGTATTA
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 82 1.00
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:343457 original size:20 final size:20
Alignment explanation
Indices: 343311--343457 Score: 161
Period size: 20 Copynumber: 7.3 Consensus size: 20
343301 GATTCTGTAT
* *
343311 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
343331 AATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
343351 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
343371 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
343391 TATCGCGTTACGAAAGTTAG
1 TATCGCGTTGCGAAAGTCAG
** *
343411 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
343432 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
343452 TATCGC
1 TATCGC
343458 ATTGTGATTT
Statistics
Matches: 112, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
19 3 0.03
20 93 0.83
21 14 0.12
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:343620 original size:40 final size:40
Alignment explanation
Indices: 343536--343621 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
343526 ATACTTACTT
* ***
343536 TCGCAACGCGATACTGACTTTCGCAACGCGATTCTGACTT
1 TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
*
343576 TCGCAACGCGATTCTGACTTTCGCAACGAGATTCTGAAAA
1 TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
343616 TCGCAA
1 TCGCAA
343622 TCATCTTCAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
TCGCAACGCGATACTGACTTTCGCAACGAGATTCTGAAAA
Found at i:343621 original size:20 final size:20
Alignment explanation
Indices: 343516--343612 Score: 158
Period size: 20 Copynumber: 4.8 Consensus size: 20
343506 ATTGGGAAAA
* *
343516 TCGCAACGCGATACTTACTT
1 TCGCAACGCGATTCTGACTT
*
343536 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
343556 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
343576 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
343596 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
343613 AAATCGCAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:343860 original size:20 final size:20
Alignment explanation
Indices: 343835--343910 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
343825 CAACGGGGAA
*
343835 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGGCT
*
343855 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
343875 ATCGCAATGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
*
343895 ATCGCAACGAGAAAAT
1 ATCGCAACGCGAAAAT
343911 CGCATTGCGA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.39, C:0.21, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:343934 original size:19 final size:19
Alignment explanation
Indices: 343910--343955 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
343900 AACGAGAAAA
343910 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATAGCCATT
***
343929 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATAGCCATT
343948 TCGCATTG
1 TCGCATTG
343956 TGATTCTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (19 bp):
TCGCATTGCGATAGCCATT
Found at i:345593 original size:41 final size:42
Alignment explanation
Indices: 345548--345639 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
345538 CCTCTTTAAC
* *
345548 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
* * *
345589 GATGATAGGGGCCTCTTGAATGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
345631 GATGACAGG
1 GATGACAGG
345640 TGAGTCGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 19 0.43
42 25 0.57
ACGTcount: A:0.21, C:0.14, G:0.42, T:0.23
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGG
Found at i:345604 original size:21 final size:21
Alignment explanation
Indices: 345575--345635 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
345565 GAACGGTGGG
*
345575 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
345596 GGGGCCTCTTGAATGATTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
345617 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
345636 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:346014 original size:20 final size:20
Alignment explanation
Indices: 345977--346037 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
345967 GAATAATAGT
** *
345977 TTACTTTCGCAACACGAAAC
1 TTACTTTCGCAATGCGAAAA
345997 TTACTTTCGCAATGCGAAAA
1 TTACTTTCGCAATGCGAAAA
* * *
346017 TGACTATCGCAATGCGGAAA
1 TTACTTTCGCAATGCGAAAA
346037 T
1 T
346038 GGCTATCGCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.26
Consensus pattern (20 bp):
TTACTTTCGCAATGCGAAAA
Found at i:346038 original size:20 final size:20
Alignment explanation
Indices: 346003--346078 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
345993 AAACTTACTT
*
346003 TCGCAATGCGAAAATGACTA
1 TCGCAATGCGGAAATGACTA
*
346023 TCGCAATGCGGAAATGGCTA
1 TCGCAATGCGGAAATGACTA
* * *
346043 TCGCAACGCAGAAATGGCTA
1 TCGCAATGCGGAAATGACTA
346063 TCGCAATGC-GAAATGA
1 TCGCAATGCGGAAATGA
346079 AAATCGCAAC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
19 6 0.12
20 44 0.88
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGGAAATGACTA
Found at i:346097 original size:14 final size:14
Alignment explanation
Indices: 346078--346136 Score: 55
Period size: 14 Copynumber: 3.9 Consensus size: 14
346068 ATGCGAAATG
346078 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
346092 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
*
346111 AAAATCGCAATGAC
1 AAAATCGCAACGAC
346125 AAAATCGCAACG
1 AAAATCGCAACG
346137 CGAAACACAA
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 21 0.58
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.28
ACGTcount: A:0.49, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:346152 original size:33 final size:33
Alignment explanation
Indices: 346062--346141 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
346052 AGAAATGGCT
346062 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
346095 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
346128 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
346142 CACAAATCGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:346170 original size:19 final size:19
Alignment explanation
Indices: 346148--346250 Score: 99
Period size: 19 Copynumber: 5.6 Consensus size: 19
346138 GAAACACAAA
346148 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
346167 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
346186 TCGCATTACGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
346202 TCG--TTACGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
346219 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
346238 TCCGCATTGCGAT
1 T-CGCATTGCGAT
346251 AGTTATTTTC
Statistics
Matches: 69, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
14 6 0.09
15 3 0.04
16 4 0.06
17 4 0.06
18 3 0.04
19 38 0.55
20 11 0.16
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:346258 original size:20 final size:19
Alignment explanation
Indices: 346215--346252 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
346205 TTACGATTTT
346215 CATTTCGCATTGCGATAGC
1 CATTTCGCATTGCGATAGC
346234 CATTTCCGCATTGCGATAG
1 CATTT-CGCATTGCGATAG
346253 TTATTTTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.21, C:0.26, G:0.21, T:0.32
Consensus pattern (19 bp):
CATTTCGCATTGCGATAGC
Found at i:348175 original size:20 final size:20
Alignment explanation
Indices: 348150--348192 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
348140 AATAATTTCT
348150 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* * *
348170 GAAAATGACAATTGCAACGC
1 GAAAATGAAAATCGCAACAC
348190 GAA
1 GAA
348193 TTTGACTATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:348497 original size:22 final size:22
Alignment explanation
Indices: 348471--348514 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
348461 GATAGAGATA
*
348471 GACGGATTTCGACGGAGATGGG
1 GACGGATTTCGACAGAGATGGG
*
348493 GACGGATTTCGTCAGAGATGGG
1 GACGGATTTCGACAGAGATGGG
348515 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:0.23, C:0.14, G:0.43, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGACAGAGATGGG
Found at i:348800 original size:41 final size:41
Alignment explanation
Indices: 348681--348818 Score: 188
Period size: 41 Copynumber: 3.4 Consensus size: 41
348671 CGTTTTGAAA
* * *
348681 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
** * * *
348722 ATCGCGTTGCGAAATT-AAGTATCGCATTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
*
348762 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
348803 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
348819 CCAAATTCGC
Statistics
Matches: 82, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 34 0.41
41 48 0.59
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:348815 original size:20 final size:20
Alignment explanation
Indices: 348701--348814 Score: 131
Period size: 20 Copynumber: 5.7 Consensus size: 20
348691 GATTATGTAT
*
348701 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
348721 TATCGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
348741 TATCGCATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
348761 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
348782 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
348802 TATCGCGTTGCGA
1 TATCGCGTTGCGA
348815 TTTTCCAAAT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 60 0.76
21 14 0.18
22 2 0.03
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:348836 original size:41 final size:40
Alignment explanation
Indices: 348708--348835 Score: 159
Period size: 41 Copynumber: 3.1 Consensus size: 40
348698 TATTATCTCG
** *
348708 TTGCGAAAGTCAGTATCGCGTTGCGAAATTAAGTATCGCA
1 TTGCGAAAGTCAGTATCGCGTTGCGATTTTAAATATCGCA
* * *
348748 TTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCGCG
1 TTGCGAAAGTCAGTATCGCGTTGCGATTTT-AAATATCGCA
*
348789 TTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAAT-TCGCA
1 TTGCGAAAGTCAGTATCGCGTTGCGATTTT--AAATATCGCA
348830 TTGCGA
1 TTGCGA
348836 TTTACTTTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
40 28 0.37
41 46 0.61
42 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (40 bp):
TTGCGAAAGTCAGTATCGCGTTGCGATTTTAAATATCGCA
Found at i:348897 original size:21 final size:22
Alignment explanation
Indices: 348845--348897 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
348835 ATTTACTTTT
348845 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
* **
348866 TCGTAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
348887 TCGCATTGCGA
1 TCGCATTGCGA
348898 TAATCATAAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:361478 original size:39 final size:39
Alignment explanation
Indices: 361406--361498 Score: 98
Period size: 39 Copynumber: 2.4 Consensus size: 39
361396 TCCTTGATAA
* **
361406 AAGATGCCATGCACTCCTGAGGTCTTTTCCATTTACCTG
1 AAGATGCCATGCAGTCCTGAAATCTTTTCCATTTACCTG
* **
361445 AAGATGCCATGCAGTCGTGAAATCTTCTT-CATTTGTCTG
1 AAGATGCCATGCAGTCCTGAAATCTT-TTCCATTTACCTG
**
361484 AAGACACCATGCAGT
1 AAGATGCCATGCAGT
361499 TAGGAGTCTT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
39 43 0.96
40 2 0.04
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (39 bp):
AAGATGCCATGCAGTCCTGAAATCTTTTCCATTTACCTG
Found at i:367156 original size:21 final size:21
Alignment explanation
Indices: 367130--367182 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
367120 ATTCTGACTA
367130 TCGCATTGCGA-TTTTCCAAAT
1 TCGCATTGCGACTTTT-CAAAT
*
367151 TCGCATTGCGACTTTTCTAAT
1 TCGCATTGCGACTTTTCAAAT
*
367172 TCGCAATGCGA
1 TCGCATTGCGA
367183 ATACATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 25 0.86
22 4 0.14
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGACTTTTCAAAT
Found at i:367197 original size:20 final size:20
Alignment explanation
Indices: 367172--367244 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
367162 CTTTTCTAAT
*
367172 TCGCAATGCGAATACATAAA
1 TCGCAATGCGAATACGTAAA
367192 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
367212 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
367232 TCGCAACGCGAAT
1 TCGCAATGCGAAT
367245 CTGACTATCG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:367466 original size:22 final size:22
Alignment explanation
Indices: 367441--367506 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
367431 TGCGACATCC
367441 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
* *
367463 GTCCTCATCTCCGACGATATCA
1 GTCCCCATCTCCGACGAAATCA
* *
367485 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
367507 TTCACGGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.38, G:0.15, T:0.23
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:367930 original size:20 final size:20
Alignment explanation
Indices: 367842--367932 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
367832 GCGATTCTGT
367842 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
** **
367861 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTTTCATTTTCG
** *
367881 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATTTTCATTTTCG
*
367901 TGTTGCGATTTTCATTTTCG
1 CGTTGCGATTTTCATTTTCG
*
367921 TGTTGCGATTTT
1 CGTTGCGATTTT
367933 AAGTTTCAAA
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
19 12 0.20
20 49 0.80
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:367939 original size:20 final size:20
Alignment explanation
Indices: 367900--367939 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
367890 AGTCATTTTT
* *
367900 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGATTTTAAGTTTC
367920 GTGTTGCGATTTTAAGTTTC
1 GTGTTGCGATTTTAAGTTTC
367940 AAAAACTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.23, T:0.53
Consensus pattern (20 bp):
GTGTTGCGATTTTAAGTTTC
Found at i:369840 original size:20 final size:20
Alignment explanation
Indices: 369813--369858 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
369803 AGAATAGTTT
*
369813 ACTATCGCAATGCGAAAATG
1 ACTATCGCAACGCGAAAATG
*
369833 ATTATCGCAACGCGAAAATG
1 ACTATCGCAACGCGAAAATG
369853 ACTATC
1 ACTATC
369859 ATAACGAGAG
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:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (20 bp):
ACTATCGCAACGCGAAAATG
Found at i:369864 original size:20 final size:20
Alignment explanation
Indices: 369813--369864 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
369803 AGAATAGTTT
* *
369813 ACTATCGCAATGCGAAAATG
1 ACTATCACAACGCGAAAATG
* *
369833 ATTATCGCAACGCGAAAATG
1 ACTATCACAACGCGAAAATG
*
369853 ACTATCATAACG
1 ACTATCACAACG
369865 AGAGAATCGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
ACTATCACAACGCGAAAATG
Found at i:369927 original size:34 final size:34
Alignment explanation
Indices: 369836--369929 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 34
369826 GAAAATGATT
** * * *
369836 ATCGCAACGCGAAAATGACTATCATAACGAGAGA
1 ATCGCAACGCGAAAATGACTATCGCAACAACAAA
* **
369870 ATCGCAATGCG-AAATGAAAATCGCAACAACAAA
1 ATCGCAACGCGAAAATGACTATCGCAACAACAAA
369903 ATCGCAACGCGAAAATGACTATCGCAA
1 ATCGCAACGCGAAAATGACTATCGCAA
369930 TGCAAAAATG
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
33 25 0.52
34 23 0.48
ACGTcount: A:0.46, C:0.22, G:0.18, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAACAACAAA
Found at i:369938 original size:34 final size:34
Alignment explanation
Indices: 369836--369938 Score: 88
Period size: 34 Copynumber: 3.1 Consensus size: 34
369826 GAAAATGATT
** * *
369836 ATCGCAACGCGAAAATGACTATCATAA-CGAGAGA
1 ATCGCAACGCGAAAATGACTATCGCAAGC-ACAAA
* **
369870 ATCGCAATGCG-AAATGAAAATCGCAA-CAACAAA
1 ATCGCAACGCGAAAATGACTATCGCAAGC-ACAAA
369903 ATCGCAACGCGAAAATGACTATCGCAATGCA-AAA
1 ATCGCAACGCGAAAATGACTATCGCAA-GCACAAA
369937 AT
1 AT
369939 GGCTATCGCA
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
33 25 0.45
34 28 0.51
35 1 0.02
36 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.17, T:0.15
Consensus pattern (34 bp):
ATCGCAACGCGAAAATGACTATCGCAAGCACAAA
Found at i:369964 original size:20 final size:20
Alignment explanation
Indices: 369903--369951 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
369893 CAACAACAAA
* *
369903 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCAAAAATGACT
*
369923 ATCGCAATGCAAAAATGGCT
1 ATCGCAATGCAAAAATGACT
369943 ATCGCAATG
1 ATCGCAATG
369952 TGAATTTGAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCAAAAATGACT
Found at i:370041 original size:20 final size:20
Alignment explanation
Indices: 370016--370082 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
370006 GATTCTCTCG
370016 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
*
370036 TTGCGATAGTCAAATTTGCA
1 TTGCGATAGTCAAATTCGCA
** *
370056 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
370076 TTGCGAT
1 TTGCGAT
370083 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:372075 original size:14 final size:14
Alignment explanation
Indices: 372056--372091 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
372046 ATTGTTTAAT
372056 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
372070 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
372084 TGATTTGT
1 TGATTTGT
372092 TTAATTGATG
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:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:372218 original size:20 final size:19
Alignment explanation
Indices: 372193--372244 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
372183 ATGCAAAACA
372193 GACTATCGCAACGCGGAAAT
1 GACTATCGCAACGC-GAAAT
*
372213 GACTATCGCAATGCGAAAT
1 GACTATCGCAACGCGAAAT
**
372232 GAAAATCGCAACG
1 GACTATCGCAACG
372245 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (19 bp):
GACTATCGCAACGCGAAAT
Found at i:372274 original size:20 final size:19
Alignment explanation
Indices: 372197--372283 Score: 76
Period size: 20 Copynumber: 4.7 Consensus size: 19
372187 AAAACAGACT
**
372197 ATCGCAACGCGGAAATGACT
1 ATCGCAACGC-GAAATGAAA
*
372217 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
372236 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
*
372250 ATCGCAATGCGAAAATGAAA
1 ATCGCAACGCG-AAATGAAA
372270 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
372284 CTAAATTCGC
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
19 18 0.33
20 22 0.40
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:372355 original size:33 final size:33
Alignment explanation
Indices: 372293--372388 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
372283 ACTAAATTCG
* *
372293 CGTTGCGATTTTTATTTTCGCATTTCGATTCTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
* *
372327 CGTTGCAATTTTCATTTCGCATTGCGATTTTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
372360 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
372389 AGTCAATTCC
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 31 0.58
34 22 0.42
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:372383 original size:20 final size:20
Alignment explanation
Indices: 372360--372448 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
372350 GCGATTTTCT
372360 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
372380 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
372400 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
372420 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
372440 CGTTGCGAT
1 CGTTGCGAT
372449 TTCCGCGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 62 0.97
21 2 0.03
ACGTcount: A:0.17, C:0.22, G:0.26, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:375792 original size:20 final size:20
Alignment explanation
Indices: 375767--375853 Score: 111
Period size: 20 Copynumber: 4.3 Consensus size: 20
375757 AAATTAAGTA
*
375767 TTGCGATAGTTAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
375787 TTGCGATAGTCGGAATCTCG
1 TTGCGATAGTCAGAATCGCG
* * *
375807 TTGCGATAGCCAGATTCGTG
1 TTGCGATAGTCAGAATCGCG
*
375827 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
375847 TTGCGAT
1 TTGCGAT
375854 TTACGTATTC
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:375863 original size:20 final size:20
Alignment explanation
Indices: 375840--375912 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
375830 CGATAGTCAG
*
375840 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
375860 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
375880 ATTCGCATTGCGAATTACGT
1 ATTCGCATTGCGATTTACGT
375900 ATTCGCATTGCGA
1 ATTCGCATTGCGA
375913 ATTAGGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:375952 original size:41 final size:40
Alignment explanation
Indices: 375902--375997 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 40
375892 AATTACGTAT
* *
375902 TCGCATTGCGAATTAGGAAAATCGCA-ATGCGATAGTCAGA-A
1 TCGCGTTGCGAATTAGGAAAAT-G-ATATGCGATA-CCAGAGA
* *
375943 TCGCGTTGCGAATCT-GGAAACTGATTTGCGATACCAGAGA
1 TCGCGTTGCGAAT-TAGGAAAATGATATGCGATACCAGAGA
375983 TCGCGTTGCGAATTA
1 TCGCGTTGCGAATTA
375998 TCGATCGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
39 6 0.13
40 22 0.47
41 18 0.38
42 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (40 bp):
TCGCGTTGCGAATTAGGAAAATGATATGCGATACCAGAGA
Found at i:380802 original size:2 final size:2
Alignment explanation
Indices: 380795--380843 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
380785 CGACGTGTTA
*
380795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
380837 AT -T AT AT
1 AT AT AT AT
380844 TTTTTTATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:382048 original size:2 final size:2
Alignment explanation
Indices: 382041--382095 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
382031 AGTTTATTTC
382041 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
382083 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
382096 ATTATTAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:382356 original size:45 final size:45
Alignment explanation
Indices: 382305--382393 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
382295 TAAAAAAACA
*
382305 TTAAACTTATTTTCATTTTTAAGTCTTACATTAACTATAATTTAT
1 TTAAACTTATTTTCATTTCTAAGTCTTACATTAACTATAATTTAT
382350 TTAAACTTATTTTCATTTCTAAGTCTTACATTAACTATAATTTA
1 TTAAACTTATTTTCATTTCTAAGTCTTACATTAACTATAATTTA
382394 ATATATATGT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (45 bp):
TTAAACTTATTTTCATTTCTAAGTCTTACATTAACTATAATTTAT
Found at i:390671 original size:44 final size:44
Alignment explanation
Indices: 390603--390706 Score: 154
Period size: 44 Copynumber: 2.4 Consensus size: 44
390593 TTGTGCACTG
*
390603 TGCATCGATACAATATGAAAGTGTACCGATGCATCCCTTGAATA
1 TGCATCGATACACTATGAAAGTGTACCGATGCATCCCTTGAATA
* * * * *
390647 TGCATCGATACACTATGAAGGTGTATCGATTCATTCCTTGAATG
1 TGCATCGATACACTATGAAAGTGTACCGATGCATCCCTTGAATA
390691 TGCATCGATACACTAT
1 TGCATCGATACACTAT
390707 ACAGTGCATC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 54 1.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGTACCGATGCATCCCTTGAATA
Found at i:390697 original size:23 final size:22
Alignment explanation
Indices: 390629--390702 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
390619 GAAAGTGTAC
* *
390629 CGATGCATCCCTTGAATATGCAT
1 CGATACAT-CCTTGAATGTGCAT
* *
390652 CGATACA--CTATGAAGGTGTAT
1 CGATACATCCT-TGAATGTGCAT
*
390673 CGATTCATTCCTTGAATGTGCAT
1 CGATACA-TCCTTGAATGTGCAT
390696 CGATACA
1 CGATACA
390703 CTATACAGTG
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
20 2 0.05
21 14 0.36
23 21 0.54
24 2 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (22 bp):
CGATACATCCTTGAATGTGCAT
Found at i:392678 original size:27 final size:27
Alignment explanation
Indices: 392627--392678 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
392617 TGTTTTATTT
*
392627 TGGATGTTTGAATATTTAAATTTGATA
1 TGGATGTTTGAATATTTAAACTTGATA
* * *
392654 TGGATGTTTGGATGTTTGAACTTGA
1 TGGATGTTTGAATATTTAAACTTGA
392679 ATGCTTATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (27 bp):
TGGATGTTTGAATATTTAAACTTGATA
Found at i:393457 original size:65 final size:64
Alignment explanation
Indices: 393325--393480 Score: 181
Period size: 65 Copynumber: 2.4 Consensus size: 64
393315 ACACCCTAAT
* *
393325 TCGAATGCATTTTGTGTACCGATGCACAACCATGCATCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
* * * * * *
393389 TCGAAAGCATTTTATGTACCGATGCACAGTCTATGCATTGATGCACTCCTGGCTCTT-TTGAAAT
1 TCGAATGCATTTTATGTACCGATGCACA-ACCATGCATCGATGCACTCCT-GATCTTATTGAAAC
393453 A
64 A
* *
393454 TCGAATGTA-ATTAGTGTACCGATGCAC
1 TCGAATGCATTTTA-TGTACCGATGCAC
393481 CCCAAGTGTA
Statistics
Matches: 78, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 29 0.37
65 45 0.58
66 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (64 bp):
TCGAATGCATTTTATGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
Found at i:397264 original size:21 final size:22
Alignment explanation
Indices: 397238--397283 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
397228 GGGTTAAAAA
397238 AATTTCTATAGAT-GAAATTTG
1 AATTTCTATAGATGGAAATTTG
* * *
397259 AATTTCTTTATATGGGAATTTG
1 AATTTCTATAGATGGAAATTTG
397281 AAT
1 AAT
397284 GCAAAATATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (22 bp):
AATTTCTATAGATGGAAATTTG
Found at i:398376 original size:25 final size:25
Alignment explanation
Indices: 398347--398397 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
398337 TTTTTTAGTC
398347 GAGTCTAGTGGAGTCAAATTTTTGA
1 GAGTCTAGTGGAGTCAAATTTTTGA
398372 GAGTCTAGTGGAGTCAAATTTTTGA
1 GAGTCTAGTGGAGTCAAATTTTTGA
398397 G
1 G
398398 GTTTTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.27, C:0.08, G:0.29, T:0.35
Consensus pattern (25 bp):
GAGTCTAGTGGAGTCAAATTTTTGA
Found at i:408658 original size:2 final size:2
Alignment explanation
Indices: 408653--408998 Score: 53
Period size: 2 Copynumber: 178.5 Consensus size: 2
408643 TGAAAAAATA
* *
408653 AT AT AT AT AT AT AT AT A- AT AT A- AA AT -T AT AT AT AA ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * * * *
408693 AT TT AT AT -T AT AA ACT AT AT AT AT AA AT -T AT AT TT AT GT GA-
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * * *
408734 ACT AT AT AT AT AA ACT AT GT AT AT A- AA AT -T AT AA ACT AT AT
1 A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
408775 TT AT AT -T AT AA AT -T AT AT A- AT -T AT -T AT A- AGT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * * * *
408811 AT AT AA AT -T AT GT TT AT GT GAT CT AT AT AT AT AA ACT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT A-T AT AT AT
* * * * * *
408854 AT AA ACT AT AT AT GT AT AA ACT AT AA AA AGT AT AT AGT TT AT A-
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT A-T AT AT AT
* * *
408897 AA AT AT -T AT TT AT AT -T A- AT AT AGT AT AT AT AT AT AT AA ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* * * *
408938 AT AT A- AA AT AT A- AA AT AT AT A- AT TT AT AT GT -T AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
408975 TT AT AT -T A- AT AT AGT AT AT AT AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT A
408999 AAAAATGGCT
Statistics
Matches: 242, Mismatches: 59, Indels: 86
0.63 0.15 0.22
Matches are distributed among these distances:
1 27 0.11
2 199 0.82
3 16 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:408672 original size:17 final size:17
Alignment explanation
Indices: 408654--408717 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 17
408644 GAAAAAATAA
408654 TATATATATATATATAA-
1 TATATATATATATA-AAC
*
408671 TATAAAATTATATATAAAC
1 TAT-ATA-TATATATAAAC
*
408690 TATATTTATATTATAAAC
1 TATATATATA-TATAAAC
408708 TATATATATA
1 TATATATATA
408718 AATTATATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
17 7 0.18
18 21 0.54
19 11 0.28
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATATATATATAAAC
Found at i:408682 original size:15 final size:17
Alignment explanation
Indices: 408650--408687 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
408640 AATTGAAAAA
*
408650 ATAATATATATATATAT
1 ATAATATATAAATATAT
408667 ATAATATA-AAATTATAT
1 ATAATATATAAA-TATAT
408684 ATAA
1 ATAA
408688 ACTATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAATATATAAATATAT
Found at i:408699 original size:13 final size:13
Alignment explanation
Indices: 408696--408878 Score: 55
Period size: 13 Copynumber: 14.3 Consensus size: 13
408686 AAACTATATT
408696 TATA-TTATAAAC
1 TATATTTATAAAC
* *
408708 TATATATATAAAT
1 TATATTTATAAAC
*
408721 TATATTTATGTGAAC
1 TATATTTA--TAAAC
*
408736 TATATATATAAAC
1 TATATTTATAAAC
* *
408749 TATGTATAT-AA-
1 TATATTTATAAAC
408760 -A-A-TTATAAAC
1 TATATTTATAAAC
*
408770 TATATTTAT--AT
1 TATATTTATAAAC
*
408781 TATAAATTATATAA-
1 TAT-ATTTATA-AAC
**
408795 T-TA-TTATAAGT
1 TATATTTATAAAC
* *
408806 TATATATATAAAT
1 TATATTTATAAAC
* * *
408819 TATGTTTATGTGATC
1 TATATTTA--TAAAC
*
408834 TATATATATAAAC
1 TATATTTATAAAC
* *
408847 TATGTATATAAAC
1 TATATTTATAAAC
408860 TATATATGTATAAAC
1 TATAT-T-TATAAAC
408875 TATA
1 TATA
408879 AAAAGTATAT
Statistics
Matches: 125, Mismatches: 27, Indels: 35
0.67 0.14 0.19
Matches are distributed among these distances:
8 3 0.02
9 2 0.02
10 2 0.02
11 11 0.09
12 15 0.12
13 61 0.49
14 1 0.01
15 30 0.24
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (13 bp):
TATATTTATAAAC
Found at i:408706 original size:18 final size:17
Alignment explanation
Indices: 408656--408717 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
408646 AAAAATAATA
*
408656 TATATATATATATAATA-
1 TATATTTATATATAA-AC
* *
408673 TAAAATTATATATAAAC
1 TATATTTATATATAAAC
408690 TATATTTATATTATAAAC
1 TATATTTATA-TATAAAC
*
408708 TATATATATA
1 TATATTTATA
408718 AATTATATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
16 1 0.03
17 20 0.54
18 16 0.43
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TATATTTATATATAAAC
Found at i:408856 original size:15 final size:15
Alignment explanation
Indices: 408834--408878 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
408824 TTATGTGATC
408834 TATATATATAAAC--
1 TATATATATAAACTA
*
408847 TATGTATATAAACTA
1 TATATATATAAACTA
*
408862 TATATGTATAAACTA
1 TATATATATAAACTA
408877 TA
1 TA
408879 AAAAGTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 12 0.44
15 15 0.56
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (15 bp):
TATATATATAAACTA
Found at i:408923 original size:69 final size:69
Alignment explanation
Indices: 408868--408998 Score: 190
Period size: 69 Copynumber: 1.9 Consensus size: 69
408858 ACTATATATG
* * *
408868 TATAAACTATAAAAAGTATATAGTTTATAAAATATTATTTATATTAATATAGTATATATATATAT
1 TATAAAATAT-AAAA-TATATAATTTATAAAATATAATTTATATTAATATAGTATATATATATAT
408933 AAACTA
64 AAACTA
***
408939 TATAAAATATAAAATATATAATTTATATGTTATAATTTATATTAATATAGTATATATATA
1 TATAAAATATAAAATATATAATTTATAAAATATAATTTATATTAATATAGTATATATATA
408999 AAAAATGGCT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 41 0.76
70 4 0.07
71 9 0.17
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (69 bp):
TATAAAATATAAAATATATAATTTATAAAATATAATTTATATTAATATAGTATATATATATATAA
ACTA
Found at i:409384 original size:14 final size:14
Alignment explanation
Indices: 409361--409419 Score: 66
Period size: 14 Copynumber: 4.2 Consensus size: 14
409351 TATATATACA
*
409361 TTAGGATTTATGGT
1 TTAGGGTTTATGGT
409375 TTAGGGTTTAGTGG-
1 TTAGGGTTTA-TGGT
* *
409389 TTAGGTTTTATGAT
1 TTAGGGTTTATGGT
*
409403 TTAGGGTTTAAGGT
1 TTAGGGTTTATGGT
409417 TTA
1 TTA
409420 TATAAACTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
13 2 0.05
14 32 0.86
15 3 0.08
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:409701 original size:17 final size:19
Alignment explanation
Indices: 409649--409706 Score: 66
Period size: 17 Copynumber: 3.1 Consensus size: 19
409639 AATTTTTCTA
* *
409649 TTCCCTCTAAATTTTCCAAT
1 TTCCCACTAAATTCT-CAAT
409669 TTCCCACTAAATTCTCAAT
1 TTCCCACTAAATTCTCAAT
*
409688 TT-CC-CTATATTCTCAAT
1 TTCCCACTAAATTCTCAAT
409705 TT
1 TT
409707 TCTAATTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 14 0.40
18 2 0.06
19 6 0.17
20 13 0.37
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (19 bp):
TTCCCACTAAATTCTCAAT
Found at i:410271 original size:2 final size:2
Alignment explanation
Indices: 410264--410292 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
410254 TATGTTTAAT
410264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
410293 TATTCAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:410427 original size:19 final size:20
Alignment explanation
Indices: 410405--410445 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
410395 GAATATAGGG
410405 AAATTGTG-AATTTAGAGGA
1 AAATTGTGAAATTTAGAGGA
410424 AAATTGTGAAATTTAGAGGA
1 AAATTGTGAAATTTAGAGGA
410444 AA
1 AA
410446 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (20 bp):
AAATTGTGAAATTTAGAGGA
Found at i:410446 original size:19 final size:18
Alignment explanation
Indices: 410403--410446 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 18
410393 GAGAATATAG
410403 GGAAATTGTGAATTTAGA
1 GGAAATTGTGAATTTAGA
410421 GGAAAATTGTGAAATTTAGA
1 GG-AAATTGTG-AATTTAGA
410441 GGAAAT
1 GGAAAT
410447 AAAAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.08
19 12 0.50
20 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (18 bp):
GGAAATTGTGAATTTAGA
Found at i:410455 original size:46 final size:46
Alignment explanation
Indices: 410366--410455 Score: 103
Period size: 46 Copynumber: 2.0 Consensus size: 46
410356 TTTTATTTGG
* * ***
410366 GAATTTAGAGGGAAATTAGTAAATTTTGAGAATATAGGGAAATTGT
1 GAATTTAGAGGAAAATTAGTAAATTTAGAGAATATAAAAAAATTGT
410412 GAATTTAGAGGAAAATT-GTGAAATTTAGAGGAA-ATAAAAAAATT
1 GAATTTAGAGGAAAATTAGT-AAATTTAGA-GAATATAAAAAAATT
410456 TGGGAAGCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.05
46 32 0.86
47 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (46 bp):
GAATTTAGAGGAAAATTAGTAAATTTAGAGAATATAAAAAAATTGT
Found at i:410939 original size:14 final size:14
Alignment explanation
Indices: 410920--410966 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
410910 ATTTTTTCTT
410920 TATATAAATTAAAC
1 TATATAAATTAAAC
410934 TATAT-AATT----
1 TATATAAATTAAAC
410943 TATATAAATTAAAC
1 TATATAAATTAAAC
*
410957 TATATTAATT
1 TATATAAATT
410967 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:410944 original size:23 final size:24
Alignment explanation
Indices: 410918--410967 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
410908 TTATTTTTTC
410918 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
410941 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
410965 TTT
1 TTT
410968 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:411275 original size:16 final size:16
Alignment explanation
Indices: 411201--411299 Score: 117
Period size: 16 Copynumber: 6.2 Consensus size: 16
411191 CGGATCATTT
* *
411201 ACAGGTTAGGTTAAAA
1 ACAGGTCAGGTTGAAA
* * *
411217 ACGGGTCAAGTTAAAA
1 ACAGGTCAGGTTGAAA
411233 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
411249 ACAAGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
*
411265 ACAGGTTAGGTTGAAA
1 ACAGGTCAGGTTGAAA
* *
411281 GCATGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
411297 ACA
1 ACA
411300 AGTCGGGTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 70 1.00
ACGTcount: A:0.40, C:0.11, G:0.27, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:411451 original size:64 final size:63
Alignment explanation
Indices: 411328--411475 Score: 140
Period size: 64 Copynumber: 2.3 Consensus size: 63
411318 ATTTACCAGG
* * *
411328 TCAATATCGGGTTCAGGTTCATATCAGTCGGATGCAGTTCGAGTTCGGGTATCATA-TTTTCGGT
1 TCAAT-TCGGGTTCAGG-TCATATCAGTCGGATGCAGGTCGAGTTCGGGTATCAAATTTTTAGGT
* * *
411392 TCAATTCGGGTTCAGGTCGTTCTCAGGTCGGATGCAGGTCGGGTTC-GG-ATCCACAATTTTTAG
1 TCAATTCGGGTTCAGGTC-ATATCA-GTCGGATGCAGGTCGAGTTCGGGTAT-CA-AATTTTTAG
411455 GT
62 GT
* * *
411457 CCAAATCGGATTCAGGTCA
1 TCAATTCGGGTTCAGGTCA
411476 ACACCAGTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
62 4 0.06
63 19 0.28
64 24 0.35
65 22 0.32
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (63 bp):
TCAATTCGGGTTCAGGTCATATCAGTCGGATGCAGGTCGAGTTCGGGTATCAAATTTTTAGGT
Found at i:423517 original size:64 final size:65
Alignment explanation
Indices: 423404--423550 Score: 192
Period size: 64 Copynumber: 2.3 Consensus size: 65
423394 CATTCATAAG
* * *
423404 TGCATCGATGCATTCC-TTTAAAAGAAAGAACATCGAATGCCTTTGATGCATCGATGCA-TAGCT
1 TGCATCGATGCA-TCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAG-T
423467 AA
64 AA
* * *
423469 TGCATCGATGCATCCTTTTAAAATAAA-AACATCGAATGCATTTTATGCACCGATGCACAAGTAG
1 TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
423533 TGCATCGATGCATACCTT
1 TGCATCGATGCAT-CCTT
423551 CATTGAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
64 45 0.62
65 28 0.38
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (65 bp):
TGCATCGATGCATCCTTTTAAAAGAAAGAACATCGAATGCATTTGATGCACCGATGCACAAGTAA
Found at i:424296 original size:31 final size:31
Alignment explanation
Indices: 424202--424309 Score: 103
Period size: 31 Copynumber: 3.5 Consensus size: 31
424192 AGTCGAGGGT
* *
424202 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * ** *
424233 TATACCTATGTTCTAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
424264 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
424295 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
424310 ATGACCTCTG
Statistics
Matches: 63, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
30 13 0.21
31 47 0.75
32 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:424316 original size:30 final size:30
Alignment explanation
Indices: 424224--424330 Score: 90
Period size: 31 Copynumber: 3.5 Consensus size: 30
424214 TTTCGAGACA
* * * *
424224 TATGGACAGTATACCTATGTTC-TAAGGAACA
1 TATGGACAGT-TACCGAGGTTCTTTAGG-ACC
* *
424255 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAG-TTACCGAGGTTCTTTAGGACC
* *
424286 TATGGACAGTTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTACCGAGGTTCTTTAGGACC
* *
424316 TCTGGATAGTTACCG
1 TATGGACAGTTACCG
424331 GGGTCTGTGT
Statistics
Matches: 63, Mismatches: 11, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
30 29 0.46
31 30 0.48
32 4 0.06
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGTTCTTTAGGACC
Found at i:428961 original size:20 final size:20
Alignment explanation
Indices: 428924--428961 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
428914 TCTCAGTCAT
*
428924 TCCTTCCTCCAAGGTCTGTA
1 TCCTTCCTCCAAGCTCTGTA
428944 TCCTTCCCTCC-AGCTCTG
1 TCCTT-CCTCCAAGCTCTG
428962 CTTTCTGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.11, C:0.42, G:0.13, T:0.34
Consensus pattern (20 bp):
TCCTTCCTCCAAGCTCTGTA
Found at i:431273 original size:24 final size:24
Alignment explanation
Indices: 431246--431300 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
431236 GTGGTTTCGT
431246 CCGGATGAACCATAGCTGGTCCGA
1 CCGGATGAACCATAGCTGGTCCGA
431270 CCGGATGAACCATAGCTGGTCCGA
1 CCGGATGAACCATAGCTGGTCCGA
431294 CCGGATG
1 CCGGATG
431301 CTGCTTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.29, G:0.31, T:0.16
Consensus pattern (24 bp):
CCGGATGAACCATAGCTGGTCCGA
Found at i:438152 original size:15 final size:15
Alignment explanation
Indices: 438129--438158 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
438119 TATTAAAAAA
*
438129 TAATTTAATATTATT
1 TAATATAATATTATT
438144 TAATATAATATTATT
1 TAATATAATATTATT
438159 ATTTTTATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAATATAATATTATT
Found at i:438154 original size:33 final size:33
Alignment explanation
Indices: 438092--438156 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
438082 TATTAATCAG
**
438092 AAAATAATTAATATTATTATTTTAAAATATTAA
1 AAAATAATTAATATTATTATAATAAAATATTAA
*
438125 AAAATAATTTAATATTATT-TAATATAATATTA
1 AAAATAA-TTAATATTATTATAATAAAATATTA
438157 TTATTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 17 0.61
34 11 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (33 bp):
AAAATAATTAATATTATTATAATAAAATATTAA
Found at i:441301 original size:17 final size:18
Alignment explanation
Indices: 441279--441319 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
441269 CGATTGAAGC
* *
441279 TCAAACTTGAGCTC-AGT
1 TCAAACTCGAACTCAAGT
441296 TCAAACTCGAACTCAAGT
1 TCAAACTCGAACTCAAGT
441314 TCAAAC
1 TCAAAC
441320 CTGAACCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (18 bp):
TCAAACTCGAACTCAAGT
Found at i:441325 original size:18 final size:17
Alignment explanation
Indices: 441279--441325 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
441269 CGATTGAAGC
* *
441279 TCAAACTTGAGCTCAGT
1 TCAAACCTGAACTCAGT
441296 TCAAA-CTCGAACTCAAGT
1 TCAAACCT-GAACTC-AGT
441314 TCAAACCTGAAC
1 TCAAACCTGAAC
441326 CTTAAGTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
16 1 0.04
17 10 0.40
18 12 0.48
19 2 0.08
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (17 bp):
TCAAACCTGAACTCAGT
Found at i:441727 original size:23 final size:24
Alignment explanation
Indices: 441684--441729 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
441674 ATTTTAGAAT
*
441684 TATACAAATTAATTAATAATAAAA
1 TATACAAATTAATTAAAAATAAAA
441708 TATAC-AATTGAA-TAAAAATAAA
1 TATACAAATT-AATTAAAAATAAA
441730 TTTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.30
Consensus pattern (24 bp):
TATACAAATTAATTAAAAATAAAA
Found at i:442363 original size:52 final size:49
Alignment explanation
Indices: 442293--442397 Score: 138
Period size: 49 Copynumber: 2.1 Consensus size: 49
442283 CAAAATTTTT
* * *
442293 ACCTCGATATGATAAATTTTAATAAAAAAATTATATTTTATTGGAACTCGTC
1 ACCTCGAGATGATAAATTTGAAT--AAAAATTAT-TTTTATTAGAACTCGTC
* *
442345 ACCTCGAGGTGATGAATTTGAATAAAAATTATTTTTATTAGAACTCGTC
1 ACCTCGAGATGATAAATTTGAATAAAAATTATTTTTATTAGAACTCGTC
442394 ACCT
1 ACCT
442398 TGACTTAACG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 20 0.42
50 9 0.19
52 19 0.40
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (49 bp):
ACCTCGAGATGATAAATTTGAATAAAAATTATTTTTATTAGAACTCGTC
Found at i:452172 original size:21 final size:23
Alignment explanation
Indices: 452146--452196 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
452136 AGGGAATCAA
452146 TCCCCCCTTG-A-GGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
*
452167 TCCCCCTTTGAAGGGGAACCGAT
1 TCCCCCCTTGAAGGGGAACCGAT
452190 TCCCCCC
1 TCCCCCC
452197 ACAGGGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 9 0.35
22 1 0.04
23 16 0.62
ACGTcount: A:0.18, C:0.41, G:0.22, T:0.20
Consensus pattern (23 bp):
TCCCCCCTTGAAGGGGAACCGAT
Found at i:452204 original size:21 final size:21
Alignment explanation
Indices: 452178--452217 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
452168 CCCCCTTTGA
*
452178 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
452199 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
452218 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:455891 original size:24 final size:24
Alignment explanation
Indices: 455846--455895 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
455836 TGGTGGTTGG
*
455846 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATATTTAAACTTTATT
*
455870 TTTAATGGTATATTT-AAGTTTATT
1 TTTAATGG-ATATTTAAACTTTATT
455894 TT
1 TT
455896 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (24 bp):
TTTAATGGATATTTAAACTTTATT
Found at i:460720 original size:13 final size:14
Alignment explanation
Indices: 460697--460726 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
460687 TTCCCATTAC
460697 AGACGTGCATATGA
1 AGACGTGCATATGA
460711 AGAC-TGCATATGA
1 AGACGTGCATATGA
460724 AGA
1 AGA
460727 TTGTCCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Done.