Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008061.1 Hibiscus syriacus cultivar Beakdansim tig00110556_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: 5800122
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 26
Found at i:1321218 original size:12 final size:12
Alignment explanation
Indices: 1321199--1321240 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
1321189 GGGCCGCTAA
*
1321199 AAATAAATTAAT
1 AAATAAATCAAT
*
1321211 ACATAAATCAAT
1 AAATAAATCAAT
1321223 AAATAAA-CAAAT
1 AAATAAATC-AAT
1321235 AAATAA
1 AAATAA
1321241 CGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 1 0.04
12 25 0.96
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:1323182 original size:20 final size:19
Alignment explanation
Indices: 1323158--1323205 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
1323148 TTCTGAAACT
1323158 TAAAATCGCAACGCGAAAA
1 TAAAATCGCAACGCGAAAA
* *
1323177 TGAAAACCGCAACGCGAAAC
1 T-AAAATCGCAACGCGAAAA
1323197 TAAAATCGC
1 TAAAATCGC
1323206 GTTGCGATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.48, C:0.25, G:0.17, T:0.10
Consensus pattern (19 bp):
TAAAATCGCAACGCGAAAA
Found at i:1323608 original size:22 final size:22
Alignment explanation
Indices: 1323562--1323632 Score: 106
Period size: 22 Copynumber: 3.2 Consensus size: 22
1323552 GATGGAGATA
* *
1323562 GACGGATTTCATCGGGAGATGGG
1 GACGAATTTCGTC-GGAGATGGG
*
1323585 GACGAATTTCGTCGGAGATTGG
1 GACGAATTTCGTCGGAGATGGG
1323607 GACGAATTTCGTCGGAGATGGG
1 GACGAATTTCGTCGGAGATGGG
1323629 GACG
1 GACG
1323633 GATGTCGCCG
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 33 0.75
23 11 0.25
ACGTcount: A:0.23, C:0.14, G:0.41, T:0.23
Consensus pattern (22 bp):
GACGAATTTCGTCGGAGATGGG
Found at i:1323832 original size:20 final size:20
Alignment explanation
Indices: 1323809--1323878 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
1323799 TGACTTCTGT
* *
1323809 GTTGCAAATTACAGATTCAC
1 GTTGCGAATTACAGATTCGC
*
1323829 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
*
1323849 GTTGCGATTTACAGATTCGC
1 GTTGCGAATTACAGATTCGC
1323869 GTTGCGAATT
1 GTTGCGAATT
1323879 TAGAAACTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (20 bp):
GTTGCGAATTACAGATTCGC
Found at i:1323834 original size:40 final size:39
Alignment explanation
Indices: 1323790--1323880 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
1323780 TAAACGCGCT
*
1323790 TTGCGAATTTGAC-TTCTGTGTTGCAAATTACAGATTCACG
1 TTGCGAATTT-ACATTC-GCGTTGCAAATTACAGATTCACG
* * *
1323830 TTGCG-ATTTACAGATTCGCGTTGCGATTTACAGATTCGCG
1 TTGCGAATTTAC--ATTCGCGTTGCAAATTACAGATTCACG
1323870 TTGCGAATTTA
1 TTGCGAATTTA
1323881 GAAACTAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
38 2 0.05
39 4 0.09
40 29 0.67
41 8 0.19
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (39 bp):
TTGCGAATTTACATTCGCGTTGCAAATTACAGATTCACG
Found at i:1324179 original size:26 final size:26
Alignment explanation
Indices: 1324160--1324219 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
1324150 ATTATATATG
* **
1324160 AAATATATCAATTTAAATTATAATAA
1 AAATATATAAATAAAAATTATAATAA
1324186 AAATATATAAATAAAAATTATAATAA
1 AAATATATAAATAAAAATTATAATAA
*
1324212 AATTATAT
1 AAATATAT
1324220 TTTATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
AAATATATAAATAAAAATTATAATAA
Found at i:1324215 original size:11 final size:12
Alignment explanation
Indices: 1324174--1324218 Score: 65
Period size: 11 Copynumber: 3.7 Consensus size: 12
1324164 ATATCAATTT
1324174 AAATTATAATAA
1 AAATTATAATAA
1324186 AAATATATAAATAA
1 AAAT-TAT-AATAA
1324200 AAATTATAAT-A
1 AAATTATAATAA
1324211 AAATTATA
1 AAATTATA
1324219 TTTTATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.29
12 7 0.23
13 6 0.19
14 9 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAATTATAATAA
Found at i:1326328 original size:16 final size:14
Alignment explanation
Indices: 1326292--1326319 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1326282 ATGTAATATT
1326292 TTAAATATTGATAC
1 TTAAATATTGATAC
1326306 TTAAATATTGATAC
1 TTAAATATTGATAC
1326320 AATTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
TTAAATATTGATAC
Found at i:1326582 original size:90 final size:90
Alignment explanation
Indices: 1326429--1326608 Score: 351
Period size: 90 Copynumber: 2.0 Consensus size: 90
1326419 AAATAAACTA
1326429 ATTTTACATCAATAAATAATGAAAAAATATCTAAAATATTAAGACTGACTTGCTAATGAATTTCG
1 ATTTTACATCAATAAATAATGAAAAAATATCTAAAATATTAAGACTGACTTGCTAATGAATTTCG
*
1326494 ATTTTAAGGTACTTCAATAGCACAT
66 ATTTTAAGGTACTTCAATAACACAT
1326519 ATTTTACATCAATAAATAATGAAAAAATATCTAAAATATTAAGACTGACTTGCTAATGAATTTCG
1 ATTTTACATCAATAAATAATGAAAAAATATCTAAAATATTAAGACTGACTTGCTAATGAATTTCG
1326584 ATTTTAAGGTACTTCAATAACACAT
66 ATTTTAAGGTACTTCAATAACACAT
1326609 TCTTTAAACA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 89 1.00
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.34
Consensus pattern (90 bp):
ATTTTACATCAATAAATAATGAAAAAATATCTAAAATATTAAGACTGACTTGCTAATGAATTTCG
ATTTTAAGGTACTTCAATAACACAT
Found at i:1326899 original size:20 final size:22
Alignment explanation
Indices: 1326866--1326911 Score: 78
Period size: 20 Copynumber: 2.2 Consensus size: 22
1326856 CAGGAAATAT
1326866 TAAAAAATATTAATATTTTAGA
1 TAAAAAATATTAATATTTTAGA
1326888 TAAAAAA-A-TAATATTTTAGA
1 TAAAAAATATTAATATTTTAGA
1326908 TAAA
1 TAAA
1326912 TTTTTATCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 16 0.67
21 1 0.04
22 7 0.29
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
TAAAAAATATTAATATTTTAGA
Found at i:1330437 original size:31 final size:31
Alignment explanation
Indices: 1330391--1330470 Score: 81
Period size: 31 Copynumber: 2.6 Consensus size: 31
1330381 TTTATTTAAA
*
1330391 TTTTAAA-AATTATAAAACAGCCATTAAGTT
1 TTTTAAATAATTATAAAACAGCCATTAAATT
* * **
1330421 TTTTAAATGATTATAAAATATTCATTAAATT
1 TTTTAAATAATTATAAAACAGCCATTAAATT
* *
1330452 TTATCAAATTATTATAAAA
1 TT-TTAAATAATTATAAAA
1330471 TGATCATTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 7 0.17
31 20 0.49
32 14 0.34
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (31 bp):
TTTTAAATAATTATAAAACAGCCATTAAATT
Found at i:1330471 original size:32 final size:32
Alignment explanation
Indices: 1330412--1330500 Score: 103
Period size: 31 Copynumber: 2.8 Consensus size: 32
1330402 ATAAAACAGC
* * *
1330412 CATTAAGTTTT-TTAAATGATTATAAAAT-ATT
1 CATTAAATTTTATCAAATTATTATAAAATGA-T
1330443 CATTAAATTTTATCAAATTATTATAAAATGAT
1 CATTAAATTTTATCAAATTATTATAAAATGAT
* *
1330475 CATTAAA-CTTATCAAATTTTTATAAA
1 CATTAAATTTTATCAAATTATTATAAA
1330501 TTAGTCTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
31 27 0.53
32 23 0.45
33 1 0.02
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (32 bp):
CATTAAATTTTATCAAATTATTATAAAATGAT
Found at i:1330490 original size:31 final size:32
Alignment explanation
Indices: 1330425--1330500 Score: 102
Period size: 32 Copynumber: 2.4 Consensus size: 32
1330415 TAAGTTTTTT
* *
1330425 AAATGATTATAAAATATTCATTAAATTTTATC
1 AAATTATTATAAAATATTCATTAAATCTTATC
1330457 AAATTATTATAAAATGA-TCATTAAA-CTTATC
1 AAATTATTATAAAAT-ATTCATTAAATCTTATC
*
1330488 AAATTTTTATAAA
1 AAATTATTATAAA
1330501 TTAGTCTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 17 0.43
32 22 0.55
33 1 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.42
Consensus pattern (32 bp):
AAATTATTATAAAATATTCATTAAATCTTATC
Found at i:1334468 original size:48 final size:48
Alignment explanation
Indices: 1334397--1334493 Score: 176
Period size: 48 Copynumber: 2.0 Consensus size: 48
1334387 CGATAATGTC
1334397 GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
1 GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
* *
1334445 GGAAGAAAGTATGATGTTGATGTGTGAAAAGTTGGCATTATTTGTACG
1 GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
1334493 G
1 G
1334494 CTCTGTAAGT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.32
Consensus pattern (48 bp):
GGAAGAAAGTATGATGTTGATGTGAGAAAAGTTCGCATTATTTGTACG
Found at i:1344267 original size:51 final size:52
Alignment explanation
Indices: 1344173--1344272 Score: 166
Period size: 51 Copynumber: 1.9 Consensus size: 52
1344163 ATTATAATAT
* *
1344173 CCTTGTGATTAGTTGTAATCCCCTAACTTTAGGCTAGTCTCCTATTTATGTG
1 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTG
*
1344225 CCTTGTAATTAGTTGTAAT-CCCTAACTCTAGGCTAGTTTCCTATTTAT
1 CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTAT
1344273 ATATGCCCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 27 0.60
52 18 0.40
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (52 bp):
CCTTGTAATTAGTTGTAATCCCCTAACTCTAGGCTAGTCTCCTATTTATGTG
Found at i:1348053 original size:15 final size:15
Alignment explanation
Indices: 1348035--1348093 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
1348025 GAAAAGATGA
*
1348035 TATTAGAAATATTAT
1 TATTATAAATATTAT
* *
1348050 TATTTTAAATATTTT
1 TATTATAAATATTAT
*
1348065 TTTTATAAA-A-TAT
1 TATTATAAATATTAT
1348078 TATT-TAAAATATTAT
1 TATTAT-AAATATTAT
1348093 T
1 T
1348094 TTTTTATCAT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
12 1 0.03
13 8 0.24
14 2 0.06
15 23 0.68
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
TATTATAAATATTAT
Found at i:1348087 original size:28 final size:32
Alignment explanation
Indices: 1348047--1348111 Score: 93
Period size: 28 Copynumber: 2.2 Consensus size: 32
1348037 TTAGAAATAT
*
1348047 TATTATTTTAAATA-T-TTTTTTTAT-A-AAA
1 TATTATTTAAAATATTATTTTTTTATCATAAA
1348075 TATTATTTAAAATATTATTTTTTTATCATAAA
1 TATTATTTAAAATATTATTTTTTTATCATAAA
1348107 TATTA
1 TATTA
1348112 ATATTAGACG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 13 0.41
29 1 0.03
30 9 0.28
31 1 0.03
32 8 0.25
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (32 bp):
TATTATTTAAAATATTATTTTTTTATCATAAA
Found at i:1348182 original size:45 final size:45
Alignment explanation
Indices: 1348077--1348193 Score: 175
Period size: 44 Copynumber: 2.6 Consensus size: 45
1348067 TTATAAAATA
* *
1348077 TTATTTAAAATATTATTTTTTTATCATAAATATTAATATTAGACG
1 TTATTTAAAATATTATTTTTTTATCAAAAATATTAATATTAAACG
* *
1348122 TTACTT-AAATATTATTTTTTTATTAAAAATATTAATATTAAACG
1 TTATTTAAAATATTATTTTTTTATCAAAAATATTAATATTAAACG
*
1348166 TTATTTAAAACATTA-TTTTTTATCAAAA
1 TTATTTAAAATATTATTTTTTTATCAAAA
1348194 TTAGTTAACA
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
44 52 0.81
45 12 0.19
ACGTcount: A:0.42, C:0.05, G:0.03, T:0.50
Consensus pattern (45 bp):
TTATTTAAAATATTATTTTTTTATCAAAAATATTAATATTAAACG
Found at i:1349233 original size:36 final size:38
Alignment explanation
Indices: 1349149--1349238 Score: 141
Period size: 38 Copynumber: 2.4 Consensus size: 38
1349139 TTTTCACCCT
1349149 AAACCCGAACCCGACCTGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCTGACCCGAATATCACACTTAAAA
1349188 AAACCCGACCCGA-CTCGACCCGAATATCACACTT-AAA
1 AAACCCGACCCGACCT-GACCCGAATATCACACTTAAAA
1349225 AAA-CCGACCCGACC
1 AAACCCGACCCGACC
1349239 CAAACAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
36 9 0.18
37 9 0.18
38 24 0.49
39 7 0.14
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.11
Consensus pattern (38 bp):
AAACCCGACCCGACCTGACCCGAATATCACACTTAAAA
Found at i:1349460 original size:37 final size:37
Alignment explanation
Indices: 1349409--1349488 Score: 142
Period size: 37 Copynumber: 2.2 Consensus size: 37
1349399 TTCACCCTAA
1349409 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
* *
1349446 ACCCGACTCGACCCGAATATCACACTTAAAAAACCCG
1 ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
1349483 ACCCGA
1 ACCCGA
1349489 ACAAAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.39, C:0.40, G:0.10, T:0.11
Consensus pattern (37 bp):
ACCCGACCCAACCCGAATATCACACTTAAAAAACCCG
Found at i:1349712 original size:42 final size:37
Alignment explanation
Indices: 1349657--1349743 Score: 138
Period size: 37 Copynumber: 2.4 Consensus size: 37
1349647 CCTAAACCCG
*
1349657 AACCCGACCCGACCCGACCCAAATATCACACTTAAAA
1 AACCCGACCCGACCCGACCCGAATATCACACTTAAAA
* * *
1349694 AACCCGACCCGACTCGACCCGAATATCATACTTTAAA
1 AACCCGACCCGACCCGACCCGAATATCACACTTAAAA
1349731 AACCCGACCCGAC
1 AACCCGACCCGAC
1349744 ATAAACAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.37, C:0.40, G:0.10, T:0.13
Consensus pattern (37 bp):
AACCCGACCCGACCCGACCCGAATATCACACTTAAAA
Found at i:1349925 original size:258 final size:255
Alignment explanation
Indices: 1349107--1349971 Score: 1209
Period size: 258 Copynumber: 3.4 Consensus size: 255
1349097 TATAAAGTAA
*
1349107 AATTATATATATTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGA---ACCCGACCTGAC
1 AATTATATATA-TTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGACCGACCCGACCCGAC
* *
1349169 CCGAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACAC-TTAAAAAACCGAC
65 CCAAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTTAAAAACCCGAC
* *
1349233 CCGACCCAAACAAAATAAAGTTTCATCCGACCTGACCCGAATATATAAATTAGAAATCCGACCCG
130 CCGA--CAAACAAAATAAAGTTTCAT-C--CC-GACCCGAATATATGAATTAGAAATTCGACCCG
*
1349298 ACCAGACCCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGAC
189 ACCTGA-CCGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGAC
1349363 CCG
253 CCG
* *
1349366 AATTATATATATTTTCGGGTCGATCCGATTTTTTTCACCCTAAA--C--CCGACCC-A----ACC
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGACCGACCCGACCCGACC
* *
1349422 CGAATATCACACTT-AAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGACC
66 CAAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTTAAAAACCCGACC
* *
1349486 CG---AACAAAATAAAATTTCATCCGACCCGACCCGAATATATGAATTAAAAATTCGACCCGA--
131 CGACAAACAAAATAAAGTTTCAT----CCCGACCCGAATATATGAATTAGAAATTCGACCCGACC
1349546 T--CCGAAATAATAAAAAAAGTATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCG
192 TGACCGAAATAATAAAAAAA-TATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCG
1349609 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGACCCGA
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCG-A-CCGACCCGACCCGA
*
1349674 CCCAAATATCACACTT-AAAAAACCCGACCCGACTCGACCCGAATATCATACTTTAAAAACCCGA
64 CCCAAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTTAAAAACCCGA
*
1349738 CCCGACATAAACAAAATAAAGTTTCAT-CCGACCCGAATATATGAATTAGAAATTCAACCCGACC
129 CCCGAC--AAACAAAATAAAGTTTCATCCCGACCCGAATATATGAATTAGAAATTCGACCCGACC
* * *
1349802 TGACCTGAAATAATAAAAAAATATTTTTATTTAATAAAAACAGTGACTTAATCCGATCCGACCTG
192 TGACC-GAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCG
*
1349867 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACTCTAAACCCGAACTCGACCCGACCCGA
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCG-AC-CGACCCGACCCGA
* *
1349932 CCCAAATATCACACTTAAAAAAACCCGATCCGACCCGACC
64 CCCAAATATCACACTTAAAAAAACCCGACCCGACTCGACC
1349972 AAAATAAAGT
Statistics
Matches: 551, Mismatches: 24, Indels: 62
0.86 0.04 0.10
Matches are distributed among these distances:
242 17 0.03
243 86 0.16
245 1 0.00
247 47 0.09
248 2 0.00
249 7 0.01
250 2 0.00
251 35 0.06
252 31 0.06
254 99 0.18
256 3 0.01
257 5 0.01
258 152 0.28
259 64 0.12
ACGTcount: A:0.37, C:0.28, G:0.11, T:0.24
Consensus pattern (255 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGACCGACCCGACCCGACC
CAAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTTAAAAACCCGACC
CGACAAACAAAATAAAGTTTCATCCCGACCCGAATATATGAATTAGAAATTCGACCCGACCTGAC
CGAAATAATAAAAAAATATTTTTATTTAATAAAAACAATGACTTAATCCGACCCGACCCG
Found at i:1352386 original size:18 final size:19
Alignment explanation
Indices: 1352344--1352388 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1352334 TTTGGTTCAC
*
1352344 GGAATATAAGATTACTAGTG
1 GGAATATAAGATTACCAG-G
*
1352364 GGAATGTAAGATTACCA-G
1 GGAATATAAGATTACCAGG
1352382 GGAATAT
1 GGAATAT
1352389 GATTACTGTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.07, G:0.27, T:0.27
Consensus pattern (19 bp):
GGAATATAAGATTACCAGG
Found at i:1352627 original size:25 final size:24
Alignment explanation
Indices: 1352599--1352645 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1352589 ATTTTAAATT
1352599 TATATA-CTTTTTAATAAAATTTA
1 TATATATCTTTTTAATAAAATTTA
* *
1352622 TATATATTTTTTTTATAAAATTTA
1 TATATATCTTTTTAATAAAATTTA
1352646 AAAGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (24 bp):
TATATATCTTTTTAATAAAATTTA
Found at i:1363987 original size:21 final size:20
Alignment explanation
Indices: 1363963--1364095 Score: 65
Period size: 20 Copynumber: 6.5 Consensus size: 20
1363953 CAGTTCCCAG
1363963 AATCGCAACGCGATTATGAA
1 AATCGCAACGCGATTATGAA
**
1363983 GAATCGCAATACGA-TA-GTACA
1 -AATCGCAACGCGATTATG-A-A
** * * *
1364004 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAACGCGATTAT-GAA
* *
1364026 AATCGCAACACGAATATGAA
1 AATCGCAACGCGATTATGAA
**
1364046 AATCGCAACGCGAACAT-ATA
1 AATCGCAACGCGATTATGA-A
* *
1364066 AATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAA
*
1364086 TATCGCAACG
1 AATCGCAACG
1364096 AATATCCGTA
Statistics
Matches: 83, Mismatches: 21, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.02
20 45 0.54
21 32 0.39
22 3 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAA
Found at i:1364172 original size:20 final size:20
Alignment explanation
Indices: 1364026--1364320 Score: 219
Period size: 20 Copynumber: 14.7 Consensus size: 20
1364016 GATTTTCCAG
* ** *
1364026 AATCGCAACACGAATATGAA
1 AATCGCAACGCGAATCCGTA
**
1364046 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-CGTA
* *
1364066 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCCGTA
* *
1364085 CTATCGCAACG-AATATCCGTAA
1 -AATCGCAACGCGA-ATCCGT-A
* *
1364107 AATCGCAACACGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1364127 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
*
1364148 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
* *
1364168 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* * *
1364188 AATCACAACGCGTATCTGTA
1 AATCGCAACGCGAATCCGTA
* *
1364208 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATCCGTA
* *
1364228 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCCGTA
*
1364248 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATCCGT-A
1364269 AATCGCAACGAC-AATCCGTA
1 AATCGCAACG-CGAATCCGTA
1364289 AATCGCAACGCG-AT-CGATA
1 AATCGCAACGCGAATCCG-TA
*
1364308 ATTCGCAACGCGA
1 AATCGCAACGCGA
1364321 TCTCCGGTAT
Statistics
Matches: 219, Mismatches: 41, Indels: 30
0.76 0.14 0.10
Matches are distributed among these distances:
18 2 0.01
19 18 0.08
20 146 0.67
21 52 0.24
22 1 0.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATCCGTA
Found at i:1364202 original size:40 final size:41
Alignment explanation
Indices: 1364087--1364298 Score: 306
Period size: 41 Copynumber: 5.2 Consensus size: 41
1364077 GATTCTGACT
* *
1364087 ATCGCAACGA-ATATCCGTAAAATCGCAACACGTATCCGTAA
1 ATCGCAACGACA-ATACGTAAAATCGCAACGCGTATCCGTAA
1364128 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* * *
1364169 ATCGCAACGAGAATACGT-AAATCACAACGCGTATCTGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
* *
1364209 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
*
1364249 ATCGCAACGACAATACGTAAAATCGCAACGAC-AATCCGTAA
1 ATCGCAACGACAATACGTAAAATCGCAACG-CGTATCCGTAA
1364290 ATCGCAACG
1 ATCGCAACG
1364299 CGATCGATAA
Statistics
Matches: 157, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
40 74 0.47
41 81 0.52
42 2 0.01
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (41 bp):
ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:1364373 original size:20 final size:20
Alignment explanation
Indices: 1364350--1364395 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
1364340 GTTTCCAGAT
*
1364350 TCGCAATGCGATTAC-GTAAA
1 TCGCAATGCGAAT-CTGTAAA
1364370 TCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATCTGTAAA
1364390 TCGCAA
1 TCGCAA
1364396 CAAGATTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATCTGTAAA
Found at i:1365283 original size:22 final size:22
Alignment explanation
Indices: 1365258--1365300 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1365248 ATTCGAAATT
1365258 TGATCTTGGTCAATACCCGGAC
1 TGATCTTGGTCAATACCCGGAC
*
1365280 TGATCTTGGTCAATACTCGGA
1 TGATCTTGGTCAATACCCGGA
1365301 TTTTGATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (22 bp):
TGATCTTGGTCAATACCCGGAC
Found at i:1367771 original size:33 final size:34
Alignment explanation
Indices: 1367716--1367784 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
1367706 GCAACACAGA
1367716 ATTTTCATTTTCACATTGCGATTCACTCGTTGCG
1 ATTTTCATTTTCACATTGCGATTCACTCGTTGCG
* *
1367750 ATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCG
1 ATTTTCATTTTCACATTGCGATTCACTCGTTGCG
1367783 AT
1 AT
1367785 CAAAATCCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 26 0.79
34 7 0.21
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.45
Consensus pattern (34 bp):
ATTTTCATTTTCACATTGCGATTCACTCGTTGCG
Found at i:1368016 original size:20 final size:21
Alignment explanation
Indices: 1367991--1368079 Score: 114
Period size: 20 Copynumber: 4.4 Consensus size: 21
1367981 TAACGCGGAA
1367991 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAATATGACT
* *
1368011 ATCGCAACAC-GAAAATGACT
1 ATCGCAACGCGGAATATGACT
*
1368031 ATCGCAATGCGGAAT-TGACT
1 ATCGCAACGCGGAATATGACT
*
1368051 ATCGCAACACGGAA-ATGACT
1 ATCGCAACGCGGAATATGACT
1368071 ATCGCAACG
1 ATCGCAACG
1368080 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 56 0.95
21 3 0.05
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGGAATATGACT
Found at i:1368050 original size:40 final size:40
Alignment explanation
Indices: 1367991--1368079 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
1367981 TAACGCGGAA
1367991 ATCGCAACGCGAATATGACTATCGCAACACGAAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGAAAATGACT
* *
1368031 ATCGCAATGCGGAAT-TGACTATCGCAACACGGAAATGACT
1 ATCGCAACGC-GAATATGACTATCGCAACACGAAAATGACT
1368071 ATCGCAACG
1 ATCGCAACG
1368080 AGAGAATCGC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
40 41 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGAAAATGACT
Found at i:1368101 original size:33 final size:33
Alignment explanation
Indices: 1368073--1368138 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1368063 AAATGACTAT
1368073 CGCAACGAGAGAATCGCAATGCGAAATGAAAAC
1 CGCAACGAGAGAATCGCAATGCGAAATGAAAAC
* *
1368106 CGCAACGAGTGAATCGTAATGCGAAAATGAAAA
1 CGCAACGAGAGAATCGCAATGCG-AAATGAAAA
1368139 TCGTAACGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 21 0.70
34 9 0.30
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.12
Consensus pattern (33 bp):
CGCAACGAGAGAATCGCAATGCGAAATGAAAAC
Found at i:1368313 original size:14 final size:14
Alignment explanation
Indices: 1368294--1368330 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1368284 CATCAATTAA
1368294 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
1368308 ACAAATCATCTTTT
1 ACAAATCAACATTT
1368322 ACAAATCAA
1 ACAAATCAA
1368331 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:1369790 original size:42 final size:42
Alignment explanation
Indices: 1369683--1369794 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
1369673 TCTAGAATGT
* * *
1369683 TGGGAG-GGACCTCTTCAACGATGACAGTGGCATCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCATCTTGAACGA
* * ** * *
1369725 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCATCTTGAACGA
1369767 TAGGG-GAGGCCTCTTGAACGATGACAGG
1 T-GGGAGAGGCCTCTTGAACGATGACAGG
1369795 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
42 50 0.91
43 5 0.09
ACGTcount: A:0.23, C:0.18, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCATCTTGAACGA
Found at i:1370297 original size:20 final size:20
Alignment explanation
Indices: 1370274--1370380 Score: 151
Period size: 20 Copynumber: 5.3 Consensus size: 20
1370264 GAAACTTAAA
*
1370274 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
1370294 ATCGCAATACGAAAATGACT
1 ATCGCAATGCGAAAATGACT
1370314 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
1370334 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
* **
1370354 ATCGCAATACGAATTTGACT
1 ATCGCAATGCGAAAATGACT
1370374 ATCGCAA
1 ATCGCAA
1370381 GAGAGAATCA
Statistics
Matches: 81, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 81 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:1370436 original size:19 final size:19
Alignment explanation
Indices: 1370414--1370457 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1370404 AAATCACAAC
*
1370414 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCACGTT
* *
1370433 GCGATTTTGGTTTCACGTT
1 GCGATTATAGTTTCACGTT
1370452 GCGATT
1 GCGATT
1370458 TTGTCGTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.14, C:0.16, G:0.27, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCACGTT
Found at i:1370458 original size:19 final size:19
Alignment explanation
Indices: 1370423--1370492 Score: 87
Period size: 19 Copynumber: 3.9 Consensus size: 19
1370413 CGCGATTATA
1370423 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
1370442 GTTTCACGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
1370460 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
1370475 GTTTTGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
1370493 CATTTCTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
14 12 0.27
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.64
ACGTcount: A:0.07, C:0.14, G:0.29, T:0.50
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:1370471 original size:33 final size:33
Alignment explanation
Indices: 1370429--1370492 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1370419 TATAGTTTCG
1370429 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
1 CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
**
1370462 CGTTGCGATTTTGGTTTTGCGTTGCGATTTT
1 CGTTGCGATTTTGGTTTCACGTTGCGATTTT
1370493 CATTTCTCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.08, C:0.14, G:0.28, T:0.50
Consensus pattern (33 bp):
CGTTGCGATTTTGGTTTCACGTTGCGATTTTGT
Found at i:1370482 original size:14 final size:14
Alignment explanation
Indices: 1370448--1370474 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1370438 TTTGGTTTCA
1370448 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
1370462 CGTTGCGATTTTG
1 CGTTGCGATTTTG
1370475 GTTTTGCGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1370484 original size:52 final size:52
Alignment explanation
Indices: 1370414--1370539 Score: 148
Period size: 52 Copynumber: 2.5 Consensus size: 52
1370404 AAATCACAAC
** * * *
1370414 GCGATTATAGTTTCGCGTTGCGATTTTGGTTTCACGTTGCGATTTTGTCGTT
1 GCGATTATAGTTTCGCGTTGCGATTTTCATTTCACGTTACGATTCTCTCGTT
* * * *
1370466 GCGATTTTGGTTTTGCGTTGCGATTTTCATTTCTCGTTACGATTCTCTCGTT
1 GCGATTATAGTTTCGCGTTGCGATTTTCATTTCACGTTACGATTCTCTCGTT
*
1370518 GCGATT-CA-TTTCGCGTTGCGAT
1 GCGATTATAGTTTCGCGTTGCGAT
1370540 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
50 13 0.21
52 49 0.79
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.46
Consensus pattern (52 bp):
GCGATTATAGTTTCGCGTTGCGATTTTCATTTCACGTTACGATTCTCTCGTT
Found at i:1370503 original size:19 final size:19
Alignment explanation
Indices: 1370461--1370563 Score: 60
Period size: 19 Copynumber: 5.7 Consensus size: 19
1370451 TGCGATTTTG
**
1370461 TCGTTGCGATTTTGGTTT-
1 TCGTTGCGATTTTCATTTC
1370479 TGCGTTGCGATTTTCATTTC
1 T-CGTTGCGATTTTCATTTC
*
1370499 TCGTTACGA--TTC---TC
1 TCGTTGCGATTTTCATTTC
1370513 TCGTTGCGA--TTCATTTC
1 TCGTTGCGATTTTCATTTC
* **
1370530 GCGTTGCGATAGTCATTTTTC
1 TCGTTGCGATTTTCA--TTTC
*
1370551 ACGTTGCGATTTT
1 TCGTTGCGATTTT
1370564 AAGTTTCGTG
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
14 13 0.19
17 13 0.19
18 1 0.01
19 25 0.37
20 1 0.01
21 14 0.21
ACGTcount: A:0.12, C:0.19, G:0.21, T:0.48
Consensus pattern (19 bp):
TCGTTGCGATTTTCATTTC
Found at i:1370561 original size:52 final size:51
Alignment explanation
Indices: 1370424--1370561 Score: 125
Period size: 52 Copynumber: 2.7 Consensus size: 51
1370414 GCGATTATAG
** ** * * **
1370424 TTTCGCGTTGCGATTTTGGTTTCACGTTGCGATTTTGTCGTTGCGATTTTGG
1 TTTCGCGTTGCGATAGTCATTTCACGTTGCGATTCTCTCGTTGCGA-TTTCA
* ** * *
1370476 TTTTGCGTTGCGATTTTCATTTCTCGTTACGATTCTCTCGTTGCGA-TTCA
1 TTTCGCGTTGCGATAGTCATTTCACGTTGCGATTCTCTCGTTGCGATTTCA
1370526 TTTCGCGTTGCGATAGTCATTTTTCACGTTGCGATT
1 TTTCGCGTTGCGATAGTCA--TTTCACGTTGCGATT
1370562 TTAAGTTTCG
Statistics
Matches: 70, Mismatches: 14, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
50 18 0.26
52 52 0.74
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (51 bp):
TTTCGCGTTGCGATAGTCATTTCACGTTGCGATTCTCTCGTTGCGATTTCA
Found at i:1370773 original size:94 final size:94
Alignment explanation
Indices: 1370627--1370847 Score: 390
Period size: 94 Copynumber: 2.4 Consensus size: 94
1370617 ATGGATTGCA
*
1370627 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
*
1370691 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACAGAACAAAT
* * *
1370720 TTACTTTCAACAAAAAGACAAACCAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
1370785 TTAGCAGAATTGGCAGCAACAGAACAAAT
66 TTAGCAGAATTGGCAGCAACAGAACAAAT
1370814 TTACTTTCAACCAAAAGACAAAACAAAGACAAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAAT
1370848 CACCTCATTC
Statistics
Matches: 120, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
93 4 0.03
94 116 0.97
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.19
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACAGAACAAAT
Found at i:1372466 original size:20 final size:20
Alignment explanation
Indices: 1372443--1372498 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
1372433 TGAAATGAAA
1372443 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
1372463 ATCGCAATGCG-GA-AATGACT
1 ATCGCAA--CGAGAGAATGACT
1372483 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
1372499 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 24 0.75
21 2 0.06
22 2 0.06
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:1372520 original size:33 final size:33
Alignment explanation
Indices: 1372483--1372555 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
1372473 GGAAATGACT
* *
1372483 ATCGCAACGAGAGAATCGCAACGCGAAATTAAA
1 ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
1372516 ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
1 ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
1372549 ATCGCAA
1 ATCGCAA
1372556 TTCTCGTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAACGCAAAATGAAA
Found at i:1372551 original size:19 final size:18
Alignment explanation
Indices: 1372496--1372555 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 18
1372486 GCAACGAGAG
*
1372496 AATCGCAACGCGAAATTAA
1 AATCGCAACGC-AAATGAA
*
1372515 AATCGCAACG---A-GAG
1 AATCGCAACGCAAATGAA
1372529 AATCGCAACGCAAAATGAA
1 AATCGCAACGC-AAATGAA
1372548 AATCGCAA
1 AATCGCAA
1372556 TTCTCGTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
14 11 0.33
15 1 0.03
18 1 0.03
19 20 0.61
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (18 bp):
AATCGCAACGCAAATGAA
Found at i:1372582 original size:21 final size:20
Alignment explanation
Indices: 1372561--1372632 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
1372551 CGCAATTCTC
1372561 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
1372581 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
1372602 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
1372622 GTTGCGATTTT
1 GTTGCGATTTT
1372633 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:1373339 original size:41 final size:41
Alignment explanation
Indices: 1373191--1373384 Score: 293
Period size: 40 Copynumber: 4.8 Consensus size: 41
1373181 CTTTAAAAAT
*
1373191 CGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * **
1373232 CGCATTGTGA-TTTACGTATTCTCGTTGCGATTTAAAGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
1373272 CGCGTTGCGA-TTTACGTATTCTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
*
1373312 CGCGTTGCGATTTTACGTATTCTCGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
* * *
1373353 CGCGTTACGATTTTACGGATACTCGTTGCGAT
1 CGCGTTGCGATTTTACGTATTCTCGTTGCGAT
1373385 AGTCAGAATC
Statistics
Matches: 138, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
40 73 0.53
41 65 0.47
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (41 bp):
CGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATA
Found at i:1373358 original size:20 final size:20
Alignment explanation
Indices: 1373191--1373384 Score: 183
Period size: 20 Copynumber: 9.6 Consensus size: 20
1373181 CTTTAAAAAT
*
1373191 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1373211 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
* * * *
1373232 CGCATTGTGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* **
1373252 CTCGTTGCGATTTAAAGATA
1 CGCGTTGCGATTTACGGATA
* *
1373272 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1373292 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1373312 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
* *
1373333 CTCGTTGCGGTTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1373353 CGCGTTACGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1373374 CTCGTTGCGAT
1 CGCGTTGCGAT
1373385 AGTCAGAATC
Statistics
Matches: 136, Mismatches: 34, Indels: 8
0.76 0.19 0.04
Matches are distributed among these distances:
20 93 0.68
21 43 0.32
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1373416 original size:20 final size:20
Alignment explanation
Indices: 1373393--1373445 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1373383 ATAGTCAGAA
*
1373393 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
1373413 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
1373433 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1373446 CTGGAAAATC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:1373463 original size:21 final size:21
Alignment explanation
Indices: 1373439--1373491 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
1373429 ATATTCGCGT
1373439 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
1373460 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
1373481 TGCGATTCTGG
1 TGCGATTCTGG
1373492 GAACTGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:1373523 original size:20 final size:20
Alignment explanation
Indices: 1373433--1373527 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
1373423 ATTTTCATAT
* *
1373433 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGG-AGA
* * *
1373454 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGA-GA
1373475 TCGCATTGCGATTCTGG-GA
1 TCGCATTGCGATTCTGGAGA
*
1373494 ACTG-ATTTGCGATTCTGGAGA
1 TC-GCA-TTGCGATTCTGGAGA
*
1373515 TCGCGTTGCGATT
1 TCGCATTGCGATT
1373528 TTTATTTCGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.05
20 26 0.46
21 25 0.44
22 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTCTGGAGA
Found at i:1373896 original size:15 final size:15
Alignment explanation
Indices: 1373876--1373909 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1373866 TTAAGAGAAA
1373876 ATCTAAATAGATAAC
1 ATCTAAATAGATAAC
1373891 ATCTAAATAGATAAC
1 ATCTAAATAGATAAC
1373906 ATCT
1 ATCT
1373910 TGTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.15, G:0.06, T:0.29
Consensus pattern (15 bp):
ATCTAAATAGATAAC
Found at i:1375767 original size:11 final size:11
Alignment explanation
Indices: 1375726--1375768 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1375716 TTATAAGATA
1375726 ATCATTAAATT
1 ATCATTAAATT
*
1375737 -TTATTAAATT
1 ATCATTAAATT
* *
1375747 ATAATAAAATT
1 ATCATTAAATT
1375758 ATCATTAAATT
1 ATCATTAAATT
1375769 TAGGGTAAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (11 bp):
ATCATTAAATT
Found at i:1383646 original size:15 final size:14
Alignment explanation
Indices: 1383626--1383655 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1383616 AACATGTCTA
1383626 CTGGATTTTGAAGCT
1 CTGGATTTTG-AGCT
1383641 CTGGATTTTGAGCT
1 CTGGATTTTGAGCT
1383655 C
1 C
1383656 CACTAATCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.40
Consensus pattern (14 bp):
CTGGATTTTGAGCT
Found at i:1387215 original size:17 final size:19
Alignment explanation
Indices: 1387195--1387229 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
1387185 TCCCTGGGAA
1387195 TTTAAAA-AAAA-ACTTTG
1 TTTAAAACAAAATACTTTG
1387212 TTTAAAACAAAATACTTT
1 TTTAAAACAAAATACTTT
1387230 AATTTACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 4 0.25
19 5 0.31
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAAAACAAAATACTTTG
Found at i:1387572 original size:22 final size:22
Alignment explanation
Indices: 1387532--1387573 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
1387522 ATATGCATAT
*
1387532 ATATATATATATATTTCATGAC
1 ATATATATATATATGTCATGAC
1387554 ATATATATA-ATCATGTCATG
1 ATATATATATAT-ATGTCATG
1387574 CACACATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (22 bp):
ATATATATATATATGTCATGAC
Found at i:1388489 original size:19 final size:20
Alignment explanation
Indices: 1388452--1388490 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1388442 TTTTTCATTT
1388452 AGGGGGAATCGATACCCCCC
1 AGGGGGAATCGATACCCCCC
1388472 AGGGGGAATCGATACCCCC
1 AGGGGGAATCGATACCCCC
1388491 TGGACATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.33, G:0.31, T:0.10
Consensus pattern (20 bp):
AGGGGGAATCGATACCCCCC
Found at i:1392848 original size:20 final size:20
Alignment explanation
Indices: 1392823--1392861 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
1392813 TATGCATGGA
1392823 GGTAT-GGTATATCTTGTTTT
1 GGTATAGGTAT-TCTTGTTTT
1392843 GGTATGAGGTATTCTTGTT
1 GGTAT-AGGTATTCTTGTT
1392862 ACGGGTTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.15, C:0.05, G:0.28, T:0.51
Consensus pattern (20 bp):
GGTATAGGTATTCTTGTTTT
Found at i:1395985 original size:30 final size:30
Alignment explanation
Indices: 1395951--1396053 Score: 161
Period size: 30 Copynumber: 3.4 Consensus size: 30
1395941 CCCGAAGGAC
1395951 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* **
1395981 CTATCCAGAGGTCATAAAAATCCTTAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1396011 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1396041 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1396054 CCGAAGAACC
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1396077 original size:31 final size:31
Alignment explanation
Indices: 1396039--1396103 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1396029 GATCCTCGGT
*
1396039 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
* * **
1396070 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATAGGTCCCGAAGAACATAGGTA
1396101 AAC
1 AAC
1396104 CCTCGACTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAGAACATAGGTA
Found at i:1397098 original size:64 final size:63
Alignment explanation
Indices: 1397000--1397172 Score: 170
Period size: 64 Copynumber: 2.7 Consensus size: 63
1396990 CATCGATGCA
* * * * * *
1397000 TTCTTTAACATGTGCATCGATGCACTACTCATGCATCGATACATAAATTACCTTCGATG-TT-
1 TTCTTTAAAAAGTGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTC
* * * *
1397061 TTCATTTAAAAAGGATGCATCGATGCACTCCTTATGCATCAATGCACCAATTGCATTCGATGTTT
1 TTC-TTTAAAAA-G-TGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTT
1397126 C
63 C
* **
1397127 TTCTTTAAAGAGTGCATCGATGCACATTCAATATGCATCGATACAC
1 TTCTTTAAAAAGTGCATCGATGCAC--TCCTTATGCATCGATACAC
1397173 CTTGCCCAGA
Statistics
Matches: 90, Mismatches: 15, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
61 3 0.03
62 6 0.07
63 14 0.16
64 40 0.44
65 24 0.27
66 3 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (63 bp):
TTCTTTAAAAAGTGCATCGATGCACTCCTTATGCATCGATACACAAATTACATTCGATGTTTC
Found at i:1400541 original size:30 final size:30
Alignment explanation
Indices: 1400507--1400579 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
1400497 CCCGAAGAAC
1400507 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1400537 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1400567 CTGTCCATAGGTC
1 CTATCCAGAGGTC
1400580 TCGAAGAACC
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1401570 original size:24 final size:20
Alignment explanation
Indices: 1401517--1401574 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
1401507 TTCCCCTTGA
*
1401517 AGTGCATCGATGTATTCTAC
1 AGTGCATCGATGCATTCTAC
1401537 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1401560 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1401575 CTACTCATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1401671 original size:64 final size:63
Alignment explanation
Indices: 1401562--1401702 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 63
1401552 TCTTTAACAT
* * * *
1401562 GTGCATCGATGCACTACTCATGTATCTATACACAAATTACCTTCGATG-TT-TTCATTTAAAAGG
1 GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTC-TTT-AAAGA
* * * * *
1401625 GATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCTTCTTTAAAGA
1 G-TGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
1401689 GTGCATCGATGCAC
1 GTGCATCGATGCAC
1401703 ATTCAATATG
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
63 14 0.21
64 44 0.67
65 5 0.08
66 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACTCATGCATCGATACACAAATTACATTCGATGTTTCTTCTTTAAAGA
Found at i:1405390 original size:9 final size:9
Alignment explanation
Indices: 1405376--1405443 Score: 64
Period size: 10 Copynumber: 7.0 Consensus size: 9
1405366 GGCTGCTGGA
1405376 AACCGGTTT
1 AACCGGTTT
1405385 AACCGGTTTTT
1 AACCGG--TTT
1405396 AACCGGTTCT
1 AACCGGTT-T
*
1405406 GACCGGTTT
1 AACCGGTTT
*
1405415 GACCGGTTT
1 AACCGGTTT
*
1405424 CAACCGGTTCG
1 -AACCGGTT-T
1405435 AACCGGTTT
1 AACCGGTTT
1405444 GACTGGTCTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
9 18 0.36
10 23 0.46
11 9 0.18
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1405412 original size:10 final size:9
Alignment explanation
Indices: 1405377--1405475 Score: 72
Period size: 9 Copynumber: 10.3 Consensus size: 9
1405367 GCTGCTGGAA
*
1405377 ACCGGTTTA
1 ACCGGTTTG
*
1405386 ACCGGTTTTTA
1 ACCGG--TTTG
1405397 ACCGGTTCTG
1 ACCGGTT-TG
1405407 ACCGGTTTG
1 ACCGGTTTG
*
1405416 ACCGGTTTCA
1 ACCGGTTT-G
*
1405426 ACCGGTTCG
1 ACCGGTTTG
1405435 AACCGGTTTG
1 -ACCGGTTTG
* *
1405445 ACTGGTCTG
1 ACCGGTTTG
*
1405454 AATCGGTTTG
1 -ACCGGTTTG
*
1405464 ACCGGTCTG
1 ACCGGTTTG
1405473 ACC
1 ACC
1405476 CGACCGTTGA
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 34 0.47
10 29 0.40
11 9 0.12
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:1405421 original size:19 final size:19
Alignment explanation
Indices: 1405378--1405475 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
1405368 CTGCTGGAAA
* * *
1405378 CCGGTTTAACCGGTTTTTAA
1 CCGGTTTGACCGG-TTCTGA
1405398 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
1405417 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
*
1405437 CCGGTTTGACTGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
1405456 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
1405474 CC
1 CC
1405476 CGACCGTTGA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 16 0.25
21 6 0.09
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.32
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:1405439 original size:29 final size:31
Alignment explanation
Indices: 1405376--1405446 Score: 103
Period size: 29 Copynumber: 2.4 Consensus size: 31
1405366 GGCTGCTGGA
* *
1405376 AACCGGTTTAACCGGTTTTTAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1405407 -ACCGGTTTGACCGG-TTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTTCAACCGGTTCTG
1405435 AACCGGTTTGAC
1 AACCGGTTTGAC
1405447 TGGTCTGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
28 1 0.03
29 23 0.62
30 13 0.35
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.31
Consensus pattern (31 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCTG
Found at i:1405460 original size:29 final size:28
Alignment explanation
Indices: 1405377--1405475 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 28
1405367 GCTGCTGGAA
* * *
1405377 ACCGGTTTAACCGGTTTTTAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
1405407 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* * * *
1405435 AACCGGTTTGACTGGTCTGAATCGGTTTG
1 -ACCGGTTTGACCGGTCTCAACCGGTTCG
*
1405464 ACCGGTCTGACC
1 ACCGGTTTGACC
1405476 CGACCGTTGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 11 0.19
29 35 0.59
30 13 0.22
ACGTcount: A:0.16, C:0.25, G:0.27, T:0.31
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:1405494 original size:17 final size:17
Alignment explanation
Indices: 1405489--1405526 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1405479 CCGTTGACCC
1405489 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1405506 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1405523 GACC
1 GACC
1405527 GTTGACAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1405499 original size:22 final size:22
Alignment explanation
Indices: 1405472--1405519 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1405462 TGACCGGTCT
1405472 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
1405494 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
1405516 GACC
1 GACC
1405520 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCGTTGACCCGACCC
Found at i:1405526 original size:7 final size:7
Alignment explanation
Indices: 1405516--1405546 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1405506 GACCCGACCC
1405516 GACCGTT
1 GACCGTT
1405523 GACCGTT
1 GACCGTT
*
1405530 GACAGTT
1 GACCGTT
1405537 GACCGTT
1 GACCGTT
1405544 GAC
1 GAC
1405547 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1405526 original size:12 final size:12
Alignment explanation
Indices: 1405471--1405514 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1405461 TTGACCGGTC
1405471 TGACCCGACCGT
1 TGACCCGACCGT
1405483 TGACCCGACC--
1 TGACCCGACCGT
*
1405493 CGACCCGACCGT
1 TGACCCGACCGT
1405505 TGACCCGACC
1 TGACCCGACC
1405515 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:1412720 original size:9 final size:9
Alignment explanation
Indices: 1412706--1412799 Score: 62
Period size: 10 Copynumber: 9.8 Consensus size: 9
1412696 GGCTGCTGGA
1412706 AACCGGTTT
1 AACCGGTTT
1412715 AACCGGTTTT
1 AACCGG-TTT
1412725 CAACCGGTTCT
1 -AACCGGTT-T
* *
1412736 GACCGATTT
1 AACCGGTTT
*
1412745 GACCGGTTT
1 AACCGGTTT
*
1412754 CAACCGGTTCG
1 -AACCGGTT-T
1412765 AACCGGTTT
1 AACCGGTTT
* * *
1412774 GACTGGTCTG
1 AACCGGT-TT
1412784 AACCGGTTT
1 AACCGGTTT
*
1412793 GACCGGT
1 AACCGGT
1412800 CTGACCCGAC
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
9 27 0.41
10 32 0.48
11 7 0.11
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (9 bp):
AACCGGTTT
Found at i:1412759 original size:10 final size:10
Alignment explanation
Indices: 1412706--1412773 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 10
1412696 GGCTGCTGGA
1412706 AACCGGTTT-
1 AACCGGTTTC
1412715 AACCGGTTTTC
1 AACCGG-TTTC
1412726 AACCGG-TTC
1 AACCGGTTTC
* *
1412735 TGACCGATTT-
1 -AACCGGTTTC
*
1412745 GACCGGTTTC
1 AACCGGTTTC
1412755 AACCGG-TTC
1 AACCGGTTTC
1412764 GAACCGGTTT
1 -AACCGGTTT
1412774 GACTGGTCTG
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
9 20 0.42
10 18 0.38
11 10 0.21
ACGTcount: A:0.19, C:0.26, G:0.24, T:0.31
Consensus pattern (10 bp):
AACCGGTTTC
Found at i:1412759 original size:29 final size:29
Alignment explanation
Indices: 1412707--1412805 Score: 112
Period size: 29 Copynumber: 3.4 Consensus size: 29
1412697 GCTGCTGGAA
*
1412707 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
1412737 ACCGATTTGACCGGTTTCAACCGGTTC-G
1 ACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
1412765 AACCGGTTTGACTGGTCTGAACCGGTT-TG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCTG
*
1412794 ACCGGTCTGACC
1 ACCGGTTTGACC
1412806 CGACCGTTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
28 11 0.19
29 36 0.61
30 12 0.20
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (29 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:1412788 original size:19 final size:19
Alignment explanation
Indices: 1412706--1412803 Score: 83
Period size: 19 Copynumber: 5.1 Consensus size: 19
1412696 GGCTGCTGGA
* * *
1412706 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG-TCTG
* *
1412726 AACCGGTTCTGACCGATTTG
1 AACCGGTT-TGACCGGTCTG
*
1412746 -ACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
*
1412765 AACCGGTTTGACTGGTCTG
1 AACCGGTTTGACCGGTCTG
1412784 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
1412803 A
1 A
1412804 CCCGACCGTT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.03
19 38 0.58
20 20 0.31
21 5 0.08
ACGTcount: A:0.18, C:0.26, G:0.27, T:0.30
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:1412824 original size:17 final size:17
Alignment explanation
Indices: 1412819--1412856 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1412809 CCGTTGACCC
1412819 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1412836 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
1412853 GACC
1 GACC
1412857 GTTGACAGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.47, G:0.24, T:0.11
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:1412829 original size:22 final size:22
Alignment explanation
Indices: 1412802--1412849 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
1412792 TGACCGGTCT
1412802 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
1412824 GACCCGACCGTTGACCCGACCC
1 GACCCGACCGTTGACCCGACCC
1412846 GACC
1 GACC
1412850 GTTGACCGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.08
Consensus pattern (22 bp):
GACCCGACCGTTGACCCGACCC
Found at i:1412856 original size:7 final size:7
Alignment explanation
Indices: 1412846--1412876 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1412836 GACCCGACCC
1412846 GACCGTT
1 GACCGTT
1412853 GACCGTT
1 GACCGTT
*
1412860 GACAGTT
1 GACCGTT
1412867 GACCGTT
1 GACCGTT
1412874 GAC
1 GAC
1412877 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:1412856 original size:12 final size:12
Alignment explanation
Indices: 1412801--1412844 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1412791 TTGACCGGTC
1412801 TGACCCGACCGT
1 TGACCCGACCGT
1412813 TGACCCGACC--
1 TGACCCGACCGT
*
1412823 CGACCCGACCGT
1 TGACCCGACCGT
1412835 TGACCCGACC
1 TGACCCGACC
1412845 CGACCGTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
12 19 0.68
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.11
Consensus pattern (12 bp):
TGACCCGACCGT
Found at i:1414494 original size:15 final size:15
Alignment explanation
Indices: 1414474--1414509 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1414464 TTGCCCGTGG
1414474 TTTTTCTCTTTTGGA
1 TTTTTCTCTTTTGGA
1414489 TTTTTCTCTTTTGGA
1 TTTTTCTCTTTTGGA
1414504 TTTTTC
1 TTTTTC
1414510 GCGTAAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.06, C:0.14, G:0.11, T:0.69
Consensus pattern (15 bp):
TTTTTCTCTTTTGGA
Found at i:1415898 original size:2 final size:2
Alignment explanation
Indices: 1415893--1415923 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1415883 TTTTTCTTTA
1415893 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1415924 CTTTAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1417690 original size:2 final size:2
Alignment explanation
Indices: 1417683--1417712 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1417673 TATTTTAATC
1417683 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
1417713 TCAAAATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1419121 original size:24 final size:23
Alignment explanation
Indices: 1419072--1419118 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
1419062 TTTGTATGGC
1419072 TTTTTAAATATTTAATTTTTTAA
1 TTTTTAAATATTTAATTTTTTAA
*
1419095 TTTTTAAATTATATTTATTTTTTA
1 TTTTTAAA-TAT-TTAATTTTTTA
1419119 TTTCACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 8 0.38
24 3 0.14
25 10 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTAAATATTTAATTTTTTAA
Found at i:1422097 original size:11 final size:10
Alignment explanation
Indices: 1422072--1422096 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1422062 GTGGCTACAA
1422072 TTTTTGTTTT
1 TTTTTGTTTT
1422082 TTTTTGTTTT
1 TTTTTGTTTT
1422092 TTTTT
1 TTTTT
1422097 TCAACTGTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:1431277 original size:29 final size:30
Alignment explanation
Indices: 1431235--1431291 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1431225 TTTTTTATAT
*
1431235 AGTTTAGTGTCTAACGTTT-ATTTCGTTCC
1 AGTTTAGTGTCTAACGTTTCATTCCGTTCC
1431264 AGTTTAGT-TCCTAACGTTTCATTCCGTT
1 AGTTTAGTGT-CTAACGTTTCATTCCGTT
1431292 AGTTTGGCCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 17 0.68
30 7 0.28
ACGTcount: A:0.18, C:0.19, G:0.16, T:0.47
Consensus pattern (30 bp):
AGTTTAGTGTCTAACGTTTCATTCCGTTCC
Found at i:1433155 original size:2 final size:2
Alignment explanation
Indices: 1433148--1433179 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1433138 AGAGTAATTA
1433148 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
1433180 TATCACCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1440137 original size:195 final size:195
Alignment explanation
Indices: 1439773--1440165 Score: 736
Period size: 195 Copynumber: 2.0 Consensus size: 195
1439763 TGTATTAGAT
1439773 ATAAAATAATATTGTATTTTATATTTTTGGGGTTAATGGGGGAGTTGTGAAAGCATAAATTGTTG
1 ATAAAATAATATTGTATTTTATATTTTTGGGGTTAATGGGGGAGTTGTGAAAGCATAAATTGTTG
1439838 GAGATGTCAAAGGGATAAAGTATAGGGTGAAATAAGAAATAAATAAATGGATTAGTCGGTAACGT
66 GAGATGTCAAAGGGATAAAGTATAGGGTGAAATAAGAAATAAATAAATGGATTAGTCGGTAACGT
1439903 AACGGAAGGTTGAATGACAGATGAAACAATGATATATAGTGGCGTCATGGATTC-GTGGACGACA
131 AACGGAAGGTTGAATGACAGATGAAACAATGA-ATATAGTGGCGTCATGGATTCGGTGGACGACA
1439967 G
195 G
1439968 ATAAAATAATATTGTATTTTATATTTTTGGGGTTAATGGGGGAGTTGTGAAAGCATAAATTGTTG
1 ATAAAATAATATTGTATTTTATATTTTTGGGGTTAATGGGGGAGTTGTGAAAGCATAAATTGTTG
*
1440033 GAGGTGTCAAAGGGATAAAGTATAGGGTGAAATAAGAAATAAATAAATGGTATTAGTCGGATAAC
66 GAGATGTCAAAGGGATAAAGTATAGGGTGAAATAAGAAATAAATAAATGG-ATTAGTCGG-TAAC
1440098 GTAACGGAAGGTTGAATGACAGATGAAACAATG-ATATAGTGGCGTCATGGATTCGGTGGACGAC
129 GTAACGGAAGGTTGAATGACAGATGAAACAATGAATATAGTGGCGTCATGGATTCGGTGGACGAC
1440162 AG
194 AG
1440164 AT
1 AT
1440166 GGTATCGGTG
Statistics
Matches: 194, Mismatches: 1, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
195 135 0.70
196 22 0.11
197 37 0.19
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.29
Consensus pattern (195 bp):
ATAAAATAATATTGTATTTTATATTTTTGGGGTTAATGGGGGAGTTGTGAAAGCATAAATTGTTG
GAGATGTCAAAGGGATAAAGTATAGGGTGAAATAAGAAATAAATAAATGGATTAGTCGGTAACGT
AACGGAAGGTTGAATGACAGATGAAACAATGAATATAGTGGCGTCATGGATTCGGTGGACGACAG
Found at i:1451829 original size:295 final size:298
Alignment explanation
Indices: 1451238--1451830 Score: 1052
Period size: 294 Copynumber: 2.0 Consensus size: 298
1451228 CATCATCTCT
*
1451238 TCTTCACTGCTAGGACTCATACTGGAGGATAATTTGAAGTTAATAGGAAAAGGGGTAGAAATTGG
1 TCTTCACTGCTAGGACTCATACTGGACGATAATTTGAAGTTAATAGGAAAAGGGGTAGAAATTGG
1451303 CTTACAATCTTGCATGTTGAATCTTGACAAGATCTTATTCAAGTAATTCTTTTGTGAAAGTCAAA
66 CTTACAATCTTGCATGTTGAATCTTGACAAGATCTTATTCAAGTAATTCTTTTGTGAAAGTCAAA
*
1451368 TATTCCTATTACTTCTGTCTCGGTGAATTTGCATCCCTAGAATCTTGTTTGTTGATCCCAAGTCC
131 TATTCCTATTACTTCTGTCTCGGTGAATTTGCATCCATAGAATCTTGTTTGTTGATCCCAAGTCC
* *
1451433 TTCATTTCAAATTCTCTAGCCAGTTGTTCTTTCAATCTCTTCATATGATCTTTTTGGGTCCTGCA
196 TTCATTTCAAATTCTCTAGCCAGTTGTTCCTTCAATCTATTCATATGATCTTTTTGGGTCCTGCA
*
1451498 ACCAACATGTTATCCACATACAACAATAATATAACAAA
261 ACCAACATGTTATCCACATACAACAACAATATAACAAA
*
1451536 TCTTCACTGCTA-GACTCATACTGGACGATAATTTGAAGTTAATAGGAAGA-GGGTAG-AATTGG
1 TCTTCACTGCTAGGACTCATACTGGACGATAATTTGAAGTTAATAGGAAAAGGGGTAGAAATTGG
1451598 CTTACAATCTTGCATGTTGAATCTTGACAAGATCTTATTC-AGTAATTCTTTTGTGAAAGTCAAA
66 CTTACAATCTTGCATGTTGAATCTTGACAAGATCTTATTCAAGTAATTCTTTTGTGAAAGTCAAA
* *
1451662 TCTTCCTATTACTTCTGTTTCGGTGAATTTGCATCCATAGAATCTTGTTTGTTGATCCCAAGTCC
131 TATTCCTATTACTTCTGTCTCGGTGAATTTGCATCCATAGAATCTTGTTTGTTGATCCCAAGTCC
1451727 TTCATTTCAAATTCTCTAGCCAGTTGTTCCTTCAAT-TATTCAATATGATCTTTGTTGGGTCCTG
196 TTCATTTCAAATTCTCTAGCCAGTTGTTCCTTCAATCTATTC-ATATGATCTTT-TTGGGTCCTG
*
1451791 CAACCGACATGTTATCCACATACAACAACAATATAACAAA
259 CAACCAACATGTTATCCACATACAACAACAATATAACAAA
1451831 ATCGTTATCA
Statistics
Matches: 284, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
293 4 0.01
294 132 0.46
295 94 0.33
296 6 0.02
297 36 0.13
298 12 0.04
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (298 bp):
TCTTCACTGCTAGGACTCATACTGGACGATAATTTGAAGTTAATAGGAAAAGGGGTAGAAATTGG
CTTACAATCTTGCATGTTGAATCTTGACAAGATCTTATTCAAGTAATTCTTTTGTGAAAGTCAAA
TATTCCTATTACTTCTGTCTCGGTGAATTTGCATCCATAGAATCTTGTTTGTTGATCCCAAGTCC
TTCATTTCAAATTCTCTAGCCAGTTGTTCCTTCAATCTATTCATATGATCTTTTTGGGTCCTGCA
ACCAACATGTTATCCACATACAACAACAATATAACAAA
Found at i:1457212 original size:20 final size:20
Alignment explanation
Indices: 1457183--1457240 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 20
1457173 ATAAAAACAT
1457183 AAAATGAAATTTTTCATAATA
1 AAAAT-AAATTTTTCATAATA
*
1457204 AAAATAAATATTT-AT-A-A
1 AAAATAAATTTTTCATAATA
* *
1457221 ATAAT-AATTATTCATAATA
1 AAAATAAATTTTTCATAATA
1457240 A
1 A
1457241 GAGGATAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 5 0.17
17 7 0.23
18 2 0.07
19 4 0.13
20 7 0.23
21 5 0.17
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (20 bp):
AAAATAAATTTTTCATAATA
Found at i:1457436 original size:2 final size:2
Alignment explanation
Indices: 1457429--1457453 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1457419 ATTACTTTTC
1457429 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 T
1457454 TGGCCATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1459153 original size:18 final size:19
Alignment explanation
Indices: 1459111--1459154 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
1459101 TTATTTGACT
* *
1459111 TTATTTATAATTTTTTATA
1 TTATTTATAATTTTTAAAA
1459130 TATATTTATAA-TTTTAAAA
1 T-TATTTATAATTTTTAAAA
1459149 TTATTT
1 TTATTT
1459155 TATATGCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
18 5 0.23
19 8 0.36
20 9 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTATAATTTTTAAAA
Found at i:1460126 original size:21 final size:21
Alignment explanation
Indices: 1460102--1460141 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1460092 ATGTTATTGG
*
1460102 TTTCTCTAATAACTATGGGTT
1 TTTCTCTAATAAATATGGGTT
* *
1460123 TTTCTGTGATAAATATGGG
1 TTTCTCTAATAAATATGGG
1460142 ATGATATATG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.45
Consensus pattern (21 bp):
TTTCTCTAATAAATATGGGTT
Found at i:1470587 original size:33 final size:33
Alignment explanation
Indices: 1470550--1470691 Score: 145
Period size: 33 Copynumber: 4.5 Consensus size: 33
1470540 TAATTTGAAT
1470550 ATTAACTATAATATATAATATATATTTTTTATC
1 ATTAACTATAATATATAATATATATTTTTTATC
* *
1470583 ATTAACTATAATATAT-ATATATA--TATTATA
1 ATTAACTATAATATATAATATATATTTTTTATC
* * * * * * **
1470613 AGTCACAAT-CT-TATGAT-TATAATTTGAAT-
1 ATTAACTATAATATATAATATATATTTTTTATC
1470642 ATTAACTATAATATATAATATATATTTTTTATC
1 ATTAACTATAATATATAATATATATTTTTTATC
1470675 ATTAACTATAATATATA
1 ATTAACTATAATATATA
1470692 TATTATAATT
Statistics
Matches: 85, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
28 7 0.08
29 9 0.11
30 15 0.18
31 5 0.06
32 16 0.19
33 33 0.39
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.47
Consensus pattern (33 bp):
ATTAACTATAATATATAATATATATTTTTTATC
Found at i:1470684 original size:92 final size:91
Alignment explanation
Indices: 1470522--1470698 Score: 336
Period size: 92 Copynumber: 1.9 Consensus size: 91
1470512 TGTGACACAT
*
1470522 GTCATAATCTTATGATTATAATTTGAATATTAACTATAATATATAATATATATTTTTTATCATTA
1 GTCACAATCTTATGATTATAATTTGAATATTAACTATAATATATAATATATATTTTTTATCATTA
1470587 ACTATAATATATATATATATATTATAA
66 ACTATAATATATATAT-TATATTATAA
1470614 GTCACAATCTTATGATTATAATTTGAATATTAACTATAATATATAATATATATTTTTTATCATTA
1 GTCACAATCTTATGATTATAATTTGAATATTAACTATAATATATAATATATATTTTTTATCATTA
1470679 ACTATAATATATATATTATA
66 ACTATAATATATATATTATA
1470699 ATTTGAATAT
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
91 4 0.05
92 80 0.95
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.47
Consensus pattern (91 bp):
GTCACAATCTTATGATTATAATTTGAATATTAACTATAATATATAATATATATTTTTTATCATTA
ACTATAATATATATATTATATTATAA
Found at i:1473645 original size:20 final size:21
Alignment explanation
Indices: 1473599--1473659 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
1473589 TTCCCCTGTG
1473599 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
1473622 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
1473642 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1473660 TGTACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:1484169 original size:48 final size:48
Alignment explanation
Indices: 1484117--1484218 Score: 109
Period size: 48 Copynumber: 2.1 Consensus size: 48
1484107 CAAGATTTTA
* *
1484117 AATTTTAAAATGA-ATTTGTTATTTTTACATATT-TAAATTAAATTCAAT
1 AATTTTAAAATGAGACTTATTA-TTTTACAT-TTATAAATTAAATTCAAT
* * * **
1484165 AATTTTCAAATTAGACTTATTATTTTATATTTATAAATTAAATTCTGT
1 AATTTTAAAATGAGACTTATTATTTTACATTTATAAATTAAATTCAAT
1484213 AATTTT
1 AATTTT
1484219 TATATTTATA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
47 2 0.04
48 37 0.82
49 6 0.13
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (48 bp):
AATTTTAAAATGAGACTTATTATTTTACATTTATAAATTAAATTCAAT
Found at i:1486721 original size:16 final size:17
Alignment explanation
Indices: 1486700--1486761 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 17
1486690 AGCTAAGTGA
*
1486700 CATATGATTA-TGAAAT
1 CATATGAATAGTGAAAT
1486716 CATATGAATAGTGAAATGT
1 CATATGAATAGTGAAA--T
*
1486735 GCATGTGAATATGTGAAAT
1 -CATATGAATA-GTGAAAT
*
1486754 GATATGAA
1 CATATGAA
1486762 AGAGAATGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 9 0.24
17 5 0.14
18 6 0.16
19 2 0.05
20 9 0.24
21 6 0.16
ACGTcount: A:0.42, C:0.05, G:0.21, T:0.32
Consensus pattern (17 bp):
CATATGAATAGTGAAAT
Found at i:1486873 original size:32 final size:32
Alignment explanation
Indices: 1486826--1487019 Score: 236
Period size: 32 Copynumber: 6.1 Consensus size: 32
1486816 GAGTCAAGGG
* *
1486826 ATTACCTATGCCTTTCGGGATATATGGACAGT
1 ATTACCTATGTCTTTCGGGACATATGGACAGT
* * *
1486858 ATTACTTATGTCTTTCGGGATATATGGACAGG
1 ATTACCTATGTCTTTCGGGACATATGGACAGT
*
1486890 ATTACCTATGTCTTTCGGGACATATGGACAGG
1 ATTACCTATGTCTTTCGGGACATATGGACAGT
*
1486922 ATTACCTATGTCTTTCGGGACATATGAACA-T
1 ATTACCTATGTCTTTCGGGACATATGGACAGT
** *
1486953 GATTACCTATGT-TCTTCAAGACATATGGATAGT
1 -ATTACCTATGTCT-TTCGGGACATATGGACAGT
1486986 -TTACCTATGT-TCTTCGGGACATATGGACAG-
1 ATTACCTATGTCT-TTCGGGACATATGGACAGT
1487016 ATTA
1 ATTA
1487020 TTATACTAGT
Statistics
Matches: 144, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
31 31 0.22
32 112 0.78
33 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (32 bp):
ATTACCTATGTCTTTCGGGACATATGGACAGT
Found at i:1487694 original size:22 final size:21
Alignment explanation
Indices: 1487643--1487695 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1487633 GGATGAAATT
1487643 ACTGTAGCAAGGGTATCAGTAC
1 ACTGTAGC-AGGGTATCAGTAC
* *
1487665 ACTATAGCAGGGTATCGGTACC
1 ACTGTAGCAGGGTATCAGTA-C
*
1487687 CCTGTAGCA
1 ACTGTAGCA
1487696 TTTTGGAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 11 0.42
22 15 0.58
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
ACTGTAGCAGGGTATCAGTAC
Found at i:1488372 original size:11 final size:12
Alignment explanation
Indices: 1488340--1488374 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
1488330 AATTTCATAT
1488340 ATAATTATTAAAA
1 ATAATTA-TAAAA
1488353 ATAATTATAAAA
1 ATAATTATAAAA
1488365 ATAATATATA
1 ATAAT-TATA
1488375 TATATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
ATAATTATAAAA
Found at i:1488961 original size:51 final size:48
Alignment explanation
Indices: 1488901--1489001 Score: 141
Period size: 48 Copynumber: 2.0 Consensus size: 48
1488891 AGAGGTTAAA
1488901 ACTGTTCCTAAAGAACAATTATTTAATCAACAAAACG-AGCATGAAAACGGT
1 ACTGTTCCTAAAGAAC-A--A-TTAATCAACAAAACGCAGCATGAAAACGGT
* *
1488952 ACTGTTCCTAAAGAACAATTAATCAACCAAACGCAGCATGAAAATGGT
1 ACTGTTCCTAAAGAACAATTAATCAACAAAACGCAGCATGAAAACGGT
1489000 AC
1 AC
1489002 ATTTTATCCA
Statistics
Matches: 47, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
47 14 0.30
48 16 0.34
50 1 0.02
51 16 0.34
ACGTcount: A:0.45, C:0.20, G:0.14, T:0.22
Consensus pattern (48 bp):
ACTGTTCCTAAAGAACAATTAATCAACAAAACGCAGCATGAAAACGGT
Found at i:1496264 original size:15 final size:15
Alignment explanation
Indices: 1496244--1496321 Score: 72
Period size: 15 Copynumber: 5.4 Consensus size: 15
1496234 AAATAATTAA
1496244 AATAATATATTTTAT
1 AATAATATATTTTAT
1496259 AATAATATA-TTTAT
1 AATAATATATTTTAT
* * *
1496273 AATTATTTATTATAT
1 AATAATATATTTTAT
** * *
1496288 TTTAA-AT-TATTAA
1 AATAATATATTTTAT
1496301 AATAATATATTTTAT
1 AATAATATATTTTAT
1496316 AATAAT
1 AATAAT
1496322 TTTTATATTT
Statistics
Matches: 46, Mismatches: 14, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
13 6 0.13
14 15 0.33
15 25 0.54
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:1496315 original size:57 final size:57
Alignment explanation
Indices: 1496221--1496328 Score: 175
Period size: 57 Copynumber: 1.9 Consensus size: 57
1496211 GATATGAATA
1496221 TATTCATATTTTAAAATAATTAAAATAATATATTTTATAATAATATATTTATAATTATT
1 TATTCATATTTTAAAATAATTAAAATAATATATTTTATAATAAT-T-TTTATAATTATT
*
1496280 TATT-ATATTTT-AAATTATTAAAATAATATATTTTATAATAATTTTTATA
1 TATTCATATTTTAAAATAATTAAAATAATATATTTTATAATAATTTTTATA
1496329 TTTTTAATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
55 6 0.12
56 1 0.02
57 30 0.62
58 7 0.15
59 4 0.08
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (57 bp):
TATTCATATTTTAAAATAATTAAAATAATATATTTTATAATAATTTTTATAATTATT
Found at i:1496328 original size:42 final size:42
Alignment explanation
Indices: 1496259--1496361 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
1496249 TATATTTTAT
* *
1496259 AATAATATA-TTTATAATTATTTATTATATTTTAAATTATTAA
1 AATAATATATTTTATAATAATTTATTATATTTTAAATAATT-A
*
1496301 AATAATATATTTTATAATAATTT-TTATATTTTTAATAATTA
1 AATAATATATTTTATAATAATTTATTATATTTTAAATAATTA
*
1496342 AAGAATATATTTTAATAATA
1 AATAATATATTTT-ATAATA
1496362 TAAAAATAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
41 13 0.24
42 30 0.55
43 12 0.22
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (42 bp):
AATAATATATTTTATAATAATTTATTATATTTTAAATAATTA
Found at i:1496354 original size:21 final size:22
Alignment explanation
Indices: 1496325--1496369 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1496315 TAATAATTTT
1496325 TATATTTTTAATAAT-TAAAGAA
1 TATATTTTTAATAATATAAA-AA
1496347 TATA-TTTTAATAATATAAAAA
1 TATATTTTTAATAATATAAAAA
1496368 TA
1 TA
1496370 AAAAATCCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TATATTTTTAATAATATAAAAA
Found at i:1497463 original size:2 final size:2
Alignment explanation
Indices: 1497458--1497500 Score: 70
Period size: 2 Copynumber: 21.5 Consensus size: 2
1497448 ACACACACAC
1497458 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1497500 A
1 A
1497501 AGTACATATG
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.95
3 1 0.03
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1499013 original size:27 final size:27
Alignment explanation
Indices: 1498972--1499038 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
1498962 TATTCATACT
*
1498972 TATGTACATACATCA-TACATAAATATA
1 TATGTACATATATCATTA-ATAAATATA
*
1498999 TATGTACATATATCATTAATCAATATA
1 TATGTACATATATCATTAATAAATATA
* *
1499026 TATATATATATAT
1 TATGTACATATAT
1499039 ATATGTACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 33 0.94
28 2 0.06
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.40
Consensus pattern (27 bp):
TATGTACATATATCATTAATAAATATA
Found at i:1499034 original size:129 final size:134
Alignment explanation
Indices: 1498897--1499166 Score: 442
Period size: 138 Copynumber: 2.0 Consensus size: 134
1498887 AACATATAAG
* *
1498897 TATATATATGTATGTATGTACATGCATCATTGATTAATGATAAGTGC-T-TATATATATTAAATC
1 TATATATATATATATATGTACATGCATCATTGATTAATGATAAGTGCTTATATATATATTAAATC
1498960 TATATTCATACTTATG-T-A-CATACATCATACATAAATATATATGTACATATATCATTAATCAA
66 TATATTCATACTTATGATAATCATACATCATACATAAATATATATGTACATATATCATTAATCAA
1499022 TATA
131 TATA
*
1499026 TATATATATATATATATGTACATGCATCATTGATTAATGATAAGTGCTTATATATATATTAAATT
1 TATATATATATATATATGTACATGCATCATTGATTAATGATAAGTGCTTATATATATATTAAATC
1499091 TATATTCATACTTATGTACATACATCATACATCATACATAAATATATATGTACATATATCATTAA
66 TATATTCATACTTATG---ATA-ATCATACATCATACATAAATATATATGTACATATATCATTAA
1499156 TCAATATA
127 TCAATATA
1499164 TAT
1 TAT
1499167 TATGCATAAG
Statistics
Matches: 129, Mismatches: 3, Indels: 9
0.91 0.02 0.06
Matches are distributed among these distances:
129 45 0.35
130 1 0.01
131 30 0.23
135 1 0.01
137 1 0.01
138 51 0.40
ACGTcount: A:0.41, C:0.11, G:0.07, T:0.41
Consensus pattern (134 bp):
TATATATATATATATATGTACATGCATCATTGATTAATGATAAGTGCTTATATATATATTAAATC
TATATTCATACTTATGATAATCATACATCATACATAAATATATATGTACATATATCATTAATCAA
TATA
Found at i:1506866 original size:89 final size:92
Alignment explanation
Indices: 1506624--1506870 Score: 270
Period size: 92 Copynumber: 2.7 Consensus size: 92
1506614 TATGTAACAT
*** * *
1506624 ACAAGCTGAGGTAGGCATCATGGCACGGCTGAGGGGCTACATCTCTGAGCTTACACACCCATCTA
1 ACAAGCTGAGGTAGGCATCATGGTGTGGCTGAGGGGCTACATCTCGGAGCTTACACACCCCTCTA
*
1506689 GCCTACCCATACTACTATGCAGCACAC
66 GCCTACCCACACTACTATGCAGCACAC
* * * *
1506716 ACAAACTGAGGTAGGCATCATGGTGCT-GTTGAGGGGCTACATCTTGGAGCTCACACA-CCCTCT
1 ACAAGCTGAGGTAGGCATCATGGTG-TGGCTGAGGGGCTACATCTCGGAGCTTACACACCCCTCT
** * * *
1506779 AGGTTACCTACACTACTTTG-AG-ATAC
65 AGCCTACCCACACTACTATGCAGCACAC
* * * * *
1506805 ACGAGCTGAGGTAAGCATCATGATGTGGCTGA-GGGTTACATCTCGGAACTTACACACCCCTCTA
1 ACAAGCTGAGGTAGGCATCATGGTGTGGCTGAGGGGCTACATCTCGGAGCTTACACACCCCTCTA
1506869 GC
66 GC
1506871 TTAACTATGC
Statistics
Matches: 127, Mismatches: 25, Indels: 9
0.79 0.16 0.06
Matches are distributed among these distances:
88 21 0.17
89 36 0.28
90 2 0.02
91 20 0.16
92 48 0.38
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (92 bp):
ACAAGCTGAGGTAGGCATCATGGTGTGGCTGAGGGGCTACATCTCGGAGCTTACACACCCCTCTA
GCCTACCCACACTACTATGCAGCACAC
Found at i:1514040 original size:23 final size:21
Alignment explanation
Indices: 1513994--1514064 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 21
1513984 ATAGGGCAGA
*
1513994 GGGAATCGATATCCCCTTGAAG
1 GGGAACCGAT-TCCCCTTGAAG
1514016 GGGAACCGATTCCCCTTTTGAAG
1 GGGAACCGATTCCCC--TTGAAG
* * *
1514039 GGGAACTGATTCCCCCTGTAG
1 GGGAACCGATTCCCCTTGAAG
1514060 GGGAA
1 GGGAA
1514065 TCGCTACCCC
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
21 14 0.33
22 9 0.21
23 20 0.47
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.23
Consensus pattern (21 bp):
GGGAACCGATTCCCCTTGAAG
Found at i:1522725 original size:16 final size:18
Alignment explanation
Indices: 1522704--1522740 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1522694 AAACTTAAAC
1522704 TTTTAT-ATTTAAT-TTT
1 TTTTATAATTTAATCTTT
1522720 TTTTATCAATTTAATCTTT
1 TTTTAT-AATTTAATCTTT
1522739 TT
1 TT
1522741 GTAACACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATAATTTAATCTTT
Found at i:1528029 original size:19 final size:17
Alignment explanation
Indices: 1527987--1528029 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
1527977 ATAACATTTT
1527987 ATATATCTTAGTTTAAA
1 ATATATCTTAGTTTAAA
*
1528004 TTCATATCTTAAGTTTAAAA
1 AT-ATATCTT-AGTTT-AAA
1528024 ATATAT
1 ATATAT
1528030 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 7 0.33
19 9 0.43
20 4 0.19
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (17 bp):
ATATATCTTAGTTTAAA
Found at i:1535750 original size:32 final size:32
Alignment explanation
Indices: 1535709--1535787 Score: 149
Period size: 32 Copynumber: 2.5 Consensus size: 32
1535699 TTGTGAACCT
*
1535709 TAAGTCGCATGGAACACAATGCAATACCCACC
1 TAAGTCGCATAGAACACAATGCAATACCCACC
1535741 TAAGTCGCATAGAACACAATGCAATACCCACC
1 TAAGTCGCATAGAACACAATGCAATACCCACC
1535773 TAAGTCGCATAGAAC
1 TAAGTCGCATAGAAC
1535788 CATGCGACAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.39, C:0.29, G:0.15, T:0.16
Consensus pattern (32 bp):
TAAGTCGCATAGAACACAATGCAATACCCACC
Found at i:1536843 original size:142 final size:142
Alignment explanation
Indices: 1536587--1536852 Score: 417
Period size: 142 Copynumber: 1.9 Consensus size: 142
1536577 TCTCCTGGGT
* ** *
1536587 TGGGTTACAAGTGGCCGCATGCGTCTCCTCAGGGTCCCCTCGTGTGGCCGGCAAAGTCGCATGGC
1 TGGGTTACAAGCGGCCGCATGCGTCTCCTCAGGGTCCCCTCGCATGGCCGGAAAAGTCGCATGGC
1536652 ATGCCACTCACGTAGGTACAGTATGTAGCTGGCATTCAAATGATAAAAGTTAAACCCATGCATCT
66 ATGCCACTCACGTAGGTACAGTATGTAGCTGGCATTCAAATGATAAAAGTTAAACCCATGCATCT
1536717 CCTAAGGCGGGC
131 CCTAAGGCGGGC
* * * *
1536729 TGGGTTGCAAGCGGCCGCATGCGTCTCCTCGGGGTCCTCTCGCATGGCTGGAAAAGTCGCATGGC
1 TGGGTTACAAGCGGCCGCATGCGTCTCCTCAGGGTCCCCTCGCATGGCCGGAAAAGTCGCATGGC
* * *
1536794 ATGCCATTCACGTAGGTACAGT-TGGTAGCTGGCATTCGAATGATAAAAGTTTAACCCAT
66 ATGCCACTCACGTAGGTACAGTAT-GTAGCTGGCATTCAAATGATAAAAGTTAAACCCAT
1536853 ACCTCTATCC
Statistics
Matches: 112, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
141 1 0.01
142 111 0.99
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.24
Consensus pattern (142 bp):
TGGGTTACAAGCGGCCGCATGCGTCTCCTCAGGGTCCCCTCGCATGGCCGGAAAAGTCGCATGGC
ATGCCACTCACGTAGGTACAGTATGTAGCTGGCATTCAAATGATAAAAGTTAAACCCATGCATCT
CCTAAGGCGGGC
Found at i:1537236 original size:19 final size:21
Alignment explanation
Indices: 1537213--1537260 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
1537203 ATTTTTATAA
*
1537213 ATATATGT-TAATATTATTTTT
1 ATAT-TGTATAATATCATTTTT
1537234 ATATTGTATAATATCATTTTT
1 ATATTGTATAATATCATTTTT
1537255 ACTATT
1 A-TATT
1537261 TATTATCATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 3 0.12
21 17 0.71
22 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (21 bp):
ATATTGTATAATATCATTTTT
Found at i:1537247 original size:31 final size:30
Alignment explanation
Indices: 1537173--1537247 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 30
1537163 TTATTTGAGG
*
1537173 TATTTTACTATTG-ATTAT-TATGTTAATAT
1 TATTTTA-TATTGTATAATATATGTTAATAT
1537202 TATTTT-TA---TA-AATATATGTTAATAT
1 TATTTTATATTGTATAATATATGTTAATAT
1537227 TATTTTTATATTGTATAATAT
1 TA-TTTTATATTGTATAATAT
1537248 CATTTTTACT
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
24 2 0.05
25 14 0.38
26 4 0.11
27 4 0.11
29 6 0.16
30 2 0.05
31 5 0.14
ACGTcount: A:0.35, C:0.01, G:0.05, T:0.59
Consensus pattern (30 bp):
TATTTTATATTGTATAATATATGTTAATAT
Done.