Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000778.1 Hibiscus syriacus cultivar Beakdansim tig00001513_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: 82574
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7476 original size:20 final size:20
Alignment explanation
Indices: 7453--7491 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
7443 AAATATAAAC
*
7453 AAATAAAATTAAAACAATAA
1 AAATAAAACTAAAACAATAA
**
7473 AAATACCACTAAAACAATA
1 AAATAAAACTAAAACAATA
7492 TATTTTAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.69, C:0.13, G:0.00, T:0.18
Consensus pattern (20 bp):
AAATAAAACTAAAACAATAA
Found at i:8757 original size:3 final size:3
Alignment explanation
Indices: 8749--8855 Score: 160
Period size: 3 Copynumber: 35.7 Consensus size: 3
8739 AATATATATT
* * *
8749 TAA TAA TAA TAA TAA TGA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
8797 TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAT TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8845 TAA TAA TAA TA
1 TAA TAA TAA TA
8856 TGGATAAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 96 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:9595 original size:113 final size:113
Alignment explanation
Indices: 9174--10072 Score: 1532
Period size: 113 Copynumber: 8.0 Consensus size: 113
9164 AGAATTATGC
* * * *
9174 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * *
9239 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
*
9286 AAAAGGTTGAACAAATTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
9351 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
9399 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
9463 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
9511 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
9576 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAA-ATGATGGATTCAGGT
*
9625 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
9690 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
9738 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
9803 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
9851 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
9916 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAA-ATGATGGATTCAGGT
*
9965 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* ** *
10030 TATGAACTTTCTCTGGAAAAGCTGATCTTTCAAATGATAGATT
66 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATT
10073 TGAATCTTTG
Statistics
Matches: 747, Mismatches: 36, Indels: 7
0.95 0.05 0.01
Matches are distributed among these distances:
112 178 0.24
113 355 0.48
114 214 0.29
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGT
Found at i:9734 original size:227 final size:226
Alignment explanation
Indices: 9174--10072 Score: 1532
Period size: 227 Copynumber: 4.0 Consensus size: 226
9164 AGAATTATGC
* * * *
9174 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* *
9239 TATGAAC-TTCTCCGGAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATT
*
9303 CTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
9368 AAAGATGATCCCTCAAATGATGGATTCAGGT
196 AAAGATGATCCCTCAAATGATGGATTCAGGT
9399 AAAAGGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * *
9463 TATGAACTTTCTCTGGAAAAGCTGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATT
9528 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
* * * *
9593 AAAGATAATCCATCAATTTGATGAATTCAGGT
196 AAAGATGATCCCTCAA-ATGATGGATTCAGGT
*
9625 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
9690 TATGAACTTTCTCTGGAAAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATT
9755 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
131 CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
*
9820 AAAGCTGATCCCTCAAATGATGGATTCAGGT
196 AAAGATGATCCCTCAAATGATGGATTCAGGT
9851 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
9916 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAA-ATGATGAATTCAGGTAAAAGGTTGAACAAAT
*
9981 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
130 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* ** *
10046 AAAAGCTGATCTTTCAAATGATAGATT
195 AAAAGATGATCCCTCAAATGATGGATT
10073 TGAATCTTTG
Statistics
Matches: 639, Mismatches: 31, Indels: 6
0.95 0.05 0.01
Matches are distributed among these distances:
224 56 0.09
225 140 0.22
226 133 0.21
227 310 0.49
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (226 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATT
CTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGA
AAAGATGATCCCTCAAATGATGGATTCAGGT
Found at i:9855 original size:340 final size:339
Alignment explanation
Indices: 9174--10072 Score: 1676
Period size: 340 Copynumber: 2.7 Consensus size: 339
9164 AGAATTATGC
* * * *
9174 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
9239 TATGAAC-TTCTCCGGAAAAGATAATCCATCAA-TTGATGAATTCAGGTAAAAGGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
* *
9302 TCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
9367 AAAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAATTCTTCTCATTATGAACTT
196 AAAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAATTCTTCTCATTATGAACTT
9432 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAAA
261 CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAAA
9497 TGATGGATTCAGGT
326 TGATGGATTCAGGT
9511 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
9576 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
9641 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
9706 AAAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACT
196 AAAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAAC-AATTCTTCTCATTATGAACT
9771 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAA
260 TCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAA
9836 ATGATGGATTCAGGT
325 ATGATGGATTCAGGT
9851 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
9916 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
66 TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
9981 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
131 TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
* ** *
10046 AAAAGCTGATCTTTCAAATGATAGATT
196 AAAAGATGATCCCTCAAATGATGGATT
10073 TGAATCTTTG
Statistics
Matches: 548, Mismatches: 11, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
337 68 0.12
338 24 0.04
339 138 0.25
340 318 0.58
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (339 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAAT
TCTTCTCATTATGAACTTCTTCTTTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
AAAAGATGATCCCTCAAATGATGGATTCAGGTAAAAGGTTGAACAATTCTTCTCATTATGAACTT
CTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCCTCAAA
TGATGGATTCAGGT
Found at i:10940 original size:167 final size:166
Alignment explanation
Indices: 10700--11172 Score: 767
Period size: 167 Copynumber: 2.8 Consensus size: 166
10690 CCTACTGAAT
* * *
10700 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATGTTACGAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
*
10765 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTGGCAA
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TTGACAA
*
10830 ATTCATC-TTCTAAATTCACTGATTGGTTCTGCCAAAC
130 ATTCATCTTTC-AAATTCAATGATTGGTTCTGCCAAAC
10867 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
* *
10932 TGATTGGTTCTGCCAAACTAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACAC
66 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAA
10996 ATTCATCTTTCAAATTCAATGATTGGTTCTGCCAAAC
130 ATTCATCTTTCAAATTCAATGATTGGTTCTGCCAAAC
* * * *
11033 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTG-ACAAATTCATCTTCTAAACTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
11097 ATGATT-GTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACA
65 ATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACA
11160 AATTCATCTTTCA
129 AATTCATCTTTCA
11173 TTTAATTGTT
Statistics
Matches: 288, Mismatches: 13, Indels: 12
0.92 0.04 0.04
Matches are distributed among these distances:
165 64 0.22
166 101 0.35
167 123 0.43
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (166 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACACATTCATCTTCCAAATTCAA
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAA
TTCATCTTTCAAATTCAATGATTGGTTCTGCCAAAC
Found at i:10969 original size:83 final size:83
Alignment explanation
Indices: 10700--11169 Score: 734
Period size: 83 Copynumber: 5.7 Consensus size: 83
10690 CCTACTGAAT
* * * *
10700 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATGTTACGAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAATTCA
10764 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* *
10783 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTTGGCAAATTCATCTTCTAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TTGACAAATTCATCTTCCAAATTCA
*
10848 CTGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
*
10867 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTCCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAATTCA
10931 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* * *
10950 TAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACACATTCATCTTTCAAATTCA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACAAATTCATCTTCCAAATTCA
11014 ATGATTGGTTCTGCCAAAC
65 ATGATTGGTTCTGCCAAAC
* * *
11033 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTGACAAATTCATCTTCTAAACTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
11098 TGATT-GTTCTGTCC-AAC
66 TGATTGGTTCTG-CCAAAC
11115 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTT
11170 TCATTTAATT
Statistics
Matches: 362, Mismatches: 20, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
82 65 0.18
83 220 0.61
84 75 0.21
85 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACAAATTCATCTTCCAAATTCAA
TGATTGGTTCTGCCAAAC
Found at i:24620 original size:17 final size:16
Alignment explanation
Indices: 24582--24620 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
24572 GGTTTAGTAG
*
24582 TTTTTTTTTCTTTCTC
1 TTTTTTTTTCTGTCTC
24598 TGTTTTTTTTCTGTCTTC
1 T-TTTTTTTTCTGTC-TC
24616 TTTTT
1 TTTTT
24621 CCGTTCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 16 0.80
18 3 0.15
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTTTTTTTCTGTCTC
Found at i:25108 original size:3 final size:3
Alignment explanation
Indices: 25100--25197 Score: 160
Period size: 3 Copynumber: 32.7 Consensus size: 3
25090 AATATATATT
* *
25100 TAA TAA TAA TAA TAA TAA TGA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
25148 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
25196 TA
1 TA
25198 TGGATAAAAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:29479 original size:36 final size:36
Alignment explanation
Indices: 29392--29479 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
29382 TGTTTTGGTA
*
29392 TCTCTGTGAATATCAAGTGCGAGGAACATGATCCCT
1 TCTCTGTGAATATTAAGTGCGAGGAACATGATCCCT
*
29428 TCTCTGTGAATATTAAGTGCGAGGAACATGATCCTT
1 TCTCTGTGAATATTAAGTGCGAGGAACATGATCCCT
* *
29464 TCTGTGTGAACATTAA
1 TCTCTGTGAATATTAA
29480 TTGTATGTAA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 48 1.00
ACGTcount: A:0.28, C:0.18, G:0.22, T:0.32
Consensus pattern (36 bp):
TCTCTGTGAATATTAAGTGCGAGGAACATGATCCCT
Found at i:31003 original size:15 final size:16
Alignment explanation
Indices: 30979--31008 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
30969 GTAAAATATT
30979 AAAAATCTAAAATTAC
1 AAAAATCTAAAATTAC
30995 AAAAA-CTAAAATTA
1 AAAAATCTAAAATTA
31009 AGAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATCTAAAATTAC
Found at i:40556 original size:20 final size:20
Alignment explanation
Indices: 40527--40568 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
40517 ACGTTGAGGC
*
40527 CATCTGTGCCCTCCTTTCTG
1 CATCTCTGCCCTCCTTTCTG
40547 CATCTCTGCCCTCCTTTCTG
1 CATCTCTGCCCTCCTTTCTG
40567 CA
1 CA
40569 GAGGCCATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.43, G:0.12, T:0.38
Consensus pattern (20 bp):
CATCTCTGCCCTCCTTTCTG
Found at i:41822 original size:31 final size:31
Alignment explanation
Indices: 41787--41872 Score: 93
Period size: 30 Copynumber: 2.8 Consensus size: 31
41777 CCAACTCAAA
* *
41787 GGGAAAACATAATTAACCATAGAAAATGAGG
1 GGGAAAATATAATTAACCATAAAAAATGAGG
* *
41818 GGG-AAATATAATAAATCATAAAAAATGAGG
1 GGGAAAATATAATTAACCATAAAAAATGAGG
** **
41848 GATAAAATATAATTAAGTATAAAAA
1 GGGAAAATATAATTAACCATAAAAA
41873 TAAGGAGACA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
30 24 0.53
31 21 0.47
ACGTcount: A:0.57, C:0.05, G:0.17, T:0.21
Consensus pattern (31 bp):
GGGAAAATATAATTAACCATAAAAAATGAGG
Found at i:41886 original size:31 final size:31
Alignment explanation
Indices: 41821--41895 Score: 73
Period size: 31 Copynumber: 2.4 Consensus size: 31
41811 AATGAGGGGG
* *
41821 AAATATAATAAATCATAAAAAATGAGGGATA
1 AAATATAATAAATCATAAAAAATAAGGGACA
*
41852 AAATATAATTAAGT-AT-AAAAATAAGGAGACA
1 AAATATAA-TAAATCATAAAAAATAAGG-GACA
*
41883 AAATTAAAATAAA
1 AAA-TATAATAAA
41896 CTAAAATTAG
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
30 9 0.25
31 19 0.53
32 8 0.22
ACGTcount: A:0.64, C:0.03, G:0.11, T:0.23
Consensus pattern (31 bp):
AAATATAATAAATCATAAAAAATAAGGGACA
Found at i:45394 original size:3 final size:3
Alignment explanation
Indices: 45386--45443 Score: 89
Period size: 3 Copynumber: 19.3 Consensus size: 3
45376 GTTTAGGCCT
* * *
45386 ATA ATA ATA ATT TTA TTA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45434 ATA ATA ATA A
1 ATA ATA ATA A
45444 ATAACAAGGG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:46311 original size:177 final size:177
Alignment explanation
Indices: 45762--46532 Score: 1231
Period size: 177 Copynumber: 4.4 Consensus size: 177
45752 TCAAGTGAGA
* * * * *
45762 TAAAAT-TTATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGACCCGTAGGACTTATAAACC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* *
45826 AAGAAACTCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAACCCCTTTATTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAAACCCTTTATTAGGCTTAGCTTCCTT
45891 TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
131 TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
45938 TAAAATCTCATTTGAAAACATCATGCACTGAAGGTTTTATGGATGGCCCGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* * * * * * *
46003 AAGAAACCCCTGAAGGCTTAGTTTCTTAATTATGAA-TAAACCCTTTGTTAGGCTTAACTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAAACCCTTTATTAGGCTTAGCTTCCTT
* * * *
46067 TAACAGCTCTTTTGAGATAATTAGTAAATCCCCAAAGGCTTGGTTTC
131 TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
46114 TAAAATCTCATTTGAAAACATCCTACACTGAAGGTCTTATGGATCGCCCGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* ** *
46179 AAGAAACCCCCGAATGCTTAGTTTCTTAGTTGTCAAGGATCCCCCTTATTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAAACCCTTTATTAGGCTTAGCTTCCTT
* *
46244 TAACAACTCTTTTGAGATAATTAGTAAACCCTCGAAGGCTTGGTTTC
131 TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
*
46291 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAAAC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
* *
46356 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTGAAGGAAACCCTTTGTTAGGCTTAGCTTCCTT
66 AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAAACCCTTTATTAGGCTTAGCTTCCTT
46421 TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
131 TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
* *
46468 TAAAATCTCATTTGAAAACATCATGCACTGAATGTCTTATGGATGGCCCGTAGGACTTACAAATC
1 TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
46533 TGGGAAATAG
Statistics
Matches: 540, Mismatches: 53, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
176 165 0.31
177 375 0.69
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (177 bp):
TAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCCGTAGGACTTACAAATC
AAGAAACCCCCGAAGGCTTAGTTTCTTAGTTGTCAAGGAAACCCTTTATTAGGCTTAGCTTCCTT
TAACAACTCTTTTAAGATAATTAGTAAACCCCCGAAGGCTTGGTTTC
Found at i:48197 original size:51 final size:51
Alignment explanation
Indices: 48121--48367 Score: 309
Period size: 52 Copynumber: 4.8 Consensus size: 51
48111 ATATCCCAAC
* *
48121 CTTTTCATGCTGGTGTGAGTCTTCAAGATACCCCACATGGATTACTTCTGT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTGT
* * *
48172 CTTTTCATGATGATGTGAGCCTTCAAGATGCCCCATATGGATTACTTCTGT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTGT
* * * * *
48223 CTTTTTCATGCTTATATGAGCCTTCAAGATGCCCCATATGGATTACTTCTAT
1 C-TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTGT
** * *
48275 CTTTTCATATTGATGTGAGCCTTCAAGATA-CCCACATAGATTACTTATGT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTGT
* *
48325 TTTTTCCCATGCTGATGTGAGCTTTCAAGATA-CCCACATGGAT
1 CTTTT--CATGCTGATGTGAGCCTTCAAGATACCCCACATGGAT
48368 ATTATGGACA
Statistics
Matches: 170, Mismatches: 23, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
50 20 0.12
51 71 0.42
52 79 0.46
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (51 bp):
CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTGT
Found at i:48251 original size:52 final size:51
Alignment explanation
Indices: 48121--48367 Score: 302
Period size: 51 Copynumber: 4.8 Consensus size: 51
48111 ATATCCCAAC
* * *
48121 CTTTTCATGCTGGTGTGAGTCTTCAAGATACCCCACATGGATTACTTCTGT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCATATGGATTACTTCTGT
* *
48172 CTTTTCATGATGATGTGAGCCTTCAAGATGCCCCATATGGATTACTTCTGT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCATATGGATTACTTCTGT
* * * *
48223 CTTTTTCATGCTTATATGAGCCTTCAAGATGCCCCATATGGATTACTTCTAT
1 C-TTTTCATGCTGATGTGAGCCTTCAAGATACCCCATATGGATTACTTCTGT
** *
48275 CTTTTCATATTGATGTGAGCCTTCAAGATACCCACATA--GATTACTTATGT
1 CTTTTCATGCTGATGTGAGCCTTCAAGATACCC-CATATGGATTACTTCTGT
* * *
48325 TTTTTCCCATGCTGATGTGAGCTTTCAAGATA-CCCACATGGAT
1 CTTTT--CATGCTGATGTGAGCCTTCAAGATACCCCATATGGAT
48368 ATTATGGACA
Statistics
Matches: 169, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
50 17 0.10
51 76 0.45
52 76 0.45
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (51 bp):
CTTTTCATGCTGATGTGAGCCTTCAAGATACCCCATATGGATTACTTCTGT
Found at i:48301 original size:103 final size:101
Alignment explanation
Indices: 48122--48367 Score: 327
Period size: 103 Copynumber: 2.4 Consensus size: 101
48112 TATCCCAACC
* * *
48122 TTTTCATGCTGGTGTGAGTCTTCAAGATACCCCACATGGATTACTTCTGTCTTTTCATGATGATG
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCTTTTCATGATGATG
* *
48187 TGAGCCTTCAAGATGCCC-CATATGGATTACTTCTGTCT
66 TGAGCCTTCAAGATACCCACATA--GATTACTTATGT-T
* * * *
48225 TTTTCATGCTTATATGAGCCTTCAAGATGCCCCATATGGATTACTTCTATCTTTTCAT-ATTGAT
1 TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCTTTTCATGA-TGAT
48289 GTGAGCCTTCAAGATACCCACATAGATTACTTATGTT
65 GTGAGCCTTCAAGATACCCACATAGATTACTTATGTT
*
48326 TTTTCCCATGCTGATGTGAGCTTTCAAGATA-CCCACATGGAT
1 TTTT--CATGCTGATGTGAGCCTTCAAGATACCCCACATGGAT
48368 ATTATGGACA
Statistics
Matches: 125, Mismatches: 14, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
101 5 0.04
102 22 0.18
103 94 0.75
104 4 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (101 bp):
TTTTCATGCTGATGTGAGCCTTCAAGATACCCCACATGGATTACTTCTATCTTTTCATGATGATG
TGAGCCTTCAAGATACCCACATAGATTACTTATGTT
Found at i:49608 original size:8 final size:8
Alignment explanation
Indices: 49595--49654 Score: 68
Period size: 8 Copynumber: 7.0 Consensus size: 8
49585 CTTGATTCAA
49595 TTTTTTTC
1 TTTTTTTC
49603 TTTTTTTC
1 TTTTTTTC
49611 -TTTTTTC
1 TTTTTTTC
49618 TTTTTTCTTC
1 -TTTTT-TTC
49628 TTTTTTTTTC
1 --TTTTTTTC
49638 TTTTTTTC
1 TTTTTTTC
49646 TCTTTTTTC
1 T-TTTTTTC
49655 CATTCTTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.15
8 17 0.36
9 11 0.23
10 6 0.13
11 6 0.13
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTC
Found at i:49616 original size:10 final size:10
Alignment explanation
Indices: 49596--49653 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
49586 TTGATTCAAT
*
49596 TTTTTTCTTTT
1 TTTTTT-TTTC
49607 TTTCTTTTTTC
1 TTT-TTTTTTC
*
49618 TTTTTTCTTC
1 TTTTTTTTTC
49628 TTTTTTTTTC
1 TTTTTTTTTC
*
49638 TTTTTTTCTC
1 TTTTTTTTTC
49648 TTTTTT
1 TTTTTT
49654 CCATTCTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
10 30 0.71
11 9 0.21
12 3 0.07
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:49651 original size:7 final size:7
Alignment explanation
Indices: 49596--49643 Score: 71
Period size: 7 Copynumber: 6.9 Consensus size: 7
49586 TTGATTCAAT
49596 TTTTTTC
1 TTTTTTC
49603 TTTTTTTC
1 -TTTTTTC
49611 TTTTTTC
1 TTTTTTC
49618 TTTTTTC
1 TTTTTTC
*
49625 TTCTTT-
1 TTTTTTC
49631 TTTTTTC
1 TTTTTTC
49638 TTTTTT
1 TTTTTT
49644 TCTCTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
6 5 0.14
7 25 0.68
8 7 0.19
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:49661 original size:35 final size:35
Alignment explanation
Indices: 49595--49661 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
49585 CTTGATTCAA
***
49595 TTTTTTTCTTTTTTTCTTTTTTCTTTTTTCTTCTT
1 TTTTTTTCTTTTTTTCTTTTTTCTCCATTCTTCTT
49630 TTTTTTTCTTTTTTTCTCTTTTT-TCCATTCTT
1 TTTTTTTCTTTTTTTCT-TTTTTCTCCATTCTT
49662 TTCTCTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 23 0.82
36 5 0.18
ACGTcount: A:0.01, C:0.16, G:0.00, T:0.82
Consensus pattern (35 bp):
TTTTTTTCTTTTTTTCTTTTTTCTCCATTCTTCTT
Found at i:49663 original size:27 final size:28
Alignment explanation
Indices: 49606--49665 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
49596 TTTTTTCTTT
* ** *
49606 TTTTC-TTTTTTCTTTTTTCTTCTTTTT
1 TTTTCTTTTTTTCTCTTTTCTTCCATTC
49633 TTTTCTTTTTTTCTCTTTT-TTCCATTC
1 TTTTCTTTTTTTCTCTTTTCTTCCATTC
49660 TTTTCT
1 TTTTCT
49666 CTGATGGATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 16 0.57
28 12 0.43
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (28 bp):
TTTTCTTTTTTTCTCTTTTCTTCCATTC
Found at i:52884 original size:42 final size:42
Alignment explanation
Indices: 52825--52907 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
52815 TAATTTGGTC
* *
52825 ATTTGTTCATTTGAATCATCTTGAAACTTTTTTGCTTGATCA
1 ATTTGTTCATTTGAATCATCCTGAAACTTTTTTACTTGATCA
* *
52867 ATTTGTTCCTTTGAATCATCCTGGAACTTTTTTACTTGATC
1 ATTTGTTCATTTGAATCATCCTGAAACTTTTTTACTTGATC
52908 GATCATCTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (42 bp):
ATTTGTTCATTTGAATCATCCTGAAACTTTTTTACTTGATCA
Found at i:53279 original size:14 final size:16
Alignment explanation
Indices: 53249--53281 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
53239 TGAAAATGTA
53249 AAAAATGAAGAAATGC
1 AAAAATGAAGAAATGC
53265 AAAAAT-AAG-AATGC
1 AAAAATGAAGAAATGC
53279 AAA
1 AAA
53282 TTGTGCAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.47
15 3 0.18
16 6 0.35
ACGTcount: A:0.67, C:0.06, G:0.15, T:0.12
Consensus pattern (16 bp):
AAAAATGAAGAAATGC
Found at i:53279 original size:58 final size:61
Alignment explanation
Indices: 53174--53291 Score: 147
Period size: 58 Copynumber: 2.0 Consensus size: 61
53164 GCAAATGCAA
* **
53174 AAAATGAAAATGTAAATACAAACGTAAAAATGCAAAGATGCGAATGCAAATATGTG-AATGT
1 AAAATGAAAATGTAAATACAAACGTAAAAATGCAAAAATAAGAATGCAAAT-TGTGCAATGT
*
53235 AAAATGAAAATGT-AA-A-AAATG-AAGAAATGCAAAAATAAGAATGCAAATTGTGCAATG
1 AAAATGAAAATGTAAATACAAACGTAA-AAATGCAAAAATAAGAATGCAAATTGTGCAATG
53292 CAAATGCAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
57 6 0.12
58 29 0.57
59 1 0.02
60 2 0.04
61 13 0.25
ACGTcount: A:0.55, C:0.07, G:0.18, T:0.20
Consensus pattern (61 bp):
AAAATGAAAATGTAAATACAAACGTAAAAATGCAAAAATAAGAATGCAAATTGTGCAATGT
Found at i:54353 original size:17 final size:17
Alignment explanation
Indices: 54333--54369 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
54323 AAGTTAAAGC
54333 AAAATAA-AAAATAAATA
1 AAAATAAGAAAA-AAATA
54350 AAAATAAGAAAAAAATA
1 AAAATAAGAAAAAAATA
54367 AAA
1 AAA
54370 TGGTTAGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (17 bp):
AAAATAAGAAAAAAATA
Found at i:56526 original size:2 final size:2
Alignment explanation
Indices: 56519--56575 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
56509 TTTACCTTAA
56519 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
56561 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
56576 CAGTTAATGG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:57660 original size:3 final size:3
Alignment explanation
Indices: 57652--57730 Score: 108
Period size: 3 Copynumber: 27.0 Consensus size: 3
57642 TTTAGGCCTG
** * *
57652 TAA TAA TAA TTT TAT TAA TAA -AA TAA TAA TAA TAA TAA T-A TAA TTA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57698 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
57731 ATAACAAGGG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 4 0.06
3 64 0.94
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:58843 original size:18 final size:17
Alignment explanation
Indices: 58820--58858 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
58810 AGGGAGTTGA
58820 AATCTGTGAAGGAATTAG
1 AATCTGT-AAGGAATTAG
*
58838 AATCTGTCAGGAATTAG
1 AATCTGTAAGGAATTAG
58855 AATC
1 AATC
58859 CAATTCCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (17 bp):
AATCTGTAAGGAATTAG
Found at i:59501 original size:234 final size:232
Alignment explanation
Indices: 59255--59734 Score: 763
Period size: 234 Copynumber: 2.0 Consensus size: 232
59245 AAAGTTTCAA
59255 CCGACCCGACCCGAATATATGAATTAG-A-AACCCGACCCGACCCAAAATAATAAAAAAAGTATT
1 CCGACCCGACCCGAATATATGAATTAGAACAACCCGACCCGACCCAAAATAAT-AAAAAAGTA-T
59318 TTTTATTCAATAAAAACAGTGACTCAATTGGAAAAAATATAT-T-GAGAGGGGTATTATTGTAAT
64 TTTTATTCAATAAAAACAGTGACTCAATT-GAAAAAATATATATAGAGAGGGGTATTATTGTAAT
* *
59381 TATTCCTAAATATATAAGGTAAAATTATATATTTTTTGGGTCGGGTCGGGTATTTTTCACCCTAA
128 TATTCCTAAATATATAAGGTAAAATTATATA-TATTT---TCGGGTCGAGTATTTTTCACCCTAA
**
59446 ACCCGAACT-GACCCGACCCGAATATCACACTTAAAAAAATTAC
189 ACCCGAACTCGACCCGACCCGAATATCACACTTAAAAAAACGAC
*
59489 CCGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCAAAATAATAAAAAATTA
1 CCGACCCGACCCGAATATATGAATTAG-AA--CAACCCGACCCGACCCAAAATAATAAAAAAGTA
* *
59554 TTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAATATATATATAGAGGGGTATTATTGTAAT
63 TTTTTATTCAATAAAAACAGTGACTCAATTGAAAAAATATATATAGAGAGGGGTATTATTGTAAT
59619 TATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCC
128 TATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCC
*
59684 GAACTCGACCCGACCCGAATATCACACTTAAAAAACCGAC
193 GAACTCGACCCGACCCGAATATCACACTTAAAAAAACGAC
59724 CCGACCCGACC
1 CCGACCCGACC
59735 AAAATAAAGT
Statistics
Matches: 230, Mismatches: 8, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
234 60 0.26
235 42 0.18
236 13 0.06
237 34 0.15
238 58 0.25
239 23 0.10
ACGTcount: A:0.39, C:0.20, G:0.13, T:0.27
Consensus pattern (232 bp):
CCGACCCGACCCGAATATATGAATTAGAACAACCCGACCCGACCCAAAATAATAAAAAAGTATTT
TTATTCAATAAAAACAGTGACTCAATTGAAAAAATATATATAGAGAGGGGTATTATTGTAATTAT
TCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGAGTATTTTTCACCCTAAACCCGAA
CTCGACCCGACCCGAATATCACACTTAAAAAAACGAC
Found at i:60319 original size:10 final size:10
Alignment explanation
Indices: 60306--60350 Score: 63
Period size: 10 Copynumber: 4.5 Consensus size: 10
60296 CGGATCGACT
*
60306 AAAAACCGGA
1 AAAAATCGGA
60316 AAAAATCGGA
1 AAAAATCGGA
*
60326 AAAAATCGGG
1 AAAAATCGGA
*
60336 AAAAATCTGA
1 AAAAATCGGA
60346 AAAAA
1 AAAAA
60351 CGAGATTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.62, C:0.11, G:0.18, T:0.09
Consensus pattern (10 bp):
AAAAATCGGA
Found at i:60640 original size:14 final size:14
Alignment explanation
Indices: 60621--60648 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60611 AAGTGAAAGA
60621 ATAGTTATATAATT
1 ATAGTTATATAATT
60635 ATAGTTATATAATT
1 ATAGTTATATAATT
60649 TTGTTATGAT
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:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:61867 original size:17 final size:18
Alignment explanation
Indices: 61845--61880 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
61835 GACGGCAGCG
61845 GATGAAATA-AGCGAAAA
1 GATGAAATATAGCGAAAA
*
61862 GATGAAATATAGCGTAAA
1 GATGAAATATAGCGAAAA
61880 G
1 G
61881 TAAGAAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.25, T:0.17
Consensus pattern (18 bp):
GATGAAATATAGCGAAAA
Found at i:62619 original size:23 final size:23
Alignment explanation
Indices: 62593--62672 Score: 88
Period size: 23 Copynumber: 3.4 Consensus size: 23
62583 GAATATCATC
* *
62593 GTTTAATGTTCGTGACCATGCTT
1 GTTTAATGTTCGTGAACATGTTT
* * *
62616 GTTTAATATTCGTCAATATGTTT
1 GTTTAATGTTCGTGAACATGTTT
* *
62639 GTTTAATGTCCGTGAACACGTTT
1 GTTTAATGTTCGTGAACATGTTT
62662 GTTTATATGTT
1 GTTTA-ATGTT
62673 TAGAAAATTG
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
23 41 0.91
24 4 0.09
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.47
Consensus pattern (23 bp):
GTTTAATGTTCGTGAACATGTTT
Found at i:65124 original size:17 final size:17
Alignment explanation
Indices: 65099--65132 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
65089 TCGGTTTTGG
65099 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
* *
65116 TTTTTAAAAAATCGGTT
1 TTTTAAAAAAACCGGTT
65133 ATAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:70401 original size:28 final size:28
Alignment explanation
Indices: 70370--70458 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
70360 TAATCAAAAA
70370 CCCTAAATCACTATAAAACAAAACAAAC
1 CCCTAAATCACTATAAAACAAAACAAAC
* * *
70398 CCCT-AAT-A--AGAAAGCAATAATCAAGAA
1 CCCTAAATCACTATAAAACAA-AA-CAA-AC
70425 CCCTAAATCACTATAAAACAAAACAAAC
1 CCCTAAATCACTATAAAACAAAACAAAC
70453 CCCTAA
1 CCCTAA
70459 TTTTTGGTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
24 7 0.15
25 2 0.04
26 4 0.08
27 8 0.17
28 14 0.29
29 4 0.08
30 2 0.04
31 7 0.15
ACGTcount: A:0.55, C:0.27, G:0.03, T:0.15
Consensus pattern (28 bp):
CCCTAAATCACTATAAAACAAAACAAAC
Found at i:70419 original size:55 final size:55
Alignment explanation
Indices: 70347--70459 Score: 217
Period size: 55 Copynumber: 2.1 Consensus size: 55
70337 CTAAACATAA
70347 AATAAGAAAGCAATAATCAAAAACCCTAAATCACTATAAAACAAAACAAACCCCT
1 AATAAGAAAGCAATAATCAAAAACCCTAAATCACTATAAAACAAAACAAACCCCT
*
70402 AATAAGAAAGCAATAATCAAGAACCCTAAATCACTATAAAACAAAACAAACCCCT
1 AATAAGAAAGCAATAATCAAAAACCCTAAATCACTATAAAACAAAACAAACCCCT
70457 AAT
1 AAT
70460 TTTTGGTGAA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.58, C:0.23, G:0.04, T:0.15
Consensus pattern (55 bp):
AATAAGAAAGCAATAATCAAAAACCCTAAATCACTATAAAACAAAACAAACCCCT
Found at i:70453 original size:27 final size:27
Alignment explanation
Indices: 70367--70454 Score: 85
Period size: 27 Copynumber: 3.2 Consensus size: 27
70357 CAATAATCAA
70367 AAACCCTAAATCACTATAAAACAAAAC
1 AAACCCTAAATCACTATAAAACAAAAC
* *
70394 AAACCCCT-AAT-A--AGAAAGCAATAATC
1 AAA-CCCTAAATCACTATAAAACAA-AA-C
70420 AAGAACCCTAAATCACTATAAAACAAAAC
1 -A-AACCCTAAATCACTATAAAACAAAAC
70449 AAACCC
1 AAACCC
70455 CTAATTTTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 18
0.69 0.06 0.26
Matches are distributed among these distances:
24 7 0.15
25 2 0.04
26 2 0.04
27 16 0.33
28 10 0.21
29 2 0.04
30 2 0.04
31 7 0.15
ACGTcount: A:0.57, C:0.26, G:0.03, T:0.14
Consensus pattern (27 bp):
AAACCCTAAATCACTATAAAACAAAAC
Found at i:72217 original size:21 final size:21
Alignment explanation
Indices: 72188--72240 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
72178 ATTCTGACTA
72188 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
72209 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
72230 TCGCAATGCGA
1 TCGCATTGCGA
72241 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.25, G:0.21, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:72257 original size:20 final size:20
Alignment explanation
Indices: 72227--72285 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
72217 CGATTTTCCG
72227 AATTCGCAATGCGAATATGTA
1 AATT-GCAATGCGAATATGTA
72248 AATTGCAATGCGAATATGTA
1 AATTGCAATGCGAATATGTA
* * *
72268 AATCGTAATGCGATTATG
1 AATTGCAATGCGAATATG
72286 ACTATCGCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 31 0.89
21 4 0.11
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (20 bp):
AATTGCAATGCGAATATGTA
Found at i:72292 original size:20 final size:20
Alignment explanation
Indices: 72277--72356 Score: 142
Period size: 20 Copynumber: 4.0 Consensus size: 20
72267 AAATCGTAAT
*
72277 GCGATTATGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
72297 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
72317 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
72337 GCGATTCTGACTGTCGCAAC
1 GCGATTCTGACTATCGCAAC
72357 ACTGAATTTC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.25, C:0.29, G:0.21, T:0.25
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:72860 original size:12 final size:12
Alignment explanation
Indices: 72845--72869 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72835 ATTGAACGAT
72845 TCATTGCTTACA
1 TCATTGCTTACA
72857 TCATTGCTTACA
1 TCATTGCTTACA
72869 T
1 T
72870 TAGTGTTTCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.24, G:0.08, T:0.44
Consensus pattern (12 bp):
TCATTGCTTACA
Found at i:73240 original size:24 final size:24
Alignment explanation
Indices: 73183--73242 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
73173 TAGTCGGTAT
73183 TCGAAATTTGATCTTGGTCAATAC
1 TCGAAATTTGATCTTGGTCAATAC
* *
73207 -CTGGACTTTGATCTTGGTCAATAC
1 TC-GAAATTTGATCTTGGTCAATAC
*
73231 TCGAATTTTGAT
1 TCGAAATTTGAT
73243 GATGTTTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 28 0.93
25 1 0.03
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.40
Consensus pattern (24 bp):
TCGAAATTTGATCTTGGTCAATAC
Found at i:75519 original size:18 final size:18
Alignment explanation
Indices: 75496--75530 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
75486 AGAAAAAGGC
*
75496 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
75514 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
75531 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:75842 original size:140 final size:140
Alignment explanation
Indices: 75590--75859 Score: 522
Period size: 140 Copynumber: 1.9 Consensus size: 140
75580 AAACGTTGTA
75590 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
75655 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGTGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
75720 TATGTGTATT
131 TATGTGTATT
75730 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
75795 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
75860 CGCAACTCAA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 128 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.43
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:75855 original size:20 final size:20
Alignment explanation
Indices: 75830--76068 Score: 165
Period size: 20 Copynumber: 12.8 Consensus size: 20
75820 TTACACATTC
*
75830 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
75850 ATTTGACTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
*
75869 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
75884 ATTTGACTACCACAACACG-
1 ATTTGACTATCGCAACGCGA
75903 ATTATGACTATCGCAACGC-A
1 ATT-TGACTATCGCAACGCGA
* *
75923 A----A-AATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
75938 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
75958 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
*
75978 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
75998 A----A--ATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
76012 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
76032 ATTTGATTATCGTAACGGGT
1 ATTTGACTATCGCAACGCGA
* *
76052 GTTTGACTATCGTAACG
1 ATTTGACTATCGCAACG
76069 AGAAAATTGC
Statistics
Matches: 169, Mismatches: 30, Indels: 40
0.71 0.13 0.17
Matches are distributed among these distances:
14 29 0.17
15 6 0.04
16 1 0.01
18 1 0.01
19 7 0.04
20 125 0.74
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:75916 original size:54 final size:54
Alignment explanation
Indices: 75842--75974 Score: 187
Period size: 54 Copynumber: 2.5 Consensus size: 54
75832 TTGAATATCG
* * *
75842 CAACGCGAATTTGACTATCGCAACTCAAAAATCGCAACGCGAATTTGACTACCA
1 CAACACGAATTTGACTATCGCAACGCAAAAATCGCAACACGAATTTGACTACCA
* *
75896 CAACACG-ATTATGACTATCGCAACGCAAAAATCGCAACACGAATTTGACTATCG
1 CAACACGAATT-TGACTATCGCAACGCAAAAATCGCAACACGAATTTGACTACCA
* *
75950 CAACGCGAATTTGATTATCGCAACG
1 CAACACGAATTTGACTATCGCAACG
75975 GGTATTTGAC
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
53 3 0.04
54 64 0.91
55 3 0.04
ACGTcount: A:0.37, C:0.26, G:0.16, T:0.21
Consensus pattern (54 bp):
CAACACGAATTTGACTATCGCAACGCAAAAATCGCAACACGAATTTGACTACCA
Found at i:75945 original size:34 final size:34
Alignment explanation
Indices: 75896--76029 Score: 128
Period size: 34 Copynumber: 3.8 Consensus size: 34
75886 TTGACTACCA
75896 CAACACG-ATTATGACTATCGCAACGCAAAAATCG
1 CAACACGAATT-TGACTATCGCAACGCAAAAATCG
*
75930 CAACACGAATTTGACTATCGCAACGCGAATTTGATTATCG
1 CAACACGAATTTGACTATCGCAACGC-AA----A-AATCG
** * *
75970 CAACGGGTATTTGACTATCGCAACG-AGAAAATTG
1 CAACACGAATTTGACTATCGCAACGCA-AAAATCG
*
76004 CAACGCGAATTTGACTATCGCAACGC
1 CAACACGAATTTGACTATCGCAACGC
76030 GAATTTGATT
Statistics
Matches: 83, Mismatches: 8, Indels: 17
0.77 0.07 0.16
Matches are distributed among these distances:
34 48 0.58
35 6 0.07
38 1 0.01
39 2 0.02
40 26 0.31
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (34 bp):
CAACACGAATTTGACTATCGCAACGCAAAAATCG
Found at i:75958 original size:74 final size:74
Alignment explanation
Indices: 75872--76112 Score: 265
Period size: 74 Copynumber: 3.3 Consensus size: 74
75862 CAACTCAAAA
75872 ATCGCAACGCGAATTTGACTACCACAACACG-ATTATGACTATCGCAACGCA-AAAATCGCAACA
1 ATCGCAACGCGAATTTGACTACCACAACACGTATT-TGACTATCGCAACG-AGAAAATCGCAACA
75935 CGAATTTGACT
64 CGAATTTGACT
* * * ** * *
75946 ATCGCAACGCGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGAAAATTGCAACGCG
1 ATCGCAACGCGAATTTGACTACCACAACACGTATTTGACTATCGCAACGAGAAAATCGCAACACG
76011 AATTTGACT
66 AATTTGACT
* * ** ** * * *
76020 ATCGCAACGCGAATTTGATTATCGTAACGGGTGTTTGACTATCGTAACGAGAAAATTGCAA-AGC
1 ATCGCAACGCGAATTTGACTACCACAACACGTATTTGACTATCGCAACGAGAAAATCGCAACA-C
* *
76084 GTATTAGACT
65 GAATTTGACT
76094 ATCGCAACGCGAA-TTGACT
1 ATCGCAACGCGAATTTGACT
76113 TTCGCGTTGC
Statistics
Matches: 150, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
73 6 0.04
74 141 0.94
75 3 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTACCACAACACGTATTTGACTATCGCAACGAGAAAATCGCAACACG
AATTTGACT
Found at i:76162 original size:20 final size:20
Alignment explanation
Indices: 76111--76164 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
76101 CGCGAATTGA
*
76111 CTTTCGCGTTGCGATTTTGG
1 CTTTAGCGTTGCGATTTTGG
* *
76131 CTTTTGCATTGCGATTTTGAG
1 CTTTAGCGTTGCGATTTTG-G
76152 -TTTAGCGTTGCGA
1 CTTTAGCGTTGCGA
76165 AAGTGTACCT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.11, C:0.17, G:0.28, T:0.44
Consensus pattern (20 bp):
CTTTAGCGTTGCGATTTTGG
Found at i:76323 original size:14 final size:14
Alignment explanation
Indices: 76263--76324 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
76253 CACAAATAAG
*
76263 AATTATTTACACATC
1 AATT-TTTACAAATC
**
76278 AATATTAAACAAATC
1 AAT-TTTTACAAATC
* *
76293 AACTTTTACAAGTC
1 AATTTTTACAAATC
*
76307 AATTTTTATAAATC
1 AATTTTTACAAATC
76321 AATT
1 AATT
76325 AAACAAGCAA
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 23 0.64
15 12 0.33
16 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.02, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:78353 original size:20 final size:20
Alignment explanation
Indices: 78328--78381 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
78318 TCGTAACACG
78328 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
78348 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
78368 TTTGACTATCGCAA
1 AATGACTATCGCAA
78382 TAAGAGAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:80396 original size:20 final size:20
Alignment explanation
Indices: 80371--80480 Score: 96
Period size: 20 Copynumber: 5.5 Consensus size: 20
80361 TTCTGAACTT
80371 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
80391 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * * **
80411 ACTATCACAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
** * **
80431 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACACGAAAATG
**
80451 ACTATCGCAACACG-AAATG
1 AAAATCGCAACACGAAAATG
80470 AAAATCGCAAC
1 AAAATCGCAAC
80481 GTGAAACTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 12 0.15
20 66 0.85
ACGTcount: A:0.45, C:0.24, G:0.15, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:80905 original size:22 final size:22
Alignment explanation
Indices: 80865--80950 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
80855 CTCTGAGAGA
80865 TGGAGAT-A-GACGGATTTCGC
1 TGGAGATGAGGACGGATTTCGC
*
80885 TGGAGATGAGGACTGATTTCGC
1 TGGAGATGAGGACGGATTTCGC
* * *
80907 CGGAGATGGGGACTGATTTCG-
1 TGGAGATGAGGACGGATTTCGC
* *
80928 TCGGAGATGGGGACGGATGTCGC
1 T-GGAGATGAGGACGGATTTCGC
80951 CTTAGAGAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
20 7 0.12
21 1 0.02
22 48 0.86
ACGTcount: A:0.21, C:0.15, G:0.41, T:0.23
Consensus pattern (22 bp):
TGGAGATGAGGACGGATTTCGC
Found at i:81172 original size:20 final size:20
Alignment explanation
Indices: 81118--81268 Score: 132
Period size: 20 Copynumber: 7.7 Consensus size: 20
81108 GCACTTTGAA
*
81118 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
81138 CATCGCGTT--GATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
81156 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
81176 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
* * *
81196 AATCGC-ATGCGAT-TTACAT
1 AATCGCGTTGCGATAGT-CAG
* * *
81215 ATTCGCATTGCGATAGTCGGAA
1 AATCGCGTTGCGATAGTC--AG
**
81237 AATCGCAATGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
81257 AATCGCG-TGCGA
1 AATCGCGTTGCGA
81269 ATCTGGAAAC
Statistics
Matches: 108, Mismatches: 16, Indels: 15
0.78 0.12 0.11
Matches are distributed among these distances:
18 17 0.16
19 19 0.18
20 54 0.50
21 1 0.01
22 17 0.16
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:81181 original size:38 final size:39
Alignment explanation
Indices: 81125--81199 Score: 116
Period size: 38 Copynumber: 1.9 Consensus size: 39
81115 GAAAATCGCA
*
81125 TTGCGATAGTCAGCATCGCGTT-GATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCGTTCGATAGTCAGAATCTCG
*
81163 TTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATC
1 TTGCGATAGTCAGAATCGCGTT-CGATAGTCAGAATC
81200 GCATGCGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 21 0.64
40 12 0.36
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.29
Consensus pattern (39 bp):
TTGCGATAGTCAGAATCGCGTTCGATAGTCAGAATCTCG
Found at i:82498 original size:21 final size:19
Alignment explanation
Indices: 82455--82503 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 19
82445 ATTAGAGGGG
* *
82455 AAAAATAAAAAAATGAAAT
1 AAAAATAAAAAAATAAAAC
82474 AAAAATATAAAAATATAAAAC
1 AAAAATA-AAAAA-ATAAAAC
*
82495 AAAATTAAA
1 AAAAATAAA
82504 GAAGGTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 7 0.28
20 7 0.28
21 11 0.44
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAATAAAAAAATAAAAC
Found at i:82538 original size:21 final size:20
Alignment explanation
Indices: 82509--82564 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
82499 TTAAAGAAGG
*
82509 TAAAGATAAAAAGGCAATAAAA
1 TAAA-ATAAAAAAG-AATAAAA
*
82531 TAAAATAAAGAAAGTATAAAA
1 TAAAATAAA-AAAGAATAAAA
82552 TAAAAGTAAAAAA
1 TAAAA-TAAAAAA
82565 AGAAAATAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (20 bp):
TAAAATAAAAAAGAATAAAA
Done.