Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007000.1 Hibiscus syriacus cultivar Beakdansim tig00018060_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: 143096
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:9121 original size:4 final size:4
Alignment explanation
Indices: 9112--9145 Score: 59
Period size: 4 Copynumber: 8.5 Consensus size: 4
9102 AGCCGACCTG
*
9112 ATAC ATAC ATAC ATAC ATAC ATAC GTAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
9146 TGTTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.47, C:0.24, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:23959 original size:29 final size:29
Alignment explanation
Indices: 23921--23978 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
23911 GCAATTAAGC
23921 ACTTGAATTTGGTTTTCGATTCGCAACTT
1 ACTTGAATTTGGTTTTCGATTCGCAACTT
* *
23950 ACTTGAATTTGGTTTTTGATTTGCAACTT
1 ACTTGAATTTGGTTTTCGATTCGCAACTT
23979 GAACTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (29 bp):
ACTTGAATTTGGTTTTCGATTCGCAACTT
Found at i:29957 original size:33 final size:33
Alignment explanation
Indices: 29920--29986 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
29910 AGAAAAGATA
29920 AGCATAATTGAAGAGTTAAACAATTAACCCATG
1 AGCATAATTGAAGAGTTAAACAATTAACCCATG
29953 AGCATAATTGAAGAGTTAAACAATTAACCCATG
1 AGCATAATTGAAGAGTTAAACAATTAACCCATG
29986 A
1 A
29987 TGCCGTCAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (33 bp):
AGCATAATTGAAGAGTTAAACAATTAACCCATG
Found at i:32942 original size:39 final size:36
Alignment explanation
Indices: 32889--32961 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 36
32879 AGGATACCCC
32889 AGAAGAACAAGAAGAAGAAAAGCCAATGGCTGAACCAAA
1 AGAAGAACAAGAAGAAG-AAA--CAATGGCTGAACCAAA
*
32928 AGAAGCAA-AAGAAGAAGGAACAATGGCTGAACCA
1 AGAAG-AACAAGAAGAAGAAACAATGGCTGAACCA
32962 TAGACATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 14 0.44
38 2 0.06
39 14 0.44
40 2 0.06
ACGTcount: A:0.55, C:0.15, G:0.25, T:0.05
Consensus pattern (36 bp):
AGAAGAACAAGAAGAAGAAACAATGGCTGAACCAAA
Found at i:37012 original size:32 final size:33
Alignment explanation
Indices: 36974--37161 Score: 102
Period size: 38 Copynumber: 5.5 Consensus size: 33
36964 CTTTATTTTG
*
36974 TTCGGGTCGGGTTGGGT-TTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTGTTTTTAAGTGTGATA
*
37006 TTCGGGTCGAGTCAGGTCGGGTGTTTTTAAGTTTGATA
1 TTCGGGTC--G---GGTCGGGTGTTTTTAAGTGTGATA
* * * ** * *
37044 TTCTGGTCGGGTCAGATGAAACTTT-ATTTTG-T-
1 TTCGGGTCGGGTCGGGTG--TTTTTAAGTGTGATA
*
37076 TT-GGGTCGGGTCGAGT-TTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTGTTTTTAAGTGTGATA
*
37107 TTCGGGTTGAGTCGGGTCGGGT-TTTTTAAAGTGTGCTA
1 TTC--G--G-GTCGGGTCGGGTGTTTTT-AAGTGTGATA
*
37145 TTTGGGTCGGGTCGGGT
1 TTCGGGTCGGGTCGGGT
37162 TTAGGGTGAA
Statistics
Matches: 119, Mismatches: 19, Indels: 35
0.69 0.11 0.20
Matches are distributed among these distances:
28 3 0.03
29 4 0.03
30 1 0.01
31 12 0.10
32 10 0.08
33 20 0.17
34 8 0.07
35 3 0.03
36 3 0.03
37 23 0.19
38 32 0.27
ACGTcount: A:0.14, C:0.10, G:0.36, T:0.41
Consensus pattern (33 bp):
TTCGGGTCGGGTCGGGTGTTTTTAAGTGTGATA
Found at i:37036 original size:38 final size:37
Alignment explanation
Indices: 36987--37058 Score: 108
Period size: 38 Copynumber: 1.9 Consensus size: 37
36977 GGGTCGGGTT
36987 GGGTTTTTTAAGTGTGATATTCGGGTCGAGTCAGGTC
1 GGGTTTTTTAAGTGTGATATTCGGGTCGAGTCAGGTC
* * *
37024 GGGTGTTTTTAAGTTTGATATTCTGGTCGGGTCAG
1 GGGT-TTTTTAAGTGTGATATTCGGGTCGAGTCAG
37059 ATGAAACTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
37 4 0.13
38 27 0.87
ACGTcount: A:0.15, C:0.10, G:0.35, T:0.40
Consensus pattern (37 bp):
GGGTTTTTTAAGTGTGATATTCGGGTCGAGTCAGGTC
Found at i:37066 original size:101 final size:101
Alignment explanation
Indices: 36940--37157 Score: 314
Period size: 101 Copynumber: 2.2 Consensus size: 101
36930 TCTAATTTAT
* * * * *
36940 ATATTCGGGTCAGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTGGGTTTTTTAAGTGTGAT
1 ATATTCTGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGAT
*
37005 ATTCGGGTCGAGTCAGGTCGGGTGTTTTT-AAGTTTG
66 ATTCGGGTCGAGTCAGGTCGGGT-TTTTTAAAGTGTG
*
37041 ATATTCTGGTCGGGTCAGATGAAACTTTATTTTGTTTGGGTCGGGTCGAGTTTTTTAAGTGTGAT
1 ATATTCTGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGAT
* *
37106 ATTCGGGTTGAGTCGGGTCGGGTTTTTTAAAGTGTG
66 ATTCGGGTCGAGTCAGGTCGGGTTTTTTAAAGTGTG
*
37142 CTATT-TGGGTCGGGTC
1 ATATTCT-GGTCGGGTC
37158 GGGTTTAGGG
Statistics
Matches: 105, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
100 6 0.06
101 99 0.94
ACGTcount: A:0.16, C:0.10, G:0.33, T:0.41
Consensus pattern (101 bp):
ATATTCTGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCGAGTTTTTTAAGTGTGAT
ATTCGGGTCGAGTCAGGTCGGGTTTTTTAAAGTGTG
Found at i:37159 original size:38 final size:37
Alignment explanation
Indices: 37078--37161 Score: 114
Period size: 38 Copynumber: 2.2 Consensus size: 37
37068 TATTTTGTTT
*
37078 GGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTT
1 GGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTC
* * * *
37115 GAGTCGGGTCGGGTTTTTTAAAGTGTGCTATTTGGGTC
1 GGGTCGGGTCGAGTTTTTT-AAGTGTGATATTCGGGTC
37153 GGGTCGGGT
1 GGGTCGGGT
37162 TTAGGGTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 17 0.43
38 23 0.57
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (37 bp):
GGGTCGGGTCGAGTTTTTTAAGTGTGATATTCGGGTC
Found at i:37373 original size:37 final size:37
Alignment explanation
Indices: 37311--37381 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
37301 TTTATTTTGT
* * *
37311 TCGGGTCGGGTTTTTTAAGTTTGATATTCGGGTCAAG
1 TCGGATCGGATTTTTTAAGTGTGATATTCGGGTCAAG
37348 TCGGATCGGATTTTTTAAGTGTGATATTCGGGTC
1 TCGGATCGGATTTTTTAAGTGTGATATTCGGGTC
37382 GGGTTCGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.17, C:0.11, G:0.31, T:0.41
Consensus pattern (37 bp):
TCGGATCGGATTTTTTAAGTGTGATATTCGGGTCAAG
Found at i:38523 original size:21 final size:21
Alignment explanation
Indices: 38490--38568 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
38480 GTTTCCAGAT
* *
38490 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTAGACTA
* *
38511 TCGTAATGCGAACTAACTTGGACTA
1 TCGCAATGCG----AACTTAGACTA
*
38536 TCGCAATGTGAACTTAGACTA
1 TCGCAATGCGAACTTAGACTA
38557 TCGCAATGCGAA
1 TCGCAATGCGAA
38569 TATGTAAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
21 29 0.62
25 18 0.38
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTAGACTA
Found at i:39197 original size:6 final size:6
Alignment explanation
Indices: 39188--39224 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
39178 GCCGTCCGTC
39188 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
39225 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:39334 original size:21 final size:21
Alignment explanation
Indices: 39310--39350 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
39300 CGTTGCGATT
39310 TTGGACTATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
*
39331 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
39351 TATGTAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:39823 original size:14 final size:14
Alignment explanation
Indices: 39801--39838 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39791 TTCGTAATTC
*
39801 GTTTATTTATTTGT
1 GTTTATTTATTTAT
*
39815 GTTTGTTTATTTAT
1 GTTTATTTATTTAT
39829 GTTTATTTAT
1 GTTTATTTAT
39839 AATCAATTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (14 bp):
GTTTATTTATTTAT
Found at i:42016 original size:27 final size:27
Alignment explanation
Indices: 41986--42041 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
41976 AGCATAGGGT
41986 TAAGGTTTAATTTGTTATATATATATA
1 TAAGGTTTAATTTGTTATATATATATA
42013 TAAGGTTTAATTTGTTATATATATATA
1 TAAGGTTTAATTTGTTATATATATATA
42040 TA
1 TA
42042 TAATATATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (27 bp):
TAAGGTTTAATTTGTTATATATATATA
Found at i:42033 original size:2 final size:2
Alignment explanation
Indices: 42028--42056 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
42018 TTTAATTTGT
42028 TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42057 AAATGTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:42049 original size:13 final size:13
Alignment explanation
Indices: 42031--42057 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42021 AATTTGTTAT
42031 ATATATATATATA
1 ATATATATATATA
42044 ATATATATATATA
1 ATATATATATATA
42057 A
1 A
42058 AATGTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATATATATATA
Found at i:50695 original size:29 final size:32
Alignment explanation
Indices: 50644--50707 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 32
50634 ATTTTGGAAA
50644 AATTATTTTACTTAAAATATAATAATATTT-T
1 AATTATTTTACTTAAAATATAATAATATTTGT
* *
50675 AATT-TTTTATTTTAAA-ATAATAATATTTGT
1 AATTATTTTACTTAAAATATAATAATATTTGT
50705 AAT
1 AAT
50708 GTTAAGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
29 12 0.40
30 14 0.47
31 4 0.13
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (32 bp):
AATTATTTTACTTAAAATATAATAATATTTGT
Found at i:55792 original size:20 final size:20
Alignment explanation
Indices: 55698--56066 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
55688 GATTTTCCAT
* ** *
55698 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
55718 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
55738 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
55758 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
55778 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
55798 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
55818 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
55838 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
55858 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
55878 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
55898 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
55918 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
55938 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
55958 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
55978 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
55998 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
56018 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
56038 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
56058 AATCACAAC
1 AATCGCAAC
56067 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:56779 original size:24 final size:24
Alignment explanation
Indices: 56740--56786 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
56730 AAATTTGGTC
56740 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
56764 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
56787 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:59310 original size:19 final size:19
Alignment explanation
Indices: 59288--59592 Score: 356
Period size: 19 Copynumber: 17.4 Consensus size: 19
59278 CGGAAAATAC
*
59288 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59307 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
59321 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59340 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
59354 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59373 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59392 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
59406 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59425 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
59444 AATCG-AA--CGACAT---
1 AATCGCAATGCGAAATGAA
*
59457 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
59476 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
59495 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59514 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59533 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
59547 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59566 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
59585 AATCGCAA
1 AATCGCAA
59593 CGAGATAATC
Statistics
Matches: 249, Mismatches: 11, Indels: 52
0.80 0.04 0.17
Matches are distributed among these distances:
13 5 0.02
14 42 0.17
15 2 0.01
16 21 0.08
17 11 0.04
18 4 0.02
19 164 0.66
ACGTcount: A:0.48, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:59330 original size:33 final size:34
Alignment explanation
Indices: 59288--59614 Score: 203
Period size: 33 Copynumber: 9.5 Consensus size: 34
59278 CGGAAAATAC
*
59288 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* * * *
59321 AATCGCAACGCGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
*
59354 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * * * *
59392 AATCGCAACGAGAGAATCG-CAAT-GCGA-AATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACAATGAA
* * * *
59425 AATCGCAATGCGAAATGAAAAT-CGAACGA-CAT
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
* *
59457 AATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAAAATC-CCA-AC--AATGAA
*
59495 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
*
59533 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--C--AATGAA
* * *
59566 AATCGCAATGCGAAATGAAAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCCCAACAATGAA
59599 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
59615 TATAAACGCA
Statistics
Matches: 243, Mismatches: 28, Indels: 46
0.77 0.09 0.15
Matches are distributed among these distances:
31 1 0.00
32 29 0.12
33 118 0.49
34 4 0.02
35 9 0.04
36 8 0.03
37 3 0.01
38 64 0.26
39 6 0.02
40 1 0.00
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCCCAACAATGAA
Found at i:59348 original size:52 final size:52
Alignment explanation
Indices: 59288--59540 Score: 262
Period size: 52 Copynumber: 4.8 Consensus size: 52
59278 CGGAAAATAC
* *
59288 AATCGCAACGCGA-AAT-GAAAATCCCAACATGAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGAATCG-AAATCCGAA-ATGAAAATCGCAATGCGAAATGAA
* * *
59340 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * *
59392 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * * * *
59444 AATCG-AACGAC-ATAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAA
1 AATCGCAACG-CGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
* * *
59495 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGCG--A-G--AATCGAAATCCGAAATGAAAATCGCAA
59541 CGAAAGAATC
Statistics
Matches: 179, Mismatches: 12, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
51 47 0.26
52 95 0.53
53 9 0.05
54 2 0.01
57 26 0.15
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.14
Consensus pattern (52 bp):
AATCGCAACGCGAGAATCGAAATCCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:59572 original size:52 final size:53
Alignment explanation
Indices: 59354--59614 Score: 287
Period size: 52 Copynumber: 4.9 Consensus size: 53
59344 GCAACGAGAG
*
59354 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATG--AATCGCAATGCGAAATGAA
*
59406 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA----AAT-CG-AACGACA
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAATGAATCGCAATGCGAAATGA-A
*
59456 TAATCGCAATGCGAAATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAA
1 -AATCGCAATGCGAAATGAAAATCGC-A-ACGAAATG--AATCGCAATGCGAAATGAA
59514 AATCGCAATGCGAAATGAAAATCGCAACGAAA-GAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
*
59566 AATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAAT
59615 TATAAACGCA
Statistics
Matches: 188, Mismatches: 5, Indels: 32
0.84 0.02 0.14
Matches are distributed among these distances:
46 2 0.01
47 2 0.01
48 1 0.01
49 2 0.01
50 2 0.01
51 31 0.16
52 103 0.55
53 3 0.02
54 1 0.01
55 6 0.03
56 1 0.01
57 27 0.14
58 3 0.02
59 4 0.02
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAATGAATCGCAATGCGAAATGAA
Found at i:59730 original size:19 final size:19
Alignment explanation
Indices: 59621--59722 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
59611 AAATTATAAA
59621 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
59640 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
59660 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
59676 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
59693 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
59712 CGCATTGCGAT
1 CGCATTGCGAT
59723 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:59847 original size:14 final size:14
Alignment explanation
Indices: 59828--59864 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
59818 CATCAATTAC
59828 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
59842 ACAAATCATCTTTT
1 ACAAATCAACTTTT
59856 ACAAATCAA
1 ACAAATCAA
59865 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:61837 original size:14 final size:14
Alignment explanation
Indices: 61818--61874 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
61808 GCGAAATGAA
*
61818 AATCGCAACGACAG
1 AATCGCAACGAAAG
61832 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
61849 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
61865 AATCGCAACG
1 AATCGCAACG
61875 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:61845 original size:33 final size:33
Alignment explanation
Indices: 61799--61891 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
61789 GCGAAACCAA
*
61799 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
61832 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
61865 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
61892 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:61856 original size:19 final size:19
Alignment explanation
Indices: 61762--61896 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
61752 TAGTTTACTT
* *
61762 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
61782 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
61801 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
61820 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
61834 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
61853 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
61867 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
61886 TCGCAATGCGA
1 TCGCAACGCGA
61897 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:61914 original size:19 final size:19
Alignment explanation
Indices: 61892--62020 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
61882 AAAATCGCAA
61892 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
61911 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
61925 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
61944 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
61958 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
61977 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
61996 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
62016 TGCGA
1 TGCGA
62021 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:61934 original size:33 final size:33
Alignment explanation
Indices: 61892--61983 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
61882 AAAATCGCAA
61892 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
61925 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
61958 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
61984 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:62223 original size:93 final size:93
Alignment explanation
Indices: 62064--62535 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
62054 TTGAATGGAT
*
62064 AAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62129 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
62157 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62222 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
62250 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62315 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
62343 AAATTTACTTTCAACCAAAAGACAAAACAACGAC-AATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62406 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
62434 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62499 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
62527 AAATTTACT
1 AAATTTACT
62536 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
91 86 0.23
92 8 0.02
93 280 0.75
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:62480 original size:184 final size:186
Alignment explanation
Indices: 62064--62535 Score: 912
Period size: 184 Copynumber: 2.5 Consensus size: 186
62054 TTGAATGGAT
*
62064 AAATTTACTTTCAACCAAAAGATAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62129 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
62194 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
62250 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
62315 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAACGAC-AA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
62379 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
62434 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
62499 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
62536 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
184 155 0.55
185 4 0.01
186 125 0.44
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:64257 original size:14 final size:14
Alignment explanation
Indices: 64238--64327 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
64228 TTGAAATGAA
64238 AATCGCAACGAGAG
1 AATCGCAACGAGAG
64252 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
64269 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
64285 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
64304 AATCGCAACGAGAG
1 AATCGCAACGAGAG
64318 AATCGCAACG
1 AATCGCAACG
64328 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:64275 original size:33 final size:33
Alignment explanation
Indices: 64230--64344 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
64220 TCTTTTGGTT
64230 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
64263 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
64296 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
64329 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
64345 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:64276 original size:19 final size:18
Alignment explanation
Indices: 64237--64349 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
64227 GTTGAAATGA
64237 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
64252 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
64269 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
64285 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
64302 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
64318 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
64335 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
64350 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:64380 original size:14 final size:14
Alignment explanation
Indices: 64361--64415 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
64351 TTTGGTTTCG
64361 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
64375 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
64394 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
64408 CGTTGCGA
1 CGTTGCGA
64416 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:64576 original size:32 final size:33
Alignment explanation
Indices: 64535--64604 Score: 106
Period size: 32 Copynumber: 2.2 Consensus size: 33
64525 AATACTAACT
*
64535 TGAAAATCGCAACGAGAG-ATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
64567 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
64600 TGAAA
1 TGAAA
64605 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 17 0.50
33 17 0.50
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:64837 original size:22 final size:21
Alignment explanation
Indices: 64786--64839 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
64776 TGGTTGTGAG
**
64786 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
64807 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
64829 GGATTTCTTCG
1 GGATTTCTTCG
64840 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:65010 original size:20 final size:20
Alignment explanation
Indices: 64985--65178 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
64975 CTTTAAATAT
64985 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
65005 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
65027 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65046 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
65066 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
65086 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
65106 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
65126 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
65146 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
65166 CGCGTTGCGATTT
1 CGCGTTGCGATTT
65179 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:65172 original size:60 final size:60
Alignment explanation
Indices: 64985--65178 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
64975 CTTTAAATAT
**
64985 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
65046 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
65106 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
65166 CGCGTTGCGATTT
1 CGCGTTGCGATTT
65179 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:65195 original size:21 final size:20
Alignment explanation
Indices: 65171--65247 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
65161 ATATTCGCGT
65171 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
65192 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
65212 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
65234 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
65248 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:65258 original size:20 final size:20
Alignment explanation
Indices: 65233--65284 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
65223 AAGAATCGCG
*
65233 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
65253 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
65273 TTGCGATTCTGG
1 TTGCGATTCTGG
65285 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:67604 original size:23 final size:24
Alignment explanation
Indices: 67574--67618 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
67564 AACACATAAA
* *
67574 AATTTAAATAATTAAAA-AAATAT
1 AATTTAAAGAAATAAAAGAAATAT
67597 AATTTAAAGAAATAAAAGAAAT
1 AATTTAAAGAAATAAAAGAAAT
67619 TAGATACTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (24 bp):
AATTTAAAGAAATAAAAGAAATAT
Found at i:67747 original size:44 final size:45
Alignment explanation
Indices: 67667--67754 Score: 151
Period size: 44 Copynumber: 2.0 Consensus size: 45
67657 AAGTTATCAT
* *
67667 TTAAATATTTGTTACTAAAAAAGGAAAGATAATATAATTAAATAA
1 TTAAATATTAGATACTAAAAAAGGAAAGATAATATAATTAAATAA
67712 TTAAATATTAGATACTAAAAAA-GAAAGATAATATAATTAAATA
1 TTAAATATTAGATACTAAAAAAGGAAAGATAATATAATTAAATA
67755 TTAGGTTATC
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 21 0.51
45 20 0.49
ACGTcount: A:0.58, C:0.02, G:0.08, T:0.32
Consensus pattern (45 bp):
TTAAATATTAGATACTAAAAAAGGAAAGATAATATAATTAAATAA
Found at i:73922 original size:30 final size:30
Alignment explanation
Indices: 73883--73964 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
73873 AACGAAGATA
*
73883 TAATCTCATGCA-AGTGTCAGAACGGATAAT
1 TAATCTCATGCAGA-TGTCAGAACGGAGAAT
* *
73913 TAATTTCATGCAGATGTCAGAACGGGGAAT
1 TAATCTCATGCAGATGTCAGAACGGAGAAT
*
73943 TAATCCCATGCAGATGTCAGAA
1 TAATCTCATGCAGATGTCAGAA
73965 TAAGGACTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 45 0.98
31 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (30 bp):
TAATCTCATGCAGATGTCAGAACGGAGAAT
Found at i:74546 original size:23 final size:23
Alignment explanation
Indices: 74520--74581 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
74510 AAGTTAACAA
74520 TCAAAGTCAAAGGGTCGAGTCGG
1 TCAAAGTCAAAGGGTCGAGTCGG
* * * *
74543 TCAAAATCAACA-GATCGGGTTGG
1 TCAAAGTCAA-AGGGTCGAGTCGG
*
74566 TCAAAGTCAATGGGTC
1 TCAAAGTCAAAGGGTC
74582 AGGACCTGTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
23 29 0.97
24 1 0.03
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (23 bp):
TCAAAGTCAAAGGGTCGAGTCGG
Found at i:79089 original size:29 final size:29
Alignment explanation
Indices: 79047--79150 Score: 190
Period size: 29 Copynumber: 3.6 Consensus size: 29
79037 GACTGTGTCA
*
79047 ATGCACCTTCATGAATAAATGCAAAGTCT
1 ATGCACCTTCATGAACAAATGCAAAGTCT
79076 ATGCACCTTCATGAACAAATGCAAAGTCT
1 ATGCACCTTCATGAACAAATGCAAAGTCT
79105 ATGCACCTTCATGAACAAATGCAAAGTCT
1 ATGCACCTTCATGAACAAATGCAAAGTCT
*
79134 ATGCATCTTCATGAACA
1 ATGCACCTTCATGAACA
79151 GTAATTTTAA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (29 bp):
ATGCACCTTCATGAACAAATGCAAAGTCT
Found at i:80076 original size:75 final size:75
Alignment explanation
Indices: 79951--80125 Score: 197
Period size: 75 Copynumber: 2.3 Consensus size: 75
79941 ATGGAGCTGG
*** * * * * ** **
79951 GGAAGATGACCATGAGTTGCAGCCTGTTCATTTATGGGATAGAAAGATTGATTTTTTCCAGTGAA
1 GGAAGATGACCATGAGACACAGCTTGTTCATTTACGGAACAGAAAGATTGATTTCGTCCACCGAA
*
80016 AGGGAGCCGA
66 AGGAAGCCGA
* * *
80026 GGAAGATGACCATGAGACACAGCTTGTTCGTTTACGGAACGGAAATATTGATTTCGTCCACCGAA
1 GGAAGATGACCATGAGACACAGCTTGTTCATTTACGGAACAGAAAGATTGATTTCGTCCACCGAA
80091 AGGAAGCCGA
66 AGGAAGCCGA
* *
80101 TGAAGATGACCACGAGACACAGCTT
1 GGAAGATGACCATGAGACACAGCTT
80126 TTTTTTTTTT
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 83 1.00
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.23
Consensus pattern (75 bp):
GGAAGATGACCATGAGACACAGCTTGTTCATTTACGGAACAGAAAGATTGATTTCGTCCACCGAA
AGGAAGCCGA
Found at i:86135 original size:21 final size:21
Alignment explanation
Indices: 86097--86136 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
86087 TTCGGTTAAT
*
86097 TATAAATAAGAAATAATTTCA
1 TATAAATAAGAAAAAATTTCA
86118 TATAAATAA-AATAAAATTT
1 TATAAATAAGAA-AAAATTT
86137 TATGTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.35
Consensus pattern (21 bp):
TATAAATAAGAAAAAATTTCA
Found at i:86222 original size:29 final size:28
Alignment explanation
Indices: 86176--86230 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
86166 TTATTCACCA
*
86176 TAATTAACTTTCATATATTACTTAAAATC
1 TAATTAACTTTCAAATA-TACTTAAAATC
* * *
86205 TAATTAATTTTTAAATATATTTAAAA
1 TAATTAACTTTCAAATATACTTAAAA
86231 AAAACATCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 8 0.36
29 14 0.64
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (28 bp):
TAATTAACTTTCAAATATACTTAAAATC
Found at i:90659 original size:13 final size:13
Alignment explanation
Indices: 90641--90668 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
90631 GAAACTTCAC
90641 TTCAAAAAATGTT
1 TTCAAAAAATGTT
90654 TTCAAAAAATGTT
1 TTCAAAAAATGTT
90667 TT
1 TT
90669 ACCTTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (13 bp):
TTCAAAAAATGTT
Found at i:90953 original size:31 final size:32
Alignment explanation
Indices: 90891--90964 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
90881 CTTGCCACGG
* * *
90891 CCGACCAAACGACAAACAACTGATCATCACAT
1 CCGACCAAACGACAAACAACAGACCACCACAT
*
90923 CCGATCAAACGAC-AACAACAGACCACCACAT
1 CCGACCAAACGACAAACAACAGACCACCACAT
*
90954 CTGACCAAACG
1 CCGACCAAACG
90965 GTCGATTATC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 24 0.67
32 12 0.33
ACGTcount: A:0.43, C:0.36, G:0.11, T:0.09
Consensus pattern (32 bp):
CCGACCAAACGACAAACAACAGACCACCACAT
Found at i:92865 original size:18 final size:17
Alignment explanation
Indices: 92842--92879 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
92832 GGTAGCCCAC
92842 TTAATTTAATTATTAT-TT
1 TTAATTT-ATT-TTATGTT
92860 TTAATTTATTTTATGTT
1 TTAATTTATTTTATGTT
92877 TTA
1 TTA
92880 CGGAATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 4 0.21
17 8 0.42
18 7 0.37
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTAATTTATTTTATGTT
Found at i:96854 original size:16 final size:17
Alignment explanation
Indices: 96833--96865 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
96823 ATAAATATTT
96833 TAAAAT-TAATTAATAA
1 TAAAATATAATTAATAA
*
96849 TAAAATATATTTAATAA
1 TAAAATATAATTAATAA
96866 ATTGACATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAAATATAATTAATAA
Found at i:96868 original size:25 final size:24
Alignment explanation
Indices: 96779--96885 Score: 74
Period size: 25 Copynumber: 4.2 Consensus size: 24
96769 TAGTCATACT
*
96779 TTTAATAAACTAAAATAAATTATATA
1 TTTAATAAATTAAAATAAA--ATATA
* *
96805 TTT-TTAAATGAAAATAAAATAAATA
1 TTTAATAAATTAAAATAAAAT--ATA
*
96830 TTTTAAAATTAATTAATAATAAAATATA
1 -TTT--AATAAATTAA-AATAAAATATA
* *
96858 TTTAATAAATTGACATAAAATAT-
1 TTTAATAAATTAAAATAAAATATA
96881 TTTAA
1 TTTAA
96886 GTTAATATAT
Statistics
Matches: 65, Mismatches: 9, Indels: 17
0.71 0.10 0.19
Matches are distributed among these distances:
23 7 0.11
24 9 0.14
25 23 0.35
26 6 0.09
27 3 0.05
28 3 0.05
29 6 0.09
30 8 0.12
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTAATAAATTAAAATAAAATATA
Found at i:96899 original size:24 final size:23
Alignment explanation
Indices: 96825--96902 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 23
96815 AAAATAAAAT
96825 AAATATTTTAAAATTAATTAATAATA
1 AAATATTTT--AATTAATTAAT-ATA
* * *
96851 AAATATATTTAATAAATTGACATA
1 AAATAT-TTTAATTAATTAATATA
96875 AAATATTTTAAGTTAA-TATATATA
1 AAATATTTTAA-TTAATTA-ATATA
96899 AAAT
1 AAAT
96903 TATATTACAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 6 0.14
24 20 0.47
25 8 0.19
26 6 0.14
27 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (23 bp):
AAATATTTTAATTAATTAATATA
Found at i:97546 original size:31 final size:31
Alignment explanation
Indices: 97503--97567 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
97493 TGACCACATT
* * *
97503 TTAATTATATAAAAACGATAGTGATCATATC
1 TTAATTAAATAAAAACAAAAGTGATCATATC
*
97534 TTAATTAAATAAAAACAAAAGTGTTCATATC
1 TTAATTAAATAAAAACAAAAGTGATCATATC
97565 TTA
1 TTA
97568 TGTTTTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTGATCATATC
Found at i:106171 original size:19 final size:21
Alignment explanation
Indices: 106149--106189 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
106139 TTTGTAACAG
*
106149 TATGAT-AA-TTTTATAATAA
1 TATGATAAAGTTTAATAATAA
106168 TATGATAAAGTTTAATAATAA
1 TATGATAAAGTTTAATAATAA
106189 T
1 T
106190 TTTATAACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (21 bp):
TATGATAAAGTTTAATAATAA
Found at i:107114 original size:17 final size:17
Alignment explanation
Indices: 107092--107125 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
107082 ATATGACATT
107092 ATGATTGTTTATACAAA
1 ATGATTGTTTATACAAA
107109 ATGATTGTTTATACAAA
1 ATGATTGTTTATACAAA
107126 CATAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (17 bp):
ATGATTGTTTATACAAA
Found at i:107898 original size:19 final size:20
Alignment explanation
Indices: 107851--107900 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
107841 CACGGAATGT
*
107851 AAGATTACCAGTGAGAATAA
1 AAGATTATCAGTGAGAATAA
107871 AAGATTATCAGTGAGAATAA
1 AAGATTATCAGTGAGAATAA
107891 AA-ATTATCAG
1 AAGATTATCAG
107901 GGAATAGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 8 0.28
20 21 0.72
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (20 bp):
AAGATTATCAGTGAGAATAA
Found at i:108743 original size:60 final size:60
Alignment explanation
Indices: 108635--108749 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
108625 TCGGGTGATC
* * *
108635 ATTTTATAACTTTTAATAGTCGATGGACTTAATAAAGCAACATTCTATAGTCGGAAGATT
1 ATTTTATAACTTTTAATAGCCGATGGACTTAATAAAGCAACATCCTATAATCGGAAGATT
* ** *
108695 ATTTTCTAACTTTTAATAGCCGA-GGAACTTAATAAATTAATATCCTATAATCGGA
1 ATTTTATAACTTTTAATAGCCGATGG-ACTTAATAAAGCAACATCCTATAATCGGA
108750 TGACTGTTTG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
59 2 0.04
60 45 0.96
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGCCGATGGACTTAATAAAGCAACATCCTATAATCGGAAGATT
Found at i:109090 original size:18 final size:18
Alignment explanation
Indices: 109054--109087 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
109044 AGTAAAAGAA
109054 TATAAAAAAATCTTAAAT
1 TATAAAAAAATCTTAAAT
*
109072 TATATAAAAAT-TTAAA
1 TATAAAAAAATCTTAAA
109088 ATTTTCGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAAAAAATCTTAAAT
Found at i:116709 original size:2 final size:2
Alignment explanation
Indices: 116704--116756 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
116694 AATATTAAAT
116704 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116746 TA TA TA TA TA T
1 TA TA TA TA TA T
116757 GATTTGATGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:117620 original size:47 final size:48
Alignment explanation
Indices: 117569--117660 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
117559 TTGGATCAGA
* *
117569 TCGGGTTATTTCGAGTTTC-GATTTATTCGGGTCTATAGTAAGTCATG
1 TCGGGTCATTTCGAGTTTCGGATTTATTCGAGTCTATAGTAAGTCATG
* * * *
117616 TCGGGTCATTTTGGGTTTCGGTTTTATTCTAGTCTATAGTAAGTC
1 TCGGGTCATTTCGAGTTTCGGATTTATTCGAGTCTATAGTAAGTC
117661 TGGTTAGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
47 16 0.42
48 22 0.58
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (48 bp):
TCGGGTCATTTCGAGTTTCGGATTTATTCGAGTCTATAGTAAGTCATG
Found at i:117928 original size:16 final size:16
Alignment explanation
Indices: 117889--117939 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
117879 GGCAAATTAA
*
117889 ATTTGGGTTGATTTCG
1 ATTTGGGTTGCTTTCG
* *
117905 GTTCGGGTTGCTTTCG
1 ATTTGGGTTGCTTTCG
*
117921 ATTTGGGTTACTTTCG
1 ATTTGGGTTGCTTTCG
117937 ATT
1 ATT
117940 CTAGTTATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.10, C:0.12, G:0.29, T:0.49
Consensus pattern (16 bp):
ATTTGGGTTGCTTTCG
Found at i:117999 original size:16 final size:16
Alignment explanation
Indices: 117900--118002 Score: 57
Period size: 16 Copynumber: 6.5 Consensus size: 16
117890 TTTGGGTTGA
*
117900 TTTCGGTTCGGGTTGC
1 TTTCGGTTCGGGTTAC
* *
117916 TTTCGATTTGGGTTAC
1 TTTCGGTTCGGGTTAC
* ** *
117932 TTTCGATTCTAGTTAT
1 TTTCGGTTCGGGTTAC
* * *
117948 TTTTGGTT-TGGTTAA
1 TTTCGGTTCGGGTTAC
* * *
117963 ATTCGGGTC-GGTTTC
1 TTTCGGTTCGGGTTAC
*
117978 GGTTCGGTTCGGGTTAC
1 -TTTCGGTTCGGGTTAC
117995 TTTCGGTT
1 TTTCGGTT
118003 TTGATAAAAT
Statistics
Matches: 64, Mismatches: 20, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
15 14 0.22
16 45 0.70
17 5 0.08
ACGTcount: A:0.09, C:0.14, G:0.29, T:0.49
Consensus pattern (16 bp):
TTTCGGTTCGGGTTAC
Found at i:125717 original size:51 final size:51
Alignment explanation
Indices: 125635--125737 Score: 179
Period size: 51 Copynumber: 2.0 Consensus size: 51
125625 TTGCCGTGTC
* *
125635 ATTACCCTTAACCAAGGCCTTCGCTATCCTCTCACAAAGAAAGCTTCATCA
1 ATTACCCTTAACCAAAGCCTTCGCTACCCTCTCACAAAGAAAGCTTCATCA
*
125686 ATTACCCTTAACCAAAGCCTTCTCTACCCTCTCACAAAGAAAGCTTCATCA
1 ATTACCCTTAACCAAAGCCTTCGCTACCCTCTCACAAAGAAAGCTTCATCA
125737 A
1 A
125738 ACCCACGCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.33, C:0.34, G:0.08, T:0.25
Consensus pattern (51 bp):
ATTACCCTTAACCAAAGCCTTCGCTACCCTCTCACAAAGAAAGCTTCATCA
Found at i:129939 original size:21 final size:21
Alignment explanation
Indices: 129913--129957 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
129903 GATTTCTGGG
* *
129913 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
129934 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
129955 CAA
1 CAA
129958 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Done.