Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008235.1 Hibiscus syriacus cultivar Beakdansim tig00110879_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: 820011
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:705777 original size:22 final size:22
Alignment explanation
Indices: 705748--705802 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
705738 ATCTACACTC
705748 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
705770 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
705792 TTCAAAGATGA
1 TTCAAAGATGA
705803 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:706625 original size:166 final size:168
Alignment explanation
Indices: 706317--706648 Score: 508
Period size: 166 Copynumber: 2.0 Consensus size: 168
706307 AAAATGAGCA
706317 TTATCTTGAGATTGGGGCATATTACCCAATCAACATGTTATTTCAAAAAAAAAAACATAATGAGA
1 TTATCTTGAGATTGGGGCATATTACCCAATCAACATGTTATTT-----AAAAAAACATAATGAGA
* **
706382 AAACGATTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACG
61 AAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACG
* *
706447 ATTTTCTTAG-TTTTTTTACTTAGTAAACTATTTCCAACAACC
126 ATTTCCTTAGTTTTTTTTACTTAATAAACTATTTCCAACAACC
* **
706489 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTGAGATTGGGGCATATTACCCAATCAACATGTTATTTAAAAAAACATAATGAGAAAACG
*
706552 ATTTCCATAGTTTCTCATTCAATCTTTTTTAAAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAACGATTT
706617 CCTTAGTTTTTTTTACTTAATAAACTATTTCC
130 CCTTAGTTTTTTTTACTTAATAAACTATTTCC
706649 CACATCTGTA
Statistics
Matches: 149, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
165 40 0.27
166 43 0.29
167 24 0.16
172 42 0.28
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (168 bp):
TTATCTTGAGATTGGGGCATATTACCCAATCAACATGTTATTTAAAAAAACATAATGAGAAAACG
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTC
CTTAGTTTTTTTTACTTAATAAACTATTTCCAACAACC
Found at i:706750 original size:76 final size:76
Alignment explanation
Indices: 706651--707137 Score: 834
Period size: 76 Copynumber: 6.4 Consensus size: 76
706641 CTATTTCCCA
* *
706651 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGATCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
706716 ATCCTTAGGGT
66 AGCCTTAGGGT
*
706727 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
706792 AGCCTTAGGGT
66 AGCCTTAGGGT
706803 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
706867 AGCCTTAGGGT
66 AGCCTTAGGGT
*
706878 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
706943 AAACCTTCGGGT
65 AAGCCTTAGGGT
*
706955 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
707020 AGCCTTAGGGT
66 AGCCTTAGGGT
*
707031 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
*
707096 AAACCTTCA-GGT
65 AAGCCTT-AGGGT
*
707108 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTT
707138 TCAACATTTC
Statistics
Matches: 393, Mismatches: 14, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
75 74 0.19
76 207 0.53
77 111 0.28
78 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:707276 original size:3 final size:3
Alignment explanation
Indices: 707268--707344 Score: 73
Period size: 3 Copynumber: 24.3 Consensus size: 3
707258 TCATTTAAAT
** *
707268 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTA GTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
* *
707314 TTA TTTA TTA ATA TTA ATA TATA TATA TTA T
1 TTA -TTA TTA TTA TTA TTA T-TA T-TA TTA T
707345 AATAAATAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
3 48 0.79
4 13 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:708637 original size:20 final size:20
Alignment explanation
Indices: 708612--708685 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
708602 TTTTCCTAAT
*
708612 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
** *
708632 TCGCAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
708653 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
708673 TCGCAACGCGAAT
1 TCGCAACGCGAAT
708686 TGGGAAAATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:708655 original size:21 final size:21
Alignment explanation
Indices: 708629--708704 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
708619 GCGAATAAGT
708629 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
708650 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
708670 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* *
708691 AAATTGCAATGCGA
1 AAATCGCAACGCGA
708705 TACTGACTAT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.41, C:0.17, G:0.25, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:708719 original size:41 final size:41
Alignment explanation
Indices: 708612--708704 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
708602 TTTTCCTAAT
708612 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
708653 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
*
708694 TTGCAATGCGA
1 TCGCAATGCGA
708705 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.40, C:0.17, G:0.25, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:708721 original size:20 final size:20
Alignment explanation
Indices: 708696--708787 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
708686 TGGGAAAATT
*
708696 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* * * **
708716 GCAATGCGATAATAAAAAATC
1 GCAACGCGATACT-GACTATC
* * *
708737 GCAACGAGATACTTACTTTC
1 GCAACGCGATACTGACTATC
*
708757 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
708777 GCAACGCGATA
1 GCAACGCGATA
708788 ATACATAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:709003 original size:22 final size:22
Alignment explanation
Indices: 708975--709018 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
708965 CACTCTCTCA
708975 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
708997 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
709019 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:709288 original size:20 final size:20
Alignment explanation
Indices: 709263--709300 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
709253 CGATTCTCTC
709263 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
709283 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
709301 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:710641 original size:18 final size:18
Alignment explanation
Indices: 710620--710664 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
710610 TCCACTTCGG
*
710620 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
710638 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
710656 GAGCCATCA
1 GAGCCATCA
710665 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:711171 original size:20 final size:20
Alignment explanation
Indices: 711146--711191 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
711136 TAGTTTACTT
711146 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
711166 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
711186 TCGCAA
1 TCGCAA
711192 TGCGAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:711220 original size:14 final size:14
Alignment explanation
Indices: 711201--711258 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
711191 ATGCGAAATA
711201 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
711215 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
711231 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
711247 AAAATCGCAACG
1 AAAATCGCAACG
711259 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:711243 original size:32 final size:32
Alignment explanation
Indices: 711185--711275 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
711175 GGAAATGGCT
*
711185 ATCGCAATGCGAAATAAAAATCGCAACGACAAA
1 ATCGCAATGCGAAAT-GAAATCGCAACGACAAA
711218 ATCGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
711250 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATG-AAATCGCAA
711276 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:711405 original size:20 final size:19
Alignment explanation
Indices: 711368--711422 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
711358 TTGCGATTTT
* *
711368 CATTTCGCATTACGATAGC
1 CATTTCGCGTTGCGATAGC
* *
711387 CATTTCCGTGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
711407 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
711423 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.18, C:0.24, G:0.22, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:711420 original size:19 final size:19
Alignment explanation
Indices: 711306--711422 Score: 104
Period size: 18 Copynumber: 6.5 Consensus size: 19
711296 GCGATTTTGT
711306 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATATTCATTTCG
711324 CGTTGCGAT-TTCATTTCG
1 CGTTGCGATATTCATTTCG
*
711342 CGTTGCGAT-TT--TGT--
1 CGTTGCGATATTCATTTCG
*
711356 CGTTGCGATTTTCATTTCG
1 CGTTGCGATATTCATTTCG
* * **
711375 CATTACGATAGCCATTTCCG
1 CGTTGCGATATTCATTT-CG
* *
711395 TGTTGCGATAGTCATTTCG
1 CGTTGCGATATTCATTTCG
711414 CGTTGCGAT
1 CGTTGCGAT
711423 TTTAAGTTTC
Statistics
Matches: 81, Mismatches: 12, Indels: 11
0.78 0.12 0.11
Matches are distributed among these distances:
14 9 0.11
15 2 0.02
16 2 0.02
17 2 0.02
18 29 0.36
19 22 0.27
20 15 0.19
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (19 bp):
CGTTGCGATATTCATTTCG
Found at i:713308 original size:14 final size:14
Alignment explanation
Indices: 713289--713324 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
713279 ATTGTTTAAT
713289 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
713303 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
713317 TGATTTGT
1 TGATTTGT
713325 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:713463 original size:19 final size:19
Alignment explanation
Indices: 713441--713508 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
713431 ATCGCAACGA
713441 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
713460 GAAAATCGAAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
713479 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
713493 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
713509 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
19 28 0.64
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:713584 original size:20 final size:20
Alignment explanation
Indices: 713527--713584 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
713517 TCGCATTGCG
* *
713527 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
713547 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
713567 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
713585 TCAAATGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:714545 original size:24 final size:24
Alignment explanation
Indices: 714518--714571 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
714508 GTATTCGAAA
* *
714518 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
714542 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
714566 TTTGAT
1 TTTGAT
714572 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:714763 original size:12 final size:12
Alignment explanation
Indices: 714746--714770 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
714736 ATATAATCCT
714746 GAAGAAGAAAAA
1 GAAGAAGAAAAA
714758 GAAGAAGAAAAA
1 GAAGAAGAAAAA
714770 G
1 G
714771 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:717066 original size:20 final size:20
Alignment explanation
Indices: 717038--717090 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
717028 GGGAATTTAA
717038 TTTCGCGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
*
717058 TTTCTCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
*
717077 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
717091 AGTACTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:717216 original size:14 final size:14
Alignment explanation
Indices: 717197--717233 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
717187 CATCAATTAA
717197 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
717211 ACAAATCACCTTTT
1 ACAAATCAACTTTT
717225 ACAAATCAA
1 ACAAATCAA
717234 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:718657 original size:21 final size:21
Alignment explanation
Indices: 718591--718657 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
718581 GTGAATCGGG
*
718591 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
718611 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
718633 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
718654 CTCT
1 CTCT
718658 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:718676 original size:42 final size:41
Alignment explanation
Indices: 718591--718713 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
718581 GTGAATCGGG
* * * * *
718591 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
718633 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
718675 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
718714 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:719858 original size:21 final size:22
Alignment explanation
Indices: 719816--719858 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
719806 AATAACAAAC
*
719816 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
719838 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
719859 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:720777 original size:33 final size:33
Alignment explanation
Indices: 720721--720819 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
720711 ACGAGATAAT
*
720721 GAGAATCGCAACGCCGAAATGACTATCGCAACGA
1 GAGAATCGCAACG-CGAAATGACTATCGCAACCA
*
720755 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
720788 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
720820 GCGAAATAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.27, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:720813 original size:19 final size:19
Alignment explanation
Indices: 720696--720861 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
720686 TCTTTTGGTT
*
720696 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
720715 GATAATGAGAATCGCAACGCC
1 GA-AATGAAAATCGCAACG-C
**
720736 GAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
720753 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
720769 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
720787 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
720802 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
720822 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
720841 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
720860 GA
1 GA
720862 TTTTGGTTTC
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 19 0.16
15 3 0.03
16 2 0.02
17 2 0.02
18 3 0.03
19 43 0.36
20 45 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:720890 original size:19 final size:19
Alignment explanation
Indices: 720857--720923 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
720847 AAAATCGCAA
**
720857 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
720876 TGCGATTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
720895 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
720915 TGCGATTTT
1 TGCGATTTT
720924 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 29 0.71
20 12 0.29
ACGTcount: A:0.10, C:0.16, G:0.25, T:0.48
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:721455 original size:20 final size:20
Alignment explanation
Indices: 721430--721483 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
721420 GGCGCTATGT
721430 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
721450 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
** *
721470 GTATCTCGTTGCGA
1 AAATCGCGTTGCGA
721484 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
AAATCGCGTTGCGAAAGTCA
Found at i:721517 original size:20 final size:20
Alignment explanation
Indices: 721492--721543 Score: 81
Period size: 18 Copynumber: 2.7 Consensus size: 20
721482 GATTTTGTAT
721492 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
721512 TATCGCATTGCG--AGTCAG
1 TATCGCATTGCGATAGTAAG
721530 TATCGCATTGCGAT
1 TATCGCATTGCGAT
721544 TTTCCCAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 17 0.59
20 12 0.41
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:721576 original size:20 final size:21
Alignment explanation
Indices: 721532--721583 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
721522 CGAGTCAGTA
*
721532 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
721553 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
721573 TCGCATTGCGA
1 TCGCATTGCGA
721584 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:721654 original size:21 final size:21
Alignment explanation
Indices: 721614--721654 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
721604 ATTGTATACC
**
721614 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
721635 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
721655 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:724915 original size:21 final size:20
Alignment explanation
Indices: 724891--724943 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
724881 CAGTTTCCAA
*
724891 ATTCGCAACGCGAATATCTAG
1 ATTCGCAACGCGAATAT-AAG
* *
724912 ATTCGCAACG-GGATGTAAG
1 ATTCGCAACGCGAATATAAG
724931 ATTCGCAACGCGA
1 ATTCGCAACGCGA
724944 TTTTGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 12 0.44
20 5 0.19
21 10 0.37
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.21
Consensus pattern (20 bp):
ATTCGCAACGCGAATATAAG
Found at i:724982 original size:14 final size:14
Alignment explanation
Indices: 724959--724988 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
724949 AAAAATGTGT
724959 TGCGACAGTTAAAA
1 TGCGACAGTTAAAA
*
724973 TGCGATAGTTAAAA
1 TGCGACAGTTAAAA
724987 TG
1 TG
724989 GTGCGAGAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (14 bp):
TGCGACAGTTAAAA
Found at i:725035 original size:18 final size:18
Alignment explanation
Indices: 725012--725046 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
725002 AAAAACGTGT
725012 TGTTGCGATAGTGAAAAG
1 TGTTGCGATAGTGAAAAG
725030 TGTTGCGATAGTGAAAA
1 TGTTGCGATAGTGAAAA
725047 ATCCAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.31, T:0.29
Consensus pattern (18 bp):
TGTTGCGATAGTGAAAAG
Found at i:725429 original size:21 final size:21
Alignment explanation
Indices: 725375--725453 Score: 83
Period size: 21 Copynumber: 3.9 Consensus size: 21
725365 GGAAAATCGC
725375 ATCTTCGACTATCGCAA--CG
1 ATCTTCGACTATCGCAACGCG
* **
725394 AT-TTGGAAAATCGCAACGCG
1 ATCTTCGACTATCGCAACGCG
*
725414 ATCTTCGACTATCGCAACGTG
1 ATCTTCGACTATCGCAACGCG
* *
725435 AACTTGGACTATCGCAACG
1 ATCTTCGACTATCGCAACG
725454 AATTTGGACT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
18 11 0.23
19 2 0.04
20 4 0.08
21 31 0.65
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCTTCGACTATCGCAACGCG
Found at i:725581 original size:21 final size:21
Alignment explanation
Indices: 725557--725613 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
725547 GCGATTTTCT
*
725557 AAAATCGTAACGCGAATTTGG
1 AAAATCGCAACGCGAATTTGG
*
725578 AAAATCGCAATGCGAATTTGG
1 AAAATCGCAACGCGAATTTGG
* *
725599 AAAATTGCAATGCGA
1 AAAATCGCAACGCGA
725614 TAGTCAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.40, C:0.14, G:0.23, T:0.23
Consensus pattern (21 bp):
AAAATCGCAACGCGAATTTGG
Found at i:725702 original size:20 final size:19
Alignment explanation
Indices: 725658--725694 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
725648 TGCGATACTG
725658 GAGATCGCATTACGATTTA
1 GAGATCGCATTACGATTTA
*
725677 GAGATCGCATTGCGATTT
1 GAGATCGCATTACGATTT
725695 TATTGATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTACGATTTA
Found at i:727491 original size:31 final size:31
Alignment explanation
Indices: 727427--727494 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
727417 TTTAATAGTC
* * *
727427 GAGGGCCTCAACAAAGCATCACCTTATAGTT
1 GAGGGACTCAACAAAACATCACCTTATAATT
727458 GAGGGACTCAACAAAACATCAACC-TATAATT
1 GAGGGACTCAACAAAACATC-ACCTTATAATT
727489 GAGGGA
1 GAGGGA
727495 TTATTTGTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (31 bp):
GAGGGACTCAACAAAACATCACCTTATAATT
Found at i:729820 original size:243 final size:241
Alignment explanation
Indices: 729358--729845 Score: 917
Period size: 243 Copynumber: 2.0 Consensus size: 241
729348 ATTCTAAATG
729358 CAAAAAAAGGATAAAAAAGGAAATTAATAATAATAATAATAATAATCAGATCCTCGAAAGTAGGG
1 CAAAAAAAGGAT-AAAAAGGAAATTAATAATAATAATAATAATAATCAGATCCTCGAAAGTAGGG
729423 AATGTCTAGAGAGTCCTACGAAGGGAGTTGCTTGAGAGAATCTTAAAATTACCATAAAATCCTTT
65 AATGTCTAGAGAGTCCTACGAAGGGAGTTGCTTGAGAGAATCTTAAAATTACCATAAAATCCTTT
729488 GCACGTAAAGCCACGTTTCGACTGACATTGAATCAAGGTAATTACAGCCAATAGGAAAAGATTTA
130 GCACGTAAAGCCACGTTTCGACTGACATTGAATCAAGGTAATTACAGCCAATAGGAAAAGATTTA
729553 AAAAATAGTTAATATAATGCCTTGAGTATGAGCGCACGCGATTGTTT
195 AAAAATAGTTAATATAATGCCTTGAGTATGAGCGCACGCGATTGTTT
729600 CAAAAAAAGGAT-AAAAGGAAATTAATAATAATAATAATAATAATCAGATCCTCCGAAAGTAGGG
1 CAAAAAAAGGATAAAAAGGAAATTAATAATAATAATAATAATAATCAGATCCT-CGAAAGTAGGG
729664 AATGTCTAGAGAGTCCTACGAAGGGAGTTGCTTTGAGAGAATCTTAAAATTACCATAAAATCCTT
65 AATGTCTAGAGAGTCCTACGAAGGGAGTTGC-TTGAGAGAATCTTAAAATTACCATAAAATCCTT
729729 TGCACGTAAAAGCCACGTTTCGAACTGACATTGAATCAAGGTAATTACAGCCAATAGGAAAAGAT
129 TGCACGT-AAAGCCACGTTTCG-ACTGACATTGAATCAAGGTAATTACAGCCAATAGGAAAAGAT
729794 TT-AAAAATAGTTAATATAATGCCTTGAGTATGAGCGCACGCGATTGTTT
192 TTAAAAAATAGTTAATATAATGCCTTGAGTATGAGCGCACGCGATTGTTT
729843 CAA
1 CAA
729846 GTCAACTTGG
Statistics
Matches: 242, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
240 40 0.17
241 42 0.17
242 52 0.21
243 64 0.26
244 44 0.18
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (241 bp):
CAAAAAAAGGATAAAAAGGAAATTAATAATAATAATAATAATAATCAGATCCTCGAAAGTAGGGA
ATGTCTAGAGAGTCCTACGAAGGGAGTTGCTTGAGAGAATCTTAAAATTACCATAAAATCCTTTG
CACGTAAAGCCACGTTTCGACTGACATTGAATCAAGGTAATTACAGCCAATAGGAAAAGATTTAA
AAAATAGTTAATATAATGCCTTGAGTATGAGCGCACGCGATTGTTT
Found at i:730538 original size:6 final size:6
Alignment explanation
Indices: 730529--730918 Score: 538
Period size: 6 Copynumber: 67.8 Consensus size: 6
730519 TAGTATACGT
* *
730529 ATATAC ATATAC ATATAC ATATAC --AGAC ACATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
730575 ATATAC ATATAC -TAT-- ATATAC ATA-AC ATA-AC --ATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
730616 ATATAC -TATAC --ATAC ATATAC ATATAC --ATAC AT-TAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
730658 ATATAC ATATAC ATATAC ATATAC ATATAC ATTATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC A-TATAC ATATAC ATATAC
730707 ATATAC ATATAC --ATAC ATATAC ATATAC ATATAC ATATAC TATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC -ATATAC
730754 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
730802 ATACATAC ATATAC ATATAC ATA-AC ATATAC ATATATAC ATATAC ATATAC
1 AT--ATAC ATATAC ATATAC ATATAC ATATAC --ATATAC ATATAC ATATAC
*
730853 ATATAC ATATAC ATATAC --ATAC ATAGAC ATATAC A-ATAC ATAT--
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC
730896 ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATA
730919 TACCCACTTA
Statistics
Matches: 352, Mismatches: 5, Indels: 54
0.86 0.01 0.13
Matches are distributed among these distances:
3 1 0.00
4 28 0.08
5 30 0.09
6 269 0.76
7 12 0.03
8 12 0.03
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:730641 original size:49 final size:50
Alignment explanation
Indices: 730531--730918 Score: 463
Period size: 49 Copynumber: 8.0 Consensus size: 50
730521 GTATACGTAT
*
730531 ATACATATACATATACATATACAGACACATACATATACATATACATATAC
1 ATACATATACATATACATATACATACACATACATATACATATACATATAC
*
730581 AT--ATACTATATATACATA-ACATA-ACATACATATACATATAC-TATAC
1 ATACATA-TACATATACATATACATACACATACATATACATATACATATAC
*
730627 ATACATATACATATAC--ATACATTACATATACATATACATATAC--AT--
1 ATACATATACATATACATATACA-TACACATACATATACATATACATATAC
*
730672 ATACATATACATATACAT-T--ATACATATACATATACATATACATATAC
1 ATACATATACATATACATATACATACACATACATATACATATACATATAC
*
730719 ATACATATACATATACATATACATATACTATATACATATACATATACATATAC
1 ATACATATACATATACATATAC--ATAC-ACATACATATACATATACATATAC
*
730772 ATATACATATACATATACATATACATATACATAC--ATACATATACATATAC
1 --ATACATATACATATACATATACATACACATACATATACATATACATATAC
* * *
730822 ATAACATATACATAT--ATACATATACATATACATATACATATACATATAC
1 AT-ACATATACATATACATATACATACACATACATATACATATACATATAC
* * *
730871 ATACATAGACATATACA-ATACATATATATACATATACATATACATATA
1 ATACATATACATATACATATACATACACATACATATACATATACATATA
730919 TACCCACTTA
Statistics
Matches: 299, Mismatches: 14, Indels: 51
0.82 0.04 0.14
Matches are distributed among these distances:
43 21 0.07
44 1 0.00
45 19 0.06
46 11 0.04
47 60 0.20
48 41 0.14
49 69 0.23
50 19 0.06
52 9 0.03
53 27 0.09
55 22 0.07
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.32
Consensus pattern (50 bp):
ATACATATACATATACATATACATACACATACATATACATATACATATAC
Found at i:738425 original size:2 final size:2
Alignment explanation
Indices: 738418--738453 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
738408 ACAAGAAATA
738418 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
738454 TTTGCTTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:739582 original size:20 final size:21
Alignment explanation
Indices: 739557--739649 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
739547 TTTTCCCAAT
*
739557 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
739577 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
739598 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
739618 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
739639 TCGCAATGCGA
1 TCGCAATGCGA
739650 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:739602 original size:41 final size:41
Alignment explanation
Indices: 739557--739649 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
739547 TTTTCCCAAT
739557 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
739598 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
739639 TCGCAATGCGA
1 TCGCAATGCGA
739650 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:739662 original size:41 final size:41
Alignment explanation
Indices: 739576--739710 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
739566 GAATAAGTAA
* *
739576 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
739617 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
739658 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
739699 TTCGCAACGCGA
1 ATCGCAACGCGA
739711 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:739663 original size:20 final size:20
Alignment explanation
Indices: 739638--739729 Score: 85
Period size: 20 Copynumber: 4.5 Consensus size: 20
739628 AATTGGGAAA
*
739638 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
739658 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
739679 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
739699 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
739719 TTCGCAACGCG
1 ATCGCAACGCG
739730 GTTTACATAG
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 44 0.76
21 14 0.24
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:740310 original size:19 final size:19
Alignment explanation
Indices: 740286--740330 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
740276 GCAACGAGAT
*
740286 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
740305 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
740324 AATCGCA
1 AATCGCA
740331 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:740348 original size:19 final size:19
Alignment explanation
Indices: 740326--740510 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
740316 GAAACCAAAA
*
740326 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
740345 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
740364 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
740383 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
740403 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
740419 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
740436 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
740450 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
740469 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
740489 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
740509 TC
1 TC
740511 AACCAAAAGA
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 20 0.14
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 60 0.43
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:740403 original size:39 final size:38
Alignment explanation
Indices: 740326--740510 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
740316 GAAACCAAAA
*
740326 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
740364 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * **
740403 TCGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
740436 TCGCGTTGCGA--TTC---TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
740469 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
740509 TC
1 TC
740511 AACCAAAAGA
Statistics
Matches: 124, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
31 3 0.02
33 38 0.31
34 10 0.08
35 1 0.01
36 3 0.02
38 21 0.17
39 30 0.24
40 18 0.15
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:740487 original size:20 final size:20
Alignment explanation
Indices: 740453--740510 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
740443 GCGATTCTCT
**
740453 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
740473 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
740493 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
740511 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:742569 original size:42 final size:42
Alignment explanation
Indices: 742509--742631 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
742499 GCCCGACTCG
* * *
742509 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
742551 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
742593 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
742632 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:742589 original size:21 final size:21
Alignment explanation
Indices: 742565--742631 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
742555 TCATTCCTCG
742565 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
742586 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
742607 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
742628 AGAG
1 AGAG
742632 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:744009 original size:14 final size:14
Alignment explanation
Indices: 743990--744025 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
743980 ATTGTTTAAT
743990 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
744004 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
744018 TGATTTGT
1 TGATTTGT
744026 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:744225 original size:19 final size:19
Alignment explanation
Indices: 744203--744353 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
744193 CGAAATTAAA
744203 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
744222 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
744237 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
744255 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
744269 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
744288 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
744303 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
744321 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
744340 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
744354 GGACATAAGA
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:744249 original size:33 final size:32
Alignment explanation
Indices: 744207--744333 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
744197 ATTAAATTCG
744207 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
744240 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
744273 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
744306 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
744334 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:744285 original size:66 final size:66
Alignment explanation
Indices: 744200--744332 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
744190 ACGCGAAATT
*
744200 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
744265 G
66 G
*
744266 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
744331 G
66 G
744332 A
1 A
744333 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:746639 original size:12 final size:12
Alignment explanation
Indices: 746622--746646 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
746612 TCTTCGGGGA
746622 CTTTTTCTTCTT
1 CTTTTTCTTCTT
746634 CTTTTTCTTCTT
1 CTTTTTCTTCTT
746646 C
1 C
746647 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:746855 original size:24 final size:24
Alignment explanation
Indices: 746821--746876 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
746811 CTGAAACATC
* *
746821 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
746845 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
746869 ATCAAAAT
1 ATCAAAAT
746877 TCGAATACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:747971 original size:20 final size:20
Alignment explanation
Indices: 747914--747964 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
747904 ATTCATTTGA
747914 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
747934 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
747954 TTATCGCAACG
1 CTATCGCAACG
747965 AGGAAATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:748057 original size:14 final size:14
Alignment explanation
Indices: 747988--748019 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
747978 GCGATTTTCA
747988 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
748002 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
748016 TTTC
1 TTTC
748020 ATTTCGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.47
Consensus pattern (14 bp):
TTTCGCATTGCGAT
Found at i:748094 original size:57 final size:52
Alignment explanation
Indices: 747971--748143 Score: 238
Period size: 52 Copynumber: 3.2 Consensus size: 52
747961 AACGAGGAAA
747971 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGCATTGCGATTTTCATT
748023 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTC-----GCATTGCGATTTTCATT
* * * ***
748080 TCGCATTGCGATTTTCATTTTGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGCATTGCGATTTTCATT
*
748132 TCGCGTTGCGAT
1 TCGCATTGCGAT
748144 AGTCTGTTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 10
0.87 0.06 0.08
Matches are distributed among these distances:
52 58 0.53
57 51 0.47
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCGCATTGCGATTTTCATT
Found at i:748121 original size:19 final size:19
Alignment explanation
Indices: 747971--748114 Score: 235
Period size: 19 Copynumber: 7.8 Consensus size: 19
747961 AACGAGGAAA
747971 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
747990 TCGCATTGCGA---T--TT
1 TCGCATTGCGATTTTCATT
748004 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
748023 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
748042 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
748061 TTGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
748080 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
748099 TTGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
748115 TCGTTGCGAT
Statistics
Matches: 117, Mismatches: 3, Indels: 10
0.90 0.02 0.08
Matches are distributed among these distances:
14 13 0.11
16 1 0.01
17 1 0.01
19 102 0.87
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:750155 original size:19 final size:19
Alignment explanation
Indices: 750130--750220 Score: 112
Period size: 19 Copynumber: 4.8 Consensus size: 19
750120 CGAAACTTAA
750130 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* * *
750149 TATCGCAACACGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
750169 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
750188 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
750206 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
750221 CACAAATCGC
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
18 15 0.24
19 31 0.50
20 16 0.26
ACGTcount: A:0.42, C:0.23, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:750155 original size:39 final size:38
Alignment explanation
Indices: 750112--750220 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 38
750102 TAGTTTACTT
* **
750112 TCGCAACACGAAACTTAAAATCGCAACGCGAAATGACTA
1 TCGCAACACGAAA-TTGAAATCGCAACGCGAAATGAAAA
* ** *
750151 TCGCAACACGGAAATGGCTATCGCAATGCGAAATGAAAA
1 TCGCAACAC-GAAATTGAAATCGCAACGCGAAATGAAAA
*
750190 TCGCAACGCGAAA-TGAAATCGCAACGCGAAA
1 TCGCAACACGAAATTGAAATCGCAACGCGAAA
750221 CACAAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
37 14 0.25
38 4 0.07
39 35 0.61
40 4 0.07
ACGTcount: A:0.42, C:0.24, G:0.20, T:0.14
Consensus pattern (38 bp):
TCGCAACACGAAATTGAAATCGCAACGCGAAATGAAAA
Found at i:750229 original size:19 final size:18
Alignment explanation
Indices: 750187--750231 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
750177 TGCGAAATGA
**
750187 AAATCGCAACGCGAAATG
1 AAATCGCAACGCGAAAAC
750205 AAATCGCAACGCGAAACAC
1 AAATCGCAACGCGAAA-AC
750224 AAATCGCA
1 AAATCGCA
750232 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.47, C:0.27, G:0.18, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGCGAAAAC
Found at i:750268 original size:14 final size:14
Alignment explanation
Indices: 750249--750306 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
750239 TTTCATTTCG
750249 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
750263 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
750279 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
750295 CGTTGCGATTTT
1 CGTTGCGATTTT
750307 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:750313 original size:33 final size:33
Alignment explanation
Indices: 750232--750322 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
750222 ACAAATCGCA
*
750232 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
750265 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
750297 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
750323 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:750341 original size:20 final size:19
Alignment explanation
Indices: 750307--750361 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
750297 TTGCGATTTT
*
750307 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
750326 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
750346 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
750362 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:750860 original size:18 final size:18
Alignment explanation
Indices: 750834--750878 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
750824 GTCGATCAGA
*
750834 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
750852 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
750870 TGATGGCTC
1 TGATGGCTC
750879 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:752224 original size:20 final size:20
Alignment explanation
Indices: 752199--752252 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
752189 AATAGTTTCT
752199 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
752219 GAAAATGACTATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
752239 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
752253 GTTGCGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.50, C:0.22, G:0.15, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:752511 original size:22 final size:22
Alignment explanation
Indices: 752486--752529 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
752476 GATTTAGATA
752486 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
752508 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
752530 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:752747 original size:21 final size:21
Alignment explanation
Indices: 752714--752814 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
752704 TGCGAAAGTA
* * *
752714 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
752735 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
752755 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
752777 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
752798 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
752815 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:752789 original size:41 final size:41
Alignment explanation
Indices: 752759--752851 Score: 150
Period size: 41 Copynumber: 2.3 Consensus size: 41
752749 ATAGTCAGTA
* *
752759 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
* *
752800 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
752841 TCGCATTGCGA
1 TCGCATTGCGA
752852 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTCACGTAT
Found at i:752824 original size:21 final size:20
Alignment explanation
Indices: 752759--752851 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
752749 ATAGTCAGTA
*
752759 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
752780 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
752800 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
752821 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
752841 TCGCATTGCGA
1 TCGCATTGCGA
752852 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:761697 original size:16 final size:16
Alignment explanation
Indices: 761667--761697 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
761657 TAATATTGAA
*
761667 ACTTGAACTCAAAAAG
1 ACTTGAACTAAAAAAG
761683 ACTTGAACTAAAAAA
1 ACTTGAACTAAAAAA
761698 ATTTTAGAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTAAAAAAG
Found at i:762191 original size:23 final size:23
Alignment explanation
Indices: 762144--762188 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
762134 TATAAAAAAT
762144 TATTTTTTACTAAATATTTTTAA
1 TATTTTTTACTAAATATTTTTAA
* *
762167 TATTTTTTATTTAAT-TTTTTAA
1 TATTTTTTACTAAATATTTTTAA
762189 ATAATTATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTTTACTAAATATTTTTAA
Found at i:790541 original size:2 final size:2
Alignment explanation
Indices: 790534--790578 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
790524 AATAGATAAC
790534 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
790576 TA T
1 TA T
790579 GGTTAGGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:796093 original size:23 final size:24
Alignment explanation
Indices: 796055--796099 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
796045 TATTTTTTTT
796055 CAAAAAACAAAAAACAA-AAAAGG
1 CAAAAAACAAAAAACAACAAAAGG
796078 CAAAAAA-AAAACAACAACAAAA
1 CAAAAAACAAAA-AACAACAAAA
796100 AAGCCAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.80, C:0.16, G:0.04, T:0.00
Consensus pattern (24 bp):
CAAAAAACAAAAAACAACAAAAGG
Found at i:796096 original size:26 final size:27
Alignment explanation
Indices: 796056--796108 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
796046 ATTTTTTTTC
*
796056 AAAAAACAAAAAACAAAAAAGGCAAAA
1 AAAAAACAAAAAACAAAAAAGCCAAAA
*
796083 AAAAAAC-AACAACAAAAAAGCCAAAA
1 AAAAAACAAAAAACAAAAAAGCCAAAA
796109 TTTTAAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.79, C:0.15, G:0.06, T:0.00
Consensus pattern (27 bp):
AAAAAACAAAAAACAAAAAAGCCAAAA
Found at i:807652 original size:22 final size:21
Alignment explanation
Indices: 807626--807684 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
807616 TTAGTGCAGA
807626 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC-TGAAG
* * *
807648 GGGAACCGATTCCCCCTGTAG
1 GGGAATCGATACCCCCTGAAG
807669 GGGAATCGATACCCCC
1 GGGAATCGATACCCCC
807685 CTGGGGTTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.17
Consensus pattern (21 bp):
GGGAATCGATACCCCCTGAAG
Found at i:809261 original size:18 final size:18
Alignment explanation
Indices: 809235--809288 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
809225 GACGACTCCG
* *
809235 ACGATGAACCAGAACAGC
1 ACGAGGAACAAGAACAGC
*
809253 ACGAGGAACAAGCACGAGC
1 ACGAGGAACAAGAAC-AGC
809272 A-GAGGAACAAGAACAGC
1 ACGAGGAACAAGAACAGC
809289 CAGATGATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
17 3 0.10
18 24 0.77
19 4 0.13
ACGTcount: A:0.46, C:0.24, G:0.28, T:0.02
Consensus pattern (18 bp):
ACGAGGAACAAGAACAGC
Found at i:811234 original size:18 final size:19
Alignment explanation
Indices: 811182--811239 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 19
811172 CACTGAATAT
811182 TTGTCCCGAAGACCACTGA
1 TTGTCCCGAAGACCACTGA
*
811201 TTGTTCCGAAGAACCACT-A
1 TTGTCCCGAAG-ACCACTGA
*
811220 -TGTCCCGAATGACCATTGA
1 TTGTCCCGAA-GACCACTGA
811239 T
1 T
811240 AATCCCTCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 13 0.41
19 13 0.41
20 6 0.19
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (19 bp):
TTGTCCCGAAGACCACTGA
Found at i:813075 original size:59 final size:59
Alignment explanation
Indices: 813009--813221 Score: 245
Period size: 59 Copynumber: 3.6 Consensus size: 59
812999 GCATATATCG
* * * *
813009 ATAGTTTGAGGATAAAATTGAACGTTCAAAAGTTTGTAGACATATTTAGAATGAGGGTC
1 ATAGTTTGGGGATGAAATTGAATGTTCAAAAGTTTGAAGACATATTTAGAATGAGGGTC
* *
813068 ATAGTTTGGGGATGAAATTGAAATGTTTAAAAGTTTGAAGACCA-A-TTAGAATGAGAGTC
1 ATAGTTTGGGGATGAAATTG-AATGTTCAAAAGTTTGAAGA-CATATTTAGAATGAGGGTC
* * * *
813127 ATAGTTTGGGGATGAAATTGGAATGTTC-AAAGTTTGGAGAC-TAATTTCGAATAAGGATC
1 ATAGTTTGGGGATGAAATT-GAATGTTCAAAAGTTTGAAGACAT-ATTTAGAATGAGGGTC
* *
813186 ATAGTTTGGGGATGAAATCAGAATGTTTAAAAGTTT
1 ATAGTTTGGGGATGAAAT-TGAATGTTCAAAAGTTT
813222 ACATATCAAT
Statistics
Matches: 132, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
57 1 0.01
58 12 0.09
59 91 0.69
60 26 0.20
61 2 0.02
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (59 bp):
ATAGTTTGGGGATGAAATTGAATGTTCAAAAGTTTGAAGACATATTTAGAATGAGGGTC
Found at i:813217 original size:118 final size:118
Alignment explanation
Indices: 813009--813221 Score: 306
Period size: 118 Copynumber: 1.8 Consensus size: 118
812999 GCATATATCG
* * *
813009 ATAGTTTGAGGATAAAATTGAACGTTCAAAAGTTTGTAGACATATTTAGAATGAGGGTCATAGTT
1 ATAGTTTGAGGATAAAATTGAACGTTCAAAAGTTTGGAGACATATTTAGAATAAGGATCATAGTT
*
813074 TGGGGATGAAATTGAAATGTTTAAAAGTTTGAAGACCAATTAGAATGAGAGTC
66 TGGGGATGAAATAGAAATGTTTAAAAGTTTGAAGACCAATTAGAATGAGAGTC
* * * *
813127 ATAGTTTGGGGATGAAATTGGAATGTTC-AAAGTTTGGAGAC-TAATTTCGAATAAGGATCATAG
1 ATAGTTTGAGGATAAAATT-GAACGTTCAAAAGTTTGGAGACAT-ATTTAGAATAAGGATCATAG
813190 TTTGGGGATGAAATCAG-AATGTTTAAAAGTTT
64 TTTGGGGATGAAAT-AGAAATGTTTAAAAGTTT
813222 ACATATCAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
117 1 0.01
118 75 0.89
119 8 0.10
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (118 bp):
ATAGTTTGAGGATAAAATTGAACGTTCAAAAGTTTGGAGACATATTTAGAATAAGGATCATAGTT
TGGGGATGAAATAGAAATGTTTAAAAGTTTGAAGACCAATTAGAATGAGAGTC
Found at i:815372 original size:41 final size:41
Alignment explanation
Indices: 815326--815529 Score: 315
Period size: 41 Copynumber: 5.0 Consensus size: 41
815316 ATTCGCGTTG
*
815326 CATTTCGCGTTGCGATAGTTGGAAATCGCGTTGCGA-TTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
* *
815366 CTATTTCGAGTTGCGATAGTTGAAAATTGCGTTGCGATTTTT
1 C-ATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
815408 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
*
815449 CATTTCGAGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
*
815490 CATTTCGCGTTGCGATAGTCT-ACAAT-GTCGTTGCGATTTT
1 CATTTCGCGTTGCGATAGT-TGAAAATCG-CGTTGCGATTTT
815530 CCAAATTCGT
Statistics
Matches: 152, Mismatches: 8, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
40 2 0.01
41 144 0.95
42 6 0.04
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.40
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTT
Found at i:815419 original size:20 final size:20
Alignment explanation
Indices: 815394--815505 Score: 107
Period size: 20 Copynumber: 5.5 Consensus size: 20
815384 GTTGAAAATT
815394 GCGTTGCGATTTTTCATTTC
1 GCGTTGCGATTTTTCATTTC
* ** **
815414 GCGTTGCGATAGTTGAAAATC
1 GCGTTGCGAT-TTTTCATTTC
815435 GCGTTGCGATTTTTCATTTC
1 GCGTTGCGATTTTTCATTTC
* * ** **
815455 GAGTTGCGATAGTTGAAAATC
1 GCGTTGCGAT-TTTTCATTTC
815476 GCGTTGCGATTTTTCATTTC
1 GCGTTGCGATTTTTCATTTC
815496 GCGTTGCGAT
1 GCGTTGCGAT
815506 AGTCTACAAT
Statistics
Matches: 68, Mismatches: 22, Indels: 4
0.72 0.23 0.04
Matches are distributed among these distances:
20 39 0.57
21 29 0.43
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (20 bp):
GCGTTGCGATTTTTCATTTC
Found at i:815723 original size:20 final size:20
Alignment explanation
Indices: 815698--815749 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
815688 ACTGTAGACT
*
815698 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
815718 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
815738 ATCGCAACGCGA
1 ATCGCAACGCGA
815750 TTTTCAACTA
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:0.40, C:0.25, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:815764 original size:21 final size:21
Alignment explanation
Indices: 815738--815791 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
815728 GAAATGGAAA
815738 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
*
815759 ATCGCAACGCGATTTTCAATT
1 ATCGCAACGCGATTTTCAACT
815780 ATCGCAACGCGA
1 ATCGCAACGCGA
815792 AATGCAACGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:816374 original size:2 final size:2
Alignment explanation
Indices: 816367--816455 Score: 160
Period size: 2 Copynumber: 44.0 Consensus size: 2
816357 ATTTTAAAAC
816367 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
*
816409 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA TA TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
816452 TA TA
1 TA TA
816456 ATTATATTAT
Statistics
Matches: 84, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
2 82 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Done.