Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001452.1 Hibiscus syriacus cultivar Beakdansim tig00002804_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: 102909
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:7931 original size:112 final size:112
Alignment explanation
Indices: 7788--8363 Score: 882
Period size: 112 Copynumber: 5.1 Consensus size: 112
7778 TTGTCGGTTT
* * * * *
7788 GTGTCGATACTTTATAAAAATATATTGATCCATAATAATATAACAAGTAAACAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
7853 AGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
7900 GTGTTGATACTTTATAAAAATGTATCTATCCATAACAATATAACATGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
7965 GGTCTATAAATGACAAAACAAGTAAAACGCTACTGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
8012 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAATAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
8077 GGTCTATTAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
** *
8124 GTGTCGATACTTTATAAAAATGTATCGATCTTTAATAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
8189 GGTCTATAAATGACAAAACATGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
8236 GTGTCGATATTTTATAAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAAATGACAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
** * * *
8301 CGGTCTATAAATGACAAAACAGGTAAAATGCTACCAGATATGTTGATA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
8349 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
8364 TATAAGTATC
Statistics
Matches: 425, Mismatches: 38, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
112 351 0.83
113 74 0.17
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.27
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:8552 original size:182 final size:181
Alignment explanation
Indices: 8235--8689 Score: 662
Period size: 182 Copynumber: 2.5 Consensus size: 181
8225 ATATGTTGAT
* * * * *
8235 AGTGTCGATATTTTATAAAAATGTATCGATCTATAACAATAAAACAGGTAAAAAAAATGACAAAA
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGT-AAAAATATGACAAAA
* ** * *
8300 CCGGTCTATAAATGACAAAACAGGTAAAATGCTACCAGATATGTTGATAGTGTCGATACTTTATT
65 TCGGTCTCGAAATGACAAAAC-GGTAAAATGCTACCAGATATGTTGATACTGTCGATAATTTATT
*
8365 ATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCG-CTAATAA
129 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTC-AATAA
* *
8418 AGTGTCGATACTTTATAAAAATGTATCGATCCATAATAATATAACATGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAT
* * * *
8483 CGGTCTCGAAATGAAAAAATCGGTAAAGA-GCTATCGGATATGTTGATACTGTCGATAATTTTTT
66 CGGTCTCGAAATGACAAAA-CGGTAAA-ATGCTACCAGATATGTTGATACTGTCGATAATTTATT
*
8547 ATAAGTATCGATACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
129 ATAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
*
8600 AGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAT
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAT
*
8665 CGATCTCGAAATGACAAAACCGGTA
66 CGGTCTCGAAATGACAAAA-CGGTA
8690 GTAAAAAAGT
Statistics
Matches: 246, Mismatches: 23, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
182 199 0.81
183 47 0.19
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.29
Consensus pattern (181 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAAGTAAAAATATGACAAAAT
CGGTCTCGAAATGACAAAACGGTAAAATGCTACCAGATATGTTGATACTGTCGATAATTTATTAT
AAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGTCAATAA
Found at i:10242 original size:28 final size:31
Alignment explanation
Indices: 10194--10263 Score: 76
Period size: 28 Copynumber: 2.4 Consensus size: 31
10184 AATGATTGTT
10194 TAATTATTATATTTAAAAAAA-A-TATA-AA
1 TAATTATTATATTTAAAAAAATATTATACAA
**
10222 TAATTATTA-ACTTTATCAAAATATTATACAA
1 TAATTATTATA-TTTAAAAAAATATTATACAA
*
10253 TAATCATTATA
1 TAATTATTATA
10264 ATATTATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 1 0.03
28 17 0.50
29 1 0.03
30 4 0.12
31 10 0.29
32 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (31 bp):
TAATTATTATATTTAAAAAAATATTATACAA
Found at i:10445 original size:31 final size:30
Alignment explanation
Indices: 10410--10481 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 30
10400 TATGAAAGTG
10410 TTATTAAATTAATCAAAGA-ATTATAAAATAA
1 TTATTAAATT-ATCAAA-ATATTATAAAATAA
*
10441 TTATTAAAATTATCAAAATATTATAAATTAA
1 TTATT-AAATTATCAAAATATTATAAAATAA
*
10472 TTACTAAATT
1 TTATTAAATT
10482 TGTTAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.16
31 26 0.70
32 5 0.14
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.40
Consensus pattern (30 bp):
TTATTAAATTATCAAAATATTATAAAATAA
Found at i:19782 original size:20 final size:22
Alignment explanation
Indices: 19757--19800 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
19747 CACCCGCAAC
19757 ATCCATCCACCCAT-TA-ATAT
1 ATCCATCCACCCATATATATAT
*
19777 ATCCATCCATCCATATATATAT
1 ATCCATCCACCCATATATATAT
19799 AT
1 AT
19801 ATATATATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.34
Consensus pattern (22 bp):
ATCCATCCACCCATATATATAT
Found at i:19794 original size:2 final size:2
Alignment explanation
Indices: 19789--19831 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
19779 CCATCCATCC
*
19789 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT -T AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19830 AT
1 AT
19832 TAAAAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20177 original size:17 final size:17
Alignment explanation
Indices: 20128--20177 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
20118 TTGTTCATGT
20128 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
*
20145 TTTGAG----TATCAATG
1 TTTG-GTTTCTATGAATG
20159 TTTGGTTTCTATGAATG
1 TTTGGTTTCTATGAATG
20176 TT
1 TT
20178 AGAAGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
13 1 0.04
14 11 0.42
17 13 0.50
18 1 0.04
ACGTcount: A:0.20, C:0.06, G:0.22, T:0.52
Consensus pattern (17 bp):
TTTGGTTTCTATGAATG
Found at i:20286 original size:15 final size:16
Alignment explanation
Indices: 20259--20289 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
20249 CGCTCCACCC
20259 GCGGATGATGGATGAA
1 GCGGATGATGGATGAA
20275 GCGGAT-ATGGATGAA
1 GCGGATGATGGATGAA
20290 ATTTTTTGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.32, C:0.06, G:0.42, T:0.19
Consensus pattern (16 bp):
GCGGATGATGGATGAA
Found at i:25093 original size:21 final size:20
Alignment explanation
Indices: 25008--25164 Score: 84
Period size: 21 Copynumber: 7.8 Consensus size: 20
24998 AATGACCAAT
** *
25008 AAAATCGCAACGCGA-AATA
1 AAAATCGCAACGCGATTTTC
***
25027 AAAATCGCAACGCGATCCCC
1 AAAATCGCAACGCGATTTTC
* ** *
25047 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGA-TTTTC
*
25067 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGATT-TTC
* * *
25088 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGAT-TTTC
* **
25109 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTT-C
* * *
25130 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTC
25150 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
25165 ACACATAAAT
Statistics
Matches: 104, Mismatches: 28, Indels: 11
0.73 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTC
Found at i:25193 original size:20 final size:20
Alignment explanation
Indices: 25131--25360 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
25121 CGATTTTCCA
* ** *
25131 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
25151 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
25171 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
25191 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
25211 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
25231 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
25251 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
25271 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
25291 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
25311 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
25331 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
25351 AAATCACAAC
1 AAATCGCAAC
25361 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:26080 original size:24 final size:24
Alignment explanation
Indices: 26041--26087 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
26031 AAATTTGGTC
26041 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
26065 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
26088 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:28611 original size:33 final size:34
Alignment explanation
Indices: 28560--28792 Score: 162
Period size: 33 Copynumber: 6.9 Consensus size: 34
28550 CGGAAATTAC
* *
28560 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
28593 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGC-GAAATGAA
* *
28627 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
** * * *
28660 AATTGCAATGCGAATGAAAATCGCAACGAGAGAATCG-C
1 AATCCCAA--CG-ATGAAAATCGCAATGCGA-AAT-GAA
* * * * *
28698 AATGCGAA--ATGAAAATCGCAACGAGAGAATCG-C
1 AATCCCAACGATGAAAATCGCAATGCGA-AAT-GAA
* *
28731 AATGCGAA--ATGAAAATCGCAATGCGAAATGAA
1 AATCCCAACGATGAAAATCGCAATGCGAAATGAA
* *
28763 AATCGCAACGA-GAGAATCGCAATGCGAAAT
1 AATCCCAACGATGAAAATCGCAATGCGAAAT
28793 TATAAACGCA
Statistics
Matches: 169, Mismatches: 19, Indels: 24
0.80 0.09 0.11
Matches are distributed among these distances:
31 1 0.01
32 9 0.05
33 103 0.61
34 30 0.18
35 3 0.02
36 1 0.01
37 13 0.08
38 8 0.05
39 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (34 bp):
AATCCCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:28669 original size:19 final size:19
Alignment explanation
Indices: 28574--28770 Score: 193
Period size: 19 Copynumber: 11.4 Consensus size: 19
28564 GCAACGAGAG
28574 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
28593 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
28607 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
28627 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
28641 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
28660 AATTGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
*
28678 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
28692 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
28711 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
28725 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28744 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
28763 AATCGCAA
1 AATCGCAA
28771 CGAGAGAATC
Statistics
Matches: 147, Mismatches: 10, Indels: 42
0.74 0.05 0.21
Matches are distributed among these distances:
14 42 0.29
15 3 0.02
16 9 0.06
17 4 0.03
18 17 0.12
19 59 0.40
20 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:28697 original size:14 final size:14
Alignment explanation
Indices: 28678--28732 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
28668 TGCGAATGAA
28678 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
28692 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
28711 AATCGCAACGAGAG
1 AATCGCAACGAGAG
28725 AATCGCAA
1 AATCGCAA
28733 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:28724 original size:84 final size:85
Alignment explanation
Indices: 28574--28792 Score: 379
Period size: 85 Copynumber: 2.6 Consensus size: 85
28564 GCAACGAGAG
* *
28574 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGC-GAAATGAAAATCGCAACGA
28638 GAGAATCGCAATGCGAAATGAA
64 GAGAATCGCAATGCGAAATGAA
*
28660 AATTGCAATGCG-AATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
28724 GAATCGCAATGCGAAATGAA
66 GAATCGCAATGCGAAATGAA
28744 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAT
28793 TATAAACGCA
Statistics
Matches: 127, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
84 52 0.41
85 63 0.50
86 12 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (85 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGA
GAATCGCAATGCGAAATGAA
Found at i:28911 original size:52 final size:53
Alignment explanation
Indices: 28799--28914 Score: 216
Period size: 53 Copynumber: 2.2 Consensus size: 53
28789 AAATTATAAA
*
28799 CGCATTGCAATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
28852 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
28904 CGCATTGCGAT
1 CGCATTGCGAT
28915 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT
Found at i:28922 original size:19 final size:19
Alignment explanation
Indices: 28817--28914 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
28807 AATTCTCTCG
28817 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
28837 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
28856 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
28870 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
28889 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
28908 TTGCGAT
1 TTGCGAT
28915 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:31043 original size:33 final size:33
Alignment explanation
Indices: 30997--31089 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
30987 GCGAAACCAA
*
30997 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
* *
31030 AATCGCAATGCGAAATGAAAATCGTAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
31063 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
31090 TGCGATTTTG
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:31072 original size:14 final size:14
Alignment explanation
Indices: 31016--31072 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
31006 GCGAAATGAA
*
31016 AATCGCAACGACAG
1 AATCGCAACGAAAG
31030 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
*
31047 AAAATCGTAACGAAAG
1 --AATCGCAACGAAAG
31063 AATCGCAACG
1 AATCGCAACG
31073 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 17 0.49
16 5 0.14
17 6 0.17
19 7 0.20
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:31087 original size:19 final size:19
Alignment explanation
Indices: 30960--31094 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
30950 TAGTTTACTT
* *
30960 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
30980 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
30999 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31018 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
31032 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31051 TCGTAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
31065 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
31084 TCGCAATGCGA
1 TCGCAACGCGA
31095 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:31112 original size:19 final size:19
Alignment explanation
Indices: 31090--31218 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
31080 AAAATCGCAA
31090 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
31109 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
31123 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
31142 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
31156 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
31175 TGCGATTTGGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
31194 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
31214 TGCGA
1 TGCGA
31219 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:31132 original size:33 final size:33
Alignment explanation
Indices: 31090--31181 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
31080 AAAATCGCAA
31090 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
31123 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
31156 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
31182 TGGGTTTCGC
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:31382 original size:93 final size:93
Alignment explanation
Indices: 31266--31637 Score: 691
Period size: 93 Copynumber: 4.1 Consensus size: 93
31256 ATGGATTGCA
31266 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
31330 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
31358 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
31423 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
31451 TTACTTTCAACC-AAAGACAAAAC-AAGACAAATA-T-TTTCACACTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
31512 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
31540 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
31605 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
31633 TTACT
1 TTACT
31638 AAGCAATCTA
Statistics
Matches: 272, Mismatches: 3, Indels: 9
0.96 0.01 0.03
Matches are distributed among these distances:
89 66 0.24
90 12 0.04
91 20 0.07
92 16 0.06
93 158 0.58
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:31610 original size:182 final size:186
Alignment explanation
Indices: 31266--31637 Score: 691
Period size: 182 Copynumber: 2.0 Consensus size: 186
31256 ATGGATTGCA
*
31266 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACACTGTTAAAGAATACACAGTT
31330 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
31395 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
31451 TTACTTTCAACC-AAAGACAAAAC-AAGACAAATA-T-TTTCACACTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACACTGTTAAAGAATACACAGTT
31512 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
66 TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
*
31577 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAATAAAT
131 ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
31633 TTACT
1 TTACT
31638 AAGCAATCTA
Statistics
Matches: 184, Mismatches: 2, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
182 151 0.82
183 1 0.01
184 10 0.05
185 15 0.08
186 7 0.04
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACACTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACT
ATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:33361 original size:14 final size:14
Alignment explanation
Indices: 33342--33428 Score: 52
Period size: 14 Copynumber: 5.7 Consensus size: 14
33332 TTGAAATGAA
33342 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
33356 AATCGCAACGCGA-
1 AATCGCAACGAGAG
33369 AAT-GACAATCGCAACGAG
1 AATCG-CAA-CG--A-GAG
*
33387 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
*
33404 AAATCACAACGAGAG
1 -AATCGCAACGAGAG
33419 AATCGCAACG
1 AATCGCAACG
33429 CGAAATGAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 20
0.67 0.08 0.24
Matches are distributed among these distances:
12 1 0.02
13 6 0.11
14 23 0.41
15 1 0.02
16 5 0.09
17 4 0.07
18 13 0.23
19 3 0.05
ACGTcount: A:0.44, C:0.24, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:33379 original size:33 final size:33
Alignment explanation
Indices: 33334--33445 Score: 185
Period size: 33 Copynumber: 3.5 Consensus size: 33
33324 TCTTTTGGTT
33334 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
33367 GAAATGACAATCGCAAC--GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
33398 GAAATG-AAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
33430 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
33446 TGCGATTTTG
Statistics
Matches: 72, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
30 8 0.11
31 20 0.28
32 20 0.28
33 24 0.33
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:33413 original size:18 final size:18
Alignment explanation
Indices: 33356--33450 Score: 75
Period size: 19 Copynumber: 5.7 Consensus size: 18
33346 GCAACGAGAG
33356 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
33374 CAATCGCAA--CG--A-G-
1 -AATCGCAACGCGAAATGA
33387 AATCGCAACGCGAAATGA
1 AATCGCAACGCGAAATGA
* *
33405 AATCACAA--CGAGA-G-
1 AATCGCAACGCGAAATGA
33419 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATG-A
*
33438 AATCGCAATGCGA
1 AATCGCAACGCGA
33451 TTTTGGTTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
12 8 0.13
14 10 0.17
15 2 0.03
16 9 0.15
17 4 0.07
18 7 0.12
19 20 0.33
ACGTcount: A:0.44, C:0.23, G:0.22, T:0.11
Consensus pattern (18 bp):
AATCGCAACGCGAAATGA
Found at i:33495 original size:20 final size:21
Alignment explanation
Indices: 33470--33546 Score: 104
Period size: 20 Copynumber: 3.8 Consensus size: 21
33460 CGCGTTGCGA
33470 TTCTCTCGTTGCGA-TTTCAT
1 TTCTCTCGTTGCGACTTTCAT
**
33490 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGACTTTCAT
*
33510 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACTTTCAT
*
33531 TTATCTCGTTGCGACT
1 TTCTCTCGTTGCGACT
33547 CTTCTGCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
20 31 0.65
21 17 0.35
ACGTcount: A:0.12, C:0.26, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGACTTTCAT
Found at i:33524 original size:40 final size:41
Alignment explanation
Indices: 33469--33545 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
33459 TCGCGTTGCG
*
33469 ATTCTCTCGTTGCGA-TTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
33509 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
33546 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 15 0.43
41 20 0.57
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:33665 original size:33 final size:33
Alignment explanation
Indices: 33623--33693 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
33613 AATACTAACT
* *
33623 TGAAAATCGCAACGAGAGAATAGCAATGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
33656 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
33689 TGAAA
1 TGAAA
33694 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:33925 original size:22 final size:22
Alignment explanation
Indices: 33873--33927 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
33863 TGGTTGTGAG
**
33873 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
33895 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
33917 GGATTTCTTCG
1 GGATTTCTTCG
33928 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:34099 original size:20 final size:20
Alignment explanation
Indices: 34074--34267 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
34064 CTTTAAATAT
34074 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
34094 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
34116 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
34135 TGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
34155 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
34175 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
34195 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
34215 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
34235 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
34255 CGCGTTGCGATTT
1 CGCGTTGCGATTT
34268 TGGAAAATCG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:34239 original size:60 final size:60
Alignment explanation
Indices: 34076--34247 Score: 236
Period size: 60 Copynumber: 2.9 Consensus size: 60
34066 TTAAATATCG
** **
34076 CGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATATG
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATACA
* * *** *
34137 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
*
34197 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
34248 TCATATTCGC
Statistics
Matches: 94, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 68 0.72
61 26 0.28
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATACA
Found at i:34284 original size:21 final size:21
Alignment explanation
Indices: 34254--34336 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
34244 ATTTTCATAT
*
34254 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
34275 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
34296 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
34317 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
34337 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:34327 original size:42 final size:43
Alignment explanation
Indices: 34234--34332 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
34224 ATTTATGTGT
* *
34234 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
34275 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
34317 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
34333 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:35214 original size:11 final size:10
Alignment explanation
Indices: 35193--35251 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
35183 ATTTTTTTAA
35193 AAAAATAAAT
1 AAAAATAAAT
35203 AAAAATACAAT
1 AAAAATA-AAT
*
35214 AAAAATGAATT
1 AAAAAT-AAAT
*
35225 AAAAATGAAT
1 AAAAATAAAT
* *
35235 AAAATTCAAT
1 AAAAATAAAT
35245 AAAAATA
1 AAAAATA
35252 TATTTGTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 22 0.55
11 17 0.43
12 1 0.03
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (10 bp):
AAAAATAAAT
Found at i:35217 original size:21 final size:21
Alignment explanation
Indices: 35193--35251 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
35183 ATTTTTTTAA
35193 AAAAATAAATAAAAATACAAT
1 AAAAATAAATAAAAATACAAT
* *
35214 AAAAATGAATTAAAAAT-GAAT
1 AAAAAT-AAATAAAAATACAAT
* *
35235 AAAATTCAATAAAAATA
1 AAAAATAAATAAAAATA
35252 TATTTGTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 8 0.26
21 14 0.45
22 9 0.29
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.22
Consensus pattern (21 bp):
AAAAATAAATAAAAATACAAT
Found at i:35856 original size:26 final size:27
Alignment explanation
Indices: 35815--35866 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
35805 AAGTCAATAG
35815 ATTTTTTAAAAATATATAAA-ATTTATA
1 ATTTTTTAAAAATATA-AAATATTTATA
*
35842 ATTTTTT-AAATTATAAAATATTTAT
1 ATTTTTTAAAAATATAAAATATTTAT
35867 CATCATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 3 0.13
26 13 0.57
27 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
ATTTTTTAAAAATATAAAATATTTATA
Found at i:35938 original size:10 final size:10
Alignment explanation
Indices: 35923--35947 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35913 AAAATTATTC
35923 ATATTTTAAA
1 ATATTTTAAA
35933 ATATTTTAAA
1 ATATTTTAAA
35943 ATATT
1 ATATT
35948 ATTTTACAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATATTTTAAA
Found at i:35952 original size:13 final size:12
Alignment explanation
Indices: 35924--35965 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
35914 AAATTATTCA
35924 TATTTT-AAAA-
1 TATTTTAAAAAT
35934 TATTTTAAAATAT
1 TATTTTAAAA-AT
*
35947 TATTTTACAAAT
1 TATTTTAAAAAT
35959 TATTTTA
1 TATTTTA
35966 TAACTCGACA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 6 0.21
11 3 0.11
12 10 0.36
13 9 0.32
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (12 bp):
TATTTTAAAAAT
Found at i:40751 original size:96 final size:96
Alignment explanation
Indices: 40587--40779 Score: 368
Period size: 96 Copynumber: 2.0 Consensus size: 96
40577 GTGAGTGTTT
40587 TGTAAACACCTGTAAATTTTCTCTCTTTAGTAAAAGATCTGCAACAGTCCGAAGACGTAGGCAAA
1 TGTAAACACCTGTAAATTTTCTCTCTTTAGTAAAAGATCTGCAACAGTCCGAAGACGTAGGCAAA
*
40652 ATTGGTTGAACTCCGTTATCAATTTCGGGTA
66 ATTGGTTGAACTCCGTTATCAATTCCGGGTA
*
40683 TGTAAACACCTGTAAATTTTCTCTCTTTAGTAAAAGATCTGCAGCAGTCCGAAGACGTAGGCAAA
1 TGTAAACACCTGTAAATTTTCTCTCTTTAGTAAAAGATCTGCAACAGTCCGAAGACGTAGGCAAA
40748 ATTGGTTGAACTCCGTTATCAATTCCGGGTA
66 ATTGGTTGAACTCCGTTATCAATTCCGGGTA
40779 T
1 T
40780 TATTTTTTCG
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 95 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (96 bp):
TGTAAACACCTGTAAATTTTCTCTCTTTAGTAAAAGATCTGCAACAGTCCGAAGACGTAGGCAAA
ATTGGTTGAACTCCGTTATCAATTCCGGGTA
Found at i:40952 original size:18 final size:17
Alignment explanation
Indices: 40914--40947 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
40904 ATTTATTACT
40914 ATTTACGTGAATAGTAA
1 ATTTACGTGAATAGTAA
40931 ATTT-CGTGAATAGTAA
1 ATTTACGTGAATAGTAA
40947 A
1 A
40948 AATTTTGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
ATTTACGTGAATAGTAA
Found at i:47268 original size:39 final size:39
Alignment explanation
Indices: 47224--47301 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
47214 CTAAAATCCC
47224 TCCATTGTTTATCTATTGCTTAATCTGTGTGCATGAGGT
1 TCCATTGTTTATCTATTGCTTAATCTGTGTGCATGAGGT
47263 TCCATTGTTTATCTATTGCTTAATCTGTGTGCATGAGGT
1 TCCATTGTTTATCTATTGCTTAATCTGTGTGCATGAGGT
47302 GGTTTACAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.18, C:0.15, G:0.21, T:0.46
Consensus pattern (39 bp):
TCCATTGTTTATCTATTGCTTAATCTGTGTGCATGAGGT
Found at i:50328 original size:18 final size:18
Alignment explanation
Indices: 50305--50375 Score: 97
Period size: 18 Copynumber: 3.9 Consensus size: 18
50295 CGGGATTATC
*
50305 AGTGGTCCTTCGGGATAT
1 AGTGGTCCTTCGGGACAT
* *
50323 AGTGGTCATTCGGGACAC
1 AGTGGTCCTTCGGGACAT
50341 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
50359 AGTGGTCATACGGGACA
1 AGTGGTCCTTCGGGACA
50376 AATTTCTAGG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 46 1.00
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:50344 original size:36 final size:36
Alignment explanation
Indices: 50304--50375 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
50294 GCGGGATTAT
* *
50304 CAGTGGTCCTTCGGGATATAGTGGTCATTCGGGACA
1 CAGTGGTCCTTCGGGACATAGTGGTCATACGGGACA
50340 CAGTGGTCCTTCGGGACATAGTGGTCATACGGGACA
1 CAGTGGTCCTTCGGGACATAGTGGTCATACGGGACA
50376 AATTTCTAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.25
Consensus pattern (36 bp):
CAGTGGTCCTTCGGGACATAGTGGTCATACGGGACA
Found at i:51315 original size:21 final size:21
Alignment explanation
Indices: 51281--51320 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51271 AGTCGTATAT
51281 AGCCGTTGGAGATG-TTTTGG
1 AGCCGTTGGAGATGATTTTGG
*
51301 AGCCGTTTGGGGATGATTTT
1 AGCCG-TTGGAGATGATTTT
51321 TCTACTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 8 0.47
22 4 0.24
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTGGAGATGATTTTGG
Found at i:51375 original size:21 final size:21
Alignment explanation
Indices: 51349--51390 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
51339 CCACGATAGG
*
51349 GGGTATCGATACCCCTTCATA
1 GGGTATCAATACCCCTTCATA
*
51370 GGGTATCAATACTCCTTCATA
1 GGGTATCAATACCCCTTCATA
51391 AAATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (21 bp):
GGGTATCAATACCCCTTCATA
Found at i:51595 original size:29 final size:30
Alignment explanation
Indices: 51575--51630 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
51565 AACTTTGAAT
51575 AAATTCAATT-AAGTCCAAAAACATTTCGC
1 AAATTCAATTCAAGTCCAAAAACATTTCGC
51604 AAATTCAATTCAAGTCCAAAAACATTT
1 AAATTCAATTCAAGTCCAAAAACATTT
51631 TGCCTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (30 bp):
AAATTCAATTCAAGTCCAAAAACATTTCGC
Found at i:51767 original size:21 final size:21
Alignment explanation
Indices: 51743--51782 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
51733 ATGTTTAATG
51743 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
51764 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
51783 CCAATTGGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:54201 original size:21 final size:21
Alignment explanation
Indices: 54176--54216 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
54166 CACAATAGGG
54176 GGTATCGGTACCCCTTCATAC
1 GGTATCGGTACCCCTTCATAC
*
54197 GGTATCGGTACTCCTTCATA
1 GGTATCGGTACCCCTTCATA
54217 AAATTCAAAT
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:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (21 bp):
GGTATCGGTACCCCTTCATAC
Found at i:54285 original size:18 final size:19
Alignment explanation
Indices: 54247--54297 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
54237 GTTGCAGCCA
*
54247 GGGGGTATAGATACCCCTG
1 GGGGGTATAGATACCCATG
*
54266 GGGGGTATCGATA-CCATGG
1 GGGGGTATAGATACCCAT-G
54285 GGGGGTATAGATA
1 GGGGGTATAGATA
54298 TCATCCGAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 3 0.11
19 25 0.89
ACGTcount: A:0.24, C:0.14, G:0.41, T:0.22
Consensus pattern (19 bp):
GGGGGTATAGATACCCATG
Found at i:61652 original size:29 final size:29
Alignment explanation
Indices: 61631--61687 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
61621 AAACTTTGAA
61631 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
61660 TAAATTCAATTCAAGTCCAAAAACATTT
1 TAAATTCAATTCAAGTCCAAAAACATTT
61688 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:61678 original size:30 final size:29
Alignment explanation
Indices: 61631--61689 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 29
61621 AAACTTTGAA
61631 TAAATTCAATTAAGTCCAAAAACATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
61660 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
61690 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.38
30 18 0.62
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:62278 original size:13 final size:12
Alignment explanation
Indices: 62250--62279 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
62240 GAGTTTTATC
*
62250 AAAATTAATTTT
1 AAAAATAATTTT
62262 AAAAATAATTTT
1 AAAAATAATTTT
62274 AAAAAT
1 AAAAAT
62280 TGTTTAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAAATAATTTT
Found at i:63766 original size:20 final size:20
Alignment explanation
Indices: 63704--63757 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
63694 ACTAGACCCT
63704 TGGTATCGATACCCACCAGC
1 TGGTATCGATACCCACCAGC
63724 TGGTATCGATACCCACCAGC
1 TGGTATCGATACCCACCAGC
63744 TGGTATCGATACCC
1 TGGTATCGATACCC
63758 CATGACTGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.22
Consensus pattern (20 bp):
TGGTATCGATACCCACCAGC
Found at i:66682 original size:35 final size:36
Alignment explanation
Indices: 66625--66695 Score: 90
Period size: 35 Copynumber: 2.0 Consensus size: 36
66615 ATCATCCACT
* ** *
66625 AAATATATATTTATTGACATTAAG-ATGTGAATTAC
1 AAATATATATATATACACATTAAGAATGAGAATTAC
*
66660 AAATATATATATATACATATTAAGAATGAGAATTAC
1 AAATATATATATATACACATTAAGAATGAGAATTAC
66696 TCCTTATTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 20 0.67
36 10 0.33
ACGTcount: A:0.48, C:0.06, G:0.10, T:0.37
Consensus pattern (36 bp):
AAATATATATATATACACATTAAGAATGAGAATTAC
Found at i:68937 original size:19 final size:19
Alignment explanation
Indices: 68901--68940 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
68891 ATACAATCAA
*
68901 ATTTTATTTTATTTATATT
1 ATTTTATTTTATTCATATT
68920 ATTTTATTTT-TTCCATATT
1 ATTTTATTTTATT-CATATT
68939 AT
1 AT
68941 ACTAATAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (19 bp):
ATTTTATTTTATTCATATT
Found at i:69082 original size:2 final size:2
Alignment explanation
Indices: 69071--69109 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
69061 CGTTAAGTTA
69071 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
69110 TAAAAAAAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:71351 original size:28 final size:30
Alignment explanation
Indices: 71321--71377 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
71311 GCTACGATTA
*
71321 TTTTTT-ATAATTGTTATTAGGGGTTTAAT
1 TTTTTTAATAATTATTATTAGGGGTTTAAT
*
71350 TTTTTTCAATATTTATTATTAGGGGTTT
1 TTTTTT-AATAATTATTATTAGGGGTTT
71378 GCTCTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.25
31 18 0.75
ACGTcount: A:0.23, C:0.02, G:0.16, T:0.60
Consensus pattern (30 bp):
TTTTTTAATAATTATTATTAGGGGTTTAAT
Found at i:74506 original size:2 final size:2
Alignment explanation
Indices: 74453--74496 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
74443 TATGTCCGTC
74453 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
74495 TA
1 TA
74497 ACGGATATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:82439 original size:23 final size:22
Alignment explanation
Indices: 82379--82440 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
82369 CAGCTCGTAT
* *
82379 AAATGCACCGAAGTACCACGTAG
1 AAATGCACCGAAGT-GCAAGTAG
* *
82402 AATTGCACCGTAGTGCAGAGTAG
1 AAATGCACCGAAGTGCA-AGTAG
82425 AAATGCACCGAAGTGC
1 AAATGCACCGAAGTGC
82441 TATATAAGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 2 0.06
23 30 0.94
ACGTcount: A:0.35, C:0.23, G:0.26, T:0.16
Consensus pattern (22 bp):
AAATGCACCGAAGTGCAAGTAG
Found at i:84067 original size:24 final size:20
Alignment explanation
Indices: 84010--84068 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 20
84000 TTTCCCTTGA
*
84010 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
84030 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
84053 ATGTGCATCGATGCAT
1 A-GTGCATCGATGCAT
84069 TAATTGCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 14 0.44
21 1 0.03
22 1 0.03
23 3 0.09
24 13 0.41
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:87389 original size:23 final size:23
Alignment explanation
Indices: 87363--87431 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
87353 CACCACAGCT
*
87363 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
87386 CGTAGAATTGCACTGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
87409 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
87432 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:88932 original size:20 final size:21
Alignment explanation
Indices: 88895--88943 Score: 55
Period size: 20 Copynumber: 2.3 Consensus size: 21
88885 TTGTTCGTGC
88895 TTGATATCTATATAATTATAC-A
1 TTGATA-C-ATATAATTATACAA
* *
88917 TTGATACATATTATTATCCAA
1 TTGATACATATAATTATACAA
88938 TTGATA
1 TTGATA
88944 TACTCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 10 0.42
21 8 0.33
22 6 0.25
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (21 bp):
TTGATACATATAATTATACAA
Found at i:89198 original size:21 final size:21
Alignment explanation
Indices: 89172--89226 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
89162 TTACCCTTGA
*
89172 TGCATCGGTGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
89193 TGCATCGATGCACCTTGAATG
1 TGCATCGATGCACCTTGAATG
89214 TGCATCGATGCAC
1 TGCATCGATGCAC
89227 ATAGCCCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (21 bp):
TGCATCGATGCACCTTGAATG
Found at i:92636 original size:16 final size:17
Alignment explanation
Indices: 92615--92649 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
92605 TAATTTTTAT
*
92615 TAAAAAATA-TAAATTA
1 TAAAAAATAGAAAATTA
92631 TAAAAAATAGAAAATTA
1 TAAAAAATAGAAAATTA
92648 TA
1 TA
92650 TTATATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
TAAAAAATAGAAAATTA
Found at i:94581 original size:24 final size:24
Alignment explanation
Indices: 94554--94613 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
94544 TGATAGATCG
94554 AAATCGAATTAAATATCAAATCTA
1 AAATCGAATTAAATATCAAATCTA
*
94578 AAATCAAATTAAATATCAAATCTA
1 AAATCGAATTAAATATCAAATCTA
94602 AAATCGAATTAA
1 AAATCGAATTAA
94614 TTATATTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (24 bp):
AAATCGAATTAAATATCAAATCTA
Found at i:94585 original size:12 final size:11
Alignment explanation
Indices: 94554--94613 Score: 66
Period size: 12 Copynumber: 5.1 Consensus size: 11
94544 TGATAGATCG
*
94554 AAATCGAATTA
1 AAATCAAATTA
94565 AATATCAAATCTA
1 AA-ATCAAAT-TA
94578 AAATCAAATTA
1 AAATCAAATTA
94589 AATATCAAATCTA
1 AA-ATCAAAT-TA
*
94602 AAATCGAATTA
1 AAATCAAATTA
94613 A
1 A
94614 TTATATTGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
11 9 0.21
12 26 0.60
13 8 0.19
ACGTcount: A:0.57, C:0.12, G:0.03, T:0.28
Consensus pattern (11 bp):
AAATCAAATTA
Done.