Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006809.1 Hibiscus syriacus cultivar Beakdansim tig00017282_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: 75653
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Found at i:1142 original size:12 final size:12
Alignment explanation
Indices: 1127--1151 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1117 ACTGAGTGAC
1127 CGAGTTGAAAAA
1 CGAGTTGAAAAA
1139 CGAGTTGAAAAA
1 CGAGTTGAAAAA
1151 C
1 C
1152 CTGGTCTTCC
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:0.48, C:0.12, G:0.24, T:0.16
Consensus pattern (12 bp):
CGAGTTGAAAAA
Found at i:1422 original size:33 final size:35
Alignment explanation
Indices: 1367--1459 Score: 111
Period size: 33 Copynumber: 2.7 Consensus size: 35
1357 GGTAACCAAT
*
1367 TTTGAAAAAATAGTTTTA-AAGTTTGGTAAATGTTT-
1 TTTG-AAAAAT-GGTTTACAAGTTTGGTAAATGTTTC
1402 TTT-AAAAATGGTTTACAAGTTTGGTAAATGTTTC
1 TTTGAAAAATGGTTTACAAGTTTGGTAAATGTTTC
* *
1436 TTTGAAAAATAGTTTTCAAAGTTT
1 TTTGAAAAATGGTTTAC-AAGTTT
1460 TTGGTCGTGT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
32 5 0.10
33 23 0.45
34 3 0.06
35 14 0.27
36 6 0.12
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.45
Consensus pattern (35 bp):
TTTGAAAAATGGTTTACAAGTTTGGTAAATGTTTC
Found at i:6013 original size:35 final size:36
Alignment explanation
Indices: 5948--6068 Score: 158
Period size: 35 Copynumber: 3.4 Consensus size: 36
5938 TGGTAACCAA
5948 CTTTGAAAAAATGATTTTC-AAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
5984 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
6019 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
* *
6056 -GTCGAAAAATGAT
1 CTTTGAAAAATGAT
6069 AATGAGATAA
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
34 11 0.14
35 24 0.32
36 18 0.24
37 23 0.30
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:21250 original size:6 final size:6
Alignment explanation
Indices: 21234--21265 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
21224 TCTCGTCTCG
21234 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
21266 AATACGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:21301 original size:21 final size:21
Alignment explanation
Indices: 21277--21357 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
21267 ATACGAGAAC
21277 TTGGAATAAATCGCAACGAAT
1 TTGGAATAAATCGCAACGAAT
21298 TTGGAATAAATCGCAACGCGAACT
1 TTGGAATAAATCGCAA--CGAA-T
* *
21322 TT-GACT--ATCGCAACGAAC
1 TTGGAATAAATCGCAACGAAT
21340 TTGGAATAAATCGCAACG
1 TTGGAATAAATCGCAACG
21358 CGAACTTGGA
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
18 2 0.04
19 7 0.14
21 32 0.63
23 7 0.14
24 3 0.06
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (21 bp):
TTGGAATAAATCGCAACGAAT
Found at i:21334 original size:42 final size:42
Alignment explanation
Indices: 21286--21376 Score: 164
Period size: 42 Copynumber: 2.2 Consensus size: 42
21276 CTTGGAATAA
* *
21286 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTTGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
21328 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
21370 ATCGCAA
1 ATCGCAA
21377 TGCGAATATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT
Found at i:21373 original size:21 final size:21
Alignment explanation
Indices: 21307--21382 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
21297 TTTGGAATAA
*
21307 ATCGCAACGCGAACTTTGACT
1 ATCGCAACGCGAACTTGGACT
*
21328 ATCGCAA--CGAACTTGGAAT
1 ATCGCAACGCGAACTTGGACT
21347 AAATCGCAACGCGAACTTGGACT
1 --ATCGCAACGCGAACTTGGACT
*
21370 ATCGCAATGCGAA
1 ATCGCAACGCGAA
21383 TATGTAAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
19 10 0.21
21 26 0.55
23 11 0.23
ACGTcount: A:0.34, C:0.25, G:0.21, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:26962 original size:19 final size:20
Alignment explanation
Indices: 26928--26966 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
26918 AACCAATGAC
26928 TGAAAAATAAAAATACTTAAT
1 TGAAAAAT-AAAATACTTAAT
26949 TGAAAAAT-AAATACTTAA
1 TGAAAAATAAAATACTTAA
26967 ATTGTACTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (20 bp):
TGAAAAATAAAATACTTAAT
Found at i:27859 original size:29 final size:29
Alignment explanation
Indices: 27826--27889 Score: 128
Period size: 29 Copynumber: 2.2 Consensus size: 29
27816 TAAGTTGAAA
27826 ATTGTTGAAGTTGTTTTAATTTTAAGAAG
1 ATTGTTGAAGTTGTTTTAATTTTAAGAAG
27855 ATTGTTGAAGTTGTTTTAATTTTAAGAAG
1 ATTGTTGAAGTTGTTTTAATTTTAAGAAG
27884 ATTGTT
1 ATTGTT
27890 TTGTCGAACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (29 bp):
ATTGTTGAAGTTGTTTTAATTTTAAGAAG
Found at i:28127 original size:30 final size:30
Alignment explanation
Indices: 28064--28127 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
28054 TGTTCGTTTG
*
28064 TTGTGCTTGTTTATGTTTGTTCAGGTTCAT
1 TTGTGCTTGTTTATGTTTGTTCACGTTCAT
* *
28094 TTGTG-TTAGTTTATGTTTGTTTACGTTCGT
1 TTGTGCTT-GTTTATGTTTGTTCACGTTCAT
28124 TTGT
1 TTGT
28128 TAATATTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 2 0.07
30 28 0.93
ACGTcount: A:0.09, C:0.08, G:0.23, T:0.59
Consensus pattern (30 bp):
TTGTGCTTGTTTATGTTTGTTCACGTTCAT
Found at i:29338 original size:29 final size:29
Alignment explanation
Indices: 29283--29338 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
29273 TACTTAAAAA
***
29283 TATTATTTATCAAAATAACATTTATTTAC
1 TATTATTTATCAAAATAACACCCATTTAC
**
29312 TATTATTTATCAAAATGTCACCCATTT
1 TATTATTTATCAAAATAACACCCATTT
29339 GAATAAAACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.46
Consensus pattern (29 bp):
TATTATTTATCAAAATAACACCCATTTAC
Found at i:32415 original size:60 final size:60
Alignment explanation
Indices: 32351--32483 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
32341 ACTATATCTG
* * * ** *
32351 TCATTTTAAATTAGT-TGTT-AAATTTTTAAATATTCCAATTTCATCCTTAAATCATGAATC
1 TCATTCTAAATTAGTCT-TTCAAATTTTT-AACATTCAAATTTCATCCCAAAAACATGAATC
* *
32411 TCATTCTAAATTAGTCTTTCAACTTTTTAACATTCAAATTTCATCCCAAAAACATGAATT
1 TCATTCTAAATTAGTCTTTCAAATTTTTAACATTCAAATTTCATCCCAAAAACATGAATC
32471 TCATTCTAAATTA
1 TCATTCTAAATTA
32484 ATCCCTAAAC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
60 55 0.87
61 8 0.13
ACGTcount: A:0.36, C:0.17, G:0.04, T:0.44
Consensus pattern (60 bp):
TCATTCTAAATTAGTCTTTCAAATTTTTAACATTCAAATTTCATCCCAAAAACATGAATC
Found at i:32495 original size:60 final size:61
Alignment explanation
Indices: 32369--32497 Score: 154
Period size: 60 Copynumber: 2.1 Consensus size: 61
32359 AATTAGTTGT
* * ** * * **
32369 TAAA-TTTTTAAATATTCCAATTTCATCCTTAAATCATGAATCTCATTCTAAATTAGTCTT
1 TAAACTTTTTAAACATTCAAATTTCATCCCAAAAACATGAATCTCATTCTAAATTAATCCC
* *
32429 TCAACTTTTT-AACATTCAAATTTCATCCCAAAAACATGAATTTCATTCTAAATTAATCCC
1 TAAACTTTTTAAACATTCAAATTTCATCCCAAAAACATGAATCTCATTCTAAATTAATCCC
32489 TAAACTTTT
1 TAAACTTTT
32498 AGATTTTCGA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 52 0.91
61 5 0.09
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.42
Consensus pattern (61 bp):
TAAACTTTTTAAACATTCAAATTTCATCCCAAAAACATGAATCTCATTCTAAATTAATCCC
Found at i:33921 original size:23 final size:23
Alignment explanation
Indices: 33889--33934 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
33879 TGATTATTTT
33889 AAAT-ATTTTTAAATTTAATAATA
1 AAATAATTTTTAAATTT-ATAATA
*
33912 AAATAATTTTTATATTTATAATA
1 AAATAATTTTTAAATTTATAATA
33935 TTTTAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATAATTTTTAAATTTATAATA
Found at i:34677 original size:21 final size:21
Alignment explanation
Indices: 34560--34677 Score: 71
Period size: 21 Copynumber: 5.7 Consensus size: 21
34550 ACGCGAAATA
**
34560 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
34580 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
*
34600 AAAATCGCAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
34621 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
34642 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
*
34663 AGAATCGCAACGCGA
1 AAAATCGCAACGCGA
34678 ACACGAAAAT
Statistics
Matches: 71, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 1 0.01
20 24 0.34
21 44 0.62
22 2 0.03
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:34841 original size:20 final size:20
Alignment explanation
Indices: 34665--34913 Score: 272
Period size: 20 Copynumber: 12.4 Consensus size: 20
34655 GATTTTCCAG
* *
34665 AATCGCAACGCG-AACACGAA
1 AATCGCAACGCGTATC-CGTA
* *
34685 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
34705 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34725 AACCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
34745 AATAGCAACGCGTATCCATA
1 AATCGCAACGCGTATCCGTA
*
34765 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34785 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
34805 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
34825 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
34845 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
34865 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
34885 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
34905 AATCACAAC
1 AATCGCAAC
34914 ACTGAAATTT
Statistics
Matches: 201, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
19 1 0.00
20 198 0.99
21 2 0.01
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:35838 original size:19 final size:19
Alignment explanation
Indices: 35769--35906 Score: 134
Period size: 19 Copynumber: 7.7 Consensus size: 19
35759 GCAACGAGAG
35769 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35788 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
*
35802 AATCGCAATGTGGAAATGAA
1 AATCGCAATG-CGAAATGAA
35822 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35841 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
35855 AATCGCAATGCGGAAATAAA
1 AATCGCAATGC-GAAATGAA
*
35875 AATCGCAATTCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
35894 AATCGCATTGCGA
1 AATCGCAATGCGA
35907 TTCTCTCGTT
Statistics
Matches: 96, Mismatches: 11, Indels: 24
0.73 0.08 0.18
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 1 0.01
17 4 0.04
19 42 0.44
20 26 0.27
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:35898 original size:53 final size:53
Alignment explanation
Indices: 35769--35900 Score: 203
Period size: 53 Copynumber: 2.5 Consensus size: 53
35759 GCAACGAGAG
* * *
35769 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGTGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATAAA
*
35822 AATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATAAA
1 AATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATAAA
*
35875 AATCGCAATTCGAAATGAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
35901 TTGCGATTCT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 72 0.99
54 1 0.01
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.16
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATAAA
Found at i:35976 original size:53 final size:52
Alignment explanation
Indices: 35896--36013 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 52
35886 GAAATGAAAA
35896 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
35949 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
36001 TCCGCATTGCGAT
1 T-CGCATTGCGAT
36014 AGTCATTTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
52 19 0.30
53 45 0.70
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:36021 original size:20 final size:19
Alignment explanation
Indices: 35915--36013 Score: 136
Period size: 20 Copynumber: 5.4 Consensus size: 19
35905 GATTCTCTCG
35915 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
35935 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
35954 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
35968 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
35987 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
36007 TTGCGAT
1 TTGCGAT
36014 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 25 0.35
20 26 0.37
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:38109 original size:19 final size:19
Alignment explanation
Indices: 38067--38239 Score: 141
Period size: 19 Copynumber: 9.6 Consensus size: 19
38057 TAGTTTACTT
* *
38067 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TCAAAA
* *
38087 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATCAAAA
* *
38106 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
38125 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATCAAAA
*
38144 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
38163 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAATCAAAA
*
38177 TCGCAATGCGAAATCAAAA
1 TCGCAACGCGAAATCAAAA
* *
38196 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATCAAAA
*
38210 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATCAAAA
*
38229 TCGCAATGCGA
1 TCGCAACGCGA
38240 TTTTGCTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 2 0.02
16 4 0.03
17 4 0.03
18 2 0.02
19 84 0.67
20 12 0.10
ACGTcount: A:0.46, C:0.24, G:0.20, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATCAAAA
Found at i:38180 original size:14 final size:14
Alignment explanation
Indices: 38161--38217 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
38151 GCGAAATGAA
38161 AATCGCAACGACAG
1 AATCGCAACGACAG
*
38175 AATCGCAATGCGAAATCAA
1 AATCGCAA--CG--A-CAG
*
38194 AATCGCAACGAGAG
1 AATCGCAACGACAG
38208 AATCGCAACG
1 AATCGCAACG
38218 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.25, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGACAG
Found at i:38188 original size:33 final size:33
Alignment explanation
Indices: 38142--38234 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
38132 GCGAAACCAA
38142 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
* * *
38175 AATCGCAATGCGAAATCAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
38208 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
38235 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:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:38231 original size:52 final size:52
Alignment explanation
Indices: 38101--38239 Score: 156
Period size: 52 Copynumber: 2.7 Consensus size: 52
38091 AACGCGAAAT
* * * *
38101 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
* ** * *
38153 GA-AAT-GAAAATCGCAACGACAGAATCGCAATGCGAAATCAAAATCGCAACGA
1 GAGAATCGCAACGCGAAACGA-A-AATCGCAATGCGAAACCAAAATCGCAACGA
*
38205 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAACGAAAATCGCAATGCGA
38240 TTTTGCTTTC
Statistics
Matches: 69, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
50 8 0.12
51 4 0.06
52 44 0.64
53 4 0.06
54 9 0.13
ACGTcount: A:0.46, C:0.24, G:0.21, T:0.09
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAACGAAAATCGCAATGCGAAACCAAAATCGCAACGA
Found at i:38270 original size:14 final size:14
Alignment explanation
Indices: 38251--38309 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
38241 TTTGCTTTCG
38251 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
38265 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
38282 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
38298 CGTTGCGATTTT
1 CGTTGCGATTTT
38310 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:38277 original size:33 final size:33
Alignment explanation
Indices: 38235--38342 Score: 164
Period size: 33 Copynumber: 3.3 Consensus size: 33
38225 AAAATCGCAA
*
38235 TGCGATTTTGCTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGCTTTCGCGTTGCGATTCTGTCGT
*
38268 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGCTTTCGCGTTGCGATTCTGTCGT
* *
38301 TGCGATTTT-CATTTCGCGTTGCTATTCTCTCGT
1 TGCGATTTTGC-TTTCGCGTTGCGATTCTGTCGT
38334 TGCGATTTT
1 TGCGATTTT
38343 AAGTTTCGTG
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
33 69 1.00
ACGTcount: A:0.07, C:0.19, G:0.25, T:0.48
Consensus pattern (33 bp):
TGCGATTTTGCTTTCGCGTTGCGATTCTGTCGT
Found at i:38289 original size:19 final size:19
Alignment explanation
Indices: 38235--38293 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
38225 AAAATCGCAA
*
38235 TGCGATTTTGCTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
38254 TGCGATTTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
38268 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
38287 TGCGATT
1 TGCGATT
38294 CTGTCGTTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
14 12 0.35
15 1 0.03
16 1 0.03
17 1 0.03
19 19 0.56
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:38322 original size:19 final size:18
Alignment explanation
Indices: 38235--38322 Score: 66
Period size: 19 Copynumber: 5.2 Consensus size: 18
38225 AAAATCGCAA
38235 TGCGATTTTGCTTTCGCGT
1 TGCGATTTT-CTTTCGCGT
*
38254 TGCGA-TTT-TGT--CGT
1 TGCGATTTTCTTTCGCGT
*
38268 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-CTTTCGCGT
*
38287 TGCGA--TTCTGT--CGT
1 TGCGATTTTCTTTCGCGT
38301 TGCGATTTTCATTTCGCGT
1 TGCGATTTTC-TTTCGCGT
38320 TGC
1 TGC
38323 TATTCTCTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 20
0.68 0.06 0.25
Matches are distributed among these distances:
14 16 0.30
15 3 0.06
16 7 0.13
17 6 0.11
18 3 0.06
19 19 0.35
ACGTcount: A:0.07, C:0.19, G:0.27, T:0.47
Consensus pattern (18 bp):
TGCGATTTTCTTTCGCGT
Found at i:40302 original size:20 final size:20
Alignment explanation
Indices: 40271--40334 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
40261 TTTTGGTTGA
40271 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
40291 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
40311 AAATGAAAATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
40332 AAT
1 AAT
40335 CGCAACGCGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 20 0.54
21 17 0.46
ACGTcount: A:0.47, C:0.16, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:40323 original size:21 final size:21
Alignment explanation
Indices: 40269--40333 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
40259 TCTTTTGGTT
40269 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
40290 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
40310 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
40331 GAA
1 GAA
40334 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:40337 original size:14 final size:14
Alignment explanation
Indices: 40318--40374 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40308 GAGAAATGAA
40318 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
40332 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
40351 AATCCCAACGAGAG
1 AATCGCAACGAGAG
40365 AATCGCAACG
1 AATCGCAACG
40375 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:40350 original size:33 final size:33
Alignment explanation
Indices: 40269--40391 Score: 156
Period size: 33 Copynumber: 3.5 Consensus size: 33
40259 TCTTTTGGTT
*
40269 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
40310 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
40343 GAAATGAAAATCCCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
40376 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
40392 TGCGATTTTG
Statistics
Matches: 79, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
33 48 0.61
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.28
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:40359 original size:19 final size:19
Alignment explanation
Indices: 40269--40396 Score: 78
Period size: 19 Copynumber: 7.1 Consensus size: 19
40259 TCTTTTGGTT
*
40269 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*** *
40288 GAGAATGACTGTCGCAACGAGA
1 GA-AATGAAAATCGCAAC--GC
40310 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
40327 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40343 GAAATGAAAATCCCAA--C
1 GAAATGAAAATCGCAACGC
*
40360 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
40376 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
40395 GA
1 GA
40397 TTTTGGTTTC
Statistics
Matches: 82, Mismatches: 14, Indels: 26
0.67 0.11 0.21
Matches are distributed among these distances:
14 19 0.23
15 2 0.02
16 4 0.05
17 3 0.04
18 2 0.02
19 25 0.30
20 12 0.15
21 11 0.13
22 4 0.05
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:40427 original size:14 final size:14
Alignment explanation
Indices: 40408--40464 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40398 TTTGGTTTCG
40408 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
40422 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
40441 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
40455 CGTTGCGATT
1 CGTTGCGATT
40465 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:40440 original size:33 final size:33
Alignment explanation
Indices: 40392--40471 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
40382 AAAATCGCAA
**
40392 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
40425 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
40458 TGCGATTTTCATTT
1 TGCGATTTTCATTT
40472 TTCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.09, C:0.21, G:0.23, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:40477 original size:21 final size:21
Alignment explanation
Indices: 40452--40525 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
40442 GTTGCGATTC
40452 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
40473 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
40494 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
40515 TCTCGTTGCGA
1 TCTCGTTGCGA
40526 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:40647 original size:33 final size:33
Alignment explanation
Indices: 40605--40675 Score: 133
Period size: 33 Copynumber: 2.2 Consensus size: 33
40595 AATACTAACT
40605 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
*
40638 TGAAAATCGCAACGAGAGAATCGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
40671 TGAAA
1 TGAAA
40676 TCTAAGTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:40651 original size:19 final size:19
Alignment explanation
Indices: 40627--40675 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
40617 CGAGAGAATA
40627 GCAACGCGAAATGAAAATC
1 GCAACGCGAAATGAAAATC
*
40646 GCAA--CG--A-GAGAATC
1 GCAACGCGAAATGAAAATC
40660 GCAACGCGAAATGAAA
1 GCAACGCGAAATGAAA
40676 TCTAAGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 10
0.66 0.06 0.29
Matches are distributed among these distances:
14 10 0.43
15 1 0.04
16 2 0.09
17 2 0.09
18 1 0.04
19 7 0.30
ACGTcount: A:0.47, C:0.20, G:0.24, T:0.08
Consensus pattern (19 bp):
GCAACGCGAAATGAAAATC
Found at i:40661 original size:14 final size:14
Alignment explanation
Indices: 40609--40665 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
40599 CTAACTTGAA
40609 AATCGCAACGAGAG
1 AATCGCAACGAGAG
* *
40623 AATAGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
40642 AATCGCAACGAGAG
1 AATCGCAACGAGAG
40656 AATCGCAACG
1 AATCGCAACG
40666 CGAAATGAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 9 0.26
ACGTcount: A:0.46, C:0.21, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:41078 original size:20 final size:20
Alignment explanation
Indices: 41053--41245 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
41043 CTTTAAAAAT
41053 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41073 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
41093 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
41114 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
41134 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
41154 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
41174 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
41194 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
41214 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
41234 CGCGTTGCGATT
1 CGCGTTGCGATT
41246 CTCCAGAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:41298 original size:21 final size:20
Alignment explanation
Indices: 41050--41310 Score: 90
Period size: 20 Copynumber: 12.8 Consensus size: 20
41040 GCGCTTTAAA
*
41050 AATCGCGTTGCGATTTAC-G
1 AATCGCGTTGCGATTTTCAG
*
41069 GATACGCGTTGCGATTTT-ACG
1 AAT-CGCGTTGCGATTTTCA-G
* * *
41090 TATTGTCGTTGCGATTTAC-G
1 AATCG-CGTTGCGATTTTCAG
* * *
41110 GATACGCGTTGCGATATAC-G
1 AAT-CGCGTTGCGATTTTCAG
* * *
41130 GATACGCATTGCGATTTAC-G
1 AAT-CGCGTTGCGATTTTCAG
* *
41150 GATACGCGTTGCGATTTAC-G
1 AAT-CGCGTTGCGATTTTCAG
* * *
41170 GATACACGTTGCGATTTAC-G
1 AAT-CGCGTTGCGATTTTCAG
* **
41190 GATACGCGTTGCGATTTATGTG
1 AAT-CGCGTTGCGATTT-TCAG
* *
41212 -TTCGCGTTGCGATTTTCAT
1 AATCGCGTTGCGATTTTCAG
* *
41231 ATTCGCGTTGCGATTCTCCAG
1 AATCGCGTTGCGATT-TTCAG
** *
41252 AATCGCAATGCGAATTTGT-AC
1 AATCGCGTTGCG-ATTT-TCAG
* *
41273 TATCGCATTGCGATTTTCAAG
1 AATCGCGTTGCGATTTTC-AG
41294 AATCGCGTTGCGATTTT
1 AATCGCGTTGCGATTTT
41311 GGAAACTGAT
Statistics
Matches: 197, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
19 4 0.02
20 133 0.68
21 56 0.28
22 4 0.02
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (20 bp):
AATCGCGTTGCGATTTTCAG
Found at i:41306 original size:42 final size:43
Alignment explanation
Indices: 41213--41311 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 43
41203 ATTTATGTGT
* *
41213 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTCCAGAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAGAA
** *
41254 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTCAAGAA
*
41296 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
41312 GAAACTGATT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
41 8 0.17
42 36 0.77
43 3 0.06
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTCAAGAA
Found at i:47918 original size:11 final size:11
Alignment explanation
Indices: 47902--47927 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
47892 ACCAAACAAC
47902 AAAAAATGTCA
1 AAAAAATGTCA
47913 AAAAAATGTCA
1 AAAAAATGTCA
47924 AAAA
1 AAAA
47928 GAATAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAAATGTCA
Found at i:47944 original size:22 final size:23
Alignment explanation
Indices: 47919--47968 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
47909 GTCAAAAAAA
47919 TGTCAAAAAGA-ATAA-GAAAACG
1 TGTCAAAAAGACA-AATGAAAACG
*
47941 TGTCATAAAGACAAATGAAAACG
1 TGTCAAAAAGACAAATGAAAACG
47964 TGTCA
1 TGTCA
47969 TACAAGCATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.52, C:0.12, G:0.18, T:0.18
Consensus pattern (23 bp):
TGTCAAAAAGACAAATGAAAACG
Found at i:55911 original size:18 final size:19
Alignment explanation
Indices: 55876--55911 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
55866 CACGGAAGGT
55876 AAGATTACCAGTGGAATAA
1 AAGATTACCAGTGGAATAA
*
55895 AAGATTACTAG-GGAATA
1 AAGATTACCAGTGGAATA
55912 GGATTACTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.47, C:0.08, G:0.22, T:0.22
Consensus pattern (19 bp):
AAGATTACCAGTGGAATAA
Found at i:57862 original size:27 final size:24
Alignment explanation
Indices: 57810--57862 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
57800 GTCGGAAGAG
*
57810 GATGTTGTCAGTCGAAAGTCAGTT
1 GATGTTGTCAGTCGAAAGTCAATT
57834 GATGTTGTCAGTGCTGGAAAGTCAATT
1 GATGTTGTCAGT-C--GAAAGTCAATT
57861 GA
1 GA
57863 GAGTAGAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 12 0.48
25 1 0.04
27 12 0.48
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.32
Consensus pattern (24 bp):
GATGTTGTCAGTCGAAAGTCAATT
Found at i:68501 original size:20 final size:21
Alignment explanation
Indices: 68466--68504 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
68456 TGGCCAAAAA
*
68466 TGAAAAAGCAGTGAACCAAGT
1 TGAAAAAGCAGCGAACCAAGT
68487 TGAAAAA-CAGCGAACCAA
1 TGAAAAAGCAGCGAACCAA
68505 AGCGAGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.51, C:0.18, G:0.21, T:0.10
Consensus pattern (21 bp):
TGAAAAAGCAGCGAACCAAGT
Done.