Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004277.1 Hibiscus syriacus cultivar Beakdansim tig00009375_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: 72078
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:6168 original size:33 final size:33
Alignment explanation
Indices: 6131--6196 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
6121 ACTTATTAGT
* *
6131 TTTAATTGATTTTTAAAACATTTAAAATTGATA
1 TTTAATTGATTTTTAAAAAATATAAAATTGATA
6164 TTTAATTGATTTTTAAAAAATATAAAATTGATA
1 TTTAATTGATTTTTAAAAAATATAAAATTGATA
6197 CTTTTATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (33 bp):
TTTAATTGATTTTTAAAAAATATAAAATTGATA
Found at i:12392 original size:14 final size:14
Alignment explanation
Indices: 12381--12414 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
12371 ATCAAATATA
12381 TAACAAGGAATAAT
1 TAACAAGGAATAAT
12395 TAACAAGGAATAAT
1 TAACAAGGAATAAT
12409 TAACAA
1 TAACAA
12415 CAAAATAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.12, T:0.21
Consensus pattern (14 bp):
TAACAAGGAATAAT
Found at i:22209 original size:13 final size:13
Alignment explanation
Indices: 22191--22216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22181 GAAGCTGCAC
22191 TTCTTGACTTCCA
1 TTCTTGACTTCCA
22204 TTCTTGACTTCCA
1 TTCTTGACTTCCA
22217 ACAACTGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.31, G:0.08, T:0.46
Consensus pattern (13 bp):
TTCTTGACTTCCA
Found at i:26170 original size:9 final size:10
Alignment explanation
Indices: 26161--26238 Score: 80
Period size: 9 Copynumber: 8.3 Consensus size: 10
26151 TTTACCCATT
26161 TTATTTA-T-
1 TTATTTATTA
26169 TTATTTATTA
1 TTATTTATTA
26179 TTA-TTATTA
1 TTATTTATTA
*
26188 TTA-TTATAA
1 TTATTTATTA
26197 TTATTATATATA
1 TTATT-TAT-TA
26209 TTA-TTATTA
1 TTATTTATTA
26218 TTA-TTATTA
1 TTATTTATTA
26227 TTA-TTATTA
1 TTATTTATTA
26236 TTA
1 TTA
26239 AAAAATAATT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
8 7 0.11
9 41 0.65
10 7 0.11
11 4 0.06
12 4 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (10 bp):
TTATTTATTA
Found at i:26181 original size:3 final size:3
Alignment explanation
Indices: 26173--26238 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
26163 ATTTATTTAT
*
26173 TTA TTA TTA TTA TTA TTA TTA TAA TTA TTA -TA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
26218 TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
26239 AAAAATAATT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.92
4 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:43057 original size:11 final size:11
Alignment explanation
Indices: 43041--43070 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
43031 GTATCATAAT
43041 CGATGGTCAGA
1 CGATGGTCAGA
43052 CGATGGTCAGA
1 CGATGGTCAGA
43063 CGATGGTC
1 CGATGGTC
43071 GATATCATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.20
Consensus pattern (11 bp):
CGATGGTCAGA
Found at i:46368 original size:10 final size:10
Alignment explanation
Indices: 46353--46377 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46343 TTAAAACAAC
46353 AAATAGTAAA
1 AAATAGTAAA
46363 AAATAGTAAA
1 AAATAGTAAA
46373 AAATA
1 AAATA
46378 AAATGAAATA
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:0.72, C:0.00, G:0.08, T:0.20
Consensus pattern (10 bp):
AAATAGTAAA
Found at i:48269 original size:42 final size:42
Alignment explanation
Indices: 48146--48270 Score: 137
Period size: 42 Copynumber: 3.0 Consensus size: 42
48136 TGTTAAAAAT
* * * * *
48146 ATCATGCCCGAAGGTCTTATAGATGGCCTGAAGGACTT-ATC
1 ATCATGCTCGAAAGACTTATAGATGGCCAGAAGGACTTAAGC
* * * *
48187 ATCTTGCTCGAAAGACTTATATATGACCAGAAGGATTTAAGC
1 ATCATGCTCGAAAGACTTATAGATGGCCAGAAGGACTTAAGC
*
48229 ATCATGCTCGAAAGACTTACT-GATGGCCCGAAGGACTTAAGC
1 ATCATGCTCGAAAGACTTA-TAGATGGCCAGAAGGACTTAAGC
48271 TGATTCGAAG
Statistics
Matches: 68, Mismatches: 14, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
41 30 0.44
42 37 0.54
43 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (42 bp):
ATCATGCTCGAAAGACTTATAGATGGCCAGAAGGACTTAAGC
Found at i:48351 original size:59 final size:59
Alignment explanation
Indices: 48270--48720 Score: 418
Period size: 59 Copynumber: 7.6 Consensus size: 59
48260 AGGACTTAAG
* ** * **
48270 CTGATTCGAAGTGTTATGAATTGAGCCAAA-GAAATGTTAACTACTATGGTGGGGCATCA
1 CTGATTCGAAATGTCGTGAATCGAG-CAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * ** * **
48329 CTTATTCGAAATGTCGTGAATTGAGTGAAGGAAATGTTAACCCCTTTGGTGGGGCATTG
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * * * **
48388 CTAATTCGAAATGCCGTGAATCAAGCAAAGGAAATATTAACCCCTATGGTGGGGCATTG
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * **
48447 CTGATTCTAAATATCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGTGTCA
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * * ** * * * * **
48506 TTGATTCAAAATGTTGTGAATCGAGTGAAGGGAATATTAACCCATCTGGTGGGGCATTG
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * * * *
48565 CTGATTCGAAATGTCGTGAATCGAGCAAAGGTAATGTTAGCCCCTCTAGTGGGGCTTCA
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * *** * * *
48624 CTGATTCGAAATGCCGTGAATCAAATGAAGGAAATGTTAACCCCTCTGGTGGGACGTCA
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
* * * **
48683 CTGATTTGAAATGTCATGAATCCAGTGAAGGAAATGTT
1 CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTT
48721 GAAAACACCC
Statistics
Matches: 320, Mismatches: 71, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
58 2 0.01
59 318 0.99
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (59 bp):
CTGATTCGAAATGTCGTGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCATCA
Found at i:48565 original size:177 final size:177
Alignment explanation
Indices: 48286--48717 Score: 510
Period size: 177 Copynumber: 2.4 Consensus size: 177
48276 CGAAGTGTTA
* ** *
48286 TGAATTGAGCCAAA-GAAATGTTAACTACTATGGTGGGGCATCACTT-ATTCGAAATGTCGTGAA
1 TGAATCGAG-CAAAGGAAATGTTAACCCCTATGGTGGGGCGTCA-TTGATTCGAAATGTCGTGAA
* * * *
48349 TTGAGTGAAGGAAATGTTAACCCCTTTGGTGGGGCATTGCTAATTCGAAATGCCGTGAATCAAGC
64 TCGAGTGAAGGAAATATTAACCCATCTGGTGGGGCATTGCTAATTCGAAATGCCGTGAATCAAGC
* * * *
48414 AAAGGAAATATTAACCCCTATGGTGGGGCATT-GCTGATTCTAAATATCG
129 AAAGGAAATATTAACCCCTATAGTGGGGC-TTCACTGATTCGAAATACCG
* * *
48463 TGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGTGTCATTGATTCAAAATGTTGTGAATC
1 TGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCGTCATTGATTCGAAATGTCGTGAATC
* * * *
48528 GAGTGAAGGGAATATTAACCCATCTGGTGGGGCATTGCTGATTCGAAATGTCGTGAATCGAGCAA
66 GAGTGAAGGAAATATTAACCCATCTGGTGGGGCATTGCTAATTCGAAATGCCGTGAATCAAGCAA
* * * * *
48593 AGGTAATGTTAGCCCCTCTAGTGGGGCTTCACTGATTCGAAATGCCG
131 AGGAAATATTAACCCCTATAGTGGGGCTTCACTGATTCGAAATACCG
* *** * * * * *
48640 TGAATCAAATGAAGGAAATGTTAACCCCTCTGGTGGGACGTCACTGATTTGAAATGTCATGAATC
1 TGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCGTCATTGATTCGAAATGTCGTGAATC
*
48705 CAGTGAAGGAAAT
66 GAGTGAAGGAAAT
48718 GTTGAAAACA
Statistics
Matches: 214, Mismatches: 38, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
176 8 0.04
177 206 0.96
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (177 bp):
TGAATCGAGCAAAGGAAATGTTAACCCCTATGGTGGGGCGTCATTGATTCGAAATGTCGTGAATC
GAGTGAAGGAAATATTAACCCATCTGGTGGGGCATTGCTAATTCGAAATGCCGTGAATCAAGCAA
AGGAAATATTAACCCCTATAGTGGGGCTTCACTGATTCGAAATACCG
Found at i:48798 original size:20 final size:20
Alignment explanation
Indices: 48773--48848 Score: 57
Period size: 20 Copynumber: 3.7 Consensus size: 20
48763 TTATCATTTT
48773 GCTCGAAAGACTTATAGATG
1 GCTCGAAAGACTTATAGATG
* * *
48793 GCTCGAATGATTTACATATCAT-
1 GCTCGAAAGACTT--ATA-GATG
48815 GCTCGAAAGACTTACT-GATG
1 GCTCGAAAGACTTA-TAGATG
* *
48835 GCCCGAAGGACTTA
1 GCTCGAAAGACTTA
48849 CTTATCAAGA
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
19 2 0.05
20 24 0.56
21 1 0.02
22 14 0.33
23 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (20 bp):
GCTCGAAAGACTTATAGATG
Found at i:48824 original size:42 final size:42
Alignment explanation
Indices: 48748--48855 Score: 123
Period size: 42 Copynumber: 2.6 Consensus size: 42
48738 AGGTCTTATG
* *
48748 GATGGCCTGAAGGACTTATCAT-T-TTGCTCGAAAGACTTA-T
1 GATGGCCCGAAGGACTTA-CATATCATGCTCGAAAGACTTACT
* * *
48788 AGATGGCTCGAATGATTTACATATCATGCTCGAAAGACTTACT
1 -GATGGCCCGAAGGACTTACATATCATGCTCGAAAGACTTACT
*
48831 GATGGCCCGAAGGACTTACTTATCA
1 GATGGCCCGAAGGACTTACATATCA
48856 AGAAACCCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
40 3 0.05
41 15 0.27
42 36 0.65
43 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTACATATCATGCTCGAAAGACTTACT
Found at i:48829 original size:22 final size:21
Alignment explanation
Indices: 48772--48829 Score: 57
Period size: 22 Copynumber: 2.8 Consensus size: 21
48762 CTTATCATTT
*
48772 TGCTCGAAAGACTT--ATAGA
1 TGCTCGAAAGACTTACATACA
* *
48791 TGGCTCGAATGATTTACATATCA
1 T-GCTCGAAAGACTTACATA-CA
48814 TGCTCGAAAGACTTAC
1 TGCTCGAAAGACTTAC
48830 TGATGGCCCG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 11 0.37
22 16 0.53
23 2 0.07
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (21 bp):
TGCTCGAAAGACTTACATACA
Found at i:48971 original size:52 final size:54
Alignment explanation
Indices: 48909--49019 Score: 154
Period size: 52 Copynumber: 2.1 Consensus size: 54
48899 TTTCAGTTAT
48909 CATCAAGAAACCACTAAAAATCAGGCTTAG-T-TTCTAAAAACTCATTTGAAAA
1 CATCAAGAAACCACTAAAAATCAGGCTTAGCTCTTCTAAAAACTCATTTGAAAA
* * * **
48961 CATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTTTTAAAAGTTCATTTGAAAA
1 CATCAAGAAACCACTAAAAATCAGGCTTAGC-TCTTCTAAAAACTCATTTGAAAA
49016 CATC
1 CATC
49020 CTATCATGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
52 28 0.55
54 1 0.02
55 22 0.43
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (54 bp):
CATCAAGAAACCACTAAAAATCAGGCTTAGCTCTTCTAAAAACTCATTTGAAAA
Found at i:50990 original size:11 final size:10
Alignment explanation
Indices: 50978--51036 Score: 66
Period size: 12 Copynumber: 5.5 Consensus size: 10
50968 ATCAGTTTTC
50978 TTTTTTCTTT
1 TTTTTTCTTT
50988 CTTTCTTTCTTT
1 -TTT-TTTCTTT
51000 TCTCTTTTCTTT
1 T-T-TTTTCTTT
51012 TCTTTTTC-TT
1 T-TTTTTCTTT
51022 TTTTTTCTTT
1 TTTTTTCTTT
51032 TTTTT
1 TTTTT
51037 CTATATGTGT
Statistics
Matches: 44, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.14
10 10 0.23
11 9 0.20
12 18 0.41
13 1 0.02
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:51008 original size:12 final size:12
Alignment explanation
Indices: 50973--51038 Score: 73
Period size: 11 Copynumber: 5.5 Consensus size: 12
50963 ATTTGATCAG
50973 TTTTCTTTTTTC
1 TTTTCTTTTTTC
50985 -TTTCTTTCTTTC
1 TTTTCTTT-TTTC
*
50997 TTTTCTCTTTTC
1 TTTTCTTTTTTC
51009 TTTTC-TTTTTC
1 TTTTCTTTTTTC
* *
51020 TTTTTTTTCTTTT
1 TTTTCTTT-TTTC
51033 TTTTCT
1 TTTTCT
51039 ATATGTGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
11 16 0.36
12 15 0.33
13 14 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTCTTTTTTC
Found at i:51008 original size:31 final size:32
Alignment explanation
Indices: 50973--51032 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
50963 ATTTGATCAG
50973 TTTTCTTTT-TTCTTTC-TTTCTTTCTTTTCTC
1 TTTTCTTTTCTT-TTTCTTTTCTTTCTTTTCTC
*
51004 TTTTCTTTTCTTTTTCTTTTTTTTCTTTT
1 TTTTCTTTTCTTTTTCTTTTCTTTCTTTT
51033 TTTTCTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (32 bp):
TTTTCTTTTCTTTTTCTTTTCTTTCTTTTCTC
Found at i:51010 original size:5 final size:5
Alignment explanation
Indices: 50973--51038 Score: 59
Period size: 5 Copynumber: 13.2 Consensus size: 5
50963 ATTTGATCAG
*
50973 TTTTC TTTTT TCTTTC -TTTC -TTTC TTTTCTC TTTTC TTTTC TTTTTC
1 TTTTC TTTTC T-TTTC TTTTC TTTTC -TTT-TC TTTTC TTTTC -TTTTC
51020 TTTT- TTTTC TTTT- TTTTC T
1 TTTTC TTTTC TTTTC TTTTC T
51039 ATATGTGTTA
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
4 16 0.31
5 21 0.40
6 13 0.25
7 2 0.04
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:51010 original size:16 final size:15
Alignment explanation
Indices: 50973--51033 Score: 70
Period size: 15 Copynumber: 3.9 Consensus size: 15
50963 ATTTGATCAG
*
50973 TTTTCTTTTTTCTTTC
1 TTTTCTTTCTT-TTTC
50989 -TTTCTTTCTTTTCTC
1 TTTTCTTTCTTTT-TC
51004 TTTTCTTTTCTTTTTC
1 TTTTC-TTTCTTTTTC
*
51020 TTTTTTTTCTTTTT
1 TTTTCTTTCTTTTT
51034 TTTCTATATG
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.05
15 20 0.50
16 10 0.25
17 8 0.20
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:51036 original size:24 final size:25
Alignment explanation
Indices: 50973--51038 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
50963 ATTTGATCAG
50973 TTTTCTTTTTTCTT-TCTTTCTTTCT
1 TTTTCTTTTTT-TTCTCTTTCTTTCT
*
50998 TTTCTCTTTTCTTTTCTTTTTCTTT-T
1 TTT-TCTTTT-TTTTCTCTTTCTTTCT
51024 TTTTCTTTTTTTTCT
1 TTTTCTTTTTTTTCT
51039 ATATGTGTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
24 6 0.16
25 9 0.24
26 12 0.32
27 10 0.27
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTTCTTTTTTTTCTCTTTCTTTCT
Found at i:56863 original size:16 final size:16
Alignment explanation
Indices: 56842--56873 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56832 TGAATATTTT
*
56842 TTAATTGGGTTTAAAA
1 TTAATTGAGTTTAAAA
56858 TTAATTGAGTTTAAAA
1 TTAATTGAGTTTAAAA
56874 ATATTAATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (16 bp):
TTAATTGAGTTTAAAA
Found at i:66580 original size:44 final size:44
Alignment explanation
Indices: 66500--66620 Score: 181
Period size: 44 Copynumber: 2.8 Consensus size: 44
66490 AATATATCTA
*
66500 TATCAGTGCTGAGGCA-TTTAGTATTAGTGCTAATGCACTTCTG
1 TATCAGTGCTGAGGCACTTTAGTATTAATGCTAATGCACTTCTG
* * *
66543 TATCAGTGATGAGGTACTTTAGTATTAATGCTGATGCACTTCTG
1 TATCAGTGCTGAGGCACTTTAGTATTAATGCTAATGCACTTCTG
* *
66587 TATCAGTGCTGAGGCACTTTAATATCAATGCTAA
1 TATCAGTGCTGAGGCACTTTAGTATTAATGCTAA
66621 GGCATTTTCA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 14 0.21
44 54 0.79
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (44 bp):
TATCAGTGCTGAGGCACTTTAGTATTAATGCTAATGCACTTCTG
Found at i:66612 original size:22 final size:22
Alignment explanation
Indices: 66500--66624 Score: 112
Period size: 22 Copynumber: 5.7 Consensus size: 22
66490 AATATATCTA
66500 TATCAGTGCTGAGGCA-TTTAG
1 TATCAGTGCTGAGGCACTTTAG
* * *
66521 TATTAGTGCTAATGCACTTCT-G
1 TATCAGTGCTGAGGCACTT-TAG
* *
66543 TATCAGTGATGAGGTACTTTAG
1 TATCAGTGCTGAGGCACTTTAG
* * *
66565 TATTAATGCTGATGCACTTCT-G
1 TATCAGTGCTGAGGCACTT-TAG
*
66587 TATCAGTGCTGAGGCACTTTAA
1 TATCAGTGCTGAGGCACTTTAG
* *
66609 TATCAATGCTAAGGCA
1 TATCAGTGCTGAGGCA
66625 TTTTCATTAA
Statistics
Matches: 80, Mismatches: 19, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
21 15 0.19
22 63 0.79
23 2 0.03
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.35
Consensus pattern (22 bp):
TATCAGTGCTGAGGCACTTTAG
Found at i:71529 original size:25 final size:25
Alignment explanation
Indices: 71492--71540 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
71482 AATTTATTTT
*
71492 TTCTCTAAATTTTATAAATTCGTCC
1 TTCTCTAAATTTTAGAAATTCGTCC
*
71517 TTCT-TAAATTTTTAGAAGTTCGTC
1 TTCTCTAAA-TTTTAGAAATTCGTC
71541 TCTTGACAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (25 bp):
TTCTCTAAATTTTAGAAATTCGTCC
Done.