Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005409.1 Hibiscus syriacus cultivar Beakdansim tig00012403_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: 72306
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6639 original size:13 final size:13
Alignment explanation
Indices: 6621--6647 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6611 GTGGCTGCTG
6621 GAATATTAATCAA
1 GAATATTAATCAA
6634 GAATATTAATCAA
1 GAATATTAATCAA
6647 G
1 G
6648 TACACATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (13 bp):
GAATATTAATCAA
Found at i:8531 original size:2 final size:2
Alignment explanation
Indices: 8524--8571 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
8514 AAAATAATTT
8524 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
8566 TA -A TA T
1 TA TA TA T
8572 TAATAAATTT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8607 original size:19 final size:19
Alignment explanation
Indices: 8583--8622 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
8573 AATAAATTTA
8583 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
8602 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
8621 AT
1 AT
8623 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:9337 original size:106 final size:108
Alignment explanation
Indices: 9184--9394 Score: 302
Period size: 106 Copynumber: 2.0 Consensus size: 108
9174 AATATACTCC
* *
9184 TTCACTTATTAAAGTTTTTAAGGAATCTATAACCTTATGAGACATGAATACGATT-TTTAACGTA
1 TTCACTTATTAAAGTTTTTAAGGAATCTATAACCTCAGGAGACATGAATACGATTATTT-ACGTA
*
9248 AATTAGAAGAGATG-A-ATAAATCGCAGATGATATGAACTCTCT
65 AATTAGAAGAGATGAATATAAATCGCAGATGAGATGAACTCTCT
* * * * *
9290 TTCACTTATTAAAGTTTTTAAGGAATCTATAATCTCAGGGGATATGAATGCGATTATTTACTTAA
1 TTCACTTATTAAAGTTTTTAAGGAATCTATAACCTCAGGAGACATGAATACGATTATTTACGTAA
*
9355 ATTAGAAGAGATGAATTATAAATCGCATATGAGATGAACT
66 ATTAGAAGAGATGAA-TATAAATCGCAGATGAGATGAACT
9395 TGTTATGTCA
Statistics
Matches: 92, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
106 67 0.73
107 4 0.04
109 21 0.23
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (108 bp):
TTCACTTATTAAAGTTTTTAAGGAATCTATAACCTCAGGAGACATGAATACGATTATTTACGTAA
ATTAGAAGAGATGAATATAAATCGCAGATGAGATGAACTCTCT
Found at i:11412 original size:31 final size:31
Alignment explanation
Indices: 11375--11456 Score: 146
Period size: 31 Copynumber: 2.6 Consensus size: 31
11365 TTAAAAAACA
*
11375 TAAGTTTTGGTCACTTACATTATTGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
11406 TAAGTTTTGGTCACTTACATTATCGTTTTAT
1 TAAGTTTTGGTCACTTACATTATCGTTTTAT
*
11437 TAAGTTTTAGTCACTTACAT
1 TAAGTTTTGGTCACTTACAT
11457 AGAAAATACA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.51
Consensus pattern (31 bp):
TAAGTTTTGGTCACTTACATTATCGTTTTAT
Found at i:23347 original size:27 final size:28
Alignment explanation
Indices: 23269--23340 Score: 107
Period size: 25 Copynumber: 2.7 Consensus size: 28
23259 CCGAACGTGA
*
23269 TTTTTTTTT-AAAAATCCGATCCTGGA-
1 TTTTTTTTTAAAAAATCCGATCCTGAAT
23295 -TTTTTTTTAAAAAA-CCGATCCTGAAT
1 TTTTTTTTTAAAAAATCCGATCCTGAAT
23321 TTTTTTTTTAAAAAATCCGA
1 TTTTTTTTTAAAAAATCCGA
23341 CCCGAATACC
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
25 18 0.44
26 5 0.12
27 14 0.34
28 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (28 bp):
TTTTTTTTTAAAAAATCCGATCCTGAAT
Found at i:24088 original size:21 final size:21
Alignment explanation
Indices: 24072--24182 Score: 161
Period size: 21 Copynumber: 5.3 Consensus size: 21
24062 GTGTTGCATT
*
24072 TCGCGTTGCAATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
24093 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
24113 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
24134 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
24155 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
24176 TCGCGTT
1 TCGCGTT
24183 CCATTTCGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
20 15 0.19
21 63 0.81
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:24096 original size:41 final size:41
Alignment explanation
Indices: 24063--24179 Score: 135
Period size: 41 Copynumber: 2.8 Consensus size: 41
24053 CGCAAATTCG
* *
24063 TGTTGCATTTCGCGTTGCAATAGTTGAAAATCGCGTTGCGA
1 TGTTCCATTTCGCGTTGCAATAGTTGAAAATCGCATTGCGA
* * *
24104 TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGA
1 TGTTCCATTTCGCGTTGCAATAGTTGAAAATCGCATTGCGA
** ** *
24145 TAGTTGAAAATCGCGTTGCGATAGTTGAAAATCGC
1 T-GTTCCATTTCGCGTTGCAATAGTTGAAAATCGC
24180 GTTCCATTTC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 39 0.58
42 28 0.42
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (41 bp):
TGTTCCATTTCGCGTTGCAATAGTTGAAAATCGCATTGCGA
Found at i:24206 original size:20 final size:20
Alignment explanation
Indices: 24181--24219 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
24171 GAAAATCGCG
24181 TTCCATTTCGCGTTGCGATT
1 TTCCATTTCGCGTTGCGATT
24201 TTCCATTTCGCGTTGCGAT
1 TTCCATTTCGCGTTGCGAT
24220 AGTCCACAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.21, T:0.44
Consensus pattern (20 bp):
TTCCATTTCGCGTTGCGATT
Found at i:24225 original size:20 final size:20
Alignment explanation
Indices: 24182--24225 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
24172 AAAATCGCGT
**
24182 TCCATTTCGCGTTGCGATTT
1 TCCATTTCGCGTTGCGATAG
24202 TCCATTTCGCGTTGCGATAG
1 TCCATTTCGCGTTGCGATAG
24222 TCCA
1 TCCA
24226 CAGTTGTCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (20 bp):
TCCATTTCGCGTTGCGATAG
Found at i:24247 original size:22 final size:22
Alignment explanation
Indices: 24187--24247 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
24177 CGCGTTCCAT
*
24187 TTCGCGTTGCGATTTT-C-CAT
1 TTCGCGTTGCGATTTTCCACAG
**
24207 TTCGCGTTGCGATAGTCCACAG
1 TTCGCGTTGCGATTTTCCACAG
24229 TT-GTCGTTGCGATTTTCCA
1 TTCG-CGTTGCGATTTTCCA
24248 AATTTGTTGC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 14 0.42
21 2 0.06
22 17 0.52
ACGTcount: A:0.13, C:0.25, G:0.23, T:0.39
Consensus pattern (22 bp):
TTCGCGTTGCGATTTTCCACAG
Found at i:24254 original size:22 final size:21
Alignment explanation
Indices: 24191--24254 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
24181 TTCCATTTCG
24191 CGTTGCGATTTTCC-ATTTCG-
1 CGTTGCGATTTTCCAATTT-GT
** *
24211 CGTTGCGATAGTCCACAGTTGT
1 CGTTGCGATTTTCCA-ATTTGT
24233 CGTTGCGATTTTCCAAATTTGT
1 CGTTGCGATTTTCC-AATTTGT
24255 TGCGATAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
20 12 0.35
21 1 0.03
22 20 0.59
23 1 0.03
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (21 bp):
CGTTGCGATTTTCCAATTTGT
Found at i:25035 original size:19 final size:19
Alignment explanation
Indices: 25011--25076 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
25001 TTAACTATCG
25011 CAACGAATTTGGAAAATCA
1 CAACGAATTTGGAAAATCA
* * **
25030 CAACGACAACTATAGACTATCA
1 CAACG--AA-TTTGGAAAATCA
*
25052 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCA
25071 CAACGA
1 CAACGA
25077 CAACTGTAGA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 18 0.51
20 2 0.06
21 2 0.06
22 13 0.37
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.18
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCA
Found at i:25050 original size:41 final size:41
Alignment explanation
Indices: 25004--25097 Score: 161
Period size: 41 Copynumber: 2.3 Consensus size: 41
24994 TTTTTTTTTA
25004 ACTATCGCAACGAATTTGGAAAATCACAACGACAACTATAG
1 ACTATCGCAACGAATTTGGAAAATCACAACGACAACTATAG
* * *
25045 ACTATCACAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCACAACGACAACTATAG
25086 ACTATCGCAACG
1 ACTATCGCAACG
25098 CGAAATAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCACAACGACAACTATAG
Found at i:25112 original size:20 final size:19
Alignment explanation
Indices: 25089--25161 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 19
25079 ACTGTAGACT
25089 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAAT-GAAA
** * *
25109 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAA-A
25130 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATG-AAA
*
25150 ATCGCAATGCGA
1 ATCGCAACGCGA
25162 TTTTCAACTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:25131 original size:41 final size:41
Alignment explanation
Indices: 25086--25186 Score: 177
Period size: 41 Copynumber: 2.5 Consensus size: 41
25076 ACAACTGTAG
25086 ACTATCGCAACGCGAAAT-AGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGA-AAAATCGCAACGCGATTTTCA
*
25127 ACTATCGCAACGCGAAATGAAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
25168 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
25187 GAACACGAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
41 57 0.98
42 1 0.02
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
Found at i:25135 original size:21 final size:21
Alignment explanation
Indices: 25109--25182 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
25099 GAAATAGAAA
25109 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** * **
25130 ATCGCAACGCGA-AATGAAAA
1 ATCGCAACGCGATTTTCAACT
*
25150 ATCGCAATGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
25171 ATCGCAACGCGA
1 ATCGCAACGCGA
25183 AATGGAACAC
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 14 0.35
21 26 0.65
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.22
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:26335 original size:23 final size:22
Alignment explanation
Indices: 26309--26358 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
26299 AATTTTTGAG
*
26309 AAAATTGATTCAGTTTTTTCAAT
1 AAAATTGATTCAATTTTTT-AAT
26332 AAAATTGATTCAATTTTTTAAT
1 AAAATTGATTCAATTTTTTAAT
26354 AAAAT
1 AAAAT
26359 ATTAGTGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (22 bp):
AAAATTGATTCAATTTTTTAAT
Found at i:26348 original size:22 final size:23
Alignment explanation
Indices: 26309--26358 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
26299 AATTTTTGAG
*
26309 AAAATTGATTCAGTTTTTTCAAT
1 AAAATTGATTCAGATTTTTCAAT
*
26332 AAAATTGATTCA-ATTTTTTAAT
1 AAAATTGATTCAGATTTTTCAAT
26354 AAAAT
1 AAAAT
26359 ATTAGTGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (23 bp):
AAAATTGATTCAGATTTTTCAAT
Found at i:29091 original size:24 final size:24
Alignment explanation
Indices: 29064--29148 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
29054 ATGATAAATA
29064 AACACAAATAAAAGAACATAAACG
1 AACACAAATAAAAGAACATAAACG
* ** * **
29088 AACAGATGTAAACGAACGCAAACG
1 AACACAAATAAAAGAACATAAACG
*
29112 AACAC-AATAAATGAACATAAACG
1 AACACAAATAAAAGAACATAAACG
*
29135 AACATAAATGAAAA
1 AACACAAAT-AAAA
29149 TAGATTTTTT
Statistics
Matches: 45, Mismatches: 14, Indels: 3
0.73 0.23 0.05
Matches are distributed among these distances:
23 17 0.38
24 25 0.56
25 3 0.07
ACGTcount: A:0.61, C:0.16, G:0.12, T:0.11
Consensus pattern (24 bp):
AACACAAATAAAAGAACATAAACG
Found at i:29264 original size:21 final size:23
Alignment explanation
Indices: 29239--29284 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
29229 TAATTGAATT
*
29239 TTAAAATTTA-TGGG-TATCATA
1 TTAAAATTTACTGGGCTATAATA
29260 TTAAAATTTACTGGGCTATAATA
1 TTAAAATTTACTGGGCTATAATA
29283 TT
1 TT
29285 TTAAATGGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.45
22 4 0.18
23 8 0.36
ACGTcount: A:0.37, C:0.07, G:0.13, T:0.43
Consensus pattern (23 bp):
TTAAAATTTACTGGGCTATAATA
Found at i:29332 original size:14 final size:14
Alignment explanation
Indices: 29312--29345 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29302 GATTGAGCTA
*
29312 AACATAAATGAACG
1 AACATAAACGAACG
*
29326 CACATAAACGAACG
1 AACATAAACGAACG
29340 AACATA
1 AACATA
29346 TTACCGAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.21, G:0.12, T:0.12
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:30954 original size:6 final size:6
Alignment explanation
Indices: 30943--30973 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
30933 CCACAGTAGT
30943 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG C
1 CTCAGG CTCAGG CTCAGG CTCAGG CTCAGG C
30974 AATGGCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.16
Consensus pattern (6 bp):
CTCAGG
Found at i:38042 original size:18 final size:19
Alignment explanation
Indices: 38014--38050 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
38004 AATTTTTTTC
38014 ATTTAATATTATATAATAT
1 ATTTAATATTATATAATAT
38033 ATTT-ATATTATATAATAT
1 ATTTAATATTATATAATAT
38051 TGTACAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
ATTTAATATTATATAATAT
Found at i:39044 original size:3 final size:3
Alignment explanation
Indices: 39038--39101 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
39028 ATTGACTTCT
* * *
39038 TTA TTA TTA TTA TT- TTA TTA TTCA -TA TTC TT- TTC TGTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA T-TA TTA TTA
*
39082 TTA TTA TTA TTA TTA CTA TT
1 TTA TTA TTA TTA TTA TTA TT
39102 CATTTTACTT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:39446 original size:13 final size:13
Alignment explanation
Indices: 39416--39456 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
39406 TCTGGTATTA
*
39416 TTTATTTA-TTTG
1 TTTATTTATTTTC
39428 TTTATTTATTTTC
1 TTTATTTATTTTC
39441 TTTATTTCATTTTC
1 TTTATTT-ATTTTC
39455 TT
1 TT
39457 CATTCTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 8 0.31
13 10 0.38
14 8 0.31
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTC
Found at i:42968 original size:76 final size:77
Alignment explanation
Indices: 42818--43011 Score: 277
Period size: 76 Copynumber: 2.5 Consensus size: 77
42808 AGATTGTTCA
** *
42818 GAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGGTTTTGGCCCCGAGATT
1 GAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAAT
*
42882 TCTAGAATGCTCG
65 TCCAGAATGCTCG
*
42895 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCCGAGAATT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATT
*
42959 CCAGTATGCTCG
66 CCAGAATGCTCG
* * *
42971 GAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
43012 TTGTACAACG
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 19 0.18
76 61 0.57
77 27 0.25
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (77 bp):
GAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATT
CCAGAATGCTCG
Found at i:51390 original size:76 final size:77
Alignment explanation
Indices: 51248--51440 Score: 284
Period size: 76 Copynumber: 2.5 Consensus size: 77
51238 GATTGCTCAA
** *
51248 AGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGGTTTTGGCCCCGAGATTT
1 AGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATT
51312 CCAGAATGCTCGG
65 CCAGAATGCTCGG
*
51325 AGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTT-GCTCCGAGAATTC
1 AGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTC
*
51389 CAGTATGCTCGG
66 CAGAATGCTCGG
* * *
51401 AGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCT
51441 TTGTACAACG
Statistics
Matches: 107, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
75 19 0.18
76 62 0.58
77 26 0.24
ACGTcount: A:0.23, C:0.34, G:0.24, T:0.19
Consensus pattern (77 bp):
AGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTTTTGGCCCCGAGAATTC
CAGAATGCTCGG
Found at i:59450 original size:9 final size:8
Alignment explanation
Indices: 59435--59486 Score: 63
Period size: 9 Copynumber: 6.5 Consensus size: 8
59425 TAAATTGAAA
59435 AAAAAAAG
1 AAAAAAAG
59443 AGAAAAAAG
1 A-AAAAAAG
59452 AGAAAAAAG
1 A-AAAAAAG
*
59461 AACAAAAG
1 AAAAAAAG
59469 -AAAAAAG
1 AAAAAAAG
59476 -AAAAAAG
1 AAAAAAAG
59483 AAAA
1 AAAA
59487 GAAAATAAGG
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
7 13 0.32
8 10 0.25
9 17 0.43
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:59456 original size:22 final size:22
Alignment explanation
Indices: 59431--59488 Score: 73
Period size: 24 Copynumber: 2.6 Consensus size: 22
59421 GCCTTAAATT
59431 GAAAAAAAAAAGAGAAAAAAGA
1 GAAAAAAAAAAGAGAAAAAAGA
*
59453 GAAAAAAGAACAAAAGAAAAAAGA
1 GAAAAAA-AA-AAGAGAAAAAAGA
*
59477 -AAAAAGAAAAGA
1 GAAAAAAAAAAGA
59489 AAATAAGGTG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 3 0.10
22 9 0.29
23 7 0.23
24 12 0.39
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
GAAAAAAAAAAGAGAAAAAAGA
Found at i:59457 original size:7 final size:7
Alignment explanation
Indices: 59431--59486 Score: 69
Period size: 7 Copynumber: 7.7 Consensus size: 7
59421 GCCTTAAATT
59431 GAAAAAA
1 GAAAAAA
*
59438 -AAAAGA
1 GAAAAAA
59444 GAAAAAAGA
1 G-AAAAA-A
59453 GAAAAAA
1 GAAAAAA
59460 GAACAAAA
1 GAA-AAAA
59468 GAAAAAA
1 GAAAAAA
59475 GAAAAAA
1 GAAAAAA
59482 GAAAA
1 GAAAA
59487 GAAAATAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
6 5 0.12
7 20 0.47
8 16 0.37
9 2 0.05
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:60800 original size:111 final size:111
Alignment explanation
Indices: 60605--60809 Score: 338
Period size: 111 Copynumber: 1.8 Consensus size: 111
60595 GCTTCCTAGT
*
60605 TTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGATCAACTTCA
1 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGATCAACTTCA
60670 CAGCGAAAGGGCAAATGACTGTCAACAAACAACTTCTTCAGTTTCA
66 CAGCGAAAGGGCAAATGACTGTCAACAAACAACTTCTTCAGTTTCA
* * *
60716 TTTAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCA
1 TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGATCAACTTCA
* ** *
60781 CAGCGAAGGGGTGACTGACTGTCAACAAA
66 CAGCGAAAGGGCAAATGACTGTCAACAAA
60810 TAATTTCCCA
Statistics
Matches: 86, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 86 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (111 bp):
TTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAGACAACACAAGATCAACTTCA
CAGCGAAAGGGCAAATGACTGTCAACAAACAACTTCTTCAGTTTCA
Found at i:63118 original size:13 final size:13
Alignment explanation
Indices: 63088--63128 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
63078 TCTGGTATTA
*
63088 TTTATTTA-TTTG
1 TTTATTTATTTTC
63100 TTTATTTATTTTC
1 TTTATTTATTTTC
63113 TTTATTTCATTTTC
1 TTTATTT-ATTTTC
63127 TT
1 TT
63129 CATTCTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 8 0.31
13 10 0.38
14 8 0.31
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTATTTATTTTC
Found at i:65338 original size:17 final size:18
Alignment explanation
Indices: 65288--65339 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
65278 AAAAAAATGT
65288 AAATATATATTATGTTATA
1 AAATATATATTAT-TTATA
* **
65307 ATAATTTGGATTATTTA-A
1 A-AATATATATTATTTATA
65325 AAATATATATTATTT
1 AAATATATATTATTT
65340 TTTTATGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 11 0.42
18 2 0.08
19 4 0.15
20 9 0.35
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
AAATATATATTATTTATA
Found at i:66044 original size:29 final size:28
Alignment explanation
Indices: 65953--66044 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
65943 TTATGATCCT
65953 TATTTTAAATTCG-TCCTTAAACTTTTATA
1 TATTTTAAATT-GATCC-TAAACTTTTATA
* * *
65982 TATTTT-ACTTTATCCTAACCTTTTACTA
1 TATTTTAAATTGATCCTAAACTTTTA-TA
*
66010 TCATTTTAAATTGATCCTCAAACTTTTAAA
1 T-ATTTTAAATTGATCCT-AAACTTTTATA
66040 TATTT
1 TATTT
66045 CAATTATATC
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
27 9 0.18
28 9 0.18
29 15 0.29
30 10 0.20
31 8 0.16
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.51
Consensus pattern (28 bp):
TATTTTAAATTGATCCTAAACTTTTATA
Found at i:71158 original size:18 final size:15
Alignment explanation
Indices: 71123--71162 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
71113 TGATTACCTT
71123 TTCTTCTTCCATCTC
1 TTCTTCTTCCATCTC
71138 TTCTTCTTCCAT-TC
1 TTCTTCTTCCATCTC
*
71152 TCACTTCTTCC
1 T-TCTTCTTCC
71163 TTCACGAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.13
15 20 0.87
ACGTcount: A:0.07, C:0.40, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCTTCTTCCATCTC
Done.