Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000504.1 Hibiscus syriacus cultivar Beakdansim tig00000961_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: 64661
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:389 original size:8 final size:8
Alignment explanation
Indices: 359--421 Score: 58
Period size: 8 Copynumber: 7.6 Consensus size: 8
349 CTACAAAAAC
359 ATTTTATT
1 ATTTTATT
367 ATATATATATAT
1 AT-T-T-TAT-T
379 ATTTTATT
1 ATTTTATT
387 A--TTATT
1 ATTTTATT
* *
393 ATATTAAT
1 ATTTTATT
401 ATTTTATT
1 ATTTTATT
409 ATTTTATT
1 ATTTTATT
417 ATTTT
1 ATTTT
422 TGTAGGCCCT
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
6 6 0.13
8 27 0.59
9 4 0.09
10 2 0.04
11 4 0.09
12 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
ATTTTATT
Found at i:419 original size:11 final size:11
Alignment explanation
Indices: 378--411 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
368 TATATATATA
378 TATTTTATTAT
1 TATTTTATTAT
* *
389 TATTATATTAA
1 TATTTTATTAT
400 TATTTTATTAT
1 TATTTTATTAT
411 T
1 T
412 TTATTATTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:419 original size:22 final size:22
Alignment explanation
Indices: 359--415 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
349 CTACAAAAAC
359 ATTTTATTA-TA-TATA-TATAT
1 ATTTTATTATTATTATATTA-AT
379 ATTTTATTATTATTATATTAAT
1 ATTTTATTATTATTATATTAAT
401 ATTTTATTATT-TTAT
1 ATTTTATTATTATTAT
416 TATTTTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
20 9 0.26
21 6 0.18
22 17 0.50
23 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
ATTTTATTATTATTATATTAAT
Found at i:1074 original size:14 final size:14
Alignment explanation
Indices: 1041--1083 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1031 TTTTTGCACC
*
1041 TTATTTTATTTTACT
1 TTATTTTATTATA-T
1056 TT-TTTTA-TATAT
1 TTATTTTATTATAT
1068 TTATTTTATTATAT
1 TTATTTTATTATAT
1082 TT
1 TT
1084 TTAGTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 3 0.12
13 8 0.32
14 12 0.48
15 2 0.08
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATTTTATTATAT
Found at i:1079 original size:16 final size:16
Alignment explanation
Indices: 1041--1084 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1031 TTTTTGCACC
*
1041 TTATTTTATTTTACTT
1 TTATTATATTTTACTT
*
1057 TTTTTATATATTTA-TT
1 TTATTATAT-TTTACTT
1073 TTATTATATTTT
1 TTATTATATTTT
1085 TAGTATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 3 0.12
16 17 0.71
17 4 0.17
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTATATTTTACTT
Found at i:1125 original size:10 final size:10
Alignment explanation
Indices: 1110--1179 Score: 61
Period size: 12 Copynumber: 6.5 Consensus size: 10
1100 GGGTTATTTA
*
1110 TTATTTTGTT
1 TTATTTTATT
1120 TTA-TTTATT
1 TTATTTTATT
1129 TTATTTTATTT
1 TTATTTTA-TT
1140 TTACTTTTACTT
1 TTA-TTTTA-TT
1152 TTACTTTTACTT
1 TTA-TTTTA-TT
*
1164 TTATTATTTTT
1 TTATT-TTATT
1175 TTATT
1 TTATT
1180 GATTTATTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
9 8 0.15
10 7 0.13
11 14 0.26
12 24 0.45
ACGTcount: A:0.17, C:0.06, G:0.01, T:0.76
Consensus pattern (10 bp):
TTATTTTATT
Found at i:1129 original size:14 final size:14
Alignment explanation
Indices: 1106--1139 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1096 TTCTGGGTTA
*
1106 TTTA-TTATTTTGT
1 TTTATTTATTTTAT
1119 TTTATTTATTTTAT
1 TTTATTTATTTTAT
1133 TTTATTT
1 TTTATTT
1140 TTACTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.18, C:0.00, G:0.03, T:0.79
Consensus pattern (14 bp):
TTTATTTATTTTAT
Found at i:1147 original size:6 final size:6
Alignment explanation
Indices: 1123--1166 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
1113 TTTTGTTTTA
*
1123 TTTA-T TTTA-T TTTATT TTTACT TTTACT TTTACT TTTACT TTTA
1 TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT TTTACT TTTA
1167 TTATTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
5 9 0.24
6 28 0.76
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (6 bp):
TTTACT
Found at i:1147 original size:17 final size:16
Alignment explanation
Indices: 1041--1179 Score: 72
Period size: 18 Copynumber: 8.3 Consensus size: 16
1031 TTTTTGCACC
1041 TTATTTTATTTTACTTT
1 TTATTTTATTTTA-TTT
*
1058 TT-TTATATATTTA-TT
1 TTATTTTAT-TTTATTT
* *
1073 TTATTATATTTTTAGTAT
1 TTATTTTA-TTTTA-TTT
* * *
1091 TAATTTTCTGGGTTATTT
1 TTATTTTAT--TTTATTT
*
1109 ATTATTTTGTTTTA--T
1 -TTATTTTATTTTATTT
1124 TTATTTTATTTTATTT
1 TTATTTTATTTTATTT
*
1140 TTACTTTTACTTTTACTT
1 TTA-TTTTA-TTTTATTT
1158 TTACTTTTATTATT-TTT
1 TTA-TTTTATT-TTATTT
1175 TTATT
1 TTATT
1180 GATTTATTGT
Statistics
Matches: 96, Mismatches: 13, Indels: 27
0.71 0.10 0.20
Matches are distributed among these distances:
14 12 0.12
15 5 0.05
16 20 0.21
17 23 0.24
18 26 0.27
19 10 0.10
ACGTcount: A:0.20, C:0.04, G:0.04, T:0.72
Consensus pattern (16 bp):
TTATTTTATTTTATTT
Found at i:1184 original size:12 final size:11
Alignment explanation
Indices: 1041--1195 Score: 50
Period size: 12 Copynumber: 13.4 Consensus size: 11
1031 TTTTTGCACC
*
1041 TTATTTTATT-
1 TTATTTTTTTA
1051 TTACTTTTTTTA
1 TTA-TTTTTTTA
1063 TATATTTATTTTA
1 T-TATTT-TTTTA
*
1076 TTATATTTTTA
1 TTATTTTTTTA
* * *
1087 GTATTAATTTTC
1 TTATT-TTTTTA
*** *
1099 TGGGTTATTTA
1 TTATTTTTTTA
*
1110 TTATTTTGTT-
1 TTATTTTTTTA
1120 TTATTTATTTTA
1 TTATTT-TTTTA
1132 TT-TTATTTTTA
1 TTATT-TTTTTA
*
1143 CTT-TTACTTTTA
1 -TTATT-TTTTTA
*
1155 CTT-TTACTTTTA
1 -TTATT-TTTTTA
1167 TTATTTTTTTA
1 TTATTTTTTTA
1178 TTGATTTATTGTTA
1 TT-ATTT-TT-TTA
1192 TTAT
1 TTAT
1196 CATTTTTTTC
Statistics
Matches: 111, Mismatches: 21, Indels: 23
0.72 0.14 0.15
Matches are distributed among these distances:
10 9 0.08
11 41 0.37
12 44 0.40
13 12 0.11
14 5 0.05
ACGTcount: A:0.21, C:0.04, G:0.05, T:0.71
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:1302 original size:13 final size:13
Alignment explanation
Indices: 1284--1314 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1274 CGAATAGGAT
1284 ATTTTAAATTTTA
1 ATTTTAAATTTTA
*
1297 ATTTTAATTTTTA
1 ATTTTAAATTTTA
1310 ATTTT
1 ATTTT
1315 CGCAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
ATTTTAAATTTTA
Found at i:18133 original size:42 final size:43
Alignment explanation
Indices: 18064--18412 Score: 335
Period size: 43 Copynumber: 8.1 Consensus size: 43
18054 TGTAAAATAA
* * * *
18064 AAACGCCGTAAAAAGTCAAGATTTATAGCGGCGTTTTT-TAAAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAAC
* ** * *
18107 AAACGCCGCAAAAGGTTAGATCTATAGCAACATTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAAC
** * *
18150 AAATACCGCAAAAGGTCAAGATCTATAACGGCGTTTTTGGATAC
1 AAACGCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAAAC
* *
18194 AAACGCCGCAAAAGGTCAGATCTATAACGACGTTTTTGG-AAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAAC
* * * * * *
18236 AAACGCCGTAAAAAGTCAGATTTATAGAGGTGTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAAC
* * *
18279 AAACGCCGCAAAAGGTCATATCTATAGCAGCATTTTTGG-AAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAAC
* * * * *
18321 AAACGCCACAAAAGGTTAGATCTATAGCGGCATTTTTGGATAT
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAAC
* * * * * *
18364 AAACGCTGTAAAATGTCAGATCTATAACGGCATTTTTTGGATAC
1 AAACGCCGCAAAAGGTCAGATCTATAGCGGC-GTTTTTGGAAAC
18408 AAACG
1 AAACG
18413 TCGCTAATTA
Statistics
Matches: 250, Mismatches: 51, Indels: 9
0.81 0.16 0.03
Matches are distributed among these distances:
42 87 0.35
43 111 0.44
44 52 0.21
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (43 bp):
AAACGCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAAAC
Found at i:18296 original size:85 final size:87
Alignment explanation
Indices: 18064--18412 Score: 379
Period size: 85 Copynumber: 4.1 Consensus size: 87
18054 TGTAAAATAA
* * * * * *
18064 AAACGCCGTAAAAAGTCAAGATTTATAGCGGCGTTTTT-TAAACAAACGCCGCAAAAGGTTAGAT
1 AAACGCCGCAAAAAGTCAAGATCTATAGAGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGAT
* *
18128 CTATAGCAACATTTTTGGATAC
66 CTATAACGACATTTTTGGATAC
** *
18150 AAATACCGCAAAAGGTCAAGATCTATA-ACGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGA
1 AAACGCCGCAAAAAGTCAAGATCTATAGA-GGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGA
*
18214 TCTATAACGACGTTTTTGGA-AC
65 TCTATAACGACATTTTTGGATAC
* * * *
18236 AAACGCCGTAAAAAGTC-AGATTTATAGAGGTGTTTTTGGATACAAACGCCGCAAAAGGTCATAT
1 AAACGCCGCAAAAAGTCAAGATCTATAGAGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGAT
*
18300 CTATAGC-AGCATTTTTGGA-AC
66 CTATAACGA-CATTTTTGGATAC
* * * * * * * * *
18321 AAACGCCACAAAAGGT-TAGATCTATAGCGGCATTTTTGGATATAAACGCTGTAAAATGTCAGAT
1 AAACGCCGCAAAAAGTCAAGATCTATAGAGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGAT
*
18385 CTATAACGGCATTTTTTGGATAC
66 CTATAACGACA-TTTTTGGATAC
18408 AAACG
1 AAACG
18413 TCGCTAATTA
Statistics
Matches: 220, Mismatches: 35, Indels: 15
0.81 0.13 0.06
Matches are distributed among these distances:
84 1 0.00
85 118 0.54
86 55 0.25
87 46 0.21
ACGTcount: A:0.36, C:0.17, G:0.20, T:0.26
Consensus pattern (87 bp):
AAACGCCGCAAAAAGTCAAGATCTATAGAGGCGTTTTTGGATACAAACGCCGCAAAAGGTCAGAT
CTATAACGACATTTTTGGATAC
Found at i:25106 original size:42 final size:44
Alignment explanation
Indices: 25059--25153 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
25049 TTGTGCTTCA
* *
25059 TGCATCGATACACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
* *
25101 TGCATCGATGCACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
25145 TGCATCGAT
1 TGCATCGAT
25154 GCACAAGGCC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 13 0.28
43 13 0.28
44 20 0.43
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.24
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:25147 original size:23 final size:21
Alignment explanation
Indices: 25078--25157 Score: 106
Period size: 21 Copynumber: 3.7 Consensus size: 21
25068 ACACCTAACA
25078 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCA-CCTTGAAT
* *
25100 GTGCATCGATGCACCATGAAG
1 GTGCATCGATGCACCTTGAAT
*
25121 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCA--CCTTGAAT
25144 GTGCATCGATGCAC
1 GTGCATCGATGCAC
25158 AAGGCCATGC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
21 19 0.38
22 13 0.26
23 18 0.36
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (21 bp):
GTGCATCGATGCACCTTGAAT
Found at i:25174 original size:43 final size:42
Alignment explanation
Indices: 25077--25176 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 42
25067 TACACCTAAC
* * *
25077 AGTGCATCGATGCATCCTTGAATGTGCATCGATGCACCATGA
1 AGTGCATCGATGCAGCCTTGAATGTGCATCGATGCACAAGGA
* *
25119 AGGTGCACCGATGCACGCCTTGAATGTGCATCGATGCACAAGGCC
1 A-GTGCATCGATGCA-GCCTTGAATGTGCATCGATGCACAAGG-A
25164 A-TGCATCGATGCA
1 AGTGCATCGATGCA
25177 TCCATCAGGT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
42 1 0.02
43 23 0.47
44 24 0.49
45 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (42 bp):
AGTGCATCGATGCAGCCTTGAATGTGCATCGATGCACAAGGA
Found at i:26729 original size:21 final size:21
Alignment explanation
Indices: 26687--26729 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
26677 ACCCCGGGAG
* *
26687 CTAGTTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
26708 CTAGCTCTTCTCGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
26729 C
1 C
26730 GGCACCGGCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.09, C:0.40, G:0.16, T:0.35
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:27039 original size:14 final size:15
Alignment explanation
Indices: 27014--27042 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
27004 AGATTTTTTA
27014 TGTTTCTGGATTGTT
1 TGTTTCTGGATTGTT
27029 TGTTT-TGGATTGTT
1 TGTTTCTGGATTGTT
27043 AAATGCTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.07, C:0.03, G:0.28, T:0.62
Consensus pattern (15 bp):
TGTTTCTGGATTGTT
Found at i:27868 original size:64 final size:65
Alignment explanation
Indices: 27756--27880 Score: 200
Period size: 64 Copynumber: 1.9 Consensus size: 65
27746 GAATGCATTT
*
27756 CATGCATCGATGCACTAAGGATTTTATGAAAACATCGAATGCATTTGATGCATCGATGCACCAAC
1 CATGCATCGATGCACTAAGGATTTTATGAAAACATCGAATGCACTTGATGCATCGATGCACCAAC
**
27821 CATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCACTTGATGCATCGATGCAC
1 CATGCATCGATGCACTAAGGAT-TTTATGAAAACATCGAATGCACTTGATGCATCGATGCAC
27881 TAAGGGTCCA
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 31 0.55
65 22 0.39
66 3 0.05
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (65 bp):
CATGCATCGATGCACTAAGGATTTTATGAAAACATCGAATGCACTTGATGCATCGATGCACCAAC
Found at i:30480 original size:16 final size:17
Alignment explanation
Indices: 30448--30485 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
30438 ATGTGAAATA
*
30448 ATATGTGCTTATATGTG
1 ATATGTGATTATATGTG
*
30465 CTATGTGATT-TATGTG
1 ATATGTGATTATATGTG
30481 ATATG
1 ATATG
30486 CCATATGGGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.47
Consensus pattern (17 bp):
ATATGTGATTATATGTG
Found at i:31087 original size:23 final size:23
Alignment explanation
Indices: 31053--31139 Score: 77
Period size: 23 Copynumber: 3.7 Consensus size: 23
31043 ACATATTATA
31053 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
31076 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * **
31099 CGGTC-CTTCGGGATAAAATTCTACG
1 TGG-CACTAC-GG-TGCAATTCTACG
31124 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
31140 ATTTATACGA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
23 29 0.59
24 6 0.12
25 14 0.29
ACGTcount: A:0.21, C:0.24, G:0.26, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:32032 original size:7 final size:7
Alignment explanation
Indices: 31983--32031 Score: 71
Period size: 7 Copynumber: 7.0 Consensus size: 7
31973 GTTCATCGCG
31983 CTATTCA
1 CTATTCA
*
31990 CTGTTCA
1 CTATTCA
31997 CTATTCA
1 CTATTCA
32004 CTATTCA
1 CTATTCA
*
32011 TTATTCA
1 CTATTCA
32018 CTATTCA
1 CTATTCA
*
32025 TTATTCA
1 CTATTCA
32032 TACAGTATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.27, C:0.24, G:0.02, T:0.47
Consensus pattern (7 bp):
CTATTCA
Found at i:39300 original size:103 final size:103
Alignment explanation
Indices: 39116--39333 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
39106 GTCGAGGGTC
*
39116 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
39181 TTAATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTAATCCCTAGCATATGTATATGATTCTTAAGGAATGA
* *
39219 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
* *
39284 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTAATCCCTAGCATATGTATATGATTCTTAAGGAATGA
39322 TATGTGGTCCTT
1 TATGTGGTCCTT
39334 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTATGGTGAGACACATAC
TTAATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:39416 original size:23 final size:23
Alignment explanation
Indices: 39340--39417 Score: 102
Period size: 23 Copynumber: 3.3 Consensus size: 23
39330 CCTTATGGAC
*
39340 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
39364 ATTCTACGTGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
39387 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
39410 ATTATATG
1 ATTATATG
39418 AGCTGTGGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
23 44 0.94
24 3 0.06
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:48288 original size:22 final size:22
Alignment explanation
Indices: 48260--48307 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
48250 AGTTACATGA
48260 GTTATTTGATTTAATTCCAGGG
1 GTTATTTGATTTAATTCCAGGG
48282 GTTATTTGATTTAATTCCAGGG
1 GTTATTTGATTTAATTCCAGGG
48304 GTTA
1 GTTA
48308 CATGATATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (22 bp):
GTTATTTGATTTAATTCCAGGG
Found at i:48313 original size:22 final size:22
Alignment explanation
Indices: 48266--48319 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
48256 ATGAGTTATT
**
48266 TGATTTAATTCCAGGGGTTATT
1 TGATTTAATTCCAGGGGTTACA
48288 TGATTTAATTCCAGGGGTTACA
1 TGATTTAATTCCAGGGGTTACA
*
48310 TGATATAATT
1 TGATTTAATT
48320 TCGGGAGTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.43
Consensus pattern (22 bp):
TGATTTAATTCCAGGGGTTACA
Found at i:56544 original size:2 final size:2
Alignment explanation
Indices: 56537--56578 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
56527 TGCTATCTGA
56537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
56579 TTACTTTGGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.