Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008970.1 Hibiscus syriacus cultivar Beakdansim tig00112313_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: 124070
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:8444 original size:19 final size:19
Alignment explanation
Indices: 8412--8453 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
8402 CTATTATATT
8412 TTATTTTTCATTTCATT-C
1 TTATTTTTCATTTCATTAC
*
8430 TTATTCTTTCCTTTCATTAC
1 TTATT-TTTCATTTCATTAC
8450 TTAT
1 TTAT
8454 ATTATTACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 11 0.52
20 5 0.24
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATTTTTCATTTCATTAC
Found at i:23312 original size:20 final size:20
Alignment explanation
Indices: 23276--23313 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
23266 TTTTTATTTA
*
23276 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
23296 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
23314 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:28904 original size:20 final size:20
Alignment explanation
Indices: 28868--28905 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
28858 TTTTTATTTA
*
28868 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
28888 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
28906 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:31426 original size:16 final size:16
Alignment explanation
Indices: 31405--31437 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
31395 CAACGTCATT
31405 ATTCCAACCGATCCTA
1 ATTCCAACCGATCCTA
31421 ATTCCAACCGATCCTA
1 ATTCCAACCGATCCTA
31437 A
1 A
31438 AGAAGTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.24
Consensus pattern (16 bp):
ATTCCAACCGATCCTA
Found at i:37626 original size:21 final size:21
Alignment explanation
Indices: 37600--37645 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
37590 CACCTCCCTT
37600 CATTAAAACA-ACATGTATTTC
1 CATTAAAA-AGACATGTATTTC
*
37621 CATTAAAAAGATATGTATTTC
1 CATTAAAAAGACATGTATTTC
37642 CATT
1 CATT
37646 CGGCCACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
CATTAAAAAGACATGTATTTC
Found at i:39759 original size:14 final size:14
Alignment explanation
Indices: 39739--39775 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
39729 ATGATAGAGA
*
39739 ATGGTGATGGAAAG
1 ATGGTGATGAAAAG
*
39753 TTGGTGATGAAAAG
1 ATGGTGATGAAAAG
39767 ATGGTGATG
1 ATGGTGATG
39776 TTATAGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (14 bp):
ATGGTGATGAAAAG
Found at i:40247 original size:14 final size:14
Alignment explanation
Indices: 40227--40263 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
40217 ATGATAGAGA
*
40227 ATGGTGATGGAAAG
1 ATGGTGATGAAAAG
*
40241 TTGGTGATGAAAAG
1 ATGGTGATGAAAAG
40255 ATGGTGATG
1 ATGGTGATG
40264 TTATAGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (14 bp):
ATGGTGATGAAAAG
Found at i:40448 original size:19 final size:20
Alignment explanation
Indices: 40410--40452 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
40400 GAAACCCCTT
*
40410 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
40430 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
40449 TGAA
1 TGAA
40453 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:43843 original size:20 final size:20
Alignment explanation
Indices: 43807--43844 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
43797 TTTTTATTTA
*
43807 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
43827 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
43845 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:44144 original size:5 final size:5
Alignment explanation
Indices: 44136--44160 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
44126 ATCAGAAAAG
44136 AAGAA AAGAA AAGAA AAGAA AAGAA
1 AAGAA AAGAA AAGAA AAGAA AAGAA
44161 GTTCAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:48374 original size:20 final size:20
Alignment explanation
Indices: 48338--48375 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48328 TTTTTATTTA
*
48338 TTTCATTTCTATTCTTATTC
1 TTTCATTTCCATTCTTATTC
48358 TTTCA-TTCCATTACTTAT
1 TTTCATTTCCATT-CTTAT
48376 ATTATTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTCATTTCCATTCTTATTC
Found at i:49782 original size:90 final size:89
Alignment explanation
Indices: 49674--49836 Score: 290
Period size: 90 Copynumber: 1.8 Consensus size: 89
49664 TAATTTCAAT
*
49674 TAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGATTAGGGTAACT
1 TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAA-CCCCAATATGATTAGGGTAACT
49739 TGGATATAAGAGGATTATTAAATTC
65 TGGATATAAGAGGATTATTAAATTC
*
49764 TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAACCCTAATATGATTAGGGTAACTT
1 TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAACCCCAATATGATTAGGGTAACTT
*
49829 GGCTATAA
66 GGATATAA
49837 AAGGGTGTGT
Statistics
Matches: 70, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 29 0.41
90 41 0.59
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (89 bp):
TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAACCCCAATATGATTAGGGTAACTT
GGATATAAGAGGATTATTAAATTC
Found at i:51882 original size:15 final size:15
Alignment explanation
Indices: 51862--51907 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
51852 TTTGATATCA
51862 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
51877 TTTC-TTCTCATTTCC
1 TTTCTTTC-CATTTCC
51892 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
51908 TTATTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.11
15 15 0.56
17 6 0.22
18 3 0.11
ACGTcount: A:0.07, C:0.33, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:55387 original size:158 final size:158
Alignment explanation
Indices: 55170--55485 Score: 616
Period size: 158 Copynumber: 2.0 Consensus size: 158
55160 TATTCAAATA
55170 TCAAAACATTACTCAAAATATTTCAAAAATCATTTTAATCCTTACTAAGTGTAAAATTAAGTTTT
1 TCAAAACATTACTCAAAATATTTCAAAAATCATTTTAATCCTTACTAAGTGTAAAATTAAGTTTT
55235 AATCTTAAAACAATTTCAAAATAATCTTTCAAAGTATTTCGAACCATTTCAAAGCCAAAAATTCC
66 AATCTTAAAACAATTTCAAAATAATCTTTCAAAGTATTTCGAACCATTTCAAAGCCAAAAATTCC
55300 AGATTGCTCAGAGGGAACCGATTCCCCC
131 AGATTGCTCAGAGGGAACCGATTCCCCC
55328 TCAAAACATTACTCAAAATATTTCAAAAATCATTTTTAATCCTTAC-AAGTGTAAAATTAAGTTT
1 TCAAAACATTACTCAAAATATTTCAAAAATCA-TTTTAATCCTTACTAAGTGTAAAATTAAGTTT
55392 TAATCTTAAAACAATTTCAAAATAATCTTTCAAAGTATTTCGAACCATTTCAAAGCCAAAAATTC
65 TAATCTTAAAACAATTTCAAAATAATCTTTCAAAGTATTTCGAACCATTTCAAAGCCAAAAATTC
55457 CAGATTGCTCAGAGGGAACCGATTCCCCC
130 CAGATTGCTCAGAGGGAACCGATTCCCCC
55486 CAAGAGGGGT
Statistics
Matches: 157, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
158 144 0.92
159 13 0.08
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (158 bp):
TCAAAACATTACTCAAAATATTTCAAAAATCATTTTAATCCTTACTAAGTGTAAAATTAAGTTTT
AATCTTAAAACAATTTCAAAATAATCTTTCAAAGTATTTCGAACCATTTCAAAGCCAAAAATTCC
AGATTGCTCAGAGGGAACCGATTCCCCC
Found at i:66342 original size:20 final size:19
Alignment explanation
Indices: 66319--66387 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
66309 TTTTTTGAAA
66319 TTTTGGCTTTTTTGGCTCTTT
1 TTTTGG-TTTTTTGGCTC-TT
* * *
66340 TTTTGTTTTTTTGCCTTTT
1 TTTTGGTTTTTTGGCTCTT
* *
66359 TTTTTGTTTTTTTGC-CTT
1 TTTTGGTTTTTTGGCTCTT
66377 TTTT-GTTTTTT
1 TTTTGGTTTTTT
66388 TTTTGTTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
17 7 0.17
18 6 0.15
19 13 0.32
20 9 0.22
21 5 0.12
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.77
Consensus pattern (19 bp):
TTTTGGTTTTTTGGCTCTT
Found at i:66368 original size:28 final size:28
Alignment explanation
Indices: 66337--66400 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
66327 TTTTTGGCTC
*
66337 TTTTTTTG-TTTTTTTGCCTTTTTTTTTG
1 TTTTTTTGCCTTTTTTG-CTTTTTTTTTG
*
66365 TTTTTTTGCCTTTTTTGTTTTTTTTTTG
1 TTTTTTTGCCTTTTTTGCTTTTTTTTTG
66393 TTTTTTTG
1 TTTTTTTG
66401 AAAAAAAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.83
Consensus pattern (28 bp):
TTTTTTTGCCTTTTTTGCTTTTTTTTTG
Found at i:66388 original size:19 final size:18
Alignment explanation
Indices: 66326--66390 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 18
66316 AAATTTTGGC
* *
66326 TTTTTTGGCTCTTTTTTTG
1 TTTTTTTGC-CTTTTTTTT
66345 TTTTTTTGCCTTTTTTTTT
1 TTTTTTTGCC-TTTTTTTT
66364 GTTTTTTTGCCTTTTTTGTT
1 -TTTTTTTGCCTTTTTT-TT
66384 TTTTTTT
1 TTTTTTT
66391 TGTTTTTTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.02
19 28 0.68
20 12 0.29
ACGTcount: A:0.00, C:0.09, G:0.11, T:0.80
Consensus pattern (18 bp):
TTTTTTTGCCTTTTTTTT
Found at i:66399 original size:20 final size:20
Alignment explanation
Indices: 66326--66392 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
66316 AAATTTTGGC
* *
66326 TTTTTTGGCTCTTTTTTTGT
1 TTTTTTGCCTTTTTTTTTGT
66346 TTTTTTGCCTTTTTTTTTGT
1 TTTTTTGCCTTTTTTTTTGT
66366 TTTTTTGCCTTTTTTGTTT-T
1 TTTTTTGCCTTTTTT-TTTGT
66386 TTTTTTG
1 TTTTTTG
66393 TTTTTTTGAA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 41 0.93
21 3 0.07
ACGTcount: A:0.00, C:0.09, G:0.12, T:0.79
Consensus pattern (20 bp):
TTTTTTGCCTTTTTTTTTGT
Found at i:66400 original size:8 final size:8
Alignment explanation
Indices: 66337--66388 Score: 50
Period size: 8 Copynumber: 5.9 Consensus size: 8
66327 TTTTTGGCTC
66337 TTTTTTTG
1 TTTTTTTG
66345 TTTTTTTG
1 TTTTTTTG
66353 CCTTTTTTTTTG
1 ----TTTTTTTG
66365 TTTTTTTG
1 TTTTTTTG
*
66373 CCTTTTTTG
1 -TTTTTTTG
66382 TTTTTTT
1 TTTTTTT
66389 TTTGTTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
8 22 0.59
9 7 0.19
12 8 0.22
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.83
Consensus pattern (8 bp):
TTTTTTTG
Found at i:68986 original size:19 final size:19
Alignment explanation
Indices: 68962--69001 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
68952 GTGTTTTAAG
68962 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
68981 TGTGTTTTAAAATGATAAA
1 TGTGTTTTAAAATGATAAA
69000 TG
1 TG
69002 GGAGAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.42
Consensus pattern (19 bp):
TGTGTTTTAAAATGATAAA
Found at i:71034 original size:19 final size:18
Alignment explanation
Indices: 71002--71037 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
70992 ACATGATTTG
71002 TTTTATGAAAATACATGA
1 TTTTATGAAAATACATGA
*
71020 TTTTAATGAAGATACATG
1 TTTT-ATGAAAATACATG
71038 CTCTTGGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (18 bp):
TTTTATGAAAATACATGA
Found at i:75186 original size:15 final size:15
Alignment explanation
Indices: 75151--75179 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
75141 GTGCTTCAAC
75151 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
75165 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
75180 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:81241 original size:18 final size:17
Alignment explanation
Indices: 81198--81230 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
81188 TGGCATAAAA
81198 GAAATGGATATGGTAAT
1 GAAATGGATATGGTAAT
81215 GAAATGGATATGGTAA
1 GAAATGGATATGGTAA
81231 ATGATGTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
GAAATGGATATGGTAAT
Found at i:81570 original size:33 final size:33
Alignment explanation
Indices: 81528--81596 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
81518 GTTGATAAAT
*
81528 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
81561 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
81594 GAA
1 GAA
81597 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:85512 original size:33 final size:33
Alignment explanation
Indices: 85470--85538 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
85460 GTTGATAAAT
*
85470 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
85503 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
85536 GAA
1 GAA
85539 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:88784 original size:19 final size:20
Alignment explanation
Indices: 88760--88799 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
88750 CTATCCTTTT
88760 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
88779 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
88799 T
1 T
88800 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:89090 original size:17 final size:18
Alignment explanation
Indices: 89070--89112 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
89060 TGCAAAAATA
89070 AAGAAAAAGAT-A-AAAAG
1 AAGAAAAA-ATCAGAAAAG
89087 AAGAGAAAAATCAGAAAAG
1 AAGA-AAAAATCAGAAAAG
89106 AAGAAAA
1 AAGAAAA
89113 GAAAAGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 6 0.26
18 8 0.35
19 9 0.39
ACGTcount: A:0.74, C:0.02, G:0.19, T:0.05
Consensus pattern (18 bp):
AAGAAAAAATCAGAAAAG
Found at i:94707 original size:5 final size:5
Alignment explanation
Indices: 94697--94722 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
94687 TTAAGGTTTC
94697 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
94723 ATATATGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:94748 original size:5 final size:5
Alignment explanation
Indices: 94738--94763 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
94728 TGACTTAGAA
94738 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
94764 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:97601 original size:16 final size:16
Alignment explanation
Indices: 97567--97600 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
97557 TTCAACTTTC
*
97567 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
97583 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
97598 TTT
1 TTT
97601 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:97628 original size:23 final size:25
Alignment explanation
Indices: 97589--97642 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
97579 TTCTTTTCTT
97589 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
97614 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
97637 TTTCTT
1 TTTCTT
97643 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:103581 original size:35 final size:37
Alignment explanation
Indices: 103535--103614 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
103525 TTTGAGAATT
*
103535 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
103570 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
103607 TGGTGATG
1 TGGTGATG
103615 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:110018 original size:16 final size:15
Alignment explanation
Indices: 109999--110041 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
109989 CTTTATTATC
*
109999 TTATTTCATCTTCTGT
1 TTATTT-ATATTCTGT
*
110015 TTATTTATATTTTGT
1 TTATTTATATTCTGT
110030 TTATTT-TATTCT
1 TTATTTATATTCT
110042 AATCTTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (15 bp):
TTATTTATATTCTGT
Found at i:110629 original size:9 final size:9
Alignment explanation
Indices: 110615--110671 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
110605 TTAGAGTGCA
110615 AAAAGAAAG
1 AAAAGAAAG
110624 AAAAGAAA-
1 AAAAGAAAG
110632 AAAA-AAGAG
1 AAAAGAA-AG
*
110641 AAAA-ATCAG
1 AAAAGA-AAG
110650 AAAAG-AAG
1 AAAAGAAAG
110658 AAAAGAAAAG
1 AAAAG-AAAG
110668 AAAA
1 AAAA
110672 AGAATTCAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
7 2 0.05
8 12 0.30
9 19 0.47
10 7 0.17
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:110630 original size:5 final size:5
Alignment explanation
Indices: 110615--110671 Score: 50
Period size: 5 Copynumber: 11.8 Consensus size: 5
110605 TTAGAGTGCA
* *
110615 AAAAG -AAAG AAAAG AAAAA AAAAG AGAAA- AATCAG AAAAG --AAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG A-AAAG AA-AAG AAAAG AAAAG AAAAG
110663 AAAAG AAAA
1 AAAAG AAAA
110672 AGAATTCAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
3 3 0.07
4 5 0.12
5 29 0.69
6 5 0.12
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:110638 original size:19 final size:18
Alignment explanation
Indices: 110614--110675 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
110604 ATTAGAGTGC
110614 AAAAAGAAAGAAAAGAAAA
1 AAAAAG-AAGAAAAGAAAA
**
110633 AAAAAG-AGAAAA-ATCA
1 AAAAAGAAGAAAAGAAAA
*
110649 GAAAAGAAGAAAAGAAAA
1 AAAAAGAAGAAAAGAAAA
110667 GAAAAAGAA
1 -AAAAAGAA
110676 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 7 0.21
17 12 0.35
18 2 0.06
19 13 0.38
ACGTcount: A:0.79, C:0.02, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAGAAGAAAAGAAAA
Found at i:110659 original size:29 final size:30
Alignment explanation
Indices: 110626--110686 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
110616 AAAGAAAGAA
*
110626 AAGAAAAAAAAAGAGAAA-AA-TCAGAAAAG
1 AAGAAAAAAAAAGAAAAAGAATTCA-AAAAG
*
110655 AAGAAAAGAAAAGAAAAAGAATTCAAAAAG
1 AAGAAAAAAAAAGAAAAAGAATTCAAAAAG
110685 AA
1 AA
110687 AGCAAAGCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 16 0.57
30 9 0.32
31 3 0.11
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.05
Consensus pattern (30 bp):
AAGAAAAAAAAAGAAAAAGAATTCAAAAAG
Found at i:118342 original size:19 final size:21
Alignment explanation
Indices: 118299--118350 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
118289 GAAACCCCTT
118299 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
118320 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
118339 TGAAGATACATG
1 TGAAAATACATG
118351 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:119158 original size:18 final size:19
Alignment explanation
Indices: 119124--119164 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
119114 AAGAAAATAT
119124 ATGAGCTAGAAAATAGATGC
1 ATGAGCTAG-AAATAGATGC
119144 ATGAGCTAG-AATAGATGC
1 ATGAGCTAGAAATAGATGC
119162 ATG
1 ATG
119165 CATGCAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 12 0.57
20 9 0.43
ACGTcount: A:0.41, C:0.10, G:0.27, T:0.22
Consensus pattern (19 bp):
ATGAGCTAGAAATAGATGC
Found at i:119314 original size:30 final size:31
Alignment explanation
Indices: 119274--119333 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
119264 ACATGCTGCC
**
119274 ATGATATCTAAATGAAATGCAAACATAATAA
1 ATGATATCTAAAACAAATGCAAACATAATAA
* *
119305 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACAAATGCAAACATAATA
119334 TAAAGCTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (31 bp):
ATGATATCTAAAACAAATGCAAACATAATAA
Found at i:121760 original size:24 final size:23
Alignment explanation
Indices: 121733--121786 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
121723 TTTGAACTTC
**
121733 TCTTTTTCTTTTCTTTTCTTTTCT
1 TCTTTTTCTTTTCTGAT-TTTTCT
*
121757 TCTTCTTCTTTTCTGATTTTTCT
1 TCTTTTTCTTTTCTGATTTTTCT
121780 TCTTTTT
1 TCTTTTT
121787 TGCACTCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 12 0.46
24 14 0.54
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (23 bp):
TCTTTTTCTTTTCTGATTTTTCT
Found at i:122544 original size:18 final size:20
Alignment explanation
Indices: 122499--122547 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 20
122489 GAAACCCCTT
122499 TGAAAATACATGATTTTAAA
1 TGAAAATACATGATTTTAAA
122519 T-AAAATACA-GATTTT-AA
1 TGAAAATACATGATTTTAAA
*
122536 TGAAGATACATG
1 TGAAAATACATG
122548 CTCTTGGACG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 3 0.12
18 13 0.50
19 9 0.35
20 1 0.04
ACGTcount: A:0.49, C:0.06, G:0.12, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Done.