Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005238.1 Hibiscus syriacus cultivar Beakdansim tig00011858_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: 87379
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1973 original size:2 final size:2
Alignment explanation
Indices: 1966--1992 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1956 TAAAATTCTA
1966 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1993 GGGGTGAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2649 original size:2 final size:2
Alignment explanation
Indices: 2642--2683 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2632 ATGTGAAAGA
2642 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
2684 CTTATATGGT
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
Found at i:4525 original size:153 final size:147
Alignment explanation
Indices: 4237--4526 Score: 386
Period size: 153 Copynumber: 1.9 Consensus size: 147
4227 TCACTGAAAC
*
4237 AGTAAAACTTGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
1 AGTAAAACTGGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
* ** * *
4302 TCATCTGAACTTTGCAAGTACAATAACCCTTTTCCCATGGGATTTTGTTCTTTTAAAGGTGTATT
66 TCATCTGAACTTTGCAAGTACAATAACCCTTTTCCCAAGGGATTTTGTTCTCGTAAAGGTATAGT
*
4367 TAAAACTAGAAAAAAAA
131 GAAAACTAGAAAAAAAA
* *
4384 AGTAAAACTGGTATGTCAGATTTGATATGGGTGCTTT-TTTTTGCTATCTATAAATACAATGCTA
1 AGTAAAACTGGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
* * *
4448 TCATCTGGCATTTGAACTTTGCAAGTATAATAACTC-TTTCCTCAAGGGATTTTGTTGTCGTAAA
66 TCA--T--C---TGAACTTTGCAAGTACAATAACCCTTTTCC-CAAGGGATTTTGTTCTCGTAAA
4512 GGTATAGTGAAAACT
123 GGTATAGTGAAAACT
4527 TGCTTGTATC
Statistics
Matches: 123, Mismatches: 12, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
146 29 0.24
147 35 0.28
148 1 0.01
150 1 0.01
152 5 0.04
153 52 0.42
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (147 bp):
AGTAAAACTGGTATGTCAGAGTTGATATGGGTGCTTTCTTTTCGCTATCTATAAATACAATGCTA
TCATCTGAACTTTGCAAGTACAATAACCCTTTTCCCAAGGGATTTTGTTCTCGTAAAGGTATAGT
GAAAACTAGAAAAAAAA
Found at i:16854 original size:20 final size:21
Alignment explanation
Indices: 16821--16860 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16811 AAAAATTAGG
16821 TAAATTATACG-TTTAGTATT
1 TAAATTATACGTTTTAGTATT
16841 TAAATTATTA-GTTTTAGTAT
1 TAAATTA-TACGTTTTAGTAT
16861 GTTTCAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.53
Consensus pattern (21 bp):
TAAATTATACGTTTTAGTATT
Found at i:16979 original size:37 final size:37
Alignment explanation
Indices: 16906--16981 Score: 100
Period size: 37 Copynumber: 2.1 Consensus size: 37
16896 ATACCTAAAG
* * *
16906 TTTAGTTTTGTTTCATTTTAGTATAGTATTTGAAAAT
1 TTTAGTTTTGTTTCATTTTAGTATACTAGTTCAAAAT
*
16943 TTTAGTTTTCGTTTTATTTTAGTATACT-GTTCAAAAT
1 TTTAGTTTT-GTTTCATTTTAGTATACTAGTTCAAAAT
16980 TT
1 TT
16982 AACATTAAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 18 0.53
38 16 0.47
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (37 bp):
TTTAGTTTTGTTTCATTTTAGTATACTAGTTCAAAAT
Found at i:32121 original size:3 final size:3
Alignment explanation
Indices: 32113--32144 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
32103 GCAACCTGTA
32113 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
32145 AATAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:32369 original size:44 final size:44
Alignment explanation
Indices: 32302--32385 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
32292 TTTTCCGGAG
* * * * *
32302 TAAGGGCTCGACTCGATTCAAAAATTGTTTGACTCGTGTTGGAT
1 TAAGGGCTCAACTCAATTAAAAAATTATTTGACTCATGTTGGAT
*
32346 TAAGGGTTCAACTCAATTAAAAAATTATTTGACTCATGTT
1 TAAGGGCTCAACTCAATTAAAAAATTATTTGACTCATGTT
32386 TGATAAAGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (44 bp):
TAAGGGCTCAACTCAATTAAAAAATTATTTGACTCATGTTGGAT
Found at i:34958 original size:23 final size:22
Alignment explanation
Indices: 34932--34987 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
34922 TAATAGAAAT
** *
34932 TAATATTATTTTTTAAAACATAA
1 TAATATTATCATTTAAAA-AAAA
34955 TAATATTATCATTTAAAAAAAA
1 TAATATTATCATTTAAAAAAAA
*
34977 TAAAATTATCA
1 TAATATTATCA
34988 AAATGTGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATATTATCATTTAAAAAAAA
Found at i:34984 original size:22 final size:23
Alignment explanation
Indices: 34943--34987 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
34933 AATATTATTT
* *
34943 TTTAAAACATAATAATATTATCA
1 TTTAAAACAAAATAAAATTATCA
34966 TTTAAAA-AAAATAAAATTATCA
1 TTTAAAACAAAATAAAATTATCA
34988 AAATGTGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.36
Consensus pattern (23 bp):
TTTAAAACAAAATAAAATTATCA
Found at i:36841 original size:33 final size:34
Alignment explanation
Indices: 36799--36947 Score: 157
Period size: 33 Copynumber: 4.4 Consensus size: 34
36789 AAAACAGACT
***
36799 ATCGCAATGCGAAATGGCTATCGCAACGA-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
36832 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAA--CG--ATGAAA
*
36870 ATCGCAATGCGAAAATCG-CAAT-GCGAA--ATGAAA
1 ATCGCAATGCG-AAAT-GAAAATCGC-AACGATGAAA
36903 ATCGCAATGCGAAATGAAAATCGCAACGA-GAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
36936 ATCGCAATGCGA
1 ATCGCAATGCGA
36948 TTTTCATTTC
Statistics
Matches: 99, Mismatches: 5, Indels: 24
0.77 0.04 0.19
Matches are distributed among these distances:
31 1 0.01
32 9 0.09
33 58 0.59
34 1 0.01
35 2 0.02
37 1 0.01
38 17 0.17
39 9 0.09
40 1 0.01
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (34 bp):
ATCGCAATGCGAAATGAAAATCGCAACGATGAAA
Found at i:36850 original size:19 final size:19
Alignment explanation
Indices: 36828--36947 Score: 170
Period size: 19 Copynumber: 6.8 Consensus size: 19
36818 ATCGCAACGA
36828 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36847 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36866 GAAAATCGCAATGC-----
1 GAAAATCGCAATGCGAAAT
36880 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36899 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
36918 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
36932 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
36948 TTTTCATTTC
Statistics
Matches: 93, Mismatches: 0, Indels: 18
0.84 0.00 0.16
Matches are distributed among these distances:
14 25 0.27
15 1 0.01
16 2 0.02
17 2 0.02
19 63 0.68
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:36966 original size:52 final size:52
Alignment explanation
Indices: 36799--36947 Score: 253
Period size: 52 Copynumber: 2.9 Consensus size: 52
36789 AAAACAGACT
***
36799 ATCGCAATGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
* *
36851 ATCGCAATGCGAAATGAAAATCGCAATGCGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
36903 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGA
36948 TTTTCATTTC
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 90 1.00
ACGTcount: A:0.44, C:0.19, G:0.22, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:37023 original size:20 final size:20
Alignment explanation
Indices: 36966--37023 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
36956 TCGCATTGCG
* *
36966 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
36986 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
37006 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
37024 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:38111 original size:24 final size:24
Alignment explanation
Indices: 38084--38130 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
38074 GTATTCGAAA
* *
38084 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
38108 TTTGATATTGGTCAATACACGGA
1 TTTGATATTGGTCAATACACGGA
38131 TTTTTGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:38330 original size:12 final size:12
Alignment explanation
Indices: 38313--38337 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38303 ATATAATCCT
38313 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38325 GAAGAAGAAAAA
1 GAAGAAGAAAAA
38337 G
1 G
38338 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:40675 original size:33 final size:33
Alignment explanation
Indices: 40629--40756 Score: 177
Period size: 33 Copynumber: 3.8 Consensus size: 33
40619 GGAAATTACT
40629 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
40662 ATCGCAATACGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
40694 TTTCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
40728 ATCGCAACGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
40757 CGAATTAGAA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.01
33 62 0.77
34 18 0.22
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:40741 original size:66 final size:67
Alignment explanation
Indices: 40630--40762 Score: 223
Period size: 66 Copynumber: 2.0 Consensus size: 67
40620 GAAATTACTA
* * *
40630 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATACG-AAATGAAAATCGCAACGCTAA
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAACACGAAAATGAAAATCGCAACGCGAA
40694 TT
66 TT
*
40696 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAAATGAAAATCGCAACGCGAA
1 TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAACACGAAAATGAAAATCGCAACGCGAA
40761 TT
66 TT
40763 AGAATTATGT
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
66 40 0.65
67 22 0.35
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.15
Consensus pattern (67 bp):
TCGCAATGCAAAATGAAAATCGCAACGAGAGAATCGCAACACGAAAATGAAAATCGCAACGCGAA
TT
Found at i:40805 original size:14 final size:14
Alignment explanation
Indices: 40786--40822 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
40776 CATCAATTAA
40786 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
40800 ACAAATCACCTTTT
1 ACAAATCAACTTTT
40814 ACAAATCAA
1 ACAAATCAA
40823 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:42246 original size:21 final size:21
Alignment explanation
Indices: 42180--42246 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
42170 GTGAATCGGG
*
42180 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
42200 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
42222 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
42243 CTCT
1 CTCT
42247 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:42265 original size:42 final size:41
Alignment explanation
Indices: 42180--42302 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
42170 GTGAATCGGG
* * * * *
42180 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
42222 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
42264 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
42303 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:44333 original size:20 final size:19
Alignment explanation
Indices: 44302--44461 Score: 97
Period size: 19 Copynumber: 8.8 Consensus size: 19
44292 TCTTTTGGTT
44302 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
44321 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
44342 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
44361 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
**
44375 GAAATGACTATCG---CGA
1 GAAATGAAAATCGCAACGA
** * *
44391 -CCA-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGA
* *
44408 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
44427 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
44446 GAAATGAAAATTGCAA
1 GAAATGAAAATCGCAA
44462 TGCGATTTTG
Statistics
Matches: 110, Mismatches: 19, Indels: 24
0.72 0.12 0.16
Matches are distributed among these distances:
14 17 0.15
15 1 0.01
16 4 0.04
17 4 0.04
18 1 0.01
19 52 0.47
20 29 0.26
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:44384 original size:33 final size:33
Alignment explanation
Indices: 44327--44412 Score: 136
Period size: 33 Copynumber: 2.6 Consensus size: 33
44317 ACGAGATAAT
*
44327 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
44361 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
*
44394 GACAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
44413 AAAAATCGCA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 35 0.71
34 14 0.29
ACGTcount: A:0.38, C:0.26, G:0.24, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:44419 original size:19 final size:19
Alignment explanation
Indices: 44397--44466 Score: 113
Period size: 19 Copynumber: 3.7 Consensus size: 19
44387 GCGACCAGAC
*
44397 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAA
44416 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
44435 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
44454 AATTGCAATGCGA
1 AATCGCAACGCGA
44467 TTTTGGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:44484 original size:19 final size:19
Alignment explanation
Indices: 44462--44506 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
44452 AAAATTGCAA
*
44462 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
44481 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
44500 TGCGATT
1 TGCGATT
44507 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:45087 original size:20 final size:20
Alignment explanation
Indices: 45059--45151 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
45049 CGCTATGTAA
*
45059 ATCGTGTTGCGAAAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
45079 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGAAAGTCAGT
* *** * *
45099 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-AAGTCAGT
* *
45120 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGAAAGTCAGT
*
45140 ATCGCATTGCGA
1 ATCGCGTTGCGA
45152 TTTTCCCAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGAAAGTCAGT
Found at i:45129 original size:21 final size:19
Alignment explanation
Indices: 45105--45274 Score: 96
Period size: 20 Copynumber: 8.3 Consensus size: 19
45095 AAGTATCTCG
*
45105 TTGCGATTTTTTATTATCGCA
1 TTGCGATTTTTCA-T-TCGCA
**
45126 TTGCGA-TAGTCAGTATCGCA
1 TTGCGATTTTTCA-T-TCGCA
*
45146 TTGCGATTTTCCCAATTCGCA
1 TTGCGATTTT-TC-ATTCGCA
45167 TTGCGATTTACTT-ATTCGCA
1 TTGCGATTT--TTCATTCGCA
* *
45187 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT-TC-ATTCGCA
45208 TTGCGATTTACTT-ATTCGCA
1 TTGCGATTT--TTCATTCGCA
* *
45228 TTGCGATTTTCCCAATTCGCG
1 TTGCGATTTT-TC-ATTCGCA
45249 TTGCGATTTACTT-ATTCGCA
1 TTGCGATTT--TTCATTCGCA
45269 TTGCGA
1 TTGCGA
45275 ATTGGGAAAA
Statistics
Matches: 118, Mismatches: 16, Indels: 31
0.72 0.10 0.19
Matches are distributed among these distances:
18 2 0.02
20 59 0.50
21 51 0.43
22 2 0.02
23 4 0.03
ACGTcount: A:0.19, C:0.22, G:0.18, T:0.41
Consensus pattern (19 bp):
TTGCGATTTTTCATTCGCA
Found at i:45130 original size:41 final size:41
Alignment explanation
Indices: 45078--45155 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
45068 CGAAAGTCAG
* * *
45078 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
45119 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
45156 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:45166 original size:41 final size:41
Alignment explanation
Indices: 45141--45274 Score: 250
Period size: 41 Copynumber: 3.3 Consensus size: 41
45131 ATAGTCAGTA
45141 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
*
45182 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
*
45223 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
45264 TCGCATTGCGA
1 TCGCATTGCGA
45275 ATTGGGAAAA
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCATTGCGATTTACTTAT
Found at i:45185 original size:20 final size:21
Alignment explanation
Indices: 45141--45274 Score: 148
Period size: 20 Copynumber: 6.5 Consensus size: 21
45131 ATAGTCAGTA
*
45141 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
45162 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
*
45182 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
45203 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
*
45223 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
45244 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
45264 TCGCATTGCGA
1 TCGCATTGCGA
45275 ATTGGGAAAA
Statistics
Matches: 92, Mismatches: 19, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
20 49 0.53
21 43 0.47
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:45557 original size:18 final size:18
Alignment explanation
Indices: 45534--45569 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45524 TATAAAATCC
45534 ATTAAGTATTATTAATAG
1 ATTAAGTATTATTAATAG
45552 ATTAAGTATTATTAATAG
1 ATTAAGTATTATTAATAG
45570 TAAACGTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (18 bp):
ATTAAGTATTATTAATAG
Found at i:46276 original size:30 final size:30
Alignment explanation
Indices: 46240--46296 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
46230 TCCTTCATCG
46240 GAAAAAGAAGCTTCTTCTCCATCAGAGAAT
1 GAAAAAGAAGCTTCTTCTCCATCAGAGAAT
46270 GAAAAAGAAGCTTCTTCTCCATCAGAG
1 GAAAAAGAAGCTTCTTCTCCATCAGAG
46297 GACAGCGGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.23
Consensus pattern (30 bp):
GAAAAAGAAGCTTCTTCTCCATCAGAGAAT
Found at i:46341 original size:54 final size:54
Alignment explanation
Indices: 46259--46373 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
46249 GCTTCTTCTC
* *
46259 CATCAGAGAATGAAAAAGAAGCTTCTTCTCCATCAGAGGACA-GCGGTGCTCCTT
1 CATCAGAGAATGAAAAAGAAGCTTCTTCTCCATCAAAGGA-AGGCGATGCTCCTT
* **
46313 CATCAGAGTATGTCAAAGAAGCTTCTTCTCCATCAAAGGAAGGCGATGCTCCTT
1 CATCAGAGAATGAAAAAGAAGCTTCTTCTCCATCAAAGGAAGGCGATGCTCCTT
46367 CATCAGA
1 CATCAGA
46374 AGCTGCATCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
53 1 0.02
54 54 0.98
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (54 bp):
CATCAGAGAATGAAAAAGAAGCTTCTTCTCCATCAAAGGAAGGCGATGCTCCTT
Found at i:49005 original size:31 final size:31
Alignment explanation
Indices: 48967--49025 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
48957 AGTTGTTATC
48967 TAATTCATATAATTTTGATACTTAAAATATA
1 TAATTCATATAATTTTGATACTTAAAATATA
*
48998 TAATTCATATAATTTTGATATTTAAAAT
1 TAATTCATATAATTTTGATACTTAAAAT
49026 TTAAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (31 bp):
TAATTCATATAATTTTGATACTTAAAATATA
Found at i:49571 original size:23 final size:23
Alignment explanation
Indices: 49541--49622 Score: 155
Period size: 23 Copynumber: 3.6 Consensus size: 23
49531 CTCATTAACA
*
49541 TTGAGGTACGTACCAAAGCAACT
1 TTGAGGTACGGACCAAAGCAACT
49564 TTGAGGTACGGACCAAAGCAACT
1 TTGAGGTACGGACCAAAGCAACT
49587 TTGAGGTACGGACCAAAGCAACT
1 TTGAGGTACGGACCAAAGCAACT
49610 TTGAGGTACGGAC
1 TTGAGGTACGGAC
49623 GTTATACTTA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 58 1.00
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.20
Consensus pattern (23 bp):
TTGAGGTACGGACCAAAGCAACT
Found at i:50679 original size:31 final size:31
Alignment explanation
Indices: 50609--50679 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 31
50599 TTAAGGAAAC
*
50609 TAATA-TAGAGACTTAAATTAAACAAATCAA
1 TAATATTAGAGACTTAAATCAAACAAATCAA
** * *
50639 TAACGTTAGAGGCTTAAATCGAACAAAAT-AA
1 TAATATTAGAGACTTAAATCAAAC-AAATCAA
50670 TAATATTAGA
1 TAATATTAGA
50680 TATCATTTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
30 3 0.09
31 25 0.78
32 4 0.12
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (31 bp):
TAATATTAGAGACTTAAATCAAACAAATCAA
Found at i:64659 original size:18 final size:18
Alignment explanation
Indices: 64636--64671 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
64626 TATTTTATTG
64636 AATAAAAATAATATTTTT
1 AATAAAAATAATATTTTT
* *
64654 AATAAATATATTATTTTT
1 AATAAAAATAATATTTTT
64672 GGATTGATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAAAATAATATTTTT
Found at i:69501 original size:17 final size:17
Alignment explanation
Indices: 69479--69512 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
69469 TGTACCAATG
69479 CCCATCACATGTTAGGT
1 CCCATCACATGTTAGGT
69496 CCCATCACATGTTAGGT
1 CCCATCACATGTTAGGT
69513 GGATATAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (17 bp):
CCCATCACATGTTAGGT
Found at i:72064 original size:23 final size:22
Alignment explanation
Indices: 72011--72065 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
72001 AAACTTTAGG
*
72011 TATAGTTTTAAAAAATTGAAAC
1 TATAGTTTTAAAAAATTAAAAC
*
72033 T-TCAGGTTTTAACAAATTAAAAC
1 TAT-A-GTTTTAAAAAATTAAAAC
72056 TGATAGTTTT
1 T-ATAGTTTT
72066 GGCGTAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
21 1 0.04
22 2 0.07
23 22 0.81
24 1 0.04
25 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (22 bp):
TATAGTTTTAAAAAATTAAAAC
Found at i:74081 original size:2 final size:2
Alignment explanation
Indices: 74074--74106 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
74064 CCAGCCATTC
74074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
74107 GTAACTGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79105 original size:2 final size:2
Alignment explanation
Indices: 79088--79129 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
79078 TTCAATCACT
* *
79088 TA TA TA TG TA TG 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
79130 GAAAGTAGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Done.