Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003377.1 Hibiscus syriacus cultivar Beakdansim tig00007097_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: 84590
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:4792 original size:59 final size:59
Alignment explanation
Indices: 4729--4841 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
4719 AACATAATGA
* *
4729 ATAGTCAAATAATCATTTTGTAATTTTTAATAGTTAA-ATGACCCAACAAAACAACTCCT
1 ATAGTCAAATAATCATTTTATAACTTTTAATAGTTAATA-GACCCAACAAAACAACTCCT
* * * * * *
4788 ATAGTCGAGTGATCATTTTATAACTTTTAGTAGTTAATAGACTCAATAAAACAA
1 ATAGTCAAATAATCATTTTATAACTTTTAATAGTTAATAGACCCAACAAAACAA
4842 TATCGGATAC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
59 44 0.98
60 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.35
Consensus pattern (59 bp):
ATAGTCAAATAATCATTTTATAACTTTTAATAGTTAATAGACCCAACAAAACAACTCCT
Found at i:8551 original size:23 final size:22
Alignment explanation
Indices: 8500--8552 Score: 61
Period size: 23 Copynumber: 2.4 Consensus size: 22
8490 ATTTTTATGG
* **
8500 TAAATTTTAAAAAATAAAATTA
1 TAAATTTTAAAAAAGAAAAACA
*
8522 TATATTTTAAAAAAAGAAAAACA
1 TAAATTTT-AAAAAAGAAAAACA
8545 TAAATTTT
1 TAAATTTT
8553 GAAATAACCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 7 0.28
23 18 0.72
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAATTTTAAAAAAGAAAAACA
Found at i:9537 original size:13 final size:13
Alignment explanation
Indices: 9519--9543 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9509 CATAATCTAA
9519 AAGTTTTTTATTT
1 AAGTTTTTTATTT
9532 AAGTTTTTTATT
1 AAGTTTTTTATT
9544 ATATTCATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (13 bp):
AAGTTTTTTATTT
Found at i:10476 original size:16 final size:16
Alignment explanation
Indices: 10455--10530 Score: 125
Period size: 16 Copynumber: 4.8 Consensus size: 16
10445 TTAGAGCCTC
10455 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
10471 TGAATCATTCAGCATT
1 TGAATCATTCAGCATT
*
10487 TGAATCATTCTGCATT
1 TGAATCATTCAGCATT
* *
10503 TAAATCATTCAGTATT
1 TGAATCATTCAGCATT
10519 TGAATCATTCAG
1 TGAATCATTCAG
10531 ATATGCGAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.12, T:0.39
Consensus pattern (16 bp):
TGAATCATTCAGCATT
Found at i:15848 original size:12 final size:12
Alignment explanation
Indices: 15831--15866 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
15821 ATTCATATTA
15831 TAAATATAAAAT
1 TAAATATAAAAT
15843 TAAATATAAAAT
1 TAAATATAAAAT
*
15855 CATAATATAAAA
1 TA-AATATAAAA
15867 CGATACTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.59
13 9 0.41
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAATATAAAAT
Found at i:22406 original size:2 final size:2
Alignment explanation
Indices: 22399--22435 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22389 AATTTTATTT
22399 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22436 CCAAATATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22534 original size:12 final size:12
Alignment explanation
Indices: 22506--22538 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
22496 AACGAACTTT
22506 TAATTTTTTATG
1 TAATTTTTTATG
22518 T-ATTTTTTATG
1 TAATTTTTTATG
22529 TAATTTTTTA
1 TAATTTTTTA
22539 AATAAATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (12 bp):
TAATTTTTTATG
Found at i:24051 original size:21 final size:21
Alignment explanation
Indices: 24024--24121 Score: 110
Period size: 21 Copynumber: 4.7 Consensus size: 21
24014 GCAAATATGT
*
24024 AAATCGCAACTCGATAATACA
1 AAATCGCAACGCGATAATACA
* **
24045 TAATCGCAACGCGATTCTGAC-
1 AAATCGCAACGCGATAAT-ACA
*
24066 -TATCGCAACGCGATAATACA
1 AAATCGCAACGCGATAATACA
*
24086 AAATCGCAATGCGATAATACA
1 AAATCGCAACGCGATAATACA
*
24107 AAATCGCAATGCGAT
1 AAATCGCAACGCGAT
24122 TTTCAAAACG
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
19 2 0.03
20 14 0.22
21 47 0.72
22 2 0.03
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (21 bp):
AAATCGCAACGCGATAATACA
Found at i:24051 original size:41 final size:41
Alignment explanation
Indices: 24006--24097 Score: 105
Period size: 41 Copynumber: 2.2 Consensus size: 41
23996 GATTTTGACT
* *
24006 ATCGCAATGCAAATATGTA-AATCGCAACTCGATAATACATA
1 ATCGCAATGCAAATATG-ACAATCGCAACGCGATAATACAAA
* * * * *
24047 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACAAA
1 ATCGCAATGCAAATATGACAATCGCAACGCGATAATACAAA
24088 ATCGCAATGC
1 ATCGCAATGC
24098 GATAATACAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 1 0.02
41 41 0.98
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.22
Consensus pattern (41 bp):
ATCGCAATGCAAATATGACAATCGCAACGCGATAATACAAA
Found at i:24112 original size:62 final size:61
Alignment explanation
Indices: 23991--24122 Score: 169
Period size: 62 Copynumber: 2.1 Consensus size: 61
23981 CCAGATTCGT
* * ** *
23991 AACGCGATTTTGACTATCGCAATGCAAATATGTAAATCGCAACTCGATAATACATAATCGC
1 AACGCGATTCTGACTATCGCAACGCAAATATCAAAATCGCAACTCGATAATACAAAATCGC
24052 AACGCGATTCTGACTATCGCAACGCGATAATA-CAAAATCGCAA-TGCGATAATACAAAATCGC
1 AACGCGATTCTGACTATCGCAACGC-A-AATATCAAAATCGCAACT-CGATAATACAAAATCGC
*
24114 AATGCGATT
1 AACGCGATT
24123 TTCAAAACGC
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
61 24 0.39
62 34 0.55
63 4 0.06
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (61 bp):
AACGCGATTCTGACTATCGCAACGCAAATATCAAAATCGCAACTCGATAATACAAAATCGC
Found at i:24299 original size:20 final size:21
Alignment explanation
Indices: 24259--24301 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
24249 TCACTCTCTA
*
24259 CGGCGACATCCGTCCCTATCTC
1 CGGCGAAATCCGT-CCTATCTC
24281 CGGCGAAATCCGT-CTATCTC
1 CGGCGAAATCCGTCCTATCTC
24301 C
1 C
24302 ATCTCTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 8 0.40
22 12 0.60
ACGTcount: A:0.16, C:0.42, G:0.19, T:0.23
Consensus pattern (21 bp):
CGGCGAAATCCGTCCTATCTC
Found at i:24694 original size:20 final size:20
Alignment explanation
Indices: 24670--24772 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
24660 AAAATCGTAA
* *
24670 CGATAGTCAAATTCACGTTA
1 CGATAGTCAAATTCGCGTTG
** *
24690 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
** *
24710 CGATTTTC-ATTTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
24729 CGATAGTCAAATTCGCGTTG
1 CGATAGTCAAATTCGCGTTG
** *
24749 CGATAGTCATTTTCGTGTTG
1 CGATAGTCAAATTCGCGTTG
24769 CGAT
1 CGAT
24773 TTTAAGTTTC
Statistics
Matches: 67, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
19 15 0.22
20 52 0.78
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (20 bp):
CGATAGTCAAATTCGCGTTG
Found at i:24749 original size:39 final size:40
Alignment explanation
Indices: 24670--24772 Score: 109
Period size: 39 Copynumber: 2.6 Consensus size: 40
24660 AAAATCGTAA
** * * ** *
24670 CGATAGTCAAATTCACGTTACGATAGTCATTTTCGTGTTG
1 CGATAGTCATTTTCGCGTTGCGATAGTCAAATTCGCGTTG
**
24710 CGATTTTCA-TTTCGCGTTGCGATAGTCAAATTCGCGTTG
1 CGATAGTCATTTTCGCGTTGCGATAGTCAAATTCGCGTTG
*
24749 CGATAGTCATTTTCGTGTTGCGAT
1 CGATAGTCATTTTCGCGTTGCGAT
24773 TTTAAGTTTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 31 0.61
40 20 0.39
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (40 bp):
CGATAGTCATTTTCGCGTTGCGATAGTCAAATTCGCGTTG
Found at i:24782 original size:20 final size:19
Alignment explanation
Indices: 24700--24782 Score: 58
Period size: 20 Copynumber: 4.2 Consensus size: 19
24690 CGATAGTCAT
* *
24700 TTTCGTGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTAA
* *
24719 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGAT-TTTAA
* * * *
24739 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGAT-TTTAA
*
24759 TTTCGTGTTGCGATTTTAA
1 TTTCGCGTTGCGATTTTAA
24778 GTTTC
1 -TTTC
24783 AGAAACTATT
Statistics
Matches: 51, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
19 15 0.29
20 36 0.71
ACGTcount: A:0.16, C:0.17, G:0.23, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTAA
Found at i:26702 original size:20 final size:20
Alignment explanation
Indices: 26674--26742 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
26664 CGAAACTTAA
26674 ATCGCAACGCGAAAATGACC
1 ATCGCAACGCGAAAATGACC
* * *
26694 ATCGTAACGCGGAAATGACT
1 ATCGCAACGCGAAAATGACC
* ** *
26714 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACC
26734 ATCGCAACG
1 ATCGCAACG
26743 GGATAATCGC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACC
Found at i:26841 original size:14 final size:14
Alignment explanation
Indices: 26819--26849 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
26809 GCGAATTTAG
26819 TTTCACGTTGCGAT
1 TTTCACGTTGCGAT
*
26833 TTTCTCGTTGCGAT
1 TTTCACGTTGCGAT
26847 TTT
1 TTT
26850 TATTTCGCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (14 bp):
TTTCACGTTGCGAT
Found at i:26914 original size:19 final size:20
Alignment explanation
Indices: 26886--26928 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
26876 CGATAGTCAT
26886 TTTCGCGTTGCGA-TTTAAG
1 TTTCGCGTTGCGATTTTAAG
*
26905 TTTCGTGTTGCGATTTTAAG
1 TTTCGCGTTGCGATTTTAAG
26925 TTTC
1 TTTC
26929 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 12 0.55
20 10 0.45
ACGTcount: A:0.14, C:0.14, G:0.23, T:0.49
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTAAG
Found at i:28889 original size:27 final size:27
Alignment explanation
Indices: 28859--28970 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
28849 CATTTTTTGC
*
28859 TTGTTTAATTGATTTGTAAAAGTTGAT
1 TTGTTTAATTGATGTGTAAAAGTTGAT
* *
28886 TTGTTTAATATTGATGTGTAAATAATTCTTATTTGT
1 TTGTTT-A-ATTGATGTGT-AA-AAGT-TGA----T
*
28922 GCTTGTTTAATTGATTTGTAAAAGTTGAT
1 --TTGTTTAATTGATGTGTAAAAGTTGAT
28951 TTGTTTAATTGATGTGTAAA
1 TTGTTTAATTGATGTGTAAA
28971 TAATTCTTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
27 25 0.37
28 1 0.01
29 10 0.15
30 2 0.03
31 3 0.04
32 2 0.03
33 2 0.03
34 3 0.04
35 2 0.03
36 10 0.15
37 1 0.01
38 6 0.09
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.52
Consensus pattern (27 bp):
TTGTTTAATTGATGTGTAAAAGTTGAT
Found at i:28909 original size:72 final size:66
Alignment explanation
Indices: 28779--29022 Score: 241
Period size: 63 Copynumber: 3.6 Consensus size: 66
28769 GGGGTACACT
* * * *
28779 TTTTTTGATTGTTTAATTTATTCT-TAAAAGTCTGATTTGTTTAATTGATGAGGAAAATAAGAAT
1 TTTTTTGCTTGTTTAATTGATT-TGTAAAAGT-TGATTTGTTTAATTGATG-TGTAAATAA-AAT
28843 TATTAGCA
62 TATT---A
*
28851 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAAT--AATTC
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTT-A-ATTGATGTGTAAATAAAATTA
28914 TTA
64 TTA
* *
28917 -TTTGTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAAT--AATTCTT
1 TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAAATTATT
28979 A
66 A
* *
28980 -TTTGTGCTTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TTTTTTGCTTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
29023 GATTTCAATA
Statistics
Matches: 158, Mismatches: 7, Indels: 19
0.86 0.04 0.10
Matches are distributed among these distances:
63 42 0.27
64 1 0.01
65 39 0.25
66 1 0.01
67 18 0.11
69 6 0.04
71 11 0.07
72 33 0.21
73 7 0.04
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.51
Consensus pattern (66 bp):
TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAAAATTATT
A
Found at i:28942 original size:36 final size:36
Alignment explanation
Indices: 28886--28999 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
28876 AAAAGTTGAT
28886 TTGTTTAATATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTT-A-ATTGATGTGTAAATAATTCTTATTTGTGC
* * *
28924 TTGTTTAATTGATTTGT-AA-AAGT-TGA----T--
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
28951 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
1 TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
*
28987 TTATTTAATTGAT
1 TTGTTTAATTGAT
29000 TGAAATGTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
27 16 0.27
28 2 0.03
29 4 0.07
30 2 0.03
33 2 0.03
34 4 0.07
35 2 0.03
36 21 0.35
37 1 0.02
38 6 0.10
ACGTcount: A:0.27, C:0.04, G:0.16, T:0.54
Consensus pattern (36 bp):
TTGTTTAATTGATGTGTAAATAATTCTTATTTGTGC
Found at i:28994 original size:63 final size:65
Alignment explanation
Indices: 28856--29022 Score: 275
Period size: 63 Copynumber: 2.5 Consensus size: 65
28846 TAGCATTTTT
28856 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTG
28921 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTT-A-ATTGATGTGTAAATAATTCTTATTTG
1 TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTG
*
28984 TGCTTATTTAATTGATTGAAATGTAAAAGTTGATTTGTT
1 TGCTTGTTTAATTGATT----TGTAAAAGTTGATTTGTT
29023 GATTTCAATA
Statistics
Matches: 97, Mismatches: 1, Indels: 6
0.93 0.01 0.06
Matches are distributed among these distances:
63 42 0.43
64 1 0.01
65 36 0.37
67 18 0.19
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.51
Consensus pattern (65 bp):
TGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATATTGATGTGTAAATAATTCTTATTTG
Found at i:29099 original size:20 final size:20
Alignment explanation
Indices: 29074--29127 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
29064 AGGTACACTT
*
29074 TCGCAACGCTAAA-CTCAAAA
1 TCGCAACGCGAAAGC-CAAAA
**
29094 TCGCAATACGAAAGCCAAAA
1 TCGCAACGCGAAAGCCAAAA
29114 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
29128 TCAATTTGCG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
20 27 0.96
21 1 0.04
ACGTcount: A:0.44, C:0.28, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAGCCAAAA
Found at i:29227 original size:20 final size:20
Alignment explanation
Indices: 29170--29238 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
29160 GCGATTTTCT
* *
29170 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
* *
29190 CATTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
29210 CGTTGAGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
29230 CGTTGCGAT
1 CGTTGCGAT
29239 TTTTGAGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:29507 original size:140 final size:140
Alignment explanation
Indices: 29255--29533 Score: 513
Period size: 140 Copynumber: 2.0 Consensus size: 140
29245 GTTGCGATAA
* * *
29255 TCAAATTCGTGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCATAGC
29320 AATGTTCAAACTAAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTAAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAAAATA
29385 CACATAATAG
131 CACATAATAG
29395 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCATAGC
1 TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCATAGC
* *
29460 AATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAATA
66 AATGTTCAAACTAAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAAAATA
29525 CACATAATA
131 CACATAATA
29534 CAAAGTTTGC
Statistics
Matches: 134, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 134 1.00
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (140 bp):
TCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCATAGC
AATGTTCAAACTAAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAAAATA
CACATAATAG
Found at i:29679 original size:18 final size:19
Alignment explanation
Indices: 29656--29706 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
29646 TGAGCTTTGG
*
29656 ATTTTGAT-GAGGGTCCAT
1 ATTTTGATAGAGGATCCAT
*
29674 ATTTTGGTAGAGGATCCAT
1 ATTTTGATAGAGGATCCAT
*
29693 ATTTTGGTAGAGGA
1 ATTTTGATAGAGGA
29707 AAAGATGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 7 0.23
19 23 0.77
ACGTcount: A:0.25, C:0.08, G:0.29, T:0.37
Consensus pattern (19 bp):
ATTTTGATAGAGGATCCAT
Found at i:29691 original size:19 final size:19
Alignment explanation
Indices: 29664--29706 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
29654 GGATTTTGAT
*
29664 GAGGGTCCATATTTTGGTA
1 GAGGATCCATATTTTGGTA
29683 GAGGATCCATATTTTGGTA
1 GAGGATCCATATTTTGGTA
29702 GAGGA
1 GAGGA
29707 AAAGATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.26, C:0.09, G:0.33, T:0.33
Consensus pattern (19 bp):
GAGGATCCATATTTTGGTA
Found at i:31700 original size:14 final size:14
Alignment explanation
Indices: 31681--31707 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31671 TCCCGTGGTA
31681 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
31695 TTTTCTTCGGGGA
1 TTTTCTTCGGGGA
31708 TTTCTCCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.19, G:0.30, T:0.44
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:32935 original size:19 final size:19
Alignment explanation
Indices: 32911--32950 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
32901 ATTTGTGATA
* *
32911 TTAGAGATCGCGTTGCGAT
1 TTAGAGATCACATTGCGAT
32930 TTAGAGATCACATTGCGAT
1 TTAGAGATCACATTGCGAT
32949 TT
1 TT
32951 TATTGTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (19 bp):
TTAGAGATCACATTGCGAT
Found at i:42286 original size:87 final size:87
Alignment explanation
Indices: 42140--42315 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 87
42130 AATTGGGAAA
42140 CACATGATTATATAGTATTTCGTAATAGCCTCATTAGACTTTACATCTTTCGTAATAACTTCTAA
1 CACATGATTATATAGTATTTCGTAATAGCCTCATTAGACTTTACATCTTTCGTAATAACTTCTAA
*
42205 TGATTCTGCTACTTGACTATAC
66 AGATTCTGCTACTTGACTATAC
42227 CACATGATTATATAGTATTTCGTAATAGCCTCATTAGACTTTACATCTTTCGTAATAACTTCTAA
1 CACATGATTATATAGTATTTCGTAATAGCCTCATTAGACTTTACATCTTTCGTAATAACTTCTAA
42292 AGATTCTGCTACTTGACTATAC
66 AGATTCTGCTACTTGACTATAC
42314 CA
1 CA
42316 ACAAAGTATC
Statistics
Matches: 88, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 88 1.00
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (87 bp):
CACATGATTATATAGTATTTCGTAATAGCCTCATTAGACTTTACATCTTTCGTAATAACTTCTAA
AGATTCTGCTACTTGACTATAC
Found at i:49499 original size:27 final size:27
Alignment explanation
Indices: 49465--49523 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
49455 GGTTTAATAT
*
49465 AAAAATAATTGCCTAAACTTTACATCG
1 AAAAATAATTACCTAAACTTTACATCG
* * *
49492 AAAAATAATTACCTAAATTTTGCATTG
1 AAAAATAATTACCTAAACTTTACATCG
49519 AAAAA
1 AAAAA
49524 CGTTTAATAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAAATAATTACCTAAACTTTACATCG
Found at i:62957 original size:14 final size:14
Alignment explanation
Indices: 62938--62965 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
62928 TCGATTATAT
62938 GTTCATTTATGTTC
1 GTTCATTTATGTTC
62952 GTTCATTTATGTTC
1 GTTCATTTATGTTC
62966 ATTTATGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:62967 original size:24 final size:26
Alignment explanation
Indices: 62925--62976 Score: 90
Period size: 24 Copynumber: 2.1 Consensus size: 26
62915 TGTTCGTGAA
62925 CGTTCGATTATATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
62951 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
62975 CG
1 CG
62977 AACATAGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 18 0.69
25 3 0.12
26 5 0.19
ACGTcount: A:0.17, C:0.13, G:0.15, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:68355 original size:25 final size:25
Alignment explanation
Indices: 68296--68360 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
68286 AGAAGGAGGA
68296 AGAAT-AAGAA-AA-AAAGCAGAAG
1 AGAATGAAGAAGAAGAAAGCAGAAG
* * * *
68318 AGGAGGAATAAGAAGAAAGCAGAAT
1 AGAATGAAGAAGAAGAAAGCAGAAG
68343 AGAATGAAGAAGAAGAAA
1 AGAATGAAGAAGAAGAAA
68361 AAGCCACGTC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 3 0.09
23 4 0.12
24 2 0.06
25 24 0.73
ACGTcount: A:0.63, C:0.03, G:0.28, T:0.06
Consensus pattern (25 bp):
AGAATGAAGAAGAAGAAAGCAGAAG
Found at i:70425 original size:14 final size:14
Alignment explanation
Indices: 70403--70433 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
70393 CTCTTCAAGA
*
70403 AATTTCTTTTGTCC
1 AATTCCTTTTGTCC
70417 AATTCCTTTTGTCC
1 AATTCCTTTTGTCC
70431 AAT
1 AAT
70434 GTATTTGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (14 bp):
AATTCCTTTTGTCC
Found at i:71609 original size:6 final size:6
Alignment explanation
Indices: 71598--71694 Score: 167
Period size: 6 Copynumber: 16.2 Consensus size: 6
71588 GACACGTATT
* *
71598 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
71646 ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
71694 A
1 A
71695 GCCGAGCCGA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 89 1.00
ACGTcount: A:0.31, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:71702 original size:5 final size:5
Alignment explanation
Indices: 71692--71730 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
71682 ACCACGACCA
* * *
71692 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
71731 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:77606 original size:6 final size:6
Alignment explanation
Indices: 77595--77697 Score: 179
Period size: 6 Copynumber: 17.2 Consensus size: 6
77585 GACACGTATT
*
77595 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
* *
77643 ACCTCG ACCTCG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
77691 ACCACG A
1 ACCACG A
77698 GCCGAGCCGA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 95 1.00
ACGTcount: A:0.31, C:0.50, G:0.17, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:77705 original size:5 final size:5
Alignment explanation
Indices: 77695--77733 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
77685 ACCACGACCA
* * *
77695 CGAGC CGAGC CGAGC CGTGC CGAGC CGAGA CGAGA CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
77734 ACGGACGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.23, C:0.33, G:0.41, T:0.03
Consensus pattern (5 bp):
CGAGC
Found at i:80932 original size:21 final size:22
Alignment explanation
Indices: 80898--80942 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
80888 GACCAAATTC
**
80898 TTTTTTTATTTTAT-TATTATT
1 TTTTTTTAAATTATATATTATT
*
80919 TTTTTTTAAATTATATTTTATT
1 TTTTTTTAAATTATATATTATT
80941 TT
1 TT
80943 AAATTTCAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTTTTAAATTATATATTATT
Found at i:80935 original size:17 final size:18
Alignment explanation
Indices: 80901--80947 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
80891 CAAATTCTTT
80901 TTTTATTTT--ATTATTA
1 TTTTATTTTAAATTATTA
*
80917 TTTTTTTTTAAATTA-TA
1 TTTTATTTTAAATTATTA
80934 TTTTATTTTAAATT
1 TTTTATTTTAAATT
80948 TCAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 8 0.30
17 15 0.56
18 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTATTTTAAATTATTA
Found at i:81080 original size:17 final size:16
Alignment explanation
Indices: 81053--81097 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
81043 TTAAAATTAG
*
81053 TTTAAATTTTATAATTT
1 TTTATATTTTAT-ATTT
81070 TATT-TATTTTATATTT
1 T-TTATATTTTATATTT
81086 TTTATATTTTAT
1 TTTATATTTTAT
81098 TTTAGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 13 0.52
17 8 0.32
18 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATATTTTATATTT
Found at i:83003 original size:21 final size:22
Alignment explanation
Indices: 82978--83018 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
82968 CTAGGACTGA
*
82978 GAGTATTGATA-CTCCTTTAAT
1 GAGTATCGATATCTCCTTTAAT
*
82999 GAGTATCGATATTTCCTTTA
1 GAGTATCGATATCTCCTTTA
83019 TAATTTCTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.44
Consensus pattern (22 bp):
GAGTATCGATATCTCCTTTAAT
Done.