Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004283.1 Hibiscus syriacus cultivar Beakdansim tig00009388_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: 100031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6899 original size:3 final size:3
Alignment explanation
Indices: 6885--6965 Score: 71
Period size: 3 Copynumber: 28.0 Consensus size: 3
6875 GTTGTATCTG
* *
6885 TAA TAA -AA TAA TAA TAA TAG TAA TAA TAA -AA -AA TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
6930 TAG TAG TAA TAA AAA TAA AAA TAA TAA -ATA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA
6966 AAAACCAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
2 7 0.11
3 56 0.88
4 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:7448 original size:73 final size:73
Alignment explanation
Indices: 7361--7526 Score: 260
Period size: 73 Copynumber: 2.3 Consensus size: 73
7351 TCTTCAGATG
* * * * *
7361 AGTTCTTCTCATTATGAACTCTCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCAAAAA
1 AGTTCTTCTCATTATGAACTCGCACTGGAAAAGTTGATCCATCGAATGATAAATTCAAGCAAAAA
7426 GTTGAACA
66 GTTGAACA
* * *
7434 AGTTCTTCTCATTATGAACTCGCACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGCACTGGAAAAGTTGATCCATCGAATGATAAATTCAAGCAAAAA
7499 GTTGAACA
66 GTTGAACA
7507 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
7527 TCTTCTTCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
73 85 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (73 bp):
AGTTCTTCTCATTATGAACTCGCACTGGAAAAGTTGATCCATCGAATGATAAATTCAAGCAAAAA
GTTGAACA
Found at i:7546 original size:24 final size:23
Alignment explanation
Indices: 7511--7555 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 23
7501 TGAACAAGTT
7511 CTTCTCATTATGAACTTCTTCTTC
1 CTTCTCATTATG-ACTTCTTCTTC
*
7535 CTTCTTCA-TATGAGTTCTTCT
1 CTTC-TCATTATGACTTCTTCT
7556 CATTATGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 8 0.42
24 8 0.42
25 3 0.16
ACGTcount: A:0.16, C:0.27, G:0.07, T:0.51
Consensus pattern (23 bp):
CTTCTCATTATGACTTCTTCTTC
Found at i:7551 original size:113 final size:113
Alignment explanation
Indices: 7434--7906 Score: 867
Period size: 113 Copynumber: 4.2 Consensus size: 113
7424 AAGTTGAACA
*
7434 AGTTCTTCTCATTATGAACTCG-CACTGGCAATGTTGATCCATCGAATGATAAATTCAAGCGAAA
1 AGTTCTTCTCATTATGAACTCGAC-CTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAA
*
7498 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCATATG
65 AGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
7547 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
*
7612 GTTGAACAAGTTCTTCTAATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
7660 AGTTCTTCTCATTATGAACTCGACCTGGTAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
7725 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
* **
7773 AGTTCTTCTCATTATGAACTCGACCTGGTAATACTGATCCATCGAATGATGAATTCAAGCGAAAA
1 AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
7838 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
66 GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
7886 AGTTCTTCTCATTATGAACTC
1 AGTTCTTCTCATTATGAACTC
7907 TTCCAGAAAT
Statistics
Matches: 352, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
113 351 1.00
114 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCGAAAA
GTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:8367 original size:22 final size:22
Alignment explanation
Indices: 8342--8396 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
8332 GATAAAGCTT
*
8342 TCATCTTTGAAAAGAGAATCTG
1 TCATCTTTGAAAAGAGAATCTA
* *
8364 TCATCTTTAAAAAGGGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
8386 TCATCTTTGAA
1 TCATCTTTGAA
8397 GAGTGTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:8845 original size:54 final size:54
Alignment explanation
Indices: 8763--8918 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
8753 AGAATAGCAG
* *
8763 GTTCGTAAAACATTTGA-AAGCGCATTCATCATTTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAA-CACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
*
8817 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
* * * *
8871 GTTCGTAAAGCGTTTGACAACACATTCATCCTTTTCTATGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGC
8919 CAAGATTTCT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 91 0.98
55 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
Found at i:11191 original size:114 final size:114
Alignment explanation
Indices: 10991--11216 Score: 371
Period size: 114 Copynumber: 2.0 Consensus size: 114
10981 ACGATCATAC
* * * * *
10991 AATTCATCTTTCAATTCTAATGATTGGTTCTGGGGTTCCTACCGAACCATATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
11056 GAACACTTCTAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAGCA
66 GAACACTTCCAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAGCA
* *
11105 AATTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAA
1 AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
*
11170 GAACACTTCCAGAAGATGTTATTGGGTCTCCTTATTTCTACTATGAG
66 GAACACTTCCAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAG
11217 AACGTGGCAC
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
AATTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGTTATGGGGTCTCCTTATTTCTACTATGAGCA
Found at i:15352 original size:20 final size:20
Alignment explanation
Indices: 15329--15367 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
15319 CGAACGTAAA
*
15329 AATGCAAATATAAAAATGTG
1 AATGCAAACATAAAAATGTG
* *
15349 AATGTAACCATAAAAATGT
1 AATGCAAACATAAAAATGT
15368 AAATTGTGCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.54, C:0.08, G:0.13, T:0.26
Consensus pattern (20 bp):
AATGCAAACATAAAAATGTG
Found at i:17754 original size:30 final size:30
Alignment explanation
Indices: 17699--17755 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
17689 AAATTAATCA
** *
17699 AATAATAAATATTAATATGATTAAAATAAT
1 AATAATAAATATTAATAACAATAAAATAAT
*
17729 AATAATAATTATTAATAACAATAAAAT
1 AATAATAAATATTAATAACAATAAAAT
17756 TGCAATGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (30 bp):
AATAATAAATATTAATAACAATAAAATAAT
Found at i:19098 original size:6 final size:6
Alignment explanation
Indices: 19072--19148 Score: 75
Period size: 6 Copynumber: 13.0 Consensus size: 6
19062 GTCGTATCTG
* * * * *
19072 TAATAA -AATTA TAATAT TAATAA TAATAT TAATAT TAATAA TAAAAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
* * *
19119 TAATAA TAGTAA TAAAAA TAAAAA TAATAA
1 TAATAA TAATAA TAATAA TAATAA TAATAA
19149 ATATAAAAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
5 4 0.07
6 54 0.93
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (6 bp):
TAATAA
Found at i:19162 original size:6 final size:6
Alignment explanation
Indices: 19111--19163 Score: 52
Period size: 6 Copynumber: 8.3 Consensus size: 6
19101 TAATATTAAT
* **
19111 AATAAA AATAAT AATAGT AATAAA AATAAA AATAATAA ATATAAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AAT-A-AA A-ATAAA AATAAA
19162 AA
1 AA
19164 AACCAAATGT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 30 0.75
7 4 0.10
8 4 0.10
9 2 0.05
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
AATAAA
Found at i:19171 original size:21 final size:21
Alignment explanation
Indices: 19102--19178 Score: 66
Period size: 21 Copynumber: 3.5 Consensus size: 21
19092 TAATAATATT
* *
19102 AATATTAATAATAAAAATAATA
1 AATA-TAAAAATAAAAATAACA
*
19124 ATAGTAATAAAAATAAAAATAATA
1 A-A-T-ATAAAAATAAAAATAACA
19148 AATATAAAAATAAAAA-AACCA
1 AATATAAAAATAAAAATAA-CA
*
19169 AATGTAAAAA
1 AATATAAAAA
19179 ACTAGTGTCT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
20 2 0.04
21 23 0.48
22 2 0.04
23 2 0.04
24 18 0.38
25 1 0.02
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (21 bp):
AATATAAAAATAAAAATAACA
Found at i:21177 original size:18 final size:19
Alignment explanation
Indices: 21156--21191 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21146 ATCACAACGT
*
21156 TTTATTT-TGGATAAAAAA
1 TTTATTTGTAGATAAAAAA
21174 TTTATTTGTAGATAAAAA
1 TTTATTTGTAGATAAAAA
21192 CTGTTAGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (19 bp):
TTTATTTGTAGATAAAAAA
Found at i:27985 original size:19 final size:19
Alignment explanation
Indices: 27957--27994 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
27947 TATAATCCAA
*
27957 AATTTAATATATTTGTTTT
1 AATTTAATATAATTGTTTT
*
27976 AATTTGATATAATTGTTTT
1 AATTTAATATAATTGTTTT
27995 TATAAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
AATTTAATATAATTGTTTT
Found at i:28262 original size:31 final size:31
Alignment explanation
Indices: 28224--28302 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 31
28214 TAATATACTT
*
28224 GTCACTAATATTATCGATTTGTAACAAAATA
1 GTCACTAACATTATCGATTTGTAACAAAATA
* *
28255 GTCACTAACGTTATCGTTTTGTAACAAAATA
1 GTCACTAACATTATCGATTTGTAACAAAATA
28286 GTCACTCCAACATTATC
1 GTCACT--AACATTATC
28303 TCCGTTAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 34 0.81
33 8 0.19
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (31 bp):
GTCACTAACATTATCGATTTGTAACAAAATA
Found at i:29334 original size:11 final size:10
Alignment explanation
Indices: 29303--29339 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
29293 CCATTTCAAA
*
29303 TTTTAAATTT
1 TTTTATATTT
29313 TTTTATA-TT
1 TTTTATATTT
29322 TTTTATATTT
1 TTTTATATTT
29332 TTTT-TATT
1 TTTTATATT
29340 CAAAATAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 13 0.52
10 12 0.48
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTATATTT
Found at i:50912 original size:13 final size:13
Alignment explanation
Indices: 50894--50924 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
50884 CTCTTGTCGG
*
50894 TTGTCTTCTCCAT
1 TTGTCTTCGCCAT
50907 TTGTCTTCGCCAT
1 TTGTCTTCGCCAT
50920 TTGTC
1 TTGTC
50925 ATGCATGCAC
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:0.06, C:0.29, G:0.13, T:0.52
Consensus pattern (13 bp):
TTGTCTTCGCCAT
Found at i:54550 original size:53 final size:52
Alignment explanation
Indices: 54492--54618 Score: 159
Period size: 53 Copynumber: 2.4 Consensus size: 52
54482 TTCATATAAG
*
54492 GTCGAATGCAGGTCGGGCTT-ATTTTGACATTATTATGTTCAATTCAGATTCAA
1 GTCGAATGCAGGTCGGG-TTCA-TTTGACATTATCATGTTCAATTCAGATTCAA
* *
54545 GTCGAATGCAGGTCGGGTTCGATTTGATATTATCATGTTCAATTCAGATTTAA
1 GTCGAATGCAGGTCGGGTTC-ATTTGACATTATCATGTTCAATTCAGATTCAA
* *
54598 GTCG-TTCACAGGTCGGGTTCA
1 GTCGAAT-GCAGGTCGGGTTCA
54619 AATCCAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
52 4 0.06
53 61 0.92
54 1 0.02
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (52 bp):
GTCGAATGCAGGTCGGGTTCATTTGACATTATCATGTTCAATTCAGATTCAA
Found at i:60311 original size:29 final size:29
Alignment explanation
Indices: 60263--60351 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
60253 CTTGATAAAT
* *
60263 TAAATTAAATTAAAATCCCATATATTTTA
1 TAAATTAAAATAAAACCCCATATATTTTA
* * *
60292 TAAATTATAATAATACCCCATATTTTTTA
1 TAAATTAAAATAAAACCCCATATATTTTA
* * *
60321 CAAATTAAAATAAAAGCCCAGA-ATTTTA
1 TAAATTAAAATAAAACCCCATATATTTTA
60349 TAA
1 TAA
60352 TCATTACAGC
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.48, C:0.12, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAATTAAAATAAAACCCCATATATTTTA
Found at i:63166 original size:13 final size:13
Alignment explanation
Indices: 63148--63172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
63138 TTCATCTCAC
63148 AATAATTTTTTAA
1 AATAATTTTTTAA
63161 AATAATTTTTTA
1 AATAATTTTTTA
63173 TATTAAAAAA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATAATTTTTTAA
Found at i:65478 original size:31 final size:29
Alignment explanation
Indices: 65410--65479 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
65400 AATATTATTT
*
65410 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
65440 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
65473 TTATATT
1 TTATATT
65480 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:65577 original size:24 final size:23
Alignment explanation
Indices: 65534--65579 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
65524 ATTAATTAGT
*
65534 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAATATCTATATTAAA
65557 ATATTATTAAATTAT-TATATTAA
1 ATATT-TTAAA-TATCTATATTAA
65580 TATTAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 5 0.25
24 12 0.60
25 3 0.15
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTTTAAATATCTATATTAAA
Found at i:65604 original size:27 final size:27
Alignment explanation
Indices: 65574--65654 Score: 78
Period size: 27 Copynumber: 3.0 Consensus size: 27
65564 TAAATTATTA
*
65574 TATTAATATTAAATATATAAATAATAT
1 TATTACTATTAAATATATAAATAATAT
*
65601 TATTCACTATT-AATA-ATTTAATAATAT
1 TATT-ACTATTAAATATA-TAAATAATAT
* *
65628 TATTTCTATGAAAT-TAATAAATAATAT
1 TATTACTATTAAATAT-ATAAATAATAT
65655 AAATTTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
26 5 0.11
27 33 0.75
28 6 0.14
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (27 bp):
TATTACTATTAAATATATAAATAATAT
Found at i:65668 original size:22 final size:22
Alignment explanation
Indices: 65640--65700 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
65630 TTTCTATGAA
*
65640 ATTAATAAATAATATAAATTTT
1 ATTAATAAATAATATAAATATT
* *
65662 ATTAATAACTTAT-TAAATATT
1 ATTAATAAATAATATAAATATT
65683 ATTAAAATAAA-AATATAA
1 ATT--AATAAATAATATAA
65701 TATCTTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 10 0.32
22 13 0.42
23 8 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
ATTAATAAATAATATAAATATT
Found at i:65721 original size:29 final size:28
Alignment explanation
Indices: 65678--65770 Score: 77
Period size: 29 Copynumber: 3.3 Consensus size: 28
65668 AACTTATTAA
*
65678 ATATTATTAAAATAAAAATATAATATCTT
1 ATATTATTAATATAAAAATATAATAT-TT
* *
65707 ATATTATTATTATAATATAAT-TGAT-TATT
1 ATATTATTAATATAA-A-AATATAATAT-TT
* *
65736 GTATTA-TAATATTAAAATATAATATTT
1 ATATTATTAATATAAAAATATAATATTT
65763 -TATTATTA
1 ATATTATTA
65771 TAAATATTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
26 8 0.16
27 8 0.16
28 7 0.14
29 21 0.41
30 4 0.08
31 3 0.06
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.49
Consensus pattern (28 bp):
ATATTATTAATATAAAAATATAATATTT
Found at i:65723 original size:26 final size:24
Alignment explanation
Indices: 65692--65771 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 24
65682 TATTAAAATA
65692 AAAATATAATATCTTATATTATTATT
1 AAAATATAATAT-TT-TATTATTATT
*
65718 ATAATATAATTGATTATTGTATTATAATATT
1 AAAATATAA-T-A-T-TT-TATTAT--TATT
65749 AAAATATAATATTTTATTATTAT
1 AAAATATAATATTTTATTATTAT
65772 AAATATTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
24 3 0.07
26 14 0.31
27 3 0.07
28 2 0.04
29 10 0.22
30 1 0.02
31 12 0.27
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (24 bp):
AAAATATAATATTTTATTATTATT
Found at i:65765 original size:23 final size:23
Alignment explanation
Indices: 65745--65799 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 23
65735 TGTATTATAA
65745 TATTA-AAATA-TAATATTTTAT
1 TATTATAAATATTAATATTTTAT
**
65766 TATTATAAATATTAATA-AATA-
1 TATTATAAATATTAATATTTTAT
65787 TATTATAAATATT
1 TATTATAAATATT
65800 TTAATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 18 0.60
22 7 0.23
23 5 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTATAAATATTAATATTTTAT
Found at i:65789 original size:12 final size:12
Alignment explanation
Indices: 65774--65806 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
65764 ATTATTATAA
65774 ATATTAATAAAT
1 ATATTAATAAAT
65786 ATATT-ATAAAT
1 ATATTAATAAAT
*
65797 ATTTTAATAA
1 ATATTAATAA
65807 TTAATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATTAATAAAT
Found at i:66340 original size:15 final size:15
Alignment explanation
Indices: 66320--66349 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66310 TATTTTAATG
66320 TCGTACAAGAACTAT
1 TCGTACAAGAACTAT
*
66335 TCGTACATGAACTAT
1 TCGTACAAGAACTAT
66350 AATGACTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (15 bp):
TCGTACAAGAACTAT
Found at i:68292 original size:19 final size:19
Alignment explanation
Indices: 68268--68312 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
68258 TAAATATAAG
68268 TTTAATGCATGAATTAGTC
1 TTTAATGCATGAATTAGTC
68287 TTTAATGCATGAATTAGTC
1 TTTAATGCATGAATTAGTC
68306 TTTAATG
1 TTTAATG
68313 ATGCTTGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.44
Consensus pattern (19 bp):
TTTAATGCATGAATTAGTC
Found at i:68345 original size:24 final size:24
Alignment explanation
Indices: 68313--68363 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
68303 GTCTTTAATG
68313 ATGCTTGATTTGTTGAAATAACGT
1 ATGCTTGATTTGTTGAAATAACGT
68337 ATGCTTGATTTGTTGAAATAACGT
1 ATGCTTGATTTGTTGAAATAACGT
68361 ATG
1 ATG
68364 ATTCGGGGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (24 bp):
ATGCTTGATTTGTTGAAATAACGT
Found at i:68925 original size:43 final size:43
Alignment explanation
Indices: 68859--69070 Score: 194
Period size: 43 Copynumber: 4.9 Consensus size: 43
68849 TTGATGTTCA
* * * *
68859 ACAAACGCCGCAAAAGGTATTGATATTTAGCGGCGTTTTGCAG
1 ACAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTTGCAC
* * * *
68902 AAAAACGCCACAATAGGTGTTGATATTTAGCGGCATTTGGCAG
1 ACAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTTGCAC
* * * *
68945 ACAAACGCCACAATAGGTGTTGATGTTTAGCGACATTTT-CTTC
1 ACAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTTGC-AC
* * * * * *
68988 ACAAACGCCGCAGTAGGTGTTGATTTTTATCGGCGTTTTCCCCC
1 ACAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTT-GCAC
* * *
69032 ACAAACGCCACAGA-AGATGTTGAGATTTGGCGGCGTTTT
1 ACAAACGCCACA-ATAGGTGTTGATATTTAGCGGCGTTTT
69071 CGTTGCAAAC
Statistics
Matches: 139, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 105 0.76
44 32 0.23
45 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
ACAAACGCCACAATAGGTGTTGATATTTAGCGGCGTTTTGCAC
Found at i:69529 original size:21 final size:21
Alignment explanation
Indices: 69504--69638 Score: 105
Period size: 21 Copynumber: 6.4 Consensus size: 21
69494 TGCGCATCTC
* *
69504 TGTGCTGCCGCTGCTTCTCTA
1 TGTGCTTCCGCTGCTGCTCTA
* *
69525 TGTGCTACCGCTGCCT-CTCTC
1 TGTGCTTCCGCTG-CTGCTCTA
* * * *
69546 TGTGCTGCCACTGCTTCTCTC
1 TGTGCTTCCGCTGCTGCTCTA
* *
69567 TCTGCTTCCGCTACTGCTCTA
1 TGTGCTTCCGCTGCTGCTCTA
*
69588 -GCTGCTTCCGCTACTGCTCTA
1 TG-TGCTTCCGCTGCTGCTCTA
*
69609 -GCTGCTTCCGCTGCTGCTCTC
1 TG-TGCTTCCGCTGCTGCTCTA
*
69630 TCTGCTTCC
1 TGTGCTTCC
69639 CTTGCTTCAT
Statistics
Matches: 96, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.02
21 92 0.96
22 2 0.02
ACGTcount: A:0.05, C:0.39, G:0.19, T:0.36
Consensus pattern (21 bp):
TGTGCTTCCGCTGCTGCTCTA
Found at i:69578 original size:63 final size:63
Alignment explanation
Indices: 69500--69646 Score: 140
Period size: 63 Copynumber: 2.3 Consensus size: 63
69490 ATATTGCGCA
* * * * *
69500 TCTCTGTGCTGCCGCTGCTTCTCTATG-TGCTACCGCTGCCT-CTCTCTG-TGCTGCCACTGCTT
1 TCTCTCTGCTTCCGCTGCTTCTCTA-GCTGCTACCGCT-ACTGCTCT-AGCTGCTGCCACTGCTG
69562 C
63 C
* * * * *
69563 TCTCTCTGCTTCCGCTACTGCTCTAGCTGCTTCCGCTACTGCTCTAGCTGCTTCCGCTGCTGC
1 TCTCTCTGCTTCCGCTGCTTCTCTAGCTGCTACCGCTACTGCTCTAGCTGCTGCCACTGCTGC
69626 TCTCTCTGCTTCC-CTTGCTTC
1 TCTCTCTGCTTCCGC-TGCTTC
69647 ATTTTCCGCT
Statistics
Matches: 68, Mismatches: 12, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
62 5 0.07
63 63 0.93
ACGTcount: A:0.05, C:0.39, G:0.18, T:0.37
Consensus pattern (63 bp):
TCTCTCTGCTTCCGCTGCTTCTCTAGCTGCTACCGCTACTGCTCTAGCTGCTGCCACTGCTGC
Found at i:69644 original size:21 final size:21
Alignment explanation
Indices: 69568--69638 Score: 106
Period size: 21 Copynumber: 3.4 Consensus size: 21
69558 GCTTCTCTCT
*
69568 CTGCTTCCGCTACTGCTCTAG
1 CTGCTTCCGCTGCTGCTCTAG
*
69589 CTGCTTCCGCTACTGCTCTAG
1 CTGCTTCCGCTGCTGCTCTAG
**
69610 CTGCTTCCGCTGCTGCTCTCT
1 CTGCTTCCGCTGCTGCTCTAG
69631 CTGCTTCC
1 CTGCTTCC
69639 CTTGCTTCAT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.06, C:0.41, G:0.18, T:0.35
Consensus pattern (21 bp):
CTGCTTCCGCTGCTGCTCTAG
Found at i:78182 original size:42 final size:42
Alignment explanation
Indices: 78136--78463 Score: 512
Period size: 42 Copynumber: 7.8 Consensus size: 42
78126 ATGTTAACCA
* *
78136 TATTGCGGCGTTTGAGCTATAAAAGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
*
78178 TATTGCGGCGTTTGATCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* *
78220 TATTACGGCGTTTGAGCTATAAACGCCGCTATATTACAACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* *
78262 TATTACGGCGTTTGATCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* * *
78304 TATTGCGGCGTTTGAGCTACAAACGTCACTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* *
78346 TATTGCGGCATTTTAGCTATAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
* * *
78388 TATTACGGCGTTTTAGCTACAAACGCCGCTATATTACTACTC
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
*
78430 TATTGCGACGTTTGAGCTATAAACGCCGCTATAT
1 TATTGCGGCGTTTGAGCTATAAACGCCGCTATAT
78464 GCTTAAAGTT
Statistics
Matches: 261, Mismatches: 25, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 261 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (42 bp):
TATTGCGGCGTTTGAGCTATAAACGCCGCTATATTACTACTC
Found at i:78858 original size:41 final size:39
Alignment explanation
Indices: 78731--78940 Score: 122
Period size: 41 Copynumber: 5.1 Consensus size: 39
78721 GTTTTTGTGA
* * *
78731 CGTTTTTATAAAAGCGCCACTATAGACAAAC-ATATTGCGG
1 CGTTTTTAGAAAA-CGCCACTATAAAC-AACTCTATTGCGG
* * * ** * *
78771 CATTTGTAGGAAAATCGCCGCTA-AATTATTACTCTTTTACGG
1 CGTTTTTA-GAAAA-CGCCACTATAA--ACAACTCTATTGCGG
78813 CGTTTTTAGCACAAACGCCACTATAAACAACTCTATTGCGG
1 CGTTTTTAG-A-AAACGCCACTATAAACAACTCTATTGCGG
* *
78854 CGTTTATATA-AAAACGCCGCTA-AATTACTACTCTATTGCGG
1 CGTTT-T-TAGAAAACGCCACTATAA--ACAACTCTATTGCGG
* * * *
78895 TGTTTTTTTAGAAAACGCCACTATAAACAATTATATTCCGG
1 CG--TTTTTAGAAAACGCCACTATAAACAACTCTATTGCGG
78936 CGTTT
1 CGTTT
78941 GAGCTATAAA
Statistics
Matches: 128, Mismatches: 27, Indels: 31
0.69 0.15 0.17
Matches are distributed among these distances:
39 5 0.04
40 17 0.13
41 60 0.47
42 34 0.27
43 12 0.09
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.32
Consensus pattern (39 bp):
CGTTTTTAGAAAACGCCACTATAAACAACTCTATTGCGG
Found at i:78878 original size:82 final size:82
Alignment explanation
Indices: 78733--78940 Score: 233
Period size: 82 Copynumber: 2.5 Consensus size: 82
78723 TTTTGTGACG
* * * * *
78733 TTTTTATAAAAGCGCCACTATAGACAAAC-ATATTGCGGCATTTGTAGGAAAATCGCCGCTAAAT
1 TTTTTAGAAAA-CGCCACTATAAAC-AACTATATTGCGGCGTTTATAGGAAAAACGCCGCTAAAT
* *
78797 TATTACTCTTTTACGGCG-
64 TACTACTCTATTACGGCGT
* *
78815 TTTTTAGCACAAACGCCACTATAAACAACTCTATTGCGGCGTTTATA-TAAAAACGCCGCTAAAT
1 TTTTTAG-A-AAACGCCACTATAAACAACTATATTGCGGCGTTTATAGGAAAAACGCCGCTAAAT
* *
78879 TACTACTCTATTGCGGTGTT
64 TACTACTCTATTACGGCG-T
* *
78899 TTTTTAGAAAACGCCACTATAAACAATTATATTCCGGCGTTT
1 TTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTT
78941 GAGCTATAAA
Statistics
Matches: 107, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
82 69 0.64
83 28 0.26
84 10 0.09
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.33
Consensus pattern (82 bp):
TTTTTAGAAAACGCCACTATAAACAACTATATTGCGGCGTTTATAGGAAAAACGCCGCTAAATTA
CTACTCTATTACGGCGT
Found at i:79083 original size:12 final size:12
Alignment explanation
Indices: 79066--79091 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
79056 GGCGTTTTCC
79066 CTAAAAACGCCG
1 CTAAAAACGCCG
79078 CTAAAAACGCCG
1 CTAAAAACGCCG
79090 CT
1 CT
79092 GCATAACACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.35, G:0.15, T:0.12
Consensus pattern (12 bp):
CTAAAAACGCCG
Found at i:79873 original size:60 final size:60
Alignment explanation
Indices: 79801--79916 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 60
79791 AGTTTTTAAT
* * * *
79801 GTTCTAATTTCATCTCCAAATTATGACTTTAATTCTAAATTAATCAT-CAAACTTTTAAAG
1 GTTCCAATTTCATCTCAAAACTATGACCTTAATTCTAAATTAATC-TCCAAACTTTTAAAG
* *
79861 GTTCCAATTTCATCTCAAAACTATGACCTTCATTCTAAATTGATCTCCAAACTTTT
1 GTTCCAATTTCATCTCAAAACTATGACCTTAATTCTAAATTAATCTCCAAACTTTT
79917 GAACATACAA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 48 0.98
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.41
Consensus pattern (60 bp):
GTTCCAATTTCATCTCAAAACTATGACCTTAATTCTAAATTAATCTCCAAACTTTTAAAG
Found at i:79930 original size:60 final size:60
Alignment explanation
Indices: 79806--79943 Score: 154
Period size: 60 Copynumber: 2.3 Consensus size: 60
79796 TTAATGTTCT
* * ** * *
79806 AATTTCATCTCCAAATTATGACTTTAATTCTAAATTAATCATCAAACTTTTAAAGGTTCC
1 AATTTCATCTCCAAACTATGACCTTAATTCTAAATTAATCATCAAACTTTTAAACATACA
* * * *
79866 AATTTCATCTCAAAACTATGACCTTCATTCTAAATTGATC-TCCAAACTTTTGAACATACA
1 AATTTCATCTCCAAACTATGACCTTAATTCTAAATTAATCAT-CAAACTTTTAAACATACA
*
79926 AATTTTATC-CCAAACTAT
1 AATTTCATCTCCAAACTAT
79944 CAGTATATAA
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 9 0.14
60 56 0.86
ACGTcount: A:0.37, C:0.21, G:0.04, T:0.38
Consensus pattern (60 bp):
AATTTCATCTCCAAACTATGACCTTAATTCTAAATTAATCATCAAACTTTTAAACATACA
Found at i:80147 original size:57 final size:58
Alignment explanation
Indices: 80058--80202 Score: 150
Period size: 57 Copynumber: 2.5 Consensus size: 58
80048 TTTGGATGCT
** * * *
80058 TTTGGGAATGAAATGGGAAGATTCATAAGTTTG-GGAATCAATTTAAAATG-AGTCATAA
1 TTTGGG-ATGAAATTAGAATATTCAAAAGTTTGAGG-ATCAATTTAAAATGAAGTAATAA
* *
80116 TTTGGGATGAAATTAGAATATTCAAAAGTTTGAGGATTAATTTAGAATGAAAGTAATAA
1 TTTGGGATGAAATTAGAATATTCAAAAGTTTGAGGATCAATTTAAAATG-AAGTAATAA
* * *
80175 TTTAGGGATTAAGTTAGAATATTTAAAA
1 TTT-GGGATGAAATTAGAATATTCAAAA
80203 AATGTAAGAA
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
57 34 0.47
58 8 0.11
59 10 0.14
60 21 0.29
ACGTcount: A:0.42, C:0.03, G:0.21, T:0.34
Consensus pattern (58 bp):
TTTGGGATGAAATTAGAATATTCAAAAGTTTGAGGATCAATTTAAAATGAAGTAATAA
Found at i:86005 original size:12 final size:13
Alignment explanation
Indices: 85974--86007 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
85964 AAATTAGATG
*
85974 CACTTAATTAAAT
1 CACTTAAATAAAT
85987 CACTTAAATAAAT
1 CACTTAAATAAAT
86000 -ACTTAAAT
1 CACTTAAAT
86008 TACATATGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (13 bp):
CACTTAAATAAAT
Found at i:86257 original size:20 final size:20
Alignment explanation
Indices: 86229--86270 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
86219 AGTCAATGGG
*
86229 TCAGACCAGTTCAGGTTGAC
1 TCAGACCAGGTCAGGTTGAC
* *
86249 TCAGGCCAGGTCGGGTTGAC
1 TCAGACCAGGTCAGGTTGAC
86269 TC
1 TC
86271 GAACCGGTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (20 bp):
TCAGACCAGGTCAGGTTGAC
Found at i:90608 original size:13 final size:13
Alignment explanation
Indices: 90590--90616 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
90580 ACTCATCACC
90590 ACCAAACCAACAA
1 ACCAAACCAACAA
90603 ACCAAACCAACAA
1 ACCAAACCAACAA
90616 A
1 A
90617 GACGCATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.37, G:0.00, T:0.00
Consensus pattern (13 bp):
ACCAAACCAACAA
Done.