Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008837.1 Hibiscus syriacus cultivar Beakdansim tig00112041_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: 58080
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Found at i:3914 original size:20 final size:20
Alignment explanation
Indices: 3889--3926 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3879 AACATGTTAA
*
3889 AGAATGCATTGATGCACTGT
1 AGAATGCATCGATGCACTGT
*
3909 AGAATGTATCGATGCACT
1 AGAATGCATCGATGCACT
3927 TCAAGGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:7849 original size:15 final size:16
Alignment explanation
Indices: 7829--7863 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
7819 TTTGTAATTT
*
7829 TTAAAATTTTATTA-A
1 TTAAAATTTAATTATA
7844 TTAAAATTTAATTATA
1 TTAAAATTTAATTATA
7860 TTAA
1 TTAA
7864 GGGTTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAAAATTTAATTATA
Found at i:8164 original size:26 final size:27
Alignment explanation
Indices: 8124--8222 Score: 91
Period size: 26 Copynumber: 3.7 Consensus size: 27
8114 AAATAAATTT
8124 TAAAATAAAATATATATTTTAAATGAA-A
1 TAAAAT-AAA-ATATATTTTAAATGAAGA
* *
8152 TAAAATAAAATAT-TTTTAAATTAAGT
1 TAAAATAAAATATATTTTAAATGAAGA
* *
8178 TAATATAAAATATA-TTT-AAT-AAGT
1 TAAAATAAAATATATTTTAAATGAAGA
*
8202 TAATATAAAATTATATTTTAA
1 TAAAATAAAA-TATATTTTAA
8223 GGTAATATAT
Statistics
Matches: 63, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
24 14 0.22
25 17 0.27
26 22 0.35
27 4 0.06
28 6 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
TAAAATAAAATATATTTTAAATGAAGA
Found at i:8182 original size:24 final size:23
Alignment explanation
Indices: 8154--8219 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 23
8144 AAATGAAATA
*
8154 AAATAAAATATTTTTAAATTAAGTT
1 AAATAAAATATATTT-AA-TAAGTT
8179 AATATAAAATATATTTAATAAGTT
1 AA-ATAAAATATATTTAATAAGTT
8203 AATATAAAATTATATTT
1 AA-ATAAAA-TATATTT
8220 TAAGGTAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
24 15 0.39
25 11 0.29
26 12 0.32
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (23 bp):
AAATAAAATATATTTAATAAGTT
Found at i:8232 original size:25 final size:24
Alignment explanation
Indices: 8179--8250 Score: 67
Period size: 24 Copynumber: 2.9 Consensus size: 24
8169 AAATTAAGTT
*
8179 AATATAAAA-TATATTTAATAA-GTT
1 AATATAAAATTATATTT--TAAGGTA
8203 AATATAAAATTATATTTTAAGGTA
1 AATATAAAATTATATTTTAAGGTA
*
8227 ATATATAAAAATTATGAATTTAAG
1 A-ATAT-AAAATTAT-ATTTTAAG
8251 TATTTATACA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 3 0.07
24 12 0.29
25 11 0.27
26 8 0.20
27 7 0.17
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (24 bp):
AATATAAAATTATATTTTAAGGTA
Found at i:11848 original size:54 final size:54
Alignment explanation
Indices: 11766--11874 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
11756 CATAAACAAT
11766 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
1 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
11820 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
1 TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
11874 T
1 T
11875 TGCGGAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.38
Consensus pattern (54 bp):
TATGATGTCATTCTAGATGTCTGTTATCCATCTATTGTTGAACAAGAACTGCGA
Found at i:13796 original size:15 final size:15
Alignment explanation
Indices: 13778--13833 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
13768 TAACCGGTTT
13778 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
13793 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
13810 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
13825 CGATTTTAA
1 CGGTTTTAA
13834 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:13806 original size:17 final size:17
Alignment explanation
Indices: 13781--13831 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
13771 CCGGTTTCGG
13781 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
13798 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
13813 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
13830 TT
1 TT
13832 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:14249 original size:13 final size:13
Alignment explanation
Indices: 14228--14282 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
14218 AAGTTCGATA
*
14228 AATTCAAATACTT
1 AATTGAAATACTT
14241 AATTGAAATACTT
1 AATTGAAATACTT
* *
14254 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
14268 AATTGAAATACTT
1 AATTGAAATACTT
14281 AA
1 AA
14283 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:14364 original size:32 final size:33
Alignment explanation
Indices: 14268--14366 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
14258 AACTCAACAT
* * *
14268 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
14301 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
14334 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
14366 A
1 A
14367 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:14385 original size:21 final size:21
Alignment explanation
Indices: 14361--14400 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
14351 ACTTCAAGTT
14361 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
14382 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
14401 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:18502 original size:29 final size:29
Alignment explanation
Indices: 18460--18521 Score: 124
Period size: 29 Copynumber: 2.1 Consensus size: 29
18450 AGAGACACAT
18460 ATAACGAGAGAGTTTTCATAGTACAAAAA
1 ATAACGAGAGAGTTTTCATAGTACAAAAA
18489 ATAACGAGAGAGTTTTCATAGTACAAAAA
1 ATAACGAGAGAGTTTTCATAGTACAAAAA
18518 ATAA
1 ATAA
18522 AAAGGATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (29 bp):
ATAACGAGAGAGTTTTCATAGTACAAAAA
Found at i:22835 original size:37 final size:37
Alignment explanation
Indices: 22785--22860 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
22775 GTGGCCGCTA
22785 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
1 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
22822 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
1 GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
22859 GG
1 GG
22861 TGGCCGAGGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.21, C:0.21, G:0.42, T:0.16
Consensus pattern (37 bp):
GGCGTCCGAGAGGAACTAGCGAGCTAGGGCAGTTCGT
Found at i:23688 original size:75 final size:75
Alignment explanation
Indices: 23599--23761 Score: 211
Period size: 75 Copynumber: 2.2 Consensus size: 75
23589 TAAACTCAAG
* **
23599 TTTAGGATAATATTTTAAACATTATATTT-TATTTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTAGGATATTATTTTAAACATTATATTTGT-TTTAGGTATTTTAGTTTAAATAGGTTTTAGTAT
*
23663 TTCAATTAAGT
65 TTCAATTAAGA
* ** *
23674 TTTAGGATATTATTTTATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTAAACATTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
* *
23739 TTAATTAGGA
66 TCAATTAAGA
*
23749 TTTAGAATATTAT
1 TTTAGGATATTAT
23762 ATTATTTTTT
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
75 75 0.99
76 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (75 bp):
TTTAGGATATTATTTTAAACATTATATTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATT
TCAATTAAGA
Found at i:23690 original size:32 final size:32
Alignment explanation
Indices: 23654--23722 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
23644 TTTAAATAGG
23654 TTTTAGTATTTCA-ATTAAGTTTTAGG-ATATTA
1 TTTTA-TATTTCATATT-AGTTTTAGGTATATTA
* * *
23686 TTTTATATTTTATATTTGTTTTAGGTATTTTA
1 TTTTATATTTCATATTAGTTTTAGGTATATTA
23718 TTTTA
1 TTTTA
23723 AATAGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 14 0.44
32 18 0.56
ACGTcount: A:0.26, C:0.01, G:0.10, T:0.62
Consensus pattern (32 bp):
TTTTATATTTCATATTAGTTTTAGGTATATTA
Found at i:23728 original size:18 final size:19
Alignment explanation
Indices: 23707--23752 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
23697 ATATTTGTTT
23707 TAGGTATTT-TATTTTAAA
1 TAGGTATTTATATTTTAAA
*
23725 TAGGT-TTTAGTATTTTAAT
1 TAGGTATTTA-TATTTTAAA
23744 TAGG-ATTTA
1 TAGGTATTTA
23753 GAATATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 3 0.12
18 5 0.21
19 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TAGGTATTTATATTTTAAA
Found at i:23740 original size:19 final size:19
Alignment explanation
Indices: 23716--23753 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23706 TTAGGTATTT
*
23716 TATTTTAAATAGGTTTTAG
1 TATTTTAAATAGGATTTAG
*
23735 TATTTTAATTAGGATTTAG
1 TATTTTAAATAGGATTTAG
23754 AATATTATAT
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:0.16, T:0.53
Consensus pattern (19 bp):
TATTTTAAATAGGATTTAG
Found at i:23774 original size:65 final size:65
Alignment explanation
Indices: 23690--23817 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
23680 ATATTATTTT
* * *
23690 ATATTTTATATTTGTTTTAGGTATTTTATTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAG
1 ATATTATATATTTGTTTTAGATATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTAG
23754 A
65 A
*
23755 ATATTATATTATTT-TTTTAGATATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 ATATTATA-TATTTGTTTTAGATATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
23818 AGATGTTTTA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 5 0.09
65 47 0.82
66 5 0.09
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.57
Consensus pattern (65 bp):
ATATTATATATTTGTTTTAGATATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGA
Found at i:23798 original size:75 final size:75
Alignment explanation
Indices: 23635--23783 Score: 183
Period size: 75 Copynumber: 2.0 Consensus size: 75
23625 TTTTATTTTT
* * * * *
23635 GTATTTTAGTTTAAATAGGTTTTAGTATTTCAATTAAGTTTTAGGATATTATTTTATATTTTATA
1 GTATTATATTTTAAATAGGTTTTAGTATTTCAATTAAGATTTAGAATATTATATTATATTTTATA
** *
23700 TTTGTTTTAG
66 GATATTTTAG
* * * *
23710 GTATTTTATTTTAAATAGGTTTTAGTATTTTAATTAGGATTTAGAATATTATATTAT-TTTTTTA
1 GTATTATATTTTAAATAGGTTTTAGTATTTCAATTAAGATTTAGAATATTATATTATATTTTATA
23774 GATATTTTAG
66 GATATTTTAG
23784 TTTAAATAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
74 13 0.20
75 51 0.80
ACGTcount: A:0.30, C:0.01, G:0.13, T:0.57
Consensus pattern (75 bp):
GTATTATATTTTAAATAGGTTTTAGTATTTCAATTAAGATTTAGAATATTATATTATATTTTATA
GATATTTTAG
Found at i:27438 original size:14 final size:14
Alignment explanation
Indices: 27414--27449 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
27404 CCCATTTTGT
*
27414 TTTATTTTCATTCTA
1 TTTA-TTTCATTCCA
27429 TTTATTTCATTCCA
1 TTTATTTCATTCCA
27443 TTTATTT
1 TTTATTT
27450 TAATTTTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 16 0.80
15 4 0.20
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTATTTCATTCCA
Found at i:27473 original size:11 final size:11
Alignment explanation
Indices: 27443--27473 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
27433 TTTCATTCCA
*
27443 TTTATTTTAAT
1 TTTATTTTTAT
27454 TTTATTTTTAT
1 TTTATTTTTAT
27465 TTTATTTTT
1 TTTATTTTT
27474 CTCTGAACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTATTTTTAT
Found at i:29859 original size:22 final size:22
Alignment explanation
Indices: 29834--29909 Score: 82
Period size: 22 Copynumber: 3.5 Consensus size: 22
29824 GTCCCATAGG
* *
29834 ACCATTATGTATGTCCCGAAGA
1 ACCACTATATATGTCCCGAAGA
*
29856 ACCACTGTATATGTCCCGAA-A
1 ACCACTATATATGTCCCGAAGA
* * *
29877 GACAACTGTATATGTCCCGAAGG
1 -ACCACTATATATGTCCCGAAGA
29900 ACCACTATAT
1 ACCACTATAT
29910 CCTGAAGGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.98
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (22 bp):
ACCACTATATATGTCCCGAAGA
Found at i:31088 original size:21 final size:21
Alignment explanation
Indices: 31064--31104 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
31054 AAAAAATTAT
*
31064 CTAAAACATTATTATTTTTTC
1 CTAAAACATTAATATTTTTTC
* *
31085 CTAAAATATTAATGTTTTTT
1 CTAAAACATTAATATTTTTT
31105 ACATTTCCGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.10, G:0.02, T:0.54
Consensus pattern (21 bp):
CTAAAACATTAATATTTTTTC
Found at i:31158 original size:21 final size:21
Alignment explanation
Indices: 31128--31174 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
31118 AGTGCCCAAT
* *
31128 AATAATAAAACTGATAGAAAA
1 AATAACAAAACCGATAGAAAA
* *
31149 AATAACAAAACCGGTAGAAAT
1 AATAACAAAACCGATAGAAAA
31170 AATAA
1 AATAA
31175 TGTTTCCGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.17
Consensus pattern (21 bp):
AATAACAAAACCGATAGAAAA
Found at i:37329 original size:17 final size:17
Alignment explanation
Indices: 37303--37343 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
37293 AGCGTCAAAT
* *
37303 AATAACATTTTACTGAA
1 AATAATATTTTACCGAA
37320 AATAATATTTTACCGAA
1 AATAATATTTTACCGAA
*
37337 AGTAATA
1 AATAATA
37344 ACATTTCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (17 bp):
AATAATATTTTACCGAA
Found at i:37980 original size:28 final size:28
Alignment explanation
Indices: 37949--38037 Score: 74
Period size: 28 Copynumber: 3.1 Consensus size: 28
37939 ATATTTTTTA
*
37949 TTTATGAATTATCATTAACACTTATTAG
1 TTTATGAATCATCATTAACACTTATTAG
* ** * * *
37977 TTTAATG-ACCGATTGTTATATATTTTTTA-
1 TTT-ATGAATC-ATCATTA-ACACTTATTAG
38006 TTTATGAATCATCATTAACACTTATTAG
1 TTTATGAATCATCATTAACACTTATTAG
38034 TTTA
1 TTTA
38038 ATGACGTGAT
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
27 7 0.16
28 16 0.37
29 13 0.30
30 7 0.16
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (28 bp):
TTTATGAATCATCATTAACACTTATTAG
Found at i:37997 original size:55 final size:57
Alignment explanation
Indices: 37931--38042 Score: 201
Period size: 57 Copynumber: 2.0 Consensus size: 57
37921 CTTATATTAT
*
37931 CGATTG-T-TATATTTTTTATTTATGAATTATCATTAACACTTATTAGTTTAATGAC
1 CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
37986 CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
1 CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
38043 GTGATATATT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
55 6 0.11
56 1 0.02
57 47 0.87
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (57 bp):
CGATTGTTATATATTTTTTATTTATGAATCATCATTAACACTTATTAGTTTAATGAC
Found at i:43483 original size:55 final size:54
Alignment explanation
Indices: 43359--43516 Score: 187
Period size: 55 Copynumber: 2.9 Consensus size: 54
43349 ATATTCGGAA
*
43359 AACGGGTTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTGCG
1 AACGGGTTCGCTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGCG
* ** *
43413 AACGAGTTTACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC-
1 AACGGGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTG-CG
* * * *
43468 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
43517 ATCAATCGTG
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
53 18 0.20
54 23 0.26
55 46 0.52
56 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (54 bp):
AACGGGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGCG
Found at i:43571 original size:55 final size:55
Alignment explanation
Indices: 43510--44186 Score: 953
Period size: 55 Copynumber: 12.3 Consensus size: 55
43500 GAACTTGAAG
* * *
43510 AATCTTCATCAATCGTGTCTGCTCCCTATTTGC-TCAGAGAGTATAAGACCCAAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTT-CTTCAGAGAGTATAAGACTCGAAC
* * * *
43565 AATCTTCAACAAATCTTGTCTGCTCCCTATTCCTTCAGAGAATATAAGACCCGAAC
1 AATCTTCAAC-AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * * *
43621 AATCTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTTGAAA
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
43676 AATCTTCATCAATCGTGTCTGCTCCCTATTTCTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
** * * * *
43731 AATCTTCAACAGCCGTGTTTGCTCCCTATTTATGCAGAGAGTATAAGACTCAAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
43786 AATTTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
43841 AATCTTCATCAATCGTGTCTGTTCCCTATTTGTTCAGAGAGTATGAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
43896 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
43951 AATCTTCAACAATTGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
44006 AATCTTTAACAATCGTGTCTGCTCCCTATTTCTTCAAAGAGTATGAGACTCGAAT
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
44061 AATCTTCAACCATTGTGTTTGCTCCCTATTTCTT-ACGAGAGTATGAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCA-GAGAGTATAAGACTCGAAC
*
44116 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATGAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
44171 AATCTTCAACAATCGT
1 AATCTTCAACAATCGT
44187 TGGGAAACCT
Statistics
Matches: 562, Mismatches: 56, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
54 1 0.00
55 512 0.91
56 49 0.09
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (55 bp):
AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:45205 original size:8 final size:8
Alignment explanation
Indices: 45187--45239 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
45177 TGAACCCTTC
45187 TTTTTTCCA
1 TTTTTT-CA
45196 TTTTTTCA
1 TTTTTTCA
*
45204 TTTTTTTTA
1 -TTTTTTCA
*
45213 TTTTTTTA
1 TTTTTTCA
*
45221 TTTTCTC-
1 TTTTTTCA
45228 TTTTTTCA
1 TTTTTTCA
45236 TTTT
1 TTTT
45240 CACTCATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
7 6 0.16
8 19 0.50
9 13 0.34
ACGTcount: A:0.09, C:0.11, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTTTCA
Found at i:45224 original size:15 final size:15
Alignment explanation
Indices: 45189--45240 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
45179 AACCCTTCTT
*
45189 TTTTCCATTTTTTCA
1 TTTTCTATTTTTTCA
* *
45204 TTTTTTTTATTTTTTTA
1 --TTTTCTATTTTTTCA
*
45221 TTTTCTCTTTTTTCA
1 TTTTCTATTTTTTCA
45236 TTTTC
1 TTTTC
45241 ACTCATTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
15 17 0.59
17 12 0.41
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTCTATTTTTTCA
Found at i:55385 original size:4 final size:4
Alignment explanation
Indices: 55373--55417 Score: 81
Period size: 4 Copynumber: 11.0 Consensus size: 4
55363 TTTGCAAAAA
55373 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
55418 TCGAGGGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 36 0.90
5 4 0.10
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Done.