Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003455.1 Hibiscus syriacus cultivar Beakdansim tig00007304_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: 89129
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6742 original size:64 final size:64
Alignment explanation
Indices: 6629--6752 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
6619 GTGCACCAAG
* ** *
6629 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAGCCTGAGTGCATCGGTGCATTGCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTGCT
* * *
6693 TGTGCATCGATGTATGAAATGCATTCGATGTTTTAATAA-AACCCAAGTGCATCGATGCAT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTGAA-AATAACCCAAGTGCATCGATGCAT
6753 GAAATTCATT
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
64 50 0.96
65 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTGAAAATAACCCAAGTGCATCGATGCATTGCT
Found at i:7523 original size:20 final size:20
Alignment explanation
Indices: 7500--7545 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
7490 AGTAGTTACA
*
7500 AAACTTTCATCAAAGTTTTT
1 AAACTTTCATCAAAGTTTTG
* * *
7520 AAACTCTCTTTAAAGTTTTG
1 AAACTTTCATCAAAGTTTTG
7540 AAACTT
1 AAACTT
7546 AGGGTTCTAA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
AAACTTTCATCAAAGTTTTG
Found at i:8144 original size:77 final size:77
Alignment explanation
Indices: 8017--8170 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 77
8007 AGAAAGTTAG
* * *
8017 AACAAATTAGTGATTTTTTTTAAATCCTTAGTCTAGAAGCTAAGTTAGTGAATGTAGACTTCAGT
1 AACAAATTAGTGAATTTTTTGAAATCCTTAGTCTAGAAGCTAAGTTAGTGAATGTAGACTTCAAT
*
8082 GAGGAATTTGAA
66 GAGGAAGTTGAA
* *
8094 AACAAATTAGTGAATTTTTTGAAATCCTTAGTGTGGAAGCTAAGTTAGTGAATGTAGACTTCAAT
1 AACAAATTAGTGAATTTTTTGAAATCCTTAGTCTAGAAGCTAAGTTAGTGAATGTAGACTTCAAT
8159 GAGGAAGTTGAA
66 GAGGAAGTTGAA
8171 CCACTCTAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.34
Consensus pattern (77 bp):
AACAAATTAGTGAATTTTTTGAAATCCTTAGTCTAGAAGCTAAGTTAGTGAATGTAGACTTCAAT
GAGGAAGTTGAA
Found at i:15402 original size:19 final size:19
Alignment explanation
Indices: 15373--15409 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
15363 TTCATATCTC
15373 CTTTCATCTTCTTCACTTCA
1 CTTTCATCTTCTTC-CTTCA
15393 CTTT-ATCTTCTTCCTTC
1 CTTTCATCTTCTTCCTTC
15410 TTTTTCTCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 9 0.53
20 4 0.24
ACGTcount: A:0.11, C:0.35, G:0.00, T:0.54
Consensus pattern (19 bp):
CTTTCATCTTCTTCCTTCA
Found at i:25952 original size:19 final size:19
Alignment explanation
Indices: 25915--25952 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
25905 TTATTTGGTG
*
25915 TTTTATTTATGTTGGATGA
1 TTTTATTTATGTTGAATGA
25934 TTTTATTTTATGTT-AATGA
1 TTTTA-TTTATGTTGAATGA
25953 ATGGACTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.61
Consensus pattern (19 bp):
TTTTATTTATGTTGAATGA
Found at i:42788 original size:11 final size:12
Alignment explanation
Indices: 42772--42821 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
42762 AATTATTAAC
42772 ATATTTAA-AAT
1 ATATTTAATAAT
42783 ATATTTAATAAT
1 ATATTTAATAAT
* *
42795 ATTTTTATTAAT
1 ATATTTAATAAT
*
42807 ATTATATAATAAT
1 A-TATTTAATAAT
42820 AT
1 AT
42822 TATTATTACA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
11 8 0.25
12 15 0.47
13 9 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
ATATTTAATAAT
Found at i:42822 original size:25 final size:24
Alignment explanation
Indices: 42780--42829 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
42770 ACATATTTAA
* *
42780 AATATATTTAATAATATTTTTATT
1 AATATATATAATAATATTATTATT
42804 AATATTATATAATAATATTATTATT
1 AATA-TATATAATAATATTATTATT
42829 A
1 A
42830 CAATAATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATATATATAATAATATTATTATT
Found at i:42835 original size:42 final size:40
Alignment explanation
Indices: 42789--42931 Score: 105
Period size: 42 Copynumber: 3.5 Consensus size: 40
42779 AAATATATTT
42789 AATAATATT-TTTATTAATATTATATAATAATATTATTATTAC
1 AATAATATTATTTATTAATA-TATATAATAA-ATTATTA-TAC
* * *
42831 AATAATA-TACTTAATT-ATAT-TATAATAAAATATGATAC
1 AATAATATTA-TTTATTAATATATATAATAAATTATTATAC
* * * * *
42869 TATTATATTCTTATTTTAATAATATATAATAAATTATTAATAA
1 AATAATATTATT-TATTAAT-ATATATAATAAATTATT-ATAC
*
42912 AAGTTATATTATTTATTAAT
1 AA-TAATATTATTTATTAAT
42932 TTCTTAAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 17
0.72 0.13 0.16
Matches are distributed among these distances:
38 10 0.13
39 8 0.10
40 10 0.13
41 4 0.05
42 22 0.28
43 15 0.19
44 9 0.12
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (40 bp):
AATAATATTATTTATTAATATATATAATAAATTATTATAC
Found at i:42838 original size:25 final size:25
Alignment explanation
Indices: 42780--42874 Score: 72
Period size: 25 Copynumber: 3.8 Consensus size: 25
42770 ACATATTTAA
* *
42780 AATAT-ATTTAATAATATTTTTATT
1 AATATAATATAATAATATTATTATT
*
42804 AATATTATATAATAATATTATTATT
1 AATATAATATAATAATATTATTATT
*
42829 ACA-ATAATATACTTAAT-TATATTA-T
1 A-ATATAATATA-ATAATAT-TATTATT
* * *
42854 AATAAAATATGATACTATTAT
1 AATATAATATAATAATATTAT
42875 ATTCTTATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
24 12 0.21
25 35 0.61
26 10 0.18
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.48
Consensus pattern (25 bp):
AATATAATATAATAATATTATTATT
Found at i:43008 original size:23 final size:21
Alignment explanation
Indices: 42981--43035 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 21
42971 CTTTTATTTA
42981 ATATTATAAAAATTCCTTAAAAT
1 ATATTATAAAAATT--TTAAAAT
*
43004 ATATTTATTAATAATTTTAAAAT
1 ATA-TTA-TAAAAATTTTAAAAT
*
43027 ATAATATAA
1 ATATTATAA
43036 TATTTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 3 0.11
22 2 0.07
23 13 0.46
24 3 0.11
25 7 0.25
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATTATAAAAATTTTAAAAT
Found at i:43036 original size:21 final size:23
Alignment explanation
Indices: 42997--43043 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
42987 TAAAAATTCC
*
42997 TTAAAATATATTTATTAATAATT
1 TTAAAATATATATATTAATAATT
*
43020 TTAAAATATA-ATA-TAATATTT
1 TTAAAATATATATATTAATAATT
43041 TTA
1 TTA
43044 TTTTAATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 2 0.09
23 10 0.45
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAAATATATATATTAATAATT
Found at i:43098 original size:29 final size:29
Alignment explanation
Indices: 43017--43100 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 29
43007 TTTATTAATA
*
43017 ATTT-TAAAA-TATA-ATATAATATTTTT
1 ATTTATAAAATTATAGAAATAATATTTTT
* **
43043 ATTTTAATAGAATATACTAGAGTTAATATTTTT
1 A-TTT-ATAAAAT-TA-TAGAAATAATATTTTT
43076 ATTTATAAAATTATAGAAATAATAT
1 ATTTATAAAATTATAGAAATAATAT
43101 CTTAATAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
29 14 0.31
30 2 0.04
31 8 0.18
32 5 0.11
33 12 0.27
ACGTcount: A:0.46, C:0.01, G:0.05, T:0.48
Consensus pattern (29 bp):
ATTTATAAAATTATAGAAATAATATTTTT
Found at i:43200 original size:23 final size:21
Alignment explanation
Indices: 43147--43201 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
43137 ATTATTCTAA
*
43147 TATTTTTAAAATAATAATATT
1 TATTTTTATAATAATAATATT
*
43168 AAGTTTTTATAATAAATAATATT
1 TA-TTTTTATAAT-AATAATATT
43191 TATTTATTATA
1 TATTT-TTATA
43202 TTTTATATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 12 0.43
23 15 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATTTTTATAATAATAATATT
Found at i:43707 original size:3 final size:3
Alignment explanation
Indices: 43701--43744 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
43691 AATAATAATA
*
43701 ATT ATT ATT ATT A-T ATT AAT ATT ATT ATT -TT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
43745 AATGATAAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:43725 original size:17 final size:17
Alignment explanation
Indices: 43703--43744 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
43693 TAATAATAAT
43703 TATTATTATTATATTAA
1 TATTATTATTATATTAA
* *
43720 TATTATTATTTTATTAT
1 TATTATTATTATATTAA
43737 TATTATTA
1 TATTATTA
43745 AATGATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTATTATTATATTAA
Found at i:43734 original size:11 final size:12
Alignment explanation
Indices: 43701--43744 Score: 65
Period size: 11 Copynumber: 3.8 Consensus size: 12
43691 AATAATAATA
43701 ATTATTATTATT
1 ATTATTATTATT
*
43713 A-TATTAATATT
1 ATTATTATTATT
43724 ATTATT-TTATT
1 ATTATTATTATT
43735 ATTATTATTA
1 ATTATTATTA
43745 AATGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTATTATTATT
Found at i:43743 original size:14 final size:14
Alignment explanation
Indices: 43702--43743 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
43692 ATAATAATAA
*
43702 TTATTATTATTATA
1 TTATTATTATTATT
*
43716 TTAATATTATTATT
1 TTATTATTATTATT
43730 TTATTATTATTATT
1 TTATTATTATTATT
43744 AAATGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTATTATTATT
Found at i:45130 original size:18 final size:19
Alignment explanation
Indices: 45094--45131 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
45084 TTTTATTATC
45094 TTTTAATTTAATCATATAT
1 TTTTAATTTAATCATATAT
* *
45113 TTTTATTTTGATCA-ATAT
1 TTTTAATTTAATCATATAT
45131 T
1 T
45132 AATTACAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.61
Consensus pattern (19 bp):
TTTTAATTTAATCATATAT
Found at i:48043 original size:42 final size:42
Alignment explanation
Indices: 47985--48067 Score: 130
Period size: 42 Copynumber: 2.0 Consensus size: 42
47975 AGAGATGATC
* *
47985 GATCAAGAAAAAAAGTTCCAGGATGATTCGAAGGAACAAATT
1 GATCAAGAAAAAAAGTTCCAAGATGATTCAAAGGAACAAATT
* *
48027 GATCAAGAAAAAAAGTTTCAAGATGATTCAAATGAACAAAT
1 GATCAAGAAAAAAAGTTCCAAGATGATTCAAAGGAACAAAT
48068 GACCAAATTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (42 bp):
GATCAAGAAAAAAAGTTCCAAGATGATTCAAAGGAACAAATT
Found at i:48535 original size:165 final size:165
Alignment explanation
Indices: 48263--48596 Score: 650
Period size: 165 Copynumber: 2.0 Consensus size: 165
48253 CAGAGGTCAT
48263 GTTGAAGAGAAGCATGGAAGAAGTTCAAGTTTCATTCAAAAAAGCTAAACAAAGCAAAAATCTAG
1 GTTGAAGAGAAGCATGGAAGAAGTTCAAGTTTCATTCAAAAAAGCTAAACAAAGCAAAAATCTAG
*
48328 ACGATCATTCATAAAGTTTTCAAGATGATGGCAAAGAGAAAATTAGGTCAAAGGAATTTCTACCC
66 ACGATCATTCACAAAGTTTTCAAGATGATGGCAAAGAGAAAATTAGGTCAAAGGAATTTCTACCC
48393 AATTTTCCTTCAGTTTCGTGCAAGTTATATTACAA
131 AATTTTCCTTCAGTTTCGTGCAAGTTATATTACAA
*
48428 GTTGAAGAGAAGCATGGAAGAAGTTCAAGTTTCATTCAAGAAAGCTAAACAAAGCAAAAATCTAG
1 GTTGAAGAGAAGCATGGAAGAAGTTCAAGTTTCATTCAAAAAAGCTAAACAAAGCAAAAATCTAG
48493 ACGATCATTCACAAAGTTTTCAAGATGATGGCAAAGAGAAAATTAGGTCAAAGGAATTTCTACCC
66 ACGATCATTCACAAAGTTTTCAAGATGATGGCAAAGAGAAAATTAGGTCAAAGGAATTTCTACCC
48558 AATTTTCCTTCAGTTTCGTGCAAGTTATATTACAA
131 AATTTTCCTTCAGTTTCGTGCAAGTTATATTACAA
48593 GTTG
1 GTTG
48597 CTCCATGTCG
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
165 167 1.00
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (165 bp):
GTTGAAGAGAAGCATGGAAGAAGTTCAAGTTTCATTCAAAAAAGCTAAACAAAGCAAAAATCTAG
ACGATCATTCACAAAGTTTTCAAGATGATGGCAAAGAGAAAATTAGGTCAAAGGAATTTCTACCC
AATTTTCCTTCAGTTTCGTGCAAGTTATATTACAA
Found at i:51187 original size:7 final size:7
Alignment explanation
Indices: 51177--51292 Score: 83
Period size: 7 Copynumber: 15.9 Consensus size: 7
51167 AAAAAAGAGA
51177 AAAAAAG
1 AAAAAAG
51184 AAAAAAG
1 AAAAAAG
51191 AGAAAAA-
1 A-AAAAAG
51198 AAGGAAAA-
1 AA--AAAAG
*
51206 AAGAAAG
1 AAAAAAG
*
51213 AGAAAAG
1 AAAAAAG
51220 AAAGAAAG
1 AAA-AAAG
*
51228 AAAAAGAT
1 AAAAA-AG
51236 AGAAAAAG
1 A-AAAAAG
*
51244 AGAAAAG
1 AAAAAAG
*
51251 AGAAAAG
1 AAAAAAG
*
51258 AGAAAAG
1 AAAAAAG
*
51265 AGAAAAG
1 AAAAAAG
*
51272 AGAAAAG
1 AAAAAAG
51279 AAAAGAAG
1 AAAA-AAG
51287 AAAAAA
1 AAAAAA
51293 AATTGAATCA
Statistics
Matches: 93, Mismatches: 8, Indels: 16
0.79 0.07 0.14
Matches are distributed among these distances:
6 4 0.04
7 56 0.60
8 29 0.31
9 4 0.04
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:51234 original size:14 final size:14
Alignment explanation
Indices: 51167--51291 Score: 102
Period size: 14 Copynumber: 8.9 Consensus size: 14
51157 CCATCAGAGA
51167 AAAAAAGAGAAAA-
1 AAAAAAGAGAAAAG
*
51180 AAAGAAA-A-AAGAG
1 AAA-AAAGAGAAAAG
51193 AAAAAA-AGGAAAA-
1 AAAAAAGA-GAAAAG
*
51206 AAGAAAGAGAAAAG
1 AAAAAAGAGAAAAG
51220 AAAGAAAGA-AAAAG
1 AAA-AAAGAGAAAAG
51234 ATAGAAAAAGAGAAAAG
1 --A-AAAAAGAGAAAAG
*
51251 AGAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
*
51265 AGAAAAGAGAAAAG
1 AAAAAAGAGAAAAG
51279 AAAAGAAGA-AAAA
1 AAAA-AAGAGAAAA
51292 AAATTGAATC
Statistics
Matches: 94, Mismatches: 6, Indels: 23
0.76 0.05 0.19
Matches are distributed among these distances:
12 7 0.07
13 17 0.18
14 47 0.50
15 10 0.11
16 6 0.06
17 7 0.07
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (14 bp):
AAAAAAGAGAAAAG
Found at i:51234 original size:60 final size:59
Alignment explanation
Indices: 51164--51291 Score: 163
Period size: 59 Copynumber: 2.2 Consensus size: 59
51154 CATCCATCAG
51164 AGAA-AAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAAGGAAAAAAG-AAAGAGAAAAG-AA
1 AGAAGAAAAAGAGAAAAAAAGAAAAAAGAG-AAAAAA-GAAAAAAGAAAAGAGAAAAGAAA
* * * * *
51222 AGAAAGAAAAAGATAGAAAAAGAGAAAAGAGAAAAGAGAAAAGAGAAAAGAGAAAAGAAA
1 AG-AAGAAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAGAAAAAAGAAAAGAGAAAAGAAA
51282 AGAAGAAAAA
1 AGAAGAAAAA
51292 AAATTGAATC
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
58 9 0.15
59 26 0.43
60 26 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.01
Consensus pattern (59 bp):
AGAAGAAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAGAAAAAAGAAAAGAGAAAAGAAA
Found at i:51258 original size:45 final size:42
Alignment explanation
Indices: 51169--51293 Score: 141
Period size: 45 Copynumber: 3.0 Consensus size: 42
51159 ATCAGAGAAA
*
51169 AAAAGAGAAAA-AAAGAAA-AAAGAGAAAAAAAGGAAAAAAG
1 AAAAGAGAAAAGAAAGAAAGAAAAAGAAAAAAAGGAAAAAAG
*
51209 -AAAGAGAAAAGAAAGAAAGAAAAAGATAGAAAAAGAGAAAAGAG
1 AAAAGAGAAAAGAAAGAAAGAAAAAGA-A-AAAAAG-GAAAAAAG
* * *
51253 AAAAGAGAAAAGAGA-AAAGAGAAAAGAAAAGAAGAAAAAAA
1 AAAAGAGAAAAGAAAGAAAGA-AAAAGAAAAAAAGGAAAAAA
51294 ATTGAATCAA
Statistics
Matches: 72, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
39 10 0.14
40 7 0.10
41 6 0.08
42 6 0.08
43 11 0.15
44 13 0.18
45 19 0.26
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (42 bp):
AAAAGAGAAAAGAAAGAAAGAAAAAGAAAAAAAGGAAAAAAG
Found at i:51292 original size:60 final size:59
Alignment explanation
Indices: 51166--51292 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 59
51156 TCCATCAGAG
51166 AAAAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAAGGAAAAAAGAAAGAGAAAAGAAAGA
1 AAAAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAAGGAAAAAAGAAAGAGAAAAGAAAGA
* * * * *
51225 AAGAAAAAGATAGAAAAAGAGAAAAGAG-AAAAGA-GAAAAGAGAAAAGAGAAAAGAAAAGA
1 AA-AAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAAGGAAAAAAG-AAAGAGAAAAG-AAAGA
51285 AGAAAAAA
1 A-AAAAAA
51293 AATTGAATCA
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
58 7 0.12
59 18 0.31
60 33 0.56
61 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (59 bp):
AAAAAAAGAGAAAAAAAGAAAAAAGAGAAAAAAAGGAAAAAAGAAAGAGAAAAGAAAGA
Found at i:52558 original size:51 final size:51
Alignment explanation
Indices: 52501--52683 Score: 269
Period size: 51 Copynumber: 3.6 Consensus size: 51
52491 CCATGTAGGT
* *
52501 ATCTTGAAGGCTCACATCAGCATGAAAAGATAGAAGTAATCTATGTGCGGC
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCTATGTGGGGC
* * *
52552 ATCTTGAAGGCTCACATCAGCATAAAAAAGACAGAAGTAATCCATATGGGGC
1 ATCTTGAAGGCTCACATCAGCAT-GAAAAGACAGAAGTAATCTATGTGGGGC
* *
52604 ATCTTGAAGGCTCCCATCAGCATGAAAAGACAGAAGTAAT-TCATGTGGGGT
1 ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCT-ATGTGGGGC
*
52655 ATCTTGAAGGCTCACACCAGCATGAAAAG
1 ATCTTGAAGGCTCACATCAGCATGAAAAG
52684 GTTGGGATAT
Statistics
Matches: 118, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
51 73 0.62
52 45 0.38
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.21
Consensus pattern (51 bp):
ATCTTGAAGGCTCACATCAGCATGAAAAGACAGAAGTAATCTATGTGGGGC
Found at i:54716 original size:176 final size:177
Alignment explanation
Indices: 54270--54803 Score: 908
Period size: 177 Copynumber: 3.0 Consensus size: 177
54260 TATTTCTCGA
* *
54270 ATTTGTAAGTCTTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
1 ATTTGTAAGTCATACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
54335 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
66 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
*
54400 AAGGGGTTCCTTAACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
131 AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
*
54447 ATTTGTAAGTCATACGGGCCATCCATAAGATCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
1 ATTTGTAAGTCATACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
* * * *
54512 AAACTAAGTCTTTGGGGGTTTCCTAATTATCTCAAAAGAGTTATTAAAGGGAGCTAAGCCTAACA
66 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
*
54577 AAGGGGCTCCTTGACAACTAAGAAACTAAGCCTTC-GGGGTTTCTTG
131 AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
* * *
54623 ATTTGTAAGTCCTACAGGCCATCCATAAGACCTTAAGTGCAGGATGTTTTCAAATGAGATTTTAG
1 ATTTGTAAGTCATACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
* * *
54688 AAACCAAGCCTTCGGGGGTTTACTAATTATCTCAAAAGAGCTGTTAAAGGAAGCTAAGCCTAACA
66 AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
* *
54753 AAGGGGTTTCTTGACAACTAAGAAACTAAGCTTTCGGGGGTTTCTTG
131 AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
54800 ATTT
1 ATTT
54804 ATAGAATTCG
Statistics
Matches: 333, Mismatches: 23, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
176 162 0.49
177 171 0.51
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (177 bp):
ATTTGTAAGTCATACGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTAG
AAACTAAGCCTTCGGGGGTTTCCTAATTATCTCAAAAGAGTTGTTAAAGGAAGCTAAGCCTAACA
AAGGGGTTCCTTGACAACTAAGAAACTAAGCCTTCGGGGGTTTCTTG
Found at i:55047 original size:124 final size:124
Alignment explanation
Indices: 54821--55113 Score: 462
Period size: 124 Copynumber: 2.4 Consensus size: 124
54811 TCGTAATAAA
* * *
54821 AAGAACTCATCTGAACAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGT
1 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGA
* * * *
54886 CTCTATCGTAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATCTG
66 CTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCATAAAGGAGTTCATAATCTG
*
54945 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTGCTTGA
1 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGA
* * *
55010 CTCTATCGCAGAAGGAGATGGTGCAACAGATCCATTTCCATAAAGGAGTTCATAATCTG
66 CTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCATAAAGGAGTTCATAATCTG
* *
55069 AAGAACTCGTCTAAAGAGG-AGAAGAAGTTCATAATCTGAAGAACT
1 AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACT
55114 CGTCTGAAGA
Statistics
Matches: 156, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
123 25 0.16
124 131 0.84
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (124 bp):
AAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGA
CTCTATCGCAGAAGGAGATAGAGCAACAGAGCCATTTCCATAAAGGAGTTCATAATCTG
Found at i:55142 original size:39 final size:38
Alignment explanation
Indices: 55056--55190 Score: 189
Period size: 39 Copynumber: 3.5 Consensus size: 38
55046 TCCATAAAGG
* *
55056 AGTTCATAATCTGAAGAACTCGTCTAAAGAGGAGAAGA
1 AGTTCATAATCTGAAGAACTCGTCTGAAGAGAAGAAGA
55094 AGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGA
1 AGTTCATAATCTGAAGAACTCGTCTGAAGA-GAAGAAGA
* * *
55133 AGTTCATAATCTGAAGAACTCATTTGAAGAGAAAGAATA
1 AGTTCATAATCTGAAGAACTCGTCTGAAGAG-AAGAAGA
* *
55172 AGTTAATAATATGAAGAAC
1 AGTTCATAATCTGAAGAAC
55191 GTATTTAACT
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
38 30 0.34
39 58 0.66
ACGTcount: A:0.44, C:0.11, G:0.21, T:0.24
Consensus pattern (38 bp):
AGTTCATAATCTGAAGAACTCGTCTGAAGAGAAGAAGA
Found at i:55149 original size:20 final size:20
Alignment explanation
Indices: 55088--55150 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
55078 TCTAAAGAGG
55088 AGAAGAAGTTCATAATCTGA
1 AGAAGAAGTTCATAATCTGA
*** **
55108 AGAACTCG-TC-TGAAGATGA
1 AGAAGAAGTTCAT-AATCTGA
55127 AGAAGAAGTTCATAATCTGA
1 AGAAGAAGTTCATAATCTGA
55147 AGAA
1 AGAA
55151 CTCATTTGAA
Statistics
Matches: 30, Mismatches: 10, Indels: 6
0.65 0.22 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 16 0.53
21 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (20 bp):
AGAAGAAGTTCATAATCTGA
Found at i:55207 original size:201 final size:200
Alignment explanation
Indices: 54932--55313 Score: 516
Period size: 201 Copynumber: 1.9 Consensus size: 200
54922 TCCATACAGG
* * * * * *
54932 AGTTCATAATCTGAAGAACTCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCA
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCA
* * *
54997 ACCTTTTGCTTGACTCTATCGCAGAAGGAGATGGTGCAACAGATC-CATTTCCATAAAGGAGTTC
66 ACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAAC--ATCACATTTCCAT-AAGGAGTTC
** * *
55061 ATAATCTGAAGAACTCGTCTAAAG-AGGAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAT
128 ATAATAAGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGAT
55125 GAAGAAGA
193 GAAGAAGA
* * *
55133 AGTTCATAATCTGAAGAACTCATTTGAAGAGAAAGAATAAGTTAATAATATGAAGAACGTATTTA
1 AGTTCATAATCTGAAGAACTCATCTGAAGAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCA
* * * *
55198 ACTTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCCATAAGGAGTTCGT
66 ACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAACATC-ACATTTCCATAAGGAGTTCAT
* *
55263 AATAAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAAC
130 AATAAGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATCTGAAGAAC
55314 ATATTCAACA
Statistics
Matches: 156, Mismatches: 22, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
199 3 0.02
200 27 0.17
201 126 0.81
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (200 bp):
AGTTCATAATCTGAAGAACTCATCTGAAGAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCA
ACCTTTTGCTCGACTCTATCGCAGAAGGAGATAGAGCAACATCACATTTCCATAAGGAGTTCATA
ATAAGAAGAACTCATCTAAAGAAGAAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAA
GAAGA
Found at i:55292 original size:123 final size:123
Alignment explanation
Indices: 55127--55697 Score: 739
Period size: 123 Copynumber: 4.6 Consensus size: 123
55117 CTGAAGATGA
* * ** * * * *
55127 AGAAGAAGTTCATAATCTGAAGAACTCATTTGAAG-AGAAAGAATAAGTTAATAATATGAAGAAC
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAG-AAGAAGAAGTTCATAATCTGAAGAAC
* * *
55191 GTATTTAACTTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
65 ATATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* *
55250 ATAAGGAGTTCGTAATAAGAAGAATTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* * * * * *
55315 TATTCAACATTTTTGCTTGATTCTATCGTAGAATGAGATATAGCAGCATTAACATTTCC
66 TATTCAAC-CTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* * * *
55374 AGAAAGAGTTCGTAATAAGAAGAACTCGTCTGAAGAGGAAGAAAAAGTTCATAATCTGAAGAACA
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* * * *
55439 TATTCAACCTTTTGCTCGATTATATCGCATAAGGAGATAGAGCAGTATCAACGTTTCC
66 TATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* * *
55497 AGAAGGAGTTCGTAATAAGAAGAACTCATTTGAAGAGGAAGAAGAAGTTCATAATCTGAAGAACG
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* * * *
55562 TATTCAACCTTTTGCTTGACTCTATCGCAAAAGGAGATAGAGCAGCATCAACGTTTCC
66 TATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
* * * ** *
55620 AGAAGGAGTTCGTAATAAAAAGAACTCATATGAAGAAGAAGAAGAAGTTTATAATAAGAAGAACT
1 AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
* *
55685 TGTTCAACATTTT
66 TATTCAACCTTTT
55698 CATCTTAATC
Statistics
Matches: 394, Mismatches: 52, Indels: 4
0.88 0.12 0.01
Matches are distributed among these distances:
123 280 0.71
124 114 0.29
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.27
Consensus pattern (123 bp):
AGAAGGAGTTCGTAATAAGAAGAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACA
TATTCAACCTTTTGCTCGATTCTATCGCAGAAGGAGATAGAGCAGCATCAACATTTCC
Found at i:55424 original size:325 final size:325
Alignment explanation
Indices: 54821--55437 Score: 791
Period size: 325 Copynumber: 1.9 Consensus size: 325
54811 TCGTAATAAA
* * * * * *
54821 AAGAACTCATCTGAACAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTACTTGT
1 AAGAACTCATCTGAACAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCAACCTTTTACTCGT
* **
54886 CTCTATCGTAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATCTGAAGAAC
66 CTCTATCGCAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATAAGAAGAAC
* * * *
54951 TCGTCTGAAGAGGAAGAAGAAGTTCATAGTCTGAAGAACTTATTCAACCTTTTGCTTGACTCTAT
131 TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTTGACTCTAT
* * * **
55016 CGCAGAAGGAGATGGTGCAACAGATCCATTTCCATAAAGGAGTTCATAATCTGAAGAACTCGTCT
196 CGCAGAAGGAGATGATGCAACAGATACATTTCCAGAAAGGAGTTCATAATAAGAAGAACTCGTCT
*
55081 AAAGAGGAGAAGAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGAAGTTCATAATCTG
261 AAAGAGGAGAAAAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGAAGTTCATAATCTG
* * * * * *
55146 AAGAACTCATTTGAAGAGAAAGAATAAGTTAATAATATGAAGAACGTATTTAACTTTTTGCTCGA
1 AAGAACTCATCTGAACAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCAACCTTTTACTCG-
*
55211 T-TCTATCGCAGAAGGAGATAGAGCAGCATCA-A-C-ATTTCCATA-AGGAGTTCGTAATAAGAA
65 TCTCTATCGCAGAAGGAGATAGAGCA--AT-AGAGCTATTTCCATACAGGAGTTCATAATAAGAA
* * *
55271 GAATTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACATTTTTGCTTGAT
127 GAACTCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAAC-CTTTTGCTTGAC
* * * * *
55336 TCTATCGTAGAATGAGAT-ATAGCAGCA-TTAACATTTCCAGAAA-GAGTTCGTAATAAGAAGAA
191 TCTATCGCAGAAGGAGATGAT-GCAACAGAT-ACATTTCCAGAAAGGAGTTCATAATAAGAAGAA
*
55398 CTCGTCTGAAGAGGAAGAAAAAGTTCATAATCTGAAGAAC
254 CTCGTCTAAAGAGG-AGAAAAAGTTCATAATCTGAAGAAC
55438 ATATTCAACC
Statistics
Matches: 249, Mismatches: 35, Indels: 16
0.83 0.12 0.05
Matches are distributed among these distances:
324 93 0.37
325 150 0.60
326 2 0.01
327 3 0.01
328 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.26
Consensus pattern (325 bp):
AAGAACTCATCTGAACAGAAAGAAGAAGTTAATAATATGAAGAACGTATTCAACCTTTTACTCGT
CTCTATCGCAGAAGGAGATAGAGCAATAGAGCTATTTCCATACAGGAGTTCATAATAAGAAGAAC
TCATCTGAAGAAGAAGAAGAAGTTCATAATCTGAAGAACATATTCAACCTTTTGCTTGACTCTAT
CGCAGAAGGAGATGATGCAACAGATACATTTCCAGAAAGGAGTTCATAATAAGAAGAACTCGTCT
AAAGAGGAGAAAAAGTTCATAATCTGAAGAACTCGTCTGAAGATGAAGAAGAAGTTCATAATCTG
Found at i:55826 original size:3 final size:3
Alignment explanation
Indices: 55818--55869 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
55808 TTTCTCCCAT
* *
55818 TTA TTA TTA TTA ATA TTA -TA TTA TTA TTA TTA TTA TCA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55864 TTA TTA
1 TTA TTA
55870 AGTGATAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:55841 original size:17 final size:17
Alignment explanation
Indices: 55819--55869 Score: 77
Period size: 17 Copynumber: 3.0 Consensus size: 17
55809 TTCTCCCATT
*
55819 TATTATTATTAATATTA
1 TATTATTATTATTATTA
55836 TATTATTATTATTATTA
1 TATTATTATTATTATTA
55853 TCATT-TTATTATTATTA
1 T-ATTATTATTATTATTA
55870 AGTGATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 29 0.91
18 3 0.09
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATTATTATTATTA
Found at i:55843 original size:20 final size:20
Alignment explanation
Indices: 55818--55870 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
55808 TTTCTCCCAT
*
55818 TTATTATTATTAATATTATA
1 TTATTATTATTAATATCATA
* *
55838 TTATTATTATTATTATCATT
1 TTATTATTATTAATATCATA
55858 TTATTATTATTAA
1 TTATTATTATTAA
55871 GTGATAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTATTATTAATATCATA
Found at i:57214 original size:19 final size:21
Alignment explanation
Indices: 57182--57231 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 21
57172 TTTTATTATC
* *
57182 TTTTAATTTAATC-ATA-TAT
1 TTTTATTTTAATCAATATTAA
*
57201 TTTTATTTTGATCAATATTAA
1 TTTTATTTTAATCAATATTAA
57222 TTTTATTTTA
1 TTTTATTTTA
57232 TTTTTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 11 0.44
20 3 0.12
21 11 0.44
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTTATTTTAATCAATATTAA
Found at i:58452 original size:3 final size:3
Alignment explanation
Indices: 58444--58524 Score: 78
Period size: 3 Copynumber: 26.7 Consensus size: 3
58434 AATTTTTTCA
*
58444 TAT TAT TAT TTT TCA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
58489 ATAT TAT AAT T-T ATAT TAT TAT AAAT T-T TAT TAT TA
1 -TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TA
58525 ATAATAAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
2 4 0.06
3 55 0.85
4 6 0.09
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:59914 original size:12 final size:12
Alignment explanation
Indices: 59894--59943 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
59884 TTATTTGCAA
59894 TATTATTTT-AT
1 TATTATTTTAAT
*
59905 TATTACTTTTGA-
1 TATTA-TTTTAAT
59917 TA-TATTTTAAT
1 TATTATTTTAAT
*
59928 TATTACTTTAAT
1 TATTATTTTAAT
59940 TATT
1 TATT
59944 TTATTATCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
10 5 0.15
11 9 0.27
12 18 0.55
13 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTATTTTAAT
Found at i:60777 original size:27 final size:27
Alignment explanation
Indices: 60738--60793 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
60728 ACTTATAATA
*
60738 TTTATTATATTTTTA-TTATTAATGTT
1 TTTATTATATTTTTAGATATTAATGTT
*
60764 TTTATTTTATTTTTAGATATTAATGTT
1 TTTATTATATTTTTAGATATTAATGTT
60791 TTT
1 TTT
60794 TGTAAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (27 bp):
TTTATTATATTTTTAGATATTAATGTT
Found at i:63112 original size:7 final size:7
Alignment explanation
Indices: 63096--63135 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
63086 TTTTCATACA
63096 TGCA-TT
1 TGCATTT
63102 TGCATTT
1 TGCATTT
63109 TGCATCTT
1 TGCAT-TT
63117 TGCATTT
1 TGCATTT
63124 T-CATTT
1 TGCATTT
63130 TGCATT
1 TGCATT
63136 CATACTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
6 10 0.32
7 14 0.45
8 7 0.23
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:70291 original size:54 final size:54
Alignment explanation
Indices: 70147--70298 Score: 187
Period size: 54 Copynumber: 2.8 Consensus size: 54
70137 ATATAGGCAA
** * * * * * **
70147 AAACCACATTAAAGGATGAATGTATTGTCAAATGCTTTACAAAAATCTGGGCAG
1 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
70201 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
1 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
* * * *
70255 AAGCCACAGGAAATGATGAATGTGTTGTCAAGTGTTTTATGAAC
1 AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAAC
70299 CAGCGATTAT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 85 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (54 bp):
AAACCACAAGAAATGATGAATGTGTTGTCAAATGTTTTACGAACATCTAAGCAG
Found at i:71513 original size:45 final size:45
Alignment explanation
Indices: 71418--71526 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
71408 CTTTTTGATA
* * * **
71418 TTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAATGCATTATG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAAGATG
* * *
71463 CTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGTAAGATG
1 TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAAGATG
71508 TTTTCAAACAGCCTTCGGG
1 TTTTCAAA-A-CCTTCGGG
71527 AGCTTTTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 44 0.83
46 1 0.02
47 8 0.15
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (45 bp):
TTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAATGCAAGATG
Found at i:71513 original size:121 final size:121
Alignment explanation
Indices: 71360--71957 Score: 865
Period size: 121 Copynumber: 4.9 Consensus size: 121
71350 CTATTTCCCA
* *
71360 CATCCATAAGACCTACAGTGCAGGATGTTTTCAAAAAACCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* * *
71425 AACCTTCGGGTCATCTATAAGCCCTTCAATGCATTATGCTTTCAAAACCTTCGGGT
66 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * *
71481 CATCCATAAGACCTGCAGTGTAAGATGTTTTCAAACAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* **
71546 AACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTTAGGT
66 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * **
71602 CATCCATAAGACCTGCAGAGCAAGATGTTTTCAAAAAGCCTTAAGGAGC-TTTTGATATTTTCAA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* * * * * *
71666 AGCCTTTGGGTAATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCTGGC
66 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTC-AAAACCTTCGGGT
71723 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATGTTTCA
1 CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAT-TTTCA
* * *
71788 AAGCCTTCAGGTCATCTGTAAGCCCTTCAGTACATGATGCTTTCAAAACCTTCGGGT
65 AAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
* * *
71845 CATCCATAAGACCTGTAGTGCAGGATGTTTTTAAAAGAAAGCCTTCAGGAGCTTTTTGATATTTT
1 CATCCATAAGACCTGCAGTGCAGGATG-TTTT-CAA-AAAGCCTTCGGGAGCTTTTTGATATTTT
* * * *
71910 CAAAACCTTCGGGTCATTTCTAAGCCCTTCAGTGAATGATGTTTTCAA
63 CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAA
71958 CATTTCCATC
Statistics
Matches: 427, Mismatches: 44, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
120 54 0.13
121 209 0.49
122 46 0.11
123 48 0.11
124 46 0.11
125 24 0.06
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (121 bp):
CATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
Found at i:71634 original size:45 final size:45
Alignment explanation
Indices: 71539--71637 Score: 108
Period size: 45 Copynumber: 2.2 Consensus size: 45
71529 CTTTTTGATA
* * ** * * * *
71539 TTTTCAAAACCTTCGGGTTATCTGTAAGCCCTTCAGTGCATGATG
1 TTTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGAGCAAGATG
* *
71584 CTTTCAAAACCTTTAGGTCATCCATAAGACCTGCAGAGCAAGATG
1 TTTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGAGCAAGATG
71629 TTTTCAAAA
1 TTTTCAAAA
71638 AGCCTTAAGG
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (45 bp):
TTTTCAAAACCTTCAGGTCATCCATAAGACCTGCAGAGCAAGATG
Found at i:72083 original size:5 final size:5
Alignment explanation
Indices: 72073--72115 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
72063 ACTAATTTTT
72073 TTATA TTATA -TATA TTATA TTATA TTATA -TATA TTATTA TTAT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTA-TA TTAT
72116 TAAATAAATA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
4 8 0.23
5 22 0.63
6 5 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:72097 original size:19 final size:20
Alignment explanation
Indices: 72073--72115 Score: 79
Period size: 19 Copynumber: 2.2 Consensus size: 20
72063 ACTAATTTTT
72073 TTATATTATATATATTA-TA
1 TTATATTATATATATTATTA
72092 TTATATTATATATATTATTA
1 TTATATTATATATATTATTA
72112 TTAT
1 TTAT
72116 TAAATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATATTATATATATTATTA
Found at i:73431 original size:30 final size:29
Alignment explanation
Indices: 73359--73431 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
73349 ATTAATTGCT
*
73359 TATATTTTATAATTTTATCATTAAGTTTTA
1 TATATTTTA-AATTTTACCATTAAGTTTTA
*
73389 TATAATTT-AATTTTAACCA-TAAGTTTTA
1 TATATTTTAAATTTT-ACCATTAAGTTTTA
73417 TATATTTTACAATTT
1 TATATTTTA-AATTT
73432 AATTTTATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 22 0.59
29 3 0.08
30 12 0.32
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (29 bp):
TATATTTTAAATTTTACCATTAAGTTTTA
Found at i:73507 original size:21 final size:19
Alignment explanation
Indices: 73481--73535 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
73471 TATTTGCAAT
*
73481 ATTATTTTATTATACTTTTG
1 ATTATTTTATTATAC-TTTA
73501 ATATATTTTAATTATTACTTTA
1 AT-TATTTT-ATTA-TACTTTA
73523 ATTATTTTATTAT
1 ATTATTTTATTAT
73536 CTTAGTCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 1 0.03
20 6 0.19
21 12 0.39
22 9 0.29
23 3 0.10
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTTTATTATACTTTA
Found at i:81962 original size:17 final size:17
Alignment explanation
Indices: 81925--81964 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
81915 ATAGTCACTG
* * *
81925 TTGACTGTTGACCTGCG
1 TTGACCGTTGACCGGCA
81942 TTGACCGTTGACCGGCA
1 TTGACCGTTGACCGGCA
81959 TTGACC
1 TTGACC
81965 ACTGTTGACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (17 bp):
TTGACCGTTGACCGGCA
Found at i:84512 original size:12 final size:12
Alignment explanation
Indices: 84494--84555 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
84484 ACCTGAATTC
84494 TGTTCTGATTTT
1 TGTTCTGATTTT
* *
84506 TGATCTGGA-TTC
1 TGTTCT-GATTTT
* * *
84518 TGTTTTGATATC
1 TGTTCTGATTTT
84530 TGTTCTGATTTT
1 TGTTCTGATTTT
*
84542 TGTTTTGATTTT
1 TGTTCTGATTTT
84554 TG
1 TG
84556 ATATTTCCGT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.11, C:0.08, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTTCTGATTTT
Found at i:84517 original size:24 final size:23
Alignment explanation
Indices: 84490--84557 Score: 73
Period size: 24 Copynumber: 2.9 Consensus size: 23
84480 CATGACCTGA
*
84490 ATTCTGTTCTGATTTTTGATCTGG
1 ATTCTGTTTTGATTTTTGATCT-G
* * *
84514 ATTCTGTTTTGATATCTGTTCTG
1 ATTCTGTTTTGATTTTTGATCTG
*
84537 ATTTTTGTTTTGATTTTTGAT
1 A-TTCTGTTTTGATTTTTGAT
84558 ATTTCCGTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 2 0.06
24 33 0.94
ACGTcount: A:0.13, C:0.09, G:0.18, T:0.60
Consensus pattern (23 bp):
ATTCTGTTTTGATTTTTGATCTG
Done.