Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004654.1 Hibiscus syriacus cultivar Beakdansim tig00010431_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: 63494
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1666 original size:44 final size:43
Alignment explanation
Indices: 1558--1668 Score: 107
Period size: 44 Copynumber: 2.5 Consensus size: 43
1548 TAGCAAAGTA
* * * * *
1558 TGAAATCTTCACAGAAGAGTAGTGGAGTAATCCAAGTTTGAGTT
1 TGAAAT-TTCACGGAAGAGTAGTGGAGAAATCCAACTTTGAATC
* * *
1602 TGAAATTTCACGAAATAGTAGTGGAAGCAAATTCAACTTTGAATC
1 TGAAATTTCACGGAAGAGTAGTGG-AG-AAATCCAACTTTGAATC
*
1647 TGATA-TTCACGGAAGAGTAGTG
1 TGAAATTTCACGGAAGAGTAGTG
1669 AATTAGATTC
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 15 0.28
44 23 0.43
45 16 0.30
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (43 bp):
TGAAATTTCACGGAAGAGTAGTGGAGAAATCCAACTTTGAATC
Found at i:1778 original size:92 final size:94
Alignment explanation
Indices: 1608--1779 Score: 208
Period size: 92 Copynumber: 1.9 Consensus size: 94
1598 AGTTTGAAAT
* * * **
1608 TTCACGAAATAGTAGTGGAAGCAAATTCAACTTTGAATCTGATATTCACGGAAGAGTAGTGAATT
1 TTCACGAAAGAGTAGTGGAAGCAAATCCAACTTTGAATCTGATATTCACAGAAGAGTAGTGAAAC
*
1673 AGATTCTTGTCAAGTCATCATTTTTTTAC
66 AGATTCATGTCAAGTCATCATTTTTTTAC
* * * *
1702 TTCACGAAAGAGTAGTGG-AG-TAATCCAAGTTTGAGTTTGA-ACTTCACAGAAGAGTAGTGAAA
1 TTCACGAAAGAGTAGTGGAAGCAAATCCAACTTTGAATCTGATA-TTCACAGAAGAGTAGTGAAA
1764 CAGATTCGAT-TCAAGT
65 CAGATTC-ATGTCAAGT
1780 TATCTATATG
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
91 1 0.02
92 45 0.68
93 3 0.05
94 17 0.26
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (94 bp):
TTCACGAAAGAGTAGTGGAAGCAAATCCAACTTTGAATCTGATATTCACAGAAGAGTAGTGAAAC
AGATTCATGTCAAGTCATCATTTTTTTAC
Found at i:2080 original size:14 final size:14
Alignment explanation
Indices: 2061--2087 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2051 CGAGTGATGC
2061 TTATTATATATAAG
1 TTATTATATATAAG
2075 TTATTATATATAA
1 TTATTATATATAA
2088 TAAATAATAA
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:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
TTATTATATATAAG
Found at i:2819 original size:18 final size:17
Alignment explanation
Indices: 2796--2833 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
2786 CGGGGTTTCT
2796 AGAGAGATGCGAGAGGAG
1 AGAGAGATGCGAG-GGAG
*
2814 AGAGAGATGGGAGGGAG
1 AGAGAGATGCGAGGGAG
2831 AGA
1 AGA
2834 TGGTCCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.39, C:0.03, G:0.53, T:0.05
Consensus pattern (17 bp):
AGAGAGATGCGAGGGAG
Found at i:3193 original size:28 final size:30
Alignment explanation
Indices: 3144--3204 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
3134 AGTGCAATAT
3144 TTTTAATATATTTTAAACTAG-ATTAATTAA
1 TTTTAATATATTTTAAACTAGAATT-ATTAA
* *
3174 TTTT-ATATA-TTTATATTAGAATTATTAA
1 TTTTAATATATTTTAAACTAGAATTATTAA
3202 TTT
1 TTT
3205 ACATAATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 16 0.57
29 8 0.29
30 4 0.14
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (30 bp):
TTTTAATATATTTTAAACTAGAATTATTAA
Found at i:9862 original size:22 final size:20
Alignment explanation
Indices: 9834--9875 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
9824 GCAATTACTA
9834 CCACACCACCATCATTCCATTT
1 CCACACCA--ATCATTCCATTT
*
9856 CCACACCATTCATTCCATTT
1 CCACACCAATCATTCCATTT
9876 TGCCACATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.43, G:0.00, T:0.31
Consensus pattern (20 bp):
CCACACCAATCATTCCATTT
Found at i:20953 original size:3 final size:3
Alignment explanation
Indices: 20947--20976 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
20937 TTTGTAGTAG
*
20947 TAA TAA TAA TAA TAA TAA CAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
20977 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:21303 original size:98 final size:97
Alignment explanation
Indices: 21129--21563 Score: 543
Period size: 98 Copynumber: 4.4 Consensus size: 97
21119 AATAAAAAGT
* * * * * *
21129 AAAAAATCCTACCCAGAGGTCTTACGGATGGCCCGGATGACTTAATTTTCTAAATATTAAATGAG
1 AAAACATCCTACCCAGAGGTTTTACAGAT-GCCCGGAGGACTTAACTTTCTAAACATTAAATGAG
21194 AAACTTTGGTAATCGATTTCTCATTTTCATGTG
65 AAACTTTGGTAATCGATTTCTCATTTTCATGTG
** * * * * *
21227 AAAACATCCTACCTTGAGGTTTTAC-GAATAACCCGGAGGGCTTAATTTTTTAAACATTGAATGA
1 AAAACATCCTACCCAGAGGTTTTACAG-AT-GCCCGGAGGACTTAACTTTCTAAACATTAAATGA
21291 GAAACTTTGGTAATC-ACTTTCTCATTTTCATGTG
64 GAAACTTTGGTAATCGA-TTTCTCATTTTCATGTG
* * * *
21325 AAAACATCCTACCCAGAGGTTTTACAGATGGCCAGAGGACTTAACTTT-TCGAATATTAAATGAG
1 AAAACATCCTACCCAGAGGTTTTACAGATGCCCGGAGGACTTAACTTTCT-AAACATTAAATGAG
* *
21389 AAACTTTGGTAATCGCTTTCTCATCTTCATGTG
65 AAACTTTGGTAATCGATTTCTCATTTTCATGTG
* *
21422 AAAACATCTTACCCAGAGGTTTTACAGATGGCCCGGAGGACTTAACTTTCTGAACATTAAATGAG
1 AAAACATCCTACCCAGAGGTTTTACAGAT-GCCCGGAGGACTTAACTTTCTAAACATTAAATGAG
*
21487 AAACTTTGGTAATCGCTTTCTCATTTTCATGTG
65 AAACTTTGGTAATCGATTTCTCATTTTCATGTG
* * * **
21520 AATACATCCTACACTGAGGTTTTATGGATGGCCCGGAGGACTTA
1 AAAACATCCTACCCAGAGGTTTTACAGAT-GCCCGGAGGACTTA
21564 TCATCTTTAG
Statistics
Matches: 296, Mismatches: 34, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
96 1 0.00
97 85 0.29
98 208 0.70
99 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (97 bp):
AAAACATCCTACCCAGAGGTTTTACAGATGCCCGGAGGACTTAACTTTCTAAACATTAAATGAGA
AACTTTGGTAATCGATTTCTCATTTTCATGTG
Found at i:21487 original size:195 final size:196
Alignment explanation
Indices: 21129--21563 Score: 624
Period size: 195 Copynumber: 2.2 Consensus size: 196
21119 AATAAAAAGT
* * *
21129 AAAAAATCCTACCCAGAGGTCTTACGGATGGCCCGGATGACTTAATTTTCTAAATATTAAATGAG
1 AAAACATCCTACCCAGAGGTTTTACGGATGGCCCGGAGGACTTAATTTTCTAAATATTAAATGAG
* **
21194 AAACTTTGGTAATCGATTTCTCATTTTCATGTGAAAACATCCTACCTTGAGGTTTTACGAATAAC
66 AAACTTTGGTAATCGATTTCTCATCTTCATGTGAAAACATCCTACCCAGAGGTTTTACGAATAAC
* * * *
21259 CCGGAGGGCTTAATTTTTTAAACATTGAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGT
131 CCGGAGGACTTAACTTTCTAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGT
21324 G
196 G
* * *
21325 AAAACATCCTACCCAGAGGTTTTACAGATGG-CCAGAGGACTTAACTTTTC-GAATATTAAATGA
1 AAAACATCCTACCCAGAGGTTTTACGGATGGCCCGGAGGACTTAA-TTTTCTAAATATTAAATGA
* * *
21388 GAAACTTTGGTAATCGCTTTCTCATCTTCATGTGAAAACATCTTACCCAGAGGTTTTAC-AGATG
65 GAAACTTTGGTAATCGATTTCTCATCTTCATGTGAAAACATCCTACCCAGAGGTTTTACGA-ATA
* * *
21452 GCCCGGAGGACTTAACTTTCTGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCAT
129 ACCCGGAGGACTTAACTTTCTAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCAT
21517 GTG
194 GTG
* * * *
21520 AATACATCCTACACTGAGGTTTTATGGATGGCCCGGAGGACTTA
1 AAAACATCCTACCCAGAGGTTTTACGGATGGCCCGGAGGACTTA
21564 TCATCTTTAG
Statistics
Matches: 211, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
194 1 0.00
195 166 0.79
196 44 0.21
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (196 bp):
AAAACATCCTACCCAGAGGTTTTACGGATGGCCCGGAGGACTTAATTTTCTAAATATTAAATGAG
AAACTTTGGTAATCGATTTCTCATCTTCATGTGAAAACATCCTACCCAGAGGTTTTACGAATAAC
CCGGAGGACTTAACTTTCTAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTCATGT
G
Found at i:23058 original size:39 final size:38
Alignment explanation
Indices: 23000--23105 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 38
22990 GCCCCAACAT
*** * *
23000 TTGCTGATATGAATGTTCAAAATGCTCTAACATTATTTC
1 TTGCTGATATGAGCCTTCAAAATGCCCCAACATT-TTTC
23039 TTGCTGATATGAGCCTTCAAAATGCCCCAACATTTTTC
1 TTGCTGATATGAGCCTTCAAAATGCCCCAACATTTTTC
* * ** *
23077 ATACTGACGTGAGGCTTCAAAATGCCCCA
1 TTGCTGATATGAGCCTTCAAAATGCCCCA
23106 CATGGATCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 28 0.49
39 29 0.51
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (38 bp):
TTGCTGATATGAGCCTTCAAAATGCCCCAACATTTTTC
Found at i:23102 original size:38 final size:39
Alignment explanation
Indices: 23015--23105 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 39
23005 GATATGAATG
* * * * *
23015 TTCAAAATGCTCTAACATTATTTCTTGCTGATATGAGCC
1 TTCAAAATGCCCCAACATTATTTCATACTGACATGAGCC
* *
23054 TTCAAAATGCCCCAACATT-TTTCATACTGACGTGAGGC
1 TTCAAAATGCCCCAACATTATTTCATACTGACATGAGCC
23092 TTCAAAATGCCCCA
1 TTCAAAATGCCCCA
23106 CATGGATCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 28 0.62
39 17 0.38
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (39 bp):
TTCAAAATGCCCCAACATTATTTCATACTGACATGAGCC
Found at i:24796 original size:18 final size:18
Alignment explanation
Indices: 24773--24813 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
24763 GATTTCTTTC
24773 TTTTTTCTC-TTTTTCTCT
1 TTTTTTCTCTTTTTTC-CT
24791 TTTTTTCTCTTTTTTCCT
1 TTTTTTCTCTTTTTTCCT
24809 TTTTT
1 TTTTT
24814 AGATGAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTCTCTTTTTTCCT
Found at i:24810 original size:8 final size:9
Alignment explanation
Indices: 24771--24813 Score: 63
Period size: 8 Copynumber: 4.9 Consensus size: 9
24761 TTGATTTCTT
24771 TCTTTTTTC
1 TCTTTTTTC
24780 TC-TTTTTC
1 TCTTTTTTC
24788 TCTTTTTTTC
1 TC-TTTTTTC
24798 TCTTTTTTC
1 TCTTTTTTC
24807 -CTTTTTT
1 TCTTTTTT
24814 AGATGAGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 15 0.47
9 9 0.28
10 8 0.25
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TCTTTTTTC
Found at i:27953 original size:20 final size:20
Alignment explanation
Indices: 27900--27953 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
27890 TATGTAGAGT
*
27900 AGTATCGATACCAAGAGGGG
1 AGTATCGATACCATGAGGGG
* *
27920 AGTATTGATACCATGAGGATG
1 AGTATCGATACCATGAGG-GG
27941 -GTATCGATACCAT
1 AGTATCGATACCAT
27954 TTGATCACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (20 bp):
AGTATCGATACCATGAGGGG
Found at i:28441 original size:58 final size:58
Alignment explanation
Indices: 28374--29056 Score: 991
Period size: 58 Copynumber: 11.8 Consensus size: 58
28364 ATGGCACTAA
* *
28374 GTGTCCAAAAAGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
28432 GTGTGCAAAAAGTTAAGAAATTCATAATAAGTGTATGAATTTCCTTATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
28490 GTGTGCAAAACA-TTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAA-AGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
28548 TTGTGCAAAACGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
28606 GTGTGAAAAAAGTTAAGAAATTCATACTAATTGTATGAATTTCCGTATTGGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * * *
28664 GTGTACAAAAAGTTAAGAAATTCATACAAAGTGTATAAATTTTCGTATTGGGTACTTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC-TTT
*
28723 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
28781 GTGTGCAAAAAGTTAAGAAATTCATATTAAGTGTATAAATTTCCGTATTGGGTACTTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC-TTT
* *
28840 GTGTGCAAAAAGTTAAGAAAGTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
28898 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAGTTTCCGTATCGGGCACTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * ** * *
28956 GTGTGC-AAAA-CTAAGAAATTCATATTAAGTGTATGAATTTATGTA-TGGACACTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
29011 GTGTAC-AGAA-CTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
29057 GAGAAATATA
Statistics
Matches: 571, Mismatches: 49, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
55 48 0.08
56 30 0.05
57 4 0.01
58 381 0.67
59 108 0.19
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (58 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:28773 original size:117 final size:116
Alignment explanation
Indices: 28374--29056 Score: 991
Period size: 117 Copynumber: 5.9 Consensus size: 116
28364 ATGGCACTAA
* *
28374 GTGTCCAAAAAGTTAAGAAATTCATACTAAATGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
* *
28439 AAAAGTTAAGAAATTCATAATAAGTGTATGAATTTCCTTATTGGGCACTTT
66 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
28490 GTGTGCAAAACA-TTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTTTGTGC
1 GTGTGCAAAA-AGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGC
* *
28554 AAAACGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTT
65 AAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
28606 GTGTGAAAAAAGTTAAGAAATTCATACTAATTGTATGAATTTCCGTATTGGGTACTTTGTGTACA
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
* * * *
28671 AAAAGTTAAGAAATTCATACAAAGTGTATAAATTTTCGTATTGGGTACTTTT
66 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC-TTT
*
28723 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGTACTTTGTGTGCA
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
* * *
28788 AAAAGTTAAGAAATTCATATTAAGTGTATAAATTTCCGTATTGGGTACTTTT
66 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCAC-TTT
* *
28840 GTGTGCAAAAAGTTAAGAAAGTCATACTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCA
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
* * *
28905 AAAAGTTAAGAAATTCATACTAAGTGTATGAGTTTCCGTATCGGGCACTAT
66 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * ** * * *
28956 GTGTGC-AAAA-CTAAGAAATTCATATTAAGTGTATGAATTTATGTA-TGGACACTATGTGTAC-
1 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
* * *
29017 AGAA-CTAAGAAATTCATACTAAGTGTATGAATTTTCGTAT
66 AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
29057 GAGAAATATA
Statistics
Matches: 519, Mismatches: 45, Indels: 11
0.90 0.08 0.02
Matches are distributed among these distances:
111 33 0.06
112 3 0.01
113 12 0.02
114 30 0.06
115 5 0.01
116 216 0.42
117 220 0.42
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (116 bp):
GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTGCA
AAAAGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:29680 original size:68 final size:68
Alignment explanation
Indices: 29272--29665 Score: 590
Period size: 68 Copynumber: 5.8 Consensus size: 68
29262 CAAGGTTAAT
* * * * * *
29272 GGCCTAACTGTGCATTTGACAAAAATGTGTCAATCATGTCAGTTAAATGAAAGGCTAAGTTCTTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
*
29337 TAA
66 TGA
29340 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29405 TGA
66 TGA
* ** * *
29408 GGCCTAACTGTGCACTTGACAGAAATATGTCAATCATACCAGGTAGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29473 TGA
66 TGA
*
29476 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTACCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29541 TGA
66 TGA
* * * * *
29544 GGCCTAATTGTGCACTTGACAGAAAGGTGTCAATCATGTCATTTAGATGAAAGGCTAAGTGCCAT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
29609 TGA
66 TGA
* * * *
29612 GGCCTGATTGTGCATTTAACAGAAAGGTGTCAATGATGCCAGTTAGATGAAAGG
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGG
29666 TTCAATATCT
Statistics
Matches: 296, Mismatches: 30, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 296 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.27
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:29761 original size:81 final size:81
Alignment explanation
Indices: 29620--29768 Score: 183
Period size: 81 Copynumber: 1.8 Consensus size: 81
29610 GAGGCCTGAT
* * * * * * * *
29620 TGTGCATTTAACAGAAAGGTGTCAATGATGCCAGTTAGATGAAAGGTTCAATATCTTTGAGCAAA
1 TGTGCACTTAACAGAAAGGTGTAAATGAAGCAAGATAGATGAAAGGTTAAATACCGTTGAGCAAA
29685 AGATTAATGGCCTAGC
66 AGATTAATGGCCTAGC
* * *
29701 TGTGCACTTGACAGAAAGGTGTAAATTAAGCAAGATAGATGAACA-GTTAAATACCGTTGAGTAA
1 TGTGCACTTAACAGAAAGGTGTAAATGAAGCAAGATAGATGAA-AGGTTAAATACCGTTGAGCAA
29765 AAGA
65 AAGA
29769 CTAGATGTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 55 0.98
82 1 0.02
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.26
Consensus pattern (81 bp):
TGTGCACTTAACAGAAAGGTGTAAATGAAGCAAGATAGATGAAAGGTTAAATACCGTTGAGCAAA
AGATTAATGGCCTAGC
Found at i:30009 original size:22 final size:22
Alignment explanation
Indices: 29984--30053 Score: 54
Period size: 22 Copynumber: 3.1 Consensus size: 22
29974 CATTATAGGT
29984 ATGAAATGATGCCATAATTAAA
1 ATGAAATGATGCCATAATTAAA
* * **
30006 ATGAATATGGGTG-CATTA-TAGGC
1 ATGAA-AT-GATGCCATAATTA-AA
*
30029 ATGAAATGATGCCATAATTGAA
1 ATGAAATGATGCCATAATTAAA
30051 ATG
1 ATG
30054 TATATGGGTG
Statistics
Matches: 34, Mismatches: 9, Indels: 10
0.64 0.17 0.19
Matches are distributed among these distances:
21 3 0.09
22 16 0.47
23 12 0.35
24 3 0.09
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (22 bp):
ATGAAATGATGCCATAATTAAA
Found at i:30130 original size:45 final size:45
Alignment explanation
Indices: 29804--30114 Score: 437
Period size: 45 Copynumber: 7.0 Consensus size: 45
29794 TGTATAAAAT
* * * *
29804 GCATGAACGGATTCCATAATTG-AA-GCATATGGGTGTATTATCG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
* * *
29847 ACATGAAAGGATACCATAATTGAAATTCATATGGGTGCATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
* * *
29892 GCATGAAAGGATGCCATAATTGAAAGGCATATGGATGTATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
* *
29937 GCATGATAGGATTCCATAATTGAAATGCATATGGGTGCATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
* * * *
29982 GTATGAAATGATGCCATAATTAAAATGAATATGGGTGCATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
* * *
30027 GCATGAAATGATGCCATAATTGAAATGTATATGGGTGTATTATAG
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
30072 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTAT
1 GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTAT
30115 CGGTATGGAA
Statistics
Matches: 236, Mismatches: 30, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
43 19 0.08
44 2 0.01
45 215 0.91
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.30
Consensus pattern (45 bp):
GCATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATAG
Found at i:33824 original size:18 final size:18
Alignment explanation
Indices: 33803--33837 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
33793 TATTAATGGA
33803 GTAAAAAAAATTAAAAAG
1 GTAAAAAAAATTAAAAAG
*
33821 GTAAAAGAAATTAAAAA
1 GTAAAAAAAATTAAAAA
33838 TGAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
GTAAAAAAAATTAAAAAG
Found at i:33996 original size:2 final size:2
Alignment explanation
Indices: 33984--34013 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
33974 TAAAGTAAAA
33984 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34014 AATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:34093 original size:2 final size:2
Alignment explanation
Indices: 34086--34171 Score: 113
Period size: 2 Copynumber: 43.5 Consensus size: 2
34076 ACATCTGTAC
34086 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
34128 AT AT AT AT AT AT GAT AT A- AG GT AT AT AT A- AA AA AT AT AT AT
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
34169 AT A
1 AT A
34172 AAAAAATATA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
1 2 0.03
2 73 0.95
3 2 0.03
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:36628 original size:67 final size:65
Alignment explanation
Indices: 36510--36676 Score: 192
Period size: 65 Copynumber: 2.5 Consensus size: 65
36500 CATGAAAATG
* *
36510 GTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGATTTTGGGTTTCAAGAGAA
1 GTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTTCAAGATTTT--GTTTCAAGAGAA
36575 ACT
63 ACT
* ** *
36578 GTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAA-TTCAACTTTTTTGTTTCAAGGGAAAC
1 GTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTTCAA-GATTTTGTTTCAAGAGAAAC
36642 T
65 T
** * * *
36643 GTCTCAAAAGAGACGAAATTTGTTTCAAGAGAAA
1 GTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
36677 CTGTCTCAGG
Statistics
Matches: 86, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
65 42 0.49
66 4 0.05
67 23 0.27
68 17 0.20
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (65 bp):
GTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTTCAAGATTTTGTTTCAAGAGAAACT
Found at i:36677 original size:36 final size:36
Alignment explanation
Indices: 36625--36850 Score: 171
Period size: 36 Copynumber: 6.4 Consensus size: 36
36615 ATTCAACTTT
* *
36625 TTTGTTTCAAGGGAAACTGTCTCAAAAGAGACGAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * *
36661 TTTGTTTCAAGAGAAACTGTCTCAGGAGAGGCAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * ** * ** *
36697 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGATGAAT
1 -TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* ** * * * *
36734 TTTTTTTCAA-ATAAAATATATTC-----A-A-ATAA
1 TTTGTTTCAAGGGAAACTGT-CTCAAGAGAGACAAAA
*
36763 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
36799 TTTGTTTCAAGGGAAACTGTCTCAAGAGATACAAAA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
*
36835 TTTATTTCAAGGGAAA
1 TTTGTTTCAAGGGAAA
36851 TGTTTTCAAT
Statistics
Matches: 145, Mismatches: 35, Indels: 20
0.73 0.17 0.10
Matches are distributed among these distances:
29 11 0.08
30 6 0.04
31 1 0.01
34 1 0.01
35 7 0.05
36 92 0.63
37 27 0.19
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
Found at i:36880 original size:101 final size:101
Alignment explanation
Indices: 36659--36926 Score: 268
Period size: 101 Copynumber: 2.6 Consensus size: 101
36649 AAAGAGACGA
* * * * **
36659 AATTTGTTTCAAGAGAAACTGTCTCAGGAGAGGCAAAACTTAGTTCCAAAAGAAACTGTCTCAAG
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTGTTTCAAGGGAAACTGTCTCAAG
* ** * * *
36724 GGAGATGAATTTTTTTTCAAATAAAATATATTCAAAT
65 AGAGACAAAATTTATTTCAAAGAAAATATATTCAAAT
* *
36761 AATTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
1 AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
* * * * *
36826 GATACAAAATTTATTTCAAGGGAAATGTTTTC-AAT
66 GAGACAAAATTTATTTCAAAGAAAATATATTCAAAT
** * * * * *
36861 GTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAATATTTTGTTTCAAGGCAAACTATCTCAA
1 AATT-TGTTTCAAGAGAAACTGTCTCAAGAGAGACAA-AATTTGTTTCAAGGGAAACTGTCTCAA
36926 G
64 G
36927 CGAAATAAAA
Statistics
Matches: 136, Mismatches: 28, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
100 5 0.04
101 72 0.53
102 59 0.43
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (101 bp):
AATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAACTGTCTCAAGA
GAGACAAAATTTATTTCAAAGAAAATATATTCAAAT
Found at i:37988 original size:16 final size:16
Alignment explanation
Indices: 37967--38003 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
37957 TGGTTTCAAG
37967 ACGTCATTCGTAATTT
1 ACGTCATTCGTAATTT
37983 ACGTCATTCGTAATTT
1 ACGTCATTCGTAATTT
37999 ACGTC
1 ACGTC
38004 TTGAACCCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (16 bp):
ACGTCATTCGTAATTT
Found at i:38414 original size:69 final size:69
Alignment explanation
Indices: 38303--38437 Score: 236
Period size: 69 Copynumber: 2.0 Consensus size: 69
38293 CTCTCTCTTG
*
38303 ATGCTCTATGATCTTCGAGTAGAGTGATTCAGTGATTCAGAAATGATTGTGCTTAATCAATCTCA
1 ATGCTCTATGATCTTCGAGTAGAGTGATTCAGTGATTCAGAAATGATTATGCTTAATCAATCTCA
38368 TTTC
66 TTTC
*
38372 ATGCTCTATGATCTTCGAGT-GAAGTGATTCAGTGATTCAGAAATGATTATGCTTGATCAATCTC
1 ATGCTCTATGATCTTCGAGTAG-AGTGATTCAGTGATTCAGAAATGATTATGCTTAATCAATCTC
38436 AT
65 AT
38438 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
68 1 0.02
69 62 0.98
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.37
Consensus pattern (69 bp):
ATGCTCTATGATCTTCGAGTAGAGTGATTCAGTGATTCAGAAATGATTATGCTTAATCAATCTCA
TTTC
Found at i:38571 original size:26 final size:26
Alignment explanation
Indices: 38516--38573 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
38506 TCAATTTTCG
* *
38516 TTTGTTTTTTCTTTTTTTATTTTCTC
1 TTTGTTTTTTCTCTTTTTATTCTCTC
*
38542 TTTGCTTTTTTCTCTTTTT-TTCTCTT
1 TTTG-TTTTTTCTCTTTTTATTCTCTC
38568 TTTGTT
1 TTTGTT
38574 CTTGATTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 2 0.07
26 13 0.46
27 13 0.46
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (26 bp):
TTTGTTTTTTCTCTTTTTATTCTCTC
Found at i:41684 original size:25 final size:25
Alignment explanation
Indices: 41624--41684 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
41614 ACATGAGAAT
*
41624 AATAAATAAAACAAGAAAAAATGAA
1 AATAAATAAAACAAGAAAAAATAAA
* * *
41649 AATTAATAAAACACGTAAAAATAAA
1 AATAAATAAAACAAGAAAAAATAAA
*
41674 AATAAAAAAAA
1 AATAAATAAAA
41685 TAAACAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.15
Consensus pattern (25 bp):
AATAAATAAAACAAGAAAAAATAAA
Found at i:41779 original size:18 final size:17
Alignment explanation
Indices: 41747--41793 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
41737 TATTAATGGA
41747 GTAAAAAAATAAAAAAG
1 GTAAAAAAATAAAAAAG
*
41764 GTAAAAGAAATTAAAAAG
1 GTAAAA-AAATAAAAAAG
41782 G-AATAAAAATAA
1 GTAA-AAAAATAA
41794 TGTGTACATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (17 bp):
GTAAAAAAATAAAAAAG
Found at i:41926 original size:2 final size:2
Alignment explanation
Indices: 41914--41943 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
41904 TAAAGTAAAA
41914 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41944 AATAAAAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42014 original size:18 final size:18
Alignment explanation
Indices: 41953--42018 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 18
41943 AAATAAAAAC
*
41953 AAAAATAGAATATTAAGA
1 AAAAATATAATATTAAGA
* *
41971 AAATATATATATATATACGTA
1 AAAAATATA-ATAT-TAAG-A
*
41992 TAAAATATAATATTAAGA
1 AAAAATATAATATTAAGA
42010 AAAAATATA
1 AAAAATATA
42019 TATACATAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 16 0.42
19 7 0.18
20 7 0.18
21 8 0.21
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (18 bp):
AAAAATATAATATTAAGA
Found at i:42059 original size:2 final size:2
Alignment explanation
Indices: 42052--42117 Score: 98
Period size: 2 Copynumber: 33.0 Consensus size: 2
42042 TTAATACATC
42052 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* *
42095 TA TA TA TA AA AA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
42118 AATAAAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 1 0.02
2 57 0.95
3 2 0.03
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:42128 original size:23 final size:23
Alignment explanation
Indices: 42102--42154 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
42092 ATATATATAT
42102 AAAAATAATATATATAAATAAA-A
1 AAAAATAATATA-ATAAATAAATA
** *
42125 AAAAGGAATATAGTAAATAAATA
1 AAAAATAATATAATAAATAAATA
42148 AAAAATA
1 AAAAATA
42155 TAATTAAAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.23
Consensus pattern (23 bp):
AAAAATAATATAATAAATAAATA
Found at i:52420 original size:32 final size:32
Alignment explanation
Indices: 52379--52485 Score: 101
Period size: 32 Copynumber: 3.4 Consensus size: 32
52369 ATACCTTGGG
**
52379 AGCCTACCCAAGAGTGTACATTGGGGCCTAAA
1 AGCCTACCCAAGAGAATACATTGGGGCCTAAA
* * * *
52411 AGCCTACCCAAGGGAATACCTTGGGGCCTTAG
1 AGCCTACCCAAGAGAATACATTGGGGCCTAAA
* * * *
52443 AGCTTACCCAAG-GAAATACCTT-GGCCCTCAA
1 AGCCTACCCAAGAG-AATACATTGGGGCCTAAA
52474 AGCCTACCCAAG
1 AGCCTACCCAAG
52486 TGTCACCTTA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
31 18 0.29
32 45 0.71
ACGTcount: A:0.30, C:0.30, G:0.22, T:0.18
Consensus pattern (32 bp):
AGCCTACCCAAGAGAATACATTGGGGCCTAAA
Found at i:52485 original size:31 final size:32
Alignment explanation
Indices: 52399--52485 Score: 104
Period size: 32 Copynumber: 2.8 Consensus size: 32
52389 AGAGTGTACA
* * *
52399 TTGGGGCCTAAAAGCCTACCCAAGGGAATACC
1 TTGGGCCCTCAAAGCCTACCCAAGGAAATACC
* * * *
52431 TTGGGGCCTTAGAGCTTACCCAAGGAAATACC
1 TTGGGCCCTCAAAGCCTACCCAAGGAAATACC
52463 TT-GGCCCTCAAAGCCTACCCAAG
1 TTGGGCCCTCAAAGCCTACCCAAG
52486 TGTCACCTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 17 0.36
32 30 0.64
ACGTcount: A:0.29, C:0.30, G:0.23, T:0.18
Consensus pattern (32 bp):
TTGGGCCCTCAAAGCCTACCCAAGGAAATACC
Found at i:54853 original size:13 final size:13
Alignment explanation
Indices: 54835--54932 Score: 67
Period size: 13 Copynumber: 7.2 Consensus size: 13
54825 TTTATTTACT
54835 TTATATTTAATAC
1 TTATATTTAATAC
*
54848 TTATATTTATCTAC
1 TTATATTTA-ATAC
54862 TTTAATACTTT-ATA-
1 -TT-ATA-TTTAATAC
*
54876 TTATACTTTAGTAC
1 TTATA-TTTAATAC
* *
54890 TTATGTAATTATATAT
1 TTA--TATTTA-ATAC
54906 TTATATTTAATAC
1 TTATATTTAATAC
54919 TTATATTT-ATAC
1 TTATATTTAATAC
54931 TT
1 TT
54933 TAATACTTAT
Statistics
Matches: 68, Mismatches: 8, Indels: 19
0.72 0.08 0.20
Matches are distributed among these distances:
12 13 0.19
13 24 0.35
14 11 0.16
15 7 0.10
16 10 0.15
17 3 0.04
ACGTcount: A:0.34, C:0.08, G:0.02, T:0.56
Consensus pattern (13 bp):
TTATATTTAATAC
Found at i:54890 original size:8 final size:7
Alignment explanation
Indices: 54831--54984 Score: 69
Period size: 7 Copynumber: 21.9 Consensus size: 7
54821 GGGGTTTATT
54831 TACTTTA
1 TACTTTA
54838 TA-TTTAA
1 TACTTT-A
54845 TAC-TTA
1 TACTTTA
54851 TA-TTTA
1 TACTTTA
54857 TCTACTTTAA
1 --TACTTT-A
54867 TACTTTA
1 TACTTTA
54874 TA--TTA
1 TACTTTA
54879 TACTTTA
1 TACTTTA
*
54886 GTACTTATG
1 -TACTT-TA
*
54895 TAATTATA
1 TACTT-TA
54903 TA-TTTA
1 TACTTTA
54909 TA-TTTAA
1 TACTTT-A
54916 TAC-TTA
1 TACTTTA
54922 TA-TTTA
1 TACTTTA
54928 TACTTTAA
1 TACTTT-A
54936 TAC-TTA
1 TACTTTA
***
54942 TATCCAAA
1 TA-CTTTA
*
54950 CACTTTA
1 TACTTTA
54957 TTACTTTA
1 -TACTTTA
54965 TA-TTATA
1 TACTT-TA
54972 TACTTTA
1 TACTTTA
54979 TACTTT
1 TACTTT
54985 TATATACTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 42
0.69 0.06 0.25
Matches are distributed among these distances:
5 5 0.04
6 29 0.25
7 42 0.36
8 35 0.30
9 4 0.03
10 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.01, T:0.54
Consensus pattern (7 bp):
TACTTTA
Found at i:54955 original size:71 final size:69
Alignment explanation
Indices: 54826--54980 Score: 190
Period size: 71 Copynumber: 2.2 Consensus size: 69
54816 TTGAAGGGGT
* * *
54826 TTATTTACTTTATATTTAATACTTATATTTATCTACTTTAATACTTTATATTATACTTTAGTACT
1 TTATATACTTTATATTTAATACTTATATTTA-CTACTTTAATACTTTATATAACACTTTAGTACT
*
54891 TATGTAA
65 T-TAT-A
*
54898 TTATATA-TTTATATTTAATACTTATATTTA-TACTTTAATAC-TTATATCCAAACACTTTATTA
1 TTATATACTTTATATTTAATACTTATATTTACTACTTTAATACTTTATAT---AACACTTTAGTA
54960 CTTTATA
63 CTTTATA
54967 TTATATACTTTATA
1 TTATATACTTTATA
54981 CTTTTATATA
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
68 6 0.08
69 19 0.26
70 8 0.11
71 35 0.47
72 6 0.08
ACGTcount: A:0.34, C:0.10, G:0.01, T:0.54
Consensus pattern (69 bp):
TTATATACTTTATATTTAATACTTATATTTACTACTTTAATACTTTATATAACACTTTAGTACTT
TATA
Found at i:54989 original size:17 final size:17
Alignment explanation
Indices: 54967--55008 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
54957 TTACTTTATA
54967 TTATATACTTTATACTT
1 TTATATACTTTATACTT
* *
54984 TTATATACTTTGTAGTT
1 TTATATACTTTATACTT
55001 TATATATA
1 T-TATATA
55009 TAAAGTACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (17 bp):
TTATATACTTTATACTT
Found at i:55429 original size:20 final size:20
Alignment explanation
Indices: 55404--55444 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
55394 TGTGTGTATG
55404 TATGATGAATGT-TATGATAA
1 TATGATGAATGTATAT-ATAA
*
55424 TATGATGCATGTATATATAA
1 TATGATGAATGTATATATAA
55444 T
1 T
55445 GTACATTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.39, C:0.02, G:0.17, T:0.41
Consensus pattern (20 bp):
TATGATGAATGTATATATAA
Found at i:55479 original size:8 final size:7
Alignment explanation
Indices: 55470--55542 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 7
55460 GCATAGATTA
55470 ATATATT
1 ATATATT
*
55477 AATACATT
1 -ATATATT
*
55485 ATATAGT
1 ATATATT
55492 ATATAGTT
1 ATATA-TT
55500 ATATA-T
1 ATATATT
55506 ATATA-T
1 ATATATT
55512 ATATA-T
1 ATATATT
*
55518 ATATATA
1 ATATATT
55525 ATATA-T
1 ATATATT
*
55531 ATATATA
1 ATATATT
55538 ATATA
1 ATATA
55543 AATAATATAC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
6 23 0.42
7 20 0.36
8 12 0.22
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (7 bp):
ATATATT
Found at i:55489 original size:2 final size:2
Alignment explanation
Indices: 55484--55569 Score: 92
Period size: 2 Copynumber: 44.0 Consensus size: 2
55474 ATTAATACAT
55484 TA TA TA GTA TA TA GT- TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
55526 TA TA TA TA TA TA -A TA TA AA TA -A TA TA CA TA TA -A GTA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
55566 TA TA
1 TA TA
55570 CACACACTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
1 5 0.07
2 63 0.88
3 4 0.06
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.44
Consensus pattern (2 bp):
TA
Found at i:55718 original size:40 final size:41
Alignment explanation
Indices: 55637--55719 Score: 105
Period size: 40 Copynumber: 2.0 Consensus size: 41
55627 GTGTAAACTT
* * *
55637 TAAAGTGCATATAATATATATATAAACTATACATTAAAGTA
1 TAAAGTGCATATAATACATATATAAACTATAAAGTAAAGTA
* * *
55678 TAAAGTGTATAT-ATACATATTTAAACTATAAAGTATAGTA
1 TAAAGTGCATATAATACATATATAAACTATAAAGTAAAGTA
55718 TA
1 TA
55720 TTATAAGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
40 25 0.69
41 11 0.31
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.36
Consensus pattern (41 bp):
TAAAGTGCATATAATACATATATAAACTATAAAGTAAAGTA
Found at i:58637 original size:17 final size:19
Alignment explanation
Indices: 58617--58659 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
58607 AAAAAACTAC
58617 AAAA-TAAAAATC-GATAT
1 AAAACTAAAAATCAGATAT
58634 AAAACT--AAATCAGATAT
1 AAAACTAAAAATCAGATAT
58651 AAAACTAAA
1 AAAACTAAA
58660 TCATATTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 5 0.23
17 15 0.68
18 1 0.05
19 1 0.05
ACGTcount: A:0.65, C:0.09, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAACTAAAAATCAGATAT
Found at i:58660 original size:17 final size:17
Alignment explanation
Indices: 58624--58662 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
58614 TACAAAATAA
58624 AAATC-GATATAAAACT
1 AAATCAGATATAAAACT
58640 AAATCAGATATAAAACT
1 AAATCAGATATAAAACT
58657 AAATCA
1 AAATCA
58663 TATTTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.59, C:0.13, G:0.05, T:0.23
Consensus pattern (17 bp):
AAATCAGATATAAAACT
Found at i:60515 original size:21 final size:21
Alignment explanation
Indices: 60489--60535 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
60479 AATACATTAT
60489 GTAACTTATCCATCTCTGGAG
1 GTAACTTATCCATCTCTGGAG
60510 GTAACTTATCCATCTCTGGAG
1 GTAACTTATCCATCTCTGGAG
60531 GTAAC
1 GTAAC
60536 ACCAACTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (21 bp):
GTAACTTATCCATCTCTGGAG
Done.