Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000619.1 Hibiscus syriacus cultivar Beakdansim tig00001197_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: 59588
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6389 original size:32 final size:33
Alignment explanation
Indices: 6353--6429 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
6343 TAATTAAAAA
* *
6353 CTAAAATATAATG-TTTAATTCTATCTTAATTC
1 CTAAAAAATAATGTTTTAACTCTATCTTAATTC
* *
6385 CT-AAAGATAATGTTTTGACTCTATCTTAATTC
1 CTAAAAAATAATGTTTTAACTCTATCTTAATTC
6417 CTAATAAAATAAT
1 CTAA-AAAATAAT
6430 AAATCTAATC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 9 0.24
32 21 0.55
33 1 0.03
34 7 0.18
ACGTcount: A:0.39, C:0.13, G:0.05, T:0.43
Consensus pattern (33 bp):
CTAAAAAATAATGTTTTAACTCTATCTTAATTC
Found at i:6395 original size:31 final size:32
Alignment explanation
Indices: 6360--6420 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
6350 AAACTAAAAT
*
6360 ATAATG-TTTAATTCTATCTTAATTCCTAAAG
1 ATAATGTTTTAACTCTATCTTAATTCCTAAAG
*
6391 ATAATGTTTTGACTCTATCTTAATTCCTAA
1 ATAATGTTTTAACTCTATCTTAATTCCTAA
6421 TAAAATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.46
Consensus pattern (32 bp):
ATAATGTTTTAACTCTATCTTAATTCCTAAAG
Found at i:13148 original size:130 final size:130
Alignment explanation
Indices: 12994--13249 Score: 503
Period size: 130 Copynumber: 2.0 Consensus size: 130
12984 ATCTATTAAA
12994 ATTAAATATCAAATTAGTAGGGGCGAACCCTTAAAAATTAGTATAAATTAGTATAGCAATCAAAA
1 ATTAAATATCAAATTAGTAGGGGCGAACCCTTAAAAATTAGTATAAATTAGTATAGCAATCAAAA
*
13059 GAAGCAGCTTAATTTAAAATTTGAAAATAGTGAAAATGATTAAAAATTATAATATTTTAGAAATG
66 GAAGCAGCTTAATTTAAAATTTGAAAATAGTGAAAATGATTAAAAAATATAATATTTTAGAAATG
13124 ATTAAATATCAAATTAGTAGGGGCGAACCCTTAAAAATTAGTATAAATTAGTATAGCAATCAAAA
1 ATTAAATATCAAATTAGTAGGGGCGAACCCTTAAAAATTAGTATAAATTAGTATAGCAATCAAAA
13189 GAAGCAGCTTAATTTAAAATTTGAAAATAGTGAAAATGATTAAAAAATATAATATTTTAGA
66 GAAGCAGCTTAATTTAAAATTTGAAAATAGTGAAAATGATTAAAAAATATAATATTTTAGA
13250 TTAGACGTAA
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 125 1.00
ACGTcount: A:0.49, C:0.07, G:0.14, T:0.30
Consensus pattern (130 bp):
ATTAAATATCAAATTAGTAGGGGCGAACCCTTAAAAATTAGTATAAATTAGTATAGCAATCAAAA
GAAGCAGCTTAATTTAAAATTTGAAAATAGTGAAAATGATTAAAAAATATAATATTTTAGAAATG
Found at i:17111 original size:33 final size:31
Alignment explanation
Indices: 17074--17153 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
17064 CACCTAATTT
17074 AAAAAATAAAGTAACAATAATAAAAAATAAAAA
1 AAAAAATAAAGTAACAA-AA-AAAAAATAAAAA
*
17107 AAAAATAGTAAA--AACAAAAATAAAATAAAAA
1 AAAAA-A-TAAAGTAACAAAAAAAAAATAAAAA
*
17138 ATAAAA-AAAGT-ACAAA
1 AAAAAATAAAGTAACAAA
17154 GACCTAATTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
28 3 0.07
29 5 0.12
30 1 0.02
31 15 0.37
32 2 0.05
33 10 0.24
34 1 0.02
35 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (31 bp):
AAAAAATAAAGTAACAAAAAAAAAATAAAAA
Found at i:17113 original size:21 final size:21
Alignment explanation
Indices: 17073--17146 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
17063 ACACCTAATT
** *
17073 TAAAAAATAAAGTAACAATAA
1 TAAAAAATAAAAAAAAAATAA
*
17094 TAAAAAATAAAAAAAAAATAG
1 TAAAAAATAAAAAAAAAATAA
* *
17115 T--AAAA-ACAAAAATAA-AA
1 TAAAAAATAAAAAAAAAATAA
17132 TAAAAAATAAAAAAA
1 TAAAAAATAAAAAAA
17147 GTACAAAGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
17 2 0.05
18 8 0.19
19 8 0.19
20 6 0.14
21 18 0.43
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.15
Consensus pattern (21 bp):
TAAAAAATAAAAAAAAAATAA
Found at i:17119 original size:12 final size:11
Alignment explanation
Indices: 17095--17146 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 11
17085 TAACAATAAT
17095 AAAAAATAAAAA
1 AAAAAAT-AAAA
17107 AAAAATAGTAAAA
1 AAAAA-A-TAAAA
17120 ACAAAAATAAAA
1 A-AAAAATAAAA
17132 TAAAAAATAAAA
1 -AAAAAATAAAA
17144 AAA
1 AAA
17147 GTACAAAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
11 3 0.08
12 20 0.56
13 8 0.22
14 5 0.14
ACGTcount: A:0.85, C:0.02, G:0.02, T:0.12
Consensus pattern (11 bp):
AAAAAATAAAA
Found at i:17145 original size:26 final size:26
Alignment explanation
Indices: 17096--17146 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
17086 AACAATAATA
*
17096 AAAAATAAAAAAAAAATAGTAAAAAC
1 AAAAATAAAAAAAAAATAGAAAAAAC
17122 AAAAATAAAATAAAAAATA-AAAAAA
1 AAAAATAAAA-AAAAAATAGAAAAAA
17147 GTACAAAGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 15 0.65
27 8 0.35
ACGTcount: A:0.84, C:0.02, G:0.02, T:0.12
Consensus pattern (26 bp):
AAAAATAAAAAAAAAATAGAAAAAAC
Found at i:18758 original size:5 final size:5
Alignment explanation
Indices: 18748--18788 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
18738 TATTTCTCCC
*
18748 TTATT TTATT TTATT TTATT AT-TT TTA-T TTATT ATTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT -TTATT TT
18789 TATGGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 7 0.23
5 19 0.61
6 5 0.16
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:19494 original size:91 final size:91
Alignment explanation
Indices: 19334--19605 Score: 418
Period size: 91 Copynumber: 3.0 Consensus size: 91
19324 AGATGGAAAC
* * * * *
19334 GAGCTAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTGCCTCATAGGATGAGTTTTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTC
19399 ATTATGAACTCTCCACTAGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
* * *
19425 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGGGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTC
* *
19490 ATTATGAACTCCCCACTGGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
* * *
19516 GATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTATTTTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTC
*
19581 ATTATGAACTCTTCACTAGAAATGT
66 ATTATGAACTCTCCACTAGAAATGT
19606 CAATCCCTCA
Statistics
Matches: 164, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 164 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.37
Consensus pattern (91 bp):
GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTC
ATTATGAACTCTCCACTAGAAATGTT
Found at i:19828 original size:91 final size:92
Alignment explanation
Indices: 19657--19832 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 92
19647 ATCGAGTGAT
19657 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
19722 GAACTCCCCACTGGAAATGTTGATCCA
66 GAACTCCCCACTGGAAATGTTGATCCA
* * * * * *
19749 AGGTTGAACAAGTTCTTCTTATTATGAACTTGTTCTCCCT-TGTCGGATGAGTTCTTCTTATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
**
19813 GAACTCTTCACTGGAAATGT
66 GAACTCCCCACTGGAAATGT
19833 CAATCCCTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
91 40 0.53
92 36 0.47
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (92 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
GAACTCCCCACTGGAAATGTTGATCCA
Found at i:19832 original size:227 final size:227
Alignment explanation
Indices: 19431--19973 Score: 840
Period size: 227 Copynumber: 2.4 Consensus size: 227
19421 TGTTGAGCCA
* * * *
19431 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGGGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
19495 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
66 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
*
19560 CTCGTCGGATGAGTTATTTTCATTATGAACTCTTCACTAGAAATGTCAATCCCTCAAGCGAGGCG
131 CTCGTCGGATGAGTTATTTTCATTATGAACTCTTCACTAGAAATGTCAATCCCTCAAGCGAGGCA
***
19625 TCACTGATTCAAAATGTTGTGAATCGAGTGAT
196 TCACTGATTCAAAATGCCATGAATCGAGTGAT
*
19657 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* *
19722 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTTATTATGAACTTGTTCTCC
66 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * *
19787 CTTGTCGGATGAGTTCTTCTT-ATTATGAACTCTTCACTGGAAATGTCAATCCCTCAAGCGAGGC
131 CTCGTCGGATGAGTTATT-TTCATTATGAACTCTTCACTAGAAATGTCAATCCCTCAAGCGAGGC
** *
19851 ATCACTGATTCTTAATGCCATGAATTGAGTGAT
195 ATCACTGATTCAAAATGCCATGAATCGAGTGAT
* * *
19884 AGGTCGAACAAGCTCTTCTAATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTATTCTTATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * *
19949 AAACTCTCCA-TCAGAAATGTTGATC
66 GAACTCCCCACT-GGAAATGTTGATC
19974 AATTTATCTT
Statistics
Matches: 290, Mismatches: 24, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
226 40 0.14
227 248 0.86
228 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.17, T:0.35
Consensus pattern (227 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
CTCGTCGGATGAGTTATTTTCATTATGAACTCTTCACTAGAAATGTCAATCCCTCAAGCGAGGCA
TCACTGATTCAAAATGCCATGAATCGAGTGAT
Found at i:21560 original size:5 final size:5
Alignment explanation
Indices: 21550--21590 Score: 50
Period size: 5 Copynumber: 8.4 Consensus size: 5
21540 TATTTCTCCC
*
21550 TTATT TTATT TTATT TTATT AT-TT TTA-T TTATT ATTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TTATT -TTATT TT
21591 TATGGGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
4 7 0.23
5 19 0.61
6 5 0.16
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTATT
Found at i:22299 original size:91 final size:91
Alignment explanation
Indices: 22144--22410 Score: 408
Period size: 91 Copynumber: 2.9 Consensus size: 91
22134 GAAACAAGCT
* * * *
22144 AAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTGCCTCATAGGATGAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTCATTAT
22209 GAACTCTCCACTAGAAATGTTGAGCC
66 GAACTCTCCACTAGAAATGTTGAGCC
* * *
22235 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGGGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTCATTAT
* * * *
22300 GAACTCCCCACTGGAAATGATGATCC
66 GAACTCTCCACTAGAAATGTTGAGCC
* *
22326 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATGAGTTATTTTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTCATTAT
*
22391 GAACTCTTCACTAGAAATGT
66 GAACTCTCCACTAGAAATGT
22411 CAACCCCTCA
Statistics
Matches: 158, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 158 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (91 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTAGGATGAGTTATTCTCATTAT
GAACTCTCCACTAGAAATGTTGAGCC
Found at i:22630 original size:91 final size:92
Alignment explanation
Indices: 22462--22637 Score: 273
Period size: 91 Copynumber: 1.9 Consensus size: 92
22452 ATCGAGTGAT
*
22462 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAAATGAGTTCTTCTCATTAT
22527 GAACTCCCCACTGGAAATGTTGATCCA
66 GAACTCCCCACTGGAAATGTTGATCCA
* * * * *
22554 AGGTTGAACAAGTTCTTCTTATTATGAACTTGTTCTCCCT-TGTCAAATGAGTTCTTCTTATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAAATGAGTTCTTCTCATTAT
**
22618 GAACTCTTCACTGGAAATGT
66 GAACTCCCCACTGGAAATGT
22638 CAATACCTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
91 40 0.53
92 36 0.47
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (92 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAAATGAGTTCTTCTCATTAT
GAACTCCCCACTGGAAATGTTGATCCA
Found at i:22637 original size:227 final size:227
Alignment explanation
Indices: 22236--22778 Score: 804
Period size: 227 Copynumber: 2.4 Consensus size: 227
22226 TGTTGAGCCA
* * * *
22236 AGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTC-GTTGGATGGGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
*
22300 GAACTCCCCACTGGAAATGATGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
66 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
** *
22365 CTCGTCGGATGAGTTATTTTCATTATGAACTCTTCACTAGAAATGTCAACCCCTCAAGCGAGGCA
131 CTCGTCAAATGAGTTATTTTCATTATGAACTCTTCACTAGAAATGTCAACACCTCAAGCGAGGCA
**
22430 TCACTGATTCAAAATGCTGTGAATCGAGTGAT
196 TCACTGATTCAAAATGCCATGAATCGAGTGAT
*
22462 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCAGATGAGTTCTTCTCATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* *
22527 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTTATTATGAACTTGTTCTCC
66 GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
22592 CTTGTCAAATGAGTTCTTCTT-ATTATGAACTCTTCACTGGAAATGTCAATACCTCAAGCGAGGC
131 CTCGTCAAATGAGTTATT-TTCATTATGAACTCTTCACTAGAAATGTCAACACCTCAAGCGAGGC
** *
22656 ATCACTGATTCTTAATGCCATGAATTGAGTGAT
195 ATCACTGATTCAAAATGCCATGAATCGAGTGAT
* * * *
22689 AGGTCGAGCAAGCTCTTCTAATTATGAACTTTTTCTCCCTCTGTCGGATGAGTTCTTCTTATTAT
1 AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
* * *
22754 AAACTCTCCA-TCAGAAATGTTGATC
66 GAACTCCCCACT-GGAAATGTTGATC
22779 AATTTATCTT
Statistics
Matches: 286, Mismatches: 28, Indels: 5
0.90 0.09 0.02
Matches are distributed among these distances:
226 40 0.14
227 244 0.85
228 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.35
Consensus pattern (227 bp):
AGGTCGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTGTCGGATGAGTTCTTCTCATTAT
GAACTCCCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
CTCGTCAAATGAGTTATTTTCATTATGAACTCTTCACTAGAAATGTCAACACCTCAAGCGAGGCA
TCACTGATTCAAAATGCCATGAATCGAGTGAT
Found at i:24967 original size:12 final size:12
Alignment explanation
Indices: 24935--25010 Score: 58
Period size: 12 Copynumber: 6.8 Consensus size: 12
24925 TTTGATCTAT
24935 TTTATTTC-TTC
1 TTTATTTCTTTC
24946 -TTA-TTC-TTC
1 TTTATTTCTTTC
*
24955 TTTATTTTTTTC
1 TTTATTTCTTTC
24967 TTTTATTT-TCTT-
1 -TTTATTTCT-TTC
*
24979 TTTCTTTCTTTC
1 TTTATTTCTTTC
*
24991 TTTCTTTCTTTC
1 TTTATTTCTTTC
25003 TTT-TTTCT
1 TTTATTTCT
25011 CCATCTTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
9 6 0.11
10 6 0.11
11 15 0.27
12 20 0.36
13 9 0.16
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTATTTCTTTC
Found at i:24988 original size:4 final size:4
Alignment explanation
Indices: 24979--25010 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
24969 TTATTTTCTT
24979 TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
25011 CCATCTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.11
4 24 0.89
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:24988 original size:20 final size:22
Alignment explanation
Indices: 24934--25010 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
24924 ATTTGATCTA
24934 TTTTATTTCTTCTTATTCTTCTT
1 TTTTATTTCTT-TTATTCTTCTT
*
24957 TATTTTTTTCTTTTATT-TTC-T
1 T-TTTATTTCTTTTATTCTTCTT
*
24978 TTTTCTTTCTTTCT-TTCTTTCTT
1 TTTTATTTCTTT-TATTC-TTCTT
25001 TCTTT-TTTCT
1 T-TTTATTTCT
25011 CCATCTTTTG
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
20 12 0.26
21 3 0.07
22 6 0.13
23 13 0.28
24 12 0.26
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTATTTCTTTTATTCTTCTT
Found at i:25024 original size:23 final size:23
Alignment explanation
Indices: 24998--25054 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
24988 TTCTTTCTTT
24998 CTTTCTTTTTTCTCCATCTTTTG
1 CTTTCTTTTTTCTCCATCTTTTG
*
25021 CTTTCTTTTTTCTCTATCTTTTG
1 CTTTCTTTTTTCTCCATCTTTTG
25044 CTTTCTTTTTT
1 CTTTCTTTTTT
25055 TTTCTCTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.04, C:0.23, G:0.04, T:0.70
Consensus pattern (23 bp):
CTTTCTTTTTTCTCCATCTTTTG
Found at i:25024 original size:27 final size:26
Alignment explanation
Indices: 24973--25080 Score: 104
Period size: 23 Copynumber: 4.3 Consensus size: 26
24963 TTTCTTTTAT
* * *
24973 TTTCTTTTTCTTTCTTTC-TTTCTTTC
1 TTTCTTTTT-TCTCTATCTTTTGTTTC
*
24999 TTTCTTTTTTCTCCATCTTTTG---C
1 TTTCTTTTTTCTCTATCTTTTGTTTC
25022 TTTCTTTTTTCTCTATCTTTTGCTTTC
1 TTTCTTTTTTCTCTATCTTTTG-TTTC
25049 TTT-TTTTTTCTCTTATCTTTT-TTT-
1 TTTCTTTTTTCTC-TATCTTTTGTTTC
25073 TTTCTTTT
1 TTTCTTTT
25081 CCCCTCTTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 15
0.78 0.06 0.17
Matches are distributed among these distances:
23 22 0.31
24 3 0.04
25 12 0.17
26 21 0.30
27 12 0.17
ACGTcount: A:0.03, C:0.20, G:0.02, T:0.75
Consensus pattern (26 bp):
TTTCTTTTTTCTCTATCTTTTGTTTC
Found at i:25031 original size:12 final size:11
Alignment explanation
Indices: 24960--25079 Score: 88
Period size: 10 Copynumber: 10.9 Consensus size: 11
24950 TCTTCTTTAT
24960 TTTTTTCTTT-
1 TTTTTTCTTTC
*
24970 TATTTTCTTT-
1 TTTTTTCTTTC
*
24980 TTCTTTCTTTC
1 TTTTTTCTTTC
24991 TTTCTTTCTTTC
1 TTT-TTTCTTTC
*
25003 TTTTTTC-TCC
1 TTTTTTCTTTC
*
25013 ATCTTTTGCTTTC
1 -T-TTTTTCTTTC
25026 TTTTTTCTCTATC
1 TTTTTTCT-T-TC
*
25039 -TTTTGCTTTC
1 TTTTTTCTTTC
25049 TTTTTT-TTTC
1 TTTTTTCTTTC
* * *
25059 TCTTATCTTTT
1 TTTTTTCTTTC
25070 TTTTTTCTTT
1 TTTTTTCTTT
25080 TCCCCTCTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
10 29 0.34
11 29 0.34
12 24 0.28
13 4 0.05
ACGTcount: A:0.03, C:0.19, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:25069 original size:17 final size:16
Alignment explanation
Indices: 25047--25078 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
25037 TCTTTTGCTT
25047 TCTTTTTTTTTCTCTTA
1 TCTTTTTTTTT-TCTTA
25064 TCTTTTTTTTTTCTT
1 TCTTTTTTTTTTCTT
25079 TTCCCCTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (16 bp):
TCTTTTTTTTTTCTTA
Found at i:25080 original size:28 final size:26
Alignment explanation
Indices: 24929--25080 Score: 89
Period size: 28 Copynumber: 5.7 Consensus size: 26
24919 GAAGTATTTG
* * *
24929 ATCTATTTTATTTCTTCTTATTCTTCTTT
1 ATCT-TTTTTTTTCTT-TT-TTTTTCTCT
* *
24958 ATTTTTTTCTTTTATTTTCTTTTTCT-T
1 ATCTTTTT-TTTTCTTTT-TTTTTCTCT
*
24985 -TCTTTCTTTCTTTCTTTCTTTTTTCTCC
1 ATCTTT-TTT-TTTCTTT-TTTTTTCTCT
**
25013 ATCTTTTGCTTTC---TTTTTTCTCT
1 ATCTTTTTTTTTCTTTTTTTTTCTCT
**
25036 ATCTTTTGCTTTCTTTTTTTTTCTCTT
1 ATCTTTTTTTTTCTTTTTTTTTCTC-T
25063 ATCTTTTTTTTTTCTTTT
1 ATC-TTTTTTTTTCTTTT
25081 CCCCTCTTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
23 22 0.22
26 14 0.14
27 24 0.24
28 26 0.26
29 13 0.13
ACGTcount: A:0.06, C:0.18, G:0.01, T:0.74
Consensus pattern (26 bp):
ATCTTTTTTTTTCTTTTTTTTTCTCT
Found at i:25804 original size:21 final size:21
Alignment explanation
Indices: 25738--25794 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
25728 GTAAAAGTAC
25738 AATGTACAATGTATACCATGT
1 AATGTACAATGTATACCATGT
25759 AATGTACAATGTATACCATGT
1 AATGTACAATGTATACCATGT
25780 AATGTACAATGTATA
1 AATGTACAATGTATA
25795 TATGCTAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.33
Consensus pattern (21 bp):
AATGTACAATGTATACCATGT
Found at i:28305 original size:25 final size:26
Alignment explanation
Indices: 28277--28326 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
28267 AAAAAAATAA
*
28277 AGTAATAACAATAAT-AA-TAAAAAAC
1 AGTAAAAACAA-AATAAAGTAAAAAAC
28302 AGTAAAAACAAAATAAAGTAAAAAA
1 AGTAAAAACAAAATAAAGTAAAAAA
28327 TAAAATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 12 0.55
26 7 0.32
ACGTcount: A:0.72, C:0.06, G:0.06, T:0.16
Consensus pattern (26 bp):
AGTAAAAACAAAATAAAGTAAAAAAC
Found at i:28331 original size:17 final size:16
Alignment explanation
Indices: 28292--28335 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
28282 TAACAATAAT
28292 AATAAAA-AACAGTAAA
1 AATAAAATAA-AGTAAA
*
28308 AACAAAATAAAGTAAAA
1 AATAAAATAAAGT-AAA
28325 AATAAAATAAA
1 AATAAAATAAA
28336 CACAAGTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.14
Consensus pattern (16 bp):
AATAAAATAAAGTAAA
Found at i:29596 original size:19 final size:19
Alignment explanation
Indices: 29574--29610 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29564 TGTTTTCCCC
29574 TTTTT-TTATTATTTTTAT
1 TTTTTATTATTATTTTTAT
29592 TTTTTATTATTATTTTTAT
1 TTTTTATTATTATTTTTAT
29611 GGGTAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTTATTATTATTTTTAT
Found at i:29914 original size:21 final size:21
Alignment explanation
Indices: 29778--29915 Score: 70
Period size: 20 Copynumber: 6.4 Consensus size: 21
29768 TTTTTAAAAA
* *
29778 TATTTTTAATTTCTAATAATT
1 TATTTTTTATTTTTAATAATT
* *
29799 TATTATTTATATTT-ATAACTT
1 TATTTTTTATTTTTAATAA-TT
* *
29820 GAGATATATTTTTATTTTTATTAATG
1 ----TAT-TTTTTATTTTTAATAATT
* *
29846 T-TTTTGTATGTTTAAT-ATAT
1 TATTTTTTATTTTTAATAAT-T
*
29866 T-TTTATTATTTTTAATAATT
1 TATTTTTTATTTTTAATAATT
* *
29886 TAATTTTTATTTTTGAT-ATT
1 TATTTTTTATTTTTAATAATT
29906 TACTTTTTTA
1 TA-TTTTTTA
29916 AATATTTGGA
Statistics
Matches: 87, Mismatches: 19, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
19 2 0.02
20 35 0.40
21 33 0.38
22 1 0.01
25 3 0.03
26 10 0.11
27 3 0.03
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.64
Consensus pattern (21 bp):
TATTTTTTATTTTTAATAATT
Found at i:29954 original size:24 final size:25
Alignment explanation
Indices: 29927--29975 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
29917 ATATTTGGAT
**
29927 ATTTTA-TATTTTAAATTTAAATAA
1 ATTTTATTATTTTAAAAATAAATAA
29951 ATTTTATTATTTTAAAAATAAATAA
1 ATTTTATTATTTTAAAAATAAATAA
29976 GCCCTTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
ATTTTATTATTTTAAAAATAAATAA
Found at i:32957 original size:34 final size:34
Alignment explanation
Indices: 32919--32986 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
32909 AGTATGGCTG
32919 CAACAAAGATGATAGAAGATAGTATTAGCAAAGA
1 CAACAAAGATGATAGAAGATAGTATTAGCAAAGA
32953 CAACAAAGATGATAGAAGATAGTATTAGCAAAGA
1 CAACAAAGATGATAGAAGATAGTATTAGCAAAGA
32987 AATACGAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.18
Consensus pattern (34 bp):
CAACAAAGATGATAGAAGATAGTATTAGCAAAGA
Found at i:33116 original size:22 final size:22
Alignment explanation
Indices: 33090--33152 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
33080 GAAGATGGTT
* *
33090 GATGGTGTTGATTTTGTATTAA
1 GATGGTGATGATGTTGTATTAA
33112 GATGGTGATGATGTTGTATTAA
1 GATGGTGATGATGTTGTATTAA
*
33134 GATGGTGATGATGGTGTAT
1 GATGGTGATGATGTTGTAT
33153 CTCAAACCCG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (22 bp):
GATGGTGATGATGTTGTATTAA
Found at i:37789 original size:50 final size:50
Alignment explanation
Indices: 37705--37801 Score: 126
Period size: 50 Copynumber: 1.9 Consensus size: 50
37695 GATGAAGATG
*
37705 CATCTCCCTTGGCCGAATGGTGATATGCTTGTTCATCTTGGCGCCAAAGT
1 CATCTCCCATGGCCGAATGGTGATATGCTTGTTCATCTTGGCGCCAAAGT
* * *
37755 CATCTTCCATGGCCGAATGGT-AT-TGTGTTGGTTCATCTTGGTGCCAA
1 CATCTCCCATGGCCGAATGGTGATATG-CTT-GTTCATCTTGGCGCCAA
37802 TTTCTTCATG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
48 2 0.05
49 4 0.10
50 35 0.85
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.34
Consensus pattern (50 bp):
CATCTCCCATGGCCGAATGGTGATATGCTTGTTCATCTTGGCGCCAAAGT
Found at i:39213 original size:18 final size:20
Alignment explanation
Indices: 39164--39214 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
39154 GTTCACACAA
39164 GAGTATCGATACTTATCCCT
1 GAGTATCGATACTTATCCCT
39184 GTAGTATCGATAC-TA-CCCT
1 G-AGTATCGATACTTATCCCT
*
39203 GAGTATTGATAC
1 GAGTATCGATAC
39215 AATTTAAGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 10 0.34
19 5 0.17
20 3 0.10
21 11 0.38
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (20 bp):
GAGTATCGATACTTATCCCT
Found at i:42760 original size:165 final size:165
Alignment explanation
Indices: 42488--42809 Score: 590
Period size: 165 Copynumber: 2.0 Consensus size: 165
42478 GAGATCTGTT
42488 AGGAAAAATGAAAATATTCCTCTACCAGACCAAAATGAGGATATCTCTATGGAAGATCGCATTCG
1 AGGAAAAATGAAAATATTCCTCTACCAGACCAAAATGAGGATATCTCTATGGAAGATCGCATTCG
*
42553 GGTAGTTCCATCAGATATTGAAATCCTAAAAGCTGAGTTTGAAGCAGAAAGAGAGGGTTGGTCGA
66 GGTAGTTCCATCAGAGATTGAAATCCTAAAAGCTGAGTTTGAAGCAGAAAGAGAGGGTTGGTCGA
* *
42618 AAGAGCTATAAGAAATACGACGAAATAAATCTAAC
131 AAGAGCTAGAACAAATACGACGAAATAAATCTAAC
42653 AGGAAAAATGAAAATATTCCTCTACCAGACCAAAATGAGGATATCTCTATGGAAGATCGCATTCG
1 AGGAAAAATGAAAATATTCCTCTACCAGACCAAAATGAGGATATCTCTATGGAAGATCGCATTCG
*
42718 GGTAGTTCCATCAGAGATTGAAATCCTAAAAGCTGAGTTTGAAGCAGAAAGAGAGGGTTGTTCGA
66 GGTAGTTCCATCAGAGATTGAAATCCTAAAAGCTGAGTTTGAAGCAGAAAGAGAGGGTTGGTCGA
* *
42783 AAGAGCTAGAACAAATGCGATGAAATA
131 AAGAGCTAGAACAAATACGACGAAATA
42810 TAGCTATGTT
Statistics
Matches: 151, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
165 151 1.00
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (165 bp):
AGGAAAAATGAAAATATTCCTCTACCAGACCAAAATGAGGATATCTCTATGGAAGATCGCATTCG
GGTAGTTCCATCAGAGATTGAAATCCTAAAAGCTGAGTTTGAAGCAGAAAGAGAGGGTTGGTCGA
AAGAGCTAGAACAAATACGACGAAATAAATCTAAC
Found at i:44026 original size:15 final size:15
Alignment explanation
Indices: 44002--44033 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43992 GATCAATACC
*
44002 TTTTGTATACATTCA
1 TTTTGCATACATTCA
44017 TTTTGCATACATTCA
1 TTTTGCATACATTCA
44032 TT
1 TT
44034 ATTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:51346 original size:16 final size:16
Alignment explanation
Indices: 51297--51339 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
51287 ATTATGCTTG
51297 AAGAAAAAAATGATGA
1 AAGAAAAAAATGATGA
51313 AAGAAAAAAATGATGA
1 AAGAAAAAAATGATGA
51329 AAGAAAAAAAT
1 AAGAAAAAAAT
51340 ATAGAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (16 bp):
AAGAAAAAAATGATGA
Found at i:51718 original size:18 final size:18
Alignment explanation
Indices: 51691--51728 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
51681 CAAGTTTATC
51691 TTTTTAAAATTCAATTTA
1 TTTTTAAAATTCAATTTA
*
51709 TTTTTGAAATTCAATTTA
1 TTTTTAAAATTCAATTTA
51727 TT
1 TT
51729 CTTTCATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (18 bp):
TTTTTAAAATTCAATTTA
Found at i:52028 original size:20 final size:20
Alignment explanation
Indices: 51984--52029 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
51974 AATGTTTTAC
*
51984 GAACTAGTAAGTATGGTGCT
1 GAACCAGTAAGTATGGTGCT
* * *
52004 AAACCAGTAATTATGGTGTT
1 GAACCAGTAAGTATGGTGCT
52024 GAACCA
1 GAACCA
52030 ATGTTGCGAT
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:0.13, G:0.24, T:0.28
Consensus pattern (20 bp):
GAACCAGTAAGTATGGTGCT
Found at i:52426 original size:22 final size:22
Alignment explanation
Indices: 52371--52427 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
52361 ACATCTACAT
*
52371 TCTTTAAAGATAATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
52393 TCTTTAAAGATGATAGATTCTC
1 TCTTTAAAGATGATAGATTCTC
52415 T-TTTCAAAGATGA
1 TCTTT-AAAGATGA
52428 AAGCTTTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
21 3 0.09
22 30 0.91
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
TCTTTAAAGATGATAGATTCTC
Found at i:52981 original size:112 final size:112
Alignment explanation
Indices: 52784--53236 Score: 541
Period size: 112 Copynumber: 4.0 Consensus size: 112
52774 TAGAAAAGAT
* * * * *
52784 TCGAATCCATCACTCAATGGATCAACA-TGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
*
52848 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTC
66 AG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTC
* * *
52896 TCGAATTCATCACTTGATGGATCAACATTTCCAGATAAAGTTGATAATGAGAAGAACTTATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
52961 AGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAGCCTTTTTC
66 AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTC
* * * * *
53008 TTGAATTCATCACTCGATGGATCAACTTTTCCAGAGAAAGTTCATAGTAAGAAGAACTCATCTGA
1 TCGAATTCATCACTCGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
53073 AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTC
66 AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTT--TTC
* * ** * * * *
53123 TC-TATCACAAAAGGAGATAGATAAGAACCAACATTTCCAGATAAAGTTCATAATGAGAAGAACT
1 TCGAAT-TC---ATCA-CTCGAT--GGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACT
* * *
53187 TATCTGAAGAGGAAGAAGAAGTTCAAAATGAGAAGAACTTGTTCGACCTT
59 CATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTT
53237 AGCTTGATTC
Statistics
Matches: 291, Mismatches: 39, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
112 160 0.55
113 37 0.13
114 2 0.01
115 5 0.02
118 2 0.01
119 4 0.01
120 2 0.01
121 79 0.27
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (112 bp):
TCGAATTCATCACTCGATGGATCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTCATCTGA
AGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTC
Found at i:53206 original size:233 final size:224
Alignment explanation
Indices: 52786--53230 Score: 581
Period size: 233 Copynumber: 1.9 Consensus size: 224
52776 GAAAAGATTC
* *
52786 GAATCCATCACTCAATGGATCAACATGCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 GAATCCATCACTCAATGGATCAACATGCCAGGTAAAGTTCATAATAAGAAGAACTCATCTGAAGA
* * * * * *
52851 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTTCTCGAATTCATCACTTGATGG
66 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGAATACAGCAATAGATGA
* * *
52916 ATCAACATTTCCAGATAAAGTTGATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATA
131 ACCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCAAA
*
52981 ATGAGAAGAATTTGTTCAGCCTTTTTCTT
196 ATGAGAAGAACTTGTTCAGCCTTTTTCTT
* * * * *
53010 GAATTCATCACTCGATGGATCAACTTTTCCAGAG-AAAGTTCATAGTAAGAAGAACTCATCTGAA
1 GAATCCATCACTCAATGGATCAAC-ATGCCAG-GTAAAGTTCATAATAAGAAGAACTCATCTGAA
* *
53074 G-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTCTC-TATCACAAAAGG
64 GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC-TTT--TTCTCGAAT-AC---AGC
53137 AGATAGATAAGAACCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
122 A-ATAGAT--GAACCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAG
*
53202 AAGAAGTTCAAAATGAGAAGAACTTGTTC
184 AAGAAATTCAAAATGAGAAGAACTTGTTC
53231 GACCTTAGCT
Statistics
Matches: 189, Mismatches: 20, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
224 60 0.32
225 36 0.19
226 3 0.02
227 6 0.03
230 2 0.01
231 4 0.02
233 78 0.41
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (224 bp):
GAATCCATCACTCAATGGATCAACATGCCAGGTAAAGTTCATAATAAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTTCTCGAATACAGCAATAGATGA
ACCAACATTTCCAGATAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCAAA
ATGAGAAGAACTTGTTCAGCCTTTTTCTT
Found at i:53670 original size:3 final size:3
Alignment explanation
Indices: 53604--53651 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
53594 CCATTTTCTT
*
53604 TTA TTA TTA TTA ATA TTA TTA -TA TTTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA
53649 TTA
1 TTA
53652 ATAAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 37 0.90
4 2 0.05
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:54884 original size:21 final size:20
Alignment explanation
Indices: 54858--54905 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
54848 ATTACTAGTT
54858 TATTATTTTTTTTATATTTAA
1 TATTATTTTTTTTA-ATTTAA
**
54879 TATTA-TAGTTTTAATTTAA
1 TATTATTTTTTTTAATTTAA
54898 T-TTATTTT
1 TATTATTTT
54906 AGTTATTGTT
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
18 3 0.14
19 8 0.36
20 6 0.27
21 5 0.23
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TATTATTTTTTTTAATTTAA
Found at i:54908 original size:21 final size:21
Alignment explanation
Indices: 54859--54909 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
54849 TTACTAGTTT
54859 ATTATTTT--TTTTATATTTA
1 ATTATTTTAGTTTTATATTTA
*
54878 A-TATTATAGTTTTA-ATTTA
1 ATTATTTTAGTTTTATATTTA
54897 ATTTATTTTAGTT
1 A-TTATTTTAGTT
54910 ATTGTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.19
19 7 0.27
20 5 0.19
21 9 0.35
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
ATTATTTTAGTTTTATATTTA
Found at i:58180 original size:15 final size:17
Alignment explanation
Indices: 58162--58203 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
58152 TTGCTTTGTG
*
58162 AATTTTCTTT-CTTT-T
1 AATTTTCTTTACTTTAA
*
58177 AATTTTATTTACTTTAA
1 AATTTTCTTTACTTTAA
58194 AATTTTCTTT
1 AATTTTCTTT
58204 TGAGTGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 9 0.41
16 4 0.18
17 9 0.41
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.67
Consensus pattern (17 bp):
AATTTTCTTTACTTTAA
Done.