Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008159.1 Hibiscus syriacus cultivar Beakdansim tig00110728_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: 104804
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:657 original size:17 final size:17
Alignment explanation
Indices: 625--675 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
615 TCTTGAACCC
*
625 TCCTTTATTTATTTTTTCT
1 TCCTTT-TTCATTTTTT-T
644 T-CTTTTTCATTTTTTT
1 TCCTTTTTCATTTTTTT
660 TCCTTTTT--TTTTTTT
1 TCCTTTTTCATTTTTTT
675 T
1 T
676 TTTTAGTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 8 0.27
16 2 0.07
17 15 0.50
18 4 0.13
19 1 0.03
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (17 bp):
TCCTTTTTCATTTTTTT
Found at i:659 original size:10 final size:9
Alignment explanation
Indices: 636--678 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
626 CCTTTATTTA
636 TTTTTTCTT
1 TTTTTTCTT
*
645 CTTTTTCATT
1 TTTTTTC-TT
655 TTTTTTCCTT
1 TTTTTT-CTT
665 TTTTTT-TT
1 TTTTTTCTT
673 TTTTTT
1 TTTTTT
679 TAGTGTAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
8 8 0.27
9 6 0.20
10 15 0.50
11 1 0.03
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:14023 original size:25 final size:25
Alignment explanation
Indices: 13989--14113 Score: 225
Period size: 25 Copynumber: 5.0 Consensus size: 25
13979 GAGTAGGGGA
*
13989 TTAGGGTTTGAAACCCTAAT-TGGTT
1 TTAGGGTTTGAAACCCTAATCT-GAT
14014 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
14039 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
14064 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
14089 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
14114 GGGTTATTGG
Statistics
Matches: 98, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
25 97 0.99
26 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.21, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:14202 original size:3 final size:3
Alignment explanation
Indices: 14194--14251 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
14184 CAAAAAATTG
* **
14194 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
14238 TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA
14252 CGGAAAAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:21015 original size:195 final size:195
Alignment explanation
Indices: 20769--21174 Score: 609
Period size: 205 Copynumber: 2.0 Consensus size: 195
20759 TAATAATAAA
*
20769 AAAAATAATGTAAATAAATACAATATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTG-TAC
1 AAAACTAATGTAAATAAATACAATATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGATAC
* *
20833 -ATATATATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAAT
66 AATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAAT
** * * *
20897 GTATAAAAAACTAATAATAGTATAGAATATATATAAATATTATAATGTAATATAAAAAGATAATT
131 GTATAAAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATT
*
20962 AAAACTAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGTA
1 AAAACTAATGTAAATAAATACAAT-ATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTG--
*
21027 CATATATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAAT
62 -----ATACA-ATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAAT
*
21092 ATATACGAATGTGTAAAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAA
121 ATATACGAATGTATAAAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAA
21157 AAAGATAATT
186 AAAGATAATT
21167 AAAACTAA
1 AAAACTAA
21175 AATCCCGAGA
Statistics
Matches: 190, Mismatches: 11, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
193 22 0.12
194 13 0.07
195 24 0.13
203 3 0.02
205 128 0.67
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.30
Consensus pattern (195 bp):
AAAACTAATGTAAATAAATACAATATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGATAC
AATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAAT
GTATAAAAAAAAAAAAATAATATAAAATATATATAAATATTATAATGTAATATAAAAAGATAATT
Found at i:21038 original size:8 final size:8
Alignment explanation
Indices: 21025--21062 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
21015 ACAAAATGTG
21025 TACATATA
1 TACATATA
21033 TACATATA
1 TACATATA
*
21041 TATATATA
1 TACATATA
21049 TA-ATATA
1 TACATATA
21056 -ACATATA
1 TACATATA
21063 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:22156 original size:3 final size:3
Alignment explanation
Indices: 22148--22179 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
22138 GTAAAGAGAA
22148 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
22180 CAAATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:22845 original size:105 final size:105
Alignment explanation
Indices: 22647--23315 Score: 1135
Period size: 105 Copynumber: 6.4 Consensus size: 105
22637 ATATTGTTCC
* ** * *
22647 GAGTCCAATATCCTCCGCCGTGAAGTCGAAATTGGCTCTGAAATTGAG--ATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
22710 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
22750 GAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGGAAATGTTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
22815 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
22855 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
22920 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
22960 GAGTCAAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
23025 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
23065 GAGTCAAATATCCTTCGTCGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
23130 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
23170 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
23235 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
23275 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGA
23316 GTAAAACCTG
Statistics
Matches: 541, Mismatches: 23, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
103 43 0.08
105 498 0.92
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.32
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:23513 original size:1 final size:1
Alignment explanation
Indices: 23507--23534 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
23497 TGTTTGATGA
23507 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
23535 GAAGATGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24130 original size:1 final size:1
Alignment explanation
Indices: 24126--24156 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
24116 GTTTTTCTCC
24126 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
24157 CCAACTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34903 original size:17 final size:19
Alignment explanation
Indices: 34881--34922 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
34871 AAAATATAAT
34881 AATAATAG-AAAAAAATA-
1 AATAATAGTAAAAAAATAC
*
34898 AATAAT-GTAAATAAATAC
1 AATAATAGTAAAAAAATAC
34916 AATAATA
1 AATAATA
34923 AAGAAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 14 0.67
18 6 0.29
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (19 bp):
AATAATAGTAAAAAAATAC
Found at i:35165 original size:8 final size:8
Alignment explanation
Indices: 35152--35189 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
35142 ACAAAATGTG
35152 TACATATA
1 TACATATA
35160 TACATATA
1 TACATATA
*
35168 TATATATA
1 TACATATA
35176 TA-ATATA
1 TACATATA
35183 -ACATATA
1 TACATATA
35190 AGTGAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
6 1 0.04
7 10 0.36
8 17 0.61
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (8 bp):
TACATATA
Found at i:35200 original size:205 final size:193
Alignment explanation
Indices: 34896--35300 Score: 598
Period size: 205 Copynumber: 2.0 Consensus size: 193
34886 TAGAAAAAAA
34896 TAAA-TAATGTAAATAAATACAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTAC
1 TAAACTAATGTAAATAAATACAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTAC
* *
34960 ATATATATATATAATATAACATATAAATGAAATAATACTATACTAATAATAAATGTATACGAATG
66 ATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATG
** * *
35025 TAT-AAAAAACTAATAATAGTATAGAATATATATAAATATTATAATGTAATATAAAAAGATAAT
131 TATAAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATAT-AAAAGATAAT
*
35088 TAAAACTAATGTAAATAAATATAATAATAAAGAAGTAAACAAATAGGGTAAAATACAAAATGTGT
1 T-AAACTAATGTAAATAAATACAATAATAAAGAAGTAAA-AAATAGGGTAAAATACAAAATGTG-
*
35153 ACATATATACATATATATATATATAATATAACATATAAGTGAAATAATAATATACTAATAATAAA
63 -------TAC--ATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAA
*
35218 TATATACGAATGTGTAAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATAT
119 TATATACGAATGTATAAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATAT
35283 AAAAGATAAT
184 AAAAGATAAT
35293 TAAACTAA
1 TAAACTAA
35301 AATCCCGAGA
Statistics
Matches: 190, Mismatches: 9, Indels: 16
0.88 0.04 0.07
Matches are distributed among these distances:
192 1 0.01
193 3 0.02
194 32 0.17
195 24 0.13
203 3 0.02
204 7 0.04
205 75 0.39
206 45 0.24
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (193 bp):
TAAACTAATGTAAATAAATACAATAATAAAGAAGTAAAAAATAGGGTAAAATACAAAATGTGTAC
ATATATATATATAATATAACATATAAATGAAATAATAATATACTAATAATAAATATATACGAATG
TATAAAAAAAAAAATAATAATATAAAATATATATAAATATTATAATGTAATATAAAAGATAAT
Found at i:36286 original size:3 final size:3
Alignment explanation
Indices: 36278--36309 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
36268 GTAAAGAGAA
36278 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36310 CAAATAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40274 original size:18 final size:19
Alignment explanation
Indices: 40234--40275 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
40224 TGAAATCTTG
40234 AAAACTCTTAAACCCCACA
1 AAAACTCTTAAACCCCACA
*
40253 AAAACTCTTAAACCCCATA
1 AAAACTCTTAAACCCCACA
40272 AAAA
1 AAAA
40276 TCGTTCTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (19 bp):
AAAACTCTTAAACCCCACA
Found at i:46833 original size:2 final size:2
Alignment explanation
Indices: 46826--46862 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
46816 CTTTTAAAAC
46826 AT AT AT AT AT AT 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 AT AT AT A
46863 CCCCCATCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:47049 original size:24 final size:24
Alignment explanation
Indices: 47022--47073 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
47012 AACGGATATA
*
47022 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
47046 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
47070 TCAA
1 TCAA
47074 GTAACATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:47074 original size:24 final size:24
Alignment explanation
Indices: 47042--47160 Score: 143
Period size: 24 Copynumber: 5.0 Consensus size: 24
47032 AAACATAAAT
*
47042 CAGGTCAAGTATCATATCAGAAAT-
1 CAGGTCAAGTATCAGATCAG-AATC
* *
47066 CAGGTCAAGTAACATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
47090 CAAGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
47114 CATGTC-AGATATAAGATCAGAATC
1 CAGGTCAAG-TATCAGATCAGAATC
*
47138 CATGTCAAGTATCAGATCAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
47161 TCAAATCAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
23 5 0.06
24 78 0.92
25 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:47169 original size:24 final size:24
Alignment explanation
Indices: 47045--47178 Score: 137
Period size: 24 Copynumber: 5.6 Consensus size: 24
47035 CATAAATCAG
* *
47045 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
* *
47069 GTCAAGTAACATATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
*
47093 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
47117 GTC-AGATATAAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAA
*
47141 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
47165 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
47179 AAAATATTCA
Statistics
Matches: 95, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
23 5 0.05
24 88 0.93
25 2 0.02
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:49646 original size:18 final size:18
Alignment explanation
Indices: 49623--49661 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
49613 ATGGGTCAAC
49623 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTTGGGTCG
49641 GGTCAACGGGTTGGGTCG
1 GGTCAACGGGTTGGGTCG
49659 GGT
1 GGT
49662 TGAGACCGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.10, C:0.15, G:0.51, T:0.23
Consensus pattern (18 bp):
GGTCAACGGGTTGGGTCG
Found at i:51749 original size:24 final size:24
Alignment explanation
Indices: 51722--51773 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
51712 AACGGATATA
*
51722 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
51746 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
51770 TCAA
1 TCAA
51774 GTAACAGATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:51774 original size:24 final size:24
Alignment explanation
Indices: 51738--51860 Score: 108
Period size: 24 Copynumber: 5.1 Consensus size: 24
51728 ATCAAAACAT
*
51738 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCAGATCAG
*
51762 AAATCAGGTCAAGTAACAGATCAG
1 AAATCAGGTCAAGTATCAGATCAG
* *
51786 -AATCCAAGTCAAGTATAAGATCAG
1 AAAT-CAGGTCAAGTATCAGATCAG
*
51810 -AATCCATGTC-AGATATCAGATCAG
1 AAAT-CAGGTCAAG-TATCAGATCAG
** * *
51834 AACCCCATGTCAAGTATCAGATTAG
1 AA-ATCAGGTCAAGTATCAGATCAG
51859 AA
1 AA
51861 TTCAAATCAA
Statistics
Matches: 84, Mismatches: 10, Indels: 9
0.82 0.10 0.09
Matches are distributed among these distances:
23 5 0.06
24 58 0.69
25 19 0.23
26 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCAGATCAG
Found at i:54322 original size:7 final size:7
Alignment explanation
Indices: 54310--54348 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
54300 AGGTCAACGT
54310 CGGTCAA
1 CGGTCAA
54317 CGGTCAA
1 CGGTCAA
*
54324 TGGGTCAA
1 -CGGTCAA
54332 CGGTCAA
1 CGGTCAA
54339 CGGTCAA
1 CGGTCAA
54346 CGG
1 CGG
54349 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
7 23 0.79
8 6 0.21
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (7 bp):
CGGTCAA
Found at i:54335 original size:22 final size:22
Alignment explanation
Indices: 54310--54351 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
54300 AGGTCAACGT
*
54310 CGGTCAACGGTCAATGGGTCAA
1 CGGTCAACGGTCAACGGGTCAA
54332 CGGTCAACGGTCAACGGGTC
1 CGGTCAACGGTCAACGGGTC
54352 GGGTCAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.33, T:0.17
Consensus pattern (22 bp):
CGGTCAACGGTCAACGGGTCAA
Found at i:54351 original size:15 final size:15
Alignment explanation
Indices: 54301--54348 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
54291 TCAAAGTTTA
54301 GGTCAACGTCGGTCAAC
1 GGTCAACG--GGTCAAC
*
54318 GGTCAATGGGTCAAC
1 GGTCAACGGGTCAAC
54333 GGTCAAC-GGTCAAC
1 GGTCAACGGGTCAAC
54347 GG
1 GG
54349 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.31
15 13 0.45
17 7 0.24
ACGTcount: A:0.25, C:0.25, G:0.33, T:0.17
Consensus pattern (15 bp):
GGTCAACGGGTCAAC
Found at i:54358 original size:13 final size:13
Alignment explanation
Indices: 54340--54369 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54330 AACGGTCAAC
54340 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
54353 GGTCAACGGGTCT
1 GGTCAACGGGTCG
54366 GGTC
1 GGTC
54370 GGGTTGTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.23, G:0.43, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:68704 original size:2 final size:2
Alignment explanation
Indices: 68699--68730 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
68689 CACAAAAAAA
68699 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
68731 CAAATACCTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:71951 original size:26 final size:26
Alignment explanation
Indices: 71922--71972 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
71912 AATTTTATCC
*
71922 TTAAAATTTTATAAATTCACTCTCTA
1 TTAAAAATTTATAAATTCACTCTCTA
*
71948 TTAAAAATTTATAAATTCATTCTCT
1 TTAAAAATTTATAAATTCACTCTCT
71973 TAAATAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (26 bp):
TTAAAAATTTATAAATTCACTCTCTA
Found at i:73558 original size:2 final size:2
Alignment explanation
Indices: 73551--73601 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
73541 TTTATCTATC
73551 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
73593 TA TA TA TA T
1 TA TA TA TA T
73602 TATGATGTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:74808 original size:21 final size:21
Alignment explanation
Indices: 74782--74825 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
74772 TAAGGTCCCT
74782 TAAAATTCATGCCTATAAACA
1 TAAAATTCATGCCTATAAACA
74803 TAAAATTCATGCCTATAAACA
1 TAAAATTCATGCCTATAAACA
74824 TA
1 TA
74826 CTCTGGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAATTCATGCCTATAAACA
Found at i:79868 original size:2 final size:2
Alignment explanation
Indices: 79861--79930 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
79851 TTTTAAGATA
79861 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
79903 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
79931 TAATAATAGG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:80449 original size:32 final size:31
Alignment explanation
Indices: 80403--80494 Score: 125
Period size: 31 Copynumber: 2.9 Consensus size: 31
80393 CGATTATATA
*
80403 TATATATATATATATATATATATATATAATATTT
1 TATATAT-TTTATAT-TA-ATATATATAATATTT
80437 TATAT-TTTTATATTAATTATATATAATATTT
1 TATATATTTTATATTAA-TATATATAATATTT
80468 TATATATTTTATATTAAT-TATATAATA
1 TATATATTTTATATTAATATATATAATA
80495 CAAACCCTAA
Statistics
Matches: 55, Mismatches: 1, Indels: 8
0.86 0.02 0.12
Matches are distributed among these distances:
30 10 0.18
31 22 0.40
32 17 0.31
33 1 0.02
34 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
TATATATTTTATATTAATATATATAATATTT
Found at i:80491 original size:2 final size:2
Alignment explanation
Indices: 80397--80474 Score: 71
Period size: 2 Copynumber: 42.5 Consensus size: 2
80387 CCGCCCCGAT
*
80397 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
80437 TA TA TT TT TA TA T- TA -A T- TA TA TA TA -A TA T- TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
80474 T
1 T
80475 TTTATATTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
1 7 0.11
2 58 0.89
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:81953 original size:15 final size:15
Alignment explanation
Indices: 81935--81970 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
81925 AGAAAAAAAT
81935 TAATAAAAA-AATTAA
1 TAATAAAAATAA-TAA
81950 TAATAAAAATAATAA
1 TAATAAAAATAATAA
81965 TAATAA
1 TAATAA
81971 TCATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.90
16 2 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAAAAATAATAA
Found at i:81965 original size:12 final size:13
Alignment explanation
Indices: 81929--81967 Score: 64
Period size: 12 Copynumber: 3.2 Consensus size: 13
81919 GAAAAAAGAA
81929 AAAAATTAATAA-
1 AAAAATTAATAAT
81941 AAAAATTAATAAT
1 AAAAATTAATAAT
81954 AAAAA-TAATAAT
1 AAAAATTAATAAT
81966 AA
1 AA
81968 TAATCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 21 0.81
13 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAATTAATAAT
Found at i:82505 original size:104 final size:102
Alignment explanation
Indices: 82380--82621 Score: 288
Period size: 102 Copynumber: 2.3 Consensus size: 102
82370 GTTCTTGTGT
* *
82380 TTCAAGAGAAAATGTCTCAAGGGAGGCAAAATTTTGTTTCAA-GAAAAATATATTCAAAGATTGG
1 TTCAAGAGAAAATGTCTCAAGGGAGACAAAA-TTTGTTT-AATGAAAAACATATTCAAAGATT-G
*
82444 TGTTTCAAGAGAAGCTGTCTCAAGAGAGATAAAACTTTGC
63 TGTTTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGC
* * * *
82484 TTCAAGGGAAATTGTCTCAAGGGAGACAAAATTTGTTTAATGTAAAACATATTCAAAGATTTTGT
1 TTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTGTTTAATGAAAAACATATTCAAAGATTGTGT
* * *
82549 TTCAAGGGAAACTGTCTCAAGAGAGACAAAGACAAAATTTGT
66 TTCAAGAGAAACTGTCTCAAGAGAGATAAA-AC----TTTGC
* * *
82591 TTCAAGAGAAACTATCTCAAGAGAGACAAAA
1 TTCAAGAGAAAATGTCTCAAGGGAGACAAAA
82622 CTTAGTTCCA
Statistics
Matches: 118, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
102 32 0.27
103 27 0.23
104 28 0.24
107 31 0.26
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (102 bp):
TTCAAGAGAAAATGTCTCAAGGGAGACAAAATTTGTTTAATGAAAAACATATTCAAAGATTGTGT
TTCAAGAGAAACTGTCTCAAGAGAGATAAAACTTTGC
Found at i:82621 original size:36 final size:36
Alignment explanation
Indices: 82578--82673 Score: 113
Period size: 37 Copynumber: 2.7 Consensus size: 36
82568 AGAGAGACAA
82578 AGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAG
1 AGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAG
* * * * *
82614 AGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
1 AGACAAAA-TTTGTTTCAAGAGAAACTATCTCAAGAG
* *
82651 AGACGAAGTTTGTTTCAAG-GAAA
1 AGACAAAATTTGTTTCAAGAGAAA
82674 ACATATTTAA
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
35 4 0.08
36 16 0.33
37 29 0.59
ACGTcount: A:0.43, C:0.15, G:0.20, T:0.23
Consensus pattern (36 bp):
AGACAAAATTTGTTTCAAGAGAAACTATCTCAAGAG
Found at i:82646 original size:37 final size:39
Alignment explanation
Indices: 82556--82654 Score: 112
Period size: 37 Copynumber: 2.5 Consensus size: 39
82546 TGTTTCAAGG
* * *
82556 GAAACTGTCTCAAGAGAGACAAAGACAAAATTTGTTTCAAGA
1 GAAACTGTCTCAAGAGAGACAAAGAC---ATTAGTTCCAAAA
*
82598 GAAACTATCTCAAGAGAGACAAA-AC-TTAGTTCCAAAA
1 GAAACTGTCTCAAGAGAGACAAAGACATTAGTTCCAAAA
*
82635 GAAACTGTCTCAAGGGAGAC
1 GAAACTGTCTCAAGAGAGAC
82655 GAAGTTTGTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
37 27 0.53
41 2 0.04
42 22 0.43
ACGTcount: A:0.44, C:0.17, G:0.19, T:0.19
Consensus pattern (39 bp):
GAAACTGTCTCAAGAGAGACAAAGACATTAGTTCCAAAA
Found at i:86474 original size:21 final size:21
Alignment explanation
Indices: 86391--86475 Score: 82
Period size: 21 Copynumber: 3.9 Consensus size: 21
86381 CAGAACCCCA
* *
86391 GGGGGGTATCGATTCCC-CTG
1 GGGGGGAATCGATTCCCTCAG
* *
86411 TGGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGGAATCGATT-CCC-TC-AG
86436 GGGGGGAATCGATTCCCTCAG
1 GGGGGGAATCGATTCCCTCAG
*
86457 GGGGGGGATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
86476 TGCACCAAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
21 31 0.58
22 5 0.09
23 3 0.06
24 14 0.26
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAG
Found at i:90309 original size:22 final size:21
Alignment explanation
Indices: 90267--90306 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
90257 GAGTTTGTTT
*
90267 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
90288 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
90307 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:92985 original size:110 final size:106
Alignment explanation
Indices: 92852--93153 Score: 370
Period size: 101 Copynumber: 2.9 Consensus size: 106
92842 TATTGTTTCA
*
92852 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTTCTGAATGAAACTAGGAAGTTGTTTGTTGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG-TCTGAATGAAACTA-GAAGTTATTTGTTGA
92917 CAGTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGCGTTGTCTCG
64 CAGTC-A-CGCCCCTTCGCTGTGAAGTTGAGCTTGCGTTGTCTCG
* * *
92962 AGTCCAATATCCTTCACTGTGAAGTTGAAATT-GACT--CTG-AA--A-AAGTTATTTGTTGACA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTCTGAATGAAACTAGAAGTTATTTGTTGACA
* *
93020 GTCAGTCGACCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTCG
66 GTCA--CGCCCCTTCGCTGTGAAGTTGAGCTTGCGTTGTCTCG
* * * *
93063 AGTCCAATATCCTTCGTTGTGAAGATGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTG-GTCTGAATGAAACT-AGAAGTTATTTGTTGA
*
93128 CAGT--CGCCCCTTCGTTGTGAAGTTGA
64 CAGTCACGCCCCTTCGCTGTGAAGTTGA
93154 TCAACCACCA
Statistics
Matches: 167, Mismatches: 15, Indels: 24
0.81 0.07 0.12
Matches are distributed among these distances:
100 1 0.01
101 82 0.49
103 3 0.02
105 4 0.02
106 24 0.14
108 2 0.01
109 2 0.01
110 49 0.29
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGTCTGAATGAAACTAGAAGTTATTTGTTGACA
GTCACGCCCCTTCGCTGTGAAGTTGAGCTTGCGTTGTCTCG
Found at i:97238 original size:10 final size:10
Alignment explanation
Indices: 97220--97271 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
97210 TGAAAAAAGG
97220 AAAAATTAAT
1 AAAAATTAAT
*
97230 AAAAGTTAAT
1 AAAAATTAAT
97240 AAAAATATTAAT
1 -AAAA-ATTAAT
*
97252 AATAA-TAAT
1 AAAAATTAAT
97261 AAAAA-TAAT
1 AAAAATTAAT
97270 AA
1 AA
97272 TCATAAATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
9 14 0.39
10 10 0.28
11 7 0.19
12 5 0.14
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAAATTAAT
Found at i:97260 original size:21 final size:21
Alignment explanation
Indices: 97220--97290 Score: 67
Period size: 21 Copynumber: 3.4 Consensus size: 21
97210 TGAAAAAAGG
97220 AAAA-ATTAATAA-AAGTTAATA
1 AAAATATTAATAATAA--TAATA
97241 AAAATATTAATAATAATAATA
1 AAAATATTAATAATAATAATA
* *
97262 AAAATAATAATCATAAATAA-A
1 AAAATATTAATAAT-AATAATA
*
97283 TAAATATT
1 AAAATATT
97291 TTTTTTAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
21 28 0.65
22 13 0.30
23 2 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (21 bp):
AAAATATTAATAATAATAATA
Found at i:97288 original size:18 final size:18
Alignment explanation
Indices: 97236--97278 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
97226 TAATAAAAGT
*
97236 TAATAAAAATATTAATAA
1 TAATAAAAATAATAATAA
97254 TAATAATAAA-AATAATAA
1 TAATAA-AAATAATAATAA
*
97272 TCATAAA
1 TAATAAA
97279 TAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 1 0.05
18 18 0.82
19 3 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
TAATAAAAATAATAATAA
Found at i:98158 original size:19 final size:18
Alignment explanation
Indices: 98118--98159 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
98108 GGTGTGAGAT
98118 AATTTAATTTTTTTAATTA
1 AATTTAATTTTTTTAA-TA
98137 AATTTAATATTATTTTAA-A
1 AATTTAAT-TT-TTTTAATA
98156 AATT
1 AATT
98160 CCGGAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 13 0.62
20 2 0.10
21 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATTTAATTTTTTTAATA
Found at i:99409 original size:28 final size:28
Alignment explanation
Indices: 99355--99434 Score: 74
Period size: 28 Copynumber: 2.9 Consensus size: 28
99345 TAGAACTTAA
* *
99355 TATTATTTTTTTA--AAATATTATAATTTT
1 TATTATTTTTTTATTAAA-A-TATTATTTC
*
99383 TTTTATTTTTTTATTAAAATATTATTTC
1 TATTATTTTTTTATTAAAATATTATTTC
* * *
99411 TATAATTTTATTAATAAAATATTA
1 TATTATTTTTTTATTAAAATATTA
99435 AGATTGTTAC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
28 39 0.91
29 1 0.02
30 3 0.07
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (28 bp):
TATTATTTTTTTATTAAAATATTATTTC
Found at i:99610 original size:27 final size:28
Alignment explanation
Indices: 99564--99654 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 28
99554 ATTACTAGAG
*
99564 TATTATATTAATATTAAATACGTAAATAA
1 TATTAT-TTAATATTAAATAAGTAAATAA
* * *
99593 TATTATTTATTATT-AATAATTTAATAA
1 TATTATTTAATATTAAATAAGTAAATAA
*
99620 TATTATTT-CTATTAAATTAA-TAAATAA
1 TATTATTTAATATTAAA-TAAGTAAATAA
*
99647 TATAATTT
1 TATTATTT
99655 TATTAATATT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
26 4 0.08
27 33 0.62
28 10 0.19
29 6 0.11
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (28 bp):
TATTATTTAATATTAAATAAGTAAATAA
Found at i:99665 original size:27 final size:27
Alignment explanation
Indices: 99586--99670 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
99576 ATTAAATACG
* *
99586 TAAATAATATTA-TTTATTATTAATAA
1 TAAATAATATTATTTTATTAATATTAA
*
99612 TTTAATAATATTATTTCTATTAA-ATTAA
1 -TAAATAATATTATTT-TATTAATATTAA
* *
99640 TAAATAATATAATTTTATTAATATTAT
1 TAAATAATATTATTTTATTAATATTAA
99667 TAAA
1 TAAA
99671 ATAAAAAATA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
26 6 0.12
27 32 0.65
28 6 0.12
29 5 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (27 bp):
TAAATAATATTATTTTATTAATATTAA
Found at i:99697 original size:32 final size:32
Alignment explanation
Indices: 99638--99698 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
99628 CTATTAAATT
* *
99638 AATAAATAATATAATTTTATTAATATTATTAA
1 AATAAAAAATATAATCTTATTAATATTATTAA
*
99670 AATAAAAAATATAAATCTTA-TATTATTAT
1 AATAAAAAATAT-AATCTTATTAATATTAT
99699 AATGTAATTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 19 0.76
33 6 0.24
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (32 bp):
AATAAAAAATATAATCTTATTAATATTATTAA
Found at i:99743 original size:28 final size:30
Alignment explanation
Indices: 99711--99766 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
99701 TGTAATTGAT
*
99711 TATTTTATTA-TAATA-TTAAAAAATATAA
1 TATTTTATTAGAAATATTTAAAAAATATAA
*
99739 TATTTTTTTAGAAATATTTAAAAAATAT
1 TATTTTATTAGAAATATTTAAAAAATAT
99767 TTTCAATGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 4 0.17
30 11 0.46
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TATTTTATTAGAAATATTTAAAAAATATAA
Found at i:101266 original size:18 final size:17
Alignment explanation
Indices: 101243--101277 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
101233 CATCTCAGTC
*
101243 CAAACTGTAATTATTAAA
1 CAAACTGAAATT-TTAAA
101261 CAAACTGAAATTTTAAA
1 CAAACTGAAATTTTAAA
101278 TGAAAAACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.51, C:0.11, G:0.06, T:0.31
Consensus pattern (17 bp):
CAAACTGAAATTTTAAA
Done.