Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015242.1 Corchorus olitorius cultivar O-4 contig15275, 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: 7666
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Found at i:757 original size:20 final size:19
Alignment explanation
Indices: 712--759 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
702 ACTTTTGAGT
* **
712 AATTTGTAATTAAAACTTG
1 AATTTTTAATTAAAAAATG
731 AATTTTTAATTAAAAAATG
1 AATTTTTAATTAAAAAATG
750 AATCTTTTAA
1 AAT-TTTTAA
760 GAAATTGTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 19 0.76
20 6 0.24
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (19 bp):
AATTTTTAATTAAAAAATG
Found at i:833 original size:50 final size:51
Alignment explanation
Indices: 581--1106 Score: 507
Period size: 51 Copynumber: 10.5 Consensus size: 51
571 TAAAAATTGA
*
581 ATTTTTAATTAAAAGA-TGAATCTTTT-AAGAAATTGTAATTAAAGGTTGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
* * * *
630 ATTTTTTAGTAAAAAAATTGAATC-TTTGAACAAATTGTAAATAAAGGTTGG
1 A-TTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
* * * * ** *
681 ATTTTTAGTTAAAAGATTGAAACTTTTG-AGTAATTTGTAATTAAAACTTGA
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAG-AAATTGTAAATAAAGGTTGG
*
732 ATTTTTAATTAAAA-AATGAATCTTTT-AAGAAATTGTAAATAAAGGTTGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
*
781 ACTTTTAATTAAAAGA-TGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
* * * *
831 ACTTTTAAGTAAAAGATTGAAACTTTTGAACAAATTGTAAATAAAGGTTGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
* * * * * * *
882 ACTTTTAGTTAAAAGATTGAAAC-TTTGGAGTAATTTGTAATTAAAGATTGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAG-AAATTGTAAATAAAGGTTGG
* *
933 ATTTTTAATTAAAAGATCGAA-CTTTT-AAGAAATTTGTAAATAAAGATTGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAA-TTGTAAATAAAGGTTGG
* * * *
983 ATTTTTAATTAAAAG-TTCAAACTTTT-AAGTAATT-TAAGAATAAA--ATGG
1 ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGT-A-AATAAAGGTTGG
* * * * *
1031 AATTTTTAAGTGAAA-ATTGAAGCTTTT-AAGCAACTTGTAAATAAAGATT-G
1 -ATTTTTAATTAAAAGATTGAATCTTTTGAAG-AAATTGTAAATAAAGGTTGG
1081 ATTTTT--TTAAAAGGATTGAATCTTTT
1 ATTTTTAATTAAAA-GATTGAATCTTTT
1107 AAGTAGTTTG
Statistics
Matches: 401, Mismatches: 53, Indels: 46
0.80 0.11 0.09
Matches are distributed among these distances:
47 4 0.01
48 4 0.01
49 94 0.23
50 146 0.36
51 153 0.38
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (51 bp):
ATTTTTAATTAAAAGATTGAATCTTTTGAAGAAATTGTAAATAAAGGTTGG
Found at i:939 original size:201 final size:199
Alignment explanation
Indices: 583--1119 Score: 689
Period size: 201 Copynumber: 2.7 Consensus size: 199
573 AAAATTGAAT
* *
583 TTTTAATTAAAAGATGAATCTTTTAAGAAATTGTAATTAAAGGTTGGATTTTTTAGTAAAAAAAT
1 TTTTAATTAAAAGATGAATCTTTTAAGAAATTGTAAATAAAGGTTGGATTTTTAAGT--AAAAAT
*
648 TGAATC-TTTGAACAAATTGTAAATAAAGGTTGGATTTTTAGTTAAAAGATTGAAACTTTTGAGT
64 TGAAACTTTTGAACAAATTGTAAATAAAGGTTGGA-TTTTAGTTAAAAGATTGAAACTTTTGAGT
712 AATTTGTAATTAAAACTTGAATTTTTAATTAAAAAAT-GAATCTTTTAAGAAA-TTGTAAATAAA
128 AATTTGTAATTAAAACTTGAATTTTTAATTAAAAAATCGAA-CTTTTAAGAAATTTGTAAATAAA
*
775 GGTTGGAC
192 GATTGGAC
*
783 TTTTAATTAAAAGATGAATCTTTTGAAGAAATTGTAAATAAAGGTTGGACTTTTAAGTAAAAGAT
1 TTTTAATTAAAAGATGAATCTTTT-AAGAAATTGTAAATAAAGGTTGGATTTTTAAGTAAAA-AT
*
848 TGAAACTTTTGAACAAATTGTAAATAAAGGTTGGACTTTTAGTTAAAAGATTGAAACTTTGGAGT
64 TGAAACTTTTGAACAAATTGTAAATAAAGGTTGGA-TTTTAGTTAAAAGATTGAAACTTTTGAGT
* *
913 AATTTGTAATTAAAGA-TTGGATTTTTAATTAAAAGATCGAACTTTTAAGAAATTTGTAAATAAA
128 AATTTGTAATTAAA-ACTTGAATTTTTAATTAAAAAATCGAACTTTTAAGAAATTTGTAAATAAA
*
977 GATTGGAT
192 GATTGGAC
* * * * * *
985 TTTTAATTAAAAGTTCAAACTTTTAAGTAATT-TAAGAATAAA--ATGGAATTTTTAAGTGAAAA
1 TTTTAATTAAAAGATGAATCTTTTAAGAAATTGT-A-AATAAAGGTTGG-ATTTTTAAGTAAAAA
* * * * * *
1047 TTGAAGCTTTT-AAGCAACTTGTAAATAAAGATT-GATTTT-TTTAAAAGGATTGAATCTTTTAA
63 TTGAAACTTTTGAA-CAAATTGTAAATAAAGGTTGGATTTTAGTTAAAA-GATTGAAACTTTTGA
*
1109 GTAGTTTGTAA
126 GTAATTTGTAA
1120 ACAAAATGAG
Statistics
Matches: 301, Mismatches: 25, Indels: 24
0.86 0.07 0.07
Matches are distributed among these distances:
197 6 0.02
198 26 0.09
199 8 0.03
200 63 0.21
201 150 0.50
202 48 0.16
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.39
Consensus pattern (199 bp):
TTTTAATTAAAAGATGAATCTTTTAAGAAATTGTAAATAAAGGTTGGATTTTTAAGTAAAAATTG
AAACTTTTGAACAAATTGTAAATAAAGGTTGGATTTTAGTTAAAAGATTGAAACTTTTGAGTAAT
TTGTAATTAAAACTTGAATTTTTAATTAAAAAATCGAACTTTTAAGAAATTTGTAAATAAAGATT
GGAC
Found at i:1139 original size:98 final size:97
Alignment explanation
Indices: 643--1143 Score: 242
Period size: 100 Copynumber: 5.0 Consensus size: 97
633 TTTTAGTAAA
* * * * *
643 AAAATTGAATCTTTGAACAAA-TTGTAAATAAAGGTTGGATTTTTAGTTAAAAGATTGAAACTTT
1 AAAATTGAAGCTTTTAAGAAACTTGTAAATAAAGATTGGATTTTTA-TTAAAAG-TTCAAACTTT
* * * ** *
707 TGAGTAATTT--GTAATTAAAACTTGAATTTTTAATT
64 TAAGTAATTTAAG-AA-CAAAA-TGGAATGATTAAGT
* * * * * * *
742 AAAAAATGAATCTTTTAAGAAA-TTGTAAATAAAGGTTGGACTTTTAATTAAAAGATGAATCTTT
1 -AAAATTGAAGCTTTTAAGAAACTTGTAAATAAAGATTGGA-TTTTTATTAAAAGTTCAAACTTT
* ** * *
806 TGAAGAAATTGTAA-ATA-AAGGTTGGACT-TTTAAGT
64 T-AAGTAATT-TAAGA-ACAA-AATGGAATGATTAAGT
* * * * *
841 AAAAGATTGAAACTTTTGAACAAA-TTGTAAATAAAGGTTGGACTTTTAGTTAAAAGATTGAAAC
1 -AAA-ATTGAAGCTTTT-AAGAAACTTGTAAATAAAGATTGGATTTTTA-TTAAAAG-TTCAAAC
** * ** *
905 TTTGGAGTAATTT--GTAATTAAAGATTGG-ATTTTTAATT
61 TTTTAAGTAATTTAAG-AA-CAAA-A-TGGAATGATTAAGT
* *
943 AAAAGATCGAA-CTTTTAAGAAATTTGTAAATAAAGATTGGATTTTTAATTAAAAGTTCAAACTT
1 -AAA-ATTGAAGCTTTTAAGAAACTTGTAAATAAAGATTGGATTTTT-ATTAAAAGTTCAAACTT
* **
1007 TTAAGTAATTTAAGAATAAAATGGAATTTTTAAGT
63 TTAAGTAATTTAAGAACAAAATGGAATGATTAAGT
* * *
1042 GAAAATTGAAGCTTTTAAGCAACTTGTAAATAAAGATT-GATTTTT-TTAAAAGGATTGAATCTT
1 -AAAATTGAAGCTTTTAAGAAACTTGTAAATAAAGATTGGATTTTTATTAAAA-G-TTCAAACTT
* *
1105 TTAAGTAGTTTGTA-AACAAAATGAGAA-GATTAAGT
63 TTAAGTAATTT-AAGAACAAAATG-GAATGATTAAGT
1140 AAAA
1 AAAA
1144 GACATACCTT
Statistics
Matches: 327, Mismatches: 46, Indels: 59
0.76 0.11 0.14
Matches are distributed among these distances:
96 6 0.02
97 5 0.02
98 46 0.14
99 62 0.19
100 97 0.30
101 81 0.25
102 30 0.09
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (97 bp):
AAAATTGAAGCTTTTAAGAAACTTGTAAATAAAGATTGGATTTTTATTAAAAGTTCAAACTTTTA
AGTAATTTAAGAACAAAATGGAATGATTAAGT
Found at i:1155 original size:49 final size:50
Alignment explanation
Indices: 1102--1280 Score: 157
Period size: 50 Copynumber: 3.6 Consensus size: 50
1092 AGGATTGAAT
* *
1102 CTTTTAAGTAGTTTGTAAA-CAAAATGAGAAGATTAAGTAAAAGACATAC
1 CTTTTAAGTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAGACATAC
* * **
1151 CTTTTGATTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAGATGTAC
1 CTTTTAAGTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAGACATAC
* * * ** *** * *
1201 CTTTTGATTAAGTTGTAAATAAAGGT-AGGATCTTTAAATAAAAGAC-TAAT
1 CTTTTAAGTAATTTGTAAATAAAAATGA-GAAGATTAAGTAAAAGACAT-AC
* *
1251 CTCTTAAGTAATTTGTAAATAAGAATGAGA
1 CTTTTAAGTAATTTGTAAATAAAAATGAGA
1281 TTTTTGGAGT
Statistics
Matches: 104, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
49 18 0.17
50 85 0.82
51 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (50 bp):
CTTTTAAGTAATTTGTAAATAAAAATGAGAAGATTAAGTAAAAGACATAC
Found at i:1184 original size:50 final size:50
Alignment explanation
Indices: 1113--1223 Score: 179
Period size: 50 Copynumber: 2.2 Consensus size: 50
1103 TTTTAAGTAG
*
1113 TTTGTAAA-CAAAATGAGAAGATTAAGTAAAAGACATACCTTTTGATTAA
1 TTTGTAAATAAAAATGAGAAGATTAAGTAAAAGACATACCTTTTGATTAA
**
1162 TTTGTAAATAAAAATGAGAAGATTAAGTAAAAGATGTACCTTTTGATTAA
1 TTTGTAAATAAAAATGAGAAGATTAAGTAAAAGACATACCTTTTGATTAA
*
1212 GTTGTAAATAAA
1 TTTGTAAATAAA
1224 GGTAGGATCT
Statistics
Matches: 57, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 8 0.14
50 49 0.86
ACGTcount: A:0.47, C:0.05, G:0.15, T:0.32
Consensus pattern (50 bp):
TTTGTAAATAAAAATGAGAAGATTAAGTAAAAGACATACCTTTTGATTAA
Found at i:1965 original size:48 final size:48
Alignment explanation
Indices: 1907--2011 Score: 165
Period size: 48 Copynumber: 2.2 Consensus size: 48
1897 TTTTCTTCAA
* * *
1907 TATTCATGTTTTGCCCTTCCCAGTCGGAAGGTGGTTTTTTCAATGTTT
1 TATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGATGTTTTCAATGTTT
* *
1955 TATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTGAATGTTT
1 TATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGATGTTTTCAATGTTT
2003 TATTCCTGT
1 TATTCCTGT
2012 CTTCAATATC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 52 1.00
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (48 bp):
TATTCCTGTTTTGCCCTTCCCAGTCGGAAGGTGATGTTTTCAATGTTT
Found at i:2081 original size:20 final size:20
Alignment explanation
Indices: 2057--2122 Score: 114
Period size: 20 Copynumber: 3.3 Consensus size: 20
2047 CGGAAGGTGT
*
2057 TGTTTTCAATGTTTTATTCT
1 TGTTTTCAATGTTTTATTCC
2077 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
*
2097 TGTTGTCAATGTTTTATTCC
1 TGTTTTCAATGTTTTATTCC
2117 TGTTTT
1 TGTTTT
2123 GCCCTTCCCG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.62
Consensus pattern (20 bp):
TGTTTTCAATGTTTTATTCC
Found at i:2138 original size:88 final size:88
Alignment explanation
Indices: 1989--2184 Score: 297
Period size: 88 Copynumber: 2.2 Consensus size: 88
1979 CGGAAGGTGA
*
1989 TGTTTTGAATGTTTTATTCCTGTCTTCAATATCTCATTCTCGTTTTGCCCTTCCCGGTCGGAAGG
1 TGTTTTCAATGTTTTATTCCTGTCTTCAATATCTCATTCTCGTTTTGCCCTTCCCGGTCGGAAGG
*
2054 TGTTGTTTTCAATGTTTTATTCT
66 TGTTGTTTTCAATGTTTTATTCC
* * *
2077 TGTTTTCAATGTTTTATTCCTGT-TGTCAATGTTTTATTC-CTGTTTTGCCCTTCCCGGTCGGAA
1 TGTTTTCAATGTTTTATTCCTGTCT-TCAATATCTCATTCTC-GTTTTGCCCTTCCCGGTCGGAA
2140 GGTGTTGTTTTCAATGTTTTATTCC
64 GGTGTTGTTTTCAATGTTTTATTCC
* *
2165 CGTTTTCAATATTTTATTCC
1 TGTTTTCAATGTTTTATTCC
2185 CGTTTTGCCC
Statistics
Matches: 99, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
87 2 0.02
88 97 0.98
ACGTcount: A:0.14, C:0.19, G:0.16, T:0.51
Consensus pattern (88 bp):
TGTTTTCAATGTTTTATTCCTGTCTTCAATATCTCATTCTCGTTTTGCCCTTCCCGGTCGGAAGG
TGTTGTTTTCAATGTTTTATTCC
Found at i:2171 original size:20 final size:20
Alignment explanation
Indices: 2146--2190 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
2136 GGAAGGTGTT
*
2146 GTTTTCAATGTTTTATTCCC
1 GTTTTCAATATTTTATTCCC
2166 GTTTTCAATATTTTATTCCC
1 GTTTTCAATATTTTATTCCC
2186 GTTTT
1 GTTTT
2191 GCCCTTCCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.16, C:0.18, G:0.09, T:0.58
Consensus pattern (20 bp):
GTTTTCAATATTTTATTCCC
Found at i:2190 original size:68 final size:68
Alignment explanation
Indices: 2076--2232 Score: 244
Period size: 68 Copynumber: 2.3 Consensus size: 68
2066 TGTTTTATTC
* * * **
2076 TTGTTTTCAATGTTTTATTCCTGTTGTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAG
1 TTGTTTTCAATGTTTTATTCCCGTTGTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAG
2141 -GTG
66 AG-G
*
2144 TTGTTTTCAATGTTTTATTCCCGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAG
1 TTGTTTTCAATGTTTTATTCCCGTTGTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAG
2209 AGG
66 AGG
2212 TTGTTTTCAATGTTTTATTCC
1 TTGTTTTCAATGTTTTATTCC
2233 TTTTTTGCCC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
68 81 0.99
69 1 0.01
ACGTcount: A:0.15, C:0.19, G:0.17, T:0.49
Consensus pattern (68 bp):
TTGTTTTCAATGTTTTATTCCCGTTGTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAG
AGG
Found at i:2230 original size:156 final size:156
Alignment explanation
Indices: 1946--2231 Score: 475
Period size: 156 Copynumber: 1.8 Consensus size: 156
1936 GGTGGTTTTT
* *
1946 TCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTGAATGTTTTATTCCTG
1 TCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTATTCCCG
* **
2011 TCTTCAATATCTCATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
66 TCTTCAATATCTCATTCCCGTTTTGCCCTTCCAAGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
2076 TTGTTTTCAATGTTTTATTCCTGTTG
131 TTGTTTTCAATGTTTTATTCCTGTTG
*
2102 TCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCCG
1 TCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTATTCCCG
* * *
2167 TTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAGAG-GTTGTTTTCAATGTTTTATT
66 TCTTCAATATCTCATTCCCGTTTTGCCCTTCCAAGTCGGAAG-GTGTTGTTTTCAATGTTTTATT
2231 C
130 C
2232 CTTTTTTGCC
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
156 119 0.99
157 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (156 bp):
TCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTATTCCCG
TCTTCAATATCTCATTCCCGTTTTGCCCTTCCAAGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
TTGTTTTCAATGTTTTATTCCTGTTG
Found at i:2239 original size:48 final size:48
Alignment explanation
Indices: 2166--2279 Score: 158
Period size: 48 Copynumber: 2.4 Consensus size: 48
2156 TTTTATTCCC
* *
2166 GTTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAGAG-GTT
1 GTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAG-GTGAT
** **
2214 GTTTTCAATGTTTTATTCCTTTTTTGCCCTTCCCGGTCGGAAGGTGAT
1 GTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAGGTGAT
2262 GTTTTCAATGTTTTATTC
1 GTTTTCAATGTTTTATTC
2280 ATGTTTTCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
47 1 0.02
48 58 0.98
ACGTcount: A:0.16, C:0.19, G:0.18, T:0.46
Consensus pattern (48 bp):
GTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAGGTGAT
Found at i:2249 original size:116 final size:116
Alignment explanation
Indices: 2097--2354 Score: 410
Period size: 116 Copynumber: 2.2 Consensus size: 116
2087 GTTTTATTCC
* *
2097 TGTTGTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTAT
* *
2162 TCCCGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGTCGGAAGAG-GT
66 TCACGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCAAGTCGGAAG-GTGT
*
2213 TGTTTTCAATGTTTTATTCCTTTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTAT
1 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTAT
* * **
2278 TCATGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
66 TCACGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCAAGTCGGAAGGTGT
*
2329 TGTTTTCAATGTTTTATTCTTGTTTT
1 TGTTTTCAATGTTTTATTCCTGTTTT
2355 CAATGTTTTA
Statistics
Matches: 130, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
115 1 0.01
116 129 0.99
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.48
Consensus pattern (116 bp):
TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTAT
TCACGTTTTCAATATTTCATTCCCGTTTTGCCCTTCCAAGTCGGAAGGTGT
Found at i:2285 original size:20 final size:20
Alignment explanation
Indices: 2260--2306 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
2250 TCGGAAGGTG
* *
2260 ATGTTTTCAATGTTTTATTC
1 ATGTTTTCAATATTTCATTC
2280 ATGTTTTCAATATTTCATTC
1 ATGTTTTCAATATTTCATTC
*
2300 CTGTTTT
1 ATGTTTT
2307 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.60
Consensus pattern (20 bp):
ATGTTTTCAATATTTCATTC
Found at i:2285 original size:68 final size:68
Alignment explanation
Indices: 2212--2708 Score: 513
Period size: 68 Copynumber: 7.3 Consensus size: 68
2202 TCGGAAGAGG
* *
2212 TTGTTTTCAATGTTTTATTCCTTTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
2277 TTC
66 TTC
* * *
2280 ATGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
2345 TTC
66 TTC
*
2348 TTGTTTTCAATGTTTTATT-CTCGTTTTGCCCTTCCCGG-CAGAAGGTGTTGTTTTCAATGTTTT
1 TTGTTTTCAATGTTTTATTCCT-GTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
2411 ATTC
65 ATTC
* * *
2415 CTGTTTTCAATATTTTATTCTTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
2480 TTC
66 TTC
* ** ***** ** * ** *** *
2483 TTCTTTTCAATGTTTTATTCCTGTTTT-CAATATTTTATTC---CCGTTTTGCCCTTCCCGGTCG
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCT-TCCCGGTCGGAAGGTGTTG-TTTTCAATGT-T
** ***
2544 GAAGAGG
63 TTA-TTC
* *
2551 TTGTTTTCAATGTTTTATTACC-GTTTTGCCCTTCCCGGTCGAAAGGTGTTGTTTTCAATGCTTT
1 TTGTTTTCAATGTTTTATT-CCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
2615 ATTC
65 ATTC
* * * * * ** *
2619 ATGTTTTCAATATTTCATTCCCGTTTTGGCCTTCCTTGTCGGAGGGTGTTGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
2684 TTC
66 TTC
*
2687 TTGCTTTCAATGTTTTATTCCT
1 TTGTTTTCAATGTTTTATTCCT
2709 ACTTTCAATG
Statistics
Matches: 341, Mismatches: 75, Indels: 26
0.77 0.17 0.06
Matches are distributed among these distances:
65 5 0.01
66 5 0.01
67 68 0.20
68 249 0.73
69 5 0.01
70 4 0.01
71 5 0.01
ACGTcount: A:0.14, C:0.19, G:0.17, T:0.50
Consensus pattern (68 bp):
TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
TTC
Found at i:2353 original size:20 final size:20
Alignment explanation
Indices: 2328--2374 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2318 TCGGAAGGTG
2328 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
2348 TTGTTTTCAATGTTTTATTC
1 TTGTTTTCAATGTTTTATTC
*
2368 TCGTTTT
1 TTGTTTT
2375 GCCCTTCCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.66
Consensus pattern (20 bp):
TTGTTTTCAATGTTTTATTC
Found at i:2421 original size:20 final size:20
Alignment explanation
Indices: 2396--2441 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
2386 CAGAAGGTGT
*
2396 TGTTTTCAATGTTTTATTCC
1 TGTTTTCAATATTTTATTCC
*
2416 TGTTTTCAATATTTTATTCT
1 TGTTTTCAATATTTTATTCC
2436 TGTTTT
1 TGTTTT
2442 GCCCTTCCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.15, C:0.11, G:0.09, T:0.65
Consensus pattern (20 bp):
TGTTTTCAATATTTTATTCC
Found at i:2440 original size:135 final size:136
Alignment explanation
Indices: 2212--2509 Score: 510
Period size: 135 Copynumber: 2.2 Consensus size: 136
2202 TCGGAAGAGG
* *
2212 TTGTTTTCAATGTTTTATTCCTTTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTA
1 TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCAGAAGGTGATGTTTTCAATGTTTTA
2277 TTCATGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTT
66 TTCATGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTT
2342 TTATTC
131 TTATTC
*
2348 TTGTTTTCAATGTTTTATT-CTCGTTTTGCCCTTCCCGG-CAGAAGGTGTTGTTTTCAATGTTTT
1 TTGTTTTCAATGTTTTATTCCT-GTTTTGCCCTTCCCGGTCAGAAGGTGATGTTTTCAATGTTTT
* * *
2411 ATTCCTGTTTTCAATATTTTATTCTTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGT
65 ATTCATGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGT
2476 TTTATTC
130 TTTATTC
*
2483 TTCTTTTCAATGTTTTATTCCTGTTTT
1 TTGTTTTCAATGTTTTATTCCTGTTTT
2510 CAATATTTTA
Statistics
Matches: 153, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
135 117 0.76
136 36 0.24
ACGTcount: A:0.13, C:0.18, G:0.17, T:0.52
Consensus pattern (136 bp):
TTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCAGAAGGTGATGTTTTCAATGTTTTA
TTCATGTTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTT
TTATTC
Found at i:2491 original size:20 final size:20
Alignment explanation
Indices: 2466--2523 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
2456 GAAGGTGTTG
*
2466 TTTTCAATGTTTTATTCTTC
1 TTTTCAATGTTTTATTCCTC
*
2486 TTTTCAATGTTTTATTCCTG
1 TTTTCAATGTTTTATTCCTC
*
2506 TTTTCAATATTTTATTCC
1 TTTTCAATGTTTTATTCC
2524 CGTTTTGCCC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.16, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTCAATGTTTTATTCCTC
Found at i:2510 original size:88 final size:88
Alignment explanation
Indices: 2398--2569 Score: 310
Period size: 88 Copynumber: 2.0 Consensus size: 88
2388 GAAGGTGTTG
**
2398 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCTTGTTTTGCCCTTCCCGGTCGGAAG-GT
1 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGAG-
2462 GTTGTTTTCAATGTTTTATTCTTC
65 GTTGTTTTCAATGTTTTATTCTTC
2486 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGAGG
1 TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGAGG
2551 TTGTTTTCAATGTTTTATT
66 TTGTTTTCAATGTTTTATT
2570 ACCGTTTTGC
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
88 80 0.99
89 1 0.01
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (88 bp):
TTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGAGG
TTGTTTTCAATGTTTTATTCTTC
Found at i:2528 original size:20 final size:20
Alignment explanation
Indices: 2465--2529 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
2455 GGAAGGTGTT
*
2465 GTTTTCAATGTTTTATTCTTC
1 GTTTTCAATGTTTTATTC-CC
*
2486 -TTTTCAATGTTTTATTCCT
1 GTTTTCAATGTTTTATTCCC
*
2505 GTTTTCAATATTTTATTCCC
1 GTTTTCAATGTTTTATTCCC
2525 GTTTT
1 GTTTT
2530 GCCCTTCCCG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.15, C:0.15, G:0.08, T:0.62
Consensus pattern (20 bp):
GTTTTCAATGTTTTATTCCC
Found at i:2560 original size:48 final size:48
Alignment explanation
Indices: 2504--2618 Score: 178
Period size: 48 Copynumber: 2.4 Consensus size: 48
2494 GTTTTATTCC
* *
2504 TGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCCGGTCGGAAGAG-GT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGAAAG-GTGT
*
2552 TGTTTTCAATGTTTTATTACCGTTTTGCCCTTCCCGGTCGAAAGGTGT
1 TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGAAAGGTGT
*
2600 TGTTTTCAATGCTTTATTC
1 TGTTTTCAATGTTTTATTC
2619 ATGTTTTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
47 1 0.02
48 60 0.98
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (48 bp):
TGTTTTCAATGTTTTATTCCCGTTTTGCCCTTCCCGGTCGAAAGGTGT
Found at i:2564 original size:339 final size:340
Alignment explanation
Indices: 1943--2706 Score: 1009
Period size: 339 Copynumber: 2.2 Consensus size: 340
1933 GAAGGTGGTT
* * * *
1943 TTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTGAATGTTTTATTC
1 TTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
* * * * * *
2008 CTGTCTTCAATATCTCATTCTCGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTA
66 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCAGAAGGTGTTGTTTTCAATGTTTTA
* * *** * ** * **
2073 TTCTTGTTTTCAATGTTTTATTCCTGTTGTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCGG
131 TTCCTGTTTTCAATATTTTATTCCTGTTGTCAATGTCCCAGTCAGGTGTTGCCCTTCAAGGTCGG
* *
2138 AAGGTGTTGTTTTCAATGTTTTATTCCCGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGT
196 AAGGTCTTCTTTTCAATGTTTTATTCCCGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGT
* *
2203 CGGAAGAGGTTGTTTTCAATGTTTTATT-CCTTTTTTGCCCTTCCCGGTCGGAAGGTGATGTTTT
261 CGGAAGAGGTTGTTTTCAATGTTTTATTACC-GTTTTGCCCTTCCCGGTCGAAAGGTGATGTTTT
*
2267 CAATGTTTTATTCATG
325 CAATGCTTTATTCATG
2283 TTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
1 TTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
2348 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGG-CAGAAGGTGTTGTTTTCAATGTTTTA
66 TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCAGAAGGTGTTGTTTTCAATGTTTTA
* * ** * ** *
2412 TTCCTGTTTTCAATATTTTATTCTTGTTTTGCCCT-TCCCGGTCGGAAGGTGTTG-TTTTCAATG
131 TTCCTGTTTTCAATATTTTATTCCTGTTGT-CAATGTCCCAGTC---AGGTGTTGCCCTTCAAGG
*** * *
2475 T-TTTA-TTCTTCTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCCCGTTTTGCCCTTCC
192 TCGGAAGGTCTTCTTTTCAATGTTTTATTCCCGTTTTCAATATTTTATTCCCGTTTTGCCCTTCC
** *
2538 CGGTCGGAAGAGGTTGTTTTCAATGTTTTATTACCGTTTTGCCCTTCCCGGTCGAAAGGTGTTGT
257 AAGTCGGAAGAGGTTGTTTTCAATGTTTTATTACCGTTTTGCCCTTCCCGGTCGAAAGGTGATGT
2603 TTTCAATGCTTTATTCATG
322 TTTCAATGCTTTATTCATG
* * ** *
2622 TTTTCAATATTTCATTCCCGTTTTGGCCTTCCTTGTCGGAGGGTGTTGTTTTCAATGTTTTATTC
1 TTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
*
2687 TTGCTTTCAATGTTTTATTC
66 TTGTTTTCAATGTTTTATTC
2707 CTACTTTCAA
Statistics
Matches: 371, Mismatches: 48, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
339 262 0.71
340 99 0.27
341 5 0.01
342 5 0.01
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.49
Consensus pattern (340 bp):
TTTTCAATATTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTC
TTGTTTTCAATGTTTTATTCTCGTTTTGCCCTTCCCGGTCAGAAGGTGTTGTTTTCAATGTTTTA
TTCCTGTTTTCAATATTTTATTCCTGTTGTCAATGTCCCAGTCAGGTGTTGCCCTTCAAGGTCGG
AAGGTCTTCTTTTCAATGTTTTATTCCCGTTTTCAATATTTTATTCCCGTTTTGCCCTTCCAAGT
CGGAAGAGGTTGTTTTCAATGTTTTATTACCGTTTTGCCCTTCCCGGTCGAAAGGTGATGTTTTC
AATGCTTTATTCATG
Found at i:2638 original size:20 final size:20
Alignment explanation
Indices: 2600--2638 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2590 CGAAAGGTGT
*
2600 TGTTTTCAATGCTTTATTCA
1 TGTTTTCAATGATTTATTCA
2620 TGTTTTCAAT-ATTTCATTC
1 TGTTTTCAATGATTT-ATTC
2639 CCGTTTTGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.56
Consensus pattern (20 bp):
TGTTTTCAATGATTTATTCA
Found at i:2685 original size:204 final size:202
Alignment explanation
Indices: 1907--2759 Score: 755
Period size: 204 Copynumber: 4.2 Consensus size: 202
1897 TTTTCTTCAA
* *
1907 TATTCATGTTTTGCCCTTCCCAGTCGGAAGGTGGTT-TTTTCAATGTTTTATTCCTGTTTTGCCC
1 TATTCCTGTTTTGCCCTTCCCAGTCGGAA-GAGGTTGTTTTCAATGTTTTATTCC-GTTTTGCCC
* * * * * *
1971 TTCCCGGTCGGAAGGTGATGTTTTGAATGTTTTATTCCTGTCTTCAATATCTCATTCTCGTTTTG
64 TTCCCGGTC-AAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTCAATATTTCATTCCCGTTTTG
*
2036 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTGTTTTCAATGTTTTATTCCTGTT
128 CCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTCTTTTCAATGTTTTATTCCTGTT
*
2101 GTCAATGTTT
193 TTCAATGTTT
* **
2111 TATTCCTGTTTTGCCCTTCCCGGTCGGAAG-GTGTTGTTTTCAATGTTTTATTCCCGTTTT-CAA
1 TATTCCTGTTTTGCCCTTCCCAGTCGGAAGAG-GTTGTTTTCAATGTTTTATT-CCGTTTTGCCC
***** ** * * * **** * * * **
2174 TATTTTATTC--CCGTTTTGCCCTTCCAAGTCGGAAGAGGT--TGTTTTCAATGTTTTATTCCTT
64 T-TCCCGGTCAAAGGTGTTG--TTTTCAA-T-GTTTTA-TTCCTGTTTTCAATATTTCATTCCCG
* * * * *
2235 TTTTGCCCTTCCCGGTCGGAAGGTGATGTTTTCAATGTTTTATTCATGTTTTCAATATTTCATTC
123 TTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTCTTTTCAATGTTTTATTC
** **
2300 CTGTTTTGCCCT-TCC
188 CTGTTTT-CAATGTTT
*** ** * ** * **** **
2315 CGGTCGGAAGGTGTTG---TTTTCAAT-GTTTTATTCTTGTTTTCAATGTTTTATTCTCGTTTTG
1 TATTC---CTGTTTTGCCCTTCCCAGTCGGAAGA-GGTTGTTTTCAATGTTTTATTC-CGTTTTG
* **
2376 CCCTTCCCGG-CAGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTCAATATTTTATTCTTGTT
61 CCCTTCCCGGTCA-AAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTCAATATTTCATTCCCGTT
2440 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTCTTTTCAATGTTTTATTCCT
125 TTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTCTTTTCAATGTTTTATTCCT
*
2505 GTTTTCAATATTT
190 GTTTTCAATGTTT
* *
2518 TATTCCCGTTTTGCCCTTCCCGGTCGGAAGAGGTTGTTTTCAATGTTTTATTACCGTTTTGCCCT
1 TATTCCTGTTTTGCCCTTCCCAGTCGGAAGAGGTTGTTTTCAATGTTTTATT-CCGTTTTGCCCT
* * *
2583 TCCCGGTCGAAAGGTGTTGTTTTCAATGCTTTATTCATGTTTTCAATATTTCATTCCCGTTTTGG
65 TCCCGGTC-AAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTCAATATTTCATTCCCGTTTTGC
** * **
2648 CCTTCCTTGTCGGAGGGTGTTGTTTTCAATGTTTTATTCTTGC-TTTCAATGTTTTATTCCTACT
129 CCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTT-CTTTTCAATGTTTTATTCCTGTT
2712 TTCAATGTTT
193 TTCAATGTTT
* *
2722 TATTCTTGTTTTGCCCTTCCCCA-TCGGAAGGGGTTGTT
1 TATTCCTGTTTTGCCCTT-CCCAGTCGGAAGAGGTTGTT
2760 CCTATTCTCT
Statistics
Matches: 503, Mismatches: 114, Indels: 64
0.74 0.17 0.09
Matches are distributed among these distances:
200 5 0.01
201 5 0.01
202 5 0.01
203 143 0.28
204 321 0.64
205 13 0.03
206 6 0.01
207 5 0.01
ACGTcount: A:0.14, C:0.19, G:0.18, T:0.48
Consensus pattern (202 bp):
TATTCCTGTTTTGCCCTTCCCAGTCGGAAGAGGTTGTTTTCAATGTTTTATTCCGTTTTGCCCTT
CCCGGTCAAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTCAATATTTCATTCCCGTTTTGCCC
TTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCTTCTTTTCAATGTTTTATTCCTGTTTTC
AATGTTT
Found at i:2696 original size:20 final size:20
Alignment explanation
Indices: 2671--2729 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
2661 AGGGTGTTGT
2671 TTTCAATGTTTTATTCTTGC
1 TTTCAATGTTTTATTCTTGC
* *
2691 TTTCAATGTTTTATTCCTAC
1 TTTCAATGTTTTATTCTTGC
2711 TTTCAATGTTTTATTCTTG
1 TTTCAATGTTTTATTCTTG
2730 TTTTGCCCTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.59
Consensus pattern (20 bp):
TTTCAATGTTTTATTCTTGC
Found at i:3260 original size:15 final size:15
Alignment explanation
Indices: 3240--3277 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
3230 AATAAAATGG
3240 TTGCTTTGTGTTGTT
1 TTGCTTTGTGTTGTT
* *
3255 TTGCTTCGTTTTGTT
1 TTGCTTTGTGTTGTT
3270 TTG-TTTGT
1 TTGCTTTGT
3278 CTTGGTGTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 4 0.20
15 16 0.80
ACGTcount: A:0.00, C:0.08, G:0.24, T:0.68
Consensus pattern (15 bp):
TTGCTTTGTGTTGTT
Found at i:6445 original size:28 final size:29
Alignment explanation
Indices: 6407--6478 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 29
6397 GTCACTTAAG
6407 GGGGCATTTTGGTCATTCTGCATAAC-AA
1 GGGGCATTTTGGTCATTCTGCATAACTAA
* * * *
6435 GGGGCATTTTGCTCATTTTGCATATCTAG
1 GGGGCATTTTGGTCATTCTGCATAACTAA
6464 GGGGCATTTTGGTCA
1 GGGGCATTTTGGTCA
6479 CTTCAAGTGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 23 0.61
29 15 0.39
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.36
Consensus pattern (29 bp):
GGGGCATTTTGGTCATTCTGCATAACTAA
Found at i:6649 original size:41 final size:41
Alignment explanation
Indices: 6604--6689 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
6594 AGCATAGCTA
6604 CATTCAGTAGTTGCATTTTAATCTTTTATTTAAATCGATTT
1 CATTCAGTAGTTGCATTTTAATCTTTTATTTAAATCGATTT
*
6645 CATTCAGTAGTTGCATTTTAATCTTTTATTTAAATTGATTT
1 CATTCAGTAGTTGCATTTTAATCTTTTATTTAAATCGATTT
6686 CATT
1 CATT
6690 TTTTAATTCG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (41 bp):
CATTCAGTAGTTGCATTTTAATCTTTTATTTAAATCGATTT
Done.