Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003087.1 Hibiscus syriacus cultivar Beakdansim tig00006443_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: 85795
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:7962 original size:30 final size:31
Alignment explanation
Indices: 7923--8002 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
7913 GATTTTATTA
*
7923 ATATG-AATGTGTTCTATGTGAAAGTGCT-T
1 ATATGAAATGTGTTCTATGTGAAAATGCTCT
**
7952 -TATGTAAATGTGTTCTACATGAAAATGCTCT
1 ATATG-AAATGTGTTCTATGTGAAAATGCTCT
7983 ATATGAAA-GTGTTCTATGTG
1 ATATGAAATGTGTTCTATGTG
8003 GCTAAAAGAC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 4 0.10
30 30 0.71
31 4 0.10
32 4 0.10
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (31 bp):
ATATGAAATGTGTTCTATGTGAAAATGCTCT
Found at i:7998 original size:15 final size:15
Alignment explanation
Indices: 7923--7999 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
7913 GATTTTATTA
*
7923 ATATGAATGTGTTCT
1 ATATGAAAGTGTTCT
*
7938 ATGTGAAAGTG--CT
1 ATATGAAAGTGTTCT
*
7951 TTATGTAAATGTGTTCT
1 ATATG-AAA-GTGTTCT
* * *
7968 ACATGAAAATGCTCT
1 ATATGAAAGTGTTCT
7983 ATATGAAAGTGTTCT
1 ATATGAAAGTGTTCT
7998 AT
1 AT
8000 GTGGCTAAAA
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
13 5 0.11
14 3 0.06
15 31 0.66
16 3 0.06
17 5 0.11
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (15 bp):
ATATGAAAGTGTTCT
Found at i:8140 original size:23 final size:23
Alignment explanation
Indices: 8122--8193 Score: 74
Period size: 23 Copynumber: 3.1 Consensus size: 23
8112 GCGGTCTTTT
8122 GGAACAATTCTATGTGGTCATTC
1 GGAACAATTCTATGTGGTCATTC
* * *
8145 GGAACAAATTCTACGCGGTCCTTC
1 GGAAC-AATTCTATGTGGTCATTC
* *
8169 GGGACAAATCTATGTGG-CACTTC
1 GGAACAATTCTATGTGGTCA-TTC
8192 GG
1 GG
8194 TGCATATTCT
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 1 0.03
23 19 0.49
24 19 0.49
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (23 bp):
GGAACAATTCTATGTGGTCATTC
Found at i:8164 original size:24 final size:24
Alignment explanation
Indices: 8106--8177 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
8096 GAGTCGAGGG
* *
8106 TTCTACGCGGTCTTTTGGAAC-AA
1 TTCTACGCGGTCATTCGGAACAAA
* *
8129 TTCTATGTGGTCATTCGGAACAAA
1 TTCTACGCGGTCATTCGGAACAAA
* *
8153 TTCTACGCGGTCCTTCGGGACAAA
1 TTCTACGCGGTCATTCGGAACAAA
8177 T
1 T
8178 CTATGTGGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 17 0.43
24 23 0.57
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (24 bp):
TTCTACGCGGTCATTCGGAACAAA
Found at i:8181 original size:47 final size:47
Alignment explanation
Indices: 8106--8216 Score: 125
Period size: 47 Copynumber: 2.4 Consensus size: 47
8096 GAGTCGAGGG
* * *
8106 TTCTACGCGGTCTTTTGGAACAATTCTATGTGGTCA-TTCGGAACAAA
1 TTCTACGCGGTCCTTCGGAACAAATCTATGTGG-CACTTCGGAACAAA
* ** *
8153 TTCTACGCGGTCCTTCGGGACAAATCTATGTGGCACTTCGGTGCATA
1 TTCTACGCGGTCCTTCGGAACAAATCTATGTGGCACTTCGGAACAAA
* *
8200 TTCTACGTGGTACTTCG
1 TTCTACGCGGTCCTTCG
8217 TTGCAATTTA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 2 0.04
47 52 0.96
ACGTcount: A:0.21, C:0.23, G:0.23, T:0.33
Consensus pattern (47 bp):
TTCTACGCGGTCCTTCGGAACAAATCTATGTGGCACTTCGGAACAAA
Found at i:12842 original size:6 final size:6
Alignment explanation
Indices: 12831--12855 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12821 TAATTTTTTC
12831 ATAATT ATAATT ATAATT ATAATT A
1 ATAATT ATAATT ATAATT ATAATT A
12856 ATATAATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATAATT
Found at i:14182 original size:15 final size:15
Alignment explanation
Indices: 14162--14191 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
14152 GGAGCTTTTA
14162 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
*
14177 ATTTTAATCATTGAT
1 ATTTTAATAATTGAT
14192 TAAAAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Found at i:14794 original size:17 final size:19
Alignment explanation
Indices: 14743--14794 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
14733 CTGATATTTC
* *
14743 TAAATAAATAAATATCTTA
1 TAAATTAATAAATTTCTTA
*
14762 TTAAATTAATATATTTCTTA
1 -TAAATTAATAAATTTCTTA
14782 -AAATT-ATAAATTT
1 TAAATTAATAAATTT
14795 GAAATAACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
17 7 0.25
18 5 0.18
20 16 0.57
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATTAATAAATTTCTTA
Found at i:15302 original size:28 final size:26
Alignment explanation
Indices: 15260--15340 Score: 73
Period size: 28 Copynumber: 3.2 Consensus size: 26
15250 TAATTCTTTC
* *
15260 TTTTCAAAATGTTTATATATAATTATTA
1 TTTTCATAATATTTATATAT-A-TATTA
*
15288 TTTTCATAATATTTATATGTATATTA
1 TTTTCATAATATTTATATATATATTA
*
15314 TTTT-TTAATATTT-T-TAT-T-TTA
1 TTTTCATAATATTTATATATATATTA
15335 TTTTCA
1 TTTTCA
15341 AGTATTAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
21 7 0.15
22 1 0.02
23 2 0.04
24 1 0.02
25 8 0.17
26 9 0.20
27 1 0.02
28 17 0.37
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTCATAATATTTATATATATATTA
Found at i:15312 original size:26 final size:28
Alignment explanation
Indices: 15260--15326 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
15250 TAATTCTTTC
* *
15260 TTTTCAAAATGTTTATATATAATTATTA
1 TTTTCATAATATTTATATATAATTATTA
*
15288 TTTTCATAATATTTATATGT-A-TATTA
1 TTTTCATAATATTTATATATAATTATTA
*
15314 TTTT-TTAATATTT
1 TTTTCATAATATTT
15327 TTATTTTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.23
26 9 0.26
27 1 0.03
28 17 0.49
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (28 bp):
TTTTCATAATATTTATATATAATTATTA
Found at i:19973 original size:2 final size:2
Alignment explanation
Indices: 19966--20000 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19956 ATTTATCCTT
19966 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20001 CCTTTGTTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20316 original size:9 final size:9
Alignment explanation
Indices: 20302--20333 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
20292 GCAAAGAAAG
20302 AAAAAAGAA
1 AAAAAAGAA
20311 AAAAAA-AA
1 AAAAAAGAA
20319 AAAAAAGAA
1 AAAAAAGAA
20328 AAAAAA
1 AAAAAA
20334 CACAAAGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:20323 original size:16 final size:16
Alignment explanation
Indices: 20302--20348 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
20292 GCAAAGAAAG
20302 AAAAAAGAAAAAAAAAA
1 AAAAAAG-AAAAAAAAA
*
20319 AAAAAAGAAAAAAAAC
1 AAAAAAGAAAAAAAAA
* *
20335 ACAAAGGAAAAAAA
1 AAAAAAGAAAAAAA
20349 GGAAAATTGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 20 0.74
17 7 0.26
ACGTcount: A:0.87, C:0.04, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAGAAAAAAAAA
Found at i:25140 original size:22 final size:22
Alignment explanation
Indices: 25114--25190 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
25104 ATCTACACTC
25114 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
25136 TTCAAAGATGATTGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
25158 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
25180 TTCAAAGATGA
1 TTCAAAGATGA
25191 AAGCTTTATG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:26020 original size:165 final size:167
Alignment explanation
Indices: 25701--26025 Score: 548
Period size: 165 Copynumber: 2.0 Consensus size: 167
25691 AAAATGAGCA
*
25701 TTATCTTGAGATTGGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACG
1 TTATCTTGAGATTGGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACA
**
25766 ATTTCCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTC
66 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTC
25831 CTTAGTTTTTTTACTTAGTAAACTATTTCCAACAACT
131 CTTAGTTTTTTTACTTAGTAAACTATTTCCAACAACT
* **
25868 TTATCTTGAGATT-GGGGCATGTTACCCAATCAACGTGTTATTT-TGAAAAATAATGAGAAAACA
1 TTATCTTGAGATTGGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACA
*
25931 ATTTCCATAGTTTCTCATTCAATCTTTTTTAAAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
66 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAGAAAATGATTT
*
25996 CCTTTG-TTTTTTACTTAGTAAACTATTTCC
130 CCTTAGTTTTTTTACTTAGTAAACTATTTCC
26026 CACATCTGTA
Statistics
Matches: 149, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
165 68 0.46
166 68 0.46
167 13 0.09
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (167 bp):
TTATCTTGAGATTGGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAGAAAACA
ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAATGATTTC
CTTAGTTTTTTTACTTAGTAAACTATTTCCAACAACT
Found at i:26154 original size:76 final size:76
Alignment explanation
Indices: 26028--26755 Score: 1208
Period size: 76 Copynumber: 9.6 Consensus size: 76
26018 CTATTTCCCA
*
26028 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26093 AGCCTTAGGGT
66 AGCCTTAGGGT
* * * *
26104 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAACGCCTTCAGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26169 AGCCTTAGGGT
66 AGCCTTAGGGT
*
26180 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26245 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
26256 CATCTGTAAGTCCTACGGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26321 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
26332 CATGTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26397 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
26408 CATCTGTAATTTCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26473 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
26484 CATCTGTAAGTCCTACATTGCATAATGTTTCCAAAAAGCCTTCGGG-GTTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26548 AGCCTTAGGGT
66 AGCCTTAGGGT
*
26559 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
26624 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
26635 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTATGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* **
26700 AACCTTCTGGT
66 AGCCTTAGGGT
* * * *
26711 TATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
26756 TCATCTGTAA
Statistics
Matches: 612, Mismatches: 39, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
75 78 0.13
76 534 0.87
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:26763 original size:46 final size:46
Alignment explanation
Indices: 26687--26791 Score: 176
Period size: 46 Copynumber: 2.3 Consensus size: 46
26677 CAGGAGCTTT
* * *
26687 ATGATGTTTTC-AAAACCTTCTGGTTATCTGTAAGCCCTTCAGTGC
1 ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGC
26732 ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGC
1 ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGC
26778 ATGATGTTTTCAAA
1 ATGATGTTTTCAAA
26792 CATTTCCATC
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
45 11 0.20
46 45 0.80
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (46 bp):
ATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAATGC
Found at i:26921 original size:3 final size:3
Alignment explanation
Indices: 26915--26981 Score: 71
Period size: 3 Copynumber: 21.0 Consensus size: 3
26905 TTTTTTTAGT
* * *
26915 TTA TTA TTA TTA TTA TTA TATA ATA TCA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
26961 TATA TATA TATA TTA TTA TTA
1 T-TA T-TA T-TA TTA TTA TTA
26982 AACAAAATAT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 43 0.77
4 13 0.23
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:26956 original size:28 final size:30
Alignment explanation
Indices: 26915--26982 Score: 104
Period size: 28 Copynumber: 2.3 Consensus size: 30
26905 TTTTTTTAGT
*
26915 TTATTATTATTATTATTATATA-ATAT-CA
1 TTATTATTAATATTATTATATATATATACA
*
26943 TTATTATTAATATTATTATATATATATATA
1 TTATTATTAATATTATTATATATATATACA
26973 TTATTATTAA
1 TTATTATTAA
26983 ACAAAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 21 0.58
29 4 0.11
30 11 0.31
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
TTATTATTAATATTATTATATATATATACA
Found at i:28283 original size:2 final size:2
Alignment explanation
Indices: 28276--28300 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28266 TTTTATAAAT
28276 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
28301 TAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28352 original size:140 final size:145
Alignment explanation
Indices: 28178--28572 Score: 465
Period size: 140 Copynumber: 2.8 Consensus size: 145
28168 GATAATAATG
*
28178 TTTATTTATTTTTAAATATTAAGAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTTCTGATAT
1 TTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTTCTGATAT
* *
28243 TTTTAATTAAATAAACATCTTATTTTTATAAATTATATATATATATATA-TA-TA-TA-TATT-A
66 TTTTAAATAAATAAATATCTTATTTTTATAAATTATATATATATATATATTATTATTATTATTAA
* *
28303 AATAT-TTTATTATTA
131 AAAATGTTT-TAATTA
*
28318 TTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAAAACAACTGGATGTCCATTTTCTGATAT
1 TTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTTCTGATAT
* * *
28383 TTTTAAATAAATAAATATCCTATTTTTA-AAATTATATAT-TA-ATCTATTATTATTATTTTTAC
66 TTTTAAATAAATAAATATCTTATTTTTATAAATTATATATATATATATATTATTATTATTATTA-
28445 AAAAATGTTTTAATTA
130 AAAAATGTTTTAATTA
* * * * * * *
28461 TTTATTTATTTTTTTATATCAAAGAAAAGAGCTA-TCTTAAGGCACCTAGAAGT-CATTTTCTGA
1 TTTATTTATTTTTTAATAT-TAAG-AAAGGGC-AGTCTTAAAGCAACTGGATGTCCATTTTCTGA
* * ** *
28524 TATTTCTAAATAAATAAATAT-TT-TATTTATATTTTATATATAAATATAT
63 TATTTTTAAATAAATAAATATCTTATTTTTATAAATTATATATATATATAT
28573 TTTTTATATA
Statistics
Matches: 218, Mismatches: 24, Indels: 21
0.83 0.09 0.08
Matches are distributed among these distances:
137 4 0.02
138 4 0.02
139 13 0.06
140 90 0.41
141 3 0.01
142 5 0.02
143 38 0.17
144 37 0.17
145 23 0.11
146 1 0.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.47
Consensus pattern (145 bp):
TTTATTTATTTTTTAATATTAAGAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTTCTGATAT
TTTTAAATAAATAAATATCTTATTTTTATAAATTATATATATATATATATTATTATTATTATTAA
AAAATGTTTTAATTA
Found at i:28573 original size:17 final size:17
Alignment explanation
Indices: 28551--28588 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
28541 ATATTTTATT
28551 TATATTTTATATATAAA
1 TATATTTTATATATAAA
* *
28568 TATATTTTTTATATAAT
1 TATATTTTATATATAAA
28585 TATA
1 TATA
28589 ACTTTGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TATATTTTATATATAAA
Found at i:30175 original size:74 final size:74
Alignment explanation
Indices: 29866--30151 Score: 518
Period size: 74 Copynumber: 3.9 Consensus size: 74
29856 ATAACCTAAT
*
29866 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGTTAGTTGAATGAGCATTATCA
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATCA
29931 TTATCAAAA
66 TTATCAAAA
*
29940 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATACTAGTTGAATGAGCATTATCA
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATCA
30005 TTATCAAAA
66 TTATCAAAA
*
30014 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATGATCA
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATCA
*
30079 TTATCAACA
66 TTATCAAAA
* *
30088 TTGAGAATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGAATTATC
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATC
30152 CAATACTTAA
Statistics
Matches: 204, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 204 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (74 bp):
TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATCA
TTATCAAAA
Found at i:35542 original size:26 final size:26
Alignment explanation
Indices: 35510--35569 Score: 120
Period size: 26 Copynumber: 2.3 Consensus size: 26
35500 ATTATCAAAA
35510 TTGAGCATTATCAAGAAATGACAATT
1 TTGAGCATTATCAAGAAATGACAATT
35536 TTGAGCATTATCAAGAAATGACAATT
1 TTGAGCATTATCAAGAAATGACAATT
35562 TTGAGCAT
1 TTGAGCAT
35570 ATTTACAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (26 bp):
TTGAGCATTATCAAGAAATGACAATT
Found at i:35619 original size:74 final size:74
Alignment explanation
Indices: 35536--35746 Score: 359
Period size: 74 Copynumber: 2.9 Consensus size: 74
35526 AATGACAATT
35536 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAA
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAA
35601 TTATCAAAA
66 TTATCAAAA
* * *
35610 TTGTGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATGATCA
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAA
*
35675 TTATCAACA
66 TTATCAAAA
* * *
35684 TTGAGAATTATCAATAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATTAGCATTAT
1 TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTAT
35747 TGAATACTTA
Statistics
Matches: 128, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
74 128 1.00
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.35
Consensus pattern (74 bp):
TTGAGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAA
TTATCAAAA
Found at i:35768 original size:74 final size:72
Alignment explanation
Indices: 35539--35771 Score: 308
Period size: 74 Copynumber: 3.2 Consensus size: 72
35529 GACAATTTTG
35539 AGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAATTA
1 AGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAA-TA
*
35604 TCAAAATTGT
65 -CTAAATT-T
* *
35614 -GCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATGATCATTA
1 AGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTAT-AATA
*
35678 -TCAACATTG
65 CT-AA-ATTT
* * *
35687 AGAATTATCAATAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATTAGCATTATTGAAT
1 AGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTA-T-AAT
*
35752 ACTTAATTT
64 ACTAAATTT
35761 AGCATTATCAA
1 AGCATTATCAA
35772 CACTATCTTG
Statistics
Matches: 139, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
73 2 0.01
74 130 0.94
75 6 0.04
76 1 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (72 bp):
AGCATTATCAAGAAATGACAATTTTGAGCATATTTACAATGCTAGTTGAATGAGCATTATAATAC
TAAATTT
Found at i:38751 original size:59 final size:59
Alignment explanation
Indices: 38657--38769 Score: 154
Period size: 59 Copynumber: 1.9 Consensus size: 59
38647 ACTGTCCACT
* *
38657 GGAGATGTTTATCCCTCGAGTGAGGCGACACTGATTCGAAATGTAATGAATCGAGCAAA
1 GGAGATGTTGATCCCTCAAGTGAGGCGACACTGATTCGAAATGTAATGAATCGAGCAAA
* * ** **
38716 GGAGATGTTGATCCCTCAAGTGAGGTGTCGTTGATTCGAAATGTTGTGAATCGA
1 GGAGATGTTGATCCCTCAAGTGAGGCGACACTGATTCGAAATGTAATGAATCGA
38770 TCCAAGGTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.27
Consensus pattern (59 bp):
GGAGATGTTGATCCCTCAAGTGAGGCGACACTGATTCGAAATGTAATGAATCGAGCAAA
Found at i:38871 original size:59 final size:59
Alignment explanation
Indices: 38810--39128 Score: 381
Period size: 59 Copynumber: 5.4 Consensus size: 59
38800 TCTCTACTGG
** * *
38810 AAATGTTGGTCCCTCATGTGAGGCGTTGCTGATTCGAAGTGTTATGAATCGAGCAAAGG
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTATGAATCGAGCAAAGA
* * * * * *
38869 AAATGTTGATCCCTCAAGTGAGGCGTTGCTAATTCAAAGTGTTGTGAATCGAGAAAATA
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTATGAATCGAGCAAAGA
* * * * * *
38928 AAATGTTGATCCCTCAAGTGAGGCATTGTTGATTCGAAGTATTTTGAATCGAGCACAGA
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTATGAATCGAGCAAAGA
* * * * *
38987 AAATGTTAATCCATCAAGTGACGCGTTGCTGATTCGAAGTATTTTGAATCGAGCATAGA
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTATGAATCGAGCAAAGA
* * * *
39046 AAATGTTAATCCCTCAAGTGAGGAGTTGATGATTTGAAATGTTGA-GAATCGAGCAAATG-
1 AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTT-ATGAATCGAGCAAA-GA
39105 AAATGTTAATCCCTCAAGTGAGGC
1 AAATGTTAATCCCTCAAGTGAGGC
39129 TTAGTTTTTT
Statistics
Matches: 225, Mismatches: 33, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
59 224 1.00
60 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (59 bp):
AAATGTTAATCCCTCAAGTGAGGCGTTGCTGATTCGAAGTGTTATGAATCGAGCAAAGA
Found at i:39242 original size:36 final size:36
Alignment explanation
Indices: 39138--40110 Score: 443
Period size: 38 Copynumber: 26.1 Consensus size: 36
39128 CTTAGTTTTT
*
39138 TTTAAGAAAAATAATCTCAAGTGAGATAAATCTTCTG
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * *
39175 TTTCGAGTGAAACTATCTCAAGCGAGATAAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* *
39211 CTTTAAGAAAAACAATCTCAAGTGCGCTAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
** *
39249 TTTCAAGTGAAACTAA-CTCAAGCGAGATAAAAATCTTCTG
1 TTT-AAGAAAAAC-AATCTCAAGTGAGAT--AAATCTTC-G
* ** * *
39289 TTTCGAGTGAAACTATCTCAAGAT-AGATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAG-TGAGATAAATCTTCG
*
39325 TTTTAAGAAAAACAATCTCAAGTTAGATAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * *
39363 TTTCGAGTGAAACTACCTCAAGCGAGATAAAATCTTCTG
1 TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTC-G
** * * * **
39402 TTCGAGTAAAACTATCTCAAGCGAGACGAATC-TCG
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
39437 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * *
39475 TTTCGAGTTAAACTATCTCAAATGAGATAAAATCTTCTG
1 TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTC-G
* ** * *
39514 TTTCGAGTGAAACTATCTCAAGTGAGATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
39550 TTTTAAGAAAAA-AATCTCAAGTGAGATAAATCTTCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
** * * ** * *
39587 TTTCAAGTGAAACTATCTTAAACGAGATGAATC-TAG
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
*
39623 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTC
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * * * *
39661 TTTCGAGTGAAACTATCTTAAGCGCGATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* *
39697 TTTTAAGAAAATCAATCTCAAGTGAGATAAATCTATTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCT-TCG
* ** * * * *
39735 TTTCGAGTGAAACTATCTCAAGCGATATGAATCTT-G
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* * *
39771 CTTTAAGAAAAACAATTTTAAGTGAGATAAATCATCTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * * * **
39809 TTTCGAGTGAGACTATCTCAAGCGAGATGAATCTTAT
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCG
* * *
39846 TTTAAGACAAACAATATCAAGTGAGATAAATCATCTG
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTC-G
* ** * * *
39883 TTTTGAGTGAAACTATCTCAAGCGAGATGAATCTT-G
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
** *
39919 TTTTAAGAAAAACAATCTTGAGTGAAATGAAATGTCTT-G
1 -TTTAAGAAAAACAATCTCAAGTGAGAT-AAA--TCTTCG
* * * *
39958 TTTCGAGTAAAAATC-GTCTCAAGTTAGACAAAGT-TT-G
1 TTT-AAG-AAAAA-CAATCTCAAGTGAGATAAA-TCTTCG
* * *
39995 TTTTAAGAAAAA-AATCTCAATTTAGATAAATCTTTTG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATC-TTCG
* ** *
40032 TTTCGAGTGAAACTATCTCAAGCT-AGATAAATCTT-G
1 TTT-AAGAAAAACAATCTCAAG-TGAGATAAATCTTCG
* *
40068 TTTTAAGAAAAAGAATCTCAAGTTAGATAAATCTTCG
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
40105 TATTAA
1 T-TTAA
40111 ATTAGATTAT
Statistics
Matches: 705, Mismatches: 173, Indels: 116
0.71 0.17 0.12
Matches are distributed among these distances:
34 1 0.00
35 37 0.05
36 231 0.33
37 82 0.12
38 246 0.35
39 62 0.09
40 45 0.06
41 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (36 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCG
Found at i:39242 original size:74 final size:74
Alignment explanation
Indices: 39138--39589 Score: 364
Period size: 74 Copynumber: 6.0 Consensus size: 74
39128 CTTAGTTTTT
* *
39138 TTTAAGAAAAATAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT
1 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGAT
39203 AAATCTT-G
66 AAATCTTCG
* * * * *
39211 CTTTAAGAAAAACAATCTCAAGTGCGCTAAATCTTCTGTTTCAAGTGAAACTAACTCAAGCGAGA
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGA
39276 TAAAAATCTTCTG
65 T--AAATCTTC-G
* ** * * ** * * **
39289 TTTCGAGTGAAACTATCTCAAGAT-AGATGAATC-T-TGTTTTAAGAAAAACAATCTCAAGTTAG
1 TTT-AAGAAAAACAATCTCAAG-TGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAG
39351 ATAAATCTTCTG
64 ATAAATCTTC-G
* ** * * *
39363 TTTCGAGTGAAACTACCTCAAGCGAGATAAAATCTTCTG-TTCGAGTAAAACTATCTCAAGCGAG
1 TTT-AAGAAAAACAATCTCAAGTGAGAT-AAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAG
**
39427 ACGAATC-TCG
64 ATAAATCTTCG
* **
39437 TTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTTAAACTATCTCAAATGAGA
1 -TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGA
39502 TAAAATCTTCTG
65 T-AAATCTTC-G
* ** * * ** ** *
39514 TTTCGAGTGAAACTATCTCAAGTGAGATGAATC-T-TGTTTTAAG-AAAAAAATCTCAAGTGAGA
1 TTT-AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGA
39576 TAAATCTTCTG
65 TAAATCTTC-G
39587 TTT
1 TTT
39590 CAAGTGAAAC
Statistics
Matches: 310, Mismatches: 52, Indels: 33
0.78 0.13 0.08
Matches are distributed among these distances:
73 23 0.07
74 153 0.49
75 20 0.06
76 61 0.20
77 31 0.10
78 21 0.07
79 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (74 bp):
TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTAAAACTATCTCAAGCGAGAT
AAATCTTCG
Found at i:39465 original size:112 final size:112
Alignment explanation
Indices: 39151--40066 Score: 827
Period size: 112 Copynumber: 8.2 Consensus size: 112
39141 AAGAAAAATA
* * *
39151 ATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATAAATCTTGCTTTA
1 ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
* *
39216 AGAAAAACAATCTCAAGTGCGCTAAATCTTCTGTTTCAAGTGAAACT
66 AGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* **
39263 AACTCAAGCGAGATAAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGATAGATGAATCTTGTTT
1 ATCTCAAGCGAGAT--AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTT
* *
39328 TAAGAAAAACAATCTCAAGTTAGATAAATCTTCTGTTTCGAGTGAAACT
64 TAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* * * *
39377 ACCTCAAGCGAGATAAAATCTTCTG-TTCGAGTAAAACTATCTCAAGCGAGACGAATCTCGTTTT
1 ATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
* *
39441 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTTAAACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
** *
39489 ATCTCAAATGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGTGAGATGAATCTTGTTTT
1 ATCTCAAGCGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
39554 AAGAAAAA-AATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* * * * ** ** * * * *
39601 ATCTTAAACGAGATGAATC-T-AGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTCTTT
1 ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGT-TTT
* ** * * * * * * * *
39664 CGAGTGAAACTATCTTAAGCGCGATGAATC-T-TGTTTTAAG-AAAATCA
65 -AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAA-CT
* * *
39711 ATCTCAAGTGAGATAAATCTAT-TGTTTCGAGTGAAACTATCTCAAGCGATATGAATCTTGCTTT
1 ATCTCAAGCGAGATAAATCT-TCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTT
* * * * *
39775 AAGAAAAACAATTTTAAGTGAGATAAATCATCTGTTTCGAGTGAGACT
65 AAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
* * * ** * * * *
39823 ATCTCAAGCGAGATGAATCTTAT-TTT-AAGACAAACAATATCAAGTGAGATAAATCATCTGTTT
1 ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTT
* ** * * * * ** *
39886 TGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTTTAAGAAAAACA
64 TAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
** * * * * * * ** **
39933 ATCTTGAGTGAAATGAAAT-GTCTTGTTTCGAGTAAAAATCGTCTCAAGTTAGACAAAGT-TTGT
1 ATCTCAAGCGAGAT-AAATCTTC-TGTTTCGAGTGAAACT-ATCTCAAGCGAGATGAA-TCTTGT
* * * *
39996 TTTAAGAAAAA-AATCTCAATTTAGATAAATCTTTTGTTTCGAGTGAAACT
62 TTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
*
40046 ATCTCAAGCTAGATAAATCTT
1 ATCTCAAGCGAGATAAATCTT
40067 GTTTTAAGAA
Statistics
Matches: 643, Mismatches: 137, Indels: 47
0.78 0.17 0.06
Matches are distributed among these distances:
109 34 0.05
110 91 0.14
111 39 0.06
112 279 0.43
113 83 0.13
114 116 0.18
115 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.32
Consensus pattern (112 bp):
ATCTCAAGCGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
AGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACT
Found at i:39652 original size:74 final size:74
Alignment explanation
Indices: 39265--40103 Score: 936
Period size: 74 Copynumber: 11.3 Consensus size: 74
39255 GTGAAACTAA
* **
39265 CTCAAGCGAGATAAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGATAGATGAATCTTGTTTTA
1 CTCAAGTGAGAT--AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTA
39330 AGAAAAACAAT
64 AGAAAAACAAT
* * * * **
39341 CTCAAGTTAGATAAATCTTCTGTTTCGAGTGAAACTACCTCAAGCGAGATAAAATCTTCTGTTCG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGAT-GAATCTTGT-TTTA
* *
39406 AGTAAAACTAT
64 AGAAAAACAAT
* ** ** ** * * * **
39417 CTCAAGCGAGACGAATC-TC-GTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATC-T-TGTTTTA
** *
39480 AGTTAAACTAT
64 AGAAAAACAAT
* *
39491 CTCAAATGAGATAAAATCTTCTGTTTCGAGTGAAACTATCTCAAGTGAGATGAATCTTGTTTTAA
1 CTCAAGTGAGAT-AAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
39556 GAAAAA-AAT
65 GAAAAACAAT
* * * *
39565 CTCAAGTGAGATAAATCTTCTGTTTCAAGTGAAACTATCTTAAACGAGATGAATCTAGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
39630 AAAAACAAT
66 AAAAACAAT
* * *
39639 CTCAAGTGAGATAAATCTTCTCTTTCGAGTGAAACTATCTTAAGCGCGATGAATCTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
*
39704 AAAATCAAT
66 AAAAACAAT
* *
39713 CTCAAGTGAGATAAATCTAT-TGTTTCGAGTGAAACTATCTCAAGCGATATGAATCTTGCTTTAA
1 CTCAAGTGAGATAAATCT-TCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAA
39777 GAAAAACAAT
65 GAAAAACAAT
* * * * *
39787 TTTAAGTGAGATAAATCATCTGTTTCGAGTGAGACTATCTCAAGCGAGATGAATCTTATTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
*
39852 ACAAACAAT
66 AAAAACAAT
* * *
39861 ATCAAGTGAGATAAATCATCTGTTTTGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
39926 AAAAACAAT
66 AAAAACAAT
** * * * * * ** **
39935 CTTGAGTGAAATGAAAT-GTCTTGTTTCGAGTAAAAATCGTCTCAAGTTAGACAAAGT-TTGTTT
1 CTCAAGTGAGAT-AAATCTTC-TGTTTCGAGTGAAACT-ATCTCAAGCGAGATGAA-TCTTGTTT
39998 TAAGAAAAA-AAT
62 TAAGAAAAACAAT
* * * * *
40010 CTCAATTTAGATAAATCTTTTGTTTCGAGTGAAACTATCTCAAGCTAGATAAATCTTGTTTTAAG
1 CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
*
40075 AAAAAGAAT
66 AAAAACAAT
*
40084 CTCAAGTTAGATAAATCTTC
1 CTCAAGTGAGATAAATCTTC
40104 GTATTAAATT
Statistics
Matches: 648, Mismatches: 98, Indels: 36
0.83 0.13 0.05
Matches are distributed among these distances:
72 1 0.00
73 88 0.14
74 412 0.64
75 54 0.08
76 64 0.10
77 29 0.04
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (74 bp):
CTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCGAGATGAATCTTGTTTTAAG
AAAAACAAT
Found at i:42945 original size:24 final size:26
Alignment explanation
Indices: 42895--42945 Score: 79
Period size: 24 Copynumber: 2.0 Consensus size: 26
42885 GCAAGATCAG
42895 ACAAAAAGAAATCAATGTTAGTAGAA
1 ACAAAAAGAAATCAATGTTAGTAGAA
*
42921 ACAAAAAG-AATCAA-GTTAGTTGAA
1 ACAAAAAGAAATCAATGTTAGTAGAA
42945 A
1 A
42946 TGATTAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 10 0.42
25 6 0.25
26 8 0.33
ACGTcount: A:0.57, C:0.08, G:0.16, T:0.20
Consensus pattern (26 bp):
ACAAAAAGAAATCAATGTTAGTAGAA
Found at i:43857 original size:18 final size:19
Alignment explanation
Indices: 43822--43867 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
43812 AATAAATAAA
*
43822 AAAAAGAAAAACACAACAT
1 AAAAATAAAAACACAACAT
*
43841 AAAAATAAAAATA-AACAT
1 AAAAATAAAAACACAACAT
*
43859 AAACATAAA
1 AAAAATAAA
43868 TACAATGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 13 0.54
19 11 0.46
ACGTcount: A:0.76, C:0.11, G:0.02, T:0.11
Consensus pattern (19 bp):
AAAAATAAAAACACAACAT
Found at i:45357 original size:26 final size:26
Alignment explanation
Indices: 45319--45398 Score: 133
Period size: 26 Copynumber: 3.1 Consensus size: 26
45309 AAATATGAGG
*
45319 TCTCTAGATTCTCCTTGCTTCTTTCT
1 TCTCTATATTCTCCTTGCTTCTTTCT
* *
45345 TTTCTATATTCTCCTTGTTTCTTTCT
1 TCTCTATATTCTCCTTGCTTCTTTCT
45371 TCTCTATATTCTCCTTGCTTCTTTCT
1 TCTCTATATTCTCCTTGCTTCTTTCT
45397 TC
1 TC
45399 CCCCCAAGCT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 49 1.00
ACGTcount: A:0.07, C:0.29, G:0.05, T:0.59
Consensus pattern (26 bp):
TCTCTATATTCTCCTTGCTTCTTTCT
Found at i:46400 original size:13 final size:13
Alignment explanation
Indices: 46382--46406 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46372 AATTATTATA
46382 ATTATATTTTTAG
1 ATTATATTTTTAG
46395 ATTATATTTTTA
1 ATTATATTTTTA
46407 ATGATTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATTATATTTTTAG
Found at i:52913 original size:2 final size:2
Alignment explanation
Indices: 52906--52934 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52896 TTATAATCAT
52906 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52935 TTAAGAACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:53660 original size:45 final size:44
Alignment explanation
Indices: 53611--53768 Score: 244
Period size: 45 Copynumber: 3.5 Consensus size: 44
53601 GCTAAGAATA
53611 CACCCATATGCATTATTATTTTGGCATACTTTCATGCCGGTAATG
1 CACCCATATGCATTATTATTTTGGCAT-CTTTCATGCCGGTAATG
*
53656 CACCCATATGCATTATTATTTTGGCATCCTTTCATGTCGGTAATG
1 CACCCATATGCATTATTATTTTGGCAT-CTTTCATGCCGGTAATG
* * *
53701 CACCCATATGCATTATTATTTTGGCATCATTTCATACTGATAATG
1 CACCCATATGCATTATTATTTTGGCATC-TTTCATGCCGGTAATG
*
53746 CACCCATATCCATTATTATTTTG
1 CACCCATATGCATTATTATTTTG
53769 TTCATTCATT
Statistics
Matches: 105, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
44 1 0.01
45 104 0.99
ACGTcount: A:0.25, C:0.22, G:0.13, T:0.40
Consensus pattern (44 bp):
CACCCATATGCATTATTATTTTGGCATCTTTCATGCCGGTAATG
Found at i:54214 original size:22 final size:22
Alignment explanation
Indices: 54171--54244 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
54161 CTGGCTCTTC
*
54171 GGTATCGATAC--CCCTACCAT
1 GGTATCGATACTACCCTACTAT
54191 GGTATCGATACTACCCTACTAT
1 GGTATCGATACTACCCTACTAT
**
54213 GGTA-C--TGA-TACCCTGTTAT
1 GGTATCGAT-ACTACCCTACTAT
54232 GGTATCGATACTA
1 GGTATCGATACTA
54245 TTTTTGCATT
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
19 14 0.32
20 13 0.30
21 2 0.05
22 15 0.34
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.31
Consensus pattern (22 bp):
GGTATCGATACTACCCTACTAT
Found at i:54338 original size:20 final size:20
Alignment explanation
Indices: 54267--54337 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
54257 ATTTTGAAAT
54267 GGTATCGATACCTTCCCCTA
1 GGTATCGATACCTTCCCCTA
54287 GGTATCGATACCTTCCCCTA
1 GGTATCGATACCTTCCCCTA
* *
54307 GGTATCGATA-CTCCCCCTTC
1 GGTATCGATACCTTCCCC-TA
54327 GGTATCGATAC
1 GGTATCGATAC
54338 TGATTAAATC
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
19 6 0.13
20 41 0.87
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.30
Consensus pattern (20 bp):
GGTATCGATACCTTCCCCTA
Found at i:56026 original size:181 final size:180
Alignment explanation
Indices: 55723--56057 Score: 589
Period size: 181 Copynumber: 1.9 Consensus size: 180
55713 TTGGAGTCAT
* * * *
55723 CAACAGATGTATACGGCCTATAAATCCAACTGATCCCTAGTGCTTTCACATGTTAGTATTCCTAA
1 CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCTAA
* *
55788 AAAGAACAACGCCTTTGATTGAGAATTTTATGATGATTTGAAAACTGTGTTATCTTTCACATTCC
66 AAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTCC
*
55853 CTCTGGAAAGATCAATTATGATTTATCACTTTAGAGGACTTACATTATCA
131 CTCTGAAAAGATCAATTATGATTTATCACTTTAGAGGACTTACATTATCA
55903 CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCTTA
1 CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCC-TA
*
55968 AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTG
65 AAAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTC
56033 CCTCTGAAAAGATCAATTATGATTT
130 CCTCTGAAAAGATCAATTATGATTT
56058 CTCATAGGAG
Statistics
Matches: 146, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
180 58 0.40
181 88 0.60
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (180 bp):
CAACAGATATATACCGCCTATAAATCCAACTGATCCCGAGTACTTTCACATGTTAGTATTCCTAA
AAAGAACAACGCCTTTGATTGAGAATTTTAGGATAATTTGAAAACTGTGTTATCTTTCACATTCC
CTCTGAAAAGATCAATTATGATTTATCACTTTAGAGGACTTACATTATCA
Found at i:67281 original size:14 final size:15
Alignment explanation
Indices: 67262--67290 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
67252 TAGCACATGT
67262 GTTCATC-TTTTTAG
1 GTTCATCATTTTTAG
67276 GTTCATCATTTTTAG
1 GTTCATCATTTTTAG
67291 AAGATTTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
GTTCATCATTTTTAG
Found at i:68740 original size:60 final size:60
Alignment explanation
Indices: 68646--68815 Score: 202
Period size: 60 Copynumber: 2.8 Consensus size: 60
68636 AGTTTGAGAG
* *
68646 GAAATTTAAATATTCAAAAAGTTT-GGGA-TCAATTTAGAATGAAGGTCATAGTTTGGGGAT
1 GAAATTGAAATATTC-AAAAGTTTAGGGACT-AATTTAGAATGAAGGTCATAGTTTAGGGAT
* *
68706 GAAATTGAAATATTCAAAAGTTTAAGGACTAATTTAGAATCATA-GTCATAGTTTAGGGAT
1 GAAATTGAAATATTCAAAAGTTTAGGGACTAATTTAGAATGA-AGGTCATAGTTTAGGGAT
* * * * * *
68766 GAAATTGGAATATTTAAAAGTTTAGGGACCAATTGAAAATGAGGGTCATA
1 GAAATTGAAATATTCAAAAGTTTAGGGACTAATTTAGAATGAAGGTCATA
68816 TTGTGAGTAC
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 8 0.09
60 84 0.89
61 2 0.02
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.32
Consensus pattern (60 bp):
GAAATTGAAATATTCAAAAGTTTAGGGACTAATTTAGAATGAAGGTCATAGTTTAGGGAT
Found at i:68789 original size:29 final size:29
Alignment explanation
Indices: 68695--68793 Score: 83
Period size: 29 Copynumber: 3.3 Consensus size: 29
68685 TGAAGGTCAT
* * *
68695 AGTTTGGGGATGAAATTGAAATATTCAAA
1 AGTTTAGGGATGAAATTGGAATATTTAAA
* * * * * *
68724 AGTTTAAGGACT-AATTTAGAATCATAGTCAT
1 AGTTTAGGGA-TGAAATTGGAAT-AT-TTAAA
68755 AGTTTAGGGATGAAATTGGAATATTTAAA
1 AGTTTAGGGATGAAATTGGAATATTTAAA
68784 AGTTTAGGGA
1 AGTTTAGGGA
68794 CCAATTGAAA
Statistics
Matches: 51, Mismatches: 15, Indels: 8
0.69 0.20 0.11
Matches are distributed among these distances:
29 27 0.53
30 6 0.12
31 18 0.35
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.33
Consensus pattern (29 bp):
AGTTTAGGGATGAAATTGGAATATTTAAA
Found at i:69137 original size:13 final size:13
Alignment explanation
Indices: 69119--69143 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
69109 TTTTACAATT
69119 ATAAATAATTTTA
1 ATAAATAATTTTA
69132 ATAAATAATTTT
1 ATAAATAATTTT
69144 TTCAGAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATAAATAATTTTA
Found at i:74144 original size:2 final size:2
Alignment explanation
Indices: 74137--74167 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
74127 TTTATGTGAT
74137 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
74168 TACCATTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:79717 original size:15 final size:15
Alignment explanation
Indices: 79697--79727 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
79687 GATTGTATGC
79697 TAAATTGAGCAAATG
1 TAAATTGAGCAAATG
79712 TAAATTGAGCAAATG
1 TAAATTGAGCAAATG
79727 T
1 T
79728 CTCTGAGATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.19, T:0.29
Consensus pattern (15 bp):
TAAATTGAGCAAATG
Found at i:82627 original size:22 final size:22
Alignment explanation
Indices: 82601--82662 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
82591 TTGACCGAAC
82601 CAAACCATTGACTTTGACAGGT
1 CAAACCATTGACTTTGACAGGT
*
82623 CAAACCGTTGACTTTGACAGGT
1 CAAACCATTGACTTTGACAGGT
**
82645 CTGACCATTGACTTTGAC
1 CAAACCATTGACTTTGAC
82663 TAAAAAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (22 bp):
CAAACCATTGACTTTGACAGGT
Done.