Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006760.1 Corchorus capsularis cultivar CVL-1 contig06781, 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: 55282
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:70 original size:15 final size:15
Alignment explanation
Indices: 50--101 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
40 CAAGAGACAC
50 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATGG
* *
65 TTTTCAAGAAAA-CG
1 TTTTCAAAAAAATGG
79 TTTTC--AAAAATGAG
1 TTTTCAAAAAAATG-G
93 TTTTCAAAA
1 TTTTCAAAA
102 GGTTTAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.14
14 12 0.41
15 11 0.38
16 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (15 bp):
TTTTCAAAAAAATGG
Found at i:83 original size:14 final size:15
Alignment explanation
Indices: 50--88 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
40 CAAGAGACAC
*
50 TTTTCAAAAAAATGG
1 TTTTCAAAAAAATCG
*
65 TTTTCAAGAAAA-CG
1 TTTTCAAAAAAATCG
79 TTTTCAAAAA
1 TTTTCAAAAA
89 TGAGTTTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (15 bp):
TTTTCAAAAAAATCG
Found at i:416 original size:12 final size:12
Alignment explanation
Indices: 401--435 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
391 CATCAAATAA
401 TTCAAATCAAAG
1 TTCAAATCAAAG
413 TTCAAATCAAAG
1 TTCAAATCAAAG
425 TTCAAATCAAA
1 TTCAAATCAAA
436 AGTGAATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (12 bp):
TTCAAATCAAAG
Found at i:2168 original size:36 final size:36
Alignment explanation
Indices: 2123--2328 Score: 151
Period size: 36 Copynumber: 5.5 Consensus size: 36
2113 TATCAAAGTT
* * *
2123 GACTAGAAACAGGTCGTCTTTCAGCACTTATCTTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCTTTC
*
2159 GACTGGAAACAGGTCATCTTTCAGGAATTATCTTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCTTTC
* * * * **
2195 GGCTGGAAACAGGTCATTTTTTTTTCAACAGTTATCAAGATC
1 GACTGGAAACAGGTCA----TCTTTCAGCAATTATC--TTTC
* * * * **
2237 GACTGGAAACAGGTCGTTTTTTCAACAGTTATCAAGATC
1 GACTGGAAACAGGTC-ATCTTTCAGCAATTATC--TTTC
* *
2276 GATTGGAAACGGGTCATCTTTCAGCAATTATCTTTC
1 GACTGGAAACAGGTCATCTTTCAGCAATTATCTTTC
* *
2312 GGCTGGAAACATGTCAT
1 GACTGGAAACAGGTCAT
2329 TTTTTTTCAA
Statistics
Matches: 138, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
36 62 0.45
38 13 0.09
39 35 0.25
40 12 0.09
42 16 0.12
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (36 bp):
GACTGGAAACAGGTCATCTTTCAGCAATTATCTTTC
Found at i:2268 original size:39 final size:39
Alignment explanation
Indices: 2214--2400 Score: 209
Period size: 39 Copynumber: 4.8 Consensus size: 39
2204 CAGGTCATTT
2214 TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCG
1 TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCG
* *
2253 TTTTTTCAACAGTTATCAAGATCGATTGGAAACGGGTC-
1 TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCG
* * * * ** * * *
2291 ATCTTTCAGCAATTATC--TTTCGGCTGGAAACATGTCATT
1 TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTC--G
*
2330 TTTTTTCAACAGTTATCAAGATCGACCGGAAACAGGTCG
1 TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCG
* *
2369 TTTTTTCAACAATTATCAAGATCGATTGGAAA
1 TTTTTTCAACAGTTATCAAGATCGACTGGAAA
2401 TGGGTCATCT
Statistics
Matches: 118, Mismatches: 25, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
36 13 0.11
38 13 0.11
39 78 0.66
41 14 0.12
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (39 bp):
TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCG
Found at i:2388 original size:116 final size:117
Alignment explanation
Indices: 2157--2417 Score: 452
Period size: 116 Copynumber: 2.2 Consensus size: 117
2147 CACTTATCTT
* * *
2157 TCGACTGGAAACAGGTCATCTTTCAGGAATTATCTTTCGGCTGGAAACAGGTCATTTTTTTTTCA
1 TCGATTGGAAACGGGTCATCTTTCAGCAATTATCTTTCGGCTGGAAACAGGTCATTTTTTTTTCA
* *
2222 ACAGTTATCAAGATCGACTGGAAACAGGTCGTTTTTTCAACAGTTATCAAGA
66 ACAGTTATCAAGATCGACCGGAAACAGGTCGTTTTTTCAACAATTATCAAGA
*
2274 TCGATTGGAAACGGGTCATCTTTCAGCAATTATCTTTCGGCTGGAAACATGTCA-TTTTTTTTCA
1 TCGATTGGAAACGGGTCATCTTTCAGCAATTATCTTTCGGCTGGAAACAGGTCATTTTTTTTTCA
2338 ACAGTTATCAAGATCGACCGGAAACAGGTCGTTTTTTCAACAATTATCAAGA
66 ACAGTTATCAAGATCGACCGGAAACAGGTCGTTTTTTCAACAATTATCAAGA
*
2390 TCGATTGGAAATGGGTCATCTTTCAGCA
1 TCGATTGGAAACGGGTCATCTTTCAGCA
2418 GTTTTCGGTT
Statistics
Matches: 137, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
116 87 0.64
117 50 0.36
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (117 bp):
TCGATTGGAAACGGGTCATCTTTCAGCAATTATCTTTCGGCTGGAAACAGGTCATTTTTTTTTCA
ACAGTTATCAAGATCGACCGGAAACAGGTCGTTTTTTCAACAATTATCAAGA
Found at i:2414 original size:77 final size:76
Alignment explanation
Indices: 2214--2420 Score: 202
Period size: 77 Copynumber: 2.7 Consensus size: 76
2204 CAGGTCATTT
* * *
2214 TTTTTTCAACAGTTATCAAGATCGACTGGAAACAGGTCGTTTTTTCAACAGTTATCAAGATCGAT
1 TTTTTTCAACAATTATCAAGATCGACTGGAAACAGGTC-ATTTTTCAACAGTTATCAAGATCGAC
* *
2279 TGGAAACGGGTC
65 CGGAAACAGGTC
* * * ** * *
2291 ATCTTTCAGCAATTATC--TTTCGGCTGGAAACATGTCATTTTTTTTCAACAGTTATCAAGATCG
1 TTTTTTCAACAATTATCAAGATCGACTGGAAACAGGTCA---TTTTTCAACAGTTATCAAGATCG
2354 ACCGGAAACAGGTC
63 ACCGGAAACAGGTC
* ** * *
2368 GTTTTTTCAACAATTATCAAGATCGATTGGAAATGGGTCATCTTTCAGCAGTT
1 -TTTTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATTTTTCAACAGTT
2421 TTCGGTTGCT
Statistics
Matches: 100, Mismatches: 24, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
75 15 0.15
77 58 0.58
78 14 0.14
80 13 0.13
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (76 bp):
TTTTTTCAACAATTATCAAGATCGACTGGAAACAGGTCATTTTTCAACAGTTATCAAGATCGACC
GGAAACAGGTC
Found at i:2501 original size:43 final size:43
Alignment explanation
Indices: 2416--2626 Score: 231
Period size: 43 Copynumber: 5.1 Consensus size: 43
2406 CATCTTTCAG
*
2416 CAGTTTTCGGTTGCTCCC-AAGGGGGGCATTCCAACAAATTTT
1 CAGTTTTCGGTTGCTCCCAAAGGGGGGCATTCCAACAACTTTT
* *
2458 CAGTCTTCGGTTACTCCCAAAGGGGGGCATCTCC-ACAACTTTT
1 CAGTTTTCGGTTGCTCCCAAAGGGGGGCAT-TCCAACAACTTTT
* * * *
2501 CAGTTTTCAGTTGCACCCAAAAGGAGGCATTCCAACAACTTTT
1 CAGTTTTCGGTTGCTCCCAAAGGGGGGCATTCCAACAACTTTT
* ** **
2544 CAGTTTTCAGCAGC-CCCAAA--GGGGCATTCCAGTAACTTTT
1 CAGTTTTCGGTTGCTCCCAAAGGGGGGCATTCCAACAACTTTT
* *
2584 CAGTTTTCAGTTGCT-CC-AA-GGAGGCATTCCAACAACTTTT
1 CAGTTTTCGGTTGCTCCCAAAGGGGGGCATTCCAACAACTTTT
2624 CAG
1 CAG
2627 CATTACAACA
Statistics
Matches: 145, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
39 2 0.01
40 51 0.35
42 25 0.17
43 64 0.44
44 3 0.02
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.29
Consensus pattern (43 bp):
CAGTTTTCGGTTGCTCCCAAAGGGGGGCATTCCAACAACTTTT
Found at i:2635 original size:19 final size:19
Alignment explanation
Indices: 2607--2645 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2597 CTCCAAGGAG
*
2607 GCATTCCAACAACTTTTCA
1 GCATTACAACAACTTTTCA
2626 GCATTACAACAACTTTTCA
1 GCATTACAACAACTTTTCA
2645 G
1 G
2646 TTTTCAGCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (19 bp):
GCATTACAACAACTTTTCA
Found at i:2725 original size:99 final size:96
Alignment explanation
Indices: 2527--2711 Score: 214
Period size: 99 Copynumber: 1.9 Consensus size: 96
2517 CCAAAAGGAG
* **
2527 GCATTCCAACAACTTTTCAGTTTTCAGCAGCCCCAAAGGGGCATTCCAGTAACTTTTCAGTTTTC
1 GCATTACAACAACTTTTCAGTTTTCAGCAG--CCAAAGGGGCATTCCAACAACTTTTCAGTTTTC
* *
2592 AGTTGCTCCAAGGAGGCATTCCAACAACTTTTCA
64 AGATGCTCCAACGAGGCATT-CAACAACTTTTCA
*
2626 GCATTACAACAACTTTTCAGTTTTCAGCAG-CAAGAGGGG-GTATCTCAACAACTTTAT-AGTTT
1 GCATTACAACAACTTTTCAGTTTTCAGCAGCCAA-AGGGGCAT-TC-CAACAACTTT-TCAGTTT
2688 TCAGATGCTCACAACGAGGACATT
62 TCAGATGCTC-CAACGAGG-CATT
2712 ATAGAAGTTT
Statistics
Matches: 74, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
96 4 0.05
97 7 0.09
98 22 0.30
99 37 0.50
100 4 0.05
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (96 bp):
GCATTACAACAACTTTTCAGTTTTCAGCAGCCAAAGGGGCATTCCAACAACTTTTCAGTTTTCAG
ATGCTCCAACGAGGCATTCAACAACTTTTCA
Found at i:6204 original size:64 final size:64
Alignment explanation
Indices: 6079--6292 Score: 297
Period size: 64 Copynumber: 3.3 Consensus size: 64
6069 TAATCAAAGA
* *
6079 TGATCGGAAGATGATCTTGTCAAGAAGTACACACCAGAAGATGGTTTATTAAGAGTTTTCAGAAG
1 TGATCGGAAGACGATCTTGTCAAGAAGT--ACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAG
6144 T
64 T
6145 TGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGT
1 TGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGT
* * * * * *
6209 TGATCAGAAGACGATCTTGTCAAGAAGTAC-CAAGAAGATAG-TTACTCAAAAAGGTTTCGGAAG
1 TGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTA-TC-AAGAGTTTTCAGAAG
6272 T
64 T
*
6273 TGGTCGGAAGACGATCTTGT
1 TGATCGGAAGACGATCTTGT
6293 TAAAAGATGA
Statistics
Matches: 136, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
62 3 0.02
63 11 0.08
64 95 0.70
66 27 0.20
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.27
Consensus pattern (64 bp):
TGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTATCAAGAGTTTTCAGAAGT
Found at i:6847 original size:165 final size:167
Alignment explanation
Indices: 6569--7042 Score: 584
Period size: 169 Copynumber: 2.8 Consensus size: 167
6559 ATCCCTTTTA
* * *
6569 GAATGGATCTGAAGACAAATCACGAAAGATTTTGAATGATGGGTCGAAGGCGATCCTTTTAAGTA
1 GAATGAATCTGAAGACAAATCACGAAAGATTTTGAACGATGGATCGAAGGCGATCCTTTTAAGTA
*
6634 TGAGTCTTAAGACAGCTCATGGACGAATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATC
66 TGAGTCTTAAGACAGCTCATGGATGAATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATC
*
6699 GAAGACGATC-TT-GTATGAGTATGAAGACAGCTCAT
131 GAAGACGATCTTTAGTATGAGTATAAAGACAGCTCAT
* *
6734 GAATGAATCTGAAGACAGATCACGAAAGATTTTGAACGATGGATCGAAGGCGGTCCTTTTAAGTA
1 GAATGAATCTGAAGACAAATCACGAAAGATTTTGAACGATGGATCGAAGGCGATCCTTTTAAGTA
6799 TGAGTCTTAAGACAGCTCATGGATGAATCTGAAGACAGATCACGAAAGATTTTGAA-GTAT-GAT
66 TGAGTCTTAAGACAGCTCATGGATGAATCTGAAGACAGATCACGAAAGATTTTGAATG-ATGGAT
**** *
6862 CGTCTTCGATCCTTTTAAGTATGAGTCTAAAGACAGCTCAT
130 CGAAGACGAT-C-TTT-AGTATGAGTATAAAGACAGCTCAT
* * * * * * * * *
6903 GGATGAATTTGAAGACAAATCAATG-AAGATTTCGGAGGATGGATCGAAGACGATCATTTTGA-T
1 GAATGAATCTGAAGACAAATC-ACGAAAGATTTTGAACGATGGATCGAAGGCGATCCTTTTAAGT
* * * * **
6966 ATTGAGTCTAAAAACAGCTCA-CGAGTGAATCTGAAGACAGATCATGAAAGAAATTGAATGATGG
65 A-TGAGTCTTAAGACAGCTCATGGA-TGAATCTGAAGACAGATCACGAAAGATTTTGAATGATGG
*
7030 ATCAAAGACGATC
128 ATCGAAGACGATC
7043 CTTTTGGAGA
Statistics
Matches: 264, Mismatches: 34, Indels: 18
0.84 0.11 0.06
Matches are distributed among these distances:
164 10 0.04
165 118 0.45
167 2 0.01
168 4 0.02
169 119 0.45
170 11 0.04
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (167 bp):
GAATGAATCTGAAGACAAATCACGAAAGATTTTGAACGATGGATCGAAGGCGATCCTTTTAAGTA
TGAGTCTTAAGACAGCTCATGGATGAATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATC
GAAGACGATCTTTAGTATGAGTATAAAGACAGCTCAT
Found at i:7048 original size:85 final size:85
Alignment explanation
Indices: 6575--7047 Score: 570
Period size: 85 Copynumber: 5.6 Consensus size: 85
6565 TTTAGAATGG
* * *
6575 ATCTGAAGACAAATCACGAAAGATTTTGAATGATGGGTCGAAGGCGATCCTTTTAAGTATGAGTC
1 ATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGTC
* *
6640 TTAAGACAGCTCATGGACGA
66 TAAAGACAGCTCATGGATGA
*
6660 ATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATCGAAGACGAT-C--TT--GTATGAGTA
1 ATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGTC
* *
6720 TGAAGACAGCTCATGAATGA
66 TAAAGACAGCTCATGGATGA
* * *
6740 ATCTGAAGACAGATCACGAAAGATTTTGAACGATGGATCGAAGGCGGTCCTTTTAAGTATGAGTC
1 ATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGTC
*
6805 TTAAGACAGCTCATGGATGA
66 TAAAGACAGCTCATGGATGA
****
6825 ATCTGAAGACAGATCACGAAAGATTTTGAA-GTAT-GATCGTCTTCGATCCTTTTAAGTATGAGT
1 ATCTGAAGACAGATCACGAAAGATTTTGAATG-ATGGATCGAAGACGATCCTTTTAAGTATGAGT
6888 CTAAAGACAGCTCATGGATGA
65 CTAAAGACAGCTCATGGATGA
* * * * * * * *
6909 ATTTGAAGACAAATCAATG-AAGATTTCGGAGGATGGATCGAAGACGATCATTTTGA-TATTGAG
1 ATCTGAAGACAGATC-ACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTA-TGAG
* *
6972 TCTAAAAACAGCTCA-CGAGTGA
64 TCTAAAGACAGCTCATGGA-TGA
* ** *
6994 ATCTGAAGACAGATCATGAAAGAAATTGAATGATGGATCAAAGACGATCCTTTT
1 ATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTT
7048 GGAGAGTGAA
Statistics
Matches: 335, Mismatches: 41, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
80 70 0.21
81 1 0.00
82 2 0.01
83 2 0.01
84 77 0.23
85 183 0.55
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (85 bp):
ATCTGAAGACAGATCACGAAAGATTTTGAATGATGGATCGAAGACGATCCTTTTAAGTATGAGTC
TAAAGACAGCTCATGGATGA
Found at i:7152 original size:57 final size:60
Alignment explanation
Indices: 7073--7215 Score: 166
Period size: 60 Copynumber: 2.4 Consensus size: 60
7063 AGACAGTTCA
* ** *
7073 CACAGATGGATTTGAAGACAGTTCCT-AAAGAT-T-TTATGATTGAGACTAAAGACAACT
1 CACAGATGGATCTGAAGACAGTTCCTAAAAGATATATTAAAAATGAGACTAAAGACAACT
* * * * *
7130 CACAGATGGATCTGAAGGCAGTTCTTAAAAGATATATTAAAAATGAGGCTGAAGACAGCT
1 CACAGATGGATCTGAAGACAGTTCCTAAAAGATATATTAAAAATGAGACTAAAGACAACT
* *
7190 CACACATGGATCTGAAGACAGCTCCT
1 CACAGATGGATCTGAAGACAGTTCCT
7216 GAATGACATT
Statistics
Matches: 70, Mismatches: 13, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
57 23 0.33
58 6 0.09
59 1 0.01
60 40 0.57
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (60 bp):
CACAGATGGATCTGAAGACAGTTCCTAAAAGATATATTAAAAATGAGACTAAAGACAACT
Found at i:7242 original size:60 final size:58
Alignment explanation
Indices: 7044--7247 Score: 153
Period size: 60 Copynumber: 3.4 Consensus size: 58
7034 AAGACGATCC
* * *
7044 TTTTGGAGAGTGAATCTGAAGACAGTTCACACAGATGGATTTGAAGACAGTTCCTAA-AGA
1 TTTT-GAGAGTGAATCTGAAGACAGCTCACAC--ATGGATCTGAAGACAGTTCCTAAGACA
* * * * * * *
7104 TTTT-ATGATTGAGA-CTAAAGACAACTCACAGATGGATCTGAAGGCAGTTCTTAAAAGATA
1 TTTTGA-GAGTGA-ATCTGAAGACAGCTCACACATGGATCTGAAGACAGTTCCT--AAGACA
* * * * ** *
7164 TATTAAAAATGAGGCTGAAGACAGCTCACACATGGATCTGAAGACAGCTCCTGAATGACA
1 TTTTGAGAGTGAATCTGAAGACAGCTCACACATGGATCTGAAGACAGTTCCT-AA-GACA
7224 TTTTGAGAGTGAATCTGAAGACAG
1 TTTTGAGAGTGAATCTGAAGACAG
7248 TTCAAGGAGA
Statistics
Matches: 109, Mismatches: 27, Indels: 16
0.72 0.18 0.11
Matches are distributed among these distances:
57 18 0.17
58 1 0.01
59 22 0.20
60 67 0.61
61 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.25
Consensus pattern (58 bp):
TTTTGAGAGTGAATCTGAAGACAGCTCACACATGGATCTGAAGACAGTTCCTAAGACA
Found at i:7395 original size:156 final size:158
Alignment explanation
Indices: 7143--7434 Score: 383
Period size: 156 Copynumber: 1.9 Consensus size: 158
7133 AGATGGATCT
* * * * *
7143 GAAGGCAGTTCTTAAAAGATATATTAAAAATGAGGCTGAAGACAGCTCACACATGGATCTGAAGA
1 GAAGACAGTTCCTAAAAGATATATGAAAAATGAGACTGAAGACAGCTCACAAATGGATCTGAAGA
* * * * ** *
7208 CAGCTCCTGAATGACATTTTGAGAGTGAATCTGAAGACAGTTCAAGGAGATGGGTTCTGAAGACA
66 CAGCTCCTAAAAGACATTTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCTGAAGACA
*
7273 GTTCCTTAAGGTATTCAAGAGTGAGGTA
131 GATCCTTAAGGTATTCAAGAGTGAGGTA
* * *
7301 GAAGACAGTTCCTAAAAGAT-T-TGAAAATTGAGACTGAAGACAGCTCACAAATGGGTTTTGAAG
1 GAAGACAGTTCCTAAAAGATATATGAAAAATGAGACTGAAGACAGCTCACAAAT-GGATCTGAAG
* **
7364 ACAGTTCCTAAAAGGTA-TTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCTGAAGAC
65 ACAGCTCCTAAAAGACATTTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCTGAAGAC
7428 AGATCCT
130 AGATCCT
7435 AAAAAGTATT
Statistics
Matches: 114, Mismatches: 19, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
156 75 0.66
157 21 0.18
158 18 0.16
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.25
Consensus pattern (158 bp):
GAAGACAGTTCCTAAAAGATATATGAAAAATGAGACTGAAGACAGCTCACAAATGGATCTGAAGA
CAGCTCCTAAAAGACATTTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCTGAAGACA
GATCCTTAAGGTATTCAAGAGTGAGGTA
Found at i:7429 original size:62 final size:60
Alignment explanation
Indices: 7301--7684 Score: 304
Period size: 62 Copynumber: 6.5 Consensus size: 60
7291 GAGTGAGGTA
* * * * *
7301 GAAGACAGTTCCTAAAA-G-ATTTGAAAATTGAGA-CTGAAGACAGCTCACAAATGGGTTTT
1 GAAGACAGTTCCTAAAAGGTATTT-AAGAGTGA-ATATGAAGACAGCTCAAAAATGGGTTCT
* * *
7360 GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCT
1 GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATATGAAGACAGCTC--AAAAATGGGTTCT
* * * * *
7422 GAAGACAGATCCTAAAAAGTATTT---AG-GAGTATGAAGACAGCTCAAAGAT-CGTTCT
1 GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATATGAAGACAGCTCAAAAATGGGTTCT
* * * * *
7477 GAAGACAGTTCCTAATAGAT-TTTAAGAATGAGTATGAAGACAGCTCACAAATGGGTTCT
1 GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATATGAAGACAGCTCAAAAATGGGTTCT
* * * * * * ** * *
7536 AAAGACAGATGCTAAAAAAGTATTTAGGAGTGAATCTGAAGACAATTCACGGAGATGGGTTCT
1 GAAGACAGTTCCT-AAAAGGTATTTAAGAGTGAATATGAAGACAGCTCA--AAAATGGGTTCT
* * * * * *
7599 GAAGACAGTTCCTCAATGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGAT-AGTTCT
1 GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATATGAAGACAGCTCAAAAATGGGTTCT
* *
7658 GAAGACAGTTCCTGAAAGAT-TTTAAGA
1 GAAGACAGTTCCTAAAAGGTATTTAAGA
7685 AAGAGGCTGA
Statistics
Matches: 258, Mismatches: 53, Indels: 29
0.76 0.16 0.09
Matches are distributed among these distances:
54 3 0.01
55 21 0.08
56 5 0.02
57 1 0.00
58 41 0.16
59 57 0.22
60 26 0.10
61 25 0.10
62 59 0.23
63 20 0.08
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (60 bp):
GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATATGAAGACAGCTCAAAAATGGGTTCT
Found at i:7511 original size:58 final size:59
Alignment explanation
Indices: 7301--7742 Score: 311
Period size: 58 Copynumber: 7.5 Consensus size: 59
7291 GAGTGAGGTA
* *
7301 GAAGACAGTTCCTAAAAGAT-TTGAA-AATTGAG-ACTGAAGACAGCTCACAA-ATGGGTTTT
1 GAAGACAGTTCCT-AAAGATATTTAAGAA-TGAGTA-TGAAGACAGCTCA-AAGATGGGTTCT
* * * * * * *
7360 GAAGACAGTTCCTAAAAGGTATTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCT
1 GAAGACAGTTCCT-AAAGATATTTAAGAATGAGTATGAAGACAGCTC--AAAGATGGGTTCT
* * *
7422 GAAGACAGATCCTAAAAAGTATTT-AG---GAGTATGAAGACAGCTCAAAGAT-CGTTCT
1 GAAGACAGTTCCTAAAGA-TATTTAAGAATGAGTATGAAGACAGCTCAAAGATGGGTTCT
7477 GAAGACAGTTCCTAATAGAT-TTTAAGAATGAGTATGAAGACAGCTCACAA-ATGGGTTCT
1 GAAGACAGTTCCTAA-AGATATTTAAGAATGAGTATGAAGACAGCTCA-AAGATGGGTTCT
* * * * * * * * ** *
7536 AAAGACAGATGCTAAAAAAGTATTTAGGAGTGAATCTGAAGACAATTCACGGAGATGGGTTCT
1 GAAGACAGTTCCT-AAAGA-TATTTAAGAATGAGTATGAAGACAGCTCA--AAGATGGGTTCT
* * *
7599 GAAGACAGTTCCTCAATGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGAT-AGTTCT
1 GAAGACAGTTCCT-AAAGATATTTAAGAATGAGTATGAAGACAGCTCAAAGATGGGTTCT
* ** * * * *
7658 GAAGACAGTTCCTGAAAGAT-TTTAAGAAAGAGGCTGAAGGCAGCTCACAGAT-GGATAT
1 GAAGACAGTTCCT-AAAGATATTTAAGAATGAGTATGAAGACAGCTCAAAGATGGGTTCT
* *
7716 GAAGACAGTTACTGAAAGCT-TTTAAGA
1 GAAGACAGTTCCT-AAAGATATTTAAGA
7743 TTTAGACTGA
Statistics
Matches: 304, Mismatches: 60, Indels: 39
0.75 0.15 0.10
Matches are distributed among these distances:
54 3 0.01
55 22 0.07
56 7 0.02
58 88 0.29
59 60 0.20
60 24 0.08
61 29 0.10
62 50 0.16
63 21 0.07
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (59 bp):
GAAGACAGTTCCTAAAGATATTTAAGAATGAGTATGAAGACAGCTCAAAGATGGGTTCT
Found at i:7670 original size:181 final size:174
Alignment explanation
Indices: 7301--7711 Score: 509
Period size: 181 Copynumber: 2.3 Consensus size: 174
7291 GAGTGAGGTA
* * *
7301 GAAGACAGTTCCTAAAAGATTTGAA-AATTGAGACTGAAGACAGCTCACAAATGGGTTTTGAAGA
1 GAAGACAGTTCCT-AAAGATTTTAAGAA-TGAGA-TGAAGACAGCTCACAAATGGGTTCTAAAGA
* * *
7365 CAGTTCCTAAAAGGTATTTAAGAGTGAATCTAAAGACAGTTCAAAAAAATGGGTTCTGAAGACAG
63 CAGATCCTAAAAAGTATTTAAGAGTGAATCTAAAGACAATTCAAAAAAATGGGTTCTGAAGACAG
*
7430 ATCCTAAAAAGTATTTAGGAGTATGAAGACAGCTCAAAGATCGTTCT
128 ATCCTAAAAAGTATTTAGGAGTATGAAGACAGCTCAAAGATAGTTCT
7477 GAAGACAGTTCCTAATAGATTTTAAGAATGAGTATGAAGACAGCTCACAAATGGGTTCTAAAGAC
1 GAAGACAGTTCCTAA-AGATTTTAAGAATGAG-ATGAAGACAGCTCACAAATGGGTTCTAAAGAC
* * * *** *
7542 AGATGCTAAAAAAGTATTTAGGAGTGAATCTGAAGACAATTCACGGAGATGGGTTCTGAAGACAG
64 AGATCCT-AAAAAGTATTTAAGAGTGAATCTAAAGACAATTCAAAAAAATGGGTTCTGAAGACAG
* * **
7607 TTCCTCAATGGTATTTAAGAATGAGTATGAAGACAGCTCAAAGATAGTTCT
128 ATCCTAAAAAGTATTT-AG---GAGTATGAAGACAGCTCAAAGATAGTTCT
* * * *
7658 GAAGACAGTTCCTGAAAGATTTTAAGAAAGAGGCTGAAGGCAGCTCACAGATGG
1 GAAGACAGTTCCT-AAAGATTTTAAGAATGA-GATGAAGACAGCTCACAAATGG
7712 ATATGAAGAC
Statistics
Matches: 203, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
175 2 0.01
176 59 0.29
177 64 0.32
178 2 0.01
181 73 0.36
182 3 0.01
ACGTcount: A:0.39, C:0.13, G:0.23, T:0.25
Consensus pattern (174 bp):
GAAGACAGTTCCTAAAGATTTTAAGAATGAGATGAAGACAGCTCACAAATGGGTTCTAAAGACAG
ATCCTAAAAAGTATTTAAGAGTGAATCTAAAGACAATTCAAAAAAATGGGTTCTGAAGACAGATC
CTAAAAAGTATTTAGGAGTATGAAGACAGCTCAAAGATAGTTCT
Found at i:7753 original size:58 final size:58
Alignment explanation
Indices: 7620--7756 Score: 150
Period size: 58 Copynumber: 2.4 Consensus size: 58
7610 CTCAATGGTA
* * * *
7620 TTTAAGAATGAGTA-TGAAGACAGCTCAAAGATAGTTCTGAAGACAGTTCCTGAAAGAT
1 TTTAAGAAAGAG-ACTGAAGACAGCTCAAAGATAGATATGAAGACAGTTACTGAAAGAT
* * * * *
7678 TTTAAGAAAGAGGCTGAAGGCAGCTCACAGATGGATATGAAGACAGTTACTGAAAGCT
1 TTTAAGAAAGAGACTGAAGACAGCTCAAAGATAGATATGAAGACAGTTACTGAAAGAT
***
7736 TTTAAGATTTAGACTGAAGAC
1 TTTAAGAAAGAGACTGAAGAC
7757 GGTCATCTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (58 bp):
TTTAAGAAAGAGACTGAAGACAGCTCAAAGATAGATATGAAGACAGTTACTGAAAGAT
Found at i:18037 original size:15 final size:15
Alignment explanation
Indices: 18017--18046 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
18007 ATCGGTTGAA
18017 ATATTGTGTATCGTG
1 ATATTGTGTATCGTG
18032 ATATTGTGTATCGTG
1 ATATTGTGTATCGTG
18047 GCAGCCTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.07, G:0.27, T:0.47
Consensus pattern (15 bp):
ATATTGTGTATCGTG
Found at i:22325 original size:22 final size:22
Alignment explanation
Indices: 22297--22339 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
22287 CGGCCACCGG
22297 CCGCCGACCGGTGAGCCTCCGA
1 CCGCCGACCGGTGAGCCTCCGA
22319 CCGCCGACCGGTGAGCCTCCG
1 CCGCCGACCGGTGAGCCTCCG
22340 GCCACCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.12, C:0.47, G:0.33, T:0.09
Consensus pattern (22 bp):
CCGCCGACCGGTGAGCCTCCGA
Found at i:23497 original size:15 final size:15
Alignment explanation
Indices: 23477--23506 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
23467 GATCGGTTGA
23477 AATATTGTGTATCGT
1 AATATTGTGTATCGT
23492 AATATTGTGTATCGT
1 AATATTGTGTATCGT
23507 GGTAGCCTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
AATATTGTGTATCGT
Found at i:30077 original size:2 final size:2
Alignment explanation
Indices: 30072--30125 Score: 56
Period size: 2 Copynumber: 27.5 Consensus size: 2
30062 GTTCATTGAC
* * * * *
30072 TA TA TA AA TA TA AA TA TA -A TA TA CA TG CA 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
30113 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
30126 GTATTAATTC
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
TA
Found at i:35198 original size:6 final size:6
Alignment explanation
Indices: 35187--35219 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
35177 TTAATTCTGC
*
35187 TTTAGA TTTAGA TTTAGA TTTAAA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
35220 GCTTGCTTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:38597 original size:10 final size:10
Alignment explanation
Indices: 38582--38633 Score: 50
Period size: 10 Copynumber: 4.8 Consensus size: 10
38572 TCGACACCAA
*
38582 GCCATGTCCG
1 GCCATGCCCG
38592 GCCATGTCCGCG
1 GCCATG-CC-CG
*
38604 CACCATGCCCG
1 -GCCATGCCCG
38615 GCCATGCCCG
1 GCCATGCCCG
38625 GCCAATGCC
1 GCC-ATGCC
38634 ATGCCATCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
10 18 0.51
11 8 0.23
12 4 0.11
13 5 0.14
ACGTcount: A:0.13, C:0.46, G:0.27, T:0.13
Consensus pattern (10 bp):
GCCATGCCCG
Found at i:39262 original size:12 final size:12
Alignment explanation
Indices: 39247--39280 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
39237 AATTTTTTCG
39247 AAAATTTTGACA
1 AAAATTTTGACA
*
39259 AAAAGTTTGACA
1 AAAATTTTGACA
39271 AAAATTTTGA
1 AAAATTTTGA
39281 TTTTATATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (12 bp):
AAAATTTTGACA
Found at i:44212 original size:58 final size:58
Alignment explanation
Indices: 44136--44382 Score: 422
Period size: 58 Copynumber: 4.2 Consensus size: 58
44126 ATACTTCCTC
*
44136 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTACTGT
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
* * *
44194 TTACTACTTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGG
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
* *
44252 TTACTTCCTTTTACTTCTTGATTAACTTAATTACTCTTAATTAAGCTAATTACTAATGT
1 TTAC-TCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
*
44311 TGACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
44369 TTACTCCTTTTACT
1 TTACTCCTTTTACT
44383 GACTTCTCCT
Statistics
Matches: 175, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
58 123 0.70
59 52 0.30
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (58 bp):
TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
Found at i:44275 original size:117 final size:116
Alignment explanation
Indices: 44136--44382 Score: 422
Period size: 117 Copynumber: 2.1 Consensus size: 116
44126 ATACTTCCTC
* *
44136 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTACTGTTTACTAC
1 TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTAATGTTGACTAC
*
44201 TTTTACTTCTTGATTAACTTAATTGCTCTGAATTAAGCTAATTACTACTGG
66 TTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGG
* * *
44252 TTACTTCCTTTTACTTCTTGATTAACTTAATTACTCTTAATTAAGCTAATTACTAATGTTGACTC
1 TTAC-TCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTAATGTTGACTA
*
44317 CTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGT
65 CTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGG
44369 TTACTCCTTTTACT
1 TTACTCCTTTTACT
44383 GACTTCTCCT
Statistics
Matches: 123, Mismatches: 7, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
116 14 0.11
117 109 0.89
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (116 bp):
TTACTCCTTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAACTACTAATGTTGACTAC
TTTTACTTCTTGATTAACTTAATTACTCTGAATTAAGCTAATTACTACTGG
Found at i:44391 original size:16 final size:16
Alignment explanation
Indices: 44372--44427 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
44362 CTACTGTTTA
44372 CTCCTTTTACTGACTT
1 CTCCTTTTACTGACTT
44388 CTCC-TTT-CT-A---
1 CTCCTTTTACTGACTT
*
44398 CTGCTTTTACTGACTT
1 CTCCTTTTACTGACTT
44414 CTCCTTTCTACTGA
1 CTCCTTT-TACTGA
44428 TTACTTCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 13
0.67 0.04 0.28
Matches are distributed among these distances:
10 3 0.10
11 3 0.10
12 2 0.06
13 2 0.06
14 2 0.06
15 3 0.10
16 10 0.32
17 6 0.19
ACGTcount: A:0.12, C:0.32, G:0.07, T:0.48
Consensus pattern (16 bp):
CTCCTTTTACTGACTT
Found at i:44406 original size:26 final size:26
Alignment explanation
Indices: 44370--44426 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
44360 TACTACTGTT
*
44370 TACTCCTTTTACTGACTTCTCCTTTC
1 TACTGCTTTTACTGACTTCTCCTTTC
44396 TACTGCTTTTACTGACTTCTCCTTTC
1 TACTGCTTTTACTGACTTCTCCTTTC
44422 TACTG
1 TACTG
44427 ATTACTTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.12, C:0.32, G:0.07, T:0.49
Consensus pattern (26 bp):
TACTGCTTTTACTGACTTCTCCTTTC
Found at i:44517 original size:15 final size:14
Alignment explanation
Indices: 44477--44633 Score: 51
Period size: 16 Copynumber: 10.9 Consensus size: 14
44467 CTGACTTCTT
44477 TTTACTTTTAC-TC
1 TTTACTTTTACTTC
*
44490 TTTGACTGATTACTTC
1 TTT-ACT-TTTACTTC
44506 TCTTACTTTTAC-TC
1 T-TTACTTTTACTTC
*
44520 -TTA--ATTACTTC
1 TTTACTTTTACTTC
*
44531 TTTTACTTTTACTCTT
1 -TTTACTTTTACT-TC
*
44547 TTCTACTAATTACTTC
1 TT-TACT-TTTACTTC
*
44563 TTCTTCTTTTAC-TC
1 TT-TACTTTTACTTC
* **
44577 TTTCACTTCTACTGA
1 TTT-ACTTTTACTTC
*
44592 TTACTTCTTTTACTTC
1 TT--TACTTTTACTTC
*
44608 --TACTGATTACTTC
1 TTTACT-TTTACTTC
44621 TTTTACTTTTACT
1 -TTTACTTTTACT
44634 GATCACTCCT
Statistics
Matches: 104, Mismatches: 20, Indels: 38
0.64 0.12 0.23
Matches are distributed among these distances:
10 4 0.04
11 2 0.02
12 6 0.06
13 14 0.13
14 15 0.14
15 26 0.25
16 29 0.28
17 8 0.08
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (14 bp):
TTTACTTTTACTTC
Found at i:44553 original size:25 final size:25
Alignment explanation
Indices: 44498--44546 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
44488 TCTTTGACTG
44498 ATTACTTCTCTTACTTTTACTCTTA
1 ATTACTTCTCTTACTTTTACTCTTA
*
44523 ATTACTTCTTTTACTTTTACTCTT
1 ATTACTTCTCTTACTTTTACTCTT
44547 TTCTACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.18, C:0.22, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTACTTCTCTTACTTTTACTCTTA
Found at i:44575 original size:57 final size:56
Alignment explanation
Indices: 44470--44578 Score: 159
Period size: 57 Copynumber: 1.9 Consensus size: 56
44460 TTTACTACTG
*
44470 ACTTCTTTTTACTTTTACTCTTTGACTGATTACTTCTCTTACTTTTACTCTTAATT
1 ACTTCTTTTTACTTTTACTCTTTGACTAATTACTTCTCTTACTTTTACTCTTAATT
*
44526 ACTTC-TTTTACTTTTACTCTTTTCTACTAATTACTTCTTCTT-CTTTTACTCTT
1 ACTTCTTTTTACTTTTACTC-TTT-GACTAATTACTTC-TCTTACTTTTACTCTT
44579 TCACTTCTAC
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
55 14 0.29
56 8 0.17
57 22 0.46
58 4 0.08
ACGTcount: A:0.17, C:0.23, G:0.02, T:0.59
Consensus pattern (56 bp):
ACTTCTTTTTACTTTTACTCTTTGACTAATTACTTCTCTTACTTTTACTCTTAATT
Found at i:44585 original size:55 final size:54
Alignment explanation
Indices: 44470--44659 Score: 149
Period size: 57 Copynumber: 3.4 Consensus size: 54
44460 TTTACTACTG
* *
44470 ACTTCTTTTTACTTTTACTCTTTGACTGATTACTTCTCTTACTTTTACTCTTAATT
1 ACTTC-TTTTACTTTTACTCTTTGACTAATTACTTCTCTTACTTTTACTCTT-ATC
*
44526 ACTTCTTTTACTTTTACTCTTTTCTACTAATTACTTCTTCTT-CTTTTACTCTT-TC
1 ACTTCTTTTACTTTTACTC-TTT-GACTAATTACTTC-TCTTACTTTTACTCTTATC
* * * *
44581 ACTTCTACTGATTACTTCTTTTACT-TCT-ACTGATTACTTCTTTTACTTTTA--CTGATC
1 ACTTCT--T--TTA---CTTTTACTCTTTGACTAATTACTTCTCTTACTTTTACTCTTATC
* *
44638 ACTCCTTTTACTTTTATTCTTT
1 ACTTCTTTTACTTTTACTCTTT
44660 TACTTCTACT
Statistics
Matches: 111, Mismatches: 10, Indels: 31
0.73 0.07 0.20
Matches are distributed among these distances:
50 7 0.06
51 2 0.02
53 3 0.03
55 22 0.20
56 10 0.09
57 33 0.30
58 21 0.19
59 3 0.03
60 2 0.02
62 8 0.07
ACGTcount: A:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (54 bp):
ACTTCTTTTACTTTTACTCTTTGACTAATTACTTCTCTTACTTTTACTCTTATC
Found at i:44595 original size:36 final size:35
Alignment explanation
Indices: 44523--44749 Score: 165
Period size: 36 Copynumber: 6.2 Consensus size: 35
44513 TTTACTCTTA
*
44523 ATTACTTCTTTTACTTTTACTC--TT--TTCTACTA
1 ATTACTTCTTTT-CTTTTACTCTTTTACTTCTACTG
*
44555 ATTACTTCTTCTTCTTTTACTCTTTCACTTCTACTG
1 ATTACTTCTT-TTCTTTTACTCTTTTACTTCTACTG
*
44591 ATTACTTCTTTTACTTCTACTGATTACTTCTTTTACTTTTACTG
1 ATTACTTC--TT--TTCT--T--TTAC-TCTTTTACTTCTACTG
* * * *
44635 ATCACTCCTTTTACTTTTATTCTTTTACTTCTACTA
1 ATTACTTCTTTT-CTTTTACTCTTTTACTTCTACTG
* * * *
44671 ATTACTCCTTTTACTTTTCCTCTTTTTCTTCCACTG
1 ATTACTTCTTTT-CTTTTACTCTTTTACTTCTACTG
* * * *
44707 ATTACTTCATTTACTCTTACTCTTTTTCTTCTGCTG
1 ATTACTTC-TTTTCTTTTACTCTTTTACTTCTACTG
44743 ATTACTT
1 ATTACTT
44750 TTCTTATTTT
Statistics
Matches: 159, Mismatches: 21, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
32 19 0.12
33 2 0.01
34 1 0.01
36 92 0.58
37 6 0.04
38 2 0.01
39 6 0.04
40 2 0.01
41 3 0.02
42 2 0.01
43 4 0.03
44 20 0.13
ACGTcount: A:0.16, C:0.25, G:0.03, T:0.56
Consensus pattern (35 bp):
ATTACTTCTTTTCTTTTACTCTTTTACTTCTACTG
Found at i:44599 original size:13 final size:13
Alignment explanation
Indices: 44581--44621 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
44571 TTACTCTTTC
44581 ACTTCTACTGATT
1 ACTTCTACTGATT
44594 ACTTCT--T--TT
1 ACTTCTACTGATT
44603 ACTTCTACTGATT
1 ACTTCTACTGATT
44616 ACTTCT
1 ACTTCT
44622 TTTACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
9 8 0.33
11 2 0.08
13 14 0.58
ACGTcount: A:0.20, C:0.24, G:0.05, T:0.51
Consensus pattern (13 bp):
ACTTCTACTGATT
Found at i:44620 original size:58 final size:58
Alignment explanation
Indices: 44547--44721 Score: 187
Period size: 58 Copynumber: 3.0 Consensus size: 58
44537 TTTTACTCTT
44547 TTCTACTAATTACTTCTTCTT-CTTTTACTCTTTCACTTCTACTGATTACTTCTTTTAC
1 TTCTACTAATTACTTCTT-TTACTTTTACTCTTTCACTTCTACTGATTACTTCTTTTAC
* ** * *
44605 TTCTACTGATTACTTCTTTTACTTTTACT-GATCACTCCTTTTACT-TTTA-TTCTTTTAC
1 TTCTACTAATTACTTCTTTTACTTTTACTCTTTCA---CTTCTACTGATTACTTCTTTTAC
* * ** * *
44663 TTCTACTAATTACTCCTTTTACTTTTCCTCTTTTTCTTCCACTGATTACTTCATTTAC
1 TTCTACTAATTACTTCTTTTACTTTTACTCTTTCACTTCTACTGATTACTTCTTTTAC
44721 T
1 T
44722 CTTACTCTTT
Statistics
Matches: 94, Mismatches: 16, Indels: 14
0.76 0.13 0.11
Matches are distributed among these distances:
56 6 0.06
57 8 0.09
58 69 0.73
59 4 0.04
60 7 0.07
ACGTcount: A:0.17, C:0.25, G:0.02, T:0.55
Consensus pattern (58 bp):
TTCTACTAATTACTTCTTTTACTTTTACTCTTTCACTTCTACTGATTACTTCTTTTAC
Found at i:44653 original size:22 final size:22
Alignment explanation
Indices: 44571--44650 Score: 117
Period size: 22 Copynumber: 3.7 Consensus size: 22
44561 TCTTCTTCTT
*
44571 TTAC-TCTTTCACTTCTACTGA
1 TTACTTCTTTTACTTCTACTGA
44592 TTACTTCTTTTACTTCTACTGA
1 TTACTTCTTTTACTTCTACTGA
*
44614 TTACTTCTTTTACTTTTACTGA
1 TTACTTCTTTTACTTCTACTGA
* *
44636 TCACTCCTTTTACTT
1 TTACTTCTTTTACTT
44651 TTATTCTTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
21 4 0.07
22 50 0.93
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.54
Consensus pattern (22 bp):
TTACTTCTTTTACTTCTACTGA
Found at i:44905 original size:57 final size:57
Alignment explanation
Indices: 44844--44953 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
44834 CTCTTTCTTC
* * *
44844 TTTAGCCTAATTACTCTGAATTAAGCTA-TCTGCTGATTACTCTTTCTTTTACTTCAT
1 TTTAGCCTAATTACTCTGAATTAAACTATTCTGCT-ATTACTCCTCCTTTTACTTCAT
*
44901 TTTAGTCTAATTACTCTGAATTAAACTATTCTGCTATTACTCCTCCTTTTACT
1 TTTAGCCTAATTACTCTGAATTAAACTATTCTGCTATTACTCCTCCTTTTACT
44954 CTTTTTAATT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
57 42 0.88
58 6 0.12
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (57 bp):
TTTAGCCTAATTACTCTGAATTAAACTATTCTGCTATTACTCCTCCTTTTACTTCAT
Found at i:44981 original size:56 final size:57
Alignment explanation
Indices: 44850--44984 Score: 148
Period size: 57 Copynumber: 2.4 Consensus size: 57
44840 CTTCTTTAGC
* * * * * *
44850 CTAATTACTCTGAATTAAGCTATCTGCTGATTACTCTTTCTTTTACTTCATTTTAGT
1 CTAATTACCCAGAATTAAACTATCTGCTGATTACTCCTCCTTTTACTTCATTTTAAT
* * *
44907 CTAATTACTCTGAATTAAACTATTCTGCT-ATTACTCCTCCTTTTAC-TCTTTTTAAT
1 CTAATTACCCAGAATTAAACTA-TCTGCTGATTACTCCTCCTTTTACTTCATTTTAAT
* *
44963 TTAATTGCCCAGAATTAAACTA
1 CTAATTACCCAGAATTAAACTA
44985 ATTACTGTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
56 26 0.38
57 36 0.53
58 6 0.09
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.46
Consensus pattern (57 bp):
CTAATTACCCAGAATTAAACTATCTGCTGATTACTCCTCCTTTTACTTCATTTTAAT
Found at i:45157 original size:53 final size:53
Alignment explanation
Indices: 45073--45720 Score: 880
Period size: 53 Copynumber: 12.3 Consensus size: 53
45063 TAATTTTGCT
* * *
45073 ACCTATTTACTGA-TTACTCCTTTCACTGCTTAGGTTAATTACTCTGAATTAG
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * * *
45125 ACATGTTTACTAATTTTCTCTTTTTACTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * * * *
45178 ACCTGTTTACTGCTTTAT-TGCTTTTACTTCTTAGTTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTT-TCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* *
45231 ACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTTAATTACTCCGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
45284 ACCTACTTACTGATTTTC-CTCTTTTATTACTTAGGTTAATTACTC-GAATTAA
1 ACCTATTTACTGATTTTCTC-CTTTTACTGCTTAGGTTAATTACTCTGAATTAA
45336 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * * * *
45389 ACCTATTTACTAATTTTCCCCTTTTACTACTTAGGTTAATTACTCGGAACTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
45442 ACCTATTTACTGATTTTC-CCCTTTACTACTTAGGTTAATTACTCGGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
*
45494 ACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * * * *
45547 ACCTGTTTACTGCTTTACTGCC-TTTACTTCTTAGGTTAATTACTTTGAATTAA
1 ACCTATTTACTGATTTTCT-CCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* * *
45600 ACCTATTTACTAATTTTGTCCTTTTATTGCTTAGGTTAATTACTCTGAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
* *
45653 ACCTATTTACTGATTTTCCCCTTTTACTACTTAGGTTAATTACTC-GAAATTAA
1 ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTG-AATTAA
45706 ACCTATTTACT-ATTT
1 ACCTATTTACTGATTT
45721 ACTGTTTTCT
Statistics
Matches: 527, Mismatches: 59, Indels: 20
0.87 0.10 0.03
Matches are distributed among these distances:
52 115 0.22
53 409 0.78
54 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (53 bp):
ACCTATTTACTGATTTTCTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAA
Found at i:45393 original size:158 final size:158
Alignment explanation
Indices: 45073--45723 Score: 882
Period size: 158 Copynumber: 4.1 Consensus size: 158
45063 TAATTTTGCT
* * * * *
45073 ACCTATTTACTGA-TTACTCCTTTCACTGCTTAGGTTAATTACTCTGAATTAGACATGTTTACTA
1 ACCTATTTACTAATTTACTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTA
* * * *
45137 ATTTTCTCTTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTGTTTACTGCTTTAT-TGCTT
66 ATTTTCTC-TTTTACTACTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTT-TCTCCTT
* *
45201 TTACTTCTTAGTTTAATTACTCTGAATTAA
129 TTACTGCTTAGGTTAATTACTCTGAATTAA
* * * *
45231 ACCTATTTACTAATTTTCTCCTTTTACTGCTTAGGTTAATTACTCCGAATTAAACCTACTTACTG
1 ACCTATTTACTAATTTACTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTA
*
45296 ATTTTCCTCTTTTATTACTTAGGTTAATTACTC-GAATTAAACCTATTTACTGATTTTCTCCTTT
66 ATTTT-CTCTTTTACTACTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTTTCTCCTTT
45360 TACTGCTTAGGTTAATTACTCTGAATTAA
130 TACTGCTTAGGTTAATTACTCTGAATTAA
* * * * * *
45389 ACCTATTTACTAATTTTCCCCTTTTACTACTTAGGTTAATTACTCGGAACTAAACCTATTTACTG
1 ACCTATTTACTAATTTACTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTA
* * * *
45454 ATTTTCCCCTTTACTACTTAGGTTAATTACTCGGAATTAAACCTATTTACTAATTTTCTCCTTTT
66 ATTTTCTCTTTTACTACTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTTTCTCCTTTT
45519 ACTGCTTAGGTTAATTACTCTGAATTAA
131 ACTGCTTAGGTTAATTACTCTGAATTAA
* ** * *
45547 ACCTGTTTACTGCTTTACTGCC-TTTACTTCTTAGGTTAATTACTTTGAATTAAACCTATTTACT
1 ACCTATTTACTAATTTACT-CCTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACT
* * * *
45611 AATTTTGTCCTTTTATTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTTTCCCCTT
65 AATTTTCT-CTTTTACTACTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTTTCTCCTT
*
45676 TTACTACTTAGGTTAATTACTC-GAAATTAA
129 TTACTGCTTAGGTTAATTACTCTG-AATTAA
45706 ACCTATTTACT-ATTTACT
1 ACCTATTTACTAATTTACT
45724 GTTTTCTTCT
Statistics
Matches: 440, Mismatches: 46, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
157 25 0.06
158 253 0.57
159 159 0.36
160 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.09, T:0.46
Consensus pattern (158 bp):
ACCTATTTACTAATTTACTCCTTTTACTGCTTAGGTTAATTACTCTGAATTAAACCTATTTACTA
ATTTTCTCTTTTACTACTTAGGTTAATTACTCTGAATTAAACCTATTTACTGATTTTCTCCTTTT
ACTGCTTAGGTTAATTACTCTGAATTAA
Found at i:50367 original size:14 final size:14
Alignment explanation
Indices: 50348--50375 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
50338 GAAGCATTGG
50348 AATTTTCCAATAGT
1 AATTTTCCAATAGT
50362 AATTTTCCAATAGT
1 AATTTTCCAATAGT
50376 TGTCCCCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
AATTTTCCAATAGT
Found at i:52981 original size:133 final size:133
Alignment explanation
Indices: 52809--53083 Score: 505
Period size: 133 Copynumber: 2.1 Consensus size: 133
52799 ATTTATATAG
* *
52809 ATTGAGGTTGGATGAAGCTTTAATAATCTAAATCTCTGCCAAAGAGTTGTTTAATGCTCAAATTG
1 ATTGATGTTGGATGAAGCTTTAATAATCTAAATCTCTGCCAAAGACTTGTTTAATGCTCAAATTG
* *
52874 ATTTGTTGATCCGTGATCCATGGTATCTTTGATTGATTTCATACTTAGGTAGGGATAAGTAGGAA
66 ATTTGTTGATCCGTGATCCATGGTATCTATGATTGATTTCATACTTAGATAGGGATAAGTAGGAA
52939 AGT
131 AGT
52942 ATTGATGTTGGATGAAGCTTTAATAATCTAAATCTCTGCCAAAGACTTGTTTAATGCTCAAATTG
1 ATTGATGTTGGATGAAGCTTTAATAATCTAAATCTCTGCCAAAGACTTGTTTAATGCTCAAATTG
*
53007 ATTTGTTGATCCGTGATCCATGGTATCTATGATTGATTTCATACTTAGATGGGGATAAGTAGGAA
66 ATTTGTTGATCCGTGATCCATGGTATCTATGATTGATTTCATACTTAGATAGGGATAAGTAGGAA
53072 AGT
131 AGT
53075 ATTGATGTT
1 ATTGATGTT
53084 TTTATTATTG
Statistics
Matches: 137, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
133 137 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.37
Consensus pattern (133 bp):
ATTGATGTTGGATGAAGCTTTAATAATCTAAATCTCTGCCAAAGACTTGTTTAATGCTCAAATTG
ATTTGTTGATCCGTGATCCATGGTATCTATGATTGATTTCATACTTAGATAGGGATAAGTAGGAA
AGT
Found at i:54403 original size:150 final size:150
Alignment explanation
Indices: 54166--54468 Score: 606
Period size: 150 Copynumber: 2.0 Consensus size: 150
54156 AAGCAGCCCA
54166 TTTCGTGGCCTATAAATACAGCAGCTGCTCCAAACGAAAGTCCTCTCTTCCACACACACAACTCT
1 TTTCGTGGCCTATAAATACAGCAGCTGCTCCAAACGAAAGTCCTCTCTTCCACACACACAACTCT
54231 CTCACACAACACAAAATCTTGCCTTACGCAACAATCAAGCTTTTTCTCTGTATTTTCTCTCAAGT
66 CTCACACAACACAAAATCTTGCCTTACGCAACAATCAAGCTTTTTCTCTGTATTTTCTCTCAAGT
54296 GTTCTTCATAGTTCATCACT
131 GTTCTTCATAGTTCATCACT
54316 TTTCGTGGCCTATAAATACAGCAGCTGCTCCAAACGAAAGTCCTCTCTTCCACACACACAACTCT
1 TTTCGTGGCCTATAAATACAGCAGCTGCTCCAAACGAAAGTCCTCTCTTCCACACACACAACTCT
54381 CTCACACAACACAAAATCTTGCCTTACGCAACAATCAAGCTTTTTCTCTGTATTTTCTCTCAAGT
66 CTCACACAACACAAAATCTTGCCTTACGCAACAATCAAGCTTTTTCTCTGTATTTTCTCTCAAGT
54446 GTTCTTCATAGTTCATCACT
131 GTTCTTCATAGTTCATCACT
54466 TTT
1 TTT
54469 ACATACAAGT
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
150 153 1.00
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (150 bp):
TTTCGTGGCCTATAAATACAGCAGCTGCTCCAAACGAAAGTCCTCTCTTCCACACACACAACTCT
CTCACACAACACAAAATCTTGCCTTACGCAACAATCAAGCTTTTTCTCTGTATTTTCTCTCAAGT
GTTCTTCATAGTTCATCACT
Done.