Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016298.1 Corchorus olitorius cultivar O-4 contig16331, 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: 66273
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2207 original size:54 final size:54
Alignment explanation
Indices: 2135--2278 Score: 227
Period size: 54 Copynumber: 2.7 Consensus size: 54
2125 GTACAGGTGT
* * *
2135 TTAAAATGA-CCAATGTGGTCTTTCATAGAAGTTTTCAGAGATCTAAACAGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAAAGATCTAAACAGATC
2188 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAAAGATCTAAACAGATC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAAAGATCTAAACAGATC
* * *
2242 TTAAGATGACCAAGTGCGATCTTTCATAGAAGTTTTC
1 TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTC
2279 GATGGTCAGA
Statistics
Matches: 84, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 8 0.10
54 76 0.90
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (54 bp):
TTAAGATGACCCAGTGTGGTCTTTCATAGAAGTTTTCAAAGATCTAAACAGATC
Found at i:2309 original size:35 final size:35
Alignment explanation
Indices: 2262--2469 Score: 301
Period size: 35 Copynumber: 5.9 Consensus size: 35
2252 CAAGTGCGAT
*
2262 CTTTCATAGAAGTTTTCGATGGTCAGAGTTGATCTC
1 CTTTCA-AGAAGTTTTCGATGATCAGAGTTGATCTC
2298 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
1 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * *
2333 ATTCCAAGAAGTTTT-TATGATCAGAGTTGATCTC
1 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
*
2367 CTTTCAAGAAGTTTTCGATGATCAGAGTTAATCTC
1 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* * * *
2402 GTTTCAAGAAGTTTTTGATGGTTAGAGTTGATCTC
1 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
* *
2437 ATTTCAAGAAGTTTTCGAGGATCAGAGTTGATC
1 CTTTCAAGAAGTTTTCGATGATCAGAGTTGATC
2470 CCAGATGATC
Statistics
Matches: 153, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
34 31 0.20
35 116 0.76
36 6 0.04
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (35 bp):
CTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTC
Found at i:2449 original size:104 final size:106
Alignment explanation
Indices: 2262--2469 Score: 321
Period size: 104 Copynumber: 2.0 Consensus size: 106
2252 CAAGTGCGAT
* *
2262 CTTTCATAGAAGTTTTCGATGGTCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTT
1 CTTTCATAGAAGTTTTCGATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTT
* *
2327 GATCTCATTCCAAGAAGTTTT-TATGATCAGAGTTGATCTC
66 GATCTCATTCCAAGAAGTTTTCGAGGATCAGAGTTGATCTC
* * * *
2367 CTTTCA-AGAAGTTTTCGATGATCAGAGTTAATCTCGTTTCAAGAAGTTTTTGATGGTTAGAGTT
1 CTTTCATAGAAGTTTTCGATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTT
*
2431 GATCTCATTTCAAGAAGTTTTCGAGGATCAGAGTTGATC
66 GATCTCATTCCAAGAAGTTTTCGAGGATCAGAGTTGATC
2470 CCAGATGATC
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
104 72 0.77
105 21 0.23
ACGTcount: A:0.26, C:0.14, G:0.21, T:0.38
Consensus pattern (106 bp):
CTTTCATAGAAGTTTTCGATGATCAGAGTTAATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTT
GATCTCATTCCAAGAAGTTTTCGAGGATCAGAGTTGATCTC
Found at i:2524 original size:35 final size:35
Alignment explanation
Indices: 2483--3297 Score: 1159
Period size: 35 Copynumber: 23.2 Consensus size: 35
2473 GATGATCCAG
2483 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
** *
2518 TGATCTCATTTCAAGAAGTTTTTTATGATTAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
2553 TGATCTCATTCCAAGAAGTTTT-TATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
2587 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
2622 TGATCTCCTTTCAAGAAGTTTT-TATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
**
2656 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* **
2691 TGATCTCAGTTCAAGAAGTTTTTTTATGATCAGAGT
1 TGATCTCATTTCAAGAAG-TTTTCGATGATCAGAGT
* * * *
2727 TGTTCTCGTTTTAAGAAGTTTTTTCGTTGATCAGAGT
1 TGATCTCATTTCAAGAAG--TTTTCGATGATCAGAGT
* *
2764 TGATCTCCTTTCAAGAAGTTTTCGTTGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
**
2799 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
*
2834 TGATCTCATTTCCAAGAAGTTTTCGATGATTAGAGT
1 TGATCTCATTT-CAAGAAGTTTTCGATGATCAGAGT
**
2870 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
2905 TGATCTCATTTCCAGAAGTTTTCGATGACCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
2940 TGATCTCATTTCAAGAAAATTTT-TATGATCAGAGT
1 TGATCTCATTTCAAG-AAGTTTTCGATGATCAGAGT
*
2975 TCATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
*
3010 TGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* * **
3045 TGATCTCGTTTCAAGAAATTTTTTATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* ** *
3080 TGATCTTATTTCAAGAAGTTTTTTTATGGTCAGAGT
1 TGATCTCATTTCAAGAAG-TTTTCGATGATCAGAGT
*
3116 TGATCTCATTTCAAGAAGTTTTCAATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
3151 AGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
*
3186 TGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
*
3221 TGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
* *
3256 TGATCTTATTTCAAGAAGTTTTCGAGGATCAGAGT
1 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
3291 TGATCTC
1 TGATCTC
3298 CAAGTTGACC
Statistics
Matches: 708, Mismatches: 64, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
34 70 0.10
35 506 0.71
36 102 0.14
37 30 0.04
ACGTcount: A:0.27, C:0.13, G:0.19, T:0.40
Consensus pattern (35 bp):
TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGT
Found at i:2552 original size:88 final size:88
Alignment explanation
Indices: 2397--2557 Score: 250
Period size: 88 Copynumber: 1.8 Consensus size: 88
2387 ATCAGAGTTA
* * * *
2397 ATCTCGTTTCAAGAAGTTTTTGATGGTTAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG
1 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG
2462 AGTTGATCCCAGATGATCCAGTG
66 AGTTGATCCCAGATGATCCAGTG
** * *
2485 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATTAG
1 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG
2550 AGTTGATC
66 AGTTGATC
2558 TCATTCCAAG
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 65 1.00
ACGTcount: A:0.27, C:0.14, G:0.21, T:0.38
Consensus pattern (88 bp):
ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGAGGATCAG
AGTTGATCCCAGATGATCCAGTG
Found at i:3013 original size:246 final size:245
Alignment explanation
Indices: 2263--3297 Score: 1166
Period size: 246 Copynumber: 4.3 Consensus size: 245
2253 AAGTGCGATC
* * **
2263 TTTCATAGAAGTTTTCGATGGTCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAGAGTTG
1 TTTCA-AGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTG
* * * **
2328 ATCTCATTCCAAGAAGTTTT-TATGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGATGATCAG
65 ATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAG
* * * * * * * *
2392 AGTTAATCTCGTTTCAAGAAGTTTTTGATGGTTAGAGTTGATCTCATTTCAAG-AAGTTTTCGAG
130 AGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAAATTTT-TAT
*
2456 GATCAGAGTTGATC-C----C----A------GATGATC-CAG-TGATCTCA
194 GATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
*
2491 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATTAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGA
* * **
2556 TCTCATTCCAAGAAGTTTT-TATGATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGA
66 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGA
* * **
2620 GTTGATCTCCTTTCAAGAAGTTTT-TATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGA
131 GTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAAATTTTTATGA
* ** * *
2684 TCAGAGTTGATCTCAGTTCAAGAAGTTTTTTTATGATCAGAGTTGTTCTCG
196 TCAGAGTTGATCTCATTTCAAGAAG-TTTTCGATGATCAGAGTTGATCTCA
* * * *
2735 TTTTAAGAAGTTTTTTCGTTGATCAGAGTTGATCTCCTTTCAAGAAGTTTTCGT-TGATCAGAGT
1 TTTCAAGAAG--TTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTT-TTATGATCAGAGT
** **
2799 TGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAAGAAGTTTTCGATGAT
63 TGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTT-CAAGAAGTTTTTTATGAT
* ** * *
2864 TAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGATCTCATTTCCAG-AAGTTTTC
127 CAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAAATTTT-
* * * * *
2928 GATGACCAGAGTTGATCTCATTTCAAGAAAATTTT-TATGATCAGAGTTCATCTCA
191 TATGATCAGAGTTGATCTCATTTCAAG-AAGTTTTCGATGATCAGAGTTGATCTCA
* **
2983 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGA
* * ** * *
3048 TCTCGTTTCAAGAAATTTTTTATGATCAGAGTTGATCTTATTTCAAGAAGTTTTTTTATGGTCAG
66 TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAG-TTTTTTATGATCAG
* * * * *
3113 AGTTGATCTCATTTCAAGAAGTTTTCAATGATCAGAGTAGATCTCGTTTCAAG-AAGTTTTCGAT
130 AGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAAATTTT-TAT
* *
3177 GATCAGAGTTGATCTCGTTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCC
194 GATCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
* ** *
3229 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTTATTTCAAGAAGTTTTCGAGGATCAGAGTTGA
1 TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGA
3294 TCTC
66 TCTC
3298 CAAGTTGACC
Statistics
Matches: 714, Mismatches: 63, Indels: 42
0.87 0.08 0.05
Matches are distributed among these distances:
226 39 0.05
227 146 0.20
228 5 0.01
231 1 0.00
235 1 0.00
242 6 0.01
243 2 0.00
244 15 0.02
245 13 0.02
246 331 0.46
247 24 0.03
248 75 0.11
249 54 0.08
250 2 0.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (245 bp):
TTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGAGTTGA
TCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAGTTTTTTATGATCAGA
GTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCATTTCAAGAAAATTTTTATGA
TCAGAGTTGATCTCATTTCAAGAAGTTTTCGATGATCAGAGTTGATCTCA
Found at i:4713 original size:86 final size:85
Alignment explanation
Indices: 4553--4713 Score: 252
Period size: 86 Copynumber: 1.9 Consensus size: 85
4543 GGTTTCATGT
* *
4553 AATAAATTATAAAGTTGAATAATAATGAGAATATTTTCTAAATCTTGCCAACTTGTGGAAGGTTT
1 AATAAATTATAAAGTTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTT
*
4618 AGGAGATATTTTAAGAAATA
66 AGGAAATATTTTAAGAAATA
* *
4638 AATAAATTATAAAGATTGAATAATAATGAGAATATTTTTTAAATCTTGCCAAATTGTGGGAGATT
1 AATAAATTATAAAG-TTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATT
4703 T-GGAAAATATT
65 TAGG-AAATATT
4714 AAATAAAATA
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
85 16 0.23
86 53 0.77
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (85 bp):
AATAAATTATAAAGTTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGAAGATTT
AGGAAATATTTTAAGAAATA
Found at i:12980 original size:45 final size:45
Alignment explanation
Indices: 12916--13114 Score: 254
Period size: 45 Copynumber: 4.4 Consensus size: 45
12906 TCACTGTTAT
* * * *** * *
12916 ACCCATCCAGATTTTCACCCCCATTATTGGCTCTTACTCCCTCAA
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
* * *
12961 ACCCATCAAGATTTTCACCCTCATTCTCCTCTCTAACTCTATCAA
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
13006 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
* ***
13051 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCCTGTT
1 ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
*
13096 CCCCATCCACATTTTCACC
1 ACCCATCCACATTTTCACC
13115 TTTTGCAGCA
Statistics
Matches: 137, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 137 1.00
ACGTcount: A:0.23, C:0.43, G:0.03, T:0.32
Consensus pattern (45 bp):
ACCCATCCACATTTTCACCCTCATTCTCCTCTCTAACTCCATCAA
Found at i:14790 original size:20 final size:21
Alignment explanation
Indices: 14765--14803 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
14755 ACCGCGTTGA
14765 TTTAATGATT-TTAATTTTCT
1 TTTAATGATTATTAATTTTCT
*
14785 TTTAATTATTATTAATTTT
1 TTTAATGATTATTAATTTT
14804 TTTAATCCGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTAATGATTATTAATTTTCT
Found at i:14856 original size:20 final size:20
Alignment explanation
Indices: 14827--14875 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
14817 GGACTTTATG
*
14827 ACGTGTCCTCTGATAATTCC
1 ACGTGGCCTCTGATAATTCC
14847 ACGTGGCCTCTGATAATTCC
1 ACGTGGCCTCTGATAATTCC
*
14867 ACGTAGCCT
1 ACGTGGCCT
14876 ATATTCACGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (20 bp):
ACGTGGCCTCTGATAATTCC
Found at i:15423 original size:22 final size:22
Alignment explanation
Indices: 15380--15424 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
15370 ACAATCTTAC
**
15380 AAAAAAAACATTAAAAAAAACA
1 AAAAAAAACAACAAAAAAAACA
* *
15402 AAAAAAAACAACAACAACAACA
1 AAAAAAAACAACAAAAAAAACA
15424 A
1 A
15425 TCTTGTCTAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.80, C:0.16, G:0.00, T:0.04
Consensus pattern (22 bp):
AAAAAAAACAACAAAAAAAACA
Found at i:17176 original size:26 final size:25
Alignment explanation
Indices: 17117--17168 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
17107 ATATGAACCT
**
17117 AAAATACATCTTAATTTGTATAAAA
1 AAAATACATCTTAATTTAAATAAAA
17142 AAAATACATCTTAATTTCAAATAAAA
1 AAAATACATCTTAATTT-AAATAAAA
17168 A
1 A
17169 TATTACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 17 0.71
26 7 0.29
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (25 bp):
AAAATACATCTTAATTTAAATAAAA
Found at i:38129 original size:20 final size:21
Alignment explanation
Indices: 38104--38145 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38094 AACAAATAAT
*
38104 AATTGTAAGA-AATAACTTGA
1 AATTGTAACATAATAACTTGA
*
38124 AATTGTAACATAATAATTTGA
1 AATTGTAACATAATAACTTGA
38145 A
1 A
38146 TATTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.50, C:0.05, G:0.12, T:0.33
Consensus pattern (21 bp):
AATTGTAACATAATAACTTGA
Found at i:39276 original size:25 final size:24
Alignment explanation
Indices: 39227--39276 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
39217 AATATCATAT
**
39227 ATTTAAATTATTTTTTTGGTAAAA
1 ATTTAAATTATTTTTTTAATAAAA
39251 ATTTAAATTATTTTTCTTAAATAAAA
1 ATTTAAATTATTTTT-TT-AATAAAA
39277 GAATTTCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 15 0.68
25 2 0.09
26 5 0.23
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTAAATTATTTTTTTAATAAAA
Found at i:46283 original size:23 final size:23
Alignment explanation
Indices: 46239--46284 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
46229 TCATTTATAA
* * **
46239 AGAATATGGATTAATATTTACAG
1 AGAAAATGAATTAATAACTACAG
46262 AGAAAATGAATTAATAACTACAG
1 AGAAAATGAATTAATAACTACAG
46285 CATCCTGCAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (23 bp):
AGAAAATGAATTAATAACTACAG
Found at i:58015 original size:13 final size:13
Alignment explanation
Indices: 57997--58025 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
57987 ACGGAACTTT
57997 AATGAAACTAAGG
1 AATGAAACTAAGG
58010 AATGAAACTAAGG
1 AATGAAACTAAGG
58023 AAT
1 AAT
58026 AGGAAAGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.21, T:0.17
Consensus pattern (13 bp):
AATGAAACTAAGG
Found at i:59786 original size:19 final size:18
Alignment explanation
Indices: 59759--59800 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
59749 GGAGTAATTT
*
59759 TTAAGTAAAAATATAATA
1 TTAAATAAAAATATAATA
59777 TATAAATAAAAATATAATA
1 T-TAAATAAAAATATAATA
59796 TTAAA
1 TTAAA
59801 ATAATTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
TTAAATAAAAATATAATA
Found at i:59804 original size:19 final size:19
Alignment explanation
Indices: 59764--59800 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
59754 AATTTTTAAG
59764 TAAAAATATAATATATAAA
1 TAAAAATATAATATATAAA
59783 TAAAAATATAATAT-TAAA
1 TAAAAATATAATATATAAA
59801 ATAATTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATATAATATATAAA
Found at i:62204 original size:222 final size:226
Alignment explanation
Indices: 61802--62210 Score: 585
Period size: 222 Copynumber: 1.8 Consensus size: 226
61792 TATGGGTTTA
* * * * * *
61802 TATATAATACACTGTCATTGGAGTTTAGCAGACTGCACAAGCGAGTCTTGAAAGGTGATATGTGT
1 TATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGAGTCTTGAAAGGTAACATGTGT
* * * *
61867 CTCTACTTTCTAGGGACTAGATTGAAATATTTAAAATTTAATTAATTCAGAAAATGAGCATGTGT
66 CTC-AC-TTCTAGGGACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGT
* * * *
61932 CAACTCCACAACCCGTTTGTGGAGTTCAAAATTTACACCGTCTATGTATCAAATAATTATAACTA
129 CAACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTATAACTA
61997 TAAGTACTAAAGTTCCTTTAATGAAAAGCAAAT
194 TAAGTACTAAAGTTCCTTTAATGAAAAGCAAAT
* *
62030 TATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGCGT-TCTGAAGGGTAACATGTG
1 TATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGAGTCT-TGAAAGGTAACATGTG
*
62094 TC-C-C-T-TAGGGATTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGTC
65 TCTCACTTCTAGGGACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGTC
* *
62155 AACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCATATAAT
130 AACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATAAT
62211 CACCCTTAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
222 101 0.63
223 1 0.01
225 1 0.01
227 2 0.01
228 56 0.35
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (226 bp):
TATACAATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGAGTCTTGAAAGGTAACATGTGT
CTCACTTCTAGGGACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGTCA
ACTCCACAACCCGCTTGTGGAGTCCAAAATTTACACCGCCGATGTATCAAATAATTATAACTATA
AGTACTAAAGTTCCTTTAATGAAAAGCAAAT
Found at i:62381 original size:199 final size:199
Alignment explanation
Indices: 62036--62409 Score: 590
Period size: 199 Copynumber: 1.9 Consensus size: 199
62026 AAATTATACA
* * *
62036 ATACACCGTCAGTGGAGTTTAGCAGACTACACAAGCGCGTTCTGAAGGGTAACATGTGTCCCTTA
1 ATACACCGGCAGTGAAGTTTAGCAGACTACACAAGCGCGTTCTGAAGGGTAACATGTGTCCCCTA
*
62101 GGGATTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGTCAACTCCACAAC
66 GGGACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGTCAACTCCACAAC
* *
62166 CCGCTTGTGGAGTCCAAAATTTACACCGCCGGTGTATCATATAATCACCCTTAAAGGGGTTTATA
131 CCGCTTGTGAAGTCCAAAATTTACACCGCCGGTGTATCAAATAATCACCCTTAAAGGGGTTTATA
62231 TATG
196 TATG
* * * *
62235 ATACACCGGCGGTGAAGTTTAGCAGACTGCACAAGCG-GGTCTTGAAGGGTGACATGTGTCCCCT
1 ATACACCGGCAGTGAAGTTTAGCAGACTACACAAGCGCGTTC-TGAAGGGTAACATGTGTCCCCT
* * * *
62299 AGGGACTAGATTGAAATATTTAAAATTTAATTAATTTAGAAAAT-AGACATGTGTCAACTCCACA
65 AGGGACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGA-ACATGTGTCAACTCCACA
62363 ACCCGCTTGTGAAGTCCAAAATTTACACCGCCGGTGTATCAAATAAT
129 ACCCGCTTGTGAAGTCCAAAATTTACACCGCCGGTGTATCAAATAAT
62410 TACAAAAAAA
Statistics
Matches: 159, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
198 4 0.03
199 155 0.97
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (199 bp):
ATACACCGGCAGTGAAGTTTAGCAGACTACACAAGCGCGTTCTGAAGGGTAACATGTGTCCCCTA
GGGACTAGATTGAAATATTTAAAACTTAAATAATTCAAAAAATGAACATGTGTCAACTCCACAAC
CCGCTTGTGAAGTCCAAAATTTACACCGCCGGTGTATCAAATAATCACCCTTAAAGGGGTTTATA
TATG
Found at i:63699 original size:20 final size:20
Alignment explanation
Indices: 63662--63700 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
63652 TACTATTATT
63662 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
63682 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
63701 ATGTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:63880 original size:22 final size:22
Alignment explanation
Indices: 63852--64065 Score: 121
Period size: 22 Copynumber: 9.6 Consensus size: 22
63842 TGTCTCTGTG
63852 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* *
63874 TGGTTATTATAATTTCATAAGGA
1 TGGTTATCAAAATTTCATAA-GA
* *
63897 -GGTTATTAAAATTTCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
63918 TGGTTACCAAAATTTCATATGGA
1 TGGTTATCAAAATTTCATA-AGA
** **
63941 -ACTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * *
63962 AGGTTATCAAAAATTCATAATA
1 TGGTTATCAAAATTTCATAAGA
* * *
63984 TGCTTACCTAAATTTCAT-AGTA
1 TGGTTATCAAAATTTCATAAG-A
* * *
64006 TCAGGTTATTAAAATTTCTTAGGA
1 T--GGTTATCAAAATTTCATAAGA
* ** *
64030 AGGTTATTGAAATTTCATAATA
1 TGGTTATCAAAATTTCATAAGA
* *
64052 TGATTATCACAATT
1 TGGTTATCAAAATT
64066 ATATAGAAAT
Statistics
Matches: 142, Mismatches: 40, Indels: 20
0.70 0.20 0.10
Matches are distributed among these distances:
20 1 0.01
21 5 0.04
22 119 0.84
23 2 0.01
24 14 0.10
25 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.14, T:0.39
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:63955 original size:66 final size:66
Alignment explanation
Indices: 63849--64036 Score: 166
Period size: 66 Copynumber: 2.8 Consensus size: 66
63839 CCTTGTCTCT
* ** * * * *
63849 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATAAGG-AGGTTATTAAAATTTCA
1 GTGTGGTTACCAAAATTTCATAAGATACTTATCAAAATTTCAT-AGGAAGGTTATCAAAAATTCA
63913 TA
65 TA
* *
63915 GTGTGGTTACCAAAATTTCATATGGA-ACTTATCAAAATTTCATGGGAAGGTTATCAAAAATTCA
1 GTGTGGTTACCAAAATTTCATA-AGATACTTATCAAAATTTCATAGGAAGGTTATCAAAAATTCA
63979 TA
65 TA
* * * * * * *
63981 ATATGCTTACCTAAATTTCAT-AGTATCAGGTTATTAAAATTTCTTAGGAAGGTTAT
1 GTGTGGTTACCAAAATTTCATAAG-AT-A-CTTATCAAAATTTCATAGGAAGGTTAT
64037 TGAAATTTCA
Statistics
Matches: 98, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
64 1 0.01
65 3 0.03
66 68 0.69
67 3 0.03
68 23 0.23
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATACTTATCAAAATTTCATAGGAAGGTTATCAAAAATTCAT
A
Found at i:64125 original size:22 final size:21
Alignment explanation
Indices: 64089--64157 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
64079 ATCAAAGAGA
*
64089 TTATCAAAATGTCATAGTGAGG
1 TTAT-AAAATTTCATAGTGAGG
* *
64111 TTATAAGAATTTCATAATGTGG
1 TTATAA-AATTTCATAGTGAGG
64133 TTAATAAAATTTCATAAG-GAGG
1 TT-ATAAAATTTCAT-AGTGAGG
64155 TTA
1 TTA
64158 CTAATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
21 3 0.08
22 31 0.79
23 5 0.13
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.36
Consensus pattern (21 bp):
TTATAAAATTTCATAGTGAGG
Found at i:64633 original size:57 final size:57
Alignment explanation
Indices: 64545--64653 Score: 209
Period size: 57 Copynumber: 1.9 Consensus size: 57
64535 CCATATATAA
*
64545 ACCGCTCTTGGTAGACGATCGAGATTATTATACTGAGGATTTGATAGAGAAGCACAG
1 ACCGCTCTTGGTAGACGATCGAGATTATTATACTGAGGATTCGATAGAGAAGCACAG
64602 ACCGCTCTTGGTAGACGATCGAGATTATTATACTGAGGATTCGATAGAGAAG
1 ACCGCTCTTGGTAGACGATCGAGATTATTATACTGAGGATTCGATAGAGAAG
64654 GAACTGCGCA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.27
Consensus pattern (57 bp):
ACCGCTCTTGGTAGACGATCGAGATTATTATACTGAGGATTCGATAGAGAAGCACAG
Found at i:64810 original size:4 final size:4
Alignment explanation
Indices: 64801--64827 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
64791 AACTCTAATA
64801 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
64828 AAACCCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:65082 original size:29 final size:31
Alignment explanation
Indices: 65050--65116 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 31
65040 ACGCAATTTG
65050 GGATATAACGTTAC-AAAA-CAAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
*
65079 GGATATAACGTTACGAAAAGCGAGCAATTAA
1 GGATATAACGTTACGAAAAGCAAGCAATTAA
65110 GGATATA
1 GGATATA
65117 GTCAGTTAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
29 14 0.40
30 4 0.11
31 17 0.49
ACGTcount: A:0.48, C:0.12, G:0.19, T:0.21
Consensus pattern (31 bp):
GGATATAACGTTACGAAAAGCAAGCAATTAA
Found at i:65272 original size:31 final size:31
Alignment explanation
Indices: 65237--65315 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
65227 TTAACTGATT
*
65237 ATATCCTTAATTGCTTGAAATCGAAAACGTC
1 ATATCCTTAATTGCTTGAAATCAAAAACGTC
*
65268 ATATCCTTAATTGCTTGAAATCAAAAACGTT
1 ATATCCTTAATTGCTTGAAATCAAAAACGTC
*
65299 ATATCATTAATTGCTTG
1 ATATCCTTAATTGCTTG
65316 TTTTGTAACA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (31 bp):
ATATCCTTAATTGCTTGAAATCAAAAACGTC
Done.