Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015761.1 Corchorus olitorius cultivar O-4 contig15794, 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: 30770
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:16 original size:2 final size:2
Alignment explanation
Indices: 10--50 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1 GTATTAATA
10 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
51 AAAGACGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:632 original size:178 final size:178
Alignment explanation
Indices: 141--1116 Score: 1119
Period size: 178 Copynumber: 5.5 Consensus size: 178
131 TTTTATTTAG
* * * * * *
141 AGGTTGTTTCACGATTTACAACTTTAATGCAGGAGTT-GAAAACTAAATTTGATATTTCAAGTAT
1 AGGTTGTTTCATGATCTACAACTTTCATGAAGGA-TTCGAAAGCTAAATTTGATGTTTCAAGTAT
* *** *
205 CCAAAATGCTTT-AAAAAATTAGTTGTATCGGTTAGTAAGAATTGACGGTCTACTTAATGTTACA
65 CCAAAATGCTTTCGAAAAATTAGTTGTATCGGTTAGCGGGAATTGACAGTCTACTTAATGTTACA
* * * *
269 AAATTTTTGCTCTAGATATCTGATTGTGGTGATTCAAGTGTCTATTAAA
130 TAATTTTTACTCTAGATGTCTGATTGCGGTGATTCAAGTGTCTATTAAA
* *
318 AGGTTGTTTCATGATCTACAACTTTCATG-AGGATTGGAAAGTTAAATTTGATGTTTCAATTCAA
1 AGGTTGTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATG--T---TTCAA
* * *
382 ATATCCAAAATGCTTTCGAAAAATTAGTTTTATCGGTTAACGGGAATTGACAGTCTACTTAATGT
61 GTATCCAAAATGCTTTCGAAAAATTAGTTGTATCGGTTAGCGGGAATTGACAGTCTACTTAATGT
** * *
447 TACATAATTTTTACTCTAGATGTCTGATTGCGGCAATTCAAGTGTATGTTAAA
126 TACATAATTTTTACTCTAGATGTCTGATTGCGGTGATTCAAGTGTCTATTAAA
* * *
500 AGGTTGTTTTATGATCAACAACTTTTATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAGTATC
1 AGGTTGTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAGTATC
* * *
565 CAAAATACTTTCGAAAAATTACTTGTATCGTTTAGCGGGAATTGACAGTCTACTTAATGTTACAT
66 CAAAATGCTTTCGAAAAATTAGTTGTATCGGTTAGCGGGAATTGACAGTCTACTTAATGTTACAT
* * *
630 AATTTTTACTCTAAATGTCTGATTGCGGTGATTCAAGTGTTTGTTAAA
131 AATTTTTACTCTAGATGTCTGATTGCGGTGATTCAAGTGTCTATTAAA
* *
678 A-TTTCGTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAATAT
1 AGGTT-GTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAGTAT
** *
742 CCAAAATGCTTTCGAAAAATTAGTTGTATTAGTTAGCGGGAATTGATAGTCTACTTAATGTTACA
65 CCAAAATGCTTTCGAAAAATTAGTTGTATCGGTTAGCGGGAATTGACAGTCTACTTAATGTTACA
* * * * *
807 TAATTTTT-GTTTAAAATGTCTGATTGAGCTGATTCAAGTGTCTATTAAA
130 TAATTTTTACTCT-AGATGTCTGATTGCGGTGATTCAAGTGTCTATTAAA
* * ** * *
856 AGATTGTTTCATGA--T-C-ACTTTCATGAAAGACCCGAATGCTAAATTTGATGTTTAAAGTATC
1 AGGTTGTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAGTATC
* * * * * * * *
917 CAAAATGC-TCCTGAAAAATTAGTTTTTTCGGTTAGCAGGAATGGA-TGGCTACTTAATATTACA
66 CAAAATGCTTTC-GAAAAATTAGTTGTATCGGTTAGCGGGAATTGACAGTCTACTTAATGTTACA
* * * * * * *
980 TAAATTTTGCTCTAGACGTCCGATTGAGATGATTCAAGTGTTTATTAAA
130 TAATTTTTACTCTAGATGTCTGATTGCGGTGATTCAAGTGTCTATTAAA
* * * * * * * * * *
1029 AAGTTGTTTAACGATCTACAACTTTAATGAAGGACTCAAAAGTTAAATTTAATATTTCAAGTATA
1 AGGTTGTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAGTATC
*
1094 AAAAATGCTTTCGAAAAATTAGT
66 CAAAATGCTTTCGAAAAATTAGT
1117 GTCTTGGGTG
Statistics
Matches: 686, Mismatches: 95, Indels: 36
0.84 0.12 0.04
Matches are distributed among these distances:
173 65 0.09
174 76 0.11
175 4 0.01
176 20 0.03
177 83 0.12
178 281 0.41
179 2 0.00
181 21 0.03
182 112 0.16
183 22 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (178 bp):
AGGTTGTTTCATGATCTACAACTTTCATGAAGGATTCGAAAGCTAAATTTGATGTTTCAAGTATC
CAAAATGCTTTCGAAAAATTAGTTGTATCGGTTAGCGGGAATTGACAGTCTACTTAATGTTACAT
AATTTTTACTCTAGATGTCTGATTGCGGTGATTCAAGTGTCTATTAAA
Found at i:1266 original size:14 final size:15
Alignment explanation
Indices: 1242--1274 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1232 CTAATAAAAT
1242 ATTTCATTACTTTAA
1 ATTTCATTACTTTAA
*
1257 ATTT-ATTACTTTGA
1 ATTTCATTACTTTAA
1271 ATTT
1 ATTT
1275 TAAATCGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.30, C:0.09, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTTCATTACTTTAA
Found at i:3062 original size:41 final size:41
Alignment explanation
Indices: 3017--3122 Score: 151
Period size: 41 Copynumber: 2.6 Consensus size: 41
3007 CTGGAGTAAC
* * *
3017 ACTTCTAGTGCCAAAGGTAATTTTAGTTTACCAAAGTGACA
1 ACTTCTAGTGTCAAAGGTAATTTTAATTTACCAAAATGACA
* *
3058 ACTTCTGGTGTCAAATGTAATTTTAATTTACCAAAATGACA
1 ACTTCTAGTGTCAAAGGTAATTTTAATTTACCAAAATGACA
3099 ACTTC-AGGTGTCAAAGGTAATTTT
1 ACTTCTA-GTGTCAAAGGTAATTTT
3123 CGATATTATT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (41 bp):
ACTTCTAGTGTCAAAGGTAATTTTAATTTACCAAAATGACA
Found at i:3438 original size:11 final size:11
Alignment explanation
Indices: 3424--3479 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
3414 ATCTAAAGAG
3424 ATAAAATCTAA
1 ATAAAATCTAA
3435 ATAAAATCTAGA
1 ATAAAATCTA-A
*
3447 TTACATAATC-AA
1 ATA-A-AATCTAA
*
3459 ATAATATCTAA
1 ATAAAATCTAA
*
3470 ATATAATCTA
1 ATAAAATCTA
3480 CTTAAATCTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
10 3 0.08
11 21 0.58
12 6 0.17
13 2 0.06
14 4 0.11
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAAATCTAA
Found at i:3876 original size:3 final size:3
Alignment explanation
Indices: 3868--3905 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
3858 AAAATTTCCC
3868 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3906 GCTTTCTCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:9258 original size:18 final size:18
Alignment explanation
Indices: 9220--9261 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
9210 AGGAAATATT
*
9220 AATAATAATTATTCTGAA
1 AATAATAATTATTCTAAA
9238 AATAATAATTATT-TAATA
1 AATAATAATTATTCTAA-A
9256 AATAAT
1 AATAAT
9262 TAATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
AATAATAATTATTCTAAA
Found at i:11300 original size:21 final size:20
Alignment explanation
Indices: 11266--11306 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
11256 GTAGAATCAA
11266 GAAAATAAATAATAGATAAT
1 GAAAATAAATAATAGATAAT
*
11286 GAAAATAGATAAATAGATAAT
1 GAAAATAAAT-AATAGATAAT
11307 AGAATTAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.63, C:0.00, G:0.12, T:0.24
Consensus pattern (20 bp):
GAAAATAAATAATAGATAAT
Found at i:12303 original size:70 final size:70
Alignment explanation
Indices: 12190--12650 Score: 354
Period size: 70 Copynumber: 6.7 Consensus size: 70
12180 ACTTGTTTGC
* * * * * * * **
12190 AGAAATATGACAAAATTGACCATTTGTCCGAAAGGGCATTTTGGGAAATAAAAAAACAAGTCTAA
1 AGAAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATAAAAAATTAAGTCTAA
12255 ATGCA
66 ATGCA
*
12260 AGAAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGG-------AAATTAAATCTAA
1 AGAAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATAAAAAATTAAGTCTAA
12318 ATGCA
66 ATGCA
* * * * * *
12323 ACAAATGTGA-AAAACTGACCCTTTTTCCGAAAGGGTATTTTGGAAAATAAAAAGTTAAGTCTAC
1 AGAAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATAAAAAATTAAGTCTAA
*
12387 ATG-T
66 ATGCA
* * * * * * * *
12391 AGAAAATGTGACAAGACTGATCCTTTGTCTGAAATGATATTTTGGGAAATCAAAAATTTAGTTTG
1 AG-AAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATAAAAAATTAAGTCTA
*
12456 TATGCA
65 AATGCA
** * * * *
12462 AG-AATGTGACACCATTGACCCTTTGTT-TGAAAGGGCATTTTGGGAAATAAAACATTAAATCTA
1 AGAAATGTGACAAGACTGACCCTTT-TTCTGAAAGGGTATTTTGGGAAATAAAAAATTAAGTCTA
* **
12525 AAGGTG
65 AATGCA
* * * * * * * * * *
12531 TGAAATGTGGCATA-ACTGACCATTTGTCCGAAAGGGTATCTTAGGAAATTTAAAAATTAAATAT
1 AGAAATGTGACA-AGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAA-TAAAAAATTAAGTCT
*
12595 AAATGCG
64 AAATGCA
* *
12602 GGAAATGTGACAAGACTGA-CCTTTTGTTTGAAAGGGTATTTTGGGAAAT
1 AGAAATGTGACAAGACTGACCCTTTT-TCTGAAAGGGTATTTTGGGAAAT
12651 TAAAGTTAAA
Statistics
Matches: 300, Mismatches: 74, Indels: 34
0.74 0.18 0.08
Matches are distributed among these distances:
62 31 0.10
63 24 0.08
68 1 0.00
69 70 0.23
70 122 0.41
71 52 0.17
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (70 bp):
AGAAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATAAAAAATTAAGTCTAA
ATGCA
Found at i:12355 original size:62 final size:63
Alignment explanation
Indices: 12250--12370 Score: 199
Period size: 62 Copynumber: 1.9 Consensus size: 63
12240 AAAAAACAAG
* * * *
12250 TCTAAATGCAAGAAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATTAAA
1 TCTAAATGCAACAAATGTGACAAAACTGACCCTTTTTCCGAAAGGGTATTTTGGAAAATTAAA
12313 TCTAAATGCAACAAATGTGA-AAAACTGACCCTTTTTCCGAAAGGGTATTTTGGAAAAT
1 TCTAAATGCAACAAATGTGACAAAACTGACCCTTTTTCCGAAAGGGTATTTTGGAAAAT
12371 AAAAAGTTAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
62 35 0.65
63 19 0.35
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (63 bp):
TCTAAATGCAACAAATGTGACAAAACTGACCCTTTTTCCGAAAGGGTATTTTGGAAAATTAAA
Found at i:12383 original size:132 final size:133
Alignment explanation
Indices: 12192--12440 Score: 340
Period size: 132 Copynumber: 1.9 Consensus size: 133
12182 TTGTTTGCAG
* *
12192 AAATATGACAAAATTGACCATTTGTCCGAAAGGGCATTTTGGGAAATAAAAAAACAAGTCTAAAT
1 AAATATGACAAAACTGACCATTTGTCCGAAAGGGCATTTTGGAAAATAAAAAAACAAGTCTAAAT
* *
12257 GCAAG-AAATGTGACAAGACTGACCCTTTTTCTGAAAGGGTATTTTGGGAAATTAAATCTAAATG
66 G-AAGAAAATGTGACAAGACTGACCCTTTGTCTGAAAGGATATTTTGGGAAATTAAATCTAAATG
12321 CAAC
130 CAAC
* * * * *** *
12325 AAATGTGA-AAAACTGACCCTTTTTCCGAAAGGGTATTTTGGAAAATAAAAAGTTAAGTCTACAT
1 AAATATGACAAAACTGACCATTTGTCCGAAAGGGCATTTTGGAAAATAAAAAAACAAGTCTAAAT
* * *
12389 GTAGAAAATGTGACAAGACTGATCCTTTGTCTGAAATGATATTTTGGGAAAT
66 GAAGAAAATGTGACAAGACTGACCCTTTGTCTGAAAGGATATTTTGGGAAAT
12441 CAAAAATTTA
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
131 2 0.02
132 91 0.91
133 7 0.07
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (133 bp):
AAATATGACAAAACTGACCATTTGTCCGAAAGGGCATTTTGGAAAATAAAAAAACAAGTCTAAAT
GAAGAAAATGTGACAAGACTGACCCTTTGTCTGAAAGGATATTTTGGGAAATTAAATCTAAATGC
AAC
Found at i:12607 original size:71 final size:72
Alignment explanation
Indices: 12509--12651 Score: 173
Period size: 71 Copynumber: 2.0 Consensus size: 72
12499 TTTTGGGAAA
* * * *
12509 TAAAACATTAAATCTAAAGGTGTGAAATGTGGCATA-ACTGACCATTTGTCCGAAAGGGTATCTT
1 TAAAACATTAAATATAAAGGCGGGAAATGTGACA-AGACTGACCATTTGTCCGAAAGGGTATCTT
12573 AGGAAATT
65 AGGAAATT
* * ** * *
12581 TAAAA-ATTAAATATAAATGCGGGAAATGTGACAAGACTGACCTTTTGTTTGAAAGGGTATTTTG
1 TAAAACATTAAATATAAAGGCGGGAAATGTGACAAGACTGACCATTTGTCCGAAAGGGTATCTTA
12645 GGAAATT
66 GGAAATT
12652 AAAGTTAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
70 1 0.02
71 54 0.90
72 5 0.08
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (72 bp):
TAAAACATTAAATATAAAGGCGGGAAATGTGACAAGACTGACCATTTGTCCGAAAGGGTATCTTA
GGAAATT
Found at i:13572 original size:17 final size:17
Alignment explanation
Indices: 13550--13585 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13540 CTGTTTTGAG
*
13550 TTTTTTATTTTCCTTTC
1 TTTTTTATTTTCCCTTC
*
13567 TTTTTTCTTTTCCCTTC
1 TTTTTTATTTTCCCTTC
13584 TT
1 TT
13586 CTTCCTCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTATTTTCCCTTC
Found at i:16838 original size:22 final size:23
Alignment explanation
Indices: 16797--16848 Score: 56
Period size: 22 Copynumber: 2.3 Consensus size: 23
16787 AATTGCTTTC
*
16797 TTAA-TTAGTATTTTAGTTTAGT
1 TTAATTTAGTATTTTAGTTTACT
16819 TTAATTTAGT-TTTT-GCTTTACT
1 TTAATTTAGTATTTTAG-TTTACT
*
16841 TTTATTTA
1 TTAATTTA
16849 CTTGCTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 20 0.77
23 5 0.19
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (23 bp):
TTAATTTAGTATTTTAGTTTACT
Found at i:18082 original size:22 final size:22
Alignment explanation
Indices: 18052--18094 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18042 AAAATTCAGA
*
18052 ACAAGTCCTGCCCAGGACTTGG
1 ACAACTCCTGCCCAGGACTTGG
18074 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
18095 TTGCGGGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.35, G:0.23, T:0.19
Consensus pattern (22 bp):
ACAACTCCTGCCCAGGACTTGG
Found at i:18944 original size:22 final size:22
Alignment explanation
Indices: 18916--18958 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
18906 TTTCCCGCAA
*
18916 CAAGTCCTGGGCAGGAGTTGTC
1 CAAGTCCTGGGCAGGACTTGTC
18938 CAAGTCCTGGGCAGGACTTGT
1 CAAGTCCTGGGCAGGACTTGT
18959 TCTAAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (22 bp):
CAAGTCCTGGGCAGGACTTGTC
Found at i:20282 original size:15 final size:15
Alignment explanation
Indices: 20264--20305 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
20254 TGGAAACTTC
20264 TTCGATTGTCTCAG-A
1 TTCGATTGTCTC-GTA
20279 TTCGATTGTCTCGTA
1 TTCGATTGTCTCGTA
*
20294 TTCGATTCTCTC
1 TTCGATTGTCTC
20306 TTCATTCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 1 0.04
15 24 0.96
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (15 bp):
TTCGATTGTCTCGTA
Found at i:25726 original size:24 final size:25
Alignment explanation
Indices: 25680--25727 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
25670 ATTGGAGTAT
*
25680 TTATTTATCTTGTTGCTTAATTTTA
1 TTATTTATCTTGTTGATTAATTTTA
* *
25705 TTATTT-TCTTGTTTATTTATTTT
1 TTATTTATCTTGTTGATTAATTTT
25728 TATTGTTACT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (25 bp):
TTATTTATCTTGTTGATTAATTTTA
Found at i:27256 original size:32 final size:32
Alignment explanation
Indices: 27219--27283 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
27209 TCGGATTACC
* *
27219 TCCAGAT-TAGATAAATATCAGGTTCGGATCTT
1 TCCAGATAAAGAT-AATATCAGATTCGGATCTT
* *
27251 TCCAGATAAAGATAATTTCAGATTCGGGTCTT
1 TCCAGATAAAGATAATATCAGATTCGGATCTT
27283 T
1 T
27284 GACTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.35
Consensus pattern (32 bp):
TCCAGATAAAGATAATATCAGATTCGGATCTT
Found at i:28302 original size:33 final size:33
Alignment explanation
Indices: 28265--28336 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
28255 TGATGTCCAT
* * *
28265 AAAAAAC-ATATTTTCTCCATTAATTATTTGCAG
1 AAAAAACAAT-TTTTCTCCAATAATAATTTGCAA
28298 AAAAAACAATTTTTCTCCAATAATAATTTGCAA
1 AAAAAACAATTTTTCTCCAATAATAATTTGCAA
28331 AAAAAA
1 AAAAAA
28337 AAAATCTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 33 0.94
34 2 0.06
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (33 bp):
AAAAAACAATTTTTCTCCAATAATAATTTGCAA
Found at i:28432 original size:2 final size:2
Alignment explanation
Indices: 28425--28462 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28415 ACTAGTATTA
28425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28463 TACTACTCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.