Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold548
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: 227431
ACGTcount: A:0.14, C:0.08, G:0.08, T:0.14
Warning! 129514 characters in sequence are not A, C, G, or T
Found at i:4327 original size:8 final size:9
Alignment explanation
Indices: 4309--4335 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
4299 AATCAGATTC
4309 AAAAATAAA
1 AAAAATAAA
4318 AAAAATAAA
1 AAAAATAAA
4327 AAAAATAAA
1 AAAAATAAA
4336 GGAGAAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:8649 original size:24 final size:23
Alignment explanation
Indices: 8595--8651 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
8585 GAATAAACAA
*
8595 GAAATGGTATTTAGTTTAGGTAC
1 GAAATGGTATTTAGATTAGGTAC
**
8618 GATTTGGTATTTAGGAATT-GGTAC
1 GAAATGGTATTTA-G-ATTAGGTAC
8642 GAAATGGTAT
1 GAAATGGTAT
8652 GGAAGTTGGT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 14 0.52
25 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.28, T:0.39
Consensus pattern (23 bp):
GAAATGGTATTTAGATTAGGTAC
Found at i:11252 original size:20 final size:20
Alignment explanation
Indices: 11227--11273 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
11217 AGCTCGTTTC
*
11227 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGATCAAGT
*
11247 CAGCTCATTCGAGATCAATT
1 CAGCTCATTCGAGATCAAGT
11267 CAGCTCA
1 CAGCTCA
11274 ATTTTAACCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.28, C:0.30, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGATCAAGT
Found at i:13720 original size:20 final size:20
Alignment explanation
Indices: 13670--13724 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
13660 TTTCTCATTT
* *
13670 TTTTTCATTCTCTTTTTTTGA
1 TTTTTC-TTTTCTTTTTTTCA
*
13691 ATTTTC-TTTCTTTTTTTCA
1 TTTTTCTTTTCTTTTTTTCA
13710 TTTTTCTTTTCTTTT
1 TTTTTCTTTTCTTTT
13725 GTATTTGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 16 0.55
20 8 0.28
21 5 0.17
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTTTCTTTTCTTTTTTTCA
Found at i:17244 original size:15 final size:15
Alignment explanation
Indices: 17219--17265 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
17209 AGAAAAGAAC
17219 AAAGAAAATGAAAATG
1 AAAG-AAATGAAAATG
*
17235 AAAGAAATGAAAAAG
1 AAAGAAATGAAAATG
17250 AAA-AAGATGAAAATG
1 AAAGAA-ATGAAAATG
17265 A
1 A
17266 GATTTCAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 22 0.79
16 4 0.14
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (15 bp):
AAAGAAATGAAAATG
Found at i:17312 original size:12 final size:12
Alignment explanation
Indices: 17295--17357 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
17285 AGTGAAAAGC
*
17295 AAAAAGAGATTG
1 AAAAAGAAATTG
17307 AAAAAGAAATTG
1 AAAAAGAAATTG
17319 AAAAAG-AA--G
1 AAAAAGAAATTG
*
17328 AAAAAGAAAGAGTGG
1 AAAAAG-AA-A-TTG
17343 AAAAAGAAATTG
1 AAAAAGAAATTG
17355 AAA
1 AAA
17358 GAGAGCCTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 7 0.16
11 3 0.07
12 23 0.53
13 1 0.02
14 2 0.05
15 7 0.16
ACGTcount: A:0.67, C:0.00, G:0.22, T:0.11
Consensus pattern (12 bp):
AAAAAGAAATTG
Found at i:22043 original size:20 final size:20
Alignment explanation
Indices: 22018--22069 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
22008 AGACCGTATA
22018 CAATTTTTTTTCTTTTTTTT
1 CAATTTTTTTTCTTTTTTTT
*
22038 CAATTTTTTTTATTTTTTTT
1 CAATTTTTTTTCTTTTTTTT
*
22058 CGATTTTTTTTC
1 CAATTTTTTTTC
22070 AAATTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.77
Consensus pattern (20 bp):
CAATTTTTTTTCTTTTTTTT
Found at i:22044 original size:11 final size:11
Alignment explanation
Indices: 22018--22080 Score: 80
Period size: 11 Copynumber: 6.0 Consensus size: 11
22008 AGACCGTATA
22018 CAATTTTTTTT
1 CAATTTTTTTT
22029 C--TTTTTTTT
1 CAATTTTTTTT
22038 CAATTTTTTTT
1 CAATTTTTTTT
22049 --ATTTTTTTT
1 CAATTTTTTTT
*
22058 CGATTTTTTTT
1 CAATTTTTTTT
22069 CAAATTTTTTTT
1 C-AATTTTTTTT
22081 TCACGAGTCT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
9 18 0.39
11 19 0.41
12 9 0.20
ACGTcount: A:0.14, C:0.08, G:0.02, T:0.76
Consensus pattern (11 bp):
CAATTTTTTTT
Found at i:22416 original size:22 final size:21
Alignment explanation
Indices: 22384--22447 Score: 92
Period size: 22 Copynumber: 3.0 Consensus size: 21
22374 TTGGTATTTA
22384 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
22405 GGAAGTTGGTACGAAATGGTAT
1 GGAA-TTGGTACGAAATGGTAT
* *
22427 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
22448 ATGGTTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
21 4 0.10
22 34 0.87
23 1 0.03
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:59621 original size:31 final size:32
Alignment explanation
Indices: 59586--59647 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
59576 AATAAATATT
*
59586 ATGCATGACATAATTAAA-ATGCAAACTTATA
1 ATGCAAGACATAATTAAAGATGCAAACTTATA
* *
59617 ATGCAAGCCATTATTAAAGATGCAAACTTAT
1 ATGCAAGACATAATTAAAGATGCAAACTTAT
59648 TAAACTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (32 bp):
ATGCAAGACATAATTAAAGATGCAAACTTATA
Found at i:99222 original size:20 final size:19
Alignment explanation
Indices: 99197--99240 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
99187 CCGTATACAA
99197 TTTTTTTCTTTC-AATTTT
1 TTTTTTTCTTTCGAATTTT
99215 GTTTTTTTCTTTCGAATTTT
1 -TTTTTTTCTTTCGAATTTT
99235 TTTTTT
1 TTTTTT
99241 CAATTGCGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (19 bp):
TTTTTTTCTTTCGAATTTT
Found at i:99404 original size:17 final size:17
Alignment explanation
Indices: 99379--99419 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
99369 CCGTATGCAA
99379 TTTTT-TTTTCAAATTT
1 TTTTTCTTTTCAAATTT
* *
99395 TTTTTCTTTTCGATTTT
1 TTTTTCTTTTCAAATTT
99412 TTTTTCTT
1 TTTTTCTT
99420 GATTTTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTTTCTTTTCAAATTT
Found at i:139547 original size:22 final size:22
Alignment explanation
Indices: 139516--139580 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
139506 ACCTTTTTGA
*
139516 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
139539 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
139561 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
139581 TTCCTAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:163217 original size:20 final size:20
Alignment explanation
Indices: 163192--163327 Score: 175
Period size: 20 Copynumber: 6.8 Consensus size: 20
163182 TCCATGCGGT
*
163192 TCAGCTCACTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
163212 TCAGCTCATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
* * *
163232 CCAACTCATTCAAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
*
163252 TCAGCTTATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
163272 TCAGCTCATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
* ** * *
163292 TCACCTCACACAAGCTCAAT
1 TCAGCTCATTCGAGCTCAAG
163312 TCAGCTCATT-GAGCTC
1 TCAGCTCATTCGAGCTC
163328 GTTATTAGCT
Statistics
Matches: 98, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 5 0.05
20 93 0.95
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:163249 original size:10 final size:10
Alignment explanation
Indices: 163194--163289 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
163184 CATGCGGTTC
*
163194 AGCTCACTCG
1 AGCTCATTCG
*
163204 AGCTCAAGTC-
1 AGCTC-ATTCG
163214 AGCTCATTCG
1 AGCTCATTCG
** *
163224 AGCTCAAGCC
1 AGCTCATTCG
* *
163234 AACTCATTCA
1 AGCTCATTCG
*
163244 AGCTCAAGTC-
1 AGCTC-ATTCG
*
163254 AGCTTATTCG
1 AGCTCATTCG
*
163264 AGCTCAAGTC-
1 AGCTC-ATTCG
163274 AGCTCATTCG
1 AGCTCATTCG
163284 AGCTCA
1 AGCTCA
163290 AGTCACCTCA
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
9 9 0.14
10 46 0.72
11 9 0.14
ACGTcount: A:0.27, C:0.31, G:0.18, T:0.24
Consensus pattern (10 bp):
AGCTCATTCG
Found at i:163338 original size:60 final size:60
Alignment explanation
Indices: 163192--163327 Score: 202
Period size: 60 Copynumber: 2.3 Consensus size: 60
163182 TCCATGCGGT
* **
163192 TCAGCTCACTCGAGCTCAAGTCAGCTCATTCGAGCTCAAGCCAACTCATTCAAGCTCAAG
1 TCAGCTCATTCGAGCTCAAGTCAGCTCATTCGAGCTCAAGCCAACTCACACAAGCTCAAG
* * * *
163252 TCAGCTTATTCGAGCTCAAGTCAGCTCATTCGAGCTCAAGTCACCTCACACAAGCTCAAT
1 TCAGCTCATTCGAGCTCAAGTCAGCTCATTCGAGCTCAAGCCAACTCACACAAGCTCAAG
163312 TCAGCTCATT-GAGCTC
1 TCAGCTCATTCGAGCTC
163328 GTTATTAGCT
Statistics
Matches: 68, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
59 6 0.09
60 62 0.91
ACGTcount: A:0.27, C:0.32, G:0.16, T:0.24
Consensus pattern (60 bp):
TCAGCTCATTCGAGCTCAAGTCAGCTCATTCGAGCTCAAGCCAACTCACACAAGCTCAAG
Found at i:167629 original size:14 final size:13
Alignment explanation
Indices: 167599--167634 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
167589 TCAATCTCAA
167599 TTTCTTTTTTAAT
1 TTTCTTTTTTAAT
*
167612 TTTCTTTTCTTTAT
1 TTTCTTTT-TTAAT
167626 TTTCTTTTT
1 TTTCTTTTT
167635 CTCTCACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.08, C:0.11, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTCTTTTTTAAT
Found at i:169703 original size:20 final size:19
Alignment explanation
Indices: 169648--169692 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
169638 CATTTCATTG
*
169648 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
169669 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
169688 AGCTC
1 AGCTC
169693 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:170843 original size:17 final size:17
Alignment explanation
Indices: 170821--170857 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
170811 CAACATTTTC
170821 CTTAGTGTTGGTTCATT
1 CTTAGTGTTGGTTCATT
170838 CTTAGTGTTGGTTCATT
1 CTTAGTGTTGGTTCATT
170855 CTT
1 CTT
170858 GTTTTTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.11, C:0.14, G:0.22, T:0.54
Consensus pattern (17 bp):
CTTAGTGTTGGTTCATT
Found at i:174573 original size:22 final size:22
Alignment explanation
Indices: 174521--174585 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
174511 TATTTGGGAA
* *
174521 TTGGTACGAAACGGTAAGGGAT
1 TTGGTACGAAATGGTAATGGAT
**
174543 TTGAAACGAAATGGTAATGGAT
1 TTGGTACGAAATGGTAATGGAT
*
174565 TTGGTACGAAAATGGAAATGG
1 TTGGTACG-AAATGGTAATGG
174586 TTCAAAAAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
22 24 0.69
23 11 0.31
ACGTcount: A:0.37, C:0.06, G:0.32, T:0.25
Consensus pattern (22 bp):
TTGGTACGAAATGGTAATGGAT
Found at i:194601 original size:101 final size:102
Alignment explanation
Indices: 194488--194672 Score: 248
Period size: 101 Copynumber: 1.8 Consensus size: 102
194478 TATTATCATT
* * * * * *
194488 CGATACATGTAGTAGCCTTCATATAGTATTACACACATGATC-AAACTTTTCAGT-TCACATAGT
1 CGATACAAGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATCCAGTAT-ACATAGT
194551 AGCCTGCACATAGTACTACACACGTGACAACTAATATC
65 AGCCTGCACATAGTACTACACACGTGACAACTAATATC
* * * *
194589 CGATACAAGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTATGCATAGTA
1 CGATACAAGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATCCAGTATACATAGTA
*
194654 GCTTGCACATAGTACTACA
66 GCCTGCACATAGTACTACA
194673 TATGCGACCT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
101 37 0.52
102 33 0.46
103 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (102 bp):
CGATACAAGTAGTAGCCTGCACATAGTACTACACACATGATCGAAACTATCCAGTATACATAGTA
GCCTGCACATAGTACTACACACGTGACAACTAATATC
Found at i:194640 original size:51 final size:49
Alignment explanation
Indices: 194544--194672 Score: 156
Period size: 51 Copynumber: 2.6 Consensus size: 49
194534 TTTTCAGTTC
194544 ACATAGTAGCCTGCACATAGTACTACACACGTGACAACTAATATCC-G-AT
1 ACATAGTAGCCTGCACATAGTACTACACACGTGACAAC--ATATCCGGTAT
194593 ACAAGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TATCCGGTAT
1 AC-A-TAGTAGCCTGCACATAGTACTACACACGTGA-C-AA-CATATCCGGTAT
* *
194646 GCATAGTAGCTTGCACATAGTACTACA
1 ACATAGTAGCCTGCACATAGTACTACA
194673 TATGCGACCT
Statistics
Matches: 71, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
49 2 0.03
50 1 0.01
51 59 0.83
52 3 0.04
53 5 0.07
54 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (49 bp):
ACATAGTAGCCTGCACATAGTACTACACACGTGACAACATATCCGGTAT
Found at i:194914 original size:21 final size:21
Alignment explanation
Indices: 194888--194931 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
194878 TTCCTTATCT
194888 TTCTTGACTTATAATAGTAAA
1 TTCTTGACTTATAATAGTAAA
*
194909 TTCTTGACTTATAATTGTAAA
1 TTCTTGACTTATAATAGTAAA
194930 TT
1 TT
194932 TAACTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (21 bp):
TTCTTGACTTATAATAGTAAA
Found at i:194939 original size:19 final size:21
Alignment explanation
Indices: 194888--194939 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
194878 TTCCTTATCT
*
194888 TTCTTGACTTATAATAGTAAA
1 TTCTTAACTTATAATAGTAAA
* *
194909 TTCTTGACTTATAATTGTAAA
1 TTCTTAACTTATAATAGTAAA
194930 -T-TTAACTTAT
1 TTCTTAACTTAT
194940 TTTACACTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 8 0.28
20 1 0.03
21 20 0.69
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (21 bp):
TTCTTAACTTATAATAGTAAA
Found at i:196447 original size:20 final size:21
Alignment explanation
Indices: 196409--196449 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
196399 ATGTGTTCTC
196409 ATTTAATTAATTAGCTACATGT
1 ATTTAATT-ATTAGCTACATGT
*
196431 ATTTAATT-TTAGGTACATG
1 ATTTAATTATTAGCTACATG
196450 CAAGACGACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.34, C:0.07, G:0.12, T:0.46
Consensus pattern (21 bp):
ATTTAATTATTAGCTACATGT
Found at i:198881 original size:15 final size:14
Alignment explanation
Indices: 198849--198888 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
198839 CATATACGAA
198849 ATTTAAAAAAAGTG
1 ATTTAAAAAAAGTG
* *
198863 ATTTAAAAAATTGTT
1 ATTTAAAAAA-AGTG
198878 ATTTAAAAAAA
1 ATTTAAAAAAA
198889 AAGGGTTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.35
Consensus pattern (14 bp):
ATTTAAAAAAAGTG
Found at i:200816 original size:34 final size:34
Alignment explanation
Indices: 200765--200834 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
200755 GTTTATTAAC
200765 TTTAATTCAGCTCAAATAAGTGCTAGTAAATAAT
1 TTTAATTCAGCTCAAATAAGTGCTAGTAAATAAT
* * * *
200799 TTTAGTTCAGCTTAAATAAGTGTTAGTAATTAAT
1 TTTAATTCAGCTCAAATAAGTGCTAGTAAATAAT
200833 TT
1 TT
200835 GTTTAAATCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.09, G:0.13, T:0.41
Consensus pattern (34 bp):
TTTAATTCAGCTCAAATAAGTGCTAGTAAATAAT
Found at i:202121 original size:72 final size:71
Alignment explanation
Indices: 202004--202192 Score: 245
Period size: 72 Copynumber: 2.6 Consensus size: 71
201994 CTGAATAACA
* * *
202004 AGCTTAGAAAAATGCAACAGCAACCTCCTCTCTT-AATGCCGTCCCAAGTCCCATGCACACATTA
1 AGCTTGGAAAAATGCAGCAGCAACCT--TCTCTTAAATGTCGTCCCAAGTCCCATGCACACATTA
202068 AATTCGGC
64 AATTCGGC
* *
202076 AGCTTGGAAAAAGGCAGCAGTAACCTTCTCTTGAAATGTCGTCCCAAGTCCCATGCACACATTAA
1 AGCTTGGAAAAATGCAGCAGCAACCTTCTCTT-AAATGTCGTCCCAAGTCCCATGCACACATTAA
*
202141 ATTCGGT
65 ATTCGGC
* * *
202148 AACTTGGAAAAATGCAGTAGCAACCTTTCACTTTAAATGTCGTCC
1 AGCTTGGAAAAATGCAGCAGCAACC-TTCTC-TTAAATGTCGTCC
202193 ATGTACCTGC
Statistics
Matches: 102, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
70 6 0.06
72 79 0.77
73 15 0.15
74 2 0.02
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.25
Consensus pattern (71 bp):
AGCTTGGAAAAATGCAGCAGCAACCTTCTCTTAAATGTCGTCCCAAGTCCCATGCACACATTAAA
TTCGGC
Found at i:204534 original size:10 final size:10
Alignment explanation
Indices: 204492--204526 Score: 70
Period size: 10 Copynumber: 3.5 Consensus size: 10
204482 CTAGTTAAGT
204492 GCTGAATTGA
1 GCTGAATTGA
204502 GCTGAATTGA
1 GCTGAATTGA
204512 GCTGAATTGA
1 GCTGAATTGA
204522 GCTGA
1 GCTGA
204527 TATGAGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.29, C:0.11, G:0.31, T:0.29
Consensus pattern (10 bp):
GCTGAATTGA
Done.