Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1238
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: 43830
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4448 original size:62 final size:62
Alignment explanation
Indices: 4349--5546 Score: 1001
Period size: 62 Copynumber: 19.3 Consensus size: 62
4339 ATATCGGACG
* * *
4349 CCTTTTTCCTTTCAAAGCCCACACGAGTTGGTTGCACCCTTTAGTCCTCAAAGAGTAGCGTC
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * ** *
4411 CCTTTATGTTTTCAAAGCCCACATTAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCGTC
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * ** *
4473 CCTTTATGTTTTTAAAGCCCACATTAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAG-GATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCG-TC
* * * * *
4535 CCTTTTTCTTTTCAGAGCCCACACGGGTTGGTGGCACCCTTTAGCCCTCAAAGAGTAGCAT-
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * *
4596 GCTTTTATCTTTTCAAAAG-CCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAG-GTC
1 CCTTTT-TCTTTTC-AAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* *
4658 ACCTTTTTCTTTTCAAA-CCCTACACGAGTTGGTGGAACCCTTTAGTTCTCAAAGAGCCAGACG-
1 -CCTTTTTCTTTTCAAAGCCC-ACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAG-CAG-CGT
4721 -
62 C
* * * * * * *
4721 ACTTTTTCCTTTCAAAGCCCACACAAGTTAGTGGCACCCTTTAGTCCTCAAAGAGTAGCCTG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * * *
4783 CCTTTATATTTTCAAAGCCCACATGAGTTGGCGGCACCCTTTAGTCCTCAAAGAGTAG-G-C
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * *
4843 CACTTTTTTCTTTTCGAACCCCACATGAGTTGGTGGCACCCTTTAGTCCTTAAA-ACGCAG-GAT
1 C-C-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGA-GCAGCG-T
*
4906 G
62 C
* *
4907 CCTTTTAGC-TTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAG-GAC
1 CCTTTT-TCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * * * * * *
4968 GCATTTTTCATTGCAAAGCCCACACGGGTTGGTAGCACTACTTT-GTCCTCAAGGAATCAGAC--
1 -CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CCTTTAGTCCTCAAAG-AGCAG-CGT
*
5030 A
62 C
* * * * * *
5031 CCTTTTTCTTTTCAAACCCCACTCGTGTTGGTGGCTCCCTTTAGTTCTCAAAGAGCCAGAAG--
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAG-CAG-CGTC
* * *
5093 CCTTTTTCCTTTTCAAAGCCCACACGAGTTGATGGCACCCTTTAGTCCTCAAAGAGCA-AGAC
1 CCTTTTT-CTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * * * * * ** *
5155 ACATTTTTCTTTTCAAAGCCTACACGGGTTCGTAGCACCCTTTAATCCACAAAGGATAAGAC--A
1 -CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAA-GAGCAG-CGTC
** * * * * * * * *
5218 CAATTTTCTTTTCAAAGCCTAGA-TAGATTTGTGGCACCTTTTAGTCCTCAAATAGAAG-GAC
1 CCTTTTTCTTTTCAAAGCCCACACGAG-TTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
** * * * * * * * *
5279 ACC-TTTTCCATTCAAAGGCCACACGACTTGGAGCCACCCCTTAGTCCTCAAAGGGTAG-GAC
1 -CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * * * *
5340 GCCATTTTCCTTTCAAAGCCCACACGAGTTGGTGGCAACCTTTAGTCCTTAAAGAGCCG-GAC
1 -CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* ** * *
5402 GCCTTTTTCCTTTCAAAGCAGACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCATG
1 -CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
* * * *
5465 CCTTTATCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTTCTCAAAGAGCAG-GATG
1 CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCG-TC
*
5527 CCTTTTTCCTTTCAAAGCCC
1 CCTTTTTCTTTTCAAAGCCC
5547 GCACATTGTA
Statistics
Matches: 928, Mismatches: 163, Indels: 90
0.79 0.14 0.08
Matches are distributed among these distances:
60 4 0.00
61 70 0.08
62 776 0.84
63 76 0.08
64 1 0.00
65 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (62 bp):
CCTTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCGTC
Found at i:4690 original size:186 final size:185
Alignment explanation
Indices: 4348--5546 Score: 1189
Period size: 186 Copynumber: 6.4 Consensus size: 185
4338 GATATCGGAC
* * *
4348 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTTGCACCCTTTAGTCCTCAAAGAGTAGCGTCCC
1 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCAT-GC
* * ** * *
4413 TTTATGTTTTCAAAGCCCACATTAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCGTC-CCTT
65 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAG-GACACCTT
* * * * **
4477 TATGTTTTTAAAGCCCACATTAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGAT
129 TTTCTTTTCAAACCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGAT
* * * *
4534 GCCTTTTTCTTTTCAGAGCCCACACGGGTTGGTGGCACCCTTTAGCCCTCAAAGAGTAGCATGCT
1 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCATGCT
* * *
4599 TTTATCTTTTCAAAAG-CCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGTCACCTT
66 TTT-TCTTTTC-AAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACACCTT
* * * *
4663 TTTCTTTTCAAACCCTACACGAGTTGGTGGAACCCTTTAGTTCTCAAAGAGCCA-GAC
129 TTTCTTTTCAAACCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAG-CAGGAT
* * * *
4720 GACTTTTTCCTTTCAAAGCCCACACAAGTTAGTGGCACCCTTTAGTCCTCAAAGAGTAGCCTGCC
1 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCATG-C
* * * * * * *
4785 TTTATATTTTCAAAGCCCACATGAGTTGGCGGCACCCTTTAGTCCTCAAAGAGTAGGCCACTTTT
65 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACACCTTT
* * *
4850 TTCTTTTCGAACCCCACATGAGTTGGTGGCACCCTTTAGTCCTTAAA-ACGCAGGAT
130 TTCTTTTCAAACCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGA-GCAGGAT
** * * *
4906 GCCTTTTAGCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACGCA
1 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCATGC-
* * * * * * *
4971 TTTTTCATTGCAAAGCCCACACGGGTTGGTAGCACTACTTT-GTCCTCAAGGAATCA-GACACCT
65 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCAC-CCTTTAGTCCTCAAAG-AGCAGGACACCT
* * * * *
5034 TTTTCTTTTCAAACCCCACTCGTGTTGGTGGCTCCCTTTAGTTCTCAAAGAGCCA-GAA
128 TTTTCTTTTCAAACCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAG-CAGGAT
* *
5092 GCCTTTTTCCTTTTCAAAGCCCACACGAGTTGATGGCACCCTTTAGTCCTCAAAGAGCAAGACA-
1 GCCTTTTTCC-TTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAG-TAG-CAT
* * * * * * * *
5156 -CATTTTTCTTTTCAAAGCCTACACGGGTTCGTAGCACCCTTTAATCCACAAAG-GATAAGACAC
63 GC-TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAG-CAGGACAC
** * * * * * * * * *
5219 AATTTTCTTTTCAAAGCCTAGA-TAGATTTGTGGCACCTTTTAGTCCTCAAATAGAAGGAC
126 CTTTTTCTTTTCAAACCCCACACGAG-TTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGAT
* * * * * * * * * *
5279 ACC-TTTTCCATTCAAAGGCCACACGACTTGGAGCCACCCCTTAGTCCTCAAAGGGTAGGACGCC
1 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCATG-C
* * * * * *
5343 ATTTTCCTTTCAAAGCCCACACGAGTTGGTGGCAACCTTTAGTCCTTAAAGAGCCGGACGCCTTT
65 TTTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACACCTTT
* * ** *
5408 TTCCTTTCAAAGCAGACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGCAT
130 TTCTTTTCAAACCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGAT
* * * * * *
5464 GCCTTTATCTTTTCAAAGCCCACATGAGTTGGTGGCACCCTTTAGTTCTCAAAGAGCAGGATGCC
1 GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCATG-C
*
5529 TTTTTCCTTTCAAAGCCC
65 TTTTTCTTTTCAAAGCCC
5547 GCACATTGTA
Statistics
Matches: 828, Mismatches: 158, Indels: 54
0.80 0.15 0.05
Matches are distributed among these distances:
183 1 0.00
184 2 0.00
185 144 0.17
186 526 0.64
187 152 0.18
188 2 0.00
189 1 0.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (185 bp):
GCCTTTTTCCTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGTAGCATGCT
TTTTCTTTTCAAAGCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGACACCTTTT
TCTTTTCAAACCCCACACGAGTTGGTGGCACCCTTTAGTCCTCAAAGAGCAGGAT
Found at i:5317 original size:123 final size:124
Alignment explanation
Indices: 5125--5396 Score: 275
Period size: 123 Copynumber: 2.2 Consensus size: 124
5115 CACGAGTTGA
* ** ** *
5125 TGGCACCCTTTAGTCCTCAAAGAGCAAGACACATTTTTCTTTTCAAAGCCTACACGGGTTCGTAG
1 TGGCACCCTTTAGTCCTCAAAGAGCAAGACACACTTTTCCATTCAAAGCCTACACGACTTCGGAG
* *
5190 CACCCTTTAATCCACAAAGGATAAGACACAATTTTCTTTTCAAAGCCTAGATAGATTTG
66 CACCCCTTAATCCACAAAGGATAAGACACAATTTTCCTTTCAAAGCCTAGATAGATTTG
* *
5249 TGGCACCTTTTAGTCCTCAAATAG-AAGGACAC-CTTTTCCATTCAAAGGCC-ACACGACTT-GG
1 TGGCACCCTTTAGTCCTCAAAGAGCAA-GACACACTTTTCCATTCAAA-GCCTACACGACTTCGG
* * * * * * * * * *
5310 AGCCACCCCTTAGTCCTCAAAGGGTAGGACGCCATTTTCCTTTCAAAGCCCACA-CGAGTTGG
64 AG-CACCCCTTAATCCACAAAGGATAAGACACAATTTTCCTTTCAAAGCCTAGATAGA-TTTG
* *
5372 TGGCAACCTTTAGTCCTTAAAGAGC
1 TGGCACCCTTTAGTCCTCAAAGAGC
5397 CGGACGCCTT
Statistics
Matches: 119, Mismatches: 24, Indels: 10
0.78 0.16 0.07
Matches are distributed among these distances:
122 5 0.04
123 84 0.71
124 30 0.25
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (124 bp):
TGGCACCCTTTAGTCCTCAAAGAGCAAGACACACTTTTCCATTCAAAGCCTACACGACTTCGGAG
CACCCCTTAATCCACAAAGGATAAGACACAATTTTCCTTTCAAAGCCTAGATAGATTTG
Found at i:5627 original size:13 final size:13
Alignment explanation
Indices: 5609--5692 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
5599 AGCTTCGTAG
5609 CGATACATTGTAT
1 CGATACATTGTAT
5622 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
5641 CGATACATTGTAT
1 CGATACATTGTAT
5654 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
*
5673 TGATACATTGTAT
1 CGATACATTGTAT
5686 CGATACA
1 CGATACA
5693 AATCGTTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
13 25 0.44
14 1 0.02
15 2 0.04
16 8 0.14
17 2 0.04
18 1 0.02
19 18 0.32
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:5641 original size:19 final size:18
Alignment explanation
Indices: 5617--5679 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
5607 AGCGATACAT
5617 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
5636 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
5649 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
5668 TGTATTGATACA
1 TGTATCGATACA
5680 TTGTATCGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:5650 original size:32 final size:32
Alignment explanation
Indices: 5609--5694 Score: 154
Period size: 32 Copynumber: 2.7 Consensus size: 32
5599 AGCTTCGTAG
5609 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
5641 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
5673 TGATACATTGTATCGATACAAA
1 CGATACATTGTATCGATACAAA
5695 TCGTTGAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:15872 original size:15 final size:13
Alignment explanation
Indices: 15837--15879 Score: 61
Period size: 13 Copynumber: 3.3 Consensus size: 13
15827 ATTAAAATTT
*
15837 TTTTAAAATATAA
1 TTTTAAAACATAA
15850 TTTTAAAACATAA
1 TTTTAAAACATAA
15863 TTATTAAAA-ATAA
1 TT-TTAAAACATAA
15876 TTTT
1 TTTT
15880 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 2 0.07
13 20 0.71
14 6 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
TTTTAAAACATAA
Found at i:15891 original size:20 final size:21
Alignment explanation
Indices: 15866--15904 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
15856 AACATAATTA
15866 TTAAAAATAATT-TTTATTTT
1 TTAAAAATAATTATTTATTTT
15886 TTAAAAATAATTATTTATT
1 TTAAAAATAATTATTTATT
15905 ACTCTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAAATAATTATTTATTTT
Found at i:16072 original size:6 final size:6
Alignment explanation
Indices: 16061--16090 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
16051 CCTGAATCAC
16061 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
16091 TTCGCTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:16282 original size:5 final size:5
Alignment explanation
Indices: 16269--16317 Score: 50
Period size: 5 Copynumber: 10.2 Consensus size: 5
16259 TAATAAATAT
* *
16269 TTATC TTATA TTATA TTATA TTATA -TA-A ATATA TATATA TTA-A TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA T-TATA TTATA TTATA
16317 T
1 T
16318 AAATGTTCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
3 1 0.03
4 8 0.21
5 24 0.63
6 5 0.13
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (5 bp):
TTATA
Found at i:16318 original size:15 final size:15
Alignment explanation
Indices: 16275--16318 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
16265 ATATTTATCT
16275 TATATTATATTATAT-
1 TATATTA-ATTATATA
*
16290 TATA-TAAATATATA
1 TATATTAATTATATA
16304 TATATTAATTATATA
1 TATATTAATTATATA
16319 AATGTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 6 0.24
14 6 0.24
15 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATATTAATTATATA
Found at i:16332 original size:23 final size:24
Alignment explanation
Indices: 16275--16321 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
16265 ATATTTATCT
16275 TATAT-TATATTATATTATATAAA
1 TATATATATATTATATTATATAAA
16298 TATATATATATTA-ATTATATAAA
1 TATATATATATTATATTATATAAA
16321 T
1 T
16322 GTTCATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
TATATATATATTATATTATATAAA
Found at i:16367 original size:25 final size:27
Alignment explanation
Indices: 16326--16377 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
16316 ATAAATGTTC
16326 ATATATTTATTTATTTT-TATTATATA
1 ATATATTTATTTATTTTATATTATATA
16352 ATAT-TTTAATTT-TTTTAATATTATAT
1 ATATATTT-ATTTATTTT-ATATTATAT
16378 TTATATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
25 7 0.30
26 8 0.35
27 8 0.35
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (27 bp):
ATATATTTATTTATTTTATATTATATA
Found at i:16386 original size:25 final size:23
Alignment explanation
Indices: 16327--16391 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
16317 TAAATGTTCA
*
16327 TATATTTATTTATTTTTATTATAT
1 TATATTTATTAATTTTT-TTATAT
*
16351 AATA-TT-TTAATTTTTTTAATAT
1 TATATTTATTAATTTTTTT-ATAT
16373 TATATTTATATAATTTTTT
1 TATATTTAT-TAATTTTTT
16392 ATAGTGTATC
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.06
22 15 0.44
23 4 0.12
24 4 0.12
25 9 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TATATTTATTAATTTTTTTATAT
Found at i:17261 original size:2 final size:2
Alignment explanation
Indices: 17254--17287 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
17244 TTAATCGAAT
*
17254 TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17288 CACGTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:19861 original size:26 final size:23
Alignment explanation
Indices: 19804--19862 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 23
19794 CTTTATTTTT
19804 AATTATAT-TTTATATATAATAA
1 AATTATATATTTATATATAATAA
*
19826 AATAAAATATATTTATATAATAATTTAA
1 AAT--TATATATTTATAT-ATAA--TAA
19854 AATTATATA
1 AATTATATA
19863 ATATAATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
22 3 0.10
24 4 0.14
25 7 0.24
26 9 0.31
28 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AATTATATATTTATATATAATAA
Found at i:19871 original size:28 final size:28
Alignment explanation
Indices: 19832--19897 Score: 70
Period size: 26 Copynumber: 2.5 Consensus size: 28
19822 ATAAAATAAA
19832 ATATAT-TTAT-ATA-ATAATTTAAAATT
1 ATATATATTATAATATATAATTT-AAATT
* *
19858 ATATA-A-TATAATATATTATTTATATT
1 ATATATATTATAATATATAATTTAAATT
19884 ATATATATTATAAT
1 ATATATATTATAAT
19898 TTTAATATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
25 3 0.09
26 17 0.52
27 7 0.21
28 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATATATATTATAATATATAATTTAAATT
Found at i:19883 original size:9 final size:9
Alignment explanation
Indices: 19857--19895 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
19847 AATTTAAAAT
*
19857 TATATAATA
1 TATATATTA
19866 TAATATATTA
1 T-ATATATTA
*
19876 TTTATATTA
1 TATATATTA
19885 TATATATTA
1 TATATATTA
19894 TA
1 TA
19896 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
9 18 0.69
10 8 0.31
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
TATATATTA
Found at i:19886 original size:14 final size:15
Alignment explanation
Indices: 19832--19897 Score: 56
Period size: 14 Copynumber: 4.9 Consensus size: 15
19822 ATAAAATAAA
19832 ATATATTTAT-ATA-
1 ATATATTTATAATAT
*
19845 ATA-ATTTAAAAT-T
1 ATATATTTATAATAT
*
19858 ATATA-ATATAATAT
1 ATATATTTATAATAT
*
19872 AT-TATTTATATTAT
1 ATATATTTATAATAT
19886 ATATA-TTATAAT
1 ATATATTTATAAT
19898 TTTAATATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
12 5 0.12
13 15 0.37
14 19 0.46
15 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
ATATATTTATAATAT
Found at i:19905 original size:23 final size:23
Alignment explanation
Indices: 19808--19923 Score: 85
Period size: 23 Copynumber: 5.0 Consensus size: 23
19798 ATTTTTAATT
* **
19808 ATATTTTATATATAATAA-AATA
1 ATATTATATATATAATAATTTTA
* *
19830 AAATATATTTATATAATAA-TTTA
1 ATAT-TATATATATAATAATTTTA
* *
19853 AAATTATATAATATAATATATTATTT
1 ATATTATAT-ATATAATA-ATT-TTA
*
19879 ATATTATATATATTATAATTTTA
1 ATATTATATATATAATAATTTTA
*
19902 ATATAATA-ATATCAATAATTTT
1 ATATTATATATAT-AATAATTTT
19924 TGCTAAAAAA
Statistics
Matches: 76, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
22 11 0.14
23 43 0.57
24 4 0.05
25 8 0.11
26 10 0.13
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATTATATATATAATAATTTTA
Found at i:20027 original size:24 final size:24
Alignment explanation
Indices: 19981--20027 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
19971 AAATCGATTA
*
19981 AATTAATCAACTTAAATTGATTTT
1 AATTAATCAACTTAAATTAATTTT
*
20005 AATTTATCAACTT-AATTCAATTT
1 AATTAATCAACTTAAATT-AATTT
20028 ATTCTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.40, C:0.11, G:0.02, T:0.47
Consensus pattern (24 bp):
AATTAATCAACTTAAATTAATTTT
Found at i:21038 original size:17 final size:17
Alignment explanation
Indices: 20962--21062 Score: 65
Period size: 17 Copynumber: 6.2 Consensus size: 17
20952 TTTTTACTCA
*
20962 ATATTATAAATACAATATT
1 ATATTATAAATA-TATA-T
20981 ATATT-TAAAT-TA-AT
1 ATATTATAAATATATAT
*
20995 TTATTAT---TATATAT
1 ATATTATAAATATATAT
* * *
21009 -TATTTTTAATATAAAT
1 ATATTATAAATATATAT
21025 ATATTA-AAATTATATAT
1 ATATTATAAA-TATATAT
*
21042 ATTTTATAAATATATAT
1 ATATTATAAATATATAT
21059 ATAT
1 ATAT
21063 GATATAAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
12 1 0.02
13 7 0.11
14 7 0.11
15 2 0.03
16 9 0.14
17 25 0.39
18 8 0.12
19 5 0.08
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTATAAATATATAT
Found at i:21068 original size:19 final size:18
Alignment explanation
Indices: 21031--21070 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
21021 AAATATATTA
**
21031 AAATTATATATATTTTAT
1 AAATTATATATATGATAT
21049 AAATATATATATATGATAT
1 AAAT-TATATATATGATAT
21068 AAA
1 AAA
21071 AAATAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (18 bp):
AAATTATATATATGATAT
Found at i:21600 original size:17 final size:17
Alignment explanation
Indices: 21578--21613 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
21568 ATTTTATTAT
*
21578 TTAAAAATATTAAAATA
1 TTAAAAAAATTAAAATA
*
21595 TTAAAAAAATTAAATTA
1 TTAAAAAAATTAAAATA
21612 TT
1 TT
21614 TATTTTTATA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAAAATTAAAATA
Found at i:22800 original size:19 final size:19
Alignment explanation
Indices: 22778--22817 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
22768 TATTTTAAAA
*
22778 TTTTAAAT-TATTATTTATT
1 TTTTAAATAT-TTATATATT
22797 TTTTAAATATTTATATATT
1 TTTTAAATATTTATATATT
22816 TT
1 TT
22818 ATAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTAAATATTTATATATT
Found at i:22817 original size:17 final size:19
Alignment explanation
Indices: 22777--22824 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
22767 TTATTTTAAA
*
22777 ATTTTAAATTATTATTTAT
1 ATTTTAAATTATTATATAT
*
22796 TTTTTAAA-TATT-TATAT
1 ATTTTAAATTATTATATAT
22813 ATTTTATAATTA
1 ATTTTA-AATTA
22825 ATTTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 9 0.38
18 6 0.25
19 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
ATTTTAAATTATTATATAT
Found at i:22849 original size:19 final size:20
Alignment explanation
Indices: 22825--22876 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
22815 TTTATAATTA
22825 ATTTTAAATAAAATA-TATT
1 ATTTTAAATAAAATATTATT
*
22844 ATTTTAATTAAAA-ATTATT
1 ATTTTAAATAAAATATTATT
*
22863 ATTTTAAATTAAAT
1 ATTTTAAATAAAAT
22877 CAAACCAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 1 0.04
19 27 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAATAAAATATTATT
Found at i:26057 original size:24 final size:25
Alignment explanation
Indices: 26028--26090 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
26018 AGGGTGATAT
26028 TCATTATAATTAATCATAAT-AATA
1 TCATTATAATTAATCATAATAAATA
* *
26052 TCATTATATTTATAATTATAATAAATA
1 TCATTATA-AT-TAATCATAATAAATA
*
26079 T-AATATAATTAA
1 TCATTATAATTAA
26091 AATTATATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 11 0.34
25 2 0.06
26 14 0.44
27 5 0.16
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
TCATTATAATTAATCATAATAAATA
Found at i:26072 original size:26 final size:26
Alignment explanation
Indices: 26038--26097 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
26028 TCATTATAAT
* * *
26038 TAATCATAAT-AATATCATTATATTTA
1 TAATTATAATAAATAT-AATATAATTA
26064 TAATTATAATAAATATAATATAATTA
1 TAATTATAATAAATATAATATAATTA
*
26090 AAATTATA
1 TAATTATA
26098 TTTACGATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATTATAATAAATATAATATAATTA
Found at i:26385 original size:2 final size:2
Alignment explanation
Indices: 26373--26411 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
26363 TGAAAAATGC
*
26373 AT AT CT 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 A
26412 GTATGTGCTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26618 original size:23 final size:22
Alignment explanation
Indices: 26584--26627 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
26574 CGTGATTATA
26584 AATTTAATAAATTATT-ATAATT
1 AATTTAATAAA-TATTGATAATT
26606 AATTATAATAAATATTGATAAT
1 AATT-TAATAAATATTGATAAT
26628 AAAAAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATTTAATAAATATTGATAATT
Found at i:29979 original size:22 final size:23
Alignment explanation
Indices: 29938--29982 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
29928 TTTATTATAA
29938 TAATTTATTACAAATTAATAAAT
1 TAATTTATTACAAATTAATAAAT
29961 TAATTT-TTA-AAATTTAATAAAT
1 TAATTTATTACAAA-TTAATAAAT
29983 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 3 0.14
22 12 0.57
23 6 0.29
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTTATTACAAATTAATAAAT
Found at i:30112 original size:29 final size:30
Alignment explanation
Indices: 30078--30135 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
30068 ATATTATAAA
*
30078 TAAATTATAA-AAATTTATC-ATTATATTTT
1 TAAATTATAATAAATTAATCGA-TATATTTT
30107 TAAATTATAATAAATTAATCGATATATTT
1 TAAATTATAATAAATTAATCGATATATTT
30136 AATTTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.38
30 15 0.58
31 1 0.04
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (30 bp):
TAAATTATAATAAATTAATCGATATATTTT
Found at i:30510 original size:3 final size:3
Alignment explanation
Indices: 30502--30532 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
30492 GCCTAATTTC
30502 ATT ATT ATT ATT ATT ATT ATT -TT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
30533 AAAAATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:31151 original size:24 final size:24
Alignment explanation
Indices: 31102--31151 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
31092 TATTTAAAAC
**
31102 TTTAAAGATAATTTTTTTTTATTT
1 TTTAAAGATAATTTTAATTTATTT
31126 TTTAAAGATAATTATTAATTTATTT
1 TTTAAAGATAATT-TTAATTTATTT
31151 T
1 T
31152 AAATTTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (24 bp):
TTTAAAGATAATTTTAATTTATTT
Found at i:31614 original size:8 final size:8
Alignment explanation
Indices: 31601--31626 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
31591 GGATAATCTT
31601 AAAAAATA
1 AAAAAATA
31609 AAAAAATA
1 AAAAAATA
31617 AAAAAATA
1 AAAAAATA
31625 AA
1 AA
31627 GTAGCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:39762 original size:13 final size:13
Alignment explanation
Indices: 39744--39769 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39734 ACAAAGATCG
39744 ATGTATCGATACA
1 ATGTATCGATACA
39757 ATGTATCGATACA
1 ATGTATCGATACA
39770 TTGAGTAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:39865 original size:21 final size:19
Alignment explanation
Indices: 39818--39872 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
39808 TGTAGCGATA
39818 TTTGTATCGATACAACACT
1 TTTGTATCGATACAACACT
* **
39837 TATGTATCGATACAGTTACT
1 TTTGTATCGATACA-ACACT
39857 GTTTGTATCGATACAA
1 -TTTGTATCGATACAA
39873 ATTGTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 13 0.45
20 3 0.10
21 13 0.45
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACAACACT
Found at i:40326 original size:21 final size:20
Alignment explanation
Indices: 40300--40350 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
40290 TATAAAAATT
40300 AATTAATTTTAATTT-ATATAA
1 AATTAATTTT-ATTTAATAT-A
40321 AATTAATTTTATTTAATATA
1 AATTAATTTTATTTAATATA
40341 AATTATATTT
1 AATTA-ATTT
40351 ATCATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTAATTTTATTTAATATA
Found at i:40481 original size:3 final size:3
Alignment explanation
Indices: 40473--40521 Score: 71
Period size: 3 Copynumber: 16.0 Consensus size: 3
40463 TGAGATTGAT
* *
40473 TTA TTA TTA TTA TTA TTA CTA TTG TTA TTA TTA TTA TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
40519 TTA
1 TTA
40522 GCTTTATCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:40788 original size:19 final size:20
Alignment explanation
Indices: 40750--40796 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
40740 ATATATTATA
*
40750 AAATTAAATATTAAAAATTT
1 AAATTTAATATTAAAAATTT
* *
40770 ATATTTAATA-TAAATATTT
1 AAATTTAATATTAAAAATTT
40789 AAATTTAA
1 AAATTTAA
40797 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
AAATTTAATATTAAAAATTT
Found at i:40860 original size:16 final size:18
Alignment explanation
Indices: 40827--40863 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
40817 AGCATTGAAG
*
40827 ATTATAATTTTTAGTTAA
1 ATTATAATTTTCAGTTAA
40845 ATTAT-ATTTTCA-TTAA
1 ATTATAATTTTCAGTTAA
40861 ATT
1 ATT
40864 GTTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 6 0.33
18 5 0.28
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (18 bp):
ATTATAATTTTCAGTTAA
Found at i:40885 original size:11 final size:11
Alignment explanation
Indices: 40866--40905 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
40856 ATTAAATTGT
40866 TATTATATTTAA
1 TATT-TATTTAA
40878 TATTTATTTAA
1 TATTTATTTAA
40889 TA-TT-TTTAA
1 TATTTATTTAA
40898 -ATTTATTT
1 TATTTATTT
40906 TAAATGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.04
9 7 0.27
10 5 0.19
11 9 0.35
12 4 0.15
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATTTAA
Done.