Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01002600.1 Kokia drynarioides strain JFW-HI SEQ_114811, 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: 57913
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 38 characters in sequence are not A, C, G, or T
Found at i:2509 original size:19 final size:19
Alignment explanation
Indices: 2485--2522 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2475 CTTTGAAAAT
*
2485 GTGACAAAACAGTCACTAA
1 GTGACAAAACAATCACTAA
2504 GTGACAAAACAATCACTAA
1 GTGACAAAACAATCACTAA
2523 AATCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.16
Consensus pattern (19 bp):
GTGACAAAACAATCACTAA
Found at i:2910 original size:5 final size:6
Alignment explanation
Indices: 2878--2916 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2868 TTAGGGTTTA
* *
2878 TTTGAT TTTGAT TTTGAT TTGGAT TTTTATT TTTGAT TT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTTGA-T TTTGAT TT
2917 AGGGTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTTGAT
Found at i:10649 original size:98 final size:98
Alignment explanation
Indices: 10452--10646 Score: 218
Period size: 97 Copynumber: 2.0 Consensus size: 98
10442 TACTTTTGAA
* * * * * *
10452 AAGGATGTTCGATTATCTCGATTTAAAGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTT
1 AAGGATATTCAATTATCTCGATTTAAAGAAAAAGTCGCACATAGTAAGTTAAGGCACAAATTTTC
* *
10517 AGAATCAGAGATAAAGAAACATTGCCTCGATTT
66 AAAATCAGAGATAAAGAAACATTGCCTCAATTT
* ** *
10550 AAGGATATTCAATTAT-TCCGATTTGAAGAAAAA-TCGTGCATAGTAAGTTAAGGCACTAATTTT
1 AAGGATATTCAATTATCT-CGATTTAAAGAAAAAGTCGCACATAGTAAGTTAAGGCACAAATTTT
*
10613 CAAAACTCA-AGATAAA-AGAATATTGCCTCAATTT
65 CAAAA-TCAGAGATAAAGA-AACATTGCCTCAATTT
10647 TAAAGTTTTT
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
96 1 0.01
97 49 0.60
98 31 0.38
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (98 bp):
AAGGATATTCAATTATCTCGATTTAAAGAAAAAGTCGCACATAGTAAGTTAAGGCACAAATTTTC
AAAATCAGAGATAAAGAAACATTGCCTCAATTT
Found at i:10892 original size:28 final size:29
Alignment explanation
Indices: 10861--10923 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
10851 GAAATGTGAT
*
10861 TTTTGGATACTCG-AGGGCAAAATGGTAA
1 TTTTGGACACTCGAAGGGCAAAATGGTAA
*
10889 TTTTGGACACTCGAATGGCAAAATGGTAA
1 TTTTGGACACTCGAAGGGCAAAATGGTAA
10918 TTTTGG
1 TTTTGG
10924 GAAAGTTCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.30, C:0.11, G:0.27, T:0.32
Consensus pattern (29 bp):
TTTTGGACACTCGAAGGGCAAAATGGTAA
Found at i:10970 original size:58 final size:58
Alignment explanation
Indices: 10908--11321 Score: 342
Period size: 58 Copynumber: 7.1 Consensus size: 58
10898 CTCGAATGGC
* * * *
10908 AAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAAATGGAATTCTAGGCA-TATGAGGGT
1 AAAATGGTAATTTTGGGAAA-ATCGGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
* *
10966 AAAATGATAATTTTAGGGGAAAATCGGGG-TAGAAAATGGAATTTTAGAAAGTTTGAGGGT
1 AAAATGGTAATTTT--GGGAAAATCGGGGTTA-AAAATGGAATTTTAGGAAGTTTGAGGGT
* * * *
11026 AAAATGGTAATTTTGGAAAAATCGAGGTTAAAAAT-GACATTTTTGGAAG-TTCAGGGGT
1 AAAATGGTAATTTTGGGAAAATCGGGGTTAAAAATGGA-ATTTTAGGAAGTTTGA-GGGT
* * * * * * *
11084 AAAATGATAATTTTTGGAAAATCGAGGTCAAAAATGAAATTTTGGGAAGTTTGAGAGT
1 AAAATGGTAATTTTGGGAAAATCGGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
* * * *
11142 AAAATGGTAATTTTTAGAAAAATCGGGGTAAAAAATGG-ATGTTTGGGAAGTTTG-GGGT
1 AAAATGGTAA-TTTTGGGAAAATCGGGGTTAAAAATGGAAT-TTTAGGAAGTTTGAGGGT
* * * * *
11200 AAAATTGTAATTTTTGGAAAAATCAGGATTAAATATGGAATTTT-GGAAAGTTTGAGGGT
1 AAAATGGTAA-TTTTGGGAAAATCGGGGTTAAAAATGGAATTTTAGG-AAGTTTGAGGGT
** ** ** * *
11259 AAAAAAGTAATTTT-CAAAAAGTTTAGGGTCAAAAATGGAATTTT-GGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGGGAAAA--TCGGGGTTAAAAATGGAATTTTAGG-AAGTTTGAGGGT
11318 AAAA
1 AAAA
11322 ATATAATTTT
Statistics
Matches: 299, Mismatches: 41, Indels: 31
0.81 0.11 0.08
Matches are distributed among these distances:
57 12 0.04
58 148 0.49
59 112 0.37
60 27 0.09
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (58 bp):
AAAATGGTAATTTTGGGAAAATCGGGGTTAAAAATGGAATTTTAGGAAGTTTGAGGGT
Found at i:11044 original size:29 final size:29
Alignment explanation
Indices: 10998--11340 Score: 149
Period size: 29 Copynumber: 11.8 Consensus size: 29
10988 ATCGGGGTAG
*
10998 AAAATGG-AATTTTAGAAAGTTTGAGGGT
1 AAAATGGTAATTTTGGAAAGTTTGAGGGT
** * *
11026 AAAATGGTAATTTTGGAAAAATCGAGGTT
1 AAAATGGTAATTTTGGAAAGTTTGAGGGT
** * *
11055 AAAAATGACATTTTTGG-AAG-TTCAGGGGT
1 -AAAATGGTAATTTTGGAAAGTTTGA-GGGT
* * *
11084 AAAATGATAATTTTTGGAAA-ATCGA-GGT
1 AAAATGGTAA-TTTTGGAAAGTTTGAGGGT
* * *
11112 CAAAAAT-GAAATTTTGGGAAGTTTGAGAGT
1 --AAAATGGTAATTTTGGAAAGTTTGAGGGT
* ** *
11142 AAAATGGTAATTTTTAGAAAAATCG-GGGT
1 AAAATGGTAA-TTTTGGAAAGTTTGAGGGT
*
11171 AAAAAATGG--ATGTTTGGGAAGTTTG-GGGT
1 --AAAATGGTAAT-TTTGGAAAGTTTGAGGGT
* ** * *
11200 AAAATTGTAATTTTTGGAAA-AATCAGGATT
1 AAAATGGTAA-TTTTGGAAAGTTTGAGG-GT
11230 AAATATGG-AATTTTGGAAAGTTTGAGGGT
1 AAA-ATGGTAATTTTGGAAAGTTTGAGGGT
** **
11259 AAAAAAGTAATTTTCAAAAAGTTT-AGGGT
1 AAAATGGTAATTTT-GGAAAGTTTGAGGGT
*
11288 CAAAAATGG-AATTTTGGAAAGTTTGGGGGT
1 --AAAATGGTAATTTTGGAAAGTTTGAGGGT
*
11318 AAAAAT-ATAATTTTTGGAAAGTT
1 -AAAATGGTAA-TTTTGGAAAGTT
11341 CGGTGGTCAA
Statistics
Matches: 231, Mismatches: 55, Indels: 56
0.68 0.16 0.16
Matches are distributed among these distances:
27 6 0.03
28 37 0.16
29 100 0.43
30 73 0.32
31 15 0.06
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (29 bp):
AAAATGGTAATTTTGGAAAGTTTGAGGGT
Found at i:11335 original size:30 final size:30
Alignment explanation
Indices: 11240--11401 Score: 134
Period size: 30 Copynumber: 5.4 Consensus size: 30
11230 AAATATGGAA
*
11240 TTTTGGAAAGTTTGAGGGTAAAAA-AGTAAT
1 TTTTGGAAAGTTTGGGGGTAAAAATA-TAAT
*** * **
11270 TTTCAAAAAGTTT-AGGGTCAAAAATGGAA-
1 TTTTGGAAAGTTTGGGGGT-AAAAATATAAT
11299 TTTTGGAAAGTTTGGGGGTAAAAATATAAT
1 TTTTGGAAAGTTTGGGGGTAAAAATATAAT
* * * *
11329 TTTTGGAAAGTTCGGTGGTCAAAATATTAT
1 TTTTGGAAAGTTTGGGGGTAAAAATATAAT
* * *
11359 TTTT-GAGAAGTTTTGAGGTCAAAATATAAT
1 TTTTGGA-AAGTTTGGGGGTAAAAATATAAT
*
11389 TTTTGGACAGTTT
1 TTTTGGAAAGTTT
11402 AGGGACCTTT
Statistics
Matches: 106, Mismatches: 20, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
29 25 0.24
30 79 0.75
31 2 0.02
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.37
Consensus pattern (30 bp):
TTTTGGAAAGTTTGGGGGTAAAAATATAAT
Found at i:11353 original size:59 final size:57
Alignment explanation
Indices: 10962--11395 Score: 290
Period size: 58 Copynumber: 7.4 Consensus size: 57
10952 AGGCATATGA
* * * * *
10962 GGGTAAAATGATAATTTTAGGGGAAAATCGGGGTAGAAAATGGAATTTTAGAAAGTTTGA
1 GGGTAAAAT-ATAATTTT-TGGAAAAATCGGGGT-CAAAATGGAATTTTGGAAAGTTTGG
* * * **
11022 GGGTAAAATGGTAA-TTTTGGAAAAATCGAGGTTAAAAAT-GACATTTTTGG-AAGTTCAG
1 GGGTAAAAT-ATAATTTTTGGAAAAATCG-GGGTCAAAATGGA-A-TTTTGGAAAGTTTGG
* * * *
11080 GGGTAAAATGATAATTTTTGG-AAAATCGAGGTCAAAAATGAAATTTTGGGAAGTTTGA
1 GGGTAAAAT-ATAATTTTTGGAAAAATCGGGGTC-AAAATGGAATTTTGGAAAGTTTGG
* * * * *
11138 GAGTAAAATGGTAATTTTTAGAAAAATCGGGGTAAAAAATGG-ATGTTTGGGAAGTTT-G
1 GGGTAAAAT-ATAATTTTTGGAAAAATCGGGGT-CAAAATGGAAT-TTTGGAAAGTTTGG
* * * * *
11196 GGGTAAAATTGTAATTTTTGGAAAAATCAGGATTAAATATGGAATTTTGGAAAGTTTGA
1 GGGTAAAA-TATAATTTTTGGAAAAATCGGGGTCAAA-ATGGAATTTTGGAAAGTTTGG
* * **
11255 GGGTAAAAAAGTAA-TTTT-CAAAAAGTTTAGGGTCAAAAATGGAATTTTGGAAAGTTTGG
1 GGGTAAAATA-TAATTTTTGGAAAAA--TCGGGGTC-AAAATGGAATTTTGGAAAGTTTGG
** *** * *
11314 GGGTAAAAATATAATTTTTGGAAAGTTCGGTGGTCAAAATATTATTTTTGAGAAGTTTTG
1 GGGT-AAAATATAATTTTTGGAAAAATCGG-GGTCAAAATGGAATTTTGGA-AAGTTTGG
*
11374 AGGTCAAAATATAATTTTTGGA
1 GGGT-AAAATATAATTTTTGGA
11396 CAGTTTAGGG
Statistics
Matches: 300, Mismatches: 51, Indels: 46
0.76 0.13 0.12
Matches are distributed among these distances:
57 18 0.06
58 117 0.39
59 106 0.35
60 56 0.19
61 3 0.01
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (57 bp):
GGGTAAAATATAATTTTTGGAAAAATCGGGGTCAAAATGGAATTTTGGAAAGTTTGG
Found at i:12550 original size:3 final size:3
Alignment explanation
Indices: 12436--12538 Score: 111
Period size: 3 Copynumber: 33.3 Consensus size: 3
12426 TTTTATTAGG
* *
12436 TTA TTAA TTA TTA ATA CTTA TTA TTA TT- TCA GTTA TT- TATA TTA TTA
1 TTA TT-A TTA TTA TTA -TTA TTA TTA TTA TTA -TTA TTA T-TA TTA TTA
*
12483 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTAA TGA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA
*
12529 TCA TTA TTA T
1 TTA TTA TTA T
12539 AAACATTATT
Statistics
Matches: 86, Mismatches: 7, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
2 2 0.02
3 74 0.86
4 10 0.12
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:13321 original size:6 final size:6
Alignment explanation
Indices: 13310--13355 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
13300 TCAAATTTGA
* * *
13310 TTAAAT TTAAAT TTAAA- TCAAAT TTAAAT TTAAAA ATAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
13356 CCAATTTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
5 4 0.12
6 29 0.88
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:13874 original size:101 final size:101
Alignment explanation
Indices: 13698--13892 Score: 264
Period size: 101 Copynumber: 1.9 Consensus size: 101
13688 GCTGTTGTAG
* * * ** * *
13698 TTTTAATCCAACTTCGCTGCAACTTCAGGAAGATAGGATTTGATGTTGAAGCTTCGTCTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACATTAAAGCTTCATCTTGCTCT
* * *
13763 TACTATAACTTTAGAGAGATAAAGACTTGCTATTGT
66 TACTACAACTTCAGAGAGATAAAAACTTGCTATTGT
* * *
13799 TTTTAATCCAACTTTACTGTAACTTCAAGAGGATAGGAATTGACATTAAAGCTTCATCTTGCTCT
1 TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACATTAAAGCTTCATCTTGCTCT
*
13864 TACTGCAACTTCAGAGAGATAAAAACTTG
66 TACTACAACTTCAGAGAGATAAAAACTTG
13893 TCATTATAGT
Statistics
Matches: 80, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 80 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (101 bp):
TTTTAATCCAACTTCACTGCAACTTCAAGAAGATAGGAATTGACATTAAAGCTTCATCTTGCTCT
TACTACAACTTCAGAGAGATAAAAACTTGCTATTGT
Found at i:14158 original size:49 final size:47
Alignment explanation
Indices: 14026--14211 Score: 146
Period size: 49 Copynumber: 3.8 Consensus size: 47
14016 CAAATTTTCG
* * * *
14026 TGGTACTGGATTCGTCGTTATGGCTTAAATCTTTCCCTTTATGTCTCTGA
1 TGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCC-TTGTGTCT-T-A
* *
14076 -GGTA-TAAGG-TTCGCCGTTGCGACTTAAACCTTTCCCTCTGTGTCTTCA
1 TGGTACT--GGATTCGCCGTTACGACTTAAATCTTTCCCT-TGTGTCTT-A
* * * *
14124 TGGTACTGGATACGTCGTTACGGCTTAGATCTTTCCCTTGATGTCTT-
1 TGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTTG-TGTCTTA
* *
14171 TGCTGTACTGGATCCGCCGTTACGACTTAGATCTTTCCCTT
1 TG--GTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTT
14212 AACATCTTCC
Statistics
Matches: 111, Mismatches: 16, Indels: 19
0.76 0.11 0.13
Matches are distributed among these distances:
47 2 0.02
48 8 0.07
49 98 0.88
50 3 0.03
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (47 bp):
TGGTACTGGATTCGCCGTTACGACTTAAATCTTTCCCTTGTGTCTTA
Found at i:14220 original size:98 final size:96
Alignment explanation
Indices: 13997--14220 Score: 243
Period size: 98 Copynumber: 2.3 Consensus size: 96
13987 TTTGCCATTG
* * * *
13997 CGACTTAAACCTTTCCCTTCAAATTTTCGTGGTACTGGATTCGTCGTTATGGCTTAAATCTTTCC
1 CGACTTAAACCTTTCCCTT-AAATCTTCATGGTACTGGATACGTCGTTACGGCTTAAATCTTTCC
* * *
14062 CTTTATGTCTCTGAGGTATAAGGTTCGCCGTTG
65 CTTGATGTCTCTGAGGTAT-AGGTCCGCCGTTA
*** *
14095 CGACTTAAACCTTTCCCTCTGTGTCTTCATGGTACTGGATACGTCGTTACGGCTTAGATCTTTCC
1 CGACTTAAACCTTTCCCT-TAAATCTTCATGGTACTGGATACGTCGTTACGGCTTAAATCTTTCC
* **
14160 CTTGATGTCTTTGCTGTACT-GGATCCGCCGTTA
65 CTTGATGTCTCTGAGGTA-TAGG-TCCGCCGTTA
* *
14193 CGACTTAGATCTTTCCCTTAACATCTTC
1 CGACTTAAACCTTTCCCTTAA-ATCTTC
14221 CAAGGTACAC
Statistics
Matches: 103, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
97 3 0.03
98 98 0.95
99 2 0.02
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (96 bp):
CGACTTAAACCTTTCCCTTAAATCTTCATGGTACTGGATACGTCGTTACGGCTTAAATCTTTCCC
TTGATGTCTCTGAGGTATAGGTCCGCCGTTA
Found at i:25656 original size:51 final size:49
Alignment explanation
Indices: 25594--25697 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 49
25584 AACTTTTGAA
* *
25594 AAGGATGTTTGATTATCTCAATTTAAAGAAAAAGTCGCAG-CTAGTAAGTTT
1 AAGGATATTTGATTATCCCAATTTAAAGAAAAA-TCG-AGCCTAGTAAG-TT
* * *
25645 AAGGATATTTGATTATCCCGATTTGAAGAAAAATCGTGCCTAGTAAGTT
1 AAGGATATTTGATTATCCCAATTTAAAGAAAAATCGAGCCTAGTAAGTT
25694 AAGG
1 AAGG
25698 CACAAATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
49 7 0.15
50 11 0.23
51 29 0.62
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (49 bp):
AAGGATATTTGATTATCCCAATTTAAAGAAAAATCGAGCCTAGTAAGTT
Found at i:26128 original size:29 final size:27
Alignment explanation
Indices: 26091--26187 Score: 76
Period size: 27 Copynumber: 3.4 Consensus size: 27
26081 ATCAGGGTCA
26091 AAAATATAATTTTGAAAAGTTCGAGGGT
1 AAAAT-TAATTTTGAAAAGTTCGAGGGT
26119 AAAATGATAATTTTTAGAAAA--TCG-GGGTT
1 AAAAT--TAA-TTTT-GAAAAGTTCGAGGG-T
* *
26148 AAAATTGCATTTTG-GAAGTTCGAGGGT
1 AAAATT-AATTTTGAAAAGTTCGAGGGT
26175 AAAATGTAATTTT
1 AAAAT-TAATTTT
26188 TGGAAAAATA
Statistics
Matches: 57, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
25 2 0.04
26 1 0.02
27 19 0.33
28 13 0.23
29 13 0.23
30 4 0.07
31 5 0.09
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (27 bp):
AAAATTAATTTTGAAAAGTTCGAGGGT
Found at i:26189 original size:28 final size:27
Alignment explanation
Indices: 26002--26192 Score: 100
Period size: 28 Copynumber: 6.7 Consensus size: 27
25992 ATTTTGAGGC
*
26002 AAAATGGTAATTTTGGGAAAGTTCGGGGTT
1 AAAAT-GTAATTTTTGG-AAGTTCGGGG-T
* * * *
26032 AAAATGGAATTTTAGGCATTTCGGGGT
1 AAAATGTAATTTTTGGAAGTTCGGGGT
* ** *
26059 AAAATGGTAATTTTAGGGGAAAATCAGGGT
1 AAAAT-GTAATTTT--TGGAAGTTCGGGGT
* *
26089 CAAAAATATAA-TTTTGAAAAGTTCGAGGGT
1 --AAAATGTAATTTTTG-GAAGTTCG-GGGT
* **
26119 AAAATGATAATTTTTAGAAAATCGGGGTT
1 AAAATG-TAATTTTTGGAAGTTCGGGG-T
*
26148 AAAAT-TGCA-TTTTGGAAGTTCGAGGGT
1 AAAATGT-AATTTTTGGAAGTTCG-GGGT
26175 AAAATGTAATTTTTGGAA
1 AAAATGTAATTTTTGGAA
26193 AAATAGTGAT
Statistics
Matches: 121, Mismatches: 26, Indels: 30
0.68 0.15 0.17
Matches are distributed among these distances:
27 24 0.20
28 37 0.31
29 27 0.22
30 25 0.21
31 3 0.02
32 5 0.04
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (27 bp):
AAAATGTAATTTTTGGAAGTTCGGGGT
Found at i:26321 original size:58 final size:59
Alignment explanation
Indices: 26002--26423 Score: 361
Period size: 59 Copynumber: 7.3 Consensus size: 59
25992 ATTTTGAGGC
* ** * * *
26002 AAAATGGTAATTTTGGGAAAGTTCGGGGTT-AAAATGGAATTTT-AGGCATTTCG-GGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTGA-GAAGTTCGAGGGT
* * * ** *
26059 AAAATGGTAATTTTAGGGGAAAATCAGGGTCAAAAATATAATTTTGAAAAGTTCGAGGGT
1 AAAATGGTAATTTT-TGGAAAAATCAGGGTTAAAAATGGAATTTTGAGAAGTTCGAGGGT
* * * * *
26119 AAAATGATAATTTTTAG-AAAATCGGGGTT-AAAATTGCATTTTG-GAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTGAGAAGTTCGAGGGT
* * * * * *
26175 AAAAT-GTAATTTTTGGAAAAAT-AGTGATAAAAAATGGATTTTTGGGACGTTTGAGGGT
1 AAAATGGTAATTTTTGGAAAAATCAG-GGTTAAAAATGGAATTTTGAGAAGTTCGAGGGT
* * *
26233 AAAATGGTAATTTTTGGAGAAATTAGGGTTAAAAATGGAATTTTGAGAAGTTTTG-GGGT
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTGAGAAG-TTCGAGGGT
* * * * *
26292 -AAATGGTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTGAAAAGATGGAGGGAA
1 AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTGAGAAGTTCGAGGG-T
* *
26351 AAAAT-GTAATTTTTAGAAAAATC-GAGGTCAAAAATGGAATTTTG-GAATGTTCG-GAGGT
1 AAAATGGTAATTTTTGGAAAAATCAG-GGTTAAAAATGGAATTTTGAGAA-GTTCGAG-GGT
26409 AAAAAT-GTAATTTTT
1 -AAAATGGTAATTTTT
26424 TAAAAGTTTT
Statistics
Matches: 298, Mismatches: 49, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
55 10 0.03
56 24 0.08
57 38 0.13
58 88 0.30
59 110 0.37
60 28 0.09
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAAAATCAGGGTTAAAAATGGAATTTTGAGAAGTTCGAGGGT
Found at i:26348 original size:117 final size:116
Alignment explanation
Indices: 26002--26486 Score: 379
Period size: 117 Copynumber: 4.2 Consensus size: 116
25992 ATTTTGAGGC
** * *
26002 AAAATGGTAATTTTGGGAAAGTTCGGGGTTAAAATGGAATTTT-AGGCA-TTTCGGGGTAAAATG
1 AAAATGGTAATTTTTAGAAAATT-GGGGTTAAAATGGAATTTTGA-GAAGTTTCGGGGTAAAATG
* * * * **
26065 GTAATTTTAGGGGAAAATCAGGGTCAAAAATATAATTTTGAAAAGTTCGAGGGT
64 GTAATTTT-TGGAAAAATCAAGGTAAAAAATGGAATTTTGAAAAGTTCGAGGGT
* * * *
26119 AAAATGATAATTTTTAGAAAATCGGGGTTAAAATTGCATTTTG-GAAG-TTCGAGGGTAAAAT-G
1 AAAATGGTAATTTTTAGAAAATTGGGGTTAAAATGGAATTTTGAGAAGTTTCG-GGGTAAAATGG
* ** * *
26181 TAATTTTTGGAAAAAT--AGTGATAAAAAATGGATTTTTGGGACGTTTGAGGGT
65 TAATTTTTGGAAAAATCAAG-G-TAAAAAATGGAATTTTGAAAAGTTCGAGGGT
* * *
26233 AAAATGGTAATTTTTGGAGAAATTAGGGTTAAAAATGGAATTTTGAGAAGTTTTGGGGT-AAATG
1 AAAATGGTAATTTTTAGA-AAATTGGGGTT-AAAATGGAATTTTGAGAAGTTTCGGGGTAAAATG
* * * *
26297 GTAATTTTTGGAAAAATCAAGGTTAAAAATGGAATTTTGAAAAGATGGAGGGAA
64 GTAATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGAAAAGTTCGAGGG-T
* * *
26351 AAAAT-GTAATTTTTAGAAAAATCGAGGTCAAAAATGGAATTTTG-GAA-TGTTCGGAGGTAAAA
1 AAAATGGTAATTTTTAG-AAAATTGGGGT-TAAAATGGAATTTTGAGAAGT-TTCGG-GGT-AAA
* * *** * * **
26413 AT-GTAATTTTT-TAAAAGTTTTGGGT-CAAAATGGAATTTTGGAAAGTTTAAGGGT
61 ATGGTAATTTTTGGAAAA-ATCAAGGTAAAAAATGGAATTTTGAAAAGTTCGAGGGT
26467 AAAAAT-GTAATTTTTAGAAA
1 -AAAATGGTAATTTTTAGAAA
26487 GTATGAGGGT
Statistics
Matches: 296, Mismatches: 51, Indels: 43
0.76 0.13 0.11
Matches are distributed among these distances:
112 1 0.00
113 1 0.00
114 46 0.16
115 24 0.08
116 52 0.18
117 143 0.48
118 23 0.08
119 6 0.02
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (116 bp):
AAAATGGTAATTTTTAGAAAATTGGGGTTAAAATGGAATTTTGAGAAGTTTCGGGGTAAAATGGT
AATTTTTGGAAAAATCAAGGTAAAAAATGGAATTTTGAAAAGTTCGAGGGT
Found at i:26442 original size:29 final size:30
Alignment explanation
Indices: 26406--26521 Score: 103
Period size: 30 Copynumber: 3.9 Consensus size: 30
26396 AATGTTCGGA
* *
26406 GGTAAAAATGTAATTTTTTAAAAGTTT-TG
1 GGTAAAAATGTAATTTTTGAAAAGTTTAAG
* * *
26435 GGTCAAAATGGAA-TTTTGGAAAGTTTAAG
1 GGTAAAAATGTAATTTTTGAAAAGTTTAAG
* *
26464 GGTAAAAATGTAATTTTT-AGAAAGTATGAG
1 GGTAAAAATGTAATTTTTGA-AAAGTTTAAG
* * * *
26494 GGTCAAAATATTATTTTTGAGAAGTTTA
1 GGTAAAAATGTAATTTTTGAAAAGTTTA
26522 GGGACCTCCA
Statistics
Matches: 67, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
28 11 0.16
29 23 0.34
30 32 0.48
31 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.38
Consensus pattern (30 bp):
GGTAAAAATGTAATTTTTGAAAAGTTTAAG
Found at i:26469 original size:58 final size:59
Alignment explanation
Indices: 26078--26486 Score: 219
Period size: 58 Copynumber: 7.0 Consensus size: 59
26068 ATTTTAGGGG
** * *
26078 AAAATC-AGGGTCAAAAATATAATTTTGAAAAGTTCGAGGGT-AAAATGATAA-TTTTTAG-
1 AAAATCGA-GGTCAAAAATGGAATTTTGGAAAGTT-AAGGGTAAAAATG-TAATTTTTTAGA
* * * * * *
26136 AAAATCGGGGT-TAAAATTGCATTTTGG-AAGTTCGAGGGT-AAAATGTAA-TTTTTGGA
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTT-AAGGGTAAAAATGTAATTTTTTAGA
* * * * * * * * *
26192 AAAATAGTGATAAAAAATGGATTTTTGGGACGTTTGAGGGT-AAAATGGTAA-TTTTTGGA
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAG-TTAAGGGTAAAAAT-GTAATTTTTTAGA
* * * ** *
26251 GAAAT-TAGGGTTAAAAATGGAATTTT-GAGAAGTTTTGGGGT--AAATGGTAA-TTTTTGGA
1 AAAATCGA-GGTCAAAAATGGAATTTTGGA-AAG-TTAAGGGTAAAAAT-GTAATTTTTTAGA
* * * ** *
26309 AAAATCAAGGTTAAAAATGGAATTTTGAAAAGATGGAGGGAAAAAATGTAA-TTTTTAGA
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAG-TTAAGGGTAAAAATGTAATTTTTTAGA
* **
26368 AAAATCGAGGTCAAAAATGGAATTTTGGAATGTTCGGAGGTAAAAATGTAATTTTTTA-A
1 AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTAAG-GGTAAAAATGTAATTTTTTAGA
** *
26427 AAGTTTTG-GGTC-AAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAA-TTTTTAGA
1 AA-AATCGAGGTCAAAAATGGAATTTTGGAAAG-TTAAGGGTAAAAATGTAATTTTTTAGA
26485 AA
1 AA
26487 GTATGAGGGT
Statistics
Matches: 286, Mismatches: 48, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
55 9 0.03
56 26 0.09
57 29 0.10
58 105 0.37
59 105 0.37
60 12 0.04
ACGTcount: A:0.40, C:0.03, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAATCGAGGTCAAAAATGGAATTTTGGAAAGTTAAGGGTAAAAATGTAATTTTTTAGA
Found at i:26488 original size:58 final size:57
Alignment explanation
Indices: 26084--26502 Score: 180
Period size: 59 Copynumber: 7.2 Consensus size: 57
26074 GGGGAAAATC
** * * * *
26084 AGGGTCAAAAATATAATTTTGAAAAGTTCGAGGGT-AAAATGATAATTTTTAGAAA-ATC
1 AGGGTC-AAAATGGAATTTTGGAAAGTT-AAGGGTAAAAATG-TAATTTTTAGAAAGTTT
* * * * * * **
26142 GGGGTTAAAATTGCATTTTGG-AAGTTCGAGGGT-AAAATGTAATTTTTGGAAA-AAT
1 AGGGTCAAAATGGAATTTTGGAAAGTT-AAGGGTAAAAATGTAATTTTTAGAAAGTTT
* * * * * *
26197 AGTGATAAAAAATGGATTTTTGGGACGTTTGAGGGT-AAAATGGTAATTTTTGGAGAAA--TT
1 AG-GGT-CAAAATGGAATTTTGGAAAG-TTAAGGGTAAAAAT-GTAATTTTT--AGAAAGTTT
* ** * * **
26257 AGGGTTAAAAATGGAATTTT-GAGAAGTTTTGGGGT--AAATGGTAATTTTTGGAAAAATCA
1 AGGG-TCAAAATGGAATTTTGGA-AAG-TTAAGGGTAAAAAT-GTAATTTTTAG-AAAGTTT
* * * ** * **
26316 AGGTTAAAAATGGAATTTTGAAAAGATGGAGGGAAAAAATGTAATTTTTAGAAA-AAT
1 AGGGTCAAAATGGAATTTTGGAAAG-TTAAGGGTAAAAATGTAATTTTTAGAAAGTTT
* * **
26373 CGAGGTCAAAAATGGAATTTTGGAATGTTCGGAGGTAAAAATGTAATTTTTTA-AAAGTTT
1 AG-GGTC-AAAATGGAATTTTGGAAAGTTAAG-GGTAAAAATGTAA-TTTTTAGAAAGTTT
* *
26433 TGGGTCAAAATGGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTAGAAAGTATG
1 AGGGTCAAAATGGAATTTTGGAAAG-TTAAGGGTAAAAATGTAATTTTTAGAAAGT-TT
26492 AGGGTCAAAAT
1 AGGGTCAAAAT
26503 ATTATTTTTG
Statistics
Matches: 283, Mismatches: 55, Indels: 45
0.74 0.14 0.12
Matches are distributed among these distances:
55 14 0.05
56 21 0.07
57 33 0.12
58 97 0.34
59 98 0.35
60 16 0.06
61 4 0.01
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.33
Consensus pattern (57 bp):
AGGGTCAAAATGGAATTTTGGAAAGTTAAGGGTAAAAATGTAATTTTTAGAAAGTTT
Found at i:26496 original size:30 final size:31
Alignment explanation
Indices: 26084--26516 Score: 116
Period size: 29 Copynumber: 14.8 Consensus size: 31
26074 GGGGAAAATC
* *
26084 AGGGTCAAAAATATAATTTTGA-AAAGT-TCG
1 AGGGT-AAAAATGTAATTTTTAGAAAGTATCG
26114 AGGGT-AAAATGATAATTTTTAGAAA--ATCG
1 AGGGTAAAAATG-TAATTTTTAGAAAGTATCG
* * *
26143 -GGGTTAAAAT-TGCA-TTTT-GGAAGT-TCG
1 AGGGTAAAAATGT-AATTTTTAGAAAGTATCG
* *
26170 AGGGT-AAAATGTAATTTTTGGAAA-AAT--
1 AGGGTAAAAATGTAATTTTTAGAAAGTATCG
* * * * * *
26197 AGTGATAAAAAATG-GATTTTTGGGACGT-TTG
1 AG-GGT-AAAAATGTAATTTTTAGAAAGTATCG
26228 AGGGT-AAAATGGTAATTTTTGGAGAAA-T-T--
1 AGGGTAAAAAT-GTAATTTTT--AGAAAGTATCG
* * * *
26257 AGGGTTAAAAATGGAATTTTGAG-AAGTTTTG
1 AGGG-TAAAAATGTAATTTTTAGAAAGTATCG
* * *
26288 -GGGT--AAATGGTAATTTTTGGAAA-AATCA
1 AGGGTAAAAAT-GTAATTTTTAGAAAGTATCG
* * * *
26316 AGGTTAAAAATGGAATTTTGA-AAAG-ATGG
1 AGGGTAAAAATGTAATTTTTAGAAAGTATCG
* *
26345 AGGGAAAAAATGTAATTTTTAGAAA-AATCG
1 AGGGTAAAAATGTAATTTTTAGAAAGTATCG
* * *
26375 A-GGTCAAAAATGGAA-TTTTGGAATGT-TCG
1 AGGGT-AAAAATGTAATTTTTAGAAAGTATCG
*
26404 -GAGGTAAAAATGTAATTTTTTA-AAAGT-T-T
1 AG-GGTAAAAATGTAA-TTTTTAGAAAGTATCG
* * * * **
26433 TGGGTCAAAATGGAA-TTTTGGAAAGT-TTA
1 AGGGTAAAAATGTAATTTTTAGAAAGTATCG
26462 AGGGTAAAAATGTAATTTTTAGAAAGTAT-G
1 AGGGTAAAAATGTAATTTTTAGAAAGTATCG
* * *
26492 AGGGTCAAAATATTATTTTTGAGAA
1 AGGGTAAAAATGTAATTTTT-AGAA
26517 GTTTAGGGAC
Statistics
Matches: 297, Mismatches: 58, Indels: 95
0.66 0.13 0.21
Matches are distributed among these distances:
26 3 0.01
27 26 0.09
28 44 0.15
29 108 0.36
30 92 0.31
31 22 0.07
32 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.33
Consensus pattern (31 bp):
AGGGTAAAAATGTAATTTTTAGAAAGTATCG
Found at i:27551 original size:3 final size:3
Alignment explanation
Indices: 27480--27539 Score: 75
Period size: 3 Copynumber: 19.3 Consensus size: 3
27470 TTTTATTAGG
*
27480 TTA TTAA TTA TTA TTA TTA TTT TTA TTA TTA TTA TTA TTA TTA TTAA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* *
27527 TGA TCA TTA TTA T
1 TTA TTA TTA TTA T
27540 AAACATTATT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
3 45 0.90
4 5 0.10
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28513 original size:28 final size:28
Alignment explanation
Indices: 28469--28528 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
28459 AAATGAGACT
* *
28469 TTTTGGATATCCGGGGGTAAAATGGTAA
1 TTTTGGATATCCAGGGGCAAAATGGTAA
28497 TTTTGGATTAT-CAGGGGCAAAATGGTAA
1 TTTTGGA-TATCCAGGGGCAAAATGGTAA
28525 TTTT
1 TTTT
28529 AGGAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 26 0.90
29 3 0.10
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.37
Consensus pattern (28 bp):
TTTTGGATATCCAGGGGCAAAATGGTAA
Found at i:28614 original size:30 final size:28
Alignment explanation
Indices: 28580--28741 Score: 150
Period size: 30 Copynumber: 5.5 Consensus size: 28
28570 GTAAAATGGT
28580 AATTTTTGAGAA-TTTCGAGGTCAAAAATAG
1 AATTTTTG-GAAGTTT-GAGGTCAAAAAT-G
* * *
28610 AATTTTTGGAGGTTCGGGGGT-AAAAATG
1 AATTTTTGGAAGTT-TGAGGTCAAAAATG
* *
28638 TAATTTTTAGAAGTTTTATGGTCAAAAATGG
1 -AATTTTTGGAAGTTTGA-GGTCAAAAAT-G
*
28669 AATTTTTGGAAGTTTGAGGGTAAAAAATG
1 AATTTTTGGAAGTTTGA-GGTCAAAAATG
28698 TAATTTTTGGAAGTTTTGAGGTC-AAAATGG
1 -AATTTTTGGAAG-TTTGAGGTCAAAAAT-G
28728 AATTTTTGGAAGTT
1 AATTTTTGGAAGTT
28742 CAGGGGTAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
28 3 0.03
29 41 0.37
30 60 0.55
31 6 0.05
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (28 bp):
AATTTTTGGAAGTTTGAGGTCAAAAATG
Found at i:28642 original size:59 final size:60
Alignment explanation
Indices: 28568--28801 Score: 266
Period size: 59 Copynumber: 4.0 Consensus size: 60
28558 AGACATTCAA
* *
28568 GGGT-AAAATGGTAATTTTTGAGAA-TTTCGAGGTCAAAAATAGAATTTTTGGAGGTTCGG
1 GGGTAAAAAT-GTAATTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGG
* * *
28627 GGGTAAAAATGTAATTTTT-AGAAGTTT-TATGGTCAAAAATGGAATTTTTGGAAGTTTGA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTCGA-GGTCAAAAATGGAATTTTTGGAAGTTCGG
* *
28686 GGGTAAAAAATGTAATTTTTG-GAAGTTTTGAGGTC-AAAATGGAATTTTTGGAAGTTCAG
1 GGGT-AAAAATGTAATTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGG
* * * * * *
28745 GGGTAAAATTATAA-TTTTCAAAAGTTTCGGGGTCAAAATTGGAATTTTTGGACAGTT
1 GGGTAAAAATGTAATTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGA-AGTT
28802 TAGGGACCTT
Statistics
Matches: 150, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
57 4 0.03
58 24 0.16
59 86 0.57
60 35 0.23
61 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (60 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGG
Found at i:29896 original size:3 final size:3
Alignment explanation
Indices: 29890--29937 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
29880 AAAGCTACAT
29890 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29938 ATGATACTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:30647 original size:6 final size:6
Alignment explanation
Indices: 30600--30693 Score: 72
Period size: 6 Copynumber: 16.0 Consensus size: 6
30590 TGTAATTGAT
* *
30600 TTTAAA TTTAAGT TTTAAA -TT--A TTTCAAA TTTAAA -CTAAA TTTAAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* ** *
30646 TTTAAA -ATAAA TTTAAA TTTAAAA AATGAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
30694 GTAAAATTAA
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
3 1 0.01
4 2 0.03
5 10 0.15
6 42 0.62
7 13 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:30677 original size:19 final size:19
Alignment explanation
Indices: 30636--30687 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
30626 AAATTTAAAC
30636 TAAATTTAAATTT--AAAA
1 TAAATTTAAATTTAAAAAA
30653 TAAATTTAAATTTAAAAAA
1 TAAATTTAAATTTAAAAAA
*
30672 TGAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
30688 TTTAAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 13 0.41
19 19 0.59
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATTTAAATTTAAAAAA
Found at i:30703 original size:17 final size:17
Alignment explanation
Indices: 30602--30687 Score: 93
Period size: 17 Copynumber: 4.9 Consensus size: 17
30592 TAATTGATTT
* *
30602 TAAATTTAAGTTTTAAA
1 TAAATTTAAATTTAAAA
* *
30619 T-TATTTCAAATTTAAAC
1 TAAATTT-AAATTTAAAA
30636 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
30653 TAAATTTAAATTTAAAAAA
1 TAAATTTAAATTT--AAAA
*
30672 TGAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
30688 TTTAAAGTAA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
16 4 0.07
17 34 0.59
18 4 0.07
19 16 0.28
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:31550 original size:20 final size:18
Alignment explanation
Indices: 31507--31571 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 18
31497 CAAATTTGAT
* *
31507 TAAATTTAAATGT-AAAG
1 TAAATTTAAATTTAAAAA
*
31524 CAAATTTAAATTTAAAAAGA
1 TAAATTTAAATTT-AAAA-A
31544 TAAATTTAAATTTAAAAA
1 TAAATTTAAATTTAAAAA
31562 TAAATTTAAA
1 TAAATTTAAA
31572 CCAATTTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.27
18 11 0.27
19 7 0.17
20 12 0.29
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (18 bp):
TAAATTTAAATTTAAAAA
Found at i:34116 original size:16 final size:16
Alignment explanation
Indices: 34095--34125 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
34085 GGGCGTTACA
34095 GAACCCCTGTATGTGC
1 GAACCCCTGTATGTGC
*
34111 GAACCCTTGTATGTG
1 GAACCCCTGTATGTG
34126 AGACCATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.29
Consensus pattern (16 bp):
GAACCCCTGTATGTGC
Found at i:34216 original size:29 final size:29
Alignment explanation
Indices: 34174--34231 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
34164 GCCAAACCAT
34174 CTTGCATGCAAAACCCTATAGGTGAACCC
1 CTTGCATGCAAAACCCTATAGGTGAACCC
*
34203 CTTGCATGCAAAACCCTATTGGTGAACCC
1 CTTGCATGCAAAACCCTATAGGTGAACCC
34232 TCTATTGCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.22
Consensus pattern (29 bp):
CTTGCATGCAAAACCCTATAGGTGAACCC
Found at i:34356 original size:54 final size:54
Alignment explanation
Indices: 34271--34383 Score: 208
Period size: 54 Copynumber: 2.1 Consensus size: 54
34261 TAGGAATTAG
* *
34271 TGTGCGAGCTCTTAAGATAATCCTGCTAACCTGGTTATAGGTGAACCTCTTATA
1 TGTGCGAGCTCTTAAGATAATCATGCGAACCTGGTTATAGGTGAACCTCTTATA
34325 TGTGCGAGCTCTTAAGATAATCATGCGAACCTGGTTATAGGTGAACCTCTTATA
1 TGTGCGAGCTCTTAAGATAATCATGCGAACCTGGTTATAGGTGAACCTCTTATA
34379 TGTGC
1 TGTGC
34384 AAACCTATAG
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
54 57 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (54 bp):
TGTGCGAGCTCTTAAGATAATCATGCGAACCTGGTTATAGGTGAACCTCTTATA
Found at i:34408 original size:22 final size:22
Alignment explanation
Indices: 34380--34455 Score: 73
Period size: 22 Copynumber: 3.5 Consensus size: 22
34370 CCTCTTATAT
34380 GTGCAAACCTATAGATTAATAC
1 GTGCAAACCTATAGATTAATAC
34402 GTGCAAACCTATATG-TTAATAC
1 GTGCAAACCTATA-GATTAATAC
* * * * * * *
34424 ATACGAACCCACAGATTATTAT
1 GTGCAAACCTATAGATTAATAC
34446 GTGCAAACCT
1 GTGCAAACCT
34456 TATTAATTGT
Statistics
Matches: 41, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
21 1 0.02
22 39 0.95
23 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (22 bp):
GTGCAAACCTATAGATTAATAC
Found at i:34587 original size:15 final size:14
Alignment explanation
Indices: 34528--34645 Score: 103
Period size: 14 Copynumber: 8.2 Consensus size: 14
34518 TATGTCAGCA
*
34528 TGCAAACCCTAATG
1 TGCAAACCCTAAGG
34542 TGCAAACCCCT-AGG
1 TGCAAA-CCCTAAGG
* *
34556 TACAAACCCTAATG
1 TGCAAACCCTAAGG
34570 TGCAAACCTCTAAGG
1 TGCAAACC-CTAAGG
* *
34585 TGCGAACCCTTAAAG
1 TGCAAACCC-TAAGG
*
34600 TGCAGACCCTAAGG
1 TGCAAACCCTAAGG
* * *
34614 TGCGAACTCTTAAAG
1 TGCAAAC-CCTAAGG
*
34629 CGCAAACCCTAAGG
1 TGCAAACCCTAAGG
34643 TGC
1 TGC
34646 GAAAAGTACG
Statistics
Matches: 80, Mismatches: 19, Indels: 10
0.73 0.17 0.09
Matches are distributed among these distances:
13 4 0.05
14 39 0.49
15 37 0.46
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (14 bp):
TGCAAACCCTAAGG
Found at i:34611 original size:29 final size:29
Alignment explanation
Indices: 34532--34648 Score: 132
Period size: 29 Copynumber: 4.1 Consensus size: 29
34522 TCAGCATGCA
* * *
34532 AACCC-TAATGTGCAAACCCCT-AGGTACA
1 AACCCTTAAAGTGCAAA-CCCTAAGGTGCG
*
34560 AACCC-TAATGTGCAAACCTCTAAGGTGCG
1 AACCCTTAAAGTGCAAACC-CTAAGGTGCG
*
34589 AACCCTTAAAGTGCAGACCCTAAGGTGCG
1 AACCCTTAAAGTGCAAACCCTAAGGTGCG
* *
34618 AACTCTTAAAGCGCAAACCCTAAGGTGCG
1 AACCCTTAAAGTGCAAACCCTAAGGTGCG
34647 AA
1 AA
34649 AAGTACGAAC
Statistics
Matches: 79, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
27 2 0.03
28 18 0.23
29 48 0.61
30 11 0.14
ACGTcount: A:0.34, C:0.28, G:0.20, T:0.18
Consensus pattern (29 bp):
AACCCTTAAAGTGCAAACCCTAAGGTGCG
Found at i:36247 original size:45 final size:46
Alignment explanation
Indices: 36160--36249 Score: 107
Period size: 45 Copynumber: 2.0 Consensus size: 46
36150 ATTACTAAGT
* *
36160 AAATTTACAATTTTAATCATTTTTATAATTTTTTTATATTTTTTAA
1 AAATTTACAATTTTAATAATTTTTATAATTTTTTAATATTTTTTAA
36206 AAATTT-CAATTTCT-ATAATTTTTAT-ATTTTTACTAAT-TTTTTTA
1 AAATTTACAATTT-TAATAATTTTTATAATTTTT--TAATATTTTTTA
36250 TAACTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
44 6 0.15
45 23 0.59
46 10 0.26
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (46 bp):
AAATTTACAATTTTAATAATTTTTATAATTTTTTAATATTTTTTAA
Found at i:37600 original size:47 final size:47
Alignment explanation
Indices: 37503--37593 Score: 116
Period size: 47 Copynumber: 2.0 Consensus size: 47
37493 ATAAAATGCA
*
37503 AAAACTTGTAAAAAAATTATTAAAAGTTGTAAAAATTATAATAATAT
1 AAAACTTGTAAAAAAATTATTAAAAGTTGTAAAAATTATAAAAATAT
* *
37550 AAAATTTGTAAAAGAA-TATTAAAAAGTT-TAACAAATT-TAAAAAT
1 AAAACTTGTAAAAAAATTATT-AAAAGTTGTAA-AAATTATAAAAAT
37594 TGTAAAAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
46 13 0.33
47 26 0.67
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (47 bp):
AAAACTTGTAAAAAAATTATTAAAAGTTGTAAAAATTATAAAAATAT
Found at i:38306 original size:18 final size:19
Alignment explanation
Indices: 38279--38315 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
38269 ATAATTTACC
*
38279 AAAAATTAATGTTGTTAGG
1 AAAAATTAATGTTGATAGG
38298 AAAAA-TAATGTTGATAGG
1 AAAAATTAATGTTGATAGG
38316 TGGTAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.22, T:0.32
Consensus pattern (19 bp):
AAAAATTAATGTTGATAGG
Found at i:41054 original size:19 final size:19
Alignment explanation
Indices: 41032--41076 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
41022 TTTTATTAGG
41032 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
41051 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
41070 ATTTAAT
1 ATTTAAT
41077 TCATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:43113 original size:21 final size:21
Alignment explanation
Indices: 43089--43144 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
43079 TGTTTATGAA
* * *
43089 TTTCAATAGCAAATTGTAGAT
1 TTTCAAAAGAAAACTGTAGAT
43110 TTTCAAAAGAAAACTGTAGAT
1 TTTCAAAAGAAAACTGTAGAT
*
43131 TTT-AAAAAAAAACT
1 TTTCAAAAGAAAACT
43145 AAGGCATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (21 bp):
TTTCAAAAGAAAACTGTAGAT
Found at i:43142 original size:20 final size:21
Alignment explanation
Indices: 43103--43144 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
43093 AATAGCAAAT
*
43103 TGTAGATTTTCAAAAGAAAAC
1 TGTAGATTTTCAAAAAAAAAC
43124 TGTAGATTTT-AAAAAAAAAC
1 TGTAGATTTTCAAAAAAAAAC
43144 T
1 T
43145 AAGGCATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.31
Consensus pattern (21 bp):
TGTAGATTTTCAAAAAAAAAC
Found at i:52113 original size:29 final size:31
Alignment explanation
Indices: 52076--52152 Score: 95
Period size: 29 Copynumber: 2.5 Consensus size: 31
52066 TTGCCTCATA
*
52076 TTACATTTTAGTCACTTATATT-T-GAAATG
1 TTACTTTTTAGTCACTTATATTATCGAAATG
* *
52105 TTACTTTTTAGTCACTTATGTTATCGAATTG
1 TTACTTTTTAGTCACTTATATTATCGAAATG
*
52136 TAACATTTTTAGTCACT
1 TTAC-TTTTTAGTCACT
52153 AAACCATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
29 20 0.49
30 1 0.02
31 8 0.20
32 12 0.29
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (31 bp):
TTACTTTTTAGTCACTTATATTATCGAAATG
Found at i:53654 original size:18 final size:18
Alignment explanation
Indices: 53628--53694 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
53618 TTTGCACGTA
*
53628 AAATGATTTTTAAAAAAT
1 AAATTATTTTTAAAAAAT
53646 AAATTATTTTTCAGAAAAATT
1 AAATTATTTTT-A-AAAAA-T
*
53667 AATATT-TTTTTGAAAAAT
1 AA-ATTATTTTTAAAAAAT
*
53685 TAA-TATTTTT
1 AAATTATTTTT
53695 TTTATGTTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
16 1 0.02
17 6 0.15
18 12 0.29
19 6 0.15
20 5 0.12
21 8 0.20
22 3 0.07
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (18 bp):
AAATTATTTTTAAAAAAT
Found at i:53696 original size:19 final size:19
Alignment explanation
Indices: 53634--53696 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
53624 CGTAAAATGA
* *
53634 TTTTTAAAAAATAAATTATT
1 TTTTTGAAAAATTAA-TATT
**
53654 TTTCAGAAAAATTAATATT
1 TTTTTGAAAAATTAATATT
53673 TTTTTGAAAAATTAATATT
1 TTTTTGAAAAATTAATATT
53692 TTTTT
1 TTTTT
53697 TATGTTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 26 0.70
20 11 0.30
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (19 bp):
TTTTTGAAAAATTAATATT
Found at i:56595 original size:29 final size:30
Alignment explanation
Indices: 56554--56618 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
56544 AAATTGTAAT
* *
56554 TTTTATAATTTTTAAATAATTAAATTAAAA
1 TTTTATAATTTTTAAAGAATTAAAGTAAAA
* * *
56584 TTTTATCATTTTT-AAGAGTTAAAGTATAA
1 TTTTATAATTTTTAAAGAATTAAAGTAAAA
56613 TTTTAT
1 TTTTAT
56619 TTATATTAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.60
30 12 0.40
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (30 bp):
TTTTATAATTTTTAAAGAATTAAAGTAAAA
Done.