Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168331.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_554, 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: 23081
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Found at i:587 original size:187 final size:187
Alignment explanation
Indices: 329--727 Score: 545
Period size: 187 Copynumber: 2.1 Consensus size: 187
319 CTTAATATTG
* *
329 TTGAAGGCATTTTATACTAAAAGATGCATTTAATAATATCAAAATTTTAAAAAAAAAATTATTGA
1 TTGAAGGCATTTTATACTAAAAGAAGCATTTAATAATATCAAAATTTTAAAAAAAAAATTATTAA
*
394 AGGCGTTTATTCTCAAAAAAATACCTTAAATAATTATGTACAAAAATTAAAATGAATTAGTGAAG
66 AGGCGTTTATTCTCAAAAAAATACCTTAAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAG
***
459 GCATTTTTCTAGAATAAA-TGTTTTCACTAACCGTTTTAAAATTTAAGTAGT-AGAATA
131 GCATTTTTCTAGAATAAACACCTTT-ACTAACCGTTTTAAAATTTAAGTAGTGA-AATA
* * * * *
516 TTGAAGGCGTTTT-TCACTGAAAGAAGCCTTTAATAATCTCAAAAATTTT-AAAAGAAAATTATT
1 TTGAAGGCATTTTAT-ACTAAAAGAAGCATTTAATAATATC-AAAATTTTAAAAAAAAAATTATT
* * * *
579 AAAGGCGTTTGTTCTTAAAAAAATACCTTCAATAATTATGTACATAAATTAAAAGGAATTAGTGA
64 AAAGGCGTTTATTCTCAAAAAAATACCTTAAATAATTATGTACAAAAATTAAAAGGAATTAGTGA
**
644 AGGTGTTTTTCTAGAATAAACACCTTTACTAACCGTTTTAAAATTTAAGTAGTGAAATA
129 AGGCATTTTTCTAGAATAAACACCTTTACTAACCGTTTTAAAATTTAAGTAGTGAAATA
* * *
703 TTTAAAGGCATTTTGTACTAGAAGA
1 -TTGAAGGCATTTTATACTAAAAGA
728 CACCTTCAAT
Statistics
Matches: 185, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
186 1 0.01
187 153 0.83
188 30 0.16
189 1 0.01
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.35
Consensus pattern (187 bp):
TTGAAGGCATTTTATACTAAAAGAAGCATTTAATAATATCAAAATTTTAAAAAAAAAATTATTAA
AGGCGTTTATTCTCAAAAAAATACCTTAAATAATTATGTACAAAAATTAAAAGGAATTAGTGAAG
GCATTTTTCTAGAATAAACACCTTTACTAACCGTTTTAAAATTTAAGTAGTGAAATA
Found at i:3437 original size:21 final size:21
Alignment explanation
Indices: 3412--3452 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3402 CATATTACAC
3412 AAGTTGGTGATATTGATATTG
1 AAGTTGGTGATATTGATATTG
*
3433 AAGTTGGTGATCTTGATATT
1 AAGTTGGTGATATTGATATT
3453 CAAAATAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (21 bp):
AAGTTGGTGATATTGATATTG
Found at i:9643 original size:23 final size:21
Alignment explanation
Indices: 9613--9655 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9603 ATAATAATTA
*
9613 TATAATTAATATTGAAAAAATAT
1 TATAATT-ATAAT-AAAAAATAT
9636 TATAATTATAATAAAAAATA
1 TATAATTATAATAAAAAATA
9656 AAAAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 4 0.21
23 7 0.37
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TATAATTATAATAAAAAATAT
Found at i:9677 original size:14 final size:13
Alignment explanation
Indices: 9654--9685 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 13
9644 TAATAAAAAA
9654 TAAAAAATTTTAT
1 TAAAAAATTTTAT
9667 TAAAGAAATTTTAT
1 TAAA-AAATTTTAT
9681 TAAAA
1 TAAAA
9686 TTAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (13 bp):
TAAAAAATTTTAT
Found at i:11884 original size:20 final size:20
Alignment explanation
Indices: 11861--11904 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
11851 TGCCCAGTTT
*
11861 CCGGCGAGGAATCCCAGAAA
1 CCGGCGAAGAATCCCAGAAA
* * *
11881 CCGGTGAATATTCCCAGAAA
1 CCGGCGAAGAATCCCAGAAA
11901 CCGG
1 CCGG
11905 TCGACTTCCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.32, C:0.30, G:0.27, T:0.11
Consensus pattern (20 bp):
CCGGCGAAGAATCCCAGAAA
Found at i:12327 original size:8 final size:7
Alignment explanation
Indices: 12288--12359 Score: 62
Period size: 7 Copynumber: 10.4 Consensus size: 7
12278 CCGCTCTAGG
12288 TTTTTT-
1 TTTTTTA
12294 TTTTTTA
1 TTTTTTA
*
12301 -TTATTA
1 TTTTTTA
* *
12307 TTATTTC
1 TTTTTTA
12314 TTTGTTTA
1 TTT-TTTA
12322 TTTGTTTA
1 TTT-TTTA
12330 TTTGTTTA
1 TTT-TTTA
12338 --TTTTA
1 TTTTTTA
12343 TTTTTTA
1 TTTTTTA
12350 TTTTTTA
1 TTTTTTA
12357 TTT
1 TTT
12360 ATTAGATTAG
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
5 4 0.07
6 12 0.22
7 20 0.36
8 19 0.35
ACGTcount: A:0.14, C:0.01, G:0.04, T:0.81
Consensus pattern (7 bp):
TTTTTTA
Found at i:12335 original size:16 final size:15
Alignment explanation
Indices: 12304--12359 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 15
12294 TTTTTTATTA
* *
12304 TTATTATTTCTTTGT
1 TTATTTTTTATTTGT
12319 TTATTTGTTTATTTGT
1 TTATTT-TTTATTTGT
12335 TTA--TTTTATTT-T
1 TTATTTTTTATTTGT
12347 TTATTTTTTATTT
1 TTATTTTTTATTT
12360 ATTAGATTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 4 0.11
13 7 0.19
14 9 0.25
15 5 0.14
16 11 0.31
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (15 bp):
TTATTTTTTATTTGT
Found at i:12362 original size:4 final size:4
Alignment explanation
Indices: 12307--12362 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
12297 TTTATTATTA
* * * *
12307 TTAT TTCT TTGT TTAT TTGT TTAT TTGT TTATT TTAT TT-T TTAT TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT
12354 TTAT TTAT T
1 TTAT TTAT T
12363 AGATTAGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
3 6 0.14
4 32 0.76
5 4 0.10
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (4 bp):
TTAT
Found at i:12502 original size:60 final size:59
Alignment explanation
Indices: 12435--12953 Score: 662
Period size: 59 Copynumber: 8.7 Consensus size: 59
12425 AAAAATTTCT
12435 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAA
*
12494 AATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATCAATTTCC-A
1 AA-AAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAA
* * ** * *
12553 AAAAAGTATTTTT-GGGGAAAGTTGAAAGTATCAATTTTCCTCGGAAAAAAATTTCAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAA
*
12611 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-AGAATAAATTTTC--
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGA-AATAAATTTCCAA
* *
12668 AAAAAATATTTTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCC--AA
12729 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAATTTCCAAA
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATAAATTTCC-AA
*
12794 AAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTGT-CAA
1 AAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATT-TCCAA
**** *
12854 AAAAGGGGTTTTT-GAGGAAAAGTTGAAAGTATTAATTTTCCTT-GAAAATCAAAATTTCC--
1 AAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAAT--AAATTTCCAA
* *
12913 AAAAAATATTTTTGGGGTAAAGTTGAAAGTATCAATTTTCC
1 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCC
12954 CTAAAAAAAA
Statistics
Matches: 406, Mismatches: 32, Indels: 44
0.84 0.07 0.09
Matches are distributed among these distances:
57 89 0.22
58 27 0.07
59 109 0.27
60 62 0.15
61 57 0.14
62 1 0.00
63 2 0.00
64 2 0.00
65 9 0.02
66 48 0.12
ACGTcount: A:0.45, C:0.08, G:0.14, T:0.34
Consensus pattern (59 bp):
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAATTTCCAA
Found at i:12645 original size:116 final size:117
Alignment explanation
Indices: 12422--12953 Score: 691
Period size: 116 Copynumber: 4.5 Consensus size: 117
12412 TTCTTTAAAT
* * *
12422 AAAAAAAATTTCTAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
1 AAAATAAATTTCCAAAAAATATTTTT-GGGGAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
*
12487 TTTCCAAAATAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
65 TTTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* ** *
12540 -AAATCAATTTCCAAAAAAGTATTTTTGGGGAAAGTTGAAAGTATCAATTTTCCTCGGAAAAAAA
1 AAAATAAATTTCCAAAAAA-TATTTTTGGGGAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
12604 TTT-CAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTA-
65 TTTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * * * *
12655 AGAATAAATTTTCAAAAAATATTTTTAAGGAAAAATTGAAAGTATCAATTTTCCTTAGAAATAAA
1 AAAATAAATTTCCAAAAAATATTTTT-GGGGAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAA
12720 TTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAG
65 TTTCC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG
12777 AAAAATAAATTTCCAAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAA
1 -AAAATAAATTTCC---AAAAAA-TATTTTTGGGG-AAAGTTGAAAGTATCAATTTTCCTTAGAA
**** *
12842 ATAAATTGT-C-AAAAAAGGGGTTTTT-GAGGAAAAGTTGAAAGTATTAATTTTCCTT-G
60 ATAAATT-TCCAAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG
12898 AAAATCAAAATTTCCAAAAAATATTTTTGGGGTAAAGTTGAAAGTATCAATTTTCC
1 AAAAT--AAATTTCCAAAAAATATTTTTGGGG-AAAGTTGAAAGTATCAATTTTCC
12954 CTAAAAAAAA
Statistics
Matches: 367, Mismatches: 28, Indels: 38
0.85 0.06 0.09
Matches are distributed among these distances:
115 7 0.02
116 97 0.26
117 53 0.14
118 87 0.24
119 6 0.02
120 5 0.01
121 2 0.01
122 8 0.02
123 11 0.03
124 1 0.00
125 38 0.10
126 8 0.02
127 43 0.12
128 1 0.00
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (117 bp):
AAAATAAATTTCCAAAAAATATTTTTGGGGAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
TTCCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:18111 original size:42 final size:42
Alignment explanation
Indices: 18063--18413 Score: 536
Period size: 42 Copynumber: 8.5 Consensus size: 42
18053 CCAAGTTCGT
18063 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
*
18105 TGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
* *
18147 TACCTCTGTTGAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
*
18189 TGCCTCTGTTTAGAGGAGCAATTTATTTTTTCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
* *
18231 TACCTCTGTTGAGAGGAGCAATTTATTTTT-CAAAGTTCCGT--
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG-T-CGTGG
18272 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCC-AAGTTCGT--
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAG-TCGTGG
*
18312 TGCCTCTGTTTAGAGGAGCAATTTA-CTTTCCAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
* * *
18353 TACCTCTGTTTAGAGGAGCAATTTACTTTTCAAAAGTCGTGG
1 TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
18395 TGCCTCTGTTTAGAGGAGC
1 TGCCTCTGTTTAGAGGAGC
18414 TTTGGTAAAA
Statistics
Matches: 286, Mismatches: 16, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
39 9 0.03
40 31 0.11
41 62 0.22
42 181 0.63
43 3 0.01
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (42 bp):
TGCCTCTGTTTAGAGGAGCAATTTATTTTTCCAAAGTCGTGG
Found at i:18457 original size:23 final size:23
Alignment explanation
Indices: 18423--18508 Score: 95
Period size: 23 Copynumber: 3.7 Consensus size: 23
18413 CTTTGGTAAA
*
18423 AAAAAAATAAAAAAATAAAAAAC
1 AAAAAAACAAAAAAATAAAAAAC
*
18446 AAAAAAACAAAAAACAAAAAAAAC
1 AAAAAAACAAAAAA-ATAAAAAAC
* *
18470 -CAAAAACAAAAAAA-AAAACAAA
1 AAAAAAACAAAAAAATAAAA-AAC
18492 AAAAAAACCAAAAAAAT
1 AAAAAAA-CAAAAAAAT
18509 GTTGAGTTGA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.08
22 3 0.06
23 30 0.57
24 16 0.30
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.03
Consensus pattern (23 bp):
AAAAAAACAAAAAAATAAAAAAC
Found at i:18507 original size:1 final size:1
Alignment explanation
Indices: 18420--18498 Score: 77
Period size: 1 Copynumber: 79.0 Consensus size: 1
18410 GAGCTTTGGT
* * * * * ** *
18420 AAAAAAAAAATAAAAAAATAAAAAACAAAAAAACAAAAAACAAAAAAAACCAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
18485 AAACAAAAAAAAAA
1 AAAAAAAAAAAAAA
18499 CCAAAAAAAT
Statistics
Matches: 62, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.89, C:0.09, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:18685 original size:9 final size:9
Alignment explanation
Indices: 18661--18702 Score: 59
Period size: 9 Copynumber: 4.7 Consensus size: 9
18651 CAATTTGTCC
*
18661 TGTATTATTT
1 TGTATT-TTA
18671 TGTATTTTA
1 TGTATTTTA
18680 TGTATTTTA
1 TGTATTTTA
18689 TGTATTTTA
1 TGTATTTTA
18698 T-TATT
1 TGTATT
18703 ATGTATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
8 4 0.13
9 21 0.68
10 6 0.19
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (9 bp):
TGTATTTTA
Found at i:18694 original size:18 final size:19
Alignment explanation
Indices: 18661--18714 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
18651 CAATTTGTCC
*
18661 TGTATTATTTTGTATTTTA
1 TGTATTATTATGTATTTTA
18680 TGTATT-TTATGTATTTTA
1 TGTATTATTATGTATTTTA
*
18698 T-TATTATGTATATATTT
1 TGTATTAT-TATGTATTT
18715 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 14 0.45
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (19 bp):
TGTATTATTATGTATTTTA
Found at i:19753 original size:8 final size:7
Alignment explanation
Indices: 19713--19785 Score: 62
Period size: 8 Copynumber: 10.1 Consensus size: 7
19703 CCGCTCTAGG
19713 TTTT-TT
1 TTTTATT
19719 TTTTATT
1 TTTTATT
19726 ATTATTATT
1 -TT-TTATT
* *
19735 ATTTCTT
1 TTTTATT
19742 TGTTTATT
1 T-TTTATT
19750 TGTTTATT
1 T-TTTATT
19758 TGTTTA--
1 T-TTTATT
19764 TTTTATT
1 TTTTATT
19771 TTTTATT
1 TTTTATT
19778 TTTTATT
1 TTTTATT
19785 T
1 T
19786 ATTAGATTAG
Statistics
Matches: 57, Mismatches: 4, Indels: 11
0.79 0.06 0.15
Matches are distributed among these distances:
5 4 0.07
6 5 0.09
7 21 0.37
8 22 0.39
9 5 0.09
ACGTcount: A:0.15, C:0.01, G:0.04, T:0.79
Consensus pattern (7 bp):
TTTTATT
Found at i:19788 original size:4 final size:4
Alignment explanation
Indices: 19733--19788 Score: 53
Period size: 4 Copynumber: 14.2 Consensus size: 4
19723 ATTATTATTA
* * * *
19733 TTAT TTCT TTGT TTAT TTGT TTAT TTGT TTATT TTAT TT-T TTAT TT-T
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TTAT
19780 TTAT TTAT T
1 TTAT TTAT T
19789 AGATTAGGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
3 6 0.14
4 32 0.76
5 4 0.10
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (4 bp):
TTAT
Found at i:20010 original size:59 final size:58
Alignment explanation
Indices: 19849--20394 Score: 593
Period size: 59 Copynumber: 9.1 Consensus size: 58
19839 TCTTTAAATA
*
19849 AAAAAAATTTC-TAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
1 AAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
** * * * **
19906 AAATCAATTTCCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGG
1 AAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
19964 AAAAAAATTTCAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAG
1 AAAAAAATTTC-AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT-AG
* * * * *
20024 AATAAATTTTC--AAAAAATATTTTTAAGGAAAAATTGAAAGTATCATTTTTCCTTAG
1 AAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
*
20080 AAATAAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAG
1 AAAAAAATTT-C--AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG
*
20144 AAAAATAAATTTCCAAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT-G
1 -AAAA-AAATTT-C-AAAAAAAA-TATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* *
20206 AAAATCAAAATTTCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAACTTTCCTTAG
1 -AAA--AAAATTTC--AAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
* **** *
20269 AAATAAATTTTCAAAAAAGGGGTTTTT-GAGAAAAAGTTGAAAGTATCAATTTTCCTT-G
1 AAA-AAAATTTCAAAAAAAATATTTTTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAG
* * * *
20327 AAAATCGAAATTTC-CAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTAA
1 AAAA---AAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
20387 AAAAAAAT
1 AAAAAAAT
20395 CATTCTTTCC
Statistics
Matches: 420, Mismatches: 45, Indels: 48
0.82 0.09 0.09
Matches are distributed among these distances:
56 9 0.02
57 55 0.13
58 55 0.13
59 113 0.27
60 21 0.05
61 47 0.11
62 45 0.11
63 16 0.04
64 3 0.01
65 12 0.03
66 44 0.10
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (58 bp):
AAAAAAATTTCAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAG
Found at i:20280 original size:246 final size:238
Alignment explanation
Indices: 19853--20394 Score: 764
Period size: 246 Copynumber: 2.3 Consensus size: 238
19843 TAAATAAAAA
* *
19853 AAATTTCTAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTT---AG--AAATCAA
1 AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAA
*
19913 TTTCCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGGAAAAAAATTTCAAA
66 TTTCCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAAAAAATTTCAAA
* *
19978 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAA-T
131 AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAACTTTCCTTAAGAATAAATTTTCAAAAAAGG
*
20042 ATTTTTAAGGAAAAA-TTGAAAGTATCATTTTTCCTT-AGAAAT-
196 ATTTTTAA-GAAAAAGTTGAAAGTATCAATTTTCCTTGA-AAATC
20084 AAATTTCCAAAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAA
1 AAATTTCC----AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAA
*
20149 TAAATTTCCAAAAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAA
62 TAAATTTCC---AAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAA--AA
*
20214 AATTTCAAAAAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAACTTTCCTT-AGAAATAAATT
122 AATTTC-AAAAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAACTTTCCTTAAG-AATAAATT
* *
20278 TTCAAAAAAGGGGTTTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
185 TTCAAAAAA-GGATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
* *
20333 GAAATTTCCAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCCTAAAA-AAAAAT
1 -AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAAT
20395 CATTCTTTCC
Statistics
Matches: 277, Mismatches: 12, Indels: 30
0.87 0.04 0.09
Matches are distributed among these distances:
231 7 0.03
235 43 0.16
238 2 0.01
240 11 0.04
243 47 0.17
245 16 0.06
246 106 0.38
247 6 0.02
248 30 0.11
249 1 0.00
250 8 0.03
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (238 bp):
AAATTTCCAAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAGAAAAATAAA
TTTCCAAAAAAGTATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAAAAAAATTTCAAA
AAAAAATATTTTTAGGGAAAAGTTGAAAGTATCAACTTTCCTTAAGAATAAATTTTCAAAAAAGG
ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATC
Done.