Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2546
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: 42173
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1670 original size:30 final size:30
Alignment explanation
Indices: 1636--1698 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
1626 CCTGATTGAA
1636 TTATAATGTATAATTTCATTGCTATGAATC
1 TTATAATGTATAATTTCATTGCTATGAATC
1666 TTATAATGTATAATTTCATTGCTATGAATC
1 TTATAATGTATAATTTCATTGCTATGAATC
1696 TTA
1 TTA
1699 GTGAAAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.48
Consensus pattern (30 bp):
TTATAATGTATAATTTCATTGCTATGAATC
Found at i:6233 original size:20 final size:19
Alignment explanation
Indices: 6187--6239 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
6177 GTTACAAGCT
6187 ATGTATCGATACATTTCTTC
1 ATGTATCGATACATTTC-TC
*
6207 ATATATCGATACATTGTAC-C
1 ATGTATCGATACATT-T-CTC
6227 ATGTATCGATACA
1 ATGTATCGATACA
6240 AATAGTGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 27 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTTCTC
Found at i:6309 original size:13 final size:13
Alignment explanation
Indices: 6291--6317 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6281 CAATTTGTCC
6291 ATGTATCGATACA
1 ATGTATCGATACA
6304 ATGTATCGATACA
1 ATGTATCGATACA
6317 A
1 A
6318 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:8799 original size:13 final size:13
Alignment explanation
Indices: 8781--8809 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
8771 AAATAGTACC
8781 CAATGTATCGATA
1 CAATGTATCGATA
8794 CAATGTATCGATA
1 CAATGTATCGATA
8807 CAA
1 CAA
8810 GGAATGTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:12955 original size:18 final size:18
Alignment explanation
Indices: 12932--12971 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
12922 TTTCAATAAT
12932 TTTTAATTTATTTTATTC
1 TTTTAATTTATTTTATTC
12950 TTTTAATTTATTTTATTC
1 TTTTAATTTATTTTATTC
12968 TTTT
1 TTTT
12972 TATGTTTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTAATTTATTTTATTC
Found at i:14688 original size:18 final size:18
Alignment explanation
Indices: 14660--14702 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
14650 CAATAAAAAC
14660 AAAAGCTCTTTGAAATGTG
1 AAAA-CTCTTTGAAATGTG
* *
14679 AAAACTCTTTGAACTTTG
1 AAAACTCTTTGAAATGTG
14697 AAAACT
1 AAAACT
14703 TTGATCTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.33
Consensus pattern (18 bp):
AAAACTCTTTGAAATGTG
Found at i:16387 original size:19 final size:21
Alignment explanation
Indices: 16351--16392 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
16341 TTACACGTTT
*
16351 AATTTTTATAACTAATAT-AA
1 AATTATTATAACTAATATGAA
16371 AATTATTATAA-TAATATGAA
1 AATTATTATAACTAATATGAA
16391 AA
1 AA
16393 ATGTCGTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AATTATTATAACTAATATGAA
Found at i:17142 original size:21 final size:20
Alignment explanation
Indices: 17116--17182 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
17106 GAATTATACG
17116 AATTTAAATTT-TTTAAGATAT
1 AATTTAAATTTATTT-AG-TAT
*
17137 AATTTATATTTATTT-GTAT
1 AATTTAAATTTATTTAGTAT
*
17156 AAATTTAAATTTGTTTTAGTTAT
1 -AATTTAAATTT-ATTTAG-TAT
17179 AATT
1 AATT
17183 ATATGAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 3 0.08
20 11 0.29
21 13 0.34
22 8 0.21
23 3 0.08
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
AATTTAAATTTATTTAGTAT
Found at i:17191 original size:72 final size:73
Alignment explanation
Indices: 17107--17307 Score: 252
Period size: 72 Copynumber: 2.8 Consensus size: 73
17097 AGTTTGAAAG
* * *
17107 AATTATACGAATTTAAATTTTTTAAGATATAATTTATATTTATTTGTATAA-A-TTTAAATTTGT
1 AATTATACGAATTTAAATTTTTTAAAATATAATTTATTTTTATTTGTATAATAGTTTAAATTTAT
17170 TTTAGTTA-T
66 TTT--TTATT
*
17179 AATTATATGAATTTAAATTTTTTAAAATATAATTTATTTTTA-TT-TATAATAGTTTAAATTTAT
1 AATTATACGAATTTAAATTTTTTAAAATATAATTTATTTTTATTTGTATAATAGTTTAAATTTAT
17242 TTTTTATTT
66 TTTTTA-TT
* * * *
17251 ATTTATACGAGTTTAAA-TTTTTAAAATATGATTTATTTTTATTTGTAAAAGTAGTTT
1 AATTATACGAATTTAAATTTTTTAAAATATAATTTATTTTTATTTGTATAA-TAGTTT
17308 GATTTTTGAG
Statistics
Matches: 113, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
70 8 0.07
71 26 0.23
72 69 0.61
73 4 0.04
74 6 0.05
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (73 bp):
AATTATACGAATTTAAATTTTTTAAAATATAATTTATTTTTATTTGTATAATAGTTTAAATTTAT
TTTTTATT
Found at i:18046 original size:23 final size:22
Alignment explanation
Indices: 18001--18046 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
17991 ATCTAAGTAC
*
18001 TAAAATTTATTAATCATATATT
1 TAAAATTTATTAATCATAAATT
* *
18023 TAAAATATTATTTATTATAAATT
1 TAAAAT-TTATTAATCATAAATT
18046 T
1 T
18047 TATAACAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAAATTTATTAATCATAAATT
Found at i:20218 original size:14 final size:14
Alignment explanation
Indices: 20199--20225 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20189 TAGCTGTATT
20199 AAATCTTGTCTATA
1 AAATCTTGTCTATA
20213 AAATCTTGTCTAT
1 AAATCTTGTCTAT
20226 CAATGTTATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.44
Consensus pattern (14 bp):
AAATCTTGTCTATA
Found at i:23956 original size:39 final size:39
Alignment explanation
Indices: 23913--23989 Score: 100
Period size: 39 Copynumber: 2.0 Consensus size: 39
23903 TTGCAAATTT
* **
23913 CAATAAATAATCAATATGTTACTAACATTTTTTAGATTC
1 CAATAAAGAATCAATACATTACTAACATTTTTTAGATTC
* * *
23952 CAATAAAGAATCCATACATTAGTCACATTTTTTAGATT
1 CAATAAAGAATCAATACATTACTAACATTTTTTAGATT
23990 TTAATGAACC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.40, C:0.14, G:0.06, T:0.39
Consensus pattern (39 bp):
CAATAAAGAATCAATACATTACTAACATTTTTTAGATTC
Found at i:25229 original size:16 final size:15
Alignment explanation
Indices: 25210--25250 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
25200 GAAAGAGAGG
25210 AAAAGAAAGAAGGAAA
1 AAAAGAAAGAA-GAAA
*
25226 AAAAGGAAGAAGAAA
1 AAAAGAAAGAAGAAA
25241 AAAAGGAAAG
1 AAAA-GAAAG
25251 GTTTTCGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAGAAAGAAGAAA
Found at i:25240 original size:15 final size:16
Alignment explanation
Indices: 25210--25248 Score: 62
Period size: 15 Copynumber: 2.5 Consensus size: 16
25200 GAAAGAGAGG
*
25210 AAAAGAAAGAAGGAAA
1 AAAAGGAAGAAGGAAA
25226 AAAAGGAAGAA-GAAA
1 AAAAGGAAGAAGGAAA
25241 AAAAGGAA
1 AAAAGGAA
25249 AGGTTTTCGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (16 bp):
AAAAGGAAGAAGGAAA
Found at i:29095 original size:19 final size:20
Alignment explanation
Indices: 29058--29096 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
29048 ATTTATAAAG
29058 ATGTATCGATATATTTCATTA
1 ATGTATCGATATA-TTCATTA
29079 ATGTATCGATATA-TCATT
1 ATGTATCGATATATTCATT
29097 GAGTTTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (20 bp):
ATGTATCGATATATTCATTA
Found at i:29905 original size:13 final size:13
Alignment explanation
Indices: 29887--29932 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
29877 GGAAACTAGA
29887 AAAGAAAAAAAAG
1 AAAGAAAAAAAAG
* *
29900 AAAGAAAAGAGAG
1 AAAGAAAAAAAAG
*
29913 AAAGAGAAAAAAG
1 AAAGAAAAAAAAG
29926 -AAGAAAA
1 AAAGAAAA
29933 TAAGAAGGTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAAAG
Found at i:30696 original size:58 final size:57
Alignment explanation
Indices: 30580--30710 Score: 167
Period size: 58 Copynumber: 2.3 Consensus size: 57
30570 GATTACAATG
** * *
30580 TCATTTCATGCA-TTTAGGTACATTTAAGTCATTTTTATGATTTATAAATTATTATA
1 TCATTTCATGCATTTTAGGTACATCAAAGTCATTTTTATGATCTAGAAATTATTATA
* * *
30636 TCATTTCATGCATTTTAGAG-ATATCAAAGTTATTTTCTATGATCTAGAAATTATTTTA
1 TCATTTCATGCATTTTAG-GTACATCAAAGTCATTTT-TATGATCTAGAAATTATTATA
30694 TCATTTCATGCATTTTA
1 TCATTTCATGCATTTTA
30711 AGGTTATTTA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
56 12 0.18
57 17 0.26
58 36 0.55
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (57 bp):
TCATTTCATGCATTTTAGGTACATCAAAGTCATTTTTATGATCTAGAAATTATTATA
Found at i:30911 original size:29 final size:29
Alignment explanation
Indices: 30879--30971 Score: 66
Period size: 29 Copynumber: 3.2 Consensus size: 29
30869 TTTGCCAAGA
30879 TTTAAGACCATTTATATAATTTCATGCAT
1 TTTAAGACCATTTATATAATTTCATGCAT
* * * *
30908 TTTAGGGCCATTCTAGTA-ATTTTTCACG-A-
1 TTTAAGACCATT-TA-TATA-ATTTCATGCAT
* * * *
30937 TTTAAGACCATTTATGTACTTTTATGCTT
1 TTTAAGACCATTTATATAATTTCATGCAT
30966 TTTAAG
1 TTTAAG
30972 CCTATTTTAG
Statistics
Matches: 47, Mismatches: 11, Indels: 12
0.67 0.16 0.17
Matches are distributed among these distances:
27 6 0.13
28 3 0.06
29 26 0.55
30 4 0.09
31 8 0.17
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (29 bp):
TTTAAGACCATTTATATAATTTCATGCAT
Found at i:30925 original size:58 final size:58
Alignment explanation
Indices: 30858--30969 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
30848 AATTTAGGAT
*
30858 CATTTTAGTAATTTGCCAAGATTTAAGACCATTTATATAATTTCATGCATTTTAGGGC
1 CATTCTAGTAATTTGCCAAGATTTAAGACCATTTATATAATTTCATGCATTTTAGGGC
** * * * * *
30916 CATTCTAGTAATTTTTCACGATTTAAGACCATTTATGTACTTTTATGCTTTTTA
1 CATTCTAGTAATTTGCCAAGATTTAAGACCATTTATATAATTTCATGCATTTTA
30970 AGCCTATTTT
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 46 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.46
Consensus pattern (58 bp):
CATTCTAGTAATTTGCCAAGATTTAAGACCATTTATATAATTTCATGCATTTTAGGGC
Found at i:31322 original size:79 final size:78
Alignment explanation
Indices: 31148--31427 Score: 212
Period size: 78 Copynumber: 3.6 Consensus size: 78
31138 CGCAACACGA
* * * **
31148 GATCATGTGGGAACTTTCATATCGAAACATGTCTATTAATTGTATTTAGGTAATATTACCTTAAA
1 GATCATGTGTGAGCTTTCATGTCGAAACATGTCTATTAAGGGTATTTAGGTAATATTACCTTAAA
31213 AACTAATCCTTAG
66 AACTAATCCTTAG
* * * * *
31226 GAT-AT-TTTGAGAACTTTCCATGTCGAAACATGTTTGTTAGGGGTATTTAGGTAATATTACGTT
1 GATCATGTGTGAG--CTTT-CATGTCGAAACATGTCTATTAAGGGTATTTAGGTAATATTACCTT
* *
31289 AAAATC-AAGTCTTTAG
63 AAAAACTAA-TCCTTAG
** * * * * *
31305 GATCATGTGTGAGCTTTCATGTTAAAACATGTCCATT-AGAGATATATAGGTAATAATACC-TCA
1 GATCATGTGTGAGCTTTCATGTCGAAACATGTCTATTAAG-GGTATTTAGGTAATATTACCTTAA
* * *
31368 AAATTGAGTCCTTAA
65 AAACT-AATCCTTAG
* * * * *
31383 GATCATGTGAGAACTTTCTTGTTGAAACATGT-TCATTAAAGGTAT
1 GATCATGTGTGAGCTTTCATGTCGAAACATGTCT-ATTAAGGGTAT
31428 CATGTATGTC
Statistics
Matches: 155, Mismatches: 36, Indels: 22
0.73 0.17 0.10
Matches are distributed among these distances:
76 3 0.02
77 7 0.05
78 80 0.52
79 58 0.37
80 2 0.01
81 5 0.03
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.37
Consensus pattern (78 bp):
GATCATGTGTGAGCTTTCATGTCGAAACATGTCTATTAAGGGTATTTAGGTAATATTACCTTAAA
AACTAATCCTTAG
Found at i:34566 original size:52 final size:52
Alignment explanation
Indices: 34488--34688 Score: 341
Period size: 52 Copynumber: 3.9 Consensus size: 52
34478 CGAAATATGA
*
34488 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
34540 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
*
34592 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
**
34644 AAATTTGCCTGCATGTATCGATACAAAG-ATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGTAT-AGTGTATCGATACA
34689 ATGTATCGAT
Statistics
Matches: 143, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
51 2 0.01
52 141 0.99
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTGTATAGTGTATCGATACATCTGGGC
Found at i:34695 original size:13 final size:13
Alignment explanation
Indices: 34677--34701 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34667 CAAAGATCAG
34677 TGTATCGATACAA
1 TGTATCGATACAA
34690 TGTATCGATACA
1 TGTATCGATACA
34702 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:34782 original size:13 final size:13
Alignment explanation
Indices: 34764--34788 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34754 CAAAAAAACA
34764 TGTATCGATACAT
1 TGTATCGATACAT
34777 TGTATCGATACA
1 TGTATCGATACA
34789 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:34887 original size:21 final size:21
Alignment explanation
Indices: 34846--34887 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
34836 GTTGGGACCT
*
34846 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
34867 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
34888 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:35752 original size:52 final size:52
Alignment explanation
Indices: 35673--35831 Score: 192
Period size: 52 Copynumber: 3.2 Consensus size: 52
35663 AAAGCTGAGA
* *
35673 AAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
* *
35726 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
* *
35770 -AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTTAAAGATGG
1 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
35821 AAAAGGTGCCA
1 AAAAGGTGCCA
35832 CCGATTTGTG
Statistics
Matches: 89, Mismatches: 8, Indels: 19
0.77 0.07 0.16
Matches are distributed among these distances:
43 37 0.42
44 1 0.01
46 1 0.01
49 1 0.01
51 1 0.01
52 42 0.47
53 6 0.07
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG
Found at i:35788 original size:43 final size:43
Alignment explanation
Indices: 35727--35816 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
35717 TAAAGATGGA
*
35727 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
* * *
35770 AAAGGTGCCAATGTGCTGATTCAAGGTCGGCTACATTGGACTT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
35813 AAAG
1 AAAG
35817 ATGGAAAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.27
Consensus pattern (43 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT
Found at i:36018 original size:88 final size:87
Alignment explanation
Indices: 35822--36079 Score: 380
Period size: 88 Copynumber: 3.0 Consensus size: 87
35812 TAAAGATGGA
* * * ** *
35822 AAAGG-TGCCACCGATTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAA-TATGCCACTGACTTGTGGGCTTTTGAAAGG
* *
35883 TTGCCACTGACTTGTGGGCTTTTT
65 GTGCCACTAACTTGTGGGC-TTTT
35907 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGG
35972 GTGCCACTAACTTGTGGGCTTTT
65 GTGCCACTAACTTGTGGGCTTTT
35995 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGG
36060 GTGCCACTAACTTGTGGGCT
65 GTGCCACTAACTTGTGGGCT
36080 GAAAAGAGTG
Statistics
Matches: 159, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
85 5 0.03
86 33 0.21
87 12 0.08
88 87 0.55
89 22 0.14
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (87 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGG
TGCCACTAACTTGTGGGCTTTT
Found at i:36022 original size:58 final size:59
Alignment explanation
Indices: 35822--36293 Score: 346
Period size: 58 Copynumber: 8.0 Consensus size: 59
35812 TAAAGATGGA
* * * *
35822 AAAGG-TGCCACCGATTTGTGGGC-TTCGAAAAAGGGTGCCACTGATTTGTGGGC-TTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAAGGGTGCCACTGACTTGTGGGCTTTTG
* *
35879 -AAGGTTGCCACTGACTTGTGGGCTTTT-TAAAGGTTGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
** * *
35936 AAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-
1 AAAGGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
***
35995 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG
1 AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * * * * **
36054 AAAAGGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACT-GACTTGTGGGCTT----TTG
* * * * * * **
36115 AAAAAGCG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGG
1 --AAAG-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
* * * *
36175 AAAAGGGTGCCACTGATTTGTGGGC-TTTG--AAGGTTGCCACTGACTTGTGGGCTTTCG
1 -AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
*** *** *
36232 AAAAAAAATGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTG
1 --AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
36292 AA
1 AA
36294 GGGTGATGAA
Statistics
Matches: 332, Mismatches: 59, Indels: 47
0.76 0.13 0.11
Matches are distributed among these distances:
56 29 0.09
57 62 0.19
58 83 0.25
59 46 0.14
60 71 0.21
61 1 0.00
62 19 0.06
63 1 0.00
64 15 0.05
65 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
AAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTGACTTGTGGGCTTTTG
Found at i:36215 original size:27 final size:27
Alignment explanation
Indices: 36152--36298 Score: 105
Period size: 29 Copynumber: 5.1 Consensus size: 27
36142 TTGGAAAAGA
* *
36152 TGCCACCGACTTGTGGGCTTCGGAAAAGGG
1 TGCCACTGACTTGTGGGCTT-TG--AAGGG
* *
36182 TGCCACTGATTTGTGGGCTTTGAAGGT
1 TGCCACTGACTTGTGGGCTTTGAAGGG
***
36209 TGCCACTGACTTGTGGGCTTTCGAAAAAAAA
1 TGCCACTGACTTGTGGGCTTT-G---AAGGG
***
36240 TGCCACTGACTTGTGGGCTTTGAAAAAAA
1 TGCCACTGACTTGTGGGCTTTG--AAGGG
*
36269 TGCCACTGACTTGTGGACTTTTGAAGGG
1 TGCCACTGACTTGTGGGC-TTTGAAGGG
36297 TG
1 TG
36299 ATGAATGTCT
Statistics
Matches: 100, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
27 24 0.24
28 5 0.05
29 25 0.25
30 23 0.23
31 23 0.23
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (27 bp):
TGCCACTGACTTGTGGGCTTTGAAGGG
Found at i:36223 original size:121 final size:117
Alignment explanation
Indices: 36001--36284 Score: 320
Period size: 121 Copynumber: 2.4 Consensus size: 117
35991 TTTTAAAGGT
* **
36001 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCA
1 TGCCACTGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCA
* *
36066 CTAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAA
65 CTAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACAAAA-AAAAA
* * * * * *
36120 GCGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGC
1 ---TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGC
* * *** * * *
36185 CACTGATTTGTGGGCTTTGAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAAA
63 CACTAACTTGTGGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACAAAAAAAAA
36240 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
1 TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
36285 ACTTTTGAAG
Statistics
Matches: 136, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
117 39 0.29
120 6 0.04
121 75 0.55
122 16 0.12
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.27
Consensus pattern (117 bp):
TGCCACTGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACAAAAAAAAA
Found at i:36292 original size:30 final size:30
Alignment explanation
Indices: 35820--36293 Score: 374
Period size: 30 Copynumber: 16.1 Consensus size: 30
35810 CTTAAAGATG
* * *
35820 GAAAAGG-TGCCACCGATTTGTGGGC-TTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
35848 GAAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
*
35878 G--AAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
35906 -TAAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
35935 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * *
35965 GAACAGGGTGCCACTAACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
*
35995 --AAAGGTTGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
36023 GAAAAATATGCCACTGACTTGTGGGCTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
36053 GAAAAGGGTGCCACTAACTTGTGGGC---T
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* * * **
36080 GAAAA-GAGTGCTA-TAGAGTTGTGAGCTTACAAAA
1 GAAAAGGA-TGCCACT-GACTTGTGGGCTT----TT
* * * *
36114 GAAAAAGCG-TGCCACGGAGTTGTGGACTTTG
1 G-AAAAG-GATGCCACTGACTTGTGGGCTTTT
* **
36145 GAAAA-GATGCCACCGACTTGTGGGCTTCG
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
36174 GAAAAGGGTGCCACTGATTTGTGGGC-TTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
* *
36203 G--AAGGTTGCCACTGACTTGTGGGCTTTC
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
**
36231 GAAAAAAAATGCCACTGACTTGTGGGC-TTT
1 G-AAAAGGATGCCACTGACTTGTGGGCTTTT
** *
36261 GAAAAAAATGCCACTGACTTGTGGACTTTT
1 GAAAAGGATGCCACTGACTTGTGGGCTTTT
36291 GAA
1 GAA
36294 GGGTGATGAA
Statistics
Matches: 366, Mismatches: 52, Indels: 54
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.01
27 60 0.16
28 33 0.09
29 82 0.22
30 147 0.40
31 21 0.06
34 1 0.00
35 19 0.05
37 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (30 bp):
GAAAAGGATGCCACTGACTTGTGGGCTTTT
Found at i:37736 original size:1 final size:1
Alignment explanation
Indices: 37732--37879 Score: 116
Period size: 1 Copynumber: 148.0 Consensus size: 1
37722 CCGGACCCCC
* * * * * ** *
37732 TTTTTTTTTGTTTGTTTTTTTATTGTTTTTTGTTTTTTTTTTTTTTTTTTTTTGCTTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * ** ** ** **
37797 TTTTTTTTTTTTTTTGGTTTTTCTTTTTTTCATTTTTTTTTTGGTTTTTCATTTTTTTCGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
37862 TTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTT
37880 GGAGGACGCC
Statistics
Matches: 115, Mismatches: 32, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 115 1.00
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (1 bp):
T
Found at i:37760 original size:22 final size:19
Alignment explanation
Indices: 37732--37879 Score: 133
Period size: 19 Copynumber: 7.7 Consensus size: 19
37722 CCGGACCCCC
37732 TTTTTTTTTGTTTGTTTTTT
1 TTTTTTTTTGTTT-TTTTTT
37752 TATTGTTTTTTGTTTTTTTTT
1 T-TT-TTTTTTGTTTTTTTTT
*
37773 TTTTTTTTT-TTTGCTTTTT
1 TTTTTTTTTGTTT-TTTTTT
*
37792 TTTTGTTTT-TTTTTTTTT
1 TTTTTTTTTGTTTTTTTTT
** * *
37810 TTGGTTTTTCTTTTTTTCAT
1 TTTTTTTTTGTTTTTTT-TT
* *
37830 TTTTTTTTTG--GTTTTTC
1 TTTTTTTTTGTTTTTTTTT
* *
37847 ATTTTTTTCGTTTTTTTTT
1 TTTTTTTTTGTTTTTTTTT
37866 TTTTTTTTTGTTTT
1 TTTTTTTTTGTTTT
37880 GGAGGACGCC
Statistics
Matches: 102, Mismatches: 19, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
17 8 0.08
18 18 0.18
19 46 0.45
20 11 0.11
21 9 0.09
22 10 0.10
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTTTT
Found at i:37762 original size:27 final size:26
Alignment explanation
Indices: 37732--37879 Score: 129
Period size: 27 Copynumber: 5.5 Consensus size: 26
37722 CCGGACCCCC
* *
37732 TTTTTTTTTGTTTGTTTTTTTATTGTTT
1 TTTTTTTTTTTTTGTTTTTTT-TT-TGT
*
37760 TTTGTTTTTTTTTTTTTTTTTTTTTGCT
1 TTT-TTTTTTTTTTGTTTTTTTTTTG-T
37788 TTTTTTTTGTTTTT-TTTTTTTTTTGGT
1 TTTTTTTT-TTTTTGTTTTTTTTTT-GT
* **
37815 TTTTCTTTTTTTCATTTTTTTTTTGGT
1 TTTTTTTTTTTTTGTTTTTTTTTT-GT
* *
37842 TTTTCATTTTTTTCGTTTTTTTTTT-T
1 TTTT-TTTTTTTTTGTTTTTTTTTTGT
*
37868 TTTTTTTGTTTT
1 TTTTTTTTTTTT
37880 GGAGGACGCC
Statistics
Matches: 105, Mismatches: 9, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
25 6 0.06
26 9 0.09
27 41 0.39
28 33 0.31
29 16 0.15
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (26 bp):
TTTTTTTTTTTTTGTTTTTTTTTTGT
Found at i:37783 original size:33 final size:33
Alignment explanation
Indices: 37732--37879 Score: 142
Period size: 33 Copynumber: 4.5 Consensus size: 33
37722 CCGGACCCCC
* * *
37732 TTTTTTTTTGTTTGTTTTTTTATTGTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTCTTGTTTTTTGT
* *
37765 TTTTTTTTTTTTTTTTTTTTGCTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTCTTGTTTTTTGT
** **
37798 TTTTTTTTTTTTTTGGTTTTTCTT-TTTTTCAT
1 TTTTTTTTTTTTTTTTTTTTTCTTGTTTTTTGT
37830 TTTTTTTTTGGTTTTTCATTTTTTTC--GTTTTTT-T
1 TTTTTTTTT--TTTTT--TTTTTTTCTTGTTTTTTGT
*
37864 TTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTT
37880 GGAGGACGCC
Statistics
Matches: 96, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
30 2 0.02
32 19 0.20
33 49 0.51
34 15 0.16
35 5 0.05
36 6 0.06
ACGTcount: A:0.02, C:0.03, G:0.08, T:0.86
Consensus pattern (33 bp):
TTTTTTTTTTTTTTTTTTTTTCTTGTTTTTTGT
Done.