Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2123
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: 54017
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:210 original size:26 final size:27
Alignment explanation
Indices: 5--419 Score: 397
Period size: 27 Copynumber: 15.0 Consensus size: 27
1 ACGT
5 TCCACAACT-CGTTGGCACCCTTTTAAGG
1 TCCACAACTCCG-TGGCACCCTTTTAA-G
*
33 T-CACAACTCTGTGGCACCCTTTTAAG
1 TCCACAACTCCGTGGCACCCTTTTAAG
59 TCCACAACTCCTGTGGCATCCCTTTTAAG
1 TCCACAACTCC-GTGGCA-CCCTTTTAAG
*
88 TCCACAACCCTCCGTTGGCA-TCTCTTTAACG
1 TCCACAA--CTCCG-TGGCACCCT-TTTAA-G
119 TCCACAACTCCGTGGCCACCCTTTTTAAG
1 TCCACAACTCCGTGG-CACCC-TTTTAAG
** *
148 T-CACAACTTTGTGGCA-CCTTTGAAG
1 TCCACAACTCCGTGGCACCCTTTTAAG
* *
173 TCCACAACTCCGTAGCACCTTTTTAAG
1 TCCACAACTCCGTGGCACCCTTTTAAG
*
200 TCCACAA-TCCGTGGGCACTCTTTTTTAACG
1 TCCACAACTCCGT-GGCAC-C-CTTTTAA-G
230 TCCACAACT-CGCTCGGGCACCCTTTTAAG
1 TCCACAACTCCG-T--GGCACCCTTTTAAG
259 TCCACAACTCCGT-GCACCC-TTTAACG
1 TCCACAACTCCGTGGCACCCTTTTAA-G
285 T-CACAACTCCGTGGCACCCTTTT-A-
1 TCCACAACTCCGTGGCACCCTTTTAAG
*
309 TCCACAACTCCGTGGCATTCCTTTTAAG
1 TCCACAACTCCGTGGCA-CCCTTTTAAG
* * *
337 ACCACAATTCTGTGGCACCCTTTTAAG
1 TCCACAACTCCGTGGCACCCTTTTAAG
*
364 TTCCACAACTCCGTGGCCACACTTTTTAAG
1 -TCCACAACTCCGTGG-CAC-CCTTTTAAG
*
394 TCCACAACT-CGTGGCCATCCTTTTAA
1 TCCACAACTCCGTGG-CACCCTTTTAA
420 ATACATTTAA
Statistics
Matches: 330, Mismatches: 25, Indels: 65
0.79 0.06 0.15
Matches are distributed among these distances:
24 1 0.00
25 38 0.12
26 42 0.13
27 69 0.21
28 57 0.17
29 58 0.18
30 38 0.12
31 21 0.06
32 6 0.02
ACGTcount: A:0.22, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
TCCACAACTCCGTGGCACCCTTTTAAG
Found at i:490 original size:32 final size:32
Alignment explanation
Indices: 452--1179 Score: 1128
Period size: 32 Copynumber: 23.1 Consensus size: 32
442 CCATTTCAAC
* *
452 CAAAGCCCACACAAGTCAGTGGCAACCAATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
484 CAAAGCCCACACAAGTCGGTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
516 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
548 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
580 CAAAGCCCACACAAGTCGGTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
612 CAAAGCCCACACAAGTCGGTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
644 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
676 CCAAAGCCCACACAAGTCGGTGGCAACCCATTC
1 -CAAAGCCCACACAAGTCGGTGGCAACCCATTT
709 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
741 CAAAGCTCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
773 CAAAGCCCACACAAGTCGGT-GCAACCCA-TT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
803 CAAAG-CC-CACAAGTC-GTGGCAACCCA-TT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
831 CAAAGCCCACACAAGTCGGTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
863 CAAAGCCCCACACAAGTCGG-GTGCAA-CCATTC
1 CAAAG-CCCACACAAGTCGGTG-GCAACCCATTT
*
895 CAAAGCCCACACAAGTCGGTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
927 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
959 C-AAGCCCACACAAGTCGGTGGC-ACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
989 C-AAG-CC-CACAA-TC-GTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1016 CAAAG-CCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
* *
1047 CAAAACCCACACAAGTCGGTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
1079 CAAAGCCCACACAAGTCGGTGGCAACTCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
1111 CAAAGCCCACATAAGTCGGTGGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGT-GGCAACCCATTT
* *** * *
1144 AAAAGCCCATGTAAGTCAGTGGCAACCCTTTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1176 CAAA
1 CAAA
1180 TCACCATTTT
Statistics
Matches: 654, Mismatches: 25, Indels: 34
0.92 0.04 0.05
Matches are distributed among these distances:
26 5 0.01
27 13 0.02
28 33 0.05
29 11 0.02
30 29 0.04
31 76 0.12
32 411 0.63
33 76 0.12
ACGTcount: A:0.32, C:0.35, G:0.18, T:0.15
Consensus pattern (32 bp):
CAAAGCCCACACAAGTCGGTGGCAACCCATTT
Found at i:1734 original size:20 final size:20
Alignment explanation
Indices: 1703--1777 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1693 TCATACCCTG
*
1703 ATGTATCAATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1723 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * *
1743 ATGTATCGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1763 ATGTATCGATACATT
1 ATGTATCGATACATT
1778 ATGTCTTTTT
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1770 original size:40 final size:39
Alignment explanation
Indices: 1703--1780 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1693 TCATACCCTG
* *
1703 ATGTATCAATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCAATACATTCTACAATATATCGATACAT-TATGA
* * *
1743 ATGTATCGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCAATACATTCTACAATATATCGATACATTATG
1781 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.40
Consensus pattern (39 bp):
ATGTATCAATACATTCTACAATATATCGATACATTATGA
Found at i:2715 original size:23 final size:23
Alignment explanation
Indices: 2685--2738 Score: 87
Period size: 20 Copynumber: 2.5 Consensus size: 23
2675 TAGCCTTGAC
2685 CATGCATTTTTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2708 CATGCA---TTTTTATTATGTTT
1 CATGCATTTTTTTTATTATGTTT
2728 CATGCATTTTT
1 CATGCATTTTT
2739 AACATGTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 20 0.71
23 8 0.29
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (23 bp):
CATGCATTTTTTTTATTATGTTT
Found at i:2719 original size:20 final size:20
Alignment explanation
Indices: 2694--2739 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2684 CCATGCATTT
2694 TTTTTATTATGTTTCATGCA
1 TTTTTATTATGTTTCATGCA
2714 TTTTTATTATGTTTCATGCA
1 TTTTTATTATGTTTCATGCA
2734 TTTTTA
1 TTTTTA
2740 ACATGTCCAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.09, G:0.09, T:0.63
Consensus pattern (20 bp):
TTTTTATTATGTTTCATGCA
Found at i:2745 original size:20 final size:20
Alignment explanation
Indices: 2702--2745 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2692 TTTTTTTATT
**
2702 ATGTTTCATGCATTTTTATT
1 ATGTTTCATGCATTTTTAAC
2722 ATGTTTCATGCATTTTTAAC
1 ATGTTTCATGCATTTTTAAC
2742 ATGT
1 ATGT
2746 CCAGCATCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.55
Consensus pattern (20 bp):
ATGTTTCATGCATTTTTAAC
Found at i:6194 original size:18 final size:17
Alignment explanation
Indices: 6171--6237 Score: 61
Period size: 18 Copynumber: 4.0 Consensus size: 17
6161 TTTGAAATTA
6171 ATATTATTTAAATATATT
1 ATATT-TTTAAATATATT
*
6189 ATATTATT--AT-T-TT
1 ATATTTTTAAATATATT
6202 ATATTTATTAAATATATT
1 ATATTT-TTAAATATATT
*
6220 ATATTTATAATATATATT
1 ATATTTTTAA-ATATATT
6238 TTTATATTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.17
14 3 0.08
15 2 0.05
16 2 0.05
17 6 0.15
18 20 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTTTTAAATATATT
Found at i:6203 original size:13 final size:12
Alignment explanation
Indices: 6171--6247 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 12
6161 TTTGAAATTA
*
6171 ATATTA-TTTAA
1 ATATTATTTTAT
*
6182 ATA-TATTATAT
1 ATATTATTTTAT
6193 -TATTATTTTAT
1 ATATTATTTTAT
**
6204 AT-TTATTAAAT
1 ATATTATTTTAT
6215 ATATTATATTTAT
1 ATATTAT-TTTAT
6228 AATATATATTTT-T
1 -ATAT-TATTTTAT
6241 ATATTAT
1 ATATTAT
6248 GTTTGAAATT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
10 4 0.08
11 25 0.48
12 9 0.17
13 4 0.08
14 7 0.13
15 3 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTATTTTAT
Found at i:6236 original size:31 final size:31
Alignment explanation
Indices: 6178--6238 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
6168 TTAATATTAT
* *
6178 TTAAATATATTATATTATTATTTTATATTTA
1 TTAAATATATTATATTATTAATATATATTTA
6209 TTAAATATATTATATT-TATAATATATATTT
1 TTAAATATATTATATTAT-TAATATATATTT
6239 TTATATTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (31 bp):
TTAAATATATTATATTATTAATATATATTTA
Found at i:8722 original size:23 final size:22
Alignment explanation
Indices: 8674--8722 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
8664 AAAATAATAA
* *
8674 TTAAAAATAATATTTTTATTTT
1 TTAAAAATAATATTATTATTTC
8696 TTAAAAATAATTATTAATTA-TTC
1 TTAAAAATAA-TATT-ATTATTTC
8719 TTAA
1 TTAA
8723 TTTTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 10 0.43
23 10 0.43
24 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAAATAATATTATTATTTC
Found at i:11388 original size:6 final size:6
Alignment explanation
Indices: 11377--11403 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
11367 AACCCATTTC
11377 TTTATT TTTATT TTTATT TTTATT TTT
1 TTTATT TTTATT TTTATT TTTATT TTT
11404 TTCACTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTATT
Found at i:12009 original size:21 final size:22
Alignment explanation
Indices: 11985--12033 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
11975 AAGATAACTA
**
11985 TTAAAAATAATT-TTTTATTTT
1 TTAAAAATAATTATTCAATTTT
12006 TTAAAAATAATTATTCAATTTT
1 TTAAAAATAATTATTCAATTTT
12028 TTAAAA
1 TTAAAA
12034 TTTTGTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAAATAATTATTCAATTTT
Found at i:12027 original size:20 final size:21
Alignment explanation
Indices: 11985--12033 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
11975 AAGATAACTA
* * *
11985 TTAAAAATAATTTTTTATTTT
1 TTAAAAATAATTATTCATATT
*
12006 TTAAAAATAATTATTCAATTTT
1 TTAAAAATAATTATTC-ATATT
12028 TTAAAA
1 TTAAAA
12034 TTTTGTAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAAAAATAATTATTCATATT
Found at i:15730 original size:2 final size:2
Alignment explanation
Indices: 15723--15747 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15713 GGTTAGATTA
15723 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 A
15748 ACTACCCAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15885 original size:30 final size:32
Alignment explanation
Indices: 15849--15908 Score: 97
Period size: 30 Copynumber: 1.9 Consensus size: 32
15839 TATGTTCAAT
15849 AATAATTAAAA-TATATTTATA-TTAAAAATA
1 AATAATTAAAATTATATTTATATTTAAAAATA
*
15879 AATAATTAAAATTATCTTTATATTTAAAAA
1 AATAATTAAAATTATATTTATATTTAAAAA
15909 AGTATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.41
31 9 0.33
32 7 0.26
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (32 bp):
AATAATTAAAATTATATTTATATTTAAAAATA
Found at i:17795 original size:16 final size:16
Alignment explanation
Indices: 17776--17828 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
17766 TACGAAATAA
17776 ATAAAATAAATTTTAT
1 ATAAAATAAATTTTAT
*
17792 ATAAAATAATTTATTA-
1 ATAAAATAAATT-TTAT
* * *
17808 ATATATTAAAATTTAT
1 ATAAAATAAATTTTAT
17824 ATAAA
1 ATAAA
17829 TATGTAATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
15 3 0.10
16 23 0.79
17 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
ATAAAATAAATTTTAT
Found at i:17867 original size:12 final size:13
Alignment explanation
Indices: 17822--17877 Score: 60
Period size: 13 Copynumber: 4.1 Consensus size: 13
17812 ATTAAAATTT
*
17822 ATATAAATATGTA
1 ATATAAATATATA
17835 ATATTTTAAATATAGTA
1 ATA---TAAATATA-TA
17852 ATATAAA-ATATA
1 ATATAAATATATA
17864 ATATAAATATATA
1 ATATAAATATATA
17877 A
1 A
17878 ATTATCAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 9 0.24
13 12 0.32
14 4 0.11
16 7 0.19
17 5 0.14
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:19468 original size:19 final size:20
Alignment explanation
Indices: 19416--19491 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 20
19406 AATAGGTCCA
*
19416 TTTTTAAAAATA-TTAATAT
1 TTTTTAAAAAAATTTAATAT
* * *
19435 TTTCTAAGAAGATTTAAT-T
1 TTTTTAAAAAAATTTAATAT
19454 TTTTTAAAAAAATTTAATCAT
1 TTTTTAAAAAAATTTAAT-AT
* *
19475 TTTTTAGATAAATTTAA
1 TTTTTAAAAAAATTTAA
19492 ACAGATCTAT
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 25 0.54
20 5 0.11
21 16 0.35
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTTAAAAAAATTTAATAT
Found at i:19490 original size:40 final size:38
Alignment explanation
Indices: 19416--19491 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 38
19406 AATAGGTCCA
* *
19416 TTTTTAAAAATATTAATATTTTCTAAGAAGATTTAATT
1 TTTTTAAAAAAATTAATATTTTCTAAGAAAATTTAATT
*
19454 TTTTTAAAAAAATTTAATCATTTT-TTAGATAAATTTAA
1 TTTTTAAAAAAA-TTAAT-ATTTTCTAAGA-AAATTTAA
19492 ACAGATCTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
38 11 0.34
39 9 0.28
40 12 0.38
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (38 bp):
TTTTTAAAAAAATTAATATTTTCTAAGAAAATTTAATT
Found at i:20948 original size:30 final size:27
Alignment explanation
Indices: 20892--20952 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 27
20882 ATTATTTTTT
20892 ATTTAATATAAAAATTATTTTATTTAA
1 ATTTAATATAAAAATTATTTTATTTAA
*
20919 ATTTAATTATAAAAATATTTTTATATTTAA
1 ATTTAA-TATAAAAAT-TATTT-TATTTAA
20949 ATTT
1 ATTT
20953 TTTTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 6 0.20
28 9 0.30
29 4 0.13
30 11 0.37
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTAATATAAAAATTATTTTATTTAA
Found at i:23338 original size:14 final size:14
Alignment explanation
Indices: 23319--23348 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
23309 CCTTCTTAAT
23319 ACACACACACACGC
1 ACACACACACACGC
*
23333 ACACACACGCACGC
1 ACACACACACACGC
23347 AC
1 AC
23349 GATGCAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.50, G:0.10, T:0.00
Consensus pattern (14 bp):
ACACACACACACGC
Found at i:23750 original size:10 final size:10
Alignment explanation
Indices: 23732--23797 Score: 52
Period size: 10 Copynumber: 7.0 Consensus size: 10
23722 AAATGATTCA
*
23732 AATTCAAATT
1 AATTTAAATT
23742 AATTTAAA-T
1 AATTTAAATT
* *
23751 --TTGAAAAT
1 AATTTAAATT
*
23759 AATTTAAA-A
1 AATTTAAATT
23768 AATTTAAATT
1 AATTTAAATT
23778 -ATATTAAATT
1 AAT-TTAAATT
23788 AATTTAAATT
1 AATTTAAATT
23798 GATCTGACTC
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
7 5 0.11
8 1 0.02
9 11 0.24
10 26 0.58
11 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (10 bp):
AATTTAAATT
Found at i:24748 original size:17 final size:17
Alignment explanation
Indices: 24728--24761 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
24718 TTTTATTTAA
24728 TTAA-TTATTTTTGAATT
1 TTAATTTATTTTT-AATT
24745 TTAATTTATTTTTAATT
1 TTAATTTATTTTTAATT
24762 ATATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTAATTTATTTTTAATT
Found at i:24769 original size:18 final size:18
Alignment explanation
Indices: 24732--24770 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
24722 ATTTAATTAA
*
24732 TTATTTTTGAATTTTAAT
1 TTATTTTTGAATTATAAT
24750 TTATTTTT-AATTATATAT
1 TTATTTTTGAATTATA-AT
24768 TTA
1 TTA
24771 AAAGATTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.67
Consensus pattern (18 bp):
TTATTTTTGAATTATAAT
Found at i:24848 original size:20 final size:19
Alignment explanation
Indices: 24823--24862 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
24813 CTAAAAAATA
24823 AAAAAAATATTTTATTAATT
1 AAAAAAATA-TTTATTAATT
*
24843 AAAAAATTATTTATTAATT
1 AAAAAAATATTTATTAATT
24862 A
1 A
24863 TACATTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAAAAATATTTATTAATT
Found at i:26949 original size:29 final size:28
Alignment explanation
Indices: 26892--26955 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
26882 AGCATTTGAA
* *
26892 ATATTATAATTTTTTTATAAATTTTTAT
1 ATATTATAATTTTTTTATAAATATATAT
*
26920 ATATTAATAATTTATTTTAT-TATATATAT
1 ATATT-ATAATTT-TTTTATAAATATATAT
*
26949 ATTTTAT
1 ATATTAT
26956 TCATGTATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 7 0.23
29 17 0.57
30 6 0.20
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (28 bp):
ATATTATAATTTTTTTATAAATATATAT
Found at i:32360 original size:21 final size:21
Alignment explanation
Indices: 32321--32393 Score: 58
Period size: 22 Copynumber: 3.4 Consensus size: 21
32311 GGATCTGATA
* * *
32321 TTTTCTTTTTTTATCTATTCTC
1 TTTTC-TTTTTCATATATTATC
* *
32343 TTTTCTTTTTCATTTATTTATT
1 TTTTCTTTTTCATATA-TTATC
* *
32365 TTTTCTTTTTCA-AAATTTTC
1 TTTTCTTTTTCATATATTATC
32385 TTTTCTTTT
1 TTTTCTTTT
32394 CCTTTTAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
20 12 0.29
21 10 0.24
22 20 0.48
ACGTcount: A:0.12, C:0.14, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTCTTTTTCATATATTATC
Found at i:32488 original size:28 final size:28
Alignment explanation
Indices: 32457--32517 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 28
32447 GCAAATATAA
32457 TTAATTTATAAATATATAAAATA-TATTT
1 TTAATTTATAAATATATAAAA-ACTATTT
* * *
32485 TTAA--AATAATTCTATAAAAACTATTT
1 TTAATTTATAAATATATAAAAACTATTT
32511 TTAATTT
1 TTAATTT
32518 TTTGTTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
25 1 0.04
26 21 0.81
28 4 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (28 bp):
TTAATTTATAAATATATAAAAACTATTT
Found at i:32493 original size:26 final size:26
Alignment explanation
Indices: 32464--32514 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
32454 TAATTAATTT
32464 ATAAATATATAAAATA-TATTTTTAAA
1 ATAAATATATAAAA-ACTATTTTTAAA
* *
32490 ATAATTCTATAAAAACTATTTTTAA
1 ATAAATATATAAAAACTATTTTTAA
32515 TTTTTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 1 0.05
26 21 0.95
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (26 bp):
ATAAATATATAAAAACTATTTTTAAA
Found at i:32654 original size:21 final size:19
Alignment explanation
Indices: 32575--32658 Score: 73
Period size: 19 Copynumber: 4.2 Consensus size: 19
32565 AAACATAAAG
*
32575 AATAATTTATATTATAATTTAA
1 AATAATTTATA--A-AATATAA
*
32597 ATTAATTT-TATAAATATAA
1 AATAATTTATA-AAATATAA
32616 AATAATTTATAAAATATAA
1 AATAATTTATAAAATATAA
32635 AAT-ATTTATCAATGAATATAA
1 AATAATTTAT-AA--AATATAA
32656 AAT
1 AAT
32659 GTAAATATTT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
18 6 0.11
19 26 0.47
20 4 0.07
21 12 0.22
22 7 0.13
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
AATAATTTATAAAATATAA
Found at i:32686 original size:31 final size:29
Alignment explanation
Indices: 32618--32714 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 29
32608 AAATATAAAA
*
32618 TAATTTATAAAATATAAAATATTTATCAAT
1 TAATTTATAAAATGT-AAATATTTATCAAT
* *
32648 GAA--TATAAAATGTAAATATTTATTTATAT
1 TAATTTATAAAATGTAAATATTTA-TCA-AT
32677 TAATTTATAAAATGTAAATA-TTA--AA-
1 TAATTTATAAAATGTAAATATTTATCAAT
32702 TAATTTATAAAAT
1 TAATTTATAAAAT
32715 ATTCATTTAT
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
25 13 0.22
26 1 0.02
27 10 0.17
28 11 0.19
29 4 0.07
30 5 0.08
31 15 0.25
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
TAATTTATAAAATGTAAATATTTATCAAT
Found at i:35586 original size:2 final size:2
Alignment explanation
Indices: 35579--35615 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35569 CCTTTTGTAG
35579 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
35616 ATTTCTTGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:45500 original size:19 final size:19
Alignment explanation
Indices: 45476--45513 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
45466 ATTATGAACT
45476 TTATTAT-AATAAATCATAA
1 TTATTATAAATAAAT-ATAA
45495 TTATTATAAATAAATATAA
1 TTATTATAAATAAATATAA
45514 AAAGTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
TTATTATAAATAAATATAA
Found at i:46013 original size:2 final size:2
Alignment explanation
Indices: 46006--46047 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
45996 AGTTACATCA
* * *
46006 AT AT AT AT AT AT AT AT AT GT GT GT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
46048 TTTACTTAGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46540 original size:10 final size:10
Alignment explanation
Indices: 46525--46654 Score: 115
Period size: 10 Copynumber: 13.2 Consensus size: 10
46515 ACACATATAC
46525 ATATATACAT
1 ATATATACAT
46535 ATATATAC--
1 ATATATACAT
46543 ATATATACAT
1 ATATATACAT
46553 ATATAT--AT
1 ATATATACAT
* *
46561 ATATACATAT
1 ATATATACAT
* * *
46571 ATACAAATAT
1 ATATATACAT
46581 ATATATACAT
1 ATATATACAT
46591 ATATATACAT
1 ATATATACAT
*
46601 ATATATATAT
1 ATATATACAT
46611 ACATATATACAT
1 --ATATATACAT
***
46623 ATATATGTGT
1 ATATATACAT
*
46633 ATATATATAT
1 ATATATACAT
*
46643 ATATATATAT
1 ATATATACAT
46653 AT
1 AT
46655 GAAGTTTTCG
Statistics
Matches: 101, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
8 15 0.15
10 77 0.76
12 9 0.09
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (10 bp):
ATATATACAT
Found at i:46544 original size:24 final size:24
Alignment explanation
Indices: 46520--46654 Score: 184
Period size: 24 Copynumber: 5.6 Consensus size: 24
46510 CCCCCACACA
46520 TATACATATATACATATATATACATA
1 TATACATATAT--ATATATATACATA
46546 TATACATATATATATATATACATA
1 TATACATATATATATATATACATA
46570 TATACA-A-ATATATATATACATA
1 TATACATATATATATATATACATA
* *
46592 TATATACATATATATATATACATA
1 TATACATATATATATATATACATA
* * *
46616 TATACATATATATGTGTATATATA
1 TATACATATATATATATATACATA
*
46640 TATATATATATATAT
1 TATACATATATATAT
46655 GAAGTTTTCG
Statistics
Matches: 99, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
22 20 0.20
23 2 0.02
24 66 0.67
26 11 0.11
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (24 bp):
TATACATATATATATATATACATA
Found at i:46652 original size:8 final size:8
Alignment explanation
Indices: 46519--46654 Score: 155
Period size: 8 Copynumber: 17.0 Consensus size: 8
46509 CCCCCCACAC
*
46519 ATATACAT
1 ATATATAT
*
46527 ATATACAT
1 ATATATAT
*
46535 ATATATAC
1 ATATATAT
*
46543 ATATATAC
1 ATATATAT
46551 ATATATAT
1 ATATATAT
*
46559 ATATATAC
1 ATATATAT
*
46567 ATATATAC
1 ATATATAT
*
46575 AAATATAT
1 ATATATAT
*
46583 ATATACAT
1 ATATATAT
*
46591 ATATATAC
1 ATATATAT
46599 ATATATAT
1 ATATATAT
*
46607 ATATACAT
1 ATATATAT
*
46615 ATATACAT
1 ATATATAT
*
46623 ATATATGT
1 ATATATAT
*
46631 GTATATAT
1 ATATATAT
46639 ATATATAT
1 ATATATAT
46647 ATATATAT
1 ATATATAT
46655 GAAGTTTTCG
Statistics
Matches: 111, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
8 111 1.00
ACGTcount: A:0.49, C:0.07, G:0.01, T:0.42
Consensus pattern (8 bp):
ATATATAT
Found at i:47270 original size:21 final size:21
Alignment explanation
Indices: 47227--47289 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
47217 TTGAGTTGAA
* *
47227 TTATGATTTAATATTT-AATAT
1 TTATTATTTAA-ATTTAAAAAT
*
47248 TTTTTATTTAAATTTAAAAAT
1 TTATTATTTAAATTTAAAAAT
*
47269 TTATT-TTTACTATTTAAAAAT
1 TTATTATTTA-AATTTAAAAAT
47290 ATGAATAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 8 0.23
21 27 0.77
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTATTATTTAAATTTAAAAAT
Found at i:47822 original size:94 final size:94
Alignment explanation
Indices: 47661--47949 Score: 551
Period size: 94 Copynumber: 3.1 Consensus size: 94
47651 GGTTGCGGCC
*
47661 GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCGTGATGGAGATGTATATTTC
1 GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCATGATGGAGATGTATATTTC
47726 ATGAGATTATTTTGCAATGTCAATATATA
66 ATGAGATTATTTTGCAATGTCAATATATA
47755 GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCATGATGGAGATGTATATTTC
1 GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCATGATGGAGATGTATATTTC
47820 ATGAGATTATTTTGCAATGTCAATATATA
66 ATGAGATTATTTTGCAATGTCAATATATA
47849 GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCATGATGGAGATGTATATTTC
1 GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCATGATGGAGATGTATATTTC
47914 ATGAGATTTATTTTTGCAATGTCAATATATA
66 ATGAGA-TTA-TTTTGCAATGTCAATATATA
47945 GCCAT
1 GCCAT
47950 TCAGGTATAA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
94 164 0.85
95 3 0.02
96 25 0.13
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (94 bp):
GCCATAGACAAGAAGAAGAAGAAAATTGAGGAAAGGGTTATATGCATGATGGAGATGTATATTTC
ATGAGATTATTTTGCAATGTCAATATATA
Found at i:49000 original size:2 final size:2
Alignment explanation
Indices: 48993--49040 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
48983 ACTTCACCAC
*
48993 CT CT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
49035 GT CT CT
1 CT CT CT
49041 TGAAAGAGAC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.46, G:0.04, T:0.50
Consensus pattern (2 bp):
CT
Done.