Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1403
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: 83123
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1697 original size:20 final size:20
Alignment explanation
Indices: 1672--1709 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1662 TAGTTTCTCG
1672 AAAAAAACTAGAAAAAAATT
1 AAAAAAACTAGAAAAAAATT
* *
1692 AAAAAAATTCGAAAAAAA
1 AAAAAAACTAGAAAAAAA
1710 AACTAGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAAAAACTAGAAAAAAATT
Found at i:1706 original size:11 final size:11
Alignment explanation
Indices: 1669--1709 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1659 TAGTAGTTTC
*
1669 TCGAAAAAAAC
1 TCGAAAAAAAT
*
1680 TAGAAAAAAAT
1 TCGAAAAAAAT
1691 T--AAAAAAAT
1 TCGAAAAAAAT
1700 TCGAAAAAAA
1 TCGAAAAAAA
1710 AACTAGTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 9 0.35
11 17 0.65
ACGTcount: A:0.71, C:0.07, G:0.07, T:0.15
Consensus pattern (11 bp):
TCGAAAAAAAT
Found at i:1772 original size:12 final size:13
Alignment explanation
Indices: 1749--1800 Score: 88
Period size: 13 Copynumber: 4.0 Consensus size: 13
1739 AGATATCAAG
1749 TTGTGAAAAAAAAA
1 TTGTG-AAAAAAAA
1763 TT-TGAAAAAAAA
1 TTGTGAAAAAAAA
1775 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
1788 TTGTGAAAAAAAA
1 TTGTGAAAAAAAA
1801 GAGAAGCTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
12 10 0.27
13 25 0.68
14 2 0.05
ACGTcount: A:0.63, C:0.00, G:0.13, T:0.23
Consensus pattern (13 bp):
TTGTGAAAAAAAA
Found at i:8463 original size:22 final size:22
Alignment explanation
Indices: 8433--8479 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
8423 TTTGGTATTT
8433 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
8455 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
8477 GGG
1 GGG
8480 TTCAAAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.40, T:0.23
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:11918 original size:12 final size:12
Alignment explanation
Indices: 11886--11936 Score: 75
Period size: 12 Copynumber: 4.2 Consensus size: 12
11876 TAGTAGTTTC
*
11886 TTCAAAAAAGAAT
1 TTCAAAAAA-AAA
*
11899 TTCGAAAAAAAA
1 TTCAAAAAAAAA
11911 TTCAAAAAAAAA
1 TTCAAAAAAAAA
11923 TTCAAAAAAAAA
1 TTCAAAAAAAAA
11935 TT
1 TT
11937 TGGTTTCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
12 27 0.77
13 8 0.23
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.22
Consensus pattern (12 bp):
TTCAAAAAAAAA
Found at i:11994 original size:15 final size:15
Alignment explanation
Indices: 11974--12027 Score: 92
Period size: 15 Copynumber: 3.6 Consensus size: 15
11964 GATATCAAGT
11974 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
11989 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
12004 TG-AAAAAAAATATCG
1 TGAAAAAAAAAT-TCG
12019 TGAAAAAAA
1 TGAAAAAAA
12028 GAAGAAGCTA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
14 9 0.24
15 22 0.59
16 6 0.16
ACGTcount: A:0.63, C:0.06, G:0.13, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:15977 original size:21 final size:21
Alignment explanation
Indices: 15941--15993 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
15931 TCCACGTCTT
*
15941 TTTCTTTTGTTTCTTT-TTCTAA
1 TTTCTTTT-TCTCTTTCTTC-AA
15963 -TTCATTTTTCTCTTTCTTCAA
1 TTTC-TTTTTCTCTTTCTTCAA
15984 TTTCTTTTTC
1 TTTCTTTTTC
15994 ACTCTCAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTCTTTTTCTCTTTCTTCAA
Found at i:20821 original size:12 final size:12
Alignment explanation
Indices: 20806--20874 Score: 61
Period size: 11 Copynumber: 5.6 Consensus size: 12
20796 TTTTGCTCGA
*
20806 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
20818 TTTTTTTTGAA-
1 TTTTTTTTCAAT
20829 TTTTTTTTCAAT
1 TTTTTTTTCAAT
20841 CAATTTTTTTTCGAAT
1 ---TTTTTTTTC-AAT
*
20857 TTTTTTTT-GAT
1 TTTTTTTTCAAT
20868 TTTTTTT
1 TTTTTTT
20875 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
11 19 0.40
12 9 0.19
13 8 0.17
15 9 0.19
16 3 0.06
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:23728 original size:21 final size:21
Alignment explanation
Indices: 23702--23750 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
23692 ACGGTATTGT
23702 AAAAAAATAAAAAAAAACTT-A
1 AAAAAAATAAAAAAAAA-TTCA
**
23723 AAAAAAATTCAAAAAAATTCA
1 AAAAAAATAAAAAAAAATTCA
23744 AAAAAAA
1 AAAAAAA
23751 AAAGTTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.80, C:0.06, G:0.00, T:0.14
Consensus pattern (21 bp):
AAAAAAATAAAAAAAAATTCA
Found at i:27654 original size:18 final size:19
Alignment explanation
Indices: 27610--27655 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
27600 GATTGAGAGT
*
27610 GAAAAAGAAATTGAAGATA
1 GAAAAAGAAAATGAAGATA
* *
27629 G-AAGAGAAAATGAA-TTA
1 GAAAAAGAAAATGAAGATA
27646 GAAAAAGAAA
1 GAAAAAGAAA
27656 CAAAAGGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 3 0.14
18 18 0.82
19 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAAAGAAAATGAAGATA
Found at i:30464 original size:16 final size:16
Alignment explanation
Indices: 30443--30474 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
30433 TAATGTGTTT
30443 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
30459 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
30475 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:30796 original size:72 final size:73
Alignment explanation
Indices: 30661--30808 Score: 192
Period size: 72 Copynumber: 2.0 Consensus size: 73
30651 GCAGGTACAT
* * *
30661 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAAGCTGCCGAATTTATTGAGTGCAT
1 GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
30726 GGGACTTG
66 GGGACTTG
* * * * * *
30734 GGACGGCATTTAAAGTGAAA-GTTGCTGTTGTA-TTTTCCCAACCAGCCGAATTTAGTGTGTGCA
1 GGACGGCATTTAAAG-AAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCA
30797 TGGGACTTG
65 TGGGACTTG
30806 GGA
1 GGA
30809 TAGCATTAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
72 38 0.58
73 24 0.37
74 3 0.05
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (73 bp):
GGACGGCATTTAAAGAAAAGGTGGCTGCTGCATTTTTCCAAACCAGCCGAATTTAGTGAGTGCAT
GGGACTTG
Found at i:32031 original size:72 final size:73
Alignment explanation
Indices: 31918--32065 Score: 183
Period size: 72 Copynumber: 2.0 Consensus size: 73
31908 TCTAATGCTA
* * * *
31918 TCCCAAGTCCCATGCACACACTAAATTCGGCTGGTTGGG-AAAATACAACAG-CAACTTTCACTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTT-ACTT
31981 TAAATGCCG
65 TAAATGCCG
* * * * * *
31990 TCCCAAGTCCCATGCACTCAATAAATTCGACAGCTTTGGAAAAATGCAGCAGCCACCTTTTCTTT
1 TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTACTTT
32055 AAATGCCG
66 AAATGCCG
32063 TCC
1 TCC
32066 ATGTACCTGC
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
72 33 0.52
73 25 0.39
74 6 0.09
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (73 bp):
TCCCAAGTCCCATGCACACAATAAATTCGACAGCTTGGGAAAAATACAACAGCCAACTTTACTTT
AAATGCCG
Found at i:32273 original size:16 final size:16
Alignment explanation
Indices: 32252--32283 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
32242 CATTCTGCAT
32252 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
32268 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
32284 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:34329 original size:18 final size:18
Alignment explanation
Indices: 34308--34367 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
34298 GACCTCACTC
34308 TCTTTTTTGATTTCTTTT
1 TCTTTTTTGATTTCTTTT
** *
34326 TCTTTTTCAATCTCTTTT
1 TCTTTTTTGATTTCTTTT
34344 TCTTTTCTTTTGATTTCTTTT
1 TC--TT-TTTTGATTTCTTTT
34365 TCT
1 TCT
34368 CGCTCGCACT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
18 17 0.52
19 1 0.03
20 2 0.06
21 13 0.39
ACGTcount: A:0.07, C:0.17, G:0.03, T:0.73
Consensus pattern (18 bp):
TCTTTTTTGATTTCTTTT
Found at i:35323 original size:11 final size:12
Alignment explanation
Indices: 35300--35328 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
35290 CAAAAAAAAA
35300 TTTTTGAATTTT
1 TTTTTGAATTTT
35312 TTTTTGAATTTT
1 TTTTTGAATTTT
35324 TTTTT
1 TTTTT
35329 CAAATTTCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.07, T:0.79
Consensus pattern (12 bp):
TTTTTGAATTTT
Found at i:37021 original size:21 final size:21
Alignment explanation
Indices: 36976--37038 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
36966 TTTCAACCAT
* *
36976 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
36998 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
37019 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
37039 CAAATATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:37365 original size:24 final size:25
Alignment explanation
Indices: 37337--37398 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 25
37327 ATAGGTACGT
*
37337 AAAAAAAGAGTTCGAAAAAAAAAA-G
1 AAAAAAA-AATTCGAAAAAAAAAATG
*
37362 AAAAAAAAATTTGAAAAAAAAAATTG
1 AAAAAAAAATTCGAAAAAAAAAA-TG
37388 AAAAAAAAATT
1 AAAAAAAAATT
37399 GCATGCGGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
24 14 0.42
25 7 0.21
26 12 0.36
ACGTcount: A:0.74, C:0.02, G:0.10, T:0.15
Consensus pattern (25 bp):
AAAAAAAAATTCGAAAAAAAAAATG
Found at i:37379 original size:14 final size:13
Alignment explanation
Indices: 37350--37396 Score: 71
Period size: 13 Copynumber: 3.8 Consensus size: 13
37340 AAAAGAGTTC
37350 GAAAAAAAAAA--
1 GAAAAAAAAAATT
*
37361 GAAAAAAAAATTT
1 GAAAAAAAAAATT
37374 GAAAAAAAAAATT
1 GAAAAAAAAAATT
37387 GAAAAAAAAA
1 GAAAAAAAAA
37397 TTGCATGCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
11 10 0.31
13 22 0.69
ACGTcount: A:0.81, C:0.00, G:0.09, T:0.11
Consensus pattern (13 bp):
GAAAAAAAAAATT
Found at i:37396 original size:26 final size:24
Alignment explanation
Indices: 37350--37398 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
37340 AAAAGAGTTC
37350 GAAAAAAAAAAGAAAAAAAAATTT
1 GAAAAAAAAAAGAAAAAAAAATTT
37374 GAAAAAAAAAATTGAAAAAAAAATT
1 GAAAAAAAAAA--GAAAAAAAAATT
37399 GCATGCGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.48
26 12 0.52
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (24 bp):
GAAAAAAAAAAGAAAAAAAAATTT
Found at i:37397 original size:12 final size:12
Alignment explanation
Indices: 37350--37399 Score: 66
Period size: 12 Copynumber: 4.1 Consensus size: 12
37340 AAAAGAGTTC
*
37350 GAAAAAAAAA-A
1 GAAAAAAAAATT
37361 GAAAAAAAAATTT
1 GAAAAAAAAA-TT
37374 GAAAAAAAAAATT
1 G-AAAAAAAAATT
37387 GAAAAAAAAATT
1 GAAAAAAAAATT
37399 G
1 G
37400 CATGCGGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
11 10 0.29
12 12 0.34
13 4 0.11
14 9 0.26
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.14
Consensus pattern (12 bp):
GAAAAAAAAATT
Found at i:39649 original size:17 final size:17
Alignment explanation
Indices: 39604--39651 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
39594 AGAAAAGAGC
* *
39604 GAAAATACAAAAGAAAA
1 GAAAATTCAAAAAAAAA
* *
39621 GAAAAATGAAAAAAAAA
1 GAAAATTCAAAAAAAAA
39638 GAAAATTCAAAAAA
1 GAAAATTCAAAAAA
39652 GAGAATGAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.77, C:0.04, G:0.10, T:0.08
Consensus pattern (17 bp):
GAAAATTCAAAAAAAAA
Found at i:43723 original size:21 final size:21
Alignment explanation
Indices: 43678--43740 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
43668 TTTCAACCAT
* *
43678 TACCAATTCGTACCAAATACCA
1 TACCATTTCGTACC-AATTCCA
43700 TACCATTTCGTACCAATTCCA
1 TACCATTTCGTACCAATTCCA
* *
43721 TACTATTTCGAACCAATTCC
1 TACCATTTCGTACCAATTCC
43741 CAAATACCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.33, C:0.32, G:0.05, T:0.30
Consensus pattern (21 bp):
TACCATTTCGTACCAATTCCA
Found at i:54674 original size:20 final size:21
Alignment explanation
Indices: 54649--54695 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
54639 AAATTTGATT
54649 GAAAAAAATTC-A-AAAAAAAA
1 GAAAAAAA-TCGACAAAAAAAA
54669 GAAAAAAATCGAGCAAAAAAAA
1 GAAAAAAATCGA-CAAAAAAAA
54691 GAAAA
1 GAAAA
54696 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 2 0.08
20 9 0.38
22 13 0.54
ACGTcount: A:0.77, C:0.06, G:0.11, T:0.06
Consensus pattern (21 bp):
GAAAAAAATCGACAAAAAAAA
Found at i:54690 original size:27 final size:28
Alignment explanation
Indices: 54660--54720 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
54650 AAAAAAATTC
54660 AAAAAAAAAG-AAAAAAA-TCGAGCAAAA
1 AAAAAAAAAGAAAAAAAAGT-GAGCAAAA
*
54687 AAAAGAAAAGAAAAAAAAGGTGAGCAAAA
1 AAAAAAAAAGAAAAAAAA-GTGAGCAAAA
54716 AAAAA
1 AAAAA
54721 TCAAGTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 9 0.31
28 7 0.24
29 12 0.41
30 1 0.03
ACGTcount: A:0.77, C:0.05, G:0.15, T:0.03
Consensus pattern (28 bp):
AAAAAAAAAGAAAAAAAAGTGAGCAAAA
Found at i:55753 original size:12 final size:12
Alignment explanation
Indices: 55741--55858 Score: 50
Period size: 12 Copynumber: 9.8 Consensus size: 12
55731 GAAAGAGATT
*
55741 GAAAAAGAAATT
1 GAAAAAGAAATA
55753 G--AAAGAAA-A
1 GAAAAAGAAATA
*
55762 CAAAAAGAAA-A
1 GAAAAAGAAATA
*
55773 CGAAAAAGAAAAA
1 -GAAAAAGAAATA
**
55786 GAAATTGCAAA-A
1 GAAAAAG-AAATA
*
55798 GAAAAAGAAATC
1 GAAAAAGAAATA
** *
55810 GAAAAAGTGAGA
1 GAAAAAGAAATA
55822 GAAAAAGAAA-A
1 GAAAAAGAAATA
*
55833 TGAAGAAAAGAAAATT
1 -G-A-AAAAG-AAATA
55849 GAAAAAGAAA
1 GAAAAAGAAA
55859 AAGCGAAAAA
Statistics
Matches: 80, Mismatches: 15, Indels: 22
0.68 0.13 0.19
Matches are distributed among these distances:
10 7 0.09
11 12 0.15
12 41 0.51
13 10 0.12
14 6 0.08
15 4 0.05
ACGTcount: A:0.70, C:0.03, G:0.19, T:0.08
Consensus pattern (12 bp):
GAAAAAGAAATA
Found at i:55784 original size:18 final size:18
Alignment explanation
Indices: 55758--55861 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
55748 AAATTGAAAG
*
55758 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
55776 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
55794 AAAAGAAAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
55812 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
55830 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
55851 AAAAGAAAAAG
1 AAAAGAAAAAG
55862 CGAAAAAAGA
Statistics
Matches: 66, Mismatches: 17, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
18 47 0.71
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:55786 original size:6 final size:6
Alignment explanation
Indices: 55754--55861 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
55744 AAAGAAATTG
* * ** *
55754 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
55801 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
55852 AAAGAA AAAG
1 AAAGAA AAAG
55862 CGAAAAAAGA
Statistics
Matches: 75, Mismatches: 24, Indels: 7
0.71 0.23 0.07
Matches are distributed among these distances:
5 3 0.04
6 61 0.81
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (6 bp):
AAAGAA
Found at i:55843 original size:14 final size:13
Alignment explanation
Indices: 55822--55859 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
55812 AAAAGTGAGA
55822 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
55834 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
55849 GAAAAAGAAAA
1 GAAAAAGAAAA
55860 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:55873 original size:21 final size:21
Alignment explanation
Indices: 55823--55873 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
55813 AAAGTGAGAG
*
55823 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
55844 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
55865 AAAAAGAAA
1 AAAAAGAAA
55874 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:55913 original size:33 final size:33
Alignment explanation
Indices: 55876--55938 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
55866 AAAAGAAATT
55876 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTAT-AAAAGAAA-CAAGTGAAAAA
*
55909 GAAAGAGAGTCTATAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTATAAAAGAAACAAGTGAA
55939 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.56, C:0.06, G:0.25, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTATAAAAGAAACAAGTGAAAAA
Found at i:57738 original size:20 final size:20
Alignment explanation
Indices: 57715--57768 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
57705 AGTTTTTCCC
*
57715 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
57735 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
57755 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
57769 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:57750 original size:30 final size:30
Alignment explanation
Indices: 57715--57788 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
57705 AGTTTTTCCC
57715 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
57745 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
57775 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
57789 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:57778 original size:20 final size:20
Alignment explanation
Indices: 57715--57779 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
57705 AGTTTTTCCC
* * * *
57715 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
57735 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
57754 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
57775 AGCTC
1 AGCTC
57780 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:59350 original size:52 final size:52
Alignment explanation
Indices: 59267--59367 Score: 184
Period size: 52 Copynumber: 1.9 Consensus size: 52
59257 TAAGGCAACG
* *
59267 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
59319 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
59368 TATGTGCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 47 1.00
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (52 bp):
TAATAGACAGCAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:64188 original size:15 final size:15
Alignment explanation
Indices: 64159--64201 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
64149 CAGTTTTTCA
64159 CTCACTTT-TTCTTTT
1 CTCACTTTCTT-TTTT
64174 -TCATCTTTCTTTTTT
1 CTCA-CTTTCTTTTTT
64189 CTCACTTTCTTTT
1 CTCACTTTCTTTT
64202 CACTCTCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 3 0.12
15 17 0.68
16 5 0.20
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (15 bp):
CTCACTTTCTTTTTT
Found at i:64223 original size:26 final size:27
Alignment explanation
Indices: 64165--64226 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
64155 TTCACTCACT
* **
64165 TTTTCTTTTTCATCTTTCTTTTTTCTCA
1 TTTTC-TTTTCATCTCTCTTTTTTCAAA
*
64193 CTTTCTTTTCA-CTCTCTTTTTTCAAA
1 TTTTCTTTTCATCTCTCTTTTTTCAAA
64219 TTTTCTTT
1 TTTTCTTT
64227 CTTTTTCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 6 0.21
28 4 0.14
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTTCTTTTCATCTCTCTTTTTTCAAA
Found at i:70805 original size:33 final size:34
Alignment explanation
Indices: 70757--70822 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
70747 ATCACTCTCC
*
70757 CTCATTTAAATGCCG-TCCATTGCATGTGGAACAT
1 CTCATTTAAATGCCGTTCCA-TGCATGTAGAACAT
*
70791 CTCA-TTAATTGCCGTTCCATGCATGTAGAACA
1 CTCATTTAAATGCCGTTCCATGCATGTAGAACA
70823 ACATATTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 21 0.72
34 8 0.28
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (34 bp):
CTCATTTAAATGCCGTTCCATGCATGTAGAACAT
Found at i:70833 original size:34 final size:34
Alignment explanation
Indices: 70757--70833 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 34
70747 ATCACTCTCC
* * *
70757 CTCATTTAAATGCCGTCCATTGCATGTGGAACAT
1 CTCATTTAATTGCCGTCCATTGCATGTAGAACAA
70791 CTCA-TTAATTGCCGTTCCA-TGCATGTAGAACAA
1 CTCATTTAATTGCCG-TCCATTGCATGTAGAACAA
70824 CAT-ATTTAAT
1 C-TCATTTAAT
70834 GCATGTCTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
33 23 0.62
34 14 0.38
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (34 bp):
CTCATTTAATTGCCGTCCATTGCATGTAGAACAA
Found at i:71304 original size:20 final size:20
Alignment explanation
Indices: 71258--71304 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
71248 AGCTCGTTTC
*
71258 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
71278 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
71298 CAGCTCA
1 CAGCTCA
71305 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:74001 original size:48 final size:47
Alignment explanation
Indices: 73922--74027 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
73912 GAGTGTCATG
*
73922 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
73970 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
74018 GAAAAAGAAA
1 GAAAAAGAAA
74028 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:75742 original size:20 final size:20
Alignment explanation
Indices: 75696--75742 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
75686 AGCTCGTTTC
*
75696 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
75716 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
75736 CAGCTCA
1 CAGCTCA
75743 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:81818 original size:40 final size:40
Alignment explanation
Indices: 81771--82116 Score: 570
Period size: 40 Copynumber: 8.7 Consensus size: 40
81761 CGCAAACACT
* * *
81771 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
81811 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
81851 TTGCCTTCGGGTCATAGCCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
81891 TTGCCTTCGGGTCTTAGCCCGG--ATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* * *
81929 TTGCCTTCGGGTCATAGCCCGGACATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
81969 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
82009 TTGCCTTCGGGTCTTAGCCCGGATATATTAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
82049 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
82089 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
82117 TCCAATGCTC
Statistics
Matches: 285, Mismatches: 19, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
38 35 0.12
40 250 0.88
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Done.