Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3082
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: 64311
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5728 original size:14 final size:14
Alignment explanation
Indices: 5709--5743 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
5699 TAGTTTCTCG
*
5709 AAAAAAAATTC-AA
1 AAAAAAAAATCGAA
5722 AAAAAAAAATCGAA
1 AAAAAAAAATCGAA
5736 AAAAAAAA
1 AAAAAAAA
5744 CTAGTTTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 10 0.50
14 10 0.50
ACGTcount: A:0.83, C:0.06, G:0.03, T:0.09
Consensus pattern (14 bp):
AAAAAAAAATCGAA
Found at i:5799 original size:12 final size:13
Alignment explanation
Indices: 5778--5819 Score: 68
Period size: 13 Copynumber: 3.2 Consensus size: 13
5768 ATTGGATATC
5778 AAATTGTGAAAAA
1 AAATTGTGAAAAA
5791 AAATT-TGAAAAAA
1 AAATTGTG-AAAAA
5804 AAATTGTGAAAAA
1 AAATTGTGAAAAA
5817 AAA
1 AAA
5820 AAGATTTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.07
13 23 0.85
14 2 0.07
ACGTcount: A:0.67, C:0.00, G:0.12, T:0.21
Consensus pattern (13 bp):
AAATTGTGAAAAA
Found at i:5838 original size:15 final size:14
Alignment explanation
Indices: 5786--5836 Score: 68
Period size: 13 Copynumber: 3.5 Consensus size: 14
5776 TCAAATTGTG
5786 AAAAAAAATTTG-A
1 AAAAAAAATTTGAA
5799 AAAAAAAATTGTGAAA
1 AAAAAAAATT-TG-AA
5815 AAAAAAAGATTTGAA
1 AAAAAAA-ATTTGAA
5830 AAAAAAA
1 AAAAAAA
5837 GAGAGCTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.29
14 2 0.06
15 9 0.26
16 10 0.29
17 3 0.09
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.18
Consensus pattern (14 bp):
AAAAAAAATTTGAA
Found at i:10454 original size:20 final size:20
Alignment explanation
Indices: 10408--10454 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
10398 AGCTCGTTTC
*
10408 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
10428 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
10448 CAGCTCA
1 CAGCTCA
10455 ATCTTAATCC
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:13972 original size:22 final size:22
Alignment explanation
Indices: 13941--14005 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
13931 ACCTTTTTGA
*
13941 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
13964 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
13986 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
14006 TTCCCAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:14329 original size:15 final size:14
Alignment explanation
Indices: 14309--14378 Score: 63
Period size: 14 Copynumber: 4.8 Consensus size: 14
14299 ATAGGTACGT
*
14309 AAAAAAAAGTTCGA
1 AAAAAAAAATTCGA
*
14323 AAAAAAAAATTTG-
1 AAAAAAAAATTCGA
14336 AAAAAAAAATTCGAAA
1 AAAAAAAAATTCG--A
14352 GGAAAAAAAAATT-GA
1 --AAAAAAAAATTCGA
14367 AAGAAAAAAATT
1 AA-AAAAAAATT
14379 GTATACGGTT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
13 14 0.30
14 20 0.43
15 1 0.02
17 1 0.02
18 11 0.23
ACGTcount: A:0.70, C:0.03, G:0.11, T:0.16
Consensus pattern (14 bp):
AAAAAAAAATTCGA
Found at i:14357 original size:17 final size:16
Alignment explanation
Indices: 14335--14376 Score: 66
Period size: 18 Copynumber: 2.5 Consensus size: 16
14325 AAAAAAATTT
14335 GAAAAAAAAATTCGAAA
1 GAAAAAAAAATT-GAAA
14352 GGAAAAAAAAATTGAAA
1 -GAAAAAAAAATTGAAA
14369 GAAAAAAA
1 GAAAAAAA
14377 TTGTATACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 8 0.33
17 4 0.17
18 12 0.50
ACGTcount: A:0.74, C:0.02, G:0.14, T:0.10
Consensus pattern (16 bp):
GAAAAAAAAATTGAAA
Found at i:14358 original size:14 final size:13
Alignment explanation
Indices: 14309--14351 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
14299 ATAGGTACGT
*
14309 AAAAAAAAGTTCG
1 AAAAAAAAATTCG
*
14322 AAAAAAAAAATTTG
1 -AAAAAAAAATTCG
14336 AAAAAAAAATTCG
1 AAAAAAAAATTCG
14349 AAA
1 AAA
14352 GGAAAAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.70, C:0.05, G:0.09, T:0.16
Consensus pattern (13 bp):
AAAAAAAAATTCG
Found at i:18931 original size:19 final size:18
Alignment explanation
Indices: 18895--18934 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
18885 TTTCCACTCG
*
18895 TTTCTTTTTCAACTTCTC
1 TTTCTTTTTCAACATCTC
*
18913 TTTCTTTTTCCACAATCTC
1 TTTCTTTTTCAAC-ATCTC
18932 TTT
1 TTT
18935 GTTTGTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.12, C:0.28, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTCTTTTTCAACATCTC
Found at i:20003 original size:12 final size:12
Alignment explanation
Indices: 19986--20032 Score: 76
Period size: 13 Copynumber: 3.8 Consensus size: 12
19976 ACTAGCTCTC
19986 TTTTTTTCAAATT
1 TTTTTTTCAAA-T
19999 TTTTTTTCACAAT
1 TTTTTTTCA-AAT
20012 TTTTTTTCAAAT
1 TTTTTTTCAAAT
20024 TTTTTTTCA
1 TTTTTTTCA
20033 CAACTTGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
12 12 0.36
13 19 0.58
14 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTTTCAAAT
Found at i:20016 original size:25 final size:25
Alignment explanation
Indices: 19986--20035 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
19976 ACTAGCTCTC
19986 TTTTTTTCAAATTTTTTTTTCACAAT
1 TTTTTTTCAAA-TTTTTTTTCACAAT
20012 TTTTTTTCAAATTTTTTTTCACAA
1 TTTTTTTCAAATTTTTTTTCACAA
20036 CTTGATATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 13 0.54
26 11 0.46
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (25 bp):
TTTTTTTCAAATTTTTTTTCACAAT
Found at i:20090 original size:12 final size:11
Alignment explanation
Indices: 20073--20114 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
20063 TGGAAACTAG
20073 TTTTTTTTTGA
1 TTTTTTTTTGA
20084 -TTTTTTTTGAA
1 TTTTTTTTTG-A
*
20095 TTTTTTTTCGA
1 TTTTTTTTTGA
20106 GTTTTTTTT
1 -TTTTTTTT
20115 CGAGAAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 9 0.33
11 2 0.07
12 16 0.59
ACGTcount: A:0.10, C:0.02, G:0.10, T:0.79
Consensus pattern (11 bp):
TTTTTTTTTGA
Found at i:20115 original size:12 final size:12
Alignment explanation
Indices: 20071--20118 Score: 64
Period size: 11 Copynumber: 4.2 Consensus size: 12
20061 AATGGAAACT
*
20071 AGTTTTTTTTTG
1 AGTTTTTTTTCG
20083 A-TTTTTTTT-G
1 AGTTTTTTTTCG
*
20093 AATTTTTTTTCG
1 AGTTTTTTTTCG
20105 AGTTTTTTTTCG
1 AGTTTTTTTTCG
20117 AG
1 AG
20119 AAACTACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
10 2 0.06
11 16 0.48
12 15 0.45
ACGTcount: A:0.12, C:0.04, G:0.15, T:0.69
Consensus pattern (12 bp):
AGTTTTTTTTCG
Found at i:22429 original size:20 final size:20
Alignment explanation
Indices: 22404--22458 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
22394 GCGAAAATAC
*
22404 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
22424 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
*
22443 AAAAGAGAATGAAAAA
1 AAAAGA-AAAGAAAAA
22459 AAATGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 7 0.24
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:27082 original size:28 final size:28
Alignment explanation
Indices: 27047--27107 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
27037 GGACTTATCT
27047 TTTA-TTCTTGCTG-TTCAATTTATTTTC
1 TTTATTTCTTGCTGTTTCAATTTA-TTTC
**
27074 TTTATTTCTTGCTGTTTCGTTTTATTTC
1 TTTATTTCTTGCTGTTTCAATTTATTTC
27102 TTTATT
1 TTTATT
27108 CCTACTTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 4 0.13
28 19 0.63
29 7 0.23
ACGTcount: A:0.11, C:0.13, G:0.08, T:0.67
Consensus pattern (28 bp):
TTTATTTCTTGCTGTTTCAATTTATTTC
Found at i:30668 original size:20 final size:20
Alignment explanation
Indices: 30645--30691 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
30635 GGGTTAAGAT
*
30645 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
30665 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
30685 TGAGCTG
1 TGAGCTG
30692 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:36399 original size:13 final size:12
Alignment explanation
Indices: 36376--36400 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36366 CTAGACCGTA
36376 TGCAATTTTTTT
1 TGCAATTTTTTT
36388 TGCAATTTTTTT
1 TGCAATTTTTTT
36400 T
1 T
36401 CTTTTTTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.08, T:0.68
Consensus pattern (12 bp):
TGCAATTTTTTT
Found at i:36409 original size:22 final size:22
Alignment explanation
Indices: 36381--36423 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
36371 CCGTATGCAA
36381 TTTTTTTT-GCAATTTTTTTTC
1 TTTTTTTTCGCAATTTTTTTTC
* *
36402 TTTTTTTTCGGATTTTTTTTTC
1 TTTTTTTTCGCAATTTTTTTTC
36424 AAAACTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.77
Consensus pattern (22 bp):
TTTTTTTTCGCAATTTTTTTTC
Found at i:41125 original size:23 final size:22
Alignment explanation
Indices: 41073--41125 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41063 TCCACGTCTT
*
41073 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
41095 -TTCATTTTCTCTTCTTTTT-TCAA
1 TTTC-TTTTCT-TTCTTTTTCT-AA
41118 TTTCTTTT
1 TTTCTTTT
41126 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 6 0.23
23 14 0.54
24 3 0.12
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:46000 original size:40 final size:40
Alignment explanation
Indices: 45941--46152 Score: 259
Period size: 40 Copynumber: 5.3 Consensus size: 40
45931 CATTTGAATG
* * *
45941 ATATCCGGGCTAAGTCCCGAAGGTAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
45981 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
46021 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
46061 TTATCCGGGCTAAGACCCGAAGGCATTTGTACGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
46101 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
46141 ATATCC-GGCTAA
1 ATATCCGGGCTAA
46153 ATTCCGAAGA
Statistics
Matches: 145, Mismatches: 23, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
39 10 0.07
40 130 0.90
41 5 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:46078 original size:80 final size:80
Alignment explanation
Indices: 45945--46152 Score: 319
Period size: 80 Copynumber: 2.6 Consensus size: 80
45935 TGAATGATAT
* *
45945 CCGGGCTAAGTCCCGAAGGTAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
* *
46010 TGCGAGTTGCTATAC
66 TACGAGTTGATATAC
*
46025 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
46090 TACGAGTTGATATAT
66 TACGAGTTGATATAC
* * * *
46105 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
46153 ATTCCGAAGA
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
79 6 0.05
80 111 0.95
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
TACGAGTTGATATAC
Found at i:48349 original size:21 final size:23
Alignment explanation
Indices: 48304--48350 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
48294 TCACCTGCAA
* *
48304 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
48327 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
48348 TAA
1 TAA
48351 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:50303 original size:22 final size:22
Alignment explanation
Indices: 50266--50330 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
50256 ACCTTTTTGA
*
50266 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
* *
50289 ACCATATCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
**
50311 TTCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
50331 TTCCCAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 32 0.89
23 4 0.11
ACGTcount: A:0.34, C:0.31, G:0.05, T:0.31
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:51356 original size:22 final size:22
Alignment explanation
Indices: 51325--51389 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
51315 ACCTTTTTGA
*
51325 ACCATTACCAATTCGTACCAAAT
1 ACCA-TACCATTTCGTACCAAAT
*
51348 ACCATACCATTTCGTACCAACT
1 ACCATACCATTTCGTACCAAAT
*
51370 TCCATACCATTTCGTACCAA
1 ACCATACCATTTCGTACCAA
51390 TTCCCAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 35 0.90
23 4 0.10
ACGTcount: A:0.34, C:0.34, G:0.05, T:0.28
Consensus pattern (22 bp):
ACCATACCATTTCGTACCAAAT
Found at i:52422 original size:22 final size:22
Alignment explanation
Indices: 52396--52449 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
52386 CCATTACTAA
52396 TTCGTACCAAATACCATACCAT
1 TTCGTACCAAATACCATACCAT
* *
52418 TTCGTACCAACTTCCATACCAT
1 TTCGTACCAAATACCATACCAT
52440 TTCGTACCAA
1 TTCGTACCAA
52450 TTCCCAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.31, C:0.33, G:0.06, T:0.30
Consensus pattern (22 bp):
TTCGTACCAAATACCATACCAT
Found at i:55800 original size:20 final size:19
Alignment explanation
Indices: 55777--55841 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
55767 AAGCTCAAAC
55777 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
55797 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
55817 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
55837 GAGCT
1 GAGCT
55842 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:57654 original size:33 final size:33
Alignment explanation
Indices: 57616--57678 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
57606 GATTACTCAC
57616 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
57649 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
57679 AATTTCTTTT
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:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:57705 original size:21 final size:21
Alignment explanation
Indices: 57676--57799 Score: 56
Period size: 21 Copynumber: 5.7 Consensus size: 21
57666 CAAGCTCTCT
*
57676 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
57697 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
* *
57718 TTCATTTTCTTTTTCTTCTTTT
1 TTCATTTTCTTTTT-TCCTTTC
* *
57740 TTCGATTTTTTTCTTTTTCTTTTC
1 TTC-A-TTTTCT-TTTTTCCTTTC
*
57764 TTTCTTTTTCTTTTTGT--TTTC
1 -TTCATTTTCTTTTT-TCCTTTC
*
57785 TTTCAATTTCTTTTT
1 -TTCATTTTCTTTTT
57800 CAATCTCTTT
Statistics
Matches: 77, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.04
21 40 0.52
22 11 0.14
23 7 0.09
24 9 0.12
25 7 0.09
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:57705 original size:27 final size:27
Alignment explanation
Indices: 57675--57799 Score: 82
Period size: 27 Copynumber: 4.6 Consensus size: 27
57665 TCAAGCTCTC
57675 TTTCAATTTCTTTTTTCGCTTTTTCTT
1 TTTCAATTTCTTTTTTCGCTTTTTCTT
*
57702 TTTCAATTTTCTTTTCTT--CATTTTCTT
1 TTTCAA-TTTCTTTT-TTCGCTTTTTCTT
*
57729 TTTC---TTCTTTTTTCGATTTTTTTCTT
1 TTTCAATTTCTTTTTTCG--CTTTTTCTT
* ** *
57755 TTTC-TTTTCTTTCTTTTTCTTTTTGTTTT
1 TTTCAATTTCTTT-TTTCGC-TTTT-TCTT
57784 CTTTCAATTTCTTTTT
1 -TTTCAATTTCTTTTT
57800 CAATCTCTTT
Statistics
Matches: 77, Mismatches: 8, Indels: 23
0.71 0.07 0.21
Matches are distributed among these distances:
22 2 0.03
23 7 0.09
26 11 0.14
27 18 0.23
28 18 0.23
29 8 0.10
30 6 0.08
31 7 0.09
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.74
Consensus pattern (27 bp):
TTTCAATTTCTTTTTTCGCTTTTTCTT
Found at i:57742 original size:10 final size:9
Alignment explanation
Indices: 57727--57778 Score: 50
Period size: 10 Copynumber: 5.2 Consensus size: 9
57717 CTTCATTTTC
57727 TTTTTCTTCT
1 TTTTTCTT-T
*
57737 TTTTTCGATT
1 TTTTTC-TTT
57747 TTTTTCTTTT
1 TTTTTC-TTT
57757 TCTTTTCTTT
1 T-TTTTCTTT
57767 CTTTTTCTTT
1 -TTTTTCTTT
57777 TT
1 TT
57779 GTTTTCTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
9 2 0.06
10 27 0.75
11 7 0.19
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:57788 original size:15 final size:14
Alignment explanation
Indices: 57681--57778 Score: 83
Period size: 15 Copynumber: 6.6 Consensus size: 14
57671 TCTCTTTCAA
*
57681 TTTCTTTTTTCGCTT
1 TTTCTTTTTT-TCTT
*
57696 TTTC--TTTTTCAAT
1 TTTCTTTTTTTC-TT
* *
57709 TTTCTTTTCTTCAT
1 TTTCTTTTTTTCTT
57723 TTTCTTTTTCTTCTTT
1 TTTCTTTTT-TTC-TT
57739 TTTCGATTTTTTTCTT
1 TTTC--TTTTTTTCTT
57755 TTTCTTTTCTTTCTT
1 TTTCTTTT-TTTCTT
57770 TTTCTTTTT
1 TTTCTTTTT
57779 GTTTTCTTTC
Statistics
Matches: 70, Mismatches: 5, Indels: 17
0.76 0.05 0.18
Matches are distributed among these distances:
12 1 0.01
13 9 0.13
14 15 0.21
15 26 0.37
16 11 0.16
17 3 0.04
18 5 0.07
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:57800 original size:6 final size:6
Alignment explanation
Indices: 57693--57787 Score: 58
Period size: 6 Copynumber: 15.7 Consensus size: 6
57683 TCTTTTTTCG
* *
57693 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTTCTTT -TTTCGATT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTT-TTT CTTT---TT
*
57747 -TTTTT CTTTTT C-TTTT C--TTT CTTTTT CTTTTT -GTTTT CTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTT
57788 CAATTTCTTT
Statistics
Matches: 72, Mismatches: 7, Indels: 20
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.06
5 12 0.17
6 36 0.50
7 12 0.17
8 8 0.11
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (6 bp):
CTTTTT
Found at i:58878 original size:11 final size:11
Alignment explanation
Indices: 58864--58928 Score: 51
Period size: 12 Copynumber: 5.5 Consensus size: 11
58854 TTTTGCTCGA
*
58864 TTTTTTTCACT
1 TTTTTTTCAAT
*
58875 TTTTTTTGAATT
1 TTTTTTTCAA-T
58887 TTTTTTCAATCAAT
1 TTTTTT---TCAAT
58901 TTTTTTTCGAAT
1 TTTTTTTC-AAT
*
58913 TTTTTTT-GAT
1 TTTTTTTCAAT
58923 TTTTTT
1 TTTTTT
58929 GTTACTCCAA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
10 8 0.18
11 10 0.22
12 17 0.38
14 7 0.16
15 3 0.07
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (11 bp):
TTTTTTTCAAT
Found at i:58889 original size:12 final size:12
Alignment explanation
Indices: 58874--58928 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 12
58864 TTTTTTTCAC
58874 TTTTTTTTGAAT
1 TTTTTTTTGAAT
*
58886 TTTTTTTCAATCAAT
1 TTTTTTT---TGAAT
*
58901 TTTTTTTCGAA-
1 TTTTTTTTGAAT
58912 TTTTTTTTG-AT
1 TTTTTTTTGAAT
58923 TTTTTT
1 TTTTTT
58929 GTTACTCCAA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
10 1 0.03
11 14 0.40
12 9 0.26
15 11 0.31
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:64220 original size:20 final size:20
Alignment explanation
Indices: 64195--64248 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 20
64185 TAGTTTTTCC
64195 AGCTTAATTTAGCTCACATG
1 AGCTTAATTTAGCTCACATG
***
64215 AGCTTAATTTAGCTCGTTTG
1 AGCTTAATTTAGCTCACATG
*
64235 AGCTCAATTTAGCT
1 AGCTTAATTTAGCT
64249 TACTTTAGCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.39
Consensus pattern (20 bp):
AGCTTAATTTAGCTCACATG
Found at i:64239 original size:30 final size:30
Alignment explanation
Indices: 64205--64265 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
64195 AGCTTAATTT
64205 AGCTCACA-TGAGCTTAATTTAGCTCGTTTG
1 AGCTCA-ATTGAGCTTAATTTAGCTCGTTTG
* *
64235 AGCTCAATTTAGCTTACTTTAGCTCGTTTG
1 AGCTCAATTGAGCTTAATTTAGCTCGTTTG
64265 A
1 A
64266 CTTGCTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (30 bp):
AGCTCAATTGAGCTTAATTTAGCTCGTTTG
Found at i:64258 original size:20 final size:20
Alignment explanation
Indices: 64195--64259 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
64185 TAGTTTTTCC
* * * *
64195 AGCTTAATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
64215 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
64234 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
64255 AGCTC
1 AGCTC
64260 GTTTGACTTG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.81
21 4 0.11
22 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Done.