Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold828
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: 31051
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:6461 original size:1 final size:1
Alignment explanation
Indices: 6450--6538 Score: 61
Period size: 1 Copynumber: 89.0 Consensus size: 1
6440 CTTCATACCC
* * * * * * * ** *
6450 AAAAAATAAAAAAAAACAAAAAAAAACAAAAAACAAAAAAAGAACAAAAAAACAAAAAAACCAAG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
6515 AAAAAAATAACAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAA
6539 GGGGTCCAGA
Statistics
Matches: 64, Mismatches: 24, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:6471 original size:11 final size:11
Alignment explanation
Indices: 6457--6538 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
6447 CCCAAAAAAT
6457 AAAAAAAAAC-
1 AAAAAAAAACA
6467 AAAAAAAAACA
1 AAAAAAAAACA
6478 AAAAACAAAA-A
1 AAAAA-AAAACA
6489 AAGAACAAAAA-A
1 AA-AA-AAAAACA
*
6501 ACAAAAAAACCA
1 A-AAAAAAAACA
* *
6513 AGAAAAAAATA
1 AAAAAAAAACA
*
6524 ACAAAAAAACA
1 AAAAAAAAACA
6535 AAAA
1 AAAA
6539 GGGGTCCAGA
Statistics
Matches: 59, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
10 10 0.17
11 31 0.53
12 16 0.27
13 2 0.03
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:6515 original size:23 final size:23
Alignment explanation
Indices: 6450--6533 Score: 88
Period size: 23 Copynumber: 3.8 Consensus size: 23
6440 CTTCATACCC
6450 AAAAAATAA-AAAAAAA-CAA-A
1 AAAAAATAACAAAAAAACCAAGA
* **
6470 AAAAAACAA-AAAACAAAAAAAGA
1 AAAAAATAACAAAA-AAACCAAGA
6493 ACAAAAA-AACAAAAAAACCAAGA
1 A-AAAAATAACAAAAAAACCAAGA
6516 AAAAAATAACAAAAAAAC
1 AAAAAATAACAAAAAAAC
6534 AAAAAGGGGT
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 12 0.22
21 3 0.06
22 7 0.13
23 23 0.43
24 9 0.17
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (23 bp):
AAAAAATAACAAAAAAACCAAGA
Found at i:6518 original size:18 final size:16
Alignment explanation
Indices: 6449--6538 Score: 83
Period size: 18 Copynumber: 5.4 Consensus size: 16
6439 CCTTCATACC
*
6449 CAAAAAATAAAAAAAAA
1 CAAAAAA-ACAAAAAAA
6466 CAAAAAAAAACAAAAAACA
1 C--AAAAAAACAAAAAA-A
*
6485 AAAAAAGAACAAAAAAA
1 CAAAAA-AACAAAAAAA
* *
6502 CAAAAAAACCAAGAAA
1 CAAAAAAACAAAAAAA
*
6518 -AAAATAACAAAAAAA
1 CAAAAAAACAAAAAAA
6533 CAAAAA
1 CAAAAA
6539 GGGGTCCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 11
0.75 0.11 0.14
Matches are distributed among these distances:
15 12 0.20
16 12 0.20
17 12 0.20
18 16 0.27
19 7 0.12
ACGTcount: A:0.84, C:0.11, G:0.02, T:0.02
Consensus pattern (16 bp):
CAAAAAAACAAAAAAA
Found at i:6527 original size:31 final size:28
Alignment explanation
Indices: 6450--6538 Score: 108
Period size: 31 Copynumber: 3.1 Consensus size: 28
6440 CTTCATACCC
* *
6450 AAAAAATAAAAAAAAACAAAAAAA-AAC
1 AAAAAACAAAAAAAAACAAAAAAACAAA
6477 AAAAAACAAAAAAAGAACAAAAAAACAAA
1 AAAAAACAAAAAAA-AACAAAAAAACAAA
*
6506 AAAACCAAGAAAAAAATAACAAAAAAACAAA
1 AAAA--AACAAAAAAA-AACAAAAAAACAAA
6537 AA
1 AA
6539 GGGGTCCAGA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
27 13 0.24
28 10 0.19
29 6 0.11
31 25 0.46
ACGTcount: A:0.85, C:0.10, G:0.02, T:0.02
Consensus pattern (28 bp):
AAAAAACAAAAAAAAACAAAAAAACAAA
Found at i:7792 original size:28 final size:28
Alignment explanation
Indices: 7752--8385 Score: 746
Period size: 28 Copynumber: 21.9 Consensus size: 28
7742 CGATCATCTC
7752 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
7780 TTCAAAGCCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
7808 TTCAAAGCCCATAAGCCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
7836 TTCAAAGCCCACAAGTGAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
7864 TTCAAAGCCCACAAGTCAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCC-T
* *
7893 TTCAAAGCCCACACGAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-AC-CCT
* *
7925 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
** *
7953 TTCAAAGCCCATGAGTCAGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGC-AC-CCT
* * * *
7983 TTCAAAGCCCACAAGTTAATGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
8011 TTCAAAGCTCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
8039 TTCAAAGCCCGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
8067 TTCAAAACCCACATGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
8096 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
8124 TTCAAAGCCCACAAGTCTGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
8152 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
8181 TTCAAAGTCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
* *
8209 TTCAAAGCCCAAAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
8237 TTCAAAGCCCACAAGTCAATGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCCT
*
8265 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
8294 TTCAAAGCCCGCACGAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-AC-CCT
*
8326 TTCAAAGCCCACACGAGTCAGTGGTAACCCTT
1 TTCAAAGCCCACA--AGTCAGTGG-CACCC-T
*
8358 TTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAAAG-CC-CACAAGTCAGTGGCACC
8386 TTTTTTAAGA
Statistics
Matches: 518, Mismatches: 69, Indels: 35
0.83 0.11 0.06
Matches are distributed among these distances:
28 323 0.62
29 73 0.14
30 33 0.06
31 27 0.05
32 55 0.11
33 3 0.01
34 4 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:8146 original size:113 final size:112
Alignment explanation
Indices: 7752--8385 Score: 759
Period size: 113 Copynumber: 5.5 Consensus size: 112
7742 CGATCATCTC
*
7752 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGTACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* * * * *
7817 CATAAGCCAGTGGCATCCTTTCAAAGCCCACAAGTGAGTGGCAC-CCT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCAC-AGTCAGTGGCACTCTT
* *
7864 TTCAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACACGAGTCGGTGGCAACTCTTTTCA
1 TTCAAAGCCCACAAGTCAGTGGCACCC-TTTCAAAGCCCACA--AGTCAGTGGC-AC-CCTTTCA
* * *
7929 AAGCCCACAAGTTAGTGGCATCCTTTCAAAGCCCATGAGTCAGTGGCAACTCTT
61 AAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA-CAGTCAGTGGC-ACTCTT
* * * * * *
7983 TTCAAAGCCCACAAGTTAATGACATCCTTTCAAAGCTCACAAGTTAGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* *
8048 CGCAAGTCAGTGGCACCCTTTCAAAACCCACATGTCAGTGGCACTCTT
66 CACAAGTCAGTGGCACCCTTTCAAAGCCCACA-GTCAGTGGCACTCTT
* * *
8096 TTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCTGTGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* * * *
8161 CACAAGTCAGTGGCACTCTTTTCAAAGTCCACAAGTTAGTGGCA-TCCT
66 CACAAGTCAGTGGCAC-CCTTTCAAAGCCCAC-AGTCAGTGGCACTCTT
* * *
8209 TTCAAAGCCCAAAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAATGGCACCCTTTCAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
* *
8274 CACAAGTCAGTGGCACTCTTTTCAAAGCCCGCACGAGTCGGTGGCAACTCTT
66 CACAAGTCAGTGGCAC-CCTTTCAAAG-CC-CAC-AGTCAGTGGC-ACTCTT
* *
8326 TTCAAAGCCCACACGAGTCAGTGGTAACCCTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAAAGCCCACA--AGTCAGTGG-CACCC-TTTCAAAG-CC-CACAAGTCAGTGGCACC
8386 TTTTTTAAGA
Statistics
Matches: 451, Mismatches: 50, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
112 27 0.06
113 184 0.41
114 68 0.15
115 22 0.05
116 11 0.02
117 62 0.14
118 15 0.03
119 33 0.07
120 4 0.01
121 8 0.02
122 2 0.00
123 15 0.03
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.22
Consensus pattern (112 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCC
CACAAGTCAGTGGCACCCTTTCAAAGCCCACAGTCAGTGGCACTCTT
Found at i:9713 original size:51 final size:49
Alignment explanation
Indices: 9599--9734 Score: 177
Period size: 49 Copynumber: 2.8 Consensus size: 49
9589 ATTTTCCTGC
*
9599 ATGTATCGATACATTGAAGAATGTATCGATACATTTTCAAAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTTCAAAAACCCAGA
* * *
9648 ATGCATCGATACAATGAAGAATATATCGCTACATTTGGGTC-AAAACCCAGA
1 ATGTATCGATACAATGAAGAATGTATCGATACATTT---TCAAAAACCCAGA
* *
9699 ATGTATCAATACAATGAA-AATGTATCGATGCATTTT
1 ATGTATCGATACAATGAAGAATGTATCGATACATTTT
9735 TATTCCAAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
47 1 0.01
49 32 0.43
50 14 0.19
51 26 0.35
52 2 0.03
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (49 bp):
ATGTATCGATACAATGAAGAATGTATCGATACATTTTCAAAAACCCAGA
Found at i:11608 original size:17 final size:17
Alignment explanation
Indices: 11583--11617 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
11573 CTTAATTATT
*
11583 AAATTTTTTCTTATTAA
1 AAATGTTTTCTTATTAA
*
11600 AAATGTTTTTTTATTAA
1 AAATGTTTTCTTATTAA
11617 A
1 A
11618 TAAACTTGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
AAATGTTTTCTTATTAA
Found at i:18503 original size:12 final size:12
Alignment explanation
Indices: 18486--18513 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18476 GGAAGGCAAC
18486 AAAAAAAATCAA
1 AAAAAAAATCAA
18498 AAAAAAAATCAA
1 AAAAAAAATCAA
18510 AAAA
1 AAAA
18514 TCACATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.86, C:0.07, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAATCAA
Found at i:18609 original size:19 final size:21
Alignment explanation
Indices: 18566--18617 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
18556 TTCAATAATT
18566 TGTATCGATACAAACAGTAAA
1 TGTATCGATACAAACAGTAAA
*
18587 TGTATCGATACATA-AGT-AA
1 TGTATCGATACAAACAGTAAA
18606 TGTATCGATACA
1 TGTATCGATACA
18618 GTGTATCGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAAACAGTAAA
Found at i:19052 original size:19 final size:19
Alignment explanation
Indices: 19028--19095 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
19018 AATTCAACAA
19028 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
19047 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
19062 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
19079 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
19096 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:19067 original size:13 final size:13
Alignment explanation
Indices: 19049--19073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19039 ACATAAGTTT
19049 TGTATCGATACAA
1 TGTATCGATACAA
19062 TGTATCGATACA
1 TGTATCGATACA
19074 TAAGTATTGT
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:19071 original size:32 final size:32
Alignment explanation
Indices: 19030--19092 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
19020 TTCAACAATT
*
19030 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
19062 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
19093 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:19151 original size:33 final size:33
Alignment explanation
Indices: 19114--19180 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
19104 TGCCAAGGAA
***
19114 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
19147 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
19180 T
1 T
19181 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:19152 original size:13 final size:13
Alignment explanation
Indices: 19134--19159 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19124 CATTTTTCTG
19134 TGTATCGATACAT
1 TGTATCGATACAT
19147 TGTATCGATACAT
1 TGTATCGATACAT
19160 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21642 original size:27 final size:28
Alignment explanation
Indices: 21612--21683 Score: 101
Period size: 27 Copynumber: 2.6 Consensus size: 28
21602 TTTCTTCACA
21612 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
21639 ATCGAGGATACTCCAACCCCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
21667 CTAGGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
21684 TCCGATTTTA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.26, C:0.32, G:0.18, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:21830 original size:52 final size:51
Alignment explanation
Indices: 21504--21835 Score: 225
Period size: 52 Copynumber: 6.4 Consensus size: 51
21494 ATCAATCTTC
* * * * *
21504 CACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTCT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
* *
21555 -ATAATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTT-TT
* * * * * *
21608 CACAATCGGGGATACTCCAACCCCG--TTAATCATCGAGGATACTCCAACCCCGTTATTT
1 CACAATCGGGGATACTCCAACTCCGATTTTAT-TTCCA--AAACACCAA-----TT-TTT
* ** * *
21666 C-C--TAGGGGATACTCCAACTCCGATTTTATCGCTAAAACACTAATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
* * *
21714 CCACAATCGGGGATACT-CAA-TCCTGGTTTTATTTTCAAAACGCCAATTTCCTT
1 -CACAATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTT--TT
* *
21767 --TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
1 CACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATTTTT
*
21817 CACAATCGAGGATACTCCA
1 CACAATCGGGGATACTCCA
21836 CCTCGTTATT
Statistics
Matches: 215, Mismatches: 39, Indels: 53
0.70 0.13 0.17
Matches are distributed among these distances:
48 3 0.01
49 3 0.01
50 49 0.23
51 35 0.16
52 55 0.26
53 12 0.06
54 27 0.13
55 18 0.08
56 2 0.01
57 5 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (51 bp):
CACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTT
Found at i:21856 original size:27 final size:27
Alignment explanation
Indices: 21821--21896 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 27
21811 ATTTTTCACA
* * *
21821 ATCGAGGATACTCCACCTCGTTATTTC
1 ATCGGGGATACTCCACCCCGTTACTTC
21848 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCC-ACCCCGTTACTTC
***
21876 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCC-ACCCCG
21897 GCTTTATTCC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 13 0.31
28 29 0.69
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCACCCCGTTACTTC
Found at i:21887 original size:209 final size:211
Alignment explanation
Indices: 21501--21892 Score: 596
Period size: 209 Copynumber: 1.9 Consensus size: 211
21491 TTTATCAATC
* *
21501 TTCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTCTATAATCGGGGA
1 TTCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTATAATCGGGGA
* *
21566 TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCCAACCC
66 TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* *
21631 CGTTAATCATCGAGGATACTCCAACCCCGTTATTTCCTAGGGGATACTCCAACTCCGATTTTATC
131 CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACTCCGATTTTATC
21696 GCTAAAACACTAATTT
196 GCTAAAACACTAATTT
* * * *
21712 TTCCACAATCGGGGATACT-CAA-TCCTGGTTTTATTTTCAAAACGCCAATTTCCTTTAATCGGG
1 TTCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTT-CTATAATCGGG
*
21775 GATACTCCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATACTCC-AC
64 GATACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
21837 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAAC
129 CCCGTTA-ATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAAC
21893 CCCGGCTTTA
Statistics
Matches: 164, Mismatches: 14, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
208 8 0.05
209 66 0.40
210 38 0.23
211 52 0.32
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (211 bp):
TTCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTCTATAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGAGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACTCCGATTTTATC
GCTAAAACACTAATTT
Found at i:21903 original size:107 final size:104
Alignment explanation
Indices: 21561--21911 Score: 324
Period size: 107 Copynumber: 3.3 Consensus size: 104
21551 TTCTATAATC
*
21561 GGGGATACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGGGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATTTCC-AAAAACACCAATTT-TTCACAATCGGGGATACTCC
* *
21626 AACCCCGTTA-ATCATCGAGGATACTCCAACCCCGTTATTTCCTA
64 -ACCTCGTTATTTCATCG-GGATACTCCAACCCCGTTA-TTCC-A
* * *
21670 GGGGATACTCCAACTCCGATTTTA--TCGCTAAAACACTAATTTTTCCACAATCGGGGATACTCA
1 GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTTT-CACAATCGGGGATACTCC
* * * * ** * *
21733 ATCCTGGTTTTATTT--TC--AAAACGCCAATTTCCTTTAAT-C-
64 A-CCTCG--TTATTTCATCGGGATACTCCAA-CCCCGTTATTCCA
* *
21772 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACTCCAC
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAC
21837 CTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGA
66 CTCGTTATTTCATC-GGGATACTCCAACCCCGTTA-TTCC-A
* ** *
21879 GGGGATACTCCAACCCCGGCTTTATTCCCAAAA
1 GGGGATACTCCAACTCCGATTTTATTTCCAAAA
21912 TATTGATTTC
Statistics
Matches: 193, Mismatches: 31, Indels: 38
0.74 0.12 0.15
Matches are distributed among these distances:
99 6 0.03
101 6 0.03
102 41 0.21
103 19 0.10
104 11 0.06
105 9 0.05
106 8 0.04
107 63 0.33
108 3 0.02
109 26 0.13
110 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (104 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAC
CTCGTTATTTCATCGGGATACTCCAACCCCGTTATTCCA
Found at i:25401 original size:51 final size:51
Alignment explanation
Indices: 25346--25632 Score: 382
Period size: 51 Copynumber: 5.6 Consensus size: 51
25336 AAGTTTCTCC
* * * *
25346 ATTTTTCATAATCGGGGGTACTCCAACCCCGGTTTTA-TTTCTAAAACACTA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCA
* * * *
25397 ATTTTCCACAATCGGGGATACTTCAACTCCGATTTTATTTTCGAAACACCA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
* *
25448 ATTTTCCACAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
1 ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
* *
25499 A-TTTTCTATAATCGAGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
1 ATTTTTC-ACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
* * *
25550 A-TTTTCTATAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCA
1 ATTTTTC-ACAATCGGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCA
25602 ATTTTTCACAATCGGGGATACTCCAACCCCG
1 ATTTTTCACAATCGGGGATACTCCAACCCCG
25633 TTAATCATCG
Statistics
Matches: 213, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
50 4 0.02
51 168 0.79
52 36 0.17
53 5 0.02
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.32
Consensus pattern (51 bp):
ATTTTTCACAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCA
Found at i:25745 original size:79 final size:78
Alignment explanation
Indices: 25563--25788 Score: 195
Period size: 79 Copynumber: 2.9 Consensus size: 78
25553 TTCTATAATC
* * *
25563 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTA-TTCCAAAAACACCAATTTCTCACAATCAGGGATACTCCAA
* *
25628 CCCCGTTAATCATC
65 CCCCATTAATCATA
* ** * * *** *
25642 GGGGATACTCTAACCCCGGCTTTATTCCTAAAATATTGATTTCTCATAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGATTTTATTCCAAAAACACCAATTTCTCACAATCAGGGATACTCCAAC
* **
25707 CCCATTATTTTTAA
66 CCCATTAATCAT-A
* * * * *
25721 GGGGATACTCCATCCCCGATTTTATTTCC-AGAACACCGATTT-TCCATAATCAGGGGTACTCCA
1 GGGGATACTCCAACCCCGATTTTA-TTCCAAAAACACCAATTTCT-CACAATCAGGGATACTCCA
*
25784 GCCCC
64 ACCCC
25789 GTCGTCATCT
Statistics
Matches: 117, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
78 42 0.36
79 71 0.61
80 4 0.03
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (78 bp):
GGGGATACTCCAACCCCGATTTTATTCCAAAAACACCAATTTCTCACAATCAGGGATACTCCAAC
CCCATTAATCATA
Found at i:27868 original size:4 final size:4
Alignment explanation
Indices: 27861--27893 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
27851 TATTTTGAGG
*
27861 TATT TATT TATT TATT TATT AATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
27894 TGTTTTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Done.