Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2020
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: 47854
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Found at i:2083 original size:26 final size:25
Alignment explanation
Indices: 2054--2206 Score: 146
Period size: 26 Copynumber: 5.8 Consensus size: 25
2044 AAATTGTACA
2054 GCACTAAGTGTGCGATTCGACTATGT
1 GCACTAAGTGTGCGATT-GACTATGT
* *
2080 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCG-ATTGACTATG-T
* *
2107 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCG-ATTGACTATG-T
*
2134 GCACTAAGTGTGCGAGTCTAACTATGT
1 GCACTAAGTGTGCGA-T-TGACTATGT
* *
2161 AGCACTAAGTGTGCGATTGATTACGT
1 -GCACTAAGTGTGCGATTGACTATGT
2187 GGCACTAAGTG-GCGAGTTGA
1 -GCACTAAGTGTGCGA-TTGA
2207 TTGATTTTAG
Statistics
Matches: 107, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
25 4 0.04
26 41 0.38
27 41 0.38
28 21 0.20
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (25 bp):
GCACTAAGTGTGCGATTGACTATGT
Found at i:2117 original size:27 final size:26
Alignment explanation
Indices: 2054--2206 Score: 150
Period size: 27 Copynumber: 5.8 Consensus size: 26
2044 AAATTGTACA
2054 GCACTAAGTGTGCG-ATTCGACTATGT
1 GCACTAAGTGTGCGAATT-GACTATGT
* *
2080 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAATTGACTATG-T
* *
2107 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAATTGACTATG-T
* *
2134 GCACTAAGTGTGCGAGTCTAACTATGT
1 GCACTAAGTGTGCGAAT-TGACTATGT
* *
2161 AGCACTAAGTGTGCG-ATTGATTACGT
1 -GCACTAAGTGTGCGAATTGACTATGT
*
2187 GGCACTAAGTG-GCGAGTTGA
1 -GCACTAAGTGTGCGAATTGA
2207 TTGATTTTAG
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
25 3 0.03
26 40 0.38
27 42 0.40
28 20 0.19
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (26 bp):
GCACTAAGTGTGCGAATTGACTATGT
Found at i:2218 original size:54 final size:54
Alignment explanation
Indices: 2053--2229 Score: 175
Period size: 54 Copynumber: 3.3 Consensus size: 54
2043 TAAATTGTAC
** *
2053 AGCACTAAGTGTGCGATTCGACTATGT-GCACTAAGTGTGCGAAATGAATATGAT
1 AGCACTAAGTGTGCGATT-GACTATGTGGCACTAAGTGTGCGAGTTGAATATTAT
* * *
2107 -GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTCT-AACTA-TGT
1 AGCACTAAGTGTGCG-ATTGACTATGTGGCACTAAGTGTGCGAGT-TGAA-TATTAT
* * * *
2161 AGCACTAAGTGTGCGATTGATTACGTGGCACTAAGTG-GCGAGTTGATTGATTTT
1 AGCACTAAGTGTGCGATTGACTATGTGGCACTAAGTGTGCGAGTTGAAT-ATTAT
*
2215 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
2230 GGCTCAATAT
Statistics
Matches: 102, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
52 2 0.02
53 28 0.27
54 55 0.54
55 17 0.17
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.28
Consensus pattern (54 bp):
AGCACTAAGTGTGCGATTGACTATGTGGCACTAAGTGTGCGAGTTGAATATTAT
Found at i:4700 original size:108 final size:104
Alignment explanation
Indices: 4555--4838 Score: 337
Period size: 108 Copynumber: 2.6 Consensus size: 104
4545 AAAGTTGCCG
*
4555 AATACCCTTGTAAGCGTAGAATTACCGACAATACCCCTGTTAGGG-AGATTATCGAAATACCCTG
1 AATACCC-TGT-AG-GTAGAATTACC-AAAATACCCCTG-TAGGGTAGATTATCGAAATACCCTG
4619 TAGGGTAAAATTACTGAAATACCCCAGGTAG-GGTAGAAGTACCG-A
61 TAGGGTAAAATTACTGAAATACCCCA-GTAGAGGTAG-A-TACCGAA
4664 AATACCCCCTGTAGGTAGAATTTACCAAAATACCCCTGTAGGGTAG-TTATTCGAAATACCCTGT
1 AATA--CCCTGTAGGTAGAA-TTACCAAAATACCCCTGTAGGGTAGATTA-TCGAAATACCCTGT
* **
4728 AGGGTAGAATTACTGAAATACCCCAGTAGACGGTAGATATTGAA
62 AGGGTAAAATTACTGAAATACCCCAGTAGA-GGTAGATACCGAA
* *
4772 AATACCCTGTAGGTAGAATTACC-GAATA-CCCTGTAGGGTAGAATTACCGAAATACCCCTGTAG
1 AATACCCTGTAGGTAGAATTACCAAAATACCCCTGTAGGGTAG-ATTATCGAAATA-CCCTGTAG
4835 GGTA
64 GGTA
4839 GAATGACCCG
Statistics
Matches: 158, Mismatches: 6, Indels: 26
0.83 0.03 0.14
Matches are distributed among these distances:
103 13 0.08
104 11 0.07
105 20 0.13
106 14 0.09
107 15 0.09
108 63 0.40
109 16 0.10
110 3 0.02
111 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (104 bp):
AATACCCTGTAGGTAGAATTACCAAAATACCCCTGTAGGGTAGATTATCGAAATACCCTGTAGGG
TAAAATTACTGAAATACCCCAGTAGAGGTAGATACCGAA
Found at i:4852 original size:27 final size:27
Alignment explanation
Indices: 4555--4842 Score: 280
Period size: 27 Copynumber: 10.8 Consensus size: 27
4545 AAAGTTGCCG
* *
4555 AATACCCTTGTAAGCGTAGAATTACCGA
1 AATACCCCTGT-AGGGTAGAATTACCGA
*
4583 CAATACCCCTGTTAGGG-AG-ATTATCGA
1 -AATACCCCTG-TAGGGTAGAATTACCGA
* *
4610 AATA-CCCTGTAGGGTAAAATTACTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
* *
4636 AATACCCCAGGTAGGGTAGAAGTACCGA
1 AATACCCC-TGTAGGGTAGAATTACCGA
*
4664 AATACCCCCTGTA-GGTAGAATTTACCAA
1 AATA-CCCCTGTAGGGTAGAA-TTACCGA
*
4692 AATACCCCTGTAGGGTAG--TTATTCGA
1 AATACCCCTGTAGGGTAGAATTA-CCGA
*
4718 AATA-CCCTGTAGGGTAGAATTACTGA
1 AATACCCCTGTAGGGTAGAATTACCGA
*
4744 AATACCCCAGTAGACGGTAGATATT---GAA
1 AATACCCCTGTAG--GGTAGA-ATTACCG-A
4772 AATA-CCCTGTA-GGTAGAATTACCG-
1 AATACCCCTGTAGGGTAGAATTACCGA
4796 AATA-CCCTGTAGGGTAGAATTACCGA
1 AATACCCCTGTAGGGTAGAATTACCGA
4822 AATACCCCTGTAGGGTAGAAT
1 AATACCCCTGTAGGGTAGAAT
4843 GACCCGAATA
Statistics
Matches: 218, Mismatches: 19, Indels: 46
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.01
24 22 0.10
25 35 0.16
26 31 0.14
27 58 0.27
28 43 0.20
29 22 0.10
30 4 0.02
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAGAATTACCGA
Found at i:10576 original size:27 final size:27
Alignment explanation
Indices: 10546--10723 Score: 115
Period size: 27 Copynumber: 6.6 Consensus size: 27
10536 ATATTGAGCC
* * *
10546 CGCACACTCAGTGCTATACAATCAACT
1 CGCACACTTAGTGCTACACAATCAAAT
* **
10573 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACACAATCAAAT
* * * *
10600 CGCACACTTAGTGCTACATAGTTAGACT
1 CGCACACTTAGTGCTACACAATCA-AAT
** *** *
10628 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACACAATCAAAT
* * **
10655 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CACAATCAAAT
* * * *
10682 CGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTACACAATCAAAT
10709 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10724 GTACAATTTA
Statistics
Matches: 123, Mismatches: 25, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
27 100 0.81
28 23 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACACAATCAAAT
Found at i:10639 original size:55 final size:55
Alignment explanation
Indices: 10546--10723 Score: 204
Period size: 54 Copynumber: 3.3 Consensus size: 55
10536 ATATTGAGCC
* * *
10546 CGCACACTCAGTGCTATACA-A-TCAACTCGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTAT-CATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
* * *
10600 CGCACACTTAGTGCTA-CATAGTT-AGACTCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTATCATA-TTCA-ACTCGCACACTTAGTGCCACATAGTCAAAT
** * *
10655 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAAT
1 CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
10709 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
10724 GTACAATTTA
Statistics
Matches: 104, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
52 2 0.02
53 1 0.01
54 56 0.54
55 45 0.43
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (55 bp):
CGCACACTTAGTGCTATCATATTCAACTCGCACACTTAGTGCCACATAGTCAAAT
Found at i:10685 original size:82 final size:81
Alignment explanation
Indices: 10567--10722 Score: 215
Period size: 82 Copynumber: 1.9 Consensus size: 81
10557 TGCTATACAA
* * *
10567 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTTAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAG-TAGAATCGCA
10632 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
10649 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCA
10713 CACTTAGTGC
65 CACTTAGTGC
10723 TGTACAATTT
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
81 20 0.31
82 45 0.69
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTAGAATCGCAC
ACTTAGTGCCGCATGG
Found at i:13357 original size:6 final size:6
Alignment explanation
Indices: 13345--13438 Score: 66
Period size: 6 Copynumber: 15.3 Consensus size: 6
13335 AAGAAACATT
* * * *
13345 ATCAGA ATTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
13394 ATTAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATTAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
13439 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
5 3 0.04
6 56 0.84
7 6 0.09
8 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:13404 original size:31 final size:31
Alignment explanation
Indices: 13366--13426 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
13356 AATCAAAATG
*
13366 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
*
13397 AGAATCAGAATCAGTATCAGGTAACAGAAT
1 AGAATCAGAATCAGAATCAGGTAACAGAAT
13427 CAAAATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATT
Found at i:13438 original size:31 final size:31
Alignment explanation
Indices: 13368--13438 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
13358 TCAAAATGAG
* * *
13368 AATCAGAATCAGAATCAGGTGACAGAATTAG
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
*
13399 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
*
13430 AATTAGAAT
1 AATCAGAAT
13439 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTAACAGAATCAA
Found at i:13603 original size:27 final size:27
Alignment explanation
Indices: 13573--13629 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
13563 ATGACGAAGT
** *
13573 CACCAGATAT-AGATATTGTGGCAGAGC
1 CACCAGA-ATCAGATAACGTGGCAAAGC
13600 CACCAGAATCAGATAACGTGGCAAAGC
1 CACCAGAATCAGATAACGTGGCAAAGC
13627 CAC
1 CAC
13630 TTAACAGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 2 0.08
27 24 0.92
ACGTcount: A:0.37, C:0.25, G:0.23, T:0.16
Consensus pattern (27 bp):
CACCAGAATCAGATAACGTGGCAAAGC
Found at i:14009 original size:26 final size:27
Alignment explanation
Indices: 13933--14042 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
13923 TCGATCAGTC
* * *
13933 AACAGATA-TTGTGACAGAGTCACCAG
1 AACAGATATTTGTGGCATAGCCACCAG
*
13959 ATACAGATA-TTGTGGCAGAGCCACCAG
1 A-ACAGATATTTGTGGCATAGCCACCAG
*
13986 AACAGATATTTGTGGCATA-ACACCAG
1 AACAGATATTTGTGGCATAGCCACCAG
*
14012 AAACAGATATTTGTGACATAGCCACCAG
1 -AACAGATATTTGTGGCATAGCCACCAG
14040 AAC
1 AAC
14043 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 14 0.19
27 54 0.73
28 6 0.08
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (27 bp):
AACAGATATTTGTGGCATAGCCACCAG
Found at i:14326 original size:27 final size:27
Alignment explanation
Indices: 14266--16529 Score: 3236
Period size: 27 Copynumber: 84.2 Consensus size: 27
14256 GGGGCAAAAT
* * *
14266 GGTAATTTTACCCCACAAGGGTATCTT-
1 GGTAATTCTACCCTACAGGGGTAT-TTC
* *
14293 GGCAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
14320 AGTAATTCTACCATACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
14347 AGTAA-TCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
14373 AGTAATTCTATCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
14400 GGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
14427 -GTAATTATACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * * *
14453 GGTAATTCTACTATATAGGGGTTTTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
14480 AGAAATTCTACCGTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14507 AGTAATTCTACCCTA-ATGGGGTATTTC
1 GGTAATTCTACCCTACA-GGGGTATTTC
* * *
14534 GGTAATTCTACCATATA-GGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14560 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
14587 GGTAATTCTACCCTACAGGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14613 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
14640 GATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
14667 GGTAATTCTACCCTACATGGGT-TTAC
1 GGTAATTCTACCCTACAGGGGTATTTC
14693 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14720 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14747 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14774 TGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
14801 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
14828 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14855 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
14882 GGTAATTCTACCATATAGGGTTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14909 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
14936 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
14963 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
14990 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
15017 GGTAATTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
15044 GGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
15071 AGTAATTCTACCGTACAGGGGTATTTA
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15098 GGTGATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15125 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
15152 GGTATTTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15179 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15206 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15233 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
15260 GGTAATTCTACCCTACAAAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15287 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
15314 GGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
15341 AGTAATTCTACCATACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
15368 AGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15395 GGTAATTCTACCCTACTGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
15422 AGTAATTCTACCTTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15448 GGTAA-TCTACCCTACAGGGTTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15474 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
15501 GGTAATTCTACCCTACATGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATTTC
15528 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
15555 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15582 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
15609 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
15636 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15663 GCTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
15690 GGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15717 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15744 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
15771 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
15798 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
15825 GATAATTTTACCCTACATGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATTTC
15852 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
15879 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15906 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
15933 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
15960 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
15987 GCTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
16014 GGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16041 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16068 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16095 GGTAATTCTACCCTACAGGGATATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
16122 GAAAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
16149 GGTAATTTTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
16176 GGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* ** *
16203 AGTAATTCTACTGTACAGGGGTATTTA
1 GGTAATTCTACCCTACAGGGGTATTTC
16230 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16257 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * ** *
16284 GGTATTTCTACCATTTAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16311 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16338 GGTAATTCTACCCTACAGTGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16365 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16392 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16419 GGTAATTCTACCCTACTGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16446 AGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16472 GGTAA-TCTACCCTACAGGGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
16498 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
16525 GGTAA
1 GGTAA
16530 ATTTCCTGAT
Statistics
Matches: 1995, Mismatches: 230, Indels: 24
0.89 0.10 0.01
Matches are distributed among these distances:
25 21 0.01
26 173 0.09
27 1800 0.90
28 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:18567 original size:6 final size:6
Alignment explanation
Indices: 18555--18648 Score: 66
Period size: 6 Copynumber: 15.3 Consensus size: 6
18545 AAGAAACATT
* * * *
18555 ATCAGA ATTAGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * * *
18604 ATTAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATTAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
18649 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
5 3 0.04
6 56 0.84
7 6 0.09
8 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.18, T:0.21
Consensus pattern (6 bp):
ATCAGA
Found at i:18614 original size:31 final size:31
Alignment explanation
Indices: 18576--18636 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
18566 AATCAAAATG
*
18576 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
*
18607 AGAATCAGAATCAGTATCAGGTAACAGAAT
1 AGAATCAGAATCAGAATCAGGTAACAGAAT
18637 CAAAATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATT
Found at i:18648 original size:31 final size:31
Alignment explanation
Indices: 18578--18648 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
18568 TCAAAATGAG
* * *
18578 AATCAGAATCAGAATCAGGTGACAGAATTAG
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
*
18609 AATCAGAATCAGTATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
*
18640 AATTAGAAT
1 AATCAGAAT
18649 GTGAATGCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTAACAGAATCAA
Found at i:19220 original size:26 final size:27
Alignment explanation
Indices: 19144--19253 Score: 127
Period size: 27 Copynumber: 4.1 Consensus size: 27
19134 TCGATCAGTC
* * *
19144 AACAGATA-TTGTGACAGAGTCACCAG
1 AACAGATATTTGTGGCATAGCCACCAG
*
19170 ATACAGATA-TTGTGGCAGAGCCACCAG
1 A-ACAGATATTTGTGGCATAGCCACCAG
*
19197 AACAGATATTTGTGGCATA-ACACCAG
1 AACAGATATTTGTGGCATAGCCACCAG
*
19223 AAACAGATATTTGTGACATAGCCACCAG
1 -AACAGATATTTGTGGCATAGCCACCAG
19251 AAC
1 AAC
19254 GCTTCCTCCA
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 14 0.19
27 54 0.73
28 6 0.08
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (27 bp):
AACAGATATTTGTGGCATAGCCACCAG
Found at i:19526 original size:27 final size:27
Alignment explanation
Indices: 19477--20503 Score: 1425
Period size: 27 Copynumber: 38.2 Consensus size: 27
19467 GGGGCAAAAT
* * **
19477 GGTAATTTTACCCCACAAAGGTATCTT-
1 GGTAATTCTACCCTACAGGGGTAT-TTC
*
19504 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19531 AGTAATTCTGCCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
19558 AGTAATTCTACCCTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19585 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
19612 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19639 -GTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
** * *
19665 GGTAATTCTACTATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * * *
19692 AGAAATTCTACCTTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19719 AGTAACTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
19746 GGTAATTCTACCCTACAGGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19772 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19799 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19826 GGTAATTCTACCCTACATGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATTTC
19853 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
19880 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
19907 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
19934 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
19961 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
19988 GGTAATTCTCCCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
20015 CGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
20042 AGTAATTCTATCGTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20069 GGTAATTCAACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
20096 CGTAATTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* * ** *
20123 GGTAATTCTACCATATAGCAGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20150 AGTAATTCTACCCTACAGGGGTATTTA
1 GGTAATTCTACCCTACAGGGGTATTTC
20177 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20204 GGTAATTCTACCCTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20231 GGTAATTCTACCCTACAAGGGTATGTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
20258 GGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20285 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20312 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20339 GGTAATTCTACCATATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20366 GGTAATTTTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
20393 GGTAATTCTACCATACTGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20420 AGTAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20446 GGTAA-TCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
20472 GGTAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
20499 GGTAA
1 GGTAA
20504 CTTTCCTGAT
Statistics
Matches: 892, Mismatches: 103, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
25 11 0.01
26 80 0.09
27 801 0.90
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:22448 original size:40 final size:40
Alignment explanation
Indices: 22404--22629 Score: 289
Period size: 40 Copynumber: 5.7 Consensus size: 40
22394 GCTACTCATT
*
22404 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
22444 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
22484 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
22524 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * * * *
22564 CAAATGCCTTC-GGATCTTAGTCCGAATATGGTCACCTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AACTCGCA
22605 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
22630 CATCATTCAA
Statistics
Matches: 169, Mismatches: 13, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
39 3 0.02
40 152 0.90
41 14 0.08
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:24809 original size:6 final size:6
Alignment explanation
Indices: 24779--24872 Score: 68
Period size: 6 Copynumber: 15.3 Consensus size: 6
24769 AAGAAACATT
* * *
24779 ATCAGAA AT-AGA ATCAAA ATGAGA ATCAGA ATCAGA ATCAG- GTGACAGA
1 ATCAG-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* * *
24828 ATTAGA ATCAGA ATCAGA ATCAGGTA A-CAGA ATCAAA ATTAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
24873 GTGAATGCAA
Statistics
Matches: 69, Mismatches: 11, Indels: 15
0.73 0.12 0.16
Matches are distributed among these distances:
5 6 0.09
6 52 0.75
7 8 0.12
8 3 0.04
ACGTcount: A:0.51, C:0.12, G:0.18, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:24837 original size:31 final size:31
Alignment explanation
Indices: 24800--24860 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
24790 AATCAAAATG
*
24800 AGAATCAGAATCAGAATCAGGTGACAGAATT
1 AGAATCAGAATCAGAATCAGGTAACAGAATT
24831 AGAATCAGAATCAGAATCAGGTAACAGAAT
1 AGAATCAGAATCAGAATCAGGTAACAGAAT
24861 CAAAATTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.13, G:0.21, T:0.18
Consensus pattern (31 bp):
AGAATCAGAATCAGAATCAGGTAACAGAATT
Found at i:24872 original size:31 final size:31
Alignment explanation
Indices: 24802--24872 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
24792 TCAAAATGAG
* * *
24802 AATCAGAATCAGAATCAGGTGACAGAATTAG
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
24833 AATCAGAATCAGAATCAGGTAACAGAATCAA
1 AATCAGAATCAGAATCAGGTAACAGAATCAA
*
24864 AATTAGAAT
1 AATCAGAAT
24873 GTGAATGCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (31 bp):
AATCAGAATCAGAATCAGGTAACAGAATCAA
Found at i:25037 original size:27 final size:27
Alignment explanation
Indices: 25007--25062 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
24997 GTGACGAAGT
* *
25007 CACCAG-ATACAGATATTGTGGCAGAGC
1 CACCAGAAT-CAGATAATGTGGCAAAGC
25034 CACCAGAATCAGATAATGTGGCAAAGC
1 CACCAGAATCAGATAATGTGGCAAAGC
25061 CA
1 CA
25063 GTTAACAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 24 0.92
28 2 0.08
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CACCAGAATCAGATAATGTGGCAAAGC
Found at i:25411 original size:27 final size:26
Alignment explanation
Indices: 25370--25456 Score: 104
Period size: 27 Copynumber: 3.3 Consensus size: 26
25360 ATCAGTCAAT
* *
25370 AGATATTGTGACAGAGTCACCAGATAC
1 AGATATTGTGGCAGAGACACCAGA-AC
*
25397 AGATATTGTGGCAGAGCCACCAGAAC
1 AGATATTGTGGCAGAGACACCAGAAC
*
25423 AGATATTTGTGGCATA-ACACCAGAAAC
1 AGATA-TTGTGGCAGAGACACCAG-AAC
25450 AGATATT
1 AGATATT
25457 TATGACATGG
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
26 15 0.28
27 39 0.72
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (26 bp):
AGATATTGTGGCAGAGACACCAGAAC
Found at i:25721 original size:27 final size:27
Alignment explanation
Indices: 25691--25749 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
25681 AACACCCTAG
*
25691 GGGTAAAATGGTAATTTTACCCCACAA
1 GGGTAAAATGGTAATTCTACCCCACAA
*** * *
25718 GGGTATCTTGGTAATTCTACCCTACAG
1 GGGTAAAATGGTAATTCTACCCCACAA
25745 GGGTA
1 GGGTA
25750 TTTTAATAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (27 bp):
GGGTAAAATGGTAATTCTACCCCACAA
Found at i:26269 original size:27 final size:27
Alignment explanation
Indices: 25700--26262 Score: 808
Period size: 27 Copynumber: 20.9 Consensus size: 27
25690 GGGGTAAAAT
* * *
25700 GGTAATTTTACCCCACAAGGGTATCTT-
1 GGTAATTCTACCCTACAGGGGTAT-TTC
*
25727 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
** *
25754 AATAATTCTACCTTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
25781 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
25808 AGTAATTTTACCCTACATGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
25835 GGTAATTCTACCCTACAGGGGTACTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
25862 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
25889 GATAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
25916 AGTAATTCTACCGTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
25943 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
25970 GGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
25997 AGTAATTCTACCATATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
26024 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
26051 GGTAATGCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
26078 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
26105 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
26132 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * *
26159 GATAATTTTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
26186 GGTAATTCTA-CCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
26212 AGTAATTCTACCTTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
26238 GGTAATTCTACCCTACAGGGGTATT
1 GGTAATTCTACCCTACAGGGGTATT
26263 ACAGTAACTT
Statistics
Matches: 480, Mismatches: 53, Indels: 6
0.89 0.10 0.01
Matches are distributed among these distances:
26 50 0.10
27 430 0.90
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:30317 original size:6 final size:6
Alignment explanation
Indices: 30306--30335 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30296 CTTCAAAAAT
*
30306 AAATAA AAATAA AAGTAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA
30336 TATGAGTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:37819 original size:29 final size:29
Alignment explanation
Indices: 37755--37838 Score: 98
Period size: 29 Copynumber: 2.9 Consensus size: 29
37745 CATGCATATG
* ** **
37755 GCCCACTAGGCCC-AATCTTATTCATATG
1 GCCCATTAGGCCCAAATCACATTCATACA
37783 GCCCATTAGGCCCAAATCACATTCATACA
1 GCCCATTAGGCCCAAATCACATTCATACA
* *
37812 GCCTATTAGGCCTAAATCACATTCATA
1 GCCCATTAGGCCCAAATCACATTCATA
37839 TACATGCTCT
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 12 0.25
29 36 0.75
ACGTcount: A:0.31, C:0.31, G:0.12, T:0.26
Consensus pattern (29 bp):
GCCCATTAGGCCCAAATCACATTCATACA
Found at i:43227 original size:40 final size:40
Alignment explanation
Indices: 43043--43227 Score: 207
Period size: 40 Copynumber: 4.7 Consensus size: 40
43033 GCTCCTCGTT
* *
43043 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * ** *
43083 CAAATGCCTTCGAGACTTAACCCATATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
43123 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
43162 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
43203 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
43228 CATCATTCAA
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 30 0.25
40 76 0.63
41 12 0.10
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Done.