Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2168
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: 21249
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Found at i:1876 original size:26 final size:26
Alignment explanation
Indices: 1840--1892 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
1830 GAAATGTGAA
*
1840 AGGGGTTGCTATGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
1866 AGGGGTTGCTAAGTGCTGATTCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCG
1892 A
1 A
1893 TTCATTGGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.15, C:0.23, G:0.34, T:0.28
Consensus pattern (26 bp):
AGGGGTTGCTAAGTGCTGATTCCCCG
Found at i:2062 original size:103 final size:103
Alignment explanation
Indices: 1764--2131 Score: 625
Period size: 103 Copynumber: 3.6 Consensus size: 103
1754 TTGTATATAA
** *
1764 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
1829 TGAAATGTGAAAGGGGTTGCTATGTGCTGATT-CCCCG
66 TGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
1866 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCT-AGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
1930 TGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTG-AAA-GGGGTTGCTATGTGCTGATTCCCCCG
*
1970 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCG-TGATCCACCATATCT
2034 TTGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
** *
2073 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCA
2132 ATAACGGTTA
Statistics
Matches: 252, Mismatches: 8, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
101 30 0.12
102 43 0.17
103 100 0.40
104 49 0.19
105 29 0.12
106 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.30, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGTGATCCACCATATCTT
TGAAATGTGAAAGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:2088 original size:27 final size:27
Alignment explanation
Indices: 2046--2097 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
2036 GAAATGTGAA
*
2046 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
2073 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
2098 GATTCAGCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:5855 original size:44 final size:42
Alignment explanation
Indices: 5807--5914 Score: 121
Period size: 41 Copynumber: 2.5 Consensus size: 42
5797 AGTCTACTCC
*
5807 ACTGCAACTTCAGGGAGATAAGACTTGTAACTTTAA-CTTGCTCT
1 ACTGCAACTTCAGGGAGATAAGACTT-TAA-TATAATC-TGCTCT
* * * *
5851 ACTGCAACTTAAGGGAGATAAG-GTTTGATATGATCTGCTCT
1 ACTGCAACTTCAGGGAGATAAGACTTTAATATAATCTGCTCT
*
5892 ACTGCAACTTCAGAGAGATAAGA
1 ACTGCAACTTCAGGGAGATAAGA
5915 TCTACAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
41 29 0.53
42 3 0.05
43 2 0.04
44 21 0.38
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (42 bp):
ACTGCAACTTCAGGGAGATAAGACTTTAATATAATCTGCTCT
Found at i:6037 original size:44 final size:45
Alignment explanation
Indices: 5803--6054 Score: 140
Period size: 44 Copynumber: 5.6 Consensus size: 45
5793 TTTTAGTCTA
* * *
5803 CTCCACTGCAACTTCAGGGAGATAAGACTTG-TAACTTTAA-CTTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATC-TG
* * ** * * *
5847 CTCTACTGCAACTTAAGGGAGATAAGGTTTGATA---T-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
* * ** *
5888 CTCTACTGCAACTTCAGAGAGATAAGATCTACAATTTATAGCTTCAATCTA
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-C----GCTAGCTTCAATCTG
* * * * * *
5939 TTCAACTGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
* * * * *
5984 CTTCGCTGCAACTTCAGGGAGATAAGGCT-GGTGGCTTCAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
* *
6028 CTCCACTGCAACTTTAGAGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
6055 TCTGCCATAA
Statistics
Matches: 157, Mismatches: 39, Indels: 24
0.71 0.18 0.11
Matches are distributed among these distances:
41 27 0.17
42 3 0.02
44 60 0.38
45 34 0.22
47 3 0.02
49 1 0.01
50 2 0.01
51 27 0.17
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTCGCTAGCTTCAATCTG
Found at i:6274 original size:142 final size:143
Alignment explanation
Indices: 5883--6294 Score: 507
Period size: 142 Copynumber: 2.9 Consensus size: 143
5873 GTTTGATATG
* * * * * *
5883 ATCTGCTCTACTGCAACTTCAGAGAGATAAGATCT---ACAATTTATAGCTTCAATCTATTCAAC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
** * * * * *
5945 TGCAACTTCAGGGAAATAAGATTCGCTATCTTCAGTCTGCTTCGCTGCAACTTCAGGGAGATAAG
66 TGCAACGCCAAGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAG
6010 GCTGGTGGCTTCA
131 GCTGGTGGCTTCA
* *
6023 ATCTGCTCCACTGCAACTTTAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
* * * * * *
6088 TGCTACGCC-AGAGAAATAAGATTTGTTGTATTCAGTTTGTTCCACTGCAACTTCAAGGAGATAA
66 TGCAACGCCAAG-GAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAA
6152 GGCTGGT-GCTTCA
130 GGCTGGTGGCTTCA
*
6165 ATCTGCTCCACTGCAACTTCA-AGAAGATAAGATCTGCCATAATTTGTAGTTTTAATCTGTTCCA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCA
* * *
6229 CTGCAACGCCAAGGAAATAAGGTTTGACT-TCTTCAATCTACTCCACTGCAACTTC-AGGAAGAT
65 CTGCAACGCCAAGGAAATAAGATTTG-CTATCTTCAGTCTGCTCCACTGCAACTTCAAGG-AGAT
6292 AAG
128 AAG
6295 ATTCGCCATA
Statistics
Matches: 232, Mismatches: 32, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
140 33 0.14
141 5 0.02
142 114 0.49
143 80 0.34
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (143 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGTTCCAC
TGCAACGCCAAGGAAATAAGATTTGCTATCTTCAGTCTGCTCCACTGCAACTTCAAGGAGATAAG
GCTGGTGGCTTCA
Found at i:6294 original size:99 final size:98
Alignment explanation
Indices: 6125--6393 Score: 317
Period size: 99 Copynumber: 2.7 Consensus size: 98
6115 GTATTCAGTT
** * * * * *
6125 TGTTCCACTGCAACTTCAAGGAGATAAGG-CTGGTGCTTCAATCTGCTCCACTGCAACTTCAAGA
1 TGTTCCACTGCAACGCCAAGGAAATAAGGTTTGCTTCTTCAATCTGCTCCACTGCAACTTCAGGA
*
6189 AGATAAGA-TCTGCCATAATTTGTAGTTTTAATC
66 AGATAAGATTC-GCCATAATTTGTAGCTTTAATC
*
6222 TGTTCCACTGCAACGCCAAGGAAATAAGGTTTGACTTCTTCAATCTACTCCACTGCAACTTCAGG
1 TGTTCCACTGCAACGCCAAGGAAATAAGGTTTG-CTTCTTCAATCTGCTCCACTGCAACTTCAGG
6287 AAGATAAGATTCGCCATAATTTGTAGCTTTAATC
65 AAGATAAGATTCGCCATAATTTGTAGCTTTAATC
* * * * * * * * * *
6321 TATTCCACTGTAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTCAGG
1 TGTTCCACTGCAACGCCAAGGAAATAAGGTTTGCT-TCTTCAATCTGCTCCACTGCAACTTCAGG
*
6386 GAGATAAG
65 AAGATAAG
6394 GTTGGTGACT
Statistics
Matches: 147, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
97 26 0.18
98 4 0.03
99 115 0.78
100 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (98 bp):
TGTTCCACTGCAACGCCAAGGAAATAAGGTTTGCTTCTTCAATCTGCTCCACTGCAACTTCAGGA
AGATAAGATTCGCCATAATTTGTAGCTTTAATC
Found at i:6313 original size:241 final size:242
Alignment explanation
Indices: 6018--6491 Score: 670
Period size: 241 Copynumber: 2.0 Consensus size: 242
6008 AGGCTGGTGG
* * *
6018 CTTCAATCTGCTCCACTGCAACTTTAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTGT
1 CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTAT
* * * *
6083 TCCATTGCT-ACGCCAGAGAAATAAGATTTGTTGTATTCAGTTTG-TTCCACTGCAACTTCAAGG
66 TCCACTG-TAACGCCAGAGAAATAAGATTCGCTGTATTCAGTCTGCTT-CACTGCAACTTCAAGG
**
6146 AGATAAGGCTGGTG-CTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCTGCCATAATTT
129 AGATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTT
* * *
6210 GTAGTTTTAATCTGTTCCACTGCAACGCCAAGGAAATAAGGTTTGACTT
194 GTAGCTTTAATCTATTCCACTACAACGCCAAGGAAATAAGGTTTGACTT
6259 CTTCAATCTACTCCACTGCAACTTCAG-GAAGATAAGAT-TCGCCATAATTTGTAGCTTTAATCT
1 CTTCAATCTACTCCACTGCAACTTCAGAG-AGATAAGATCT-GCCATAATTTGTAGCTTTAATCT
* * * * * *
6322 ATTCCACTGTAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTCAGGG
64 ATTCCACTGTAACGCCAGAGAAATAAGATTCGCTGTATTCAGTCTGCTTCACTGCAACTTCAAGG
*
6387 AGATAAGGTTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTT
129 AGATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTT
* * * *
6452 TTAGCTTTAATCTATTCTACTACAACGCTAGGGAAATAAG
194 GTAGCTTTAATCTATTCCACTACAACGCCAAGGAAATAAG
6492 ATTAGTTGTC
Statistics
Matches: 205, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
240 3 0.01
241 119 0.58
242 83 0.40
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (242 bp):
CTTCAATCTACTCCACTGCAACTTCAGAGAGATAAGATCTGCCATAATTTGTAGCTTTAATCTAT
TCCACTGTAACGCCAGAGAAATAAGATTCGCTGTATTCAGTCTGCTTCACTGCAACTTCAAGGAG
ATAAGGCTGGTGACTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTGT
AGCTTTAATCTATTCCACTACAACGCCAAGGAAATAAGGTTTGACTT
Found at i:6393 original size:45 final size:44
Alignment explanation
Indices: 6338--6439 Score: 105
Period size: 44 Copynumber: 2.3 Consensus size: 44
6328 CTGTAACGCT
* * * * * *
6338 AGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTC
1 AGGGAGATAAGATT-GCTGACTTCAATCTGCTCCACTGCAACTTC
* *
6383 AGGGAGATAAGGTTGGTGACTTCAATCTGCTCCACTGCAACTTC
1 AGGGAGATAAGATTGCTGACTTCAATCTGCTCCACTGCAACTTC
* *
6427 AAGAAGATAAGAT
1 AGGGAGATAAGAT
6440 CCACCATAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
44 34 0.74
45 12 0.26
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATTGCTGACTTCAATCTGCTCCACTGCAACTTC
Found at i:6425 original size:143 final size:143
Alignment explanation
Indices: 6259--6759 Score: 620
Period size: 143 Copynumber: 3.5 Consensus size: 143
6249 GGTTTGACTT
*
6259 CTTCAATCTACTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTAT
** * *
6324 TCCACTGTAACGCTAGGGAAATAAGATTCGCTGTCTTCAGTCTGCTTCGCTGTAACTTCAGGGAG
66 TCCACTACAACGCTAGGGAAATAAGATTAGCTGTCTTCAGTCTGCTTCGCTGCAACTTCAGGGAG
* *
6389 ATAAGGTTGGTGA
131 ATAAGGCTGGTGG
* * * *
6402 CTTCAATCTGCTCCACTGCAACTTCAAGAAGATAAGATCCACCATAATTTTTAGCTTTAATCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTAT
* * * *
6467 TCTACTACAACGCTAGGGAAATAAGATTAGTTGTCTTCAGTCTGC-TCTGTTGCAACTTCAAGGA
66 TCCACTACAACGCTAGGGAAATAAGATTAGCTGTCTTCAGTCTGCTTC-GCTGCAACTTCAGGGA
6531 GATAAGGCTGGTGG
130 GATAAGGCTGGTGG
* * * *** * * *
6545 CTTCAATCTGTTCCACTGCGACTTCAGGAAGATAA-AATCTTTTATAATTAGTATCTTTAATCTG
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTC-GCCATAATTTGTAGCTTTAATCTA
* * ** * * *
6609 TTCCATTACAACG-TCAGGGAAATAAGATTTGCAATCTTTAGTCTGCTCCACTGCAACTTCAGGG
65 TTCCACTACAACGCT-AGGGAAATAAGATTAGCTGTCTTCAGTCTGCTTCGCTGCAACTTCAGGG
6673 AGATAAGGCTGGTGG
129 AGATAAGGCTGGTGG
*
6688 CTTCAATCTGCTCCATTGCAACTTCAGGAAGATAAGATTCGCCATAA--TG-A-CTTTAATCTAT
1 CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTAT
* *
6749 CCCACTGCAAC
66 TCCACTACAAC
6760 TTCAGGGGTA
Statistics
Matches: 303, Mismatches: 50, Indels: 14
0.83 0.14 0.04
Matches are distributed among these distances:
139 18 0.06
140 1 0.00
141 1 0.00
142 5 0.02
143 274 0.90
144 4 0.01
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (143 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGAAGATAAGATTCGCCATAATTTGTAGCTTTAATCTAT
TCCACTACAACGCTAGGGAAATAAGATTAGCTGTCTTCAGTCTGCTTCGCTGCAACTTCAGGGAG
ATAAGGCTGGTGG
Found at i:7626 original size:6 final size:6
Alignment explanation
Indices: 7617--7694 Score: 77
Period size: 6 Copynumber: 13.0 Consensus size: 6
7607 TTGGCCTCTC
** * * *
7617 CTTTTT CTTTTT CTTCTTT -TGCTT CTTCTT CTATTT CTTTTT CCTTTT
1 CTTTTT CTTTTT CTT-TTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
* *
7665 CTTTTT CTATTT CTTTTT CTATTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
7695 TTTAATTGAA
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
5 2 0.03
6 53 0.91
7 3 0.05
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (6 bp):
CTTTTT
Found at i:7654 original size:12 final size:12
Alignment explanation
Indices: 7617--7694 Score: 88
Period size: 12 Copynumber: 6.5 Consensus size: 12
7607 TTGGCCTCTC
*
7617 CTTTTTCTTTTT
1 CTTTTTCTATTT
**
7629 CTTCTTT-TGCTT
1 CTT-TTTCTATTT
*
7641 CTTCTTCTATTT
1 CTTTTTCTATTT
7653 CTTTTTCCT-TTT
1 CTTTTT-CTATTT
7665 CTTTTTCTATTT
1 CTTTTTCTATTT
7677 CTTTTTCTATTT
1 CTTTTTCTATTT
7689 CTTTTT
1 CTTTTT
7695 TTTAATTGAA
Statistics
Matches: 56, Mismatches: 6, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
11 4 0.07
12 47 0.84
13 5 0.09
ACGTcount: A:0.04, C:0.21, G:0.01, T:0.74
Consensus pattern (12 bp):
CTTTTTCTATTT
Found at i:11914 original size:40 final size:40
Alignment explanation
Indices: 11762--11907 Score: 181
Period size: 40 Copynumber: 3.6 Consensus size: 40
11752 TTGAATGATG
* * * *
11762 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
*
11802 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
11842 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
11883 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
11908 AACGAGTAGC
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
39 1 0.01
40 82 0.88
41 10 0.11
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:11914 original size:80 final size:80
Alignment explanation
Indices: 11762--11940 Score: 195
Period size: 80 Copynumber: 2.2 Consensus size: 80
11752 TTGAATGATG
* *
11762 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
**
11827 GTGCGAGTTA-CTAAA
66 GAACGAG-TAGCTAAA
* * * * *
11842 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCGGACTAAGAT-CCGAAGGCAT
*
11905 TTGAACGAGTAGCTATA
64 TTGAACGAGTAGCTAAA
* *
11922 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
11941 TACGTGATTT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
79 17 0.20
80 60 0.71
81 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCGGACTAAGATCCGAAGGCATTT
GAACGAGTAGCTAAA
Found at i:19841 original size:79 final size:79
Alignment explanation
Indices: 19650--19873 Score: 301
Period size: 79 Copynumber: 2.8 Consensus size: 79
19640 TTGAATGATG
* * * * *
19650 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
*
19714 TGTGCGAGATACTAAT
64 TGTGCGAGATACTAAA
*
19730 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
*
19794 TGCGAGTTACTAAA
66 TGCGAGATACTAAA
* *
19808 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
19872 TG
64 TG
19874 AACGAGTAGC
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
78 36 0.28
79 60 0.47
80 33 0.26
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
TGCGAGATACTAAA
Found at i:19887 original size:40 final size:40
Alignment explanation
Indices: 19650--19873 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
19640 TTGAATGATG
* * * *
19650 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
19690 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
19730 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
19769 TCCGGGTTAAGT-CCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
19808 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
19849 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
19874 AACGAGTAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
39 74 0.45
40 81 0.49
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:19904 original size:79 final size:79
Alignment explanation
Indices: 19650--19906 Score: 254
Period size: 79 Copynumber: 3.3 Consensus size: 79
19640 TTGAATGATG
* * * * * * *
19650 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAATCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCGAAGGCATT
** * *
19714 TGTGCGAGATACTAAT
64 TGAACGAGTTACTAAA
* * *
19730 TCCGGGCT-AAGCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGGCATTTG
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
**
19794 TGCGAGTTACTAAA
66 AACGAGTTACTAAA
* *
19808 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGT-CCGAAGGCATT
*
19872 TGAACGAG-TAGCTATA
64 TGAACGAGTTA-CTAAA
*
19888 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAATCCCGAAGG
19907 TACGTGATTT
Statistics
Matches: 152, Mismatches: 20, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
78 33 0.22
79 78 0.51
80 41 0.27
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAATCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCGAAGGCATTTG
AACGAGTTACTAAA
Done.