Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2920
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: 26939
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:1073 original size:19 final size:19
Alignment explanation
Indices: 1049--1092 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1039 ATCAATAATT
* *
1049 AAAAAAAAAAAGACAAAGA
1 AAAAAAAAAAACAAAAAGA
1068 AAAAAAAAAAACAAAAAGA
1 AAAAAAAAAAACAAAAAGA
1087 AGAAAA
1 A-AAAA
1093 GATGCCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.86, C:0.05, G:0.09, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAACAAAAAGA
Found at i:1092 original size:17 final size:18
Alignment explanation
Indices: 1049--1082 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1039 ATCAATAATT
1049 AAAAAAAAAAAGACAAAG
1 AAAAAAAAAAAGACAAAG
1067 AAAAAAAAAAA-ACAAA
1 AAAAAAAAAAAGACAAA
1083 AAGAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.88, C:0.06, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAGACAAAG
Found at i:2369 original size:23 final size:25
Alignment explanation
Indices: 2343--2389 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2333 TATCATTCAT
*
2343 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
2366 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
2390 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:2766 original size:92 final size:80
Alignment explanation
Indices: 2737--2896 Score: 238
Period size: 76 Copynumber: 2.0 Consensus size: 80
2727 CTTTTCATGT
2737 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGTTGCCATGGTATCTT
1 CACGTTGCCATGGTATCTTTCAACCATGGTCTTAC-CAT-TC-T-TCAGGTTGCCATGGTATCTT
2802 TCAACCATGGTCTTACACA
62 TCAACCATGGTCTTACACA
* *
2821 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTA-CA--C-ACAGGTTGCCATGGTATCTTTCAA
1 CACGTTGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAA
2882 CCATGGTCTTACACA
66 CCATGGTCTTACACA
2897 TTTCATATCA
Statistics
Matches: 74, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
76 38 0.51
79 1 0.01
82 2 0.03
84 33 0.45
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.33
Consensus pattern (80 bp):
CACGTTGCCATGGTATCTTTCAACCATGGTCTTACCATTCTTCAGGTTGCCATGGTATCTTTCAA
CCATGGTCTTACACA
Found at i:2818 original size:46 final size:45
Alignment explanation
Indices: 2650--2907 Score: 274
Period size: 46 Copynumber: 6.0 Consensus size: 45
2640 TTTGACGTGA
* * * * * *
2650 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCTATCAGGT
** * * *
2696 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
*
2742 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAGGT
2788 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
2826 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C-A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
2864 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTC-TATCAG
2908 AGAGCACACT
Statistics
Matches: 191, Mismatches: 12, Indels: 18
0.86 0.05 0.08
Matches are distributed among these distances:
38 71 0.37
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 106 0.55
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCTATCAGGT
Found at i:2834 original size:38 final size:38
Alignment explanation
Indices: 2783--2896 Score: 228
Period size: 38 Copynumber: 3.0 Consensus size: 38
2773 CATCTCATAT
2783 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2821 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2859 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
2897 TTTCATATCA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 76 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:5138 original size:31 final size:30
Alignment explanation
Indices: 5094--5158 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
5084 CTAATAAAAT
*
5094 AATAATAAATATCTTATTAAAGT-ATTAATAA
1 AATAATAAATATCTAATTAAA-TAATT-ATAA
**
5125 AATAATATTTATCTAATTAAATAATTATAA
1 AATAATAAATATCTAATTAAATAATTATAA
5155 AATA
1 AATA
5159 TCAAAATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (30 bp):
AATAATAAATATCTAATTAAATAATTATAA
Found at i:7780 original size:23 final size:25
Alignment explanation
Indices: 7754--7800 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
7744 TATCATTCAT
*
7754 TTCATTATAT-CA-ATATTTTATGC
1 TTCATCATATCCATATATTTTATGC
*
7777 TTCATCATTTCCATATATTTTATG
1 TTCATCATATCCATATATTTTATG
7801 TATATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 2 0.10
25 10 0.50
ACGTcount: A:0.28, C:0.15, G:0.04, T:0.53
Consensus pattern (25 bp):
TTCATCATATCCATATATTTTATGC
Found at i:8229 original size:46 final size:46
Alignment explanation
Indices: 8061--8280 Score: 260
Period size: 46 Copynumber: 5.0 Consensus size: 46
8051 TTTGACGTGA
* * * * * *
8061 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
8107 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
8153 TGCCATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
8199 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
8237 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
8281 AGAGCACACT
Statistics
Matches: 153, Mismatches: 12, Indels: 18
0.84 0.07 0.10
Matches are distributed among these distances:
38 33 0.22
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 106 0.69
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:8245 original size:38 final size:38
Alignment explanation
Indices: 8194--8269 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
8184 CATCTCATAT
8194 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
8232 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
8270 TTTCATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:12028 original size:85 final size:85
Alignment explanation
Indices: 11934--13082 Score: 1943
Period size: 85 Copynumber: 13.6 Consensus size: 85
11924 TGAATCCACA
* *
11934 CGCCTTAACCCCTTAAGAAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
*
11999 AGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
12019 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12084 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
*
12104 CGCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12169 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
* * *
12189 CGCCTTAACCCTCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGAGCTCGCCAAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12254 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
* *
12274 CGCTTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCACCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12339 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
*
12359 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGTCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12424 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
12444 CGCCTTAACCCCCTAAGCAGTAGGGT---AGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
* *
12506 GGTGGAGCAGGTCAAAAACT
66 GGTGGAGCAGGTCGAAGACT
* *
12526 CGCCTTAACCCCCTAAGCAGTAGGGTAAAAGGCTAAAATTTACAGATCTAGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12591 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
* * *
12611 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAAATCTGGGCTCGCTGAGTAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12676 GGTGGAGCAGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
* *
12696 CGCCTTAACCCCCTAAACAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCCCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
*
12761 GGTGGAG-TGGTCGAAGACT
66 GGTGGAGCAGGTCGAAGACT
12780 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
*
12845 GGTGGAGCAGGTTGAAGACT
66 GGTGGAGCAGGTCGAAGACT
* * * *
12865 CGCCTTAAGCCCCTAAGCAGTAGGGTAACAGGCTAAAGTTTACAGATTTGGGCTCACCGAGCAGT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
12930 GGTGGAGCAGGTCGAAGA-T
66 GGTGGAGCAGGTCGAAGACT
* *
12949 CCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAAATCCT-GGCTCTCCGAGCA
1 -CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGAT-CTGGGCTCGCCGAGCA
* *
13013 GTGGTGGAGTAGGTCGAAAACT
64 GTGGTGGAGCAGGTCGAAGACT
* * *
13035 CGCCTTAATCCCCTAAGTAGTAGGGTAACAGGCTAAAA-TTGCAGATCT
1 CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCT
13083 TATCCCATTA
Statistics
Matches: 1004, Mismatches: 53, Indels: 16
0.94 0.05 0.01
Matches are distributed among these distances:
82 79 0.08
83 2 0.00
84 88 0.09
85 833 0.83
86 2 0.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.20
Consensus pattern (85 bp):
CGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTTACAGATCTGGGCTCGCCGAGCAGT
GGTGGAGCAGGTCGAAGACT
Found at i:13359 original size:133 final size:135
Alignment explanation
Indices: 13120--13397 Score: 357
Period size: 133 Copynumber: 2.1 Consensus size: 135
13110 CAAATTTCGA
* ** * * *
13120 CAGATCTTATCTTCACTAAGCAGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTA
1 CAGATCTTATATTCGTTGAGCAGGAGCGAAGCAAATCAAATTTTGGCAAGTCTTATCTCCATGTA
* * * *
13185 ACGGCAATGGAGTAGATTTCAGCCATCAACCTTATCTTCACTAAGCAGGAGTGGAGCAGGCT-AA
66 ACGGCAATGGAGTAGATTCCAACCATCAACCTTATCTTCACTAAGCAGAAGTGGAACAGGCTAAA
13249 -ATAC
131 CATAC
* * *
13253 TAGATCTTATATTCGTTGAGCAGGAGCGGAGCAAATCAAATTTTGATG-AA-TCTTATCTCTATG
1 CAGATCTTATATTCGTTGAGCAGGAGCGAAGCAAATCAAATTTTG--GCAAGTCTTATCTCCATG
* * * *
13316 TATCGGCAATGGAGTAGATTCCAATCATCAGCCTTATCTTCACTGAGCAGAAGTGGAACAGGCTA
64 TAACGGCAATGGAGTAGATTCCAACCATCAACCTTATCTTCACTAAGCAGAAGTGGAACAGGCTA
13381 AACATAC
129 AACATAC
13388 CAGATCTTAT
1 CAGATCTTAT
13398 CTTTACTGGG
Statistics
Matches: 123, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
133 105 0.85
134 4 0.03
135 14 0.11
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.28
Consensus pattern (135 bp):
CAGATCTTATATTCGTTGAGCAGGAGCGAAGCAAATCAAATTTTGGCAAGTCTTATCTCCATGTA
ACGGCAATGGAGTAGATTCCAACCATCAACCTTATCTTCACTAAGCAGAAGTGGAACAGGCTAAA
CATAC
Found at i:14201 original size:26 final size:26
Alignment explanation
Indices: 14165--14214 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
14155 TAGGGGATCG
*
14165 CTTCCAGGATACATCAGTACCTATGT
1 CTTCCAGGATACATCAGTAACTATGT
* *
14191 CTTCCGGGATACATCCGTAACTAT
1 CTTCCAGGATACATCAGTAACTAT
14215 ACCAAGCTGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (26 bp):
CTTCCAGGATACATCAGTAACTATGT
Found at i:14830 original size:126 final size:126
Alignment explanation
Indices: 14672--14905 Score: 387
Period size: 126 Copynumber: 1.9 Consensus size: 126
14662 GTTTTAGCCT
*
14672 TAAGAGGATATTCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
1 TAAGAGGATATCCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
* * * * *
14737 CTTCGAATTCTTTAAATACTGACCATTGCCTTTATTTTGAAAATTTTTTAGAGTGAACTGG
66 CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTTAAAAATTTTTTAGAGTGAACTGG
* * *
14798 TAAGAGGATATCCGAATATTCAAGACAAACAAAGAAAGCGAAGCCCAGTACGTTAGGGCACTATT
1 TAAGAGGATATCCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
14863 CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTTAAAAA
66 CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTTAAAAA
14906 CAATTGAGAA
Statistics
Matches: 99, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
126 99 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (126 bp):
TAAGAGGATATCCGAATATTCAAAACAAACAAAGAAAGCGAAACCCAGTACGTTAGGGCACGATT
CTTCGAAGTCTTTAAATACCGAACATTGCCATTATTTTAAAAATTTTTTAGAGTGAACTGG
Found at i:15497 original size:3 final size:3
Alignment explanation
Indices: 15491--15654 Score: 79
Period size: 3 Copynumber: 54.7 Consensus size: 3
15481 AATAGAAGAC
* * * *
15491 AAT AAT AAT AAT -AT ATT AAT AAA AAT AAT AAT -AT AAA AAT AAT AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* ** ** *
15537 AAT AAA AAT -AT GTT TCT AAT AAT AAT AAAT CAAT AAT GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT -AAT AAT AAT AAT -AAT
* * * *
15584 ATAT ACAA AAT AAT AGT AAC AGT AAT AA- AAT AAGT -AT AAT -AT AAT
1 A-AT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
* * *
15629 AAT AAT AAT AAC AAT ATT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
15655 CACTCTCCCT
Statistics
Matches: 118, Mismatches: 33, Indels: 20
0.69 0.19 0.12
Matches are distributed among these distances:
2 11 0.09
3 92 0.78
4 15 0.13
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:15518 original size:23 final size:24
Alignment explanation
Indices: 15491--15654 Score: 72
Period size: 23 Copynumber: 6.8 Consensus size: 24
15481 AATAGAAGAC
* *
15491 AATAATAATAAT-ATATTAATAAA
1 AATAATAATAATAAAAATAATAAA
15514 AATAATAAT-ATAAAAATAATAAA
1 AATAATAATAATAAAAATAATAAA
* * ***
15537 AATAAAAATATGTTTCTAATAATAATA
1 AATAATAATA--ATAAAAATAATAA-A
* *
15564 AATCAATAATGATAATAAAT-ATATAC
1 AAT-AATAATAATAA-AAATAATA-AA
* * *
15590 AA-AATAATAGTAACAGTAAT-AA
1 AATAATAATAATAAAAATAATAAA
* *
15612 AATAAGT-ATAAT-ATAATAATAAT
1 AATAA-TAATAATAAAAATAATAAA
* *
15635 AATAACAATATTAAAAATAA
1 AATAATAATAATAAAAATAA
15655 CACTCTCCCT
Statistics
Matches: 101, Mismatches: 26, Indels: 27
0.66 0.17 0.18
Matches are distributed among these distances:
22 11 0.11
23 44 0.44
24 18 0.18
26 15 0.15
27 8 0.08
28 5 0.05
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (24 bp):
AATAATAATAATAAAAATAATAAA
Found at i:15526 original size:14 final size:15
Alignment explanation
Indices: 15508--15546 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
15498 ATAATATATT
15508 AATAAAAATAAT-AA
1 AATAAAAATAATAAA
*
15522 TATAAAAATAATAAA
1 AATAAAAATAATAAA
15537 AATAAAAATA
1 AATAAAAATA
15547 TGTTTCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:15531 original size:20 final size:21
Alignment explanation
Indices: 15494--15541 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
15484 AGAAGACAAT
**
15494 AATAATAATATATTAATAA-A
1 AATAATAATATAAAAATAATA
15514 AATAATAATATAAAAATAATA
1 AATAATAATATAAAAATAATA
15535 AA-AATAA
1 AATAATAA
15542 AAATATGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
AATAATAATATAAAAATAATA
Found at i:15639 original size:17 final size:17
Alignment explanation
Indices: 15491--15639 Score: 64
Period size: 17 Copynumber: 8.8 Consensus size: 17
15481 AATAGAAGAC
15491 AATAATAATAAT-ATATT
1 AATAATAATAATAATA-T
*
15508 AATAAAAATAATAATAT
1 AATAATAATAATAATAT
*
15525 AAAAATAATAA-AA-AT
1 AATAATAATAATAATAT
* * * *
15540 AAAAAT-AT-GT-TTCT
1 AATAATAATAATAATAT
*
15554 AATAATAATAAATCA-AT
1 AATAATAAT-AATAATAT
*
15571 AATGATAATAA-ATATAT
1 AATAATAATAATA-ATAT
* * *
15588 ACAAAATAATAGTAACAGT
1 A-ATAATAATAATAATA-T
15607 AATAA-AATAAGTATAATAT
1 AATAATAAT-A--ATAATAT
15626 AATAATAATAATAA
1 AATAATAATAATAA
15640 CAATATTAAA
Statistics
Matches: 97, Mismatches: 19, Indels: 32
0.66 0.13 0.22
Matches are distributed among these distances:
14 8 0.08
15 10 0.10
16 5 0.05
17 41 0.42
18 16 0.16
19 10 0.10
20 7 0.07
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (17 bp):
AATAATAATAATAATAT
Found at i:15940 original size:45 final size:45
Alignment explanation
Indices: 15890--15979 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
15880 GAGAATAGAC
*
15890 AAAGAAAACCTCTTTTGCTTTGATATTTGATTAATCTCCAAAAAA
1 AAAGAAAACCTATTTTGCTTTGATATTTGATTAATCTCCAAAAAA
*
15935 AAAGAAAACTTATTTTGCTTTGATATTTGATTAATCTCCAAAAAA
1 AAAGAAAACCTATTTTGCTTTGATATTTGATTAATCTCCAAAAAA
15980 GAACTCCCCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.41, C:0.13, G:0.09, T:0.37
Consensus pattern (45 bp):
AAAGAAAACCTATTTTGCTTTGATATTTGATTAATCTCCAAAAAA
Found at i:16108 original size:29 final size:30
Alignment explanation
Indices: 16060--16129 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 30
16050 TTTGTAGGCA
16060 AGTGGGGTGATAGAGATAGT-GGATGATTT
1 AGTGGGGTGATAGAGATAGTGGGATGATTT
* * *
16089 AGTGGGGTGATGGAGTTAGTGGGGTGATTT
1 AGTGGGGTGATAGAGATAGTGGGATGATTT
*
16119 AGTGGGTTGAT
1 AGTGGGGTGAT
16130 TTAGTAGGGT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 18 0.50
30 18 0.50
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (30 bp):
AGTGGGGTGATAGAGATAGTGGGATGATTT
Found at i:16122 original size:13 final size:13
Alignment explanation
Indices: 16083--16140 Score: 62
Period size: 13 Copynumber: 4.2 Consensus size: 13
16073 AGATAGTGGA
16083 TGATTTAGTGGGG
1 TGATTTAGTGGGG
16096 TGATGGAGTTAGTGGGG
1 TGAT----TTAGTGGGG
*
16113 TGATTTAGTGGGT
1 TGATTTAGTGGGG
*
16126 TGATTTAGTAGGG
1 TGATTTAGTGGGG
16139 TG
1 TG
16141 TGGGGGTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 25 0.66
17 13 0.34
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (13 bp):
TGATTTAGTGGGG
Found at i:16467 original size:13 final size:14
Alignment explanation
Indices: 16442--16483 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
16432 TTATAATATG
16442 TAAATTATATAAAA
1 TAAATTATATAAAA
16456 TAAATT-TATAAAA
1 TAAATTATATAAAA
* *
16469 -ACATTATACAAAA
1 TAAATTATATAAAA
16482 TA
1 TA
16484 TAAAATGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 4 0.17
13 13 0.54
14 7 0.29
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATTATATAAAA
Found at i:18281 original size:26 final size:27
Alignment explanation
Indices: 18252--18306 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
18242 GTTTTTGAGT
*
18252 TTAAT-TTTAATGAGAACTTTTAAAAA
1 TTAATGTTTAATGAAAACTTTTAAAAA
* *
18278 TTAATGTTTAATTAAAATTTTTAAAAA
1 TTAATGTTTAATGAAAACTTTTAAAAA
18305 TT
1 TT
18307 TTGTGTAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
TTAATGTTTAATGAAAACTTTTAAAAA
Done.