Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2483
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: 105901
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:3918 original size:104 final size:103
Alignment explanation
Indices: 3739--3961 Score: 376
Period size: 104 Copynumber: 2.2 Consensus size: 103
3729 TGTATATAAA
** * *
3739 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
3804 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
3842 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
3906 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
3946 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
3962 GATATCCATT
Statistics
Matches: 113, Mismatches: 5, Indels: 3
0.93 0.04 0.02
Matches are distributed among these distances:
103 27 0.24
104 85 0.75
105 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.31
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:4013 original size:71 final size:71
Alignment explanation
Indices: 3880--4030 Score: 241
Period size: 71 Copynumber: 2.1 Consensus size: 71
3870 TCATTGGTGG
* *
3880 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
3945 GAGGGGT
66 GA-GGGT
***
3952 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
4016 GAGGGT
66 GAGGGT
4022 TGCTAAGTG
1 TGCTAAGTG
4031 ATGATTCCCC
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
70 13 0.18
71 31 0.42
72 30 0.41
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
GAGGGT
Found at i:11393 original size:26 final size:26
Alignment explanation
Indices: 11358--11408 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
11348 AATGTGAAAG
*
11358 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
11384 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
11409 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:11459 original size:103 final size:102
Alignment explanation
Indices: 11281--11500 Score: 363
Period size: 103 Copynumber: 2.2 Consensus size: 102
11271 TTGTATATAA
** * *
11281 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGTGGTGCTATGTGCGTGATCCACCATATCTTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
11346 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
11383 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCA-TGGTGGTGCTAAGTGCG-TGATCCACCATATCT
11447 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
64 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
11486 AGGGGTT-CTAAGTGC
1 AGGGGTTGCTAAGTGC
11501 GATATCCATT
Statistics
Matches: 111, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
102 35 0.32
103 75 0.68
104 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.31, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGTGGTGCTAAGTGCGTGATCCACCATATCTTT
GAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:11565 original size:26 final size:26
Alignment explanation
Indices: 11530--11581 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
11520 AAATGAAAAG
* *
11530 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
11556 GGGGTTGCTAAGTGATGATTCCCCGA
1 GGGGTTGCTAAGTGATGATTCCCCGA
11582 TTCAGTGGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.15, C:0.21, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGATGATTCCCCGA
Found at i:11567 original size:70 final size:71
Alignment explanation
Indices: 11421--11569 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 71
11411 TCATTGGTGG
* *
11421 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
11486 AGGGGT
66 AGGGGT
***
11492 T-CTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
11555 AGGGGT
66 AGGGGT
11561 TGCTAAGTG
1 TGCTAAGTG
11570 ATGATTCCCC
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
69 36 0.50
70 35 0.49
71 1 0.01
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCG
AGGGGT
Found at i:13700 original size:46 final size:46
Alignment explanation
Indices: 13647--13822 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
13637 TATTTGGGCA
13647 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13693 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * **
13738 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGACA
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
13786 CCCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
13823 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 64 0.59
47 28 0.26
48 2 0.02
50 4 0.04
51 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:13802 original size:93 final size:93
Alignment explanation
Indices: 13643--13814 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
13633 AGGATATTTG
*** *
13643 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCATTGAG
13708 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
13736 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGGACACCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCATTGAG
13801 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
13815 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCGAACTCATTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:17901 original size:46 final size:46
Alignment explanation
Indices: 17848--17976 Score: 204
Period size: 46 Copynumber: 2.8 Consensus size: 46
17838 TATTTGGGCA
* *
17848 TCCGAACTCGTTGAGTTAAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
17894 TCCGAACTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
17940 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
17977 GCGGGTTACA
Statistics
Matches: 76, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:28523 original size:15 final size:15
Alignment explanation
Indices: 28500--28537 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
28490 ATATACTCGT
*
28500 TAATCTTTAATTCCA
1 TAATTTTTAATTCCA
28515 TAATTTTTAATTCCA
1 TAATTTTTAATTCCA
28530 TAATTTTT
1 TAATTTTT
28538 TTGAAATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATTTTTAATTCCA
Found at i:29213 original size:27 final size:27
Alignment explanation
Indices: 29183--29236 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
29173 TCATACAACC
* *
29183 CATGTAATAGTAATTTAACATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
**
29210 CATGTAACAATAATTTGCCATTCAATT
1 CATGTAACAATAATTTAACATTCAATT
29237 TCACATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (27 bp):
CATGTAACAATAATTTAACATTCAATT
Found at i:31967 original size:15 final size:15
Alignment explanation
Indices: 31949--31979 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
31939 TGAATTGTGG
31949 TTTGAGAAGAGGTTA
1 TTTGAGAAGAGGTTA
31964 TTTGAGAAGAGGTTA
1 TTTGAGAAGAGGTTA
31979 T
1 T
31980 CATGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (15 bp):
TTTGAGAAGAGGTTA
Found at i:36194 original size:13 final size:13
Alignment explanation
Indices: 36176--36203 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
36166 CTACTAATTC
36176 GTGACTCAATTAG
1 GTGACTCAATTAG
36189 GTGACTCAATTAG
1 GTGACTCAATTAG
36202 GT
1 GT
36204 TAGTAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (13 bp):
GTGACTCAATTAG
Found at i:38828 original size:48 final size:46
Alignment explanation
Indices: 38757--39074 Score: 282
Period size: 48 Copynumber: 6.8 Consensus size: 46
38747 ATGTTGACGT
* * *
38757 CATGTCCCAAACATGGTCTTACACTAGCTCACATGTCGAGGCCGATGC
1 CATGT-CC-AACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * * *
38805 CATGTCCCAGACATGGTCTTACACTAGCTCTCGTCTCCATGCCGATGC
1 CATGT-CCA-ACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* *
38853 CATGTGCAACATGGTCTTACACTAGCTCACA-ATCAACCCCGATGC
1 CATGTCCAACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * *
38898 CAAGTCCAACATGGTCTTACACTGGCTCTCA-ATCAACGTCGATGC
1 CATGTCCAACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * ** *
38943 CATGTCCAACATGGTCTTACACTGGCTCTCATAACATTGTCGATGC
1 CATGTCCAACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
* * * * ***
38989 CATGTTCCAAACATGGTCTTACACTGGCACATGAAAT-GTGGCCGATGC
1 CATG-TCC-AACATGGTCTTACACTAGCTCA-CATATCAACGCCGATGC
*
39037 CATGTCCCAGACATGGTCTTACACTAGCGCACATATCA
1 CATGT-CCA-ACATGGTCTTACACTAGCTCACATATCA
39075 CCATAGTACC
Statistics
Matches: 227, Mismatches: 35, Indels: 16
0.82 0.13 0.06
Matches are distributed among these distances:
45 79 0.35
46 36 0.16
47 11 0.05
48 99 0.44
49 2 0.01
ACGTcount: A:0.25, C:0.31, G:0.19, T:0.25
Consensus pattern (46 bp):
CATGTCCAACATGGTCTTACACTAGCTCACATATCAACGCCGATGC
Found at i:45869 original size:46 final size:43
Alignment explanation
Indices: 45769--45895 Score: 139
Period size: 46 Copynumber: 2.8 Consensus size: 43
45759 CTAGGATTTG
** *
45769 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGAAT
*
45812 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGA-AGATGTAACT
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACAGATG-AA-T
*
45860 AGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
45896 TTATGGGCGG
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
43 1 0.01
44 2 0.03
45 1 0.01
46 60 0.86
47 2 0.03
48 3 0.04
49 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (43 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGAAT
Found at i:48829 original size:15 final size:15
Alignment explanation
Indices: 48809--48871 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
48799 TTATCCTATC
48809 TCTTTATTCTGGATT
1 TCTTTATTCTGGATT
*
48824 TCTTTATTCTGGGTT
1 TCTTTATTCTGGATT
*
48839 TCTCTA-TCTTGGATT
1 TCTTTATTC-TGGATT
*
48854 TCTTTATTC-GGTTT
1 TCTTTATTCTGGATT
48868 TCTT
1 TCTT
48872 GTTATCTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 10 0.24
15 29 0.71
16 2 0.05
ACGTcount: A:0.10, C:0.16, G:0.14, T:0.60
Consensus pattern (15 bp):
TCTTTATTCTGGATT
Found at i:51333 original size:46 final size:43
Alignment explanation
Indices: 51233--51359 Score: 139
Period size: 46 Copynumber: 2.8 Consensus size: 43
51223 CTAGGATTTG
** *
51233 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGAT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGAAT
*
51276 GCGAATGTCCGAACTCGTTGAGTTGAGTCCGAGTTCGA-AGATGTAACT
1 G-GCA--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACAGATG-AA-T
*
51324 AGGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCAC
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC
51360 TTATGGGCGG
Statistics
Matches: 70, Mismatches: 6, Indels: 13
0.79 0.07 0.15
Matches are distributed among these distances:
43 1 0.01
44 2 0.03
45 1 0.01
46 60 0.86
47 2 0.03
48 3 0.04
49 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.28
Consensus pattern (43 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACAGATGAAT
Found at i:56150 original size:30 final size:30
Alignment explanation
Indices: 56114--56173 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
56104 TTCCCGAGCC
*
56114 TAGGGGCAAAAGTGTAATTATGCAAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
* *
56144 TAGGGGCAAAAATGTAATTTTGCCAAAGTT
1 TAGGGGCAAAAATGTAATTATGCAAAAGTT
56174 CGTATTAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.38, C:0.08, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGGGGCAAAAATGTAATTATGCAAAAGTT
Found at i:66712 original size:14 final size:14
Alignment explanation
Indices: 66691--66724 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
66681 TTATTTTAAA
66691 TATTATTTTTCATTG
1 TATTATTTTT-ATTG
66706 T-TTATTTTTATTG
1 TATTATTTTTATTG
66719 TATTAT
1 TATTAT
66725 AAATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.28
14 12 0.67
15 1 0.06
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.71
Consensus pattern (14 bp):
TATTATTTTTATTG
Found at i:68746 original size:30 final size:32
Alignment explanation
Indices: 68712--68770 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
68702 CAGGTGATGA
68712 AAATAAATGTG-ATA-TAAA-ATGAAATTGGCT
1 AAAT-AATGTGTATACTAAATATGAAATTGGCT
*
68742 AAATAATGTGTATACTAAATTTGAAATTG
1 AAATAATGTGTATACTAAATATGAAATTG
68771 ATACATGAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 6 0.24
30 7 0.28
31 4 0.16
32 8 0.32
ACGTcount: A:0.47, C:0.03, G:0.15, T:0.34
Consensus pattern (32 bp):
AAATAATGTGTATACTAAATATGAAATTGGCT
Found at i:74142 original size:21 final size:21
Alignment explanation
Indices: 74116--74166 Score: 102
Period size: 21 Copynumber: 2.4 Consensus size: 21
74106 ATTGACATGG
74116 GCATGGGAATTTCCCATACGA
1 GCATGGGAATTTCCCATACGA
74137 GCATGGGAATTTCCCATACGA
1 GCATGGGAATTTCCCATACGA
74158 GCATGGGAA
1 GCATGGGAA
74167 AAGCGAACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (21 bp):
GCATGGGAATTTCCCATACGA
Found at i:84001 original size:79 final size:81
Alignment explanation
Indices: 83865--84049 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
83855 TTGAATGATG
* *
83865 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
83929 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
83944 TTCCGGGCTAAG-CCCGAAGGCATTTGTG-TGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
84006 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
84024 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
84050 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.64
80 32 0.35
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:84063 original size:40 final size:40
Alignment explanation
Indices: 83866--84049 Score: 198
Period size: 40 Copynumber: 4.6 Consensus size: 40
83856 TGAATGATGT
* * * *
83866 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
83906 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
83946 CCGGGCTAAG-CCCGAAGGCATTTGTGTGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
83984 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
84025 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
84050 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.28
40 78 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:84071 original size:79 final size:79
Alignment explanation
Indices: 83918--84082 Score: 192
Period size: 79 Copynumber: 2.1 Consensus size: 79
83908 GGACTAAGAT
* * ***
83918 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGTGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
83983 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
83997 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
84060 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
84076 CCGAAGG
1 CCGAAGG
84083 TACGTGATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 24 0.33
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:91910 original size:39 final size:40
Alignment explanation
Indices: 91727--91903 Score: 197
Period size: 39 Copynumber: 4.5 Consensus size: 40
91717 GAATGATTCC
* * * *
91727 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT-CG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* *
91766 GACTAAGAT-CCGAAGGCATTTGTGCGA--TACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
91804 GGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
* * *
91843 GGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTTAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
91882 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
91904 AACGAGTAGC
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
37 22 0.19
38 8 0.07
39 53 0.45
40 34 0.29
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:91910 original size:79 final size:75
Alignment explanation
Indices: 91775--91936 Score: 184
Period size: 79 Copynumber: 2.1 Consensus size: 75
91765 GGACTAAGAT
* **
91775 CCGAAGGCATTTGTGCGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTA-CTAAA
1 CCGAAGGCAATTGTGCGATACTAA-TCCGGGCTAAGCCCGAAGGCATTTGAACGAG-TAGCTAAA
*
91839 TCCGGGTTAAGTC
64 TCC-GGTTAAATC
*
91852 CCGAAGGCAATTGTGCGAGTTACTTAA-CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTA
1 CCGAAGGCAATTGTGCGA--TAC-TAATCCGGGCTAAG-CCCGAAGGCATTTGAACGAGTAGCTA
* *
91916 TATCCGGTTAAATT
62 AATCCGGTTAAATC
91930 CCGAAGG
1 CCGAAGG
91937 TACGTGATTT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
77 17 0.23
78 25 0.34
79 28 0.38
80 3 0.04
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (75 bp):
CCGAAGGCAATTGTGCGATACTAATCCGGGCTAAGCCCGAAGGCATTTGAACGAGTAGCTAAATC
CGGTTAAATC
Done.