Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3162_ERROPOS485598
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: 92732
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:165 original size:17 final size:17
Alignment explanation
Indices: 122--181 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
112 TTTTAATTAT
*
122 ATTTTTTAT-TTCTTTGA
1 ATTTTTTATATT-TTTCA
* *
139 ATTGTCTATATTTTTCA
1 ATTTTTTATATTTTTCA
*
156 ATTTTTTATAAGTTTTTTA
1 ATTTTTTAT-A-TTTTTCA
175 ATTTTTT
1 ATTTTTT
182 TAAAAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 18 0.53
18 3 0.09
19 13 0.38
ACGTcount: A:0.22, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
ATTTTTTATATTTTTCA
Found at i:839 original size:26 final size:26
Alignment explanation
Indices: 753--839 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
743 GATATGATGT
753 CTCATATTTGTTAAAGATGTTAATAG
1 CTCATATTTGTTAAAGATGTTAATAG
* ** * * *
779 CTCACACTTTACTAATGATTAATGTGATA-
1 CTCATA-TTTGTTAAAGA-T-GT-TAATAG
808 CTTCATATTTGTTAAAGATGTTAATAG
1 C-TCATATTTGTTAAAGATGTTAATAG
835 CTCAT
1 CTCAT
840 GCAAAAGCTT
Statistics
Matches: 43, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
26 13 0.30
27 10 0.23
28 2 0.05
29 10 0.23
30 8 0.19
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (26 bp):
CTCATATTTGTTAAAGATGTTAATAG
Found at i:3237 original size:14 final size:14
Alignment explanation
Indices: 3218--3265 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 14
3208 AAAATTGATA
3218 TTTAATTTTTATAT
1 TTTAATTTTTATAT
*
3232 TTTAATTTTTAACATAA
1 TTTAATTTTT---ATAT
3249 TTTAATTTTTATAT
1 TTTAATTTTTATAT
3263 TTT
1 TTT
3266 TATAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 16 0.55
17 13 0.45
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTAATTTTTATAT
Found at i:7540 original size:20 final size:20
Alignment explanation
Indices: 7515--7557 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
7505 TGCTGAGATT
7515 ACTGCATCAACTAAATCAAG
1 ACTGCATCAACTAAATCAAG
7535 ACTGCATCAACTAAATCAAG
1 ACTGCATCAACTAAATCAAG
7555 ACT
1 ACT
7558 CAATCCGCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.26, G:0.09, T:0.21
Consensus pattern (20 bp):
ACTGCATCAACTAAATCAAG
Found at i:7623 original size:14 final size:14
Alignment explanation
Indices: 7604--7632 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
7594 TTATTTATTT
7604 TCCTGTTTAAACTC
1 TCCTGTTTAAACTC
7618 TCCTGTTTAAACTC
1 TCCTGTTTAAACTC
7632 T
1 T
7633 AGAAACGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.45
Consensus pattern (14 bp):
TCCTGTTTAAACTC
Found at i:7677 original size:34 final size:34
Alignment explanation
Indices: 7639--7708 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
7629 CTCTAGAAAC
7639 GATGGGAAATTGGGAATCCAGAAAAAGAAAGTGT
1 GATGGGAAATTGGGAATCCAGAAAAAGAAAGTGT
7673 GATGGGAAATTGGGAATCCAGAAAAAGAAAGTGT
1 GATGGGAAATTGGGAATCCAGAAAAAGAAAGTGT
7707 GA
1 GA
7709 GAAAAAGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.44, C:0.06, G:0.33, T:0.17
Consensus pattern (34 bp):
GATGGGAAATTGGGAATCCAGAAAAAGAAAGTGT
Found at i:12095 original size:88 final size:88
Alignment explanation
Indices: 11946--12119 Score: 348
Period size: 88 Copynumber: 2.0 Consensus size: 88
11936 TGAAGAGACG
11946 GCATGTGGGTTAGGGTTAATGCTAATGCTAATGATTTGCTTTATCATTGGTTGTACCATCTCTTT
1 GCATGTGGGTTAGGGTTAATGCTAATGCTAATGATTTGCTTTATCATTGGTTGTACCATCTCTTT
12011 ATATAAAAAATCAGAATAACTTA
66 ATATAAAAAATCAGAATAACTTA
12034 GCATGTGGGTTAGGGTTAATGCTAATGCTAATGATTTGCTTTATCATTGGTTGTACCATCTCTTT
1 GCATGTGGGTTAGGGTTAATGCTAATGCTAATGATTTGCTTTATCATTGGTTGTACCATCTCTTT
12099 ATATAAAAAATCAGAATAACT
66 ATATAAAAAATCAGAATAACT
12120 ATCTGATTAG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (88 bp):
GCATGTGGGTTAGGGTTAATGCTAATGCTAATGATTTGCTTTATCATTGGTTGTACCATCTCTTT
ATATAAAAAATCAGAATAACTTA
Found at i:13296 original size:29 final size:26
Alignment explanation
Indices: 13227--13298 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 26
13217 AGAGAGAACC
13227 AAAT-TATACATAAATAAATTTAAAA
1 AAATATATACATAAATAAATTTAAAA
* *
13252 GAATATATAAAT-AATAAATTTAAGAGA
1 AAATATATACATAAATAAATTTAA-A-A
*
13279 AAATATTTACATGAAATAAA
1 AAATATATACAT-AAATAAA
13299 AGGAAGTCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 14 0.38
26 7 0.19
27 10 0.27
29 6 0.16
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (26 bp):
AAATATATACATAAATAAATTTAAAA
Found at i:15372 original size:44 final size:44
Alignment explanation
Indices: 15324--15690 Score: 154
Period size: 44 Copynumber: 8.3 Consensus size: 44
15314 AACTTCAGGA
*
15324 AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACTTGG
1 AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGG
* ** * *
15368 AGATAAGACTCGCCATTTCT--AATCAGCTCCACAGCCGATACATGG
1 AGATAAGACTTG---TGGCTAAAATCTGCTCCATAGCCGATACATGG
*** ** * * *
15413 AGATAAGA-TCTGTAATTTTCAGTCTGCTTCC-TA--CAACTTCA-GG
1 AGATAAGACT-TGT-GGCTAAAATCTGC-TCCATAGCCGA-TACATGG
*
15456 AAGATAAGACTTGGGGCTAAAATCTGCTCCATAGCCGATACATGG
1 -AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGG
** * *
15501 AGATAAGACTTGCCATTTCT--GATCTGCTCCACAGCCGATACATGG
1 AGATAAGACTTG---TGGCTAAAATCTGCTCCATAGCCGATACATGG
*** **** ** *
15546 AGATAAGA-TCTGTAATTTTCGGTCTGCTTCC-T-G-TAACTTCA-GG
1 AGATAAGACT-TGT-GGCTAAAATCTGC-TCCATAGCCGA-TACATGG
15589 AAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGG
1 -AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGG
* ** *
15634 AGATAAGACTCGCATTTCT--GATCTGCTCCATAGCCGATACATGG
1 AGATAAGACTTG--TGGCTAAAATCTGCTCCATAGCCGATACATGG
*
15678 AGATAAGATTTGT
1 AGATAAGACTTGT
15691 AATTTTCAGT
Statistics
Matches: 240, Mismatches: 51, Indels: 66
0.67 0.14 0.18
Matches are distributed among these distances:
42 9 0.04
43 27 0.11
44 105 0.44
45 85 0.35
46 9 0.04
47 5 0.02
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (44 bp):
AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGG
Found at i:15415 original size:133 final size:133
Alignment explanation
Indices: 15177--15734 Score: 904
Period size: 133 Copynumber: 4.2 Consensus size: 133
15167 TAGCTAAAAT
* *
15177 CTGCAACTTTAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCTGATACATGGAGATAAG
1 CTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
* * * *
15242 ACTCGCCATTCCTGATTTA-CTCCATAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTG
66 ACTCGCCATTTCT-AATCAGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTG
15306 CTTC
130 CTTC
*
15310 CTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACTTGGAGATAAG
1 CTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
15375 ACTCGCCATTTCTAATCAGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC
66 ACTCGCCATTTCTAATCAGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC
15440 TTC
131 TTC
* *
15443 CTACAACTTCAGGAAGATAAGACTTGGGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
1 CTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
* * * *
15508 ACTTGCCATTTCTGATCTGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCGGTCTGC
66 ACTCGCCATTTCTAATCAGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC
15573 TTC
131 TTC
*
15576 CTGTAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
1 CTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
* * * *
15641 ACTCG-CATTTCTGATCTGCTCCATAGCCGATACATGGAGATAAGATTTGTAATTTTCAGTCTGC
66 ACTCGCCATTTCTAATCAGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC
15705 TTC
131 TTC
* **
15708 TTATAACTTCAGGAAGATAAGACTTGT
1 CTGCAACTTCAGGAAGATAAGACTTGT
15735 ATCTTCAATG
Statistics
Matches: 401, Mismatches: 23, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
132 87 0.22
133 314 0.78
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (133 bp):
CTGCAACTTCAGGAAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAG
ACTCGCCATTTCTAATCAGCTCCACAGCCGATACATGGAGATAAGATCTGTAATTTTCAGTCTGC
TTC
Found at i:15682 original size:88 final size:89
Alignment explanation
Indices: 15324--15690 Score: 233
Period size: 88 Copynumber: 4.1 Consensus size: 89
15314 AACTTCAGGA
*
15324 AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACTTGGAGATAAGACTCGCCATTTCTA
1 AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTA
* *
15389 ATCAGCTCCACAGCCGATACATGG
66 ATCTGCTCCATAGCCGATACATGG
*** ** * * * * ***
15413 AGATAAGA-TCTGTAATTTTCAGTCTGCTTCC-TA--CAACTTCA-GGAAGATAAGACTTG-GGG
1 AGATAAGACT-TGT-GGCTAAAATCTGC-TCCATAGCCGA-TACATGG-AGATAAGACTCGCCAT
* **
15472 CTAAAATCTGCTCCATAGCCGATACATGG
61 TTCTAATCTGCTCCATAGCCGATACATGG
** * * **
15501 AGATAAGACTTGCCATTTCT--GATCTGCTCCACAGCCGATACATGGAGATAAGA-TCTGTAATT
1 AGATAAGACTTG---TGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTC-GCCATT
** ** *
15563 T-TCGGTCTGCTTCC-T-G-TAACTTCA-GG
62 TCT-AATCTGC-TCCATAGCCGA-TACATGG
15589 AAGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCG-CATTTCT
1 -AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCT
*
15653 GATCTGCTCCATAGCCGATACATGG
65 AATCTGCTCCATAGCCGATACATGG
*
15678 AGATAAGATTTGT
1 AGATAAGACTTGT
15691 AATTTTCAGT
Statistics
Matches: 205, Mismatches: 46, Indels: 55
0.67 0.15 0.18
Matches are distributed among these distances:
86 6 0.03
87 14 0.07
88 98 0.48
89 58 0.28
90 22 0.11
91 7 0.03
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (89 bp):
AGATAAGACTTGTGGCTAAAATCTGCTCCATAGCCGATACATGGAGATAAGACTCGCCATTTCTA
ATCTGCTCCATAGCCGATACATGG
Found at i:24831 original size:5 final size:5
Alignment explanation
Indices: 24821--24852 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
24811 TTGTGTGTTC
24821 TTTAT TTTAT TTTA- TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
24853 TCACAAATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:24840 original size:14 final size:14
Alignment explanation
Indices: 24821--24851 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
24811 TTGTGTGTTC
24821 TTTATTTTATTTTA
1 TTTATTTTATTTTA
24835 TTTATTTTATTTTA
1 TTTATTTTATTTTA
24849 TTT
1 TTT
24852 TTCACAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:27754 original size:54 final size:53
Alignment explanation
Indices: 27663--27805 Score: 216
Period size: 54 Copynumber: 2.7 Consensus size: 53
27653 TACGCAACAC
* *
27663 ACACCGAAGCCATATCCCAGAC-ATGGTCTTATACGGAATCACATTATCACATT
1 ACACCGATGCCATAGCCCAG-CTATGGTCTTATACGGAATCACATTATCACATT
*
27716 ATACCGATGCCATAGCCCAGCTAATGGTCTTATACGGAATCACATTATCACATT
1 ACACCGATGCCATAGCCCAGCT-ATGGTCTTATACGGAATCACATTATCACATT
* *
27770 GCACCGATGCCATAGCCCAGCTATGGTCTTAAACGG
1 ACACCGATGCCATAGCCCAGCTATGGTCTTATACGG
27806 GCGAACTTAT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 30 0.37
54 51 0.62
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (53 bp):
ACACCGATGCCATAGCCCAGCTATGGTCTTATACGGAATCACATTATCACATT
Found at i:30110 original size:18 final size:20
Alignment explanation
Indices: 30074--30111 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
30064 TTTCTGTGGA
*
30074 TTTTTGTTTGTTCGTAGTTT
1 TTTTTGTCTGTTCGTAGTTT
30094 TTTTTGTCT-TTCG-AGTTT
1 TTTTTGTCTGTTCGTAGTTT
30112 GCTTCCACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 4 0.24
20 8 0.47
ACGTcount: A:0.05, C:0.08, G:0.18, T:0.68
Consensus pattern (20 bp):
TTTTTGTCTGTTCGTAGTTT
Found at i:37497 original size:18 final size:18
Alignment explanation
Indices: 37474--37510 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
37464 AAATTGATGT
37474 TAAATTTATTCATATAGA
1 TAAATTTATTCATATAGA
*
37492 TAAATTTATTCGTATAGA
1 TAAATTTATTCATATAGA
37510 T
1 T
37511 CCGGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (18 bp):
TAAATTTATTCATATAGA
Found at i:38019 original size:26 final size:27
Alignment explanation
Indices: 37979--38036 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
37969 TCCCATTAAA
* *
37979 GGCTCTTTCATGAGCTTTTCGATTTATT
1 GGCTCTTTCATGAGCTTCTCGA-TAATT
38007 GGCTC-TTCA-GAGCTTCTCGATAATT
1 GGCTCTTTCATGAGCTTCTCGATAATT
38032 GGCTC
1 GGCTC
38037 GCTTGAACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 9 0.32
26 10 0.36
27 4 0.14
28 5 0.18
ACGTcount: A:0.16, C:0.22, G:0.21, T:0.41
Consensus pattern (27 bp):
GGCTCTTTCATGAGCTTCTCGATAATT
Found at i:44564 original size:21 final size:21
Alignment explanation
Indices: 44539--44582 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
44529 GAAATGCAAG
*
44539 AAAAGAAAATTTGCTCAAGAT
1 AAAAGAAAATTTGCTCAAAAT
* * *
44560 AAAAGGATATTTTCTCAAAAT
1 AAAAGAAAATTTGCTCAAAAT
44581 AA
1 AA
44583 GACATGAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.52, C:0.09, G:0.11, T:0.27
Consensus pattern (21 bp):
AAAAGAAAATTTGCTCAAAAT
Found at i:60217 original size:12 final size:12
Alignment explanation
Indices: 60200--60224 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60190 TCCTGCAAAA
60200 TTGAAAATTAAG
1 TTGAAAATTAAG
60212 TTGAAAATTAAG
1 TTGAAAATTAAG
60224 T
1 T
60225 ATAAGATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TTGAAAATTAAG
Found at i:70860 original size:5 final size:5
Alignment explanation
Indices: 70850--70874 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
70840 AATACAAATA
70850 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
70875 ATAAATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:70907 original size:22 final size:21
Alignment explanation
Indices: 70865--70910 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
70855 TTTATTTTAT
70865 TTTATTTTATATAAATATTTG
1 TTTATTTTATATAAATATTTG
* *
70886 TTTATTTATATTTATATATTTG
1 TTTATTT-TATATAAATATTTG
70908 TTT
1 TTT
70911 GTCAACGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATTTTATATAAATATTTG
Found at i:73135 original size:16 final size:17
Alignment explanation
Indices: 73111--73150 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
73101 ATATATATAT
* *
73111 AAAGTAAAAGAA-ATAA
1 AAAGAAAAAGAATAGAA
73127 AAAGAAAAAGAATAGAA
1 AAAGAAAAAGAATAGAA
73144 AAAGAAA
1 AAAGAAA
73151 GAAAGGATGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (17 bp):
AAAGAAAAAGAATAGAA
Found at i:73145 original size:11 final size:10
Alignment explanation
Indices: 73117--73154 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
73107 ATATAAAGTA
73117 AAAGAAATAA-
1 AAAGAAA-AAG
73127 AAAGAAAAAG
1 AAAGAAAAAG
73137 AATAGAAAAAG
1 AA-AGAAAAAG
73148 AAAGAAA
1 AAAGAAA
73155 GGATGAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 2 0.08
10 14 0.54
11 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:73217 original size:16 final size:16
Alignment explanation
Indices: 73173--73211 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
73163 CGAGAGCAGG
* *
73173 GGAAAGAAAGAAGGAA
1 GGAAAAAAAGAAAGAA
73189 GGAAAAAAAGAAAGAA
1 GGAAAAAAAGAAAGAA
73205 GGAAAAA
1 GGAAAAA
73212 GGGAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
GGAAAAAAAGAAAGAA
Found at i:75337 original size:46 final size:46
Alignment explanation
Indices: 75270--75587 Score: 537
Period size: 46 Copynumber: 6.9 Consensus size: 46
75260 TGCTCTCTGG
75270 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
*
75316 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
*
75362 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
** *
75408 TATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
* * **
75454 CATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
75500 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
**
75546 TATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
75588 GTGACATGGC
Statistics
Matches: 260, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 260 1.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
TATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGA
Found at i:75597 original size:13 final size:13
Alignment explanation
Indices: 75579--75608 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
75569 TGAAAGATAC
75579 CATGGCAACGTGA
1 CATGGCAACGTGA
75592 CATGGCAACGTGA
1 CATGGCAACGTGA
75605 CATG
1 CATG
75609 AAAAGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.30, C:0.23, G:0.30, T:0.17
Consensus pattern (13 bp):
CATGGCAACGTGA
Found at i:75610 original size:59 final size:59
Alignment explanation
Indices: 75533--75652 Score: 195
Period size: 59 Copynumber: 2.0 Consensus size: 59
75523 TGAAAGATAC
* * * *
75533 CATGGCAACCTGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACGTGA
1 CATGGCAACCTGACATGAAAAGAATAAGACCATGATTGAAAGATACCATGGCAACATGA
*
75592 CATGGCAACGTGACATGAAAAGAATAAGACCATGATTGAAAGATACCATGGCAACATGA
1 CATGGCAACCTGACATGAAAAGAATAAGACCATGATTGAAAGATACCATGGCAACATGA
75651 CA
1 CA
75653 GAAAATGAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (59 bp):
CATGGCAACCTGACATGAAAAGAATAAGACCATGATTGAAAGATACCATGGCAACATGA
Found at i:86507 original size:14 final size:15
Alignment explanation
Indices: 86479--86507 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
86469 TATATCACAC
86479 ATAGAGCATGCAAGA
1 ATAGAGCATGCAAGA
86494 ATAGAGCA-GCAAGA
1 ATAGAGCATGCAAGA
86508 TACTCCATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.14, G:0.28, T:0.10
Consensus pattern (15 bp):
ATAGAGCATGCAAGA
Found at i:88351 original size:52 final size:52
Alignment explanation
Indices: 88273--88374 Score: 161
Period size: 52 Copynumber: 2.0 Consensus size: 52
88263 TATAAGGTAT
* *
88273 ATATGGCACACCATATGTAATTGTCAGGTTATTCCGTTAA-TTACGCCAGTAC
1 ATATGGCACACCATATGTAATTGTCAGATTATTCAG-TAATTTACGCCAGTAC
*
88325 ATATGGCACACTATATGTAATTGTCAGATTATTCAGTAATTTACGCCAGT
1 ATATGGCACACCATATGTAATTGTCAGATTATTCAGTAATTTACGCCAGT
88375 TTTTAATAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 3 0.07
52 43 0.93
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (52 bp):
ATATGGCACACCATATGTAATTGTCAGATTATTCAGTAATTTACGCCAGTAC
Found at i:88691 original size:40 final size:40
Alignment explanation
Indices: 88636--88716 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
88626 TGTAGACAAC
*
88636 CCTTTGTTCTTTGATAATTACAAAGCTGCATATAGTAAAA
1 CCTTTGTTCTTTGATAATTACAAAGCTGCATATAGCAAAA
* *
88676 CCTTTGTTCTTTGATAATTACAGAGTTGCATATAGCAAAA
1 CCTTTGTTCTTTGATAATTACAAAGCTGCATATAGCAAAA
88716 C
1 C
88717 AAGCATAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (40 bp):
CCTTTGTTCTTTGATAATTACAAAGCTGCATATAGCAAAA
Done.