Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold717
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: 37141
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:3937 original size:21 final size:20
Alignment explanation
Indices: 3846--3990 Score: 136
Period size: 20 Copynumber: 7.1 Consensus size: 20
3836 AAGAGGACAG
*
3846 AATGTATCGATACATTGAAG-
1 AATGTATCGATACATTG-GGT
**
3866 AATGTATCGATACATT-CAT
1 AATGTATCGATACATTGGGT
**
3885 ACATGTATCGATACATT-GAA
1 A-ATGTATCGATACATTGGGT
*
3905 AGATGTACCGATACATTTGGGT
1 A-ATGTATCGATACA-TTGGGT
*
3927 AATGTATCGATACATT-GGA
1 AATGTATCGATACATTGGGT
3946 AGATGTATCGATACATCTGGGT
1 A-ATGTATCGATACAT-TGGGT
3968 AATGTATCGATACATCTGGGT
1 AATGTATCGATACAT-TGGGT
3989 AA
1 AA
3991 AAATGTGACT
Statistics
Matches: 107, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
19 4 0.04
20 61 0.57
21 37 0.35
22 5 0.05
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGGGT
Found at i:3949 original size:41 final size:41
Alignment explanation
Indices: 3846--3982 Score: 190
Period size: 41 Copynumber: 3.4 Consensus size: 41
3836 AAGAGGACAG
**
3846 AATGTATCGATACATT-GAAGAATGTATCGATACA-TT-CAT
1 AATGTATCGATACATTGGAAG-ATGTATCGATACATTTGGGT
* *
3885 ACATGTATCGATACATTGAAAGATGTACCGATACATTTGGGT
1 A-ATGTATCGATACATTGGAAGATGTATCGATACATTTGGGT
*
3927 AATGTATCGATACATTGGAAGATGTATCGATACATCTGGGT
1 AATGTATCGATACATTGGAAGATGTATCGATACATTTGGGT
3968 AATGTATCGATACAT
1 AATGTATCGATACAT
3983 CTGGGTAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
39 1 0.01
40 27 0.31
41 57 0.66
42 2 0.02
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (41 bp):
AATGTATCGATACATTGGAAGATGTATCGATACATTTGGGT
Found at i:5082 original size:29 final size:29
Alignment explanation
Indices: 4890--5280 Score: 458
Period size: 28 Copynumber: 13.4 Consensus size: 29
4880 CACTAACTTG
* *
4890 TGTGGGCTTTGAAAAAAGTTGCCA-TCGACT
1 TGTGGGCTTTG-AAAAGGATGCCACT-GACT
* * *
4920 TGCGTGGGCTTTGAAAAGAGTTACCGCTGACT
1 T--GTGGGCTTTGAAAAG-GATGCCACTGACT
*
4952 TGTGGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
4980 TATGGGCTTTG-AAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
5008 TGTGGACTTTG-AAAGGAGTTGCCACCGACTT
1 TGTGGGCTTTGAAAAGGA--TGCCACTGAC-T
5039 GTGTGGGCTTTGAAAAGGATGCCACTGACT
1 -TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5069 TGTGGGCTTTG-AAAGGATGCCAATGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5097 TGTGGGCTTTG-AAAGGATGCCAATGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5125 TGTGGGCTTTG-AAAGGATGCCACTGACC
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5153 TGTGAGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5181 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
*
5210 TGTGGGCTTTGAAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAAGGATGCCACTGACT
* *
5239 TGTGGGCTTTTGAAGA-GATGCCACTGACC
1 TGTGGGC-TTTGAAAAGGATGCCACTGACT
*
5268 TGTAGGCTTTGAA
1 TGTGGGCTTTGAA
5281 GAGATGAACG
Statistics
Matches: 322, Mismatches: 27, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.02
28 154 0.48
29 79 0.25
30 33 0.10
31 14 0.04
32 30 0.09
33 7 0.02
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (29 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACT
Found at i:7067 original size:78 final size:78
Alignment explanation
Indices: 6968--7168 Score: 226
Period size: 79 Copynumber: 2.6 Consensus size: 78
6958 AATAACAGGG
* * * * *
6968 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTA
*
7031 GAAAAAAAATCGGGA
64 GAAAAAAAACCGGGA
* *
7046 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATA-TTTAG
* * * *
7111 GAATAAAGCCGGGG
65 AAAAAAAACCGGGA
* * *
7125 TTGGAGTATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGAT
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGAT
7169 GAAATAACGA
Statistics
Matches: 104, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
77 7 0.07
78 45 0.43
79 52 0.50
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.25
Consensus pattern (78 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGA
AAAAAAACCGGGA
Found at i:7176 original size:28 final size:28
Alignment explanation
Indices: 7120--7196 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
7110 GGAATAAAGC
*** *
7120 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
7148 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * *
7176 CGAGGTTGGAGCATCCTCGAT
1 CGGGGTTGGAGTATCCCCGAT
7197 TGTGAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 42 1.00
ACGTcount: A:0.23, C:0.21, G:0.34, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:7249 original size:52 final size:52
Alignment explanation
Indices: 7180--7518 Score: 162
Period size: 52 Copynumber: 6.4 Consensus size: 52
7170 AAATAACGAG
* *
7180 GTTGGAGCATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
** * ** * *
7232 GTTGGAGTATCCCCGATTAAAGGAAAATTGG-CGTTTTGAAAATAAAACTAGGA
1 GTTGGAGTATCCCCGATT-GTGAAAAATTGGTATTTTTGGAAATAAAA-TCGGA
* * * * *
7285 -TTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCG--ATAAAACCGGA
1 GTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTG-GAAATAAAATCGGA
* **** * * *
7336 GTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGG-AGTATCCCCGATGAT-TAA-CGGG
1 GTTGGAGTATCCCCGATTGTGAAA-AA-----TTGGTA-T-TTTTGGA-AATAAAATCGGA
*
7391 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAA-AAATT-G-G-TATTTTTGGAAATAAAATCGGA
* * * * *
7447 GTTAGAGTATCCCCGATTAT-AGAAAATTAGT-GTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGGAAATAAAATCGGA
* *
7498 GTTGGAATATCCTCGATTGTG
1 GTTGGAGTATCCCCGATTGTG
7519 GAGAATTGAT
Statistics
Matches: 211, Mismatches: 47, Indels: 58
0.67 0.15 0.18
Matches are distributed among these distances:
48 4 0.02
49 2 0.01
50 2 0.01
51 37 0.18
52 73 0.35
53 20 0.09
54 8 0.04
55 30 0.14
56 25 0.12
57 4 0.02
58 5 0.02
59 1 0.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGA
Found at i:7376 original size:28 final size:27
Alignment explanation
Indices: 7336--7406 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
7326 TAAAACCGGA
**
7336 GTTGGAGTATCCCCTCGGAAATAACGGG
1 GTTGGAGTATCCCCGAGG-AATAACGGG
* *
7364 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCGAGGAATAACGGG
7391 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
7407 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 24 0.62
28 15 0.38
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (27 bp):
GTTGGAGTATCCCCGAGGAATAACGGG
Found at i:7419 original size:107 final size:105
Alignment explanation
Indices: 7066--7460 Score: 293
Period size: 107 Copynumber: 3.7 Consensus size: 105
7056 CCTTCGAAAA
* * * * * *
7066 TAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAG
1 TAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTAGTATTTT-GGAATAAAACCGGAGTTGGAG
* *
7131 TATCCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAA
65 TATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-AT
* * * * * *
7173 TAACGAGGTTGGAGCATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGA
1 TAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTAGTA-TTTTGG-AATAAAACCGGAGTTGGA
* * ** * ** **
7238 GTAT-CCC-C-G-ATTAAAGGAAAATTGGCGT-T--TTGAAAAT
64 GTATCCCCTCGGAAATAACGG--GGTTGGAGTATCCCCGATGAT
* * * *
7275 AAAACTAGGATTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCG-ATAAAACCGGAGTT
1 -TAAC-GGGGTTGGAGTATCCCCAATTGT-GAAAAATTAGTATTTT-G-GAATAAAACCGGAGTT
7339 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
61 GGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
* * * *
7384 TAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGT
1 TAACGGGGTTGGAGTATCCCCAATTGTGAA-AAATT--AG--TATTTTGG-AATAAAACCGGAGT
*
7449 TAGAGTATCCCC
60 TGGAGTATCCCC
7461 GATTATAGAA
Statistics
Matches: 216, Mismatches: 49, Indels: 42
0.70 0.16 0.14
Matches are distributed among these distances:
102 1 0.00
103 5 0.02
104 47 0.22
105 16 0.07
106 18 0.08
107 62 0.29
108 32 0.15
109 6 0.03
110 1 0.00
111 28 0.13
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (105 bp):
TAACGGGGTTGGAGTATCCCCAATTGTGAAAAATTAGTATTTTGGAATAAAACCGGAGTTGGAGT
ATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAT
Found at i:7462 original size:56 final size:51
Alignment explanation
Indices: 7395--7523 Score: 134
Period size: 51 Copynumber: 2.4 Consensus size: 51
7385 AACGGGGTTG
* *
7395 GAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTATCCCCGATTGTG-AGAAATTAGTG----TTTTGAAAATAAAATCGGAGTTA
* *
7451 GAGTATCCCCGATTAT-AGAAAATTAGTGTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCCGATTGTGAG-AAATTAGTGTTTTGAAAATAAAATCGGAGTTA
* *
7502 GAATATCCTCGATTGTGGAGAA
1 GAGTATCCCCGATTGT-GAGAA
7524 TTGATAAACT
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
51 34 0.54
52 2 0.03
53 2 0.03
54 2 0.03
55 8 0.13
56 15 0.24
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (51 bp):
GAGTATCCCCGATTGTGAGAAATTAGTGTTTTGAAAATAAAATCGGAGTTA
Found at i:9908 original size:13 final size:13
Alignment explanation
Indices: 9890--9915 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9880 ACAAAGATCC
9890 ATGTATCGATACA
1 ATGTATCGATACA
9903 ATGTATCGATACA
1 ATGTATCGATACA
9916 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:9911 original size:33 final size:33
Alignment explanation
Indices: 9869--9935 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
9859 AAAATTTCCA
***
9869 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
9902 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
9935 A
1 A
9936 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:9979 original size:19 final size:18
Alignment explanation
Indices: 9955--10022 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
9945 CAGTAGCTAA
9955 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
9974 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
9989 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
10006 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
10023 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:9995 original size:13 final size:13
Alignment explanation
Indices: 9977--10001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9967 ACAATACTTA
9977 TGTATCGATACAT
1 TGTATCGATACAT
9990 TGTATCGATACA
1 TGTATCGATACA
10002 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:9999 original size:32 final size:32
Alignment explanation
Indices: 9958--10020 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
9948 TAGCTAATTA
*
9958 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
9990 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
10021 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:10084 original size:21 final size:21
Alignment explanation
Indices: 10058--10135 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
10048 GTTGGGATCC
10058 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
10079 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
10099 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
10120 TGTATCGATACATTTG
1 TGTATCGATACATTTG
10136 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:10122 original size:41 final size:40
Alignment explanation
Indices: 10058--10139 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
10048 GTTGGGATCC
* *
10058 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
10099 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
10139 T
1 T
10140 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:10806 original size:16 final size:16
Alignment explanation
Indices: 10787--10842 Score: 76
Period size: 17 Copynumber: 3.4 Consensus size: 16
10777 TTTGGACCCC
*
10787 TTTTTTTATTTGTTTG
1 TTTTTTTATTTTTTTG
10803 TTTTTTTATTTATTTTG
1 TTTTTTTATTT-TTTTG
*
10820 TTTTTGTTTTTTTTTTG
1 TTTTT-TTATTTTTTTG
10837 TTTTTT
1 TTTTTT
10843 GTCCTTATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
16 12 0.33
17 19 0.53
18 5 0.14
ACGTcount: A:0.05, C:0.00, G:0.09, T:0.86
Consensus pattern (16 bp):
TTTTTTTATTTTTTTG
Found at i:10829 original size:11 final size:11
Alignment explanation
Indices: 10799--10842 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
10789 TTTTTATTTG
10799 TTTGTTTTTTT
1 TTTGTTTTTTT
* *
10810 ATTTATTTTGTT
1 -TTTGTTTTTTT
10822 TTTGTTTTTTT
1 TTTGTTTTTTT
10833 TTTGTTTTTT
1 TTTGTTTTTT
10843 GTCCTTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.05, C:0.00, G:0.09, T:0.86
Consensus pattern (11 bp):
TTTGTTTTTTT
Found at i:10853 original size:18 final size:18
Alignment explanation
Indices: 10787--10854 Score: 63
Period size: 16 Copynumber: 4.0 Consensus size: 18
10777 TTTGGACCCC
*
10787 TTTTTT-TATTT-GTTTG
1 TTTTTTGTATTTATTTTG
10803 TTTTTT-TATTTATTTTG
1 TTTTTTGTATTTATTTTG
* *
10820 -TTTTTGTTTTTTTTTTG
1 TTTTTTGTATTTATTTTG
**
10837 TTTTTTGTCCTTATTTTG
1 TTTTTTGTATTTATTTTG
10855 GTACGAAGGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
16 16 0.37
17 13 0.30
18 14 0.33
ACGTcount: A:0.06, C:0.03, G:0.10, T:0.81
Consensus pattern (18 bp):
TTTTTTGTATTTATTTTG
Found at i:15609 original size:21 final size:19
Alignment explanation
Indices: 15583--15656 Score: 85
Period size: 19 Copynumber: 3.7 Consensus size: 19
15573 CTGCCAGTTT
**
15583 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
15604 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
* *
15623 CATGTATCGATACAAAGCAG
1 CATGTATCGATACAATG-AA
15643 CATGTATCGATACA
1 CATGTATCGATACA
15657 TCTAGATGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 18 0.38
20 15 0.31
21 15 0.31
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:16201 original size:18 final size:19
Alignment explanation
Indices: 16178--16221 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
16168 TTCATTTTTT
16178 CCTTAAAAAAAT-TCTCCC
1 CCTTAAAAAAATATCTCCC
** *
16196 CCTTAAACGATTATCTCCC
1 CCTTAAAAAAATATCTCCC
16215 CCTTAAA
1 CCTTAAA
16222 CAATTATCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (19 bp):
CCTTAAAAAAATATCTCCC
Found at i:16214 original size:19 final size:19
Alignment explanation
Indices: 16190--16230 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
16180 TTAAAAAAAT
*
16190 TCTCCCCCTTAAACGATTA
1 TCTCCCCCTTAAACAATTA
16209 TCTCCCCCTTAAACAATTA
1 TCTCCCCCTTAAACAATTA
16228 TCT
1 TCT
16231 TCTCCCCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.27, C:0.37, G:0.02, T:0.34
Consensus pattern (19 bp):
TCTCCCCCTTAAACAATTA
Found at i:24233 original size:19 final size:19
Alignment explanation
Indices: 24188--24244 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
24178 CTGCCAGTTT
**
24188 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
24209 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
24228 CATGTATCGATACAATG
1 CATGTATCGATACAATG
24245 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.56
21 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:24247 original size:13 final size:13
Alignment explanation
Indices: 24229--24288 Score: 60
Period size: 13 Copynumber: 5.1 Consensus size: 13
24219 TACAATGAAC
24229 ATGTATCGATACA
1 ATGTATCGATACA
24242 ATGTATCGATACA
1 ATGTATCGATACA
* *
24255 A---AGC-A-GC-
1 ATGTATCGATACA
24262 ATGTATCGATACA
1 ATGTATCGATACA
24275 ATGTATCGATACA
1 ATGTATCGATACA
24288 A
1 A
24289 AGCAGCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 1 0.03
10 4 0.11
11 1 0.03
12 1 0.03
13 28 0.76
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24267 original size:20 final size:20
Alignment explanation
Indices: 24242--24307 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
24232 TATCGATACA
24242 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAAAGCAGC
24262 ATGTATCGAT----A-CA--
1 ATGTATCGATACAAAGCAGC
24275 ATGTATCGATACAAAGCAGC
1 ATGTATCGATACAAAGCAGC
24295 ATGTATCGATACA
1 ATGTATCGATACA
24308 TCTAGATGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 23 0.59
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAGC
Found at i:24270 original size:33 final size:33
Alignment explanation
Indices: 24210--24307 Score: 171
Period size: 33 Copynumber: 3.0 Consensus size: 33
24200 CAATTTGTCC
* *
24210 ATGTATCGATACAATG-AACATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
24242 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
24275 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAGCAGCATGTATCGATACA
24308 TCTAGATGTG
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 15 0.24
33 48 0.76
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (33 bp):
ATGTATCGATACAAAGCAGCATGTATCGATACA
Found at i:35579 original size:1 final size:1
Alignment explanation
Indices: 35573--35612 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
35563 AAAGTGTTTG
***
35573 AAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35613 TTTTACAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:35593 original size:18 final size:18
Alignment explanation
Indices: 35570--35605 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
35560 GATAAAGTGT
35570 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
35588 TTGAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAA
35606 AAAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (18 bp):
TTGAAAAAAAAAAAAAAA
Done.