Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2606
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: 36339
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:1043 original size:18 final size:18
Alignment explanation
Indices: 1020--1054 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1010 GAGCATCGGC
*
1020 TTTTTTTCTTC-TTTCTT
1 TTTTTTTTTTCGTTTCTT
1037 TTTTTTTTTTCGTTTCTT
1 TTTTTTTTTTCGTTTCTT
1055 GGTCCCACTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (18 bp):
TTTTTTTTTTCGTTTCTT
Found at i:1550 original size:18 final size:18
Alignment explanation
Indices: 1523--1558 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1513 TCTGTGTGCA
1523 CATTAACACAACTTCCTC
1 CATTAACACAACTTCCTC
*
1541 CATTAGCACAACTTCCTC
1 CATTAACACAACTTCCTC
1559 GAAACTTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.39, G:0.03, T:0.28
Consensus pattern (18 bp):
CATTAACACAACTTCCTC
Found at i:4151 original size:2 final size:2
Alignment explanation
Indices: 4144--4178 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
4134 TATTGTATTT
4144 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4179 TTGTACTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4735 original size:12 final size:12
Alignment explanation
Indices: 4718--4744 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
4708 AATGGCCTAA
4718 CCACATATCTGG
1 CCACATATCTGG
4730 CCACATATCTGG
1 CCACATATCTGG
4742 CCA
1 CCA
4745 GCAGATGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (12 bp):
CCACATATCTGG
Found at i:5629 original size:21 final size:21
Alignment explanation
Indices: 5603--5645 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5593 TGTATCGATA
5603 TAATGTATCAATACATTTCCT
1 TAATGTATCAATACATTTCCT
*
5624 TAATGTATCGATACATTTCCT
1 TAATGTATCAATACATTTCCT
5645 T
1 T
5646 GGCAGTAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (21 bp):
TAATGTATCAATACATTTCCT
Found at i:5694 original size:19 final size:17
Alignment explanation
Indices: 5670--5732 Score: 62
Period size: 19 Copynumber: 3.7 Consensus size: 17
5660 AGCAATACAT
5670 TGTATCGATACAAAATTTA
1 TGTATCGATAC-AAA-TTA
5689 TGTATCGATAC--A-T-
1 TGTATCGATACAAATTA
5702 TGTATCGATACAACACTTA
1 TGTATCGATACAA-A-TTA
5721 TGTATCGATACA
1 TGTATCGATACA
5733 TTTTCTGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.61
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (17 bp):
TGTATCGATACAAATTA
Found at i:5705 original size:32 final size:32
Alignment explanation
Indices: 5664--5734 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
5654 CTTCGTAGCA
*
5664 ATACATTGTATCGATACAAAATTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
*
5696 ATACATTGTATCGATACAACACTTATGTATCG
1 ATACATTGTATCGATACAAAACTTATGTATCG
5728 ATACATT
1 ATACATT
5735 TTCTGTTTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTTATGTATCG
Found at i:5707 original size:13 final size:13
Alignment explanation
Indices: 5689--5713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5679 ACAAAATTTA
5689 TGTATCGATACAT
1 TGTATCGATACAT
5702 TGTATCGATACA
1 TGTATCGATACA
5714 ACACTTATGT
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:5761 original size:19 final size:19
Alignment explanation
Indices: 5701--5762 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
5691 TATCGATACA
5701 TTGTATCGATACAACACT-T
1 TTGTATCGATACAA-ACTGT
* **
5720 ATGTATCGATACATTTTCTGT
1 TTGTATCGATACA--AACTGT
5741 TTGTATCGATACAAACTGT
1 TTGTATCGATACAAACTGT
5760 TTG
1 TTG
5763 AAGTTCAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
19 19 0.56
20 2 0.06
21 13 0.38
ACGTcount: A:0.27, C:0.16, G:0.15, T:0.42
Consensus pattern (19 bp):
TTGTATCGATACAAACTGT
Found at i:5824 original size:21 final size:21
Alignment explanation
Indices: 5795--5864 Score: 131
Period size: 21 Copynumber: 3.3 Consensus size: 21
5785 GGACCTTATA
5795 ATCGATACATTCTACAAATGT
1 ATCGATACATTCTACAAATGT
*
5816 ATTGATACATTCTACAAATGT
1 ATCGATACATTCTACAAATGT
5837 ATCGATACATTCTACAAATGT
1 ATCGATACATTCTACAAATGT
5858 ATCGATA
1 ATCGATA
5865 TATTTGGATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
ATCGATACATTCTACAAATGT
Found at i:15368 original size:17 final size:16
Alignment explanation
Indices: 15348--15395 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
15338 AAAAAAAGAG
15348 AAGAAAAAAATACAAAA
1 AAGAAAAAAA-ACAAAA
*
15365 AAGATAAAAAAACAACA
1 AAGA-AAAAAAACAAAA
*
15382 AACAAAAAAAACAA
1 AAGAAAAAAAACAA
15396 CAACAAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 10 0.36
17 12 0.43
18 6 0.21
ACGTcount: A:0.81, C:0.10, G:0.04, T:0.04
Consensus pattern (16 bp):
AAGAAAAAAAACAAAA
Found at i:15389 original size:16 final size:16
Alignment explanation
Indices: 15351--15404 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
15341 AAAAGAGAAG
* *
15351 AAAAAAATACAAAAAAG
1 AAAAAAA-ACAACAAAC
15368 ATAAAAAAACAACAAAC
1 A-AAAAAAACAACAAAC
15385 AAAAAAAACAAC-AAC
1 AAAAAAAACAACAAAC
15400 AAAAA
1 AAAAA
15405 GGGTCCGGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 9 0.26
18 6 0.18
ACGTcount: A:0.81, C:0.13, G:0.02, T:0.04
Consensus pattern (16 bp):
AAAAAAAACAACAAAC
Found at i:16868 original size:29 final size:30
Alignment explanation
Indices: 16825--16914 Score: 123
Period size: 29 Copynumber: 3.1 Consensus size: 30
16815 TTCCTCACCC
16825 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
* * *
16855 TTC-AAAGCCCACAAATCAGTGGCAAC--C
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
*
16882 TTCAAAAGCCCACAAGTCTGTGGCATCTTT
1 TTCAAAAGCCCACAAGTCAGTGGCATCTTT
16912 TTC
1 TTC
16915 CTTTTAAGCC
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.06
28 20 0.40
29 21 0.42
30 6 0.12
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.26
Consensus pattern (30 bp):
TTCAAAAGCCCACAAGTCAGTGGCATCTTT
Found at i:16938 original size:33 final size:32
Alignment explanation
Indices: 16887--16968 Score: 92
Period size: 32 Copynumber: 2.5 Consensus size: 32
16877 CAACCTTCAA
* * * *
16887 AAGCCCACAAGTCTGTGGCATCTTTTTCCTTTT
1 AAGCCCACAACTCCGTGGC-GCCTTTTCCTTTT
* *
16920 AAGCCCATAACTCCGTGGCGCCTTTTCTTTTT
1 AAGCCCACAACTCCGTGGCGCCTTTTCCTTTT
*
16952 AAGTCCACAACTCCGTG
1 AAGCCCACAACTCCGTG
16969 ACACCTTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
32 25 0.61
33 16 0.39
ACGTcount: A:0.20, C:0.30, G:0.16, T:0.34
Consensus pattern (32 bp):
AAGCCCACAACTCCGTGGCGCCTTTTCCTTTT
Found at i:17129 original size:28 final size:29
Alignment explanation
Indices: 17063--17132 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 29
17053 TTTTCCTTTT
*
17063 AAGCCCACAAGTCAGTGGCACCCTTTTCAA
1 AAGCCCACAAGTCAGTGGCAACC-TTTCAA
17093 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGCAACCTTTCAA
*
17121 AAGCACACAAGT
1 AAGCCCACAAGT
17133 TGGTGGCGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 16 0.42
30 22 0.58
ACGTcount: A:0.36, C:0.31, G:0.17, T:0.16
Consensus pattern (29 bp):
AAGCCCACAAGTCAGTGGCAACCTTTCAA
Found at i:17210 original size:43 final size:44
Alignment explanation
Indices: 17144--17408 Score: 257
Period size: 43 Copynumber: 5.7 Consensus size: 44
17134 GGTGGCGTCT
*
17144 TCTTCTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 TCTT-TAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* *
17189 -CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCC
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGC-AC
* * * *
17233 TTTGTCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACACTGGCAC
1 ----TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
* * *
17281 -CTTTAAGTCCAATATCGCTAGCTTTGAATCAGCATATTGGCACCTC
1 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCA---C
* *
17327 ATCTTTAAGACCAATGTCAG-TGGCCTTGAATCAGCACATTGGCACCTTC
1 -TCTTTAAGTCCAATATC-GCTGGCCTTGAATCAGCACATTGGCA----C
17376 ATCTTTAAGTCCAATATCGCTGGCCTTGAATCA
1 -TCTTTAAGTCCAATATCGCTGGCCTTGAATCA
17409 ACATATTAGC
Statistics
Matches: 184, Mismatches: 22, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
43 73 0.40
44 4 0.02
46 1 0.01
48 37 0.20
49 69 0.38
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.31
Consensus pattern (44 bp):
TCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:17262 original size:49 final size:46
Alignment explanation
Indices: 17144--17617 Score: 289
Period size: 49 Copynumber: 9.9 Consensus size: 46
17134 GGTGGCGTCT
17144 TCTTCTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGG--C-A
1 TCTT-TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCCTA
* * * *
17188 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCTCCTTTG
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC-CC--TA
* * *
17237 TCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACACTGG--C-A
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCCTA
* * * * *
17280 CCTTTAAGTCCAATATCGCTAGCTTTGAATCAGCATATTGGCACCTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC-CCT-A
*
17328 TCTTTAAGACCAATGTCAG-TGGCCTTGAATCAGCACATTGGCACCTTCA
1 TCTTTAAGTCCAATGTC-GCTGGCCTTGAATCAGCACATTGGC-CC-T-A
* * *
17377 TCTTTAAGTCCAATATCGCTGGCCTTGAATCAACATATTAGCGCCTTCGTCA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATT-G-GCC--C-T-A
* * *
17429 TCTTTCAAAT-CAATGTCGCTGGCCTTGATTCAGCACATTGACACCTTCA
1 TCTTT-AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC-CC-T-A
* * ** * ** *
17478 TCCTTAAGTCTAAAATCGTTGGCCTTGAATCAGCGTATTGGCATCTTTA
1 TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC--C-CTA
* * * ** * ** *
17527 ACATTCCTAAGTCCAATGTCACTGCCCTTGCCTTAGCACATTGGCATTTT
1 TC-TT--TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGC-CCTA
* * *
17577 TCTTCAAGTCTAAATGTCGCTGGCCATGAATCAGCACATTG
1 TCTTTAAGTC-CAATGTCGCTGGCCTTGAATCAGCACATTG
17618 TCATTCTTCG
Statistics
Matches: 331, Mismatches: 72, Indels: 50
0.73 0.16 0.11
Matches are distributed among these distances:
43 70 0.21
44 3 0.01
46 3 0.01
47 5 0.02
48 65 0.20
49 108 0.33
50 9 0.03
51 4 0.01
52 61 0.18
53 3 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.32
Consensus pattern (46 bp):
TCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCCCTA
Found at i:17271 original size:92 final size:92
Alignment explanation
Indices: 17144--17572 Score: 414
Period size: 101 Copynumber: 4.5 Consensus size: 92
17134 GGTGGCGTCT
*
17144 TCTTCTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTG
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTG
* *
17209 GCCTTGAATCAGCATATTGGCTCCTTTG
65 GCCTTGAATCAGCATATTGGCACCTTTA
* * *
17237 TCTTTAAGACCAATGTCGCTAGCCTTGAATCAGCACACTGGCACCTTTAAGTCCAATATCGCTAG
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGG
* *
17302 CTTTGAATCAGCATATTGGCACC-TCA
66 CCTTGAATCAGCATATTGGCACCTTTA
17328 TCTTTAAGACCAATGTCAG-TGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATA
1 TCTTTAAGACCAATGTC-GCTGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATA
* * *
17392 TCGCTGGCCTTGAATCAACATATTAGCGCCTTCGTCA
59 TCGCTGGCCTTGAATCAGCATATTGGCACCTT--T-A
* * * * *
17429 TCTTTCAA-ATCAATGTCGCTGGCCTTGATTCAGCACATTGACACCTTCATCCTTAAGTCTAAAA
1 TCTTT-AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-C--C-T--TTAAGTCCAATA
* * *
17493 TCGTTGGCCTTGAATCAGCGTATTGGCATCTTTA
59 TCGCTGGCCTTGAATCAGCATATTGGCACCTTTA
* * * * ** *
17527 ACATTCCTAAGTCCAATGTCACTGCCCTTGCCTTAGCACATTGGCA
1 TC-TT--TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCA
17573 TTTTTCTTCA
Statistics
Matches: 278, Mismatches: 38, Indels: 32
0.80 0.11 0.09
Matches are distributed among these distances:
91 40 0.14
92 79 0.28
93 4 0.01
95 1 0.00
97 39 0.14
98 6 0.02
99 4 0.01
100 3 0.01
101 100 0.36
102 2 0.01
ACGTcount: A:0.25, C:0.27, G:0.17, T:0.31
Consensus pattern (92 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGG
CCTTGAATCAGCATATTGGCACCTTTA
Found at i:18405 original size:13 final size:13
Alignment explanation
Indices: 18387--18411 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18377 TTCAACGAAT
18387 TGTATCGATACAA
1 TGTATCGATACAA
18400 TGTATCGATACA
1 TGTATCGATACA
18412 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:18501 original size:13 final size:13
Alignment explanation
Indices: 18483--18507 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18473 ATTACTCAAA
18483 TGTATCGATACAT
1 TGTATCGATACAT
18496 TGTATCGATACA
1 TGTATCGATACA
18508 CTGATCTTTG
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:18561 original size:52 final size:52
Alignment explanation
Indices: 18516--18644 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
18506 CACTGATCTT
* * * *
18516 TGTATCGATACATGCAAGCAAATTTGCCCAGATGTATCAATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
*
18568 TGTATCGATACATACAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
18620 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
18645 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCAAGATGTATCGATACACTATAAAA
Found at i:26682 original size:486 final size:486
Alignment explanation
Indices: 25766--26716 Score: 1866
Period size: 486 Copynumber: 2.0 Consensus size: 486
25756 TTTATAGTCA
* *
25766 AGAGTAAGCGTACTTATCTTTGACTTGGTCTGTCCTTTCATGTGTGGTGGCAAGTTTATCCCACA
1 AGAGCAAGCGTACTAATCTTTGACTTGGTCTGTCCTTTCATGTGTGGTGGCAAGTTTATCCCACA
*
25831 CTTGTTTGGCATTATCGTAGAGCGAGTCTCTGTTATACTCACTTGGGCTGAGAGCACAAAATAAC
66 CTTGTTTGGCATTATCGTAGAGCGAGTCTCTGTTATACCCACTTGGGCTGAGAGCACAAAATAAC
25896 GTGTGCAACACTTTAGGCTGAGTTGTGCATCTTTATGTCTTGATCATTCCATTCTTCTTTTTCTT
131 GTGTGCAACACTTTAGGCTGAGTTGTGCATCTTTATGTCTTGATCATTCCATTCTTCTTTTTCTT
*
25961 TGGGCATGAGGACGTCATTAACTCTTTTCATTGGAATACGAGGTCCATTTATGATTATCTTCCAC
196 TGGGCACGAGGACGTCATTAACTCTTTTCATTGGAATACGAGGTCCATTTATGATTATCTTCCAC
26026 ACTTTGTAATCATTTGCTTGAATAAATAACCTCATTCTTGTCCTCCAATATGAGTAGTTGTAACC
261 ACTTTGTAATCATTTGCTTGAATAAATAACCTCATTCTTGTCCTCCAATATGAGTAGTTGTAACC
26091 ATTAAAGAATGGAGGTCTCATGATTGAGTAACCTTCGAGTCCAATAGCATTTGAGTTTGTTTCCA
326 ATTAAAGAATGGAGGTCTCATGATTGAGTAACCTTCGAGTCCAATAGCATTTGAGTTTGTTTCCA
26156 AGGCCATGAGACACACTTTGTCTTGGCTCATCACTTCTTGTGAAACTTTGATCATTAATGAGTTT
391 AGGCCATGAGACACACTTTGTCTTGGCTCATCACTTCTTGTGAAACTTTGATCATTAATGAGTTT
26221 TTCATTTAAGTGTGGTGGCAAGTTTAGGCTG
456 TTCATTTAAGTGTGGTGGCAAGTTTAGGCTG
26252 AGAGCAAGCGTACTAATCTTTGACTTGGTCTGTCCTTTCATGTGTGGTGGCAAGTTTATCCCACA
1 AGAGCAAGCGTACTAATCTTTGACTTGGTCTGTCCTTTCATGTGTGGTGGCAAGTTTATCCCACA
26317 CTTGTTTGGCATTATCGTAGAGCGAGTCTCTGTTATACCCACTTGGGCTGAGAGCACAAAATAAC
66 CTTGTTTGGCATTATCGTAGAGCGAGTCTCTGTTATACCCACTTGGGCTGAGAGCACAAAATAAC
26382 GTGTGCAACACTTTAGGCTGAGTTGTGCATCTTTATGTCTTGATCATTCCATTCTTCTTTTTCTT
131 GTGTGCAACACTTTAGGCTGAGTTGTGCATCTTTATGTCTTGATCATTCCATTCTTCTTTTTCTT
26447 TGGGCACGAGGACGTCATTAACTCTTTTCATTGGAATACGAGGTCCATTTATGATTATCTTCCAC
196 TGGGCACGAGGACGTCATTAACTCTTTTCATTGGAATACGAGGTCCATTTATGATTATCTTCCAC
26512 ACTTTGTAATCATTTGCTTGAATAAATAACCTCATTCTTGTCCTCCAATATGAGTAGTTGTAACC
261 ACTTTGTAATCATTTGCTTGAATAAATAACCTCATTCTTGTCCTCCAATATGAGTAGTTGTAACC
26577 ATTAAAGAATGGAGGTCTCATGATTGAGTAACCTTCGAGTCCAATAGCATTTGAGTTTGTTTCCA
326 ATTAAAGAATGGAGGTCTCATGATTGAGTAACCTTCGAGTCCAATAGCATTTGAGTTTGTTTCCA
26642 AGGCCATGAGACACACTTTGTCTTGGCTCATCACTTCTTGTGAAACTTTGATCATTAATGAGTTT
391 AGGCCATGAGACACACTTTGTCTTGGCTCATCACTTCTTGTGAAACTTTGATCATTAATGAGTTT
26707 TTCATTTAAG
456 TTCATTTAAG
26717 CTAGTAGGAT
Statistics
Matches: 461, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
486 461 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (486 bp):
AGAGCAAGCGTACTAATCTTTGACTTGGTCTGTCCTTTCATGTGTGGTGGCAAGTTTATCCCACA
CTTGTTTGGCATTATCGTAGAGCGAGTCTCTGTTATACCCACTTGGGCTGAGAGCACAAAATAAC
GTGTGCAACACTTTAGGCTGAGTTGTGCATCTTTATGTCTTGATCATTCCATTCTTCTTTTTCTT
TGGGCACGAGGACGTCATTAACTCTTTTCATTGGAATACGAGGTCCATTTATGATTATCTTCCAC
ACTTTGTAATCATTTGCTTGAATAAATAACCTCATTCTTGTCCTCCAATATGAGTAGTTGTAACC
ATTAAAGAATGGAGGTCTCATGATTGAGTAACCTTCGAGTCCAATAGCATTTGAGTTTGTTTCCA
AGGCCATGAGACACACTTTGTCTTGGCTCATCACTTCTTGTGAAACTTTGATCATTAATGAGTTT
TTCATTTAAGTGTGGTGGCAAGTTTAGGCTG
Found at i:27653 original size:33 final size:33
Alignment explanation
Indices: 27610--27674 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
27600 TAATTCATGG
*
27610 TGTATTGATACAAAGCAATTTGTATCGATACAA
1 TGTATCGATACAAAGCAATTTGTATCGATACAA
**
27643 TGTATCGATACTTAGCAATTTGTATCGATACA
1 TGTATCGATACAAAGCAATTTGTATCGATACA
27675 TTTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAAAGCAATTTGTATCGATACAA
Found at i:28236 original size:33 final size:32
Alignment explanation
Indices: 28140--28236 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
28130 GACTGACCAG
* * *
28140 GGCAAAACCATGATAGTCAATGATATGACTAA
1 GGCAAAACCATGATAGTTAAAGATGTGACTAA
* * * *
28172 GGCGAAACC-T-TTAGTTAAAAAAGTTGACTAA
1 GGCAAAACCATGATAGTTAAAGATG-TGACTAA
*
28203 GGCAAAACCATGATAGTTAAAGTTGTGACCTAA
1 GGCAAAACCATGATAGTTAAAGATGTGA-CTAA
28236 G
1 G
28237 CGAAACCTTT
Statistics
Matches: 49, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
30 7 0.14
31 16 0.33
32 12 0.24
33 14 0.29
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (32 bp):
GGCAAAACCATGATAGTTAAAGATGTGACTAA
Found at i:31129 original size:14 final size:14
Alignment explanation
Indices: 31094--31131 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
31084 ACTTATACCA
31094 TAAAAATT-AATTG
1 TAAAAATTAAATTG
31107 -AAAAGATTAAATTG
1 TAAAA-ATTAAATTG
31121 TAAAAATTAAA
1 TAAAAATTAAA
31132 AATCATGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.18
13 3 0.14
14 11 0.50
15 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (14 bp):
TAAAAATTAAATTG
Done.