Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1783
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: 24204
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Found at i:726 original size:19 final size:19
Alignment explanation
Indices: 702--769 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
692 AATTCAACGA
702 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
721 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
736 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
753 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
770 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:740 original size:32 final size:32
Alignment explanation
Indices: 704--766 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
694 TTCAACGATT
*
704 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
736 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
767 TAATTAGCTA
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:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:741 original size:13 final size:13
Alignment explanation
Indices: 723--747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
713 ACATAAGTTT
723 TGTATCGATACAA
1 TGTATCGATACAA
736 TGTATCGATACA
1 TGTATCGATACA
748 TAAGTATTGT
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:827 original size:13 final size:13
Alignment explanation
Indices: 809--834 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
799 CATTTTTCTG
809 TGTATCGATACAT
1 TGTATCGATACAT
822 TGTATCGATACAT
1 TGTATCGATACAT
835 GGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:831 original size:33 final size:33
Alignment explanation
Indices: 789--855 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
779 GCCAAGGAAA
***
789 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
822 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
855 T
1 T
856 TGGAAATTTT
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:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:3340 original size:27 final size:27
Alignment explanation
Indices: 3307--3384 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
3297 TTTCTTCACA
3307 ATCGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
*
3334 ATTGGGGATACTCCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
3361 ATCGGGGATACTCCAACCCCGTTA
1 ATCGGGGATACTCCAACCCCGTTA
3385 TTTCTGAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:3404 original size:28 final size:27
Alignment explanation
Indices: 3310--3405 Score: 140
Period size: 27 Copynumber: 3.5 Consensus size: 27
3300 CTTCACAATC
*
3310 GGGGATACTCCAACCCCGTTAATCATT
1 GGGGATACTCCAACCCCGTTAATCATA
*
3337 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
3364 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
3392 GGGGATACTCCAAC
1 GGGGATACTCCAAC
3406 TCCGGTTTTA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
27 48 0.75
28 16 0.25
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.24
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:3477 original size:52 final size:53
Alignment explanation
Indices: 3392--3561 Score: 181
Period size: 52 Copynumber: 3.3 Consensus size: 53
3382 TTATTTCTGA
* *
3392 GGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTATTTC-CAAAAACACTAATTTTTCCATAATC
* * *
3444 GGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCTAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATTTCCAAAAACACTAATTTTTCC-ATAATC
* * * *
3496 GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTCT-CATAATC
1 GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACTAATTTTTCCATAATC
*
3548 GAGGATACTCCAAC
1 GGGGATACTCCAAC
3562 CTCGTTATTT
Statistics
Matches: 99, Mismatches: 12, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
51 9 0.09
52 74 0.75
53 12 0.12
54 4 0.04
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
GGGGATACTCCAACTCCGGTTTTATTTCCAAAAACACTAATTTTTCCATAATC
Found at i:3581 original size:28 final size:28
Alignment explanation
Indices: 3545--3621 Score: 95
Period size: 28 Copynumber: 2.8 Consensus size: 28
3535 ATTTCTCATA
* * *
3545 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3573 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
3601 --CGAGGGAATACTCCAACCCCG
1 ATCG-GGG-ATACTCCAACCCCG
3622 ACTTTATTCC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
26 2 0.05
27 3 0.07
28 39 0.89
ACGTcount: A:0.25, C:0.34, G:0.18, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:3661 original size:107 final size:107
Alignment explanation
Indices: 3500--3700 Score: 271
Period size: 107 Copynumber: 1.9 Consensus size: 107
3490 TTAATCGGGG
* * *
3500 ATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAACCTC
1 ATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAACCCC
3565 GTTATTTCATCG-GGGATACTCCAACCCCGTTACTTCCGAGGGA
66 GTTATTT--TCGAGGGATACTCCAACCCCGTTACTTCCGAGGGA
* *** * *
3608 ATACTCCAACCCCGACTTTA-TTCCCAAAATATTGATTTCTCATAATTGGGGATACTCCAACCCC
1 ATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAACCCC
*
3672 GTTATTTTCGAAGGGATACTCCAATCCCG
66 GTTATTTTCG-AGGGATACTCCAACCCCG
3701 ATTTTTTTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 5
0.84 0.10 0.05
Matches are distributed among these distances:
105 3 0.04
107 60 0.74
108 18 0.22
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.30
Consensus pattern (107 bp):
ATACTCCAACCCCGACTTTATTTCCAAAAATACCAATTTCTCATAATCGAGGATACTCCAACCCC
GTTATTTTCGAGGGATACTCCAACCCCGTTACTTCCGAGGGA
Found at i:7335 original size:50 final size:50
Alignment explanation
Indices: 7253--7512 Score: 351
Period size: 50 Copynumber: 5.2 Consensus size: 50
7243 AGTTGTTGAC
* * * * *
7253 ATTGTTGACTATTCTTCACTAATCTTTTACAATCGAGAGAGGTGGCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
* * *
7303 ATTATTGACTATTCTTCACCAACCTTTAACAATAGAGAGAGAT-GTCCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGT-CATA
* * **
7353 ATTGTTGACTATTCTTCACCAACCTTTGACAATAAAGGGAGGTGGTTGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
* * *
7403 ATTGTTGACTACTCTTCACCAACCTTTGACAATAGAAAGAGGTGGTCGTA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
* *
7453 ATTGTTGACTATTCTTCACCAACCTTTGATAATAGAGAGAAGTGGTCATA
1 ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
7503 ATTGTTGACT
1 ATTGTTGACT
7513 CTAAGCAACT
Statistics
Matches: 184, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
49 1 0.01
50 181 0.98
51 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (50 bp):
ATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGTCATA
Found at i:13350 original size:40 final size:39
Alignment explanation
Indices: 13302--13379 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
13292 GGTAAAAAGA
* *
13302 CATAATGTATCAATACATTGTAGAATATATCGATACATT
1 CATAATGTATCAATACATTGAAAAATATATCGATACATT
* * *
13341 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCAATACATTGAAAAATATATCGATACAT
13380 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.35
Consensus pattern (39 bp):
CATAATGTATCAATACATTGAAAAATATATCGATACATT
Found at i:13352 original size:20 final size:20
Alignment explanation
Indices: 13305--13379 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
13295 AAAAAGACAT
* ** *
13305 AATGTATCAATACATTGTAG
1 AATGTATCGATACATTCAAA
* *
13325 AATATATCGATACATTCATA
1 AATGTATCGATACATTCAAA
* * *
13345 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCAAA
13365 AATGTATCGATACAT
1 AATGTATCGATACAT
13380 CAGGGTATGA
Statistics
Matches: 42, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCAAA
Found at i:14087 original size:28 final size:28
Alignment explanation
Indices: 13987--15087 Score: 1135
Period size: 28 Copynumber: 38.6 Consensus size: 28
13977 CACTGACACA
* **
13987 TGTGGGCTTTGAAAAGAGTGTTACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
14016 TGCGTGGGCTTTAAAAGGGTGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
*
14046 TGCGTGGGCTTTGAAATGATGCCACTGACT
1 T--GTGGGCTTTGAAAGGATGCCACTGACT
* *
14076 CGTGGGCTTTGAAA-GAGTACCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
14104 TATGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
14131 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
14159 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
14186 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
14214 CGTGGGCTTTGAAAAGG-TGCCATTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
14242 TGCGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
* *
14274 GTGTGGGCTTTGAAAGGGTGCTACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
14303 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
14331 CGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
14359 TGTGGGCTTTGAAAGG-TGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
14386 CGTGGGCTTTGAAAAGG-TACCACTGACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
14414 CGTGGGC-TTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
14441 GGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
14469 CGTAGGCTTTGAAAAGG-TGCCACTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
* *
14497 TGCGTGGGCTTTAAAAGGAGTGCCACTAACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
14529 GTGTGGGCTTTGAAAGGGA-GCCACTGACT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
14558 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
14586 TGTGGGCTTCGCAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
14614 TGTGTGCTTCGAAAGGGTGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
14642 TGTGGGCTTTGAAAGG-TGCCATTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
14669 CGTGGG-ATTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
14696 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
14724 CGTGGGCTTTGAAAAGG-TGCCATTAACT
1 TGTGGGCTTTG-AAAGGATGCCACTGACT
*
14752 TGCGTGGGCTTTAAAAGGAGTGCCACTGACTT
1 T--GTGGGCTTTGAAAGGA-TGCCACTGAC-T
14784 GTGTGGGCTTTGAAAGGGA-GCCACTGACT
1 -TGTGGGCTTTGAAA-GGATGCCACTGACT
14813 TGTGGGCTTTGAAA-GAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * *
14841 TGTGGGCTTCGCAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
14869 TGTGGGCTTCGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
14897 TGTGGGCTTTGAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* *
14926 TGTGGGCTTTGAAAAGAGTGCCACTGATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* **
14955 TGTGGGCTTTAAAAATAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
* * * *
14984 TGTGGGCTTTAAAAAGAGTGCCACTAATT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
**
15013 TGTGGGCTTTGAAAATAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
15042 TGTGGGCTTTGAAAGGAGTGCCACTGACTT
1 TGTGGGCTTTGAAAGGA-TGCCACTGAC-T
15072 TGTGGGCTTTGAAAGG
1 TGTGGGCTTTGAAAGG
15088 GATGAACATT
Statistics
Matches: 931, Mismatches: 90, Indels: 101
0.83 0.08 0.09
Matches are distributed among these distances:
26 22 0.02
27 114 0.12
28 423 0.45
29 172 0.18
30 109 0.12
31 79 0.08
32 9 0.01
33 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:14383 original size:227 final size:228
Alignment explanation
Indices: 13941--15088 Score: 1384
Period size: 227 Copynumber: 5.0 Consensus size: 228
13931 TAAAAAAAAT
* *
13941 GTGCCACT-AGCTTGTGTAGGCTTTGAAAAAAGTTGCCACTGACACATGTGGGCTTTGAAAAGAG
1 GTGCCACTGA-CTTGTG--GGCTTTG-AAAGAG-TGCCACTGACTC--GTGGGCTTTGAAAAGAG
** * * *
14005 TGTTACTGACTTGCGTGGGCTTT-AAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAATGATGCC
59 TGCCACTGACTT-CGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCC
* * * *
14069 ACTGACTCGTGGGCTTTGAAA-GAGTACCACTGACTTATGGGCTTTGAAAG-GTGCCACTGACTC
123 ACTGACTTGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTT
* *
14132 GTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGG
188 GTGGGCTTTG-AAAGGTGCCACTGACTTGTGGGCTTGAAAGG
*
14174 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCATT
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
* * *
14238 GACTTGCGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCTACTGACT
66 GACTT-CGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACT
*
14303 TGTGGGCTTTGAAAGGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
130 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCT
* *
14367 TTGAAAGGTGCCACTGACTCGTGGGCTTTGAAAAG
195 TTGAAAGGTGCCACTGACTTGTGGGC-TTGAAAGG
* * * *
14402 GTACCACTGACTCGTGGGC-TTGAAAGGGTGCCACTGACTGGTGGGCTTTG-AAAGAGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
* * * *
14465 GAC-TCGTAGGCTTTGAAAAG-GTGCCACTAACTTGCGTGGGCTTTAAAAGGAGTGCCACTAACT
66 GACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGG-GTGCCACTGAC-
*
14528 TGTGTGGGCTTTGAAAGG-GAGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGG
129 T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGG
* * * *
14592 CTTCGCAAGGGTGCCATTGACTTGTGTGCTTCGAAAGG
193 CTTTG-AAAGGTGCCACTGACTTGTGGGCTT-GAAAGG
* * * *
14630 GTGCCACTAACTTGTGGGCTTTGAAAG-GTGCCATTGACTCGTGGG-ATTG-AAAGGGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
* * *
14692 GACTT-GTGGGCTTTG-AAAGAGTGCCACTGAC-T-CGTGGGCTTTGAAAAGGTGCCATTAACTT
66 GACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACTT
* * *
14753 GCGTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGAGCCACTGACTTGTGG
131 --GTGGGCTTTGAAAGGAGTGCCACTGAC-T-TGTGGGCTTTGAAAGAGTGCCACTGACTTGTGG
*
14818 GCTTTGAAAGAGTGCCACTGACTTGTGGGCTTCGCAAGG
192 GCTTTGAAAG-GTGCCACTGACTTGTGGGCTT-GAAAGG
* * *
14857 GTGCCACTGACTTGTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACT
1 GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
* * * **
14922 AACTT-GTGGGCTTTGAAAAGAGTGCCACTGA-TT-TGTGGGCTTTAAAAATAGTGCCACTGACT
66 GACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTT-GAAAGGGTGCCACTGACT
* * * * *
14984 TGTGGGCTTTAAAAAGAGTGCCACTAATTTGTGGGCTTTGAAAATAGTGCCACTGACTTGTGGGC
130 TGTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGTGGGC
15049 TTTGAAAGGAGTGCCACTGACTTTGTGGGCTTTGAAAGG
194 TTTGAAA-G-GTGCCACTGAC-TTGTGGGC-TTGAAAGG
15088 G
1 G
15089 ATGAACATTC
Statistics
Matches: 805, Mismatches: 79, Indels: 64
0.85 0.08 0.07
Matches are distributed among these distances:
222 1 0.00
223 1 0.00
224 51 0.06
225 47 0.06
226 36 0.04
227 342 0.42
228 132 0.16
229 50 0.06
230 68 0.08
231 46 0.06
232 16 0.02
233 14 0.02
234 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (228 bp):
GTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGAGTGCCACT
GACTTCGTGGGCTTTGAAAAGAGTGCCACTGACTTGCGTGGGCTTTGAAAGGGTGCCACTGACTT
GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTT
TGAAAGGTGCCACTGACTTGTGGGCTTGAAAGG
Found at i:14448 original size:255 final size:256
Alignment explanation
Indices: 13988--15086 Score: 1604
Period size: 255 Copynumber: 4.3 Consensus size: 256
13978 ACTGACACAT
* ** * *
13988 GTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTT--GTGG
* * * *
14053 GCTTTGAAATGA-TGCCACTGACTCGTGGGCTTTGAAAGAGTACCACTGACTTATGGGCTTTGAA
64 GCTTTGAAA-GAGTGCCACTGACTCGTGGGCTTCGAAAGAGTGCCACTGACTTGTGGGCTTCGAA
14117 A-GGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCAC
128 AGGGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCAC
* *
14181 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCATTGACTTGC
193 TGACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTTGC
*
14245 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCTACTGACTTGTGGGC
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* *
14310 TTTGAAAG-GATGCCACTGACTCGTGGGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAA-
66 TTTGAAAGAG-TGCCACTGACTCGTGGGCTTCGAAAGAGTGCCACTGACTTGTGGGCTTCGAAAG
14373 GGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTG
130 GGTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTG
* *
14438 ACTGGTGGGCTTTGAAAGAGTGCCACTGACTCGTAGGCTTTGAAAAGGTGCCACTAACTTGC
195 ACTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTTGC
* * *
14500 GTGGGCTTTAAAAGGAGTGCCACTAACTTGTGTGGGCTTTGAAAGGGAGCCACTGACTTGTGGGC
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * * * *
14565 TTTGAAAGAGTGCCACTGACTTGTGGGCTTCGCAAGGGTGCCATTGACTTGTGTGCTTCGAAAGG
66 TTTGAAAGAGTGCCACTGACTCGTGGGCTTCGAAAGAGTGCCACTGACTTGTGGGCTTCGAAAGG
* * * * *
14630 GTGCCACTAACTTGTGGGCTTTG-AAAGGTGCCATTGACTCGTGGGATTGAAAGGGTGCCACTGA
131 GTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGA
*
14694 CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCATTAACTTGC
196 CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTTGC
* *
14755 GTGGGCTTTAAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGAGCCACTGACTTGTGGGC
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
* * *
14820 TTTGAAAGAGTGCCACTGACTTGTGGGCTTCGCAAGGGTGCCACTGACTTGTGGGCTTCGAAAGG
66 TTTGAAAGAGTGCCACTGACTCGTGGGCTTCGAAAGAGTGCCACTGACTTGTGGGCTTCGAAAGG
* * * * *
14885 GTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCAC
131 GTGCCACTGACTCGTGGGCTTTGAAAAG-GTACCACTGACTCGTGGGC-TTG-AAAGGGTGCCAC
* * * * *
14950 TGATTTGTGGGCTTTAAAAATAGTGCCACTGACTTGTGGGCTTTAAAAAGAGTGCCACTAA-TT-
193 TGACTTGTGGGCTTT-GAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAG-GTGCCACTAACTTG
*
15013 T
256 C
**
15014 GTGGGCTTTGAAAATAGTGCCACTGAC-T-TGTGGGCTTTGAAAGGAGTGCCACTGACTTTGTGG
1 GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGG-GTGCCACTGAC-TTGTGG
15077 GCTTTGAAAG
64 GCTTTGAAAG
15087 GGATGAACAT
Statistics
Matches: 779, Mismatches: 51, Indels: 22
0.91 0.06 0.03
Matches are distributed among these distances:
254 1 0.00
255 547 0.70
256 27 0.03
257 84 0.11
258 14 0.02
259 65 0.08
260 32 0.04
261 9 0.01
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.28
Consensus pattern (256 bp):
GTGGGCTTTGAAAGGAGTGCCACTGACTTGTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
TTTGAAAGAGTGCCACTGACTCGTGGGCTTCGAAAGAGTGCCACTGACTTGTGGGCTTCGAAAGG
GTGCCACTGACTCGTGGGCTTTGAAAAGGTACCACTGACTCGTGGGCTTGAAAGGGTGCCACTGA
CTTGTGGGCTTTGAAAGAGTGCCACTGACTCGTGGGCTTTGAAAAGGTGCCACTAACTTGC
Found at i:16322 original size:1 final size:1
Alignment explanation
Indices: 16318--16369 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
16308 TTTTTTGCTA
* * * * *
16318 TTTTTCTTTTTTTTTTGTTTTTTTTTGTTTTGTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16370 GGGTGTAAAG
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (1 bp):
T
Found at i:16341 original size:14 final size:14
Alignment explanation
Indices: 16318--16369 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
16308 TTTTTTGCTA
*
16318 TTTTTCTTTTTTT-
1 TTTTTTTTTTTTTG
*
16331 TTTGTTTTTTTTTG
1 TTTTTTTTTTTTTG
*
16345 TTTTGTTTTTTTTG
1 TTTTTTTTTTTTTG
16359 TTTTTTTTTTT
1 TTTTTTTTTTT
16370 GGGTGTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (14 bp):
TTTTTTTTTTTTTG
Found at i:16342 original size:15 final size:15
Alignment explanation
Indices: 16319--16369 Score: 68
Period size: 15 Copynumber: 3.3 Consensus size: 15
16309 TTTTTGCTAT
16319 TTTTCTTTTTTTTTTG
1 TTTT-TTTTTTTTTTG
*
16335 TTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTG
16350 TTTTTTTTGTTTTTT-
1 TTTTTTTT-TTTTTTG
16365 TTTTT
1 TTTTT
16370 GGGTGTAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 23 0.72
16 9 0.28
ACGTcount: A:0.00, C:0.02, G:0.08, T:0.90
Consensus pattern (15 bp):
TTTTTTTTTTTTTTG
Found at i:16364 original size:26 final size:26
Alignment explanation
Indices: 16319--16370 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
16309 TTTTTGCTAT
16319 TTTTCTTTTTTTTTTGTTTTTTTTTG
1 TTTTCTTTTTTTTTTGTTTTTTTTTG
*
16345 TTTTGTTTTTTTTGTT-TTTTTTTTTG
1 TTTTCTTTTTTTT-TTGTTTTTTTTTG
16371 GGTGTAAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 22 0.92
27 2 0.08
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.88
Consensus pattern (26 bp):
TTTTCTTTTTTTTTTGTTTTTTTTTG
Done.