Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1462
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: 106782
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:7253 original size:11 final size:11
Alignment explanation
Indices: 7237--7273 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
7227 GTAGTTTTCG
7237 AAAAAAATTCA
1 AAAAAAATTCA
7248 AAAAAAA---A
1 AAAAAAATTCA
7256 AAAAAAATTCA
1 AAAAAAATTCA
7267 AAAAAAA
1 AAAAAAA
7274 GTTTCCATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 8 0.35
11 15 0.65
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAAAATTCA
Found at i:7261 original size:19 final size:19
Alignment explanation
Indices: 7237--7273 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
7227 GTAGTTTTCG
7237 AAAAAAATTCAAAAAAAAA
1 AAAAAAATTCAAAAAAAAA
7256 AAAAAAATTCAAAAAAAA
1 AAAAAAATTCAAAAAAAA
7274 GTTTCCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.84, C:0.05, G:0.00, T:0.11
Consensus pattern (19 bp):
AAAAAAATTCAAAAAAAAA
Found at i:7327 original size:15 final size:14
Alignment explanation
Indices: 7307--7344 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
7297 GATATCAAGT
7307 TGAAAAAAAAATTTG
1 TGAAAAAAAAA-TTG
7322 TG-AAAAAAAATTG
1 TGAAAAAAAAATTG
7335 TGAAAAAAAA
1 TGAAAAAAAA
7345 GAAGAAGCTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.23
14 15 0.68
15 2 0.09
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (14 bp):
TGAAAAAAAAATTG
Found at i:7329 original size:14 final size:13
Alignment explanation
Indices: 7310--7344 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
7300 ATCAAGTTGA
7310 AAAAAAAATTTGTG
1 AAAAAAAA-TTGTG
7324 AAAAAAAATTGTG
1 AAAAAAAATTGTG
7337 AAAAAAAA
1 AAAAAAAA
7345 GAAGAAGCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:8280 original size:17 final size:18
Alignment explanation
Indices: 8256--8299 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
8246 AAGAGTGACG
8256 AGAGAAAAAAACCGAAAA
1 AGAGAAAAAAACCGAAAA
**
8274 AGA-AAAAAAATTGAAAA
1 AGAGAAAAAAACCGAAAA
8291 AGAGAAAAA
1 AGAGAAAAA
8300 GATTGGAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.05
Consensus pattern (18 bp):
AGAGAAAAAAACCGAAAA
Found at i:8304 original size:18 final size:17
Alignment explanation
Indices: 8269--8315 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 17
8259 GAAAAAAACC
8269 GAAAAAGAAAAAAAATT
1 GAAAAAGAAAAAAAATT
*
8286 GAAAAAGAGAAAAAGATT
1 GAAAAAGA-AAAAAAATT
*
8304 GGAGAAAGAAAA
1 -GAAAAAGAAAA
8316 GAAAGAGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 8 0.31
18 11 0.42
19 7 0.27
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (17 bp):
GAAAAAGAAAAAAAATT
Found at i:13075 original size:307 final size:307
Alignment explanation
Indices: 12521--13135 Score: 921
Period size: 307 Copynumber: 2.0 Consensus size: 307
12511 TAAAGTCTAA
* *
12521 ATGATACGAGTCACAAAGGCCCAATTCAAGCTCAAAGACGTGATGGGCTCAAATTACCACAAGGC
1 ATGATACGAGTCACAAAGGCCCAATCCAAGCTCAAAGACATGATGGGCTCAAATTACCACAAGGC
* ** * * *
12586 CCAATAACGAGGTCAAAGGCCAGGCAAATGCGTATGAAACTAAATGGAATCATTCAAGCCTTCAT
66 CCAATAACGAGATCAAAGGCCAGAAAAATGCGTATCAAACTAAATGGAACCATTCAAGACTTCAT
* *
12651 TAGCAAGGCCTTAGATGCGTATACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAG
131 TAGCAAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAG
* * *
12716 AAAATCAAGAAACCAAATCTTGGTCCAATTTTGCTGTTTTGAGCGATTTCAAGAATCAAGAAAAT
196 AAAATCAAGAAACCAAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGAATCAAGAAAAT
12781 CAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
261 CAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
*
12828 ATGATACGAGTCACAAAGGCCCAATCCAAGTTC-AAGAACATGATGGGCTCAAATTACCACAAGG
1 ATGATACGAGTCACAAAGGCCCAATCCAAGCTCAAAG-ACATGATGGGCTCAAATTACCACAAGG
* * *
12892 CCCAATAACGAGATCAAAGGCCCGAAAAATGCGT-TCCAAACTAAATAGG-ACCATTCAGGAGTT
65 CCCAATAACGAGATCAAAGGCCAGAAAAATGCGTAT-CAAACTAAAT-GGAACCATTCAAGACTT
** * ** *
12955 TGTTAGCAAGGCCTTAGATGCATACACGAAGGAACGAGAAAATCAAGATTCCCTTTCTTGTTTTC
128 CATTAGCAAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTC
* * *
13020 AAGAAAATCAAGAAACCGAATCTTGGCCCAATTTTATTGTTTGGAGCGATTTCAAGACTCAAGAA
193 AAGAAAATCAAGAAACCAAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGAATCAAGAA
* **
13085 AATCAAGATTTCAAATCTTGGAAATCTTGGTCCAAGAAACTGAATCTTGC
258 AATCAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
13135 A
1 A
13136 GCTAAAACGC
Statistics
Matches: 276, Mismatches: 29, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
306 4 0.01
307 270 0.98
308 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.24
Consensus pattern (307 bp):
ATGATACGAGTCACAAAGGCCCAATCCAAGCTCAAAGACATGATGGGCTCAAATTACCACAAGGC
CCAATAACGAGATCAAAGGCCAGAAAAATGCGTATCAAACTAAATGGAACCATTCAAGACTTCAT
TAGCAAGGCCTTAGATGCATACACAAAGGAAAAAGAAAATCAAGATTCACTTTCTTGTTTTCAAG
AAAATCAAGAAACCAAATCTTGGCCCAATTTTACTGTTTGGAGCGATTTCAAGAATCAAGAAAAT
CAAGATTTCAAACCTTGGAAATCTTGGTCCAAGAAACCAAATCTTGC
Found at i:13227 original size:18 final size:18
Alignment explanation
Indices: 13204--13239 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
13194 GATCACAAGC
13204 CCAAATTCTCGAAGGCAA
1 CCAAATTCTCGAAGGCAA
13222 CCAAATTCTCGAAGGCAA
1 CCAAATTCTCGAAGGCAA
13240 GGCCCAATAA
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:0.39, C:0.28, G:0.17, T:0.17
Consensus pattern (18 bp):
CCAAATTCTCGAAGGCAA
Found at i:13662 original size:25 final size:25
Alignment explanation
Indices: 13566--13660 Score: 181
Period size: 25 Copynumber: 3.8 Consensus size: 25
13556 GTTTAAGTGC
13566 AGAATTCTCTTTGAGTTTTTCTCCA
1 AGAATTCTCTTTGAGTTTTTCTCCA
13591 AGAATTCTCTTTGAGTTTTTCTCCA
1 AGAATTCTCTTTGAGTTTTTCTCCA
13616 AGAATTCTCTTTGAGTTTTTCTCCA
1 AGAATTCTCTTTGAGTTTTTCTCCA
13641 AGAATTCTCTCTTGAGTTTT
1 AGAATTCTCT-TTGAGTTTT
13661 CTTTAGAAGT
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
25 60 0.87
26 9 0.13
ACGTcount: A:0.20, C:0.19, G:0.13, T:0.48
Consensus pattern (25 bp):
AGAATTCTCTTTGAGTTTTTCTCCA
Found at i:23796 original size:12 final size:12
Alignment explanation
Indices: 23750--23795 Score: 74
Period size: 12 Copynumber: 3.8 Consensus size: 12
23740 TTGTAGATTC
23750 AAAAAAAATCGA
1 AAAAAAAATCGA
23762 AAAAAAAATCGA
1 AAAAAAAATCGA
*
23774 GAAAAAAAATTGA
1 -AAAAAAAATCGA
23787 AAAAAAAAT
1 AAAAAAAAT
23796 TTTTGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 21 0.66
13 11 0.34
ACGTcount: A:0.76, C:0.04, G:0.09, T:0.11
Consensus pattern (12 bp):
AAAAAAAATCGA
Found at i:30837 original size:26 final size:25
Alignment explanation
Indices: 30783--30839 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
30773 CTACTTCTAA
* * *
30783 AGAAAACTCAAGATAGAATTCTTTG
1 AGAAAACTCAAGAGAGAATTCTCTC
30808 AGAAAACTCAA-AGAGAATTTCTACTC
1 AGAAAACTCAAGAGAGAA-TTCT-CTC
30834 AGAAAA
1 AGAAAA
30840 ATCTAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 5 0.19
25 15 0.56
26 7 0.26
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (25 bp):
AGAAAACTCAAGAGAGAATTCTCTC
Found at i:42679 original size:15 final size:15
Alignment explanation
Indices: 42659--42697 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
42649 CTTCTTCTTC
42659 TTTTTTTCACGAAAT
1 TTTTTTTCACGAAAT
*
42674 TTTTTTTCACGAATT
1 TTTTTTTCACGAAAT
42689 TTTTTTTCA
1 TTTTTTTCA
42698 ACTTGATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.05, T:0.62
Consensus pattern (15 bp):
TTTTTTTCACGAAAT
Found at i:42771 original size:11 final size:12
Alignment explanation
Indices: 42737--42768 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
42727 GGAAACCAAT
42737 TTTTTTTTTGAA
1 TTTTTTTTTGAA
42749 TTTTTTTTTGAA
1 TTTTTTTTTGAA
42761 TTTTTTTT
1 TTTTTTTT
42769 GAAGAAACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:46389 original size:21 final size:21
Alignment explanation
Indices: 46363--46402 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
46353 CAAATACCAT
46363 ACCATTTCATACCAATTCCAA
1 ACCATTTCATACCAATTCCAA
*
46384 ACCATTTCGTACCAATTCC
1 ACCATTTCATACCAATTCC
46403 CAAATACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.35, G:0.03, T:0.30
Consensus pattern (21 bp):
ACCATTTCATACCAATTCCAA
Found at i:46717 original size:10 final size:10
Alignment explanation
Indices: 46702--46750 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
46692 GTAAGTGATT
46702 AAAAAAATT-
1 AAAAAAATTA
*
46711 AAAAAAATCGA
1 AAAAAAAT-TA
*
46722 AAAAAAATAA
1 AAAAAAATTA
*
46732 AAAAAAAGTA
1 AAAAAAATTA
46742 AAAAAAATT
1 AAAAAAATT
46751 CGTGGATTGA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
9 8 0.24
10 17 0.52
11 8 0.24
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (10 bp):
AAAAAAATTA
Found at i:46727 original size:20 final size:21
Alignment explanation
Indices: 46702--46750 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
46692 GTAAGTGATT
**
46702 AAAAAAATTAAAAAAATCG-A
1 AAAAAAATTAAAAAAAAAGTA
46722 AAAAAAA-TAAAAAAAAAGTA
1 AAAAAAATTAAAAAAAAAGTA
46742 AAAAAAATT
1 AAAAAAATT
46751 CGTGGATTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 9 0.36
20 15 0.60
21 1 0.04
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.14
Consensus pattern (21 bp):
AAAAAAATTAAAAAAAAAGTA
Found at i:47727 original size:6 final size:6
Alignment explanation
Indices: 47701--47798 Score: 63
Period size: 6 Copynumber: 15.8 Consensus size: 6
47691 AATGAATTCA
** * **
47701 AAAAAG AAAGTG AAGAAG AAAAAG AAAACA- AAAAAG AAAAAG AAAATT
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG
** * * *
47749 AAAAAG TGAGAG AAAAAG AAAATG AAGAAAAG AAAATTG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG -A-AAAAG AAAA-AG AAAAAG AAAAA
47799 TATGAAAATG
Statistics
Matches: 67, Mismatches: 20, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
5 1 0.01
6 54 0.81
7 8 0.12
8 4 0.06
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.07
Consensus pattern (6 bp):
AAAAAG
Found at i:47752 original size:18 final size:18
Alignment explanation
Indices: 47701--47798 Score: 79
Period size: 18 Copynumber: 5.3 Consensus size: 18
47691 AATGAATTCA
* *
47701 AAAAAGAAAGTGAAGAAG
1 AAAAAGAAAATGAAAAAG
**
47719 AAAAAGAAAACAAAAAAG
1 AAAAAGAAAATGAAAAAG
*
47737 AAAAAGAAAATTAAAAAG
1 AAAAAGAAAATGAAAAAG
** * * *
47755 TGAGAGAAAAAGAAAATG
1 AAAAAGAAAATGAAAAAG
47773 AAGAAAAGAAAATTGAAAAAG
1 -A-AAAAGAAAA-TGAAAAAG
47794 AAAAA
1 AAAAA
47799 TATGAAAATG
Statistics
Matches: 60, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
18 42 0.70
19 4 0.07
20 8 0.13
21 6 0.10
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAAGAAAATGAAAAAG
Found at i:47781 original size:14 final size:13
Alignment explanation
Indices: 47760--47797 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
47750 AAAAGTGAGA
47760 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
47772 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
47787 GAAAAAGAAAA
1 GAAAAAGAAAA
47798 ATATGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:47794 original size:13 final size:12
Alignment explanation
Indices: 47701--47797 Score: 72
Period size: 12 Copynumber: 7.8 Consensus size: 12
47691 AATGAATTCA
*
47701 AAAAAGAAAGTG
1 AAAAAGAAAATG
* *
47713 AAGAAGAAAAAG
1 AAAAAGAAAATG
*
47725 AAAACA-AAAAAG
1 AAAA-AGAAAATG
*
47737 AAAAAGAAAATT
1 AAAAAGAAAATG
* *
47749 AAAAAGTGAGA-G
1 AAAAAG-AAAATG
47761 AAAAAGAAAATG
1 AAAAAGAAAATG
47773 AAGAAAAGAAAATTG
1 -A-AAAAGAAAA-TG
47788 AAAAAGAAAA
1 AAAAAGAAAA
47798 ATATGAAAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
11 3 0.04
12 39 0.58
13 13 0.19
14 10 0.15
15 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.19, T:0.07
Consensus pattern (12 bp):
AAAAAGAAAATG
Found at i:47841 original size:17 final size:18
Alignment explanation
Indices: 47816--47855 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
47806 ATGAGATTTC
47816 AAAAACAAAA-GAGAGTG
1 AAAAACAAAATGAGAGTG
* *
47833 AAAAGCAAAATGAGATTG
1 AAAAACAAAATGAGAGTG
47851 AAAAA
1 AAAAA
47856 GAAAGAGAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.65, C:0.05, G:0.20, T:0.10
Consensus pattern (18 bp):
AAAAACAAAATGAGAGTG
Found at i:47847 original size:18 final size:17
Alignment explanation
Indices: 47816--47865 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
47806 ATGAGATTTC
47816 AAAAACAAAAGAGAGTG
1 AAAAACAAAAGAGAGTG
* *
47833 AAAAGCAAAATGAGATTG
1 AAAAACAAAA-GAGAGTG
*
47851 AAAAA-GAAAGAGAGT
1 AAAAACAAAAGAGAGT
47866 TTGAAAAGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 5 0.19
17 12 0.44
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.10
Consensus pattern (17 bp):
AAAAACAAAAGAGAGTG
Found at i:47871 original size:36 final size:34
Alignment explanation
Indices: 47802--47897 Score: 92
Period size: 36 Copynumber: 2.8 Consensus size: 34
47792 AGAAAAATAT
* *
47802 GAAAATGAGATTTCAAAAACAAAAGAGAG-TGAAAA
1 GAAAATGAGA-TTGAAAAA-GAAAGAGAGTTGAAAA
47837 GCAAAATGAGATTGAAAAAGAAAGAGAGTTTGAAAA
1 G-AAAATGAGATTGAAAAAGAAAGAGAG-TTGAAAA
* *
47873 GAAAACGAG--TGAAGAAG-AAGAGAGT
1 GAAAATGAGATTGAAAAAGAAAGAGAGT
47898 GCTCAAACAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
31 1 0.02
32 7 0.13
33 7 0.13
34 8 0.15
35 15 0.28
36 16 0.30
ACGTcount: A:0.56, C:0.04, G:0.26, T:0.14
Consensus pattern (34 bp):
GAAAATGAGATTGAAAAAGAAAGAGAGTTGAAAA
Found at i:47874 original size:17 final size:16
Alignment explanation
Indices: 47823--47897 Score: 52
Period size: 16 Copynumber: 4.6 Consensus size: 16
47813 TTCAAAAACA
47823 AAAGAGAG-TGAAAAG
1 AAAGAGAGTTGAAAAG
47838 CAAA-ATGAGATTGAAAAAG
1 -AAAGA-GAG-TTG-AAAAG
47857 AAAGAGAGTTTGAAAAG
1 AAAGAGAG-TTGAAAAG
47874 AAA-ACGAG-TGAAGAAG
1 AAAGA-GAGTTGAA-AAG
47890 -AAGAGAGT
1 AAAGAGAGT
47898 GCTCAAACAC
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
15 10 0.20
16 11 0.22
17 11 0.22
18 11 0.22
19 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.29, T:0.12
Consensus pattern (16 bp):
AAAGAGAGTTGAAAAG
Found at i:49166 original size:20 final size:21
Alignment explanation
Indices: 49131--49169 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
49121 CAGCTCGTTG
49131 AGCTCAATTCAGCTCATTTCC
1 AGCTCAATTCAGCTCATTTCC
*
49152 AGCTC-ATTGAGCTCATTT
1 AGCTCAATTCAGCTCATTT
49170 GCTTGTTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.28, G:0.13, T:0.36
Consensus pattern (21 bp):
AGCTCAATTCAGCTCATTTCC
Found at i:49577 original size:13 final size:13
Alignment explanation
Indices: 49559--49584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49549 TGTGTCCTAA
49559 TATGAATTAAATT
1 TATGAATTAAATT
49572 TATGAATTAAATT
1 TATGAATTAAATT
49585 GCTTTCAGGT
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:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGAATTAAATT
Found at i:57656 original size:20 final size:20
Alignment explanation
Indices: 57610--57647 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57600 AGCTCGTTTC
*
57610 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
57630 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
57648 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:66842 original size:20 final size:20
Alignment explanation
Indices: 66796--66842 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
66786 AGCTCGTTTC
*
66796 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
66816 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
66836 CAGCTCA
1 CAGCTCA
66843 ATCTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:69765 original size:23 final size:22
Alignment explanation
Indices: 69714--69765 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
69704 CCTCGTCTTT
*
69714 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
69736 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
69759 TTCTTTT
1 TTCTTTT
69766 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:72158 original size:11 final size:10
Alignment explanation
Indices: 72133--72193 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
72123 ACCAATAAAA
72133 TAAA-TGAGC
1 TAAATTGAGC
*
72142 TGAATTGTAGC
1 TAAATTG-AGC
72153 TAAATTGAGC
1 TAAATTGAGC
**
72163 TCGATTGAGC
1 TAAATTGAGC
72173 TGAAA-TGAGC
1 T-AAATTGAGC
*
72183 TCAATTGAGC
1 TAAATTGAGC
72193 T
1 T
72194 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:72194 original size:20 final size:20
Alignment explanation
Indices: 72134--72194 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
72124 CCAATAAAAT
*
72134 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
72154 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
72175 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
72195 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:74279 original size:18 final size:18
Alignment explanation
Indices: 74258--74292 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
74248 TTTTTATTTT
74258 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
74276 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
74293 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:74289 original size:6 final size:6
Alignment explanation
Indices: 74280--74384 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
74270 TCAATCTCAA
* * * ** **
74280 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
74332 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
74378 TTTCTT T
1 TTTCTT T
74385 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:74397 original size:6 final size:6
Alignment explanation
Indices: 74331--74384 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
74321 ACTATTTTGA
* ** * *
74331 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
74378 TTTCTT T
1 TTTCTT T
74385 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:75447 original size:12 final size:12
Alignment explanation
Indices: 75432--75475 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
75422 TTGTCACTTC
75432 TTTTTTTTTTAA
1 TTTTTTTTTTAA
*
75444 TTTTTTTTTGAA
1 TTTTTTTTTTAA
*
75456 -TTTTTTTTTGA
1 TTTTTTTTTTAA
75467 TTTTTTTTT
1 TTTTTTTTT
75476 CACGTTTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 9 0.32
12 19 0.68
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:75449 original size:11 final size:11
Alignment explanation
Indices: 75433--75475 Score: 68
Period size: 11 Copynumber: 3.8 Consensus size: 11
75423 TGTCACTTCT
75433 TTTTTTTTTAA
1 TTTTTTTTTAA
75444 TTTTTTTTTGAA
1 TTTTTTTTT-AA
*
75456 TTTTTTTTTGA
1 TTTTTTTTTAA
75467 TTTTTTTTT
1 TTTTTTTTT
75476 CACGTTTCGA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 19 0.63
12 11 0.37
ACGTcount: A:0.12, C:0.00, G:0.05, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTAA
Found at i:76751 original size:11 final size:10
Alignment explanation
Indices: 76726--76787 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
76716 ACCAATAAAA
76726 TAAA-TGAGC
1 TAAATTGAGC
*
76735 TGAATTGTAGC
1 TAAATTG-AGC
76746 TAAATTGAGC
1 TAAATTGAGC
**
76756 TCGATTGAGC
1 TAAATTGAGC
76766 TGAAA-TGAGC
1 T-AAATTGAGC
*
76776 TCAATTGAGC
1 TAAATTGAGC
76786 TA
1 TA
76788 GTCGGAGTTG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:76766 original size:20 final size:19
Alignment explanation
Indices: 76726--76787 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 19
76716 ACCAATAAAA
76726 TAAATGAGCT-GAATTGTAGC
1 TAAATGAGCTCG-ATTG-AGC
76746 TAAATTGAGCTCGATTGAGC
1 TAAA-TGAGCTCGATTGAGC
*
76766 TGAAATGAGCTCAATTGAGC
1 T-AAATGAGCTCGATTGAGC
76786 TA
1 TA
76788 GTCGGAGTTG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
19 1 0.03
20 23 0.61
21 13 0.34
22 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (19 bp):
TAAATGAGCTCGATTGAGC
Found at i:81128 original size:14 final size:14
Alignment explanation
Indices: 81109--81136 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
81099 GACGTCACGC
81109 ACGAAGAATTGATT
1 ACGAAGAATTGATT
81123 ACGAAGAATTGATT
1 ACGAAGAATTGATT
81137 GTGATATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (14 bp):
ACGAAGAATTGATT
Found at i:81284 original size:24 final size:24
Alignment explanation
Indices: 81232--81287 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
81222 AATCGAAAAA
81232 GAAAAAGAAAAAGAAAAAAAAGTT
1 GAAAAAGAAAAAGAAAAAAAAGTT
* ** * *
81256 AAAAAAGAAATTGAGAAAGAAGTT
1 GAAAAAGAAAAAGAAAAAAAAGTT
81280 GAAAAAGA
1 GAAAAAGA
81288 GATAGAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.11
Consensus pattern (24 bp):
GAAAAAGAAAAAGAAAAAAAAGTT
Found at i:81289 original size:18 final size:18
Alignment explanation
Indices: 81268--81305 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
81258 AAAAGAAATT
81268 GAGAAAGAAGTTGAAAAA
1 GAGAAAGAAGTTGAAAAA
* *
81286 GAGATAGAATTTGAAAAA
1 GAGAAAGAAGTTGAAAAA
81304 GA
1 GA
81306 ACATAAGAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.26, T:0.16
Consensus pattern (18 bp):
GAGAAAGAAGTTGAAAAA
Found at i:81306 original size:12 final size:12
Alignment explanation
Indices: 81232--81287 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
81222 AATCGAAAAA
**
81232 GAAAAAGAAAAA
1 GAAAAAGAAATT
81244 GAAAAA-AAAGTT
1 GAAAAAGAAA-TT
*
81256 AAAAAAGAAATT
1 GAAAAAGAAATT
* *
81268 GAGAAAGAAGTT
1 GAAAAAGAAATT
81280 GAAAAAGA
1 GAAAAAGA
81288 GATAGAATTT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 3 0.09
12 29 0.83
13 3 0.09
ACGTcount: A:0.70, C:0.00, G:0.20, T:0.11
Consensus pattern (12 bp):
GAAAAAGAAATT
Found at i:83196 original size:12 final size:11
Alignment explanation
Indices: 83176--83222 Score: 76
Period size: 11 Copynumber: 4.2 Consensus size: 11
83166 TAGTAGTTTC
83176 TTCAAAAAAAA
1 TTCAAAAAAAA
*
83187 TTCGAAAAAAA
1 TTCAAAAAAAA
83198 TTCAAAAAAAAA
1 TTC-AAAAAAAA
83210 TTCAAAAAAAA
1 TTCAAAAAAAA
83221 TT
1 TT
83223 GGTTTCCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
11 23 0.70
12 10 0.30
ACGTcount: A:0.68, C:0.09, G:0.02, T:0.21
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:83209 original size:23 final size:23
Alignment explanation
Indices: 83179--83222 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
83169 TAGTTTCTTC
*
83179 AAAAAAAATTCGAAAAAAATTCA
1 AAAAAAAATTCAAAAAAAATTCA
83202 AAAAAAAATTCAAAAAAAATT
1 AAAAAAAATTCAAAAAAAATT
83223 GGTTTCCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.73, C:0.07, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAAAAATTCAAAAAAAATTCA
Found at i:84130 original size:20 final size:20
Alignment explanation
Indices: 84084--84130 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
84074 AGCTCGTTTC
*
84084 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* *
84104 CAACTCACTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
84124 CAGCTCA
1 CAGCTCA
84131 ATTTTAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.36, G:0.13, T:0.21
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:101054 original size:21 final size:23
Alignment explanation
Indices: 101009--101055 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
100999 TCACCTGCAA
* *
101009 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
101032 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
101053 TAA
1 TAA
101056 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:106182 original size:17 final size:16
Alignment explanation
Indices: 106160--106199 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 16
106150 GCTTCTTTTC
106160 TTTTTTTTCACGAAATT
1 TTTTTTTTCACG-AATT
106177 TTTTTTTTCACGAATT
1 TTTTTTTTCACGAATT
106193 TTTTTTT
1 TTTTTTT
106200 CAACTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTTTCACGAATT
Found at i:106259 original size:13 final size:13
Alignment explanation
Indices: 106241--106265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
106231 GGAAACCAAA
106241 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
106254 TTTTTTTTTGAA
1 TTTTTTTTTGAA
106266 GAAACTACTT
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:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Done.