Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1558
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: 66954
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:10851 original size:81 final size:81
Alignment explanation
Indices: 10742--10953 Score: 370
Period size: 81 Copynumber: 2.6 Consensus size: 81
10732 TGTATAATTG
* *
10742 ATCTTTGCATCACATATATGCATATTTATATGCGATACAAAAGAAAGCAAATTACTACAATATTG
1 ATCTTTGTATCACATATATGCATATTTATATGTGATACAAAAGAAAGCAAATTACTACAATATTG
10807 CGATTTCATTGATGGA
66 CGATTTCATTGATGGA
10823 ATCTTTGTATCACATATATGCATATTTATATGTGATACAAAAGAAAGCAAATTACTACAATATTG
1 ATCTTTGTATCACATATATGCATATTTATATGTGATACAAAAGAAAGCAAATTACTACAATATTG
**
10888 TTATTTCATTGATGGA
66 CGATTTCATTGATGGA
* *
10904 ATCTTTGTATCACATGTATGCATGTTTATATGTGATACAAAAGAAAGCAA
1 ATCTTTGTATCACATATATGCATATTTATATGTGATACAAAAGAAAGCAA
10954 GGGTGAGTTT
Statistics
Matches: 125, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
81 125 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (81 bp):
ATCTTTGTATCACATATATGCATATTTATATGTGATACAAAAGAAAGCAAATTACTACAATATTG
CGATTTCATTGATGGA
Found at i:16759 original size:36 final size:36
Alignment explanation
Indices: 16714--16802 Score: 139
Period size: 35 Copynumber: 2.5 Consensus size: 36
16704 TTTGTAAAAT
16714 AATTT-TTGAAATTTTTATAAAAATATATAAT-GATA
1 AATTTATTGAAATTTTTATAAAAATATAT-ATCGATA
16749 AATTTATTGAAA-TTTTATAAAAATATATATCGATA
1 AATTTATTGAAATTTTTATAAAAATATATATCGATA
16784 AATTTATTGACAATTTTTA
1 AATTTATTGA-AATTTTTA
16803 AATATGTATA
Statistics
Matches: 50, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
34 2 0.04
35 35 0.70
36 8 0.16
37 5 0.10
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (36 bp):
AATTTATTGAAATTTTTATAAAAATATATATCGATA
Found at i:19050 original size:21 final size:20
Alignment explanation
Indices: 19022--19065 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
19012 GTCTTAACAG
*
19022 AACTGCTGATGTGACAAGTT
1 AACTGCTGACGTGACAAGTT
* *
19042 AACTAGCTGACGTGGCCAGTT
1 AACT-GCTGACGTGACAAGTT
19063 AAC
1 AAC
19066 CTGCCACGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (20 bp):
AACTGCTGACGTGACAAGTT
Found at i:19098 original size:5 final size:6
Alignment explanation
Indices: 19083--19144 Score: 52
Period size: 6 Copynumber: 9.3 Consensus size: 6
19073 GTTGGATGAA
* *
19083 AAAAAG AAAAAG AAAAAG AAGCAGCAG CAACAGAAG AAAAAG AAGAAG
1 AAAAAG AAAAAG AAAAAG AA--A-AAG -AA-A-AAG AAAAAG AAAAAG
19131 AAAAAG AAAAAG AA
1 AAAAAG AAAAAG AA
19145 GCAGCAGCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
6 35 0.73
7 1 0.02
8 3 0.06
9 7 0.15
10 2 0.04
ACGTcount: A:0.73, C:0.06, G:0.21, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:19135 original size:42 final size:42
Alignment explanation
Indices: 19086--19167 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
19076 GGATGAAAAA
19086 AAGAAAAAGAAAAAGAAGCAGCAGCAACAGAAGAAAAAGAAG
1 AAGAAAAAGAAAAAGAAGCAGCAGCAACAGAAGAAAAAGAAG
*
19128 AAGAAAAAGAAAAAGAAGCAGCAGCAACAGAAGAAGAAGA
1 AAGAAAAAGAAAAAGAAGCAGCAGCAACAGAAGAAAAAGA
19168 GACTGTTGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.66, C:0.10, G:0.24, T:0.00
Consensus pattern (42 bp):
AAGAAAAAGAAAAAGAAGCAGCAGCAACAGAAGAAAAAGAAG
Found at i:20064 original size:30 final size:31
Alignment explanation
Indices: 19998--20066 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
19988 ACTGTTAGTC
* *
19998 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
*
20029 AGTGACTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
20058 AGGTGACTG
1 A-GTGACTG
20067 AAATGAACCC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 6 0.18
30 13 0.38
31 15 0.44
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:20082 original size:20 final size:20
Alignment explanation
Indices: 20057--20105 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
20047 TTTCAAAAGT
*
20057 TAGGTGACTGAAATGAACCC
1 TAGGTGACTGAAATGAAACC
20077 TAGGTGACTGAAATGAAACC
1 TAGGTGACTGAAATGAAACC
20097 TAGGTGACT
1 TAGGTGACT
20106 ATTTTATCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (20 bp):
TAGGTGACTGAAATGAAACC
Found at i:21850 original size:23 final size:23
Alignment explanation
Indices: 21823--21873 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
21813 AGTTTGATTT
*
21823 AAATTTTAAAATATAAAAA-ATTA
1 AAATTTTAAAAT-TAAAAATATGA
21846 AAATTTTAAAATTAAAAATATGA
1 AAATTTTAAAATTAAAAATATGA
21869 AAATT
1 AAATT
21874 AAATTTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATTTTAAAATTAAAAATATGA
Found at i:21861 original size:29 final size:28
Alignment explanation
Indices: 21820--21883 Score: 83
Period size: 30 Copynumber: 2.2 Consensus size: 28
21810 AGGAGTTTGA
* *
21820 TTTAAATTTTAAAATATAAAAAATTAAAAT
1 TTTAAAATTAAAAATAT-AAAAATT-AAAT
*
21850 TTTAAAATTAAAAATATGAAAATTAAAT
1 TTTAAAATTAAAAATATAAAAATTAAAT
21878 TTTAAA
1 TTTAAA
21884 TTTTGAAAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 10 0.32
29 6 0.19
30 15 0.48
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
TTTAAAATTAAAAATATAAAAATTAAAT
Found at i:23145 original size:12 final size:12
Alignment explanation
Indices: 23128--23152 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
23118 AAGTATTTCA
23128 GCTTTAGTTTTT
1 GCTTTAGTTTTT
23140 GCTTTAGTTTTT
1 GCTTTAGTTTTT
23152 G
1 G
23153 AGGTATAGAG
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:0.08, C:0.08, G:0.20, T:0.64
Consensus pattern (12 bp):
GCTTTAGTTTTT
Found at i:24180 original size:22 final size:24
Alignment explanation
Indices: 24119--24187 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 24
24109 CTCGACTTTC
24119 ATTTTCATATGCTTATCAAATATA
1 ATTTTCATATGCTTATCAAATATA
* *
24143 AGTATT-ATAT--TAATCAAAT-T-
1 A-TTTTCATATGCTTATCAAATATA
24163 ATTTTCATATGCTTATCAAATATA
1 ATTTTCATATGCTTATCAAATATA
24187 A
1 A
24188 GTATGCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
19 3 0.09
20 5 0.14
21 1 0.03
22 16 0.46
23 1 0.03
24 6 0.17
25 3 0.09
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTTCATATGCTTATCAAATATA
Found at i:24838 original size:13 final size:13
Alignment explanation
Indices: 24820--24857 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
24810 ATACTCAAAT
24820 TTCTCAAAAGCAC
1 TTCTCAAAAGCAC
*
24833 TTCTCAAAAACAC
1 TTCTCAAAAGCAC
24846 TTCTCAAAAGCA
1 TTCTCAAAAGCA
24858 ATGAATAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.29, G:0.05, T:0.24
Consensus pattern (13 bp):
TTCTCAAAAGCAC
Found at i:29311 original size:21 final size:21
Alignment explanation
Indices: 29285--29340 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
29275 AACAGCGGTG
*
29285 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGATACTGTA
*
29306 GCGGTGAGATTGGATACTGTA
1 GCGGTGAGATTAGATACTGTA
* *
29327 GCTGTAAGATTAGA
1 GCGGTGAGATTAGA
29341 AACAATGGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.27, C:0.09, G:0.34, T:0.30
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:29795 original size:29 final size:30
Alignment explanation
Indices: 29746--30043 Score: 364
Period size: 31 Copynumber: 10.1 Consensus size: 30
29736 GAATATGCCG
* *
29746 AATATACTACATATATTTTTTTTATTTTTAC
1 AATACACTACATATA-TTTTTTTATTTTTAA
*
29777 AATACACTACATATATTTTTTTAAATTTTAA
1 AATACACTACATATATTTTTTT-ATTTTTAA
29808 AATACACTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTTATTTTTAA
29839 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
*
29868 AATACACT--AT-T-TTTTTTTACTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
* * * *
29894 AATACACTTCATATA--TATATA-TATTAA
1 AATACACTACATATATTTTTTTATTTTTAA
* * *
29921 AATACACTACATATATATTTTTATTTCTAG
1 AATACACTACATATATTTTTTTATTTTTAA
29951 AATACACTACATATA-TTTTTTATTTTTAA
1 AATACACTACATATATTTTTTTATTTTTAA
29980 AATACACTACA-AGTATTTTTTTATTTTTAA
1 AATACACTACATA-TATTTTTTTATTTTTAA
* *
30010 AATCCATTACATATATTTTTTTTATTTTTAA
1 AATACACTACATATA-TTTTTTTATTTTTAA
30041 AAT
1 AAT
30044 TTTAAATACA
Statistics
Matches: 234, Mismatches: 19, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
26 22 0.09
27 21 0.09
28 7 0.03
29 51 0.22
30 50 0.21
31 76 0.32
32 7 0.03
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (30 bp):
AATACACTACATATATTTTTTTATTTTTAA
Found at i:30024 original size:112 final size:112
Alignment explanation
Indices: 29804--30025 Score: 308
Period size: 112 Copynumber: 2.0 Consensus size: 112
29794 TTTTTAAATT
* *
29804 TTAAAATACACTACATATATTTTTTTTATTTTTAAAATACACTACATATATTTTTTATTTTTAAA
1 TTAAAATACACTACATATATTATTTTTATTTCTAAAATACACTACATATATTTTTTATTTTTAAA
* * *
29869 ATACACTATTTTTTTTTACTTTTAAAATACACTTCATATATATATATA
66 ATACACTATATTTTTTTACTTTTAAAATACACAT-ATACATATATATA
*
29917 TTAAAATACACTACATATA-TATTTTTATTTCTAGAATACACTACATATATTTTTTATTTTTAAA
1 TTAAAATACACTACATATATTATTTTTATTTCTAAAATACACTACATATATTTTTTATTTTTAAA
*
29981 ATACACTACAAGTATTTTTTTATTTTTAAAAT-C-CAT-TACATATAT
66 ATACACT---A-TATTTTTTTACTTTTAAAATACACATATACATATAT
30026 TTTTTTTATT
Statistics
Matches: 98, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
112 57 0.58
113 19 0.19
114 2 0.02
115 2 0.02
116 18 0.18
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (112 bp):
TTAAAATACACTACATATATTATTTTTATTTCTAAAATACACTACATATATTTTTTATTTTTAAA
ATACACTATATTTTTTTACTTTTAAAATACACATATACATATATATA
Found at i:30140 original size:6 final size:6
Alignment explanation
Indices: 30131--30281 Score: 117
Period size: 6 Copynumber: 23.0 Consensus size: 6
30121 CCATGCAATA
* *
30131 CCCATT CCCATTT CCCATT CCCATTT CCCATT CCACCGTG CCC-TCCT
1 CCCATT CCCA-TT CCCATT CCCA-TT CCCATT -C-CCATT CCCAT--T
* *
30178 CCCATTT CCCATT CCCATCT CCCCTCTT CCACCGTT CCC-TCCT CCCATT
1 CCCA-TT CCCATT CCCAT-T -CCC-ATT -C-CCATT CCCAT--T CCCATT
30227 CCCATT CCCATTT CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT
1 CCCATT CCCA-TT CCCATT CCCATT CCCATT CCCATT CCCATT CCCATT
30276 CCCATT
1 CCCATT
30282 ATCAACAATA
Statistics
Matches: 124, Mismatches: 5, Indels: 32
0.77 0.03 0.20
Matches are distributed among these distances:
5 2 0.02
6 72 0.58
7 34 0.27
8 12 0.10
9 4 0.03
ACGTcount: A:0.13, C:0.52, G:0.02, T:0.33
Consensus pattern (6 bp):
CCCATT
Found at i:30149 original size:13 final size:13
Alignment explanation
Indices: 30131--30281 Score: 125
Period size: 13 Copynumber: 11.5 Consensus size: 13
30121 CCATGCAATA
30131 CCCATTCCCATTT
1 CCCATTCCCATTT
30144 CCCATTCCCATTT
1 CCCATTCCCATTT
** *
30157 CCCATTCCACCGTG
1 CCCATTCC-CATTT
30171 CCC-TCCTCCCATTT
1 CCCAT--TCCCATTT
*
30185 CCCATTCCCATCTC
1 CCCATTCCCAT-TT
* **
30199 CCCTCTTCCACCGTT
1 CCC-ATTCC-CATTT
30214 CCC-TCCTCCCA-TT
1 CCCAT--TCCCATTT
30227 CCCATTCCCATTT
1 CCCATTCCCATTT
30240 CCCATTCCCA-TT
1 CCCATTCCCATTT
30252 CCCATTCCCA-TT
1 CCCATTCCCATTT
30264 CCCATTCCCA-TT
1 CCCATTCCCATTT
30276 CCCATT
1 CCCATT
30282 ATCAACAATA
Statistics
Matches: 115, Mismatches: 12, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
12 37 0.32
13 46 0.40
14 16 0.14
15 15 0.13
16 1 0.01
ACGTcount: A:0.13, C:0.52, G:0.02, T:0.33
Consensus pattern (13 bp):
CCCATTCCCATTT
Found at i:30154 original size:43 final size:41
Alignment explanation
Indices: 30106--30281 Score: 137
Period size: 43 Copynumber: 4.2 Consensus size: 41
30096 CGTATCCTTC
* *
30106 TCCCATTTCCCATCCCCATGCAATACCCATTCCCATTTCCCAT
1 TCCCATTTCCCATCCCCATGCCATTCCC-TTCCCA-TTCCCAT
* *
30149 TCCCATTTCCCATTCCACCGTGCC-CT-CC-TCCCATTTCCCAT
1 TCCCATTTCCCA-TCC-CCATGCCATTCCCTTCCCA-TTCCCAT
* * * *
30190 TCCCATCTCCCCTCTTCCA--CCGTTCCCTCCTCCCATTCCCAT
1 TCCCATTTCCCATC-CCCATGCCATTCCCT--TCCCATTCCCAT
* *
30232 TCCCATTTCCCATTCCCATTCCCATTCCCATTCCCATTCCCAT
1 TCCCATTTCCCATCCCCA-TGCCATTCCC-TTCCCATTCCCAT
30275 TCCCATT
1 TCCCATT
30282 ATCAACAATA
Statistics
Matches: 107, Mismatches: 14, Indels: 24
0.74 0.10 0.17
Matches are distributed among these distances:
38 2 0.02
39 1 0.01
40 6 0.06
41 26 0.24
42 18 0.17
43 38 0.36
44 10 0.09
45 6 0.06
ACGTcount: A:0.15, C:0.51, G:0.02, T:0.32
Consensus pattern (41 bp):
TCCCATTTCCCATCCCCATGCCATTCCCTTCCCATTCCCAT
Found at i:30182 original size:21 final size:21
Alignment explanation
Indices: 30156--30228 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 21
30146 CATTCCCATT
*
30156 TCCCATTCCACCGTGCCCTCC
1 TCCCATTCCACCGTTCCCTCC
* *
30177 TCCCATTTC-CCATTCCCAT-C
1 TCCCATTCCACCGTTCCC-TCC
*
30197 TCCCCTCTTCCACCGTTCCCTCC
1 T-CCC-ATTCCACCGTTCCCTCC
30220 TCCCATTCC
1 TCCCATTCC
30229 CATTCCCATT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
20 8 0.20
21 16 0.40
22 7 0.17
23 9 0.22
ACGTcount: A:0.10, C:0.56, G:0.04, T:0.30
Consensus pattern (21 bp):
TCCCATTCCACCGTTCCCTCC
Found at i:30222 original size:23 final size:22
Alignment explanation
Indices: 30156--30226 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
30146 CATTCCCATT
*
30156 TCCCA-TTCCACCGTGCCCTCC
1 TCCCATTTCCACCGTTCCCTCC
*
30177 TCCCATTT-C-CCATTCCCAT-C
1 TCCCATTTCCACCGTTCCC-TCC
*
30197 TCCCCTCTTCCACCGTTCCCTCC
1 TCCCAT-TTCCACCGTTCCCTCC
30220 TCCCATT
1 TCCCATT
30227 CCCATTCCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
20 12 0.31
21 9 0.23
22 5 0.13
23 13 0.33
ACGTcount: A:0.10, C:0.55, G:0.04, T:0.31
Consensus pattern (22 bp):
TCCCATTTCCACCGTTCCCTCC
Found at i:31998 original size:6 final size:6
Alignment explanation
Indices: 31987--32035 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
31977 TTAGTGATTT
* *
31987 AATATA AATATA AATATA AATATA AATAT- AACATA AATAATT AATATA
1 AATATA AATATA AATATA AATATA AATATA AATATA AAT-ATA AATATA
32035 A
1 A
32036 TATTTTTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
5 4 0.11
6 28 0.76
7 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (6 bp):
AATATA
Found at i:41451 original size:29 final size:30
Alignment explanation
Indices: 41401--41462 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
41391 CCAACTAAAA
* *
41401 GATCTGATTTAATAGTACAGGGACCAAATT
1 GATCTGATTGAATAATACAGGGACCAAATT
* *
41431 GATCT-ATTGAATAATAGAGGGACCAATTT
1 GATCTGATTGAATAATACAGGGACCAAATT
41460 GAT
1 GAT
41463 AAGGTCCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (30 bp):
GATCTGATTGAATAATACAGGGACCAAATT
Found at i:48235 original size:207 final size:201
Alignment explanation
Indices: 47881--48260 Score: 589
Period size: 207 Copynumber: 1.9 Consensus size: 201
47871 ACAGGACCAA
* *
47881 AAACACAAGAAAAACTATACCCAAGATAGAGAATAAAACCAGAGGAAAACTCATTTGGAATAGAA
1 AAACACAAGAAAAACTATACCCAAGATAGAGAATAAAACCAGAGGAAAACTCATTCGAAATAGAA
* * * *
47946 AATATTGAAGAGATATTCAACTTAGAAGCTGCTTTGAATAGAGAACCATTACCAAATTAAACTTT
66 AATATTCAAAAAATATTCAACTTAAAAGCTGCTTTGAATAGAGAACCATTACCAAATTAAACTTT
48011 CAAACTAAATTAAGAGGAAAACAATAGAAAGCAAACTGAATTGCTTTCACTTTTATACACAAAGT
131 CAAACTAAATTAAGAGGAAAACAATAGAAAGCAAACTGAATTGCTTTCACTTTTATACACAAAGT
48076 ACATTG
196 ACATTG
* * *
48082 AAACTCAAGAAAAGCTATTCCCAAGATAGAGAATAAAACCAGGAGAAAGGGAAAACTCATTCGAA
1 AAACACAAGAAAAACTATACCCAAGATAGAGAATAAAACC---AG--A-GGAAAACTCATTCGAA
**
48147 ATAGAATCTATTCAAAAAATATTCAACTTAAAAGCTGCTTTGAATAGAGAACCATTACCAAATTA
60 ATAGAAAATATTCAAAAAATATTCAACTTAAAAGCTGCTTTGAATAGAGAACCATTACCAAATTA
* *
48212 AACTTTCAAACTAAATTAAGAGGATAATAATAGAAAGCAAACTGAATTG
125 AACTTTCAAACTAAATTAAGAGGAAAACAATAGAAAGCAAACTGAATTG
48261 AAACATGGGC
Statistics
Matches: 160, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
201 37 0.23
204 2 0.01
206 1 0.01
207 120 0.75
ACGTcount: A:0.48, C:0.15, G:0.14, T:0.23
Consensus pattern (201 bp):
AAACACAAGAAAAACTATACCCAAGATAGAGAATAAAACCAGAGGAAAACTCATTCGAAATAGAA
AATATTCAAAAAATATTCAACTTAAAAGCTGCTTTGAATAGAGAACCATTACCAAATTAAACTTT
CAAACTAAATTAAGAGGAAAACAATAGAAAGCAAACTGAATTGCTTTCACTTTTATACACAAAGT
ACATTG
Found at i:48968 original size:16 final size:16
Alignment explanation
Indices: 48947--48978 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
48937 ATCTCCATCG
48947 TTAGTAAACATGTACC
1 TTAGTAAACATGTACC
48963 TTAGTAAACATGTACC
1 TTAGTAAACATGTACC
48979 AATATGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (16 bp):
TTAGTAAACATGTACC
Found at i:51982 original size:31 final size:31
Alignment explanation
Indices: 51947--52005 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
51937 CAAAATAATC
* * *
51947 ATTAAATTATTCAAATGTTTTCATTTAATTT
1 ATTAAACTATTAAAAAGTTTTCATTTAATTT
*
51978 ATTAAACTATTAAAAAGTTTTTATTTAA
1 ATTAAACTATTAAAAAGTTTTCATTTAA
52006 ACCACTGGCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (31 bp):
ATTAAACTATTAAAAAGTTTTCATTTAATTT
Found at i:52909 original size:18 final size:19
Alignment explanation
Indices: 52886--52927 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
52876 TTTGGGTATC
*
52886 TAAAATTGAT-TTCATTAT
1 TAAAATTAATATTCATTAT
*
52904 TAAAATTAATATTGATTAT
1 TAAAATTAATATTCATTAT
52923 TAAAA
1 TAAAA
52928 AGAATTACAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (19 bp):
TAAAATTAATATTCATTAT
Found at i:53093 original size:6 final size:6
Alignment explanation
Indices: 53082--53123 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
53072 ACGGGAGGGA
53082 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
1 GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG GAGAGG
53124 AACGAAGCTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:57938 original size:28 final size:29
Alignment explanation
Indices: 57898--57954 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
57888 TTTTCCTCCC
57898 TTTTTGTGGCCATC-AAGCTCATAGTTTG
1 TTTTTGTGGCCATCAAAGCTCATAGTTTG
57926 TTTTTGTGGCCATCAAAGCTCATAGTTTG
1 TTTTTGTGGCCATCAAAGCTCATAGTTTG
57955 GTAGACTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.42
Consensus pattern (29 bp):
TTTTTGTGGCCATCAAAGCTCATAGTTTG
Found at i:58962 original size:31 final size:31
Alignment explanation
Indices: 58924--58987 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
58914 AAGCCTTCCT
*
58924 TGTCATACCTCTATGCCTTCGCTCATCATAG
1 TGTCATACCTCTATGCCTTAGCTCATCATAG
58955 TGTCATACCTCTATGCCTTAGCTCATCATAG
1 TGTCATACCTCTATGCCTTAGCTCATCATAG
58986 TG
1 TG
58988 AGTAAACGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (31 bp):
TGTCATACCTCTATGCCTTAGCTCATCATAG
Found at i:59202 original size:24 final size:25
Alignment explanation
Indices: 59160--59209 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
59150 CAAGTGAGTC
59160 GATCAGGACTTCCATCAAGCATTGG
1 GATCAGGACTTCCATCAAGCATTGG
59185 GATCAGGAC-TCCATCAAGCATTGG
1 GATCAGGACTTCCATCAAGCATTGG
59209 G
1 G
59210 GGCATTAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.28, C:0.24, G:0.26, T:0.22
Consensus pattern (25 bp):
GATCAGGACTTCCATCAAGCATTGG
Found at i:66113 original size:2 final size:2
Alignment explanation
Indices: 66095--66127 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
66085 AAAGAGAAAC
*
66095 AG AG A- AG AG AT AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
66128 GGCTTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.45, T:0.03
Consensus pattern (2 bp):
AG
Done.