Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1623
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: 29275
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2917 original size:23 final size:24
Alignment explanation
Indices: 2890--2942 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
2880 ATAAATAGTA
2890 ATAGTGTTAGAA-ATATAC-TATAG
1 ATAGTGTTAGAAGATATACATA-AG
*
2913 ATAGTGTTTGAAGTATATACATAAG
1 ATAGTGTTAGAAG-ATATACATAAG
2938 ATAGT
1 ATAGT
2943 AAAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
25 13 0.50
26 2 0.08
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (24 bp):
ATAGTGTTAGAAGATATACATAAG
Found at i:3008 original size:19 final size:21
Alignment explanation
Indices: 2970--3008 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2960 AATGTTAAAC
*
2970 TATATATAATATATACATATA
1 TATATATAATATATAAATATA
2991 TATATATAA-A-ATAAATAT
1 TATATATAATATATAAATAT
3009 TGAAAATGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 1 0.06
21 9 0.53
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (21 bp):
TATATATAATATATAAATATA
Found at i:4980 original size:3 final size:3
Alignment explanation
Indices: 4966--5108 Score: 128
Period size: 3 Copynumber: 47.7 Consensus size: 3
4956 TATAACAATA
* * * * *
4966 ATT ATT ACT ATT ATT ATT ATT TTT ACT ATT ACT ATT ATT TTCT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT
** **
5012 ATT ATT ATT ATT ATT ATT ATT ACC ATT ACG ATT -TCT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
* * * * *
5057 ATT GTT ATT ATT ATC ATT A-T AGT ATT ATT ATT ATT ACT ATT ATT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5104 ATT AT
1 ATT AT
5109 CATTTTTACT
Statistics
Matches: 109, Mismatches: 27, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
2 3 0.03
3 103 0.94
4 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:5269 original size:12 final size:12
Alignment explanation
Indices: 5233--5270 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
5223 TATTCCTTTA
5233 TTATTTTATTTAT
1 TTATTTTATTT-T
*
5246 TTATTTCATTTT
1 TTATTTTATTTT
5258 TTATTTTATTTT
1 TTATTTTATTTT
5270 T
1 T
5271 GTTCTCATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:10574 original size:25 final size:25
Alignment explanation
Indices: 10506--10577 Score: 92
Period size: 25 Copynumber: 2.9 Consensus size: 25
10496 CAACCTATAC
* *
10506 CTTTTCAACTTCTTCAATTTATATT
1 CTTTTGAACTTCTTCAATTTCTATT
* *
10531 CTTCTGAACTTTTTCAATTTCTATT
1 CTTTTGAACTTCTTCAATTTCTATT
10556 CTTTTGAACTTC-TCTAATTTCT
1 CTTTTGAACTTCTTC-AATTTCT
10578 CTCGCTGTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
24 2 0.05
25 38 0.95
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.56
Consensus pattern (25 bp):
CTTTTGAACTTCTTCAATTTCTATT
Found at i:10934 original size:128 final size:128
Alignment explanation
Indices: 10645--10958 Score: 388
Period size: 128 Copynumber: 2.5 Consensus size: 128
10635 AAGCAGGATG
* * * *
10645 TACTATAGAAAAAGAGCGTCCAGA-TGG-GA--TTTTTTCAGTACTTTTACTGATAGTGCATCCT
1 TACTATAGAAAAAAAGCGTCCATAGTGGTGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCT
* *
10706 TCTTGAAGCATTTTTGACACTATTTTTTTAAAACCATATTCTCAAAATTATTTTTTCAAAAAC
66 GCATGAAGCATTTTTGACACTATTTTTTTAAAACCATATTCTCAAAATTATTTTTTCAAAAAC
* ** ***
10769 TACTATAGAAAAATAGCGTCCATCTTGGTGTTTTTTTTTCAGTACTTTTGCTGACAGTGCATCCT
1 TACTATAGAAAAAAAGCGTCCATAGTGGTGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCT
* * * *
10834 GCATGAAGCATTTTTGACATTATTTTTTTCAAAACCATCTTCTCAAAATTATTTTTTTTATAAAC
66 GCATGAAGCATTTTTGACACTATTTTTTT-AAAACCATATTCTCAAAATTA-TTTTTTCAAAAAC
* * * *
10899 TACTGTATAAAAAAAGTGTTCA-AGTGG-GAGCTTTTTTCAGTACTTTTGCTGACAGTGCAT
1 TACTATAGAAAAAAAGCGTCCATAGTGGTGAGCTTTTTTCAGTACTTTTGCTGACAGTGCAT
10959 GTAACTCCCT
Statistics
Matches: 162, Mismatches: 22, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
124 21 0.13
125 3 0.02
126 1 0.01
128 86 0.53
129 23 0.14
130 28 0.17
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (128 bp):
TACTATAGAAAAAAAGCGTCCATAGTGGTGAGCTTTTTTCAGTACTTTTGCTGACAGTGCATCCT
GCATGAAGCATTTTTGACACTATTTTTTTAAAACCATATTCTCAAAATTATTTTTTCAAAAAC
Found at i:12986 original size:48 final size:48
Alignment explanation
Indices: 12931--13200 Score: 177
Period size: 48 Copynumber: 5.6 Consensus size: 48
12921 TATAAGAGCC
12931 AGTGTAAGACCATGTCTGGGACATGGCATCGATGTTGAGTCGAGTGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATGTTGAGTCGAGTGCT
*** * * *
12979 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGACGTA-AGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATGTTGAGTCG-AGTGCT
* * * * *
13027 AGTGTAAGA-TATGTCTAGGACAT-GCATC-A-GCT-ACG-AGATGTGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGATGTTGA-GTCGA-GTGCT
* * * *
13071 AGTGTAAGACCATGTCTGGGACATGGCATTGGCACAGAT-A-TGCGAGAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCA-TCG-A-TGTTGAGT-CGAGTGCT
* * * *
13121 AGTGTAAGACCATGTCTAGGACAAGACATCAGCCTCGTTGA-T-GA-TAGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATC-G-AT-GTTGAGTCGAGT-GCT
*
13170 AGTGTAAGACCATGCCTGGGACATGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
13201 GCATACTTAC
Statistics
Matches: 171, Mismatches: 34, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 12 0.07
45 12 0.07
46 8 0.05
47 13 0.08
48 50 0.29
49 34 0.20
50 32 0.19
51 7 0.04
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGATGTTGAGTCGAGTGCT
Found at i:13191 original size:99 final size:96
Alignment explanation
Indices: 12925--13203 Score: 306
Period size: 92 Copynumber: 2.9 Consensus size: 96
12915 CCACATTATA
* * *
12925 AGAGCCAGTGTAAGACCATGTCTGGGACATGGCATC-GAT-GTTGAGTCGAGTGCTAGTGTAAGA
1 AGAGCTAGTGTAAGACCATGTCTAGGACAT-GCATCAGCTCGTTGA-T-GA-TGCTAGTGTAAGA
*
12988 CCATGTCTGGGACATGGCATCGGC-CTCGAGACGT
62 CCATGTCTGGGACATGGCATCGGCACTAGAGACGT
* * *
13022 A-AGCTAGTGTAAGA-TATGTCTAGGACATGCATCAGCTACG-AGATG-TGTTAGTGTAAGACCA
1 AGAGCTAGTGTAAGACCATGTCTAGGACATGCATCAGCT-CGTTGATGATGCTAGTGTAAGACCA
* *
13083 TGTCTGGGACATGGCATTGGCAC-AGATATGCG-
65 TGTCTGGGACATGGCATCGGCACTAGAGA--CGT
*
13115 AGAGCTAGTGTAAGACCATGTCTAGGACAAGACATCAGCCTCGTTGATGATAGCTAGTGTAAGAC
1 AGAGCTAGTGTAAGACCATGTCTAGGACATG-CATCAG-CTCGTTGATGAT-GCTAGTGTAAGAC
*
13180 CATGCCTGGGACATGGCATCGGCA
63 CATGTCTGGGACATGGCATCGGCA
13204 TACTTACTCC
Statistics
Matches: 154, Mismatches: 15, Indels: 24
0.80 0.08 0.12
Matches are distributed among these distances:
92 38 0.25
93 2 0.01
94 21 0.14
95 28 0.18
96 22 0.14
97 8 0.05
98 1 0.01
99 34 0.22
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.23
Consensus pattern (96 bp):
AGAGCTAGTGTAAGACCATGTCTAGGACATGCATCAGCTCGTTGATGATGCTAGTGTAAGACCAT
GTCTGGGACATGGCATCGGCACTAGAGACGT
Found at i:16100 original size:18 final size:19
Alignment explanation
Indices: 16063--16106 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
16053 GTAAAGTAAC
16063 AAATAAACATATTAAATTAT
1 AAAT-AACATATTAAATTAT
* *
16083 ATATAACA-ATTAATTTAT
1 AAATAACATATTAAATTAT
16101 AAATAA
1 AAATAA
16107 ACTATTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 14 0.67
19 4 0.19
20 3 0.14
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATAACATATTAAATTAT
Found at i:17690 original size:21 final size:21
Alignment explanation
Indices: 17666--17705 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17656 TATTTAATTT
17666 ATAAAATAATAAAATAATAAA
1 ATAAAATAATAAAATAATAAA
** *
17687 ATAATCTAATTAAATAATA
1 ATAAAATAATAAAATAATA
17706 TTTATAAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAAATAATAAAATAATAAA
Found at i:17704 original size:8 final size:8
Alignment explanation
Indices: 17666--17691 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
17656 TATTTAATTT
17666 ATAAAATA
1 ATAAAATA
17674 ATAAAATA
1 ATAAAATA
17682 ATAAAATA
1 ATAAAATA
17690 AT
1 AT
17692 CTAATTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATAAAATA
Found at i:19662 original size:125 final size:125
Alignment explanation
Indices: 19431--20024 Score: 734
Period size: 125 Copynumber: 4.8 Consensus size: 125
19421 ACGGGTTGTT
19431 ACAGTGCATCCTGCTTGAAGCATTTTTTACACTATTTTTTCAGAACCATCATT-TCAAAATTA-T
1 ACAGTGCATCCTGCTTGAAGCATTTTTTACACT-TTTTTTCAGAACCATC-TTCTCAAAATTATT
* * * *
19494 TTTTCAGAAACTACTGTAGAAAAATAGCGTCCAGCTTGAAGCTTTTTTTAGTACTTTTGCTG
64 TTTTCAGAAACTACTGTAGAAAAATAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTG
* * *
19556 ACAGTGCATCCTGCTTGAAGCATTTTTGACACTGTTTTTAAGAACCATCTTCTCAAAATTATTTT
1 ACAGTGCATCCTGCTTGAAGCATTTTTTACACTTTTTTTCAGAACCATCTTCTCAAAATTATTTT
* * * *
19621 TTCAGAAACTACTGTATAAAAAGAGTGTCCAGGTGGGAGCTTTTTTTAGTACTTTTGCTG
66 TTCAGAAACTACTGTAGAAAAATAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTG
* * * * *
19681 ACAGTGCATCCTGCTTGGAGCATTTTTGACATTATTTTTTCAG-ATCATCTTTTCAAAATTATTT
1 ACAGTGCATCCTGCTTGAAGCATTTTTTACACT-TTTTTTCAGAACCATCTTCTCAAAATTATTT
* * *
19745 TTTCAGAAACTCCTGTAGAAAAATAGTGTCCATGTGGGAGC-TTTTTCAGTACTTTTGCTG
65 TTTCAGAAACTACTGTAGAAAAATAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTG
* * * * * *
19805 AAAGTGCATCCTGCTTGAAGCGTTTTTTACCCTATTTTTCAAAACCATCTTCTCAAAATTATTGT
1 ACAGTGCATCCTGCTTGAAGCATTTTTTACACTTTTTTTCAGAACCATCTTCTCAAAATTATTTT
* * * *
19870 TTCAGAAACTCCTGTAGAAAAATAGCATCCAGGT--GAGCTTTTTTCATTACTTTTGTTG
66 TTCAGAAACTACTGTAGAAAAATAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTG
** * * * * * ***
19928 ACAGTATATCCTGCTTAAAGCGTTTTTTACCCATTTTTTTCATAACCATCTTCTCAAAA-AAAAA
1 ACAGTGCATCCTGCTTGAAGCATTTTTTACAC-TTTTTTTCAGAACCATCTTCTCAAAATTATTT
* *
19992 TTTCAGAAATTACTGTAGAAAAATAGCATCCAG
65 TTTCAGAAACTACTGTAGAAAAATAGCGTCCAG
20025 CTTTTTTTCA
Statistics
Matches: 415, Mismatches: 48, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
122 4 0.01
123 86 0.21
124 142 0.34
125 176 0.42
126 7 0.02
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (125 bp):
ACAGTGCATCCTGCTTGAAGCATTTTTTACACTTTTTTTCAGAACCATCTTCTCAAAATTATTTT
TTCAGAAACTACTGTAGAAAAATAGCGTCCAGGTGGGAGCTTTTTTCAGTACTTTTGCTG
Found at i:19875 original size:249 final size:248
Alignment explanation
Indices: 19431--20026 Score: 754
Period size: 249 Copynumber: 2.4 Consensus size: 248
19421 ACGGGTTGTT
*
19431 ACAGTGCATCCTGCTTGAAGCATTTTTTACACTATTTTTTCAGAACCATCATTTCAAAATTATTT
1 ACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCATTTCAAAATTATTT
* * *
19496 TTCAGAAACTACTGTAGAAAAATAGCGTCCAGCTTGAAGCTTTTTTTAGTACTTTTGCTGACAGT
66 TTCAGAAACTACTGTAGAAAAATAGCGTCCAGCTGGAAGCTTTTTTCAGTACTTTTGCTGAAAGT
* *
19561 GCATCCTGCTTGAAGCATTTTTGACACTGTTTTTAAGAACCATCTTCTCAAAATTATTTTTTCAG
131 GCATCCTGCTTGAAGCATTTTTGACACTATTTTTAAGAACCATCTTCTCAAAATTATTGTTTCAG
* ** *
19626 AAACTACTGTATAAAAAGAGTGTCCAGGTGGGAGCTTTTTTTAGTACTTTTGCTG
196 AAACTACTGTAGAAAAAGAGCATCCAGGT--GAGCTTTTTTCAGTACTTTTGCTG
* * * *
19681 ACAGTGCATCCTGCTTGGAGCATTTTTGACATTATTTTTTCAG-ATCATCTTTTCAAAATTATTT
1 ACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCATTTCAAAATTA-TT
* * *
19745 TTTCAGAAACTCCTGTAGAAAAATAGTGTCCATG-TGGGAGC-TTTTTCAGTACTTTTGCTGAAA
65 TTTCAGAAACTACTGTAGAAAAATAGCGTCCA-GCTGGAAGCTTTTTTCAGTACTTTTGCTGAAA
* * *
19808 GTGCATCCTGCTTGAAGCGTTTTTTACCCTATTTTTCAA-AACCATCTTCTCAAAATTATTGTTT
129 GTGCATCCTGCTTGAAGCATTTTTGACACTATTTTT-AAGAACCATCTTCTCAAAATTATTGTTT
* * * *
19872 CAGAAACTCCTGTAGAAAAATAGCATCCAGGTGAGCTTTTTTCATTACTTTTGTTG
193 CAGAAACTACTGTAGAAAAAGAGCATCCAGGTGAGCTTTTTTCAGTACTTTTGCTG
** * * * * * ** *
19928 ACAGTATATCCTGCTTAAAGCGTTTTTTAC-CCATTTTTTTCATAACCATC-TTCTCAAAAAAAA
1 ACAGTGCATCCTGCTTGAAGCATTTTTGACACTA-TTTTTTCAGAACCATCATT-TCAAAATTAT
* * *
19991 ATTTCAGAAATTACTGTAGAAAAATAGCATCCAGCT
64 TTTTCAGAAACTACTGTAGAAAAATAGCGTCCAGCT
20027 TTTTTTCAGT
Statistics
Matches: 297, Mismatches: 42, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
246 2 0.01
247 84 0.28
248 12 0.04
249 119 0.40
250 79 0.27
251 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (248 bp):
ACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAGAACCATCATTTCAAAATTATTT
TTCAGAAACTACTGTAGAAAAATAGCGTCCAGCTGGAAGCTTTTTTCAGTACTTTTGCTGAAAGT
GCATCCTGCTTGAAGCATTTTTGACACTATTTTTAAGAACCATCTTCTCAAAATTATTGTTTCAG
AAACTACTGTAGAAAAAGAGCATCCAGGTGAGCTTTTTTCAGTACTTTTGCTG
Found at i:20163 original size:27 final size:26
Alignment explanation
Indices: 20125--20179 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
20115 ACAAAAATCC
20125 TAAAACCCTAAACACAAATTTATTTT
1 TAAAACCCTAAACACAAATTTATTTT
* * *
20151 TAAAATCCTTAAACCCTAATTTATTTT
1 TAAAA-CCCTAAACACAAATTTATTTT
20178 TA
1 TA
20180 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.40
Consensus pattern (26 bp):
TAAAACCCTAAACACAAATTTATTTT
Found at i:20284 original size:29 final size:28
Alignment explanation
Indices: 20126--20284 Score: 128
Period size: 28 Copynumber: 5.6 Consensus size: 28
20116 CAAAAATCCT
* * *
20126 AAAACCCTAAACACAAATTTA-TTTTTA
1 AAAACCATAAACTCTAATTTATTTTTTA
* * *
20153 AAATCCTTAAACCCTAATTTATTTTTATA
1 AAAACCATAAACTCTAATTTATTTTT-TA
** * *
20182 AAAATAATCTTAA-TTTAATTTATTTTTTA
1 AAAACCA--TAAACTCTAATTTATTTTTTA
20211 AAAACCATAAACAT-TAATTTATTTTTTA
1 AAAACCATAAAC-TCTAATTTATTTTTTA
* *
20239 AAAACTC-TAAACCCTAATTTATTTTTTCC
1 AAAAC-CATAAACTCTAATTTATTTTTT-A
20268 AAAACCATAAACTCTAA
1 AAAACCATAAACTCTAA
20285 ACATATAAAA
Statistics
Matches: 105, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
27 20 0.19
28 42 0.40
29 28 0.27
30 12 0.11
31 3 0.03
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (28 bp):
AAAACCATAAACTCTAATTTATTTTTTA
Found at i:22295 original size:95 final size:97
Alignment explanation
Indices: 22167--22371 Score: 240
Period size: 95 Copynumber: 2.1 Consensus size: 97
22157 GGTTTTTAAA
* * * ** *
22167 GTTTAGAG-TTTTAAGGAAAAAAATTAAATAAATTAAGGTTTAGTGTTTGTTAATTAAATTAATT
1 GTTTAGGGTTTTTAAGG-AAAAAATCAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATT
* *
22231 ACT-AATTTTAAAAAA-TTAGATTATGG-TTTAGT
65 A-TAAATTTAAAAAAATTTAGATTA-GGATTTAGG
* * *
22263 GTTTATGGTTTTTAAGG-AAAAATCAAATAAATTAGGGTTTAGGGTTACTTGAGTAAATTAATTA
1 GTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA
22327 TAAATTTAAAAAAATTTAGATTAGGATTTTAGG
66 TAAATTTAAAAAAATTTAGATTAGGA-TTTAGG
22360 GTTTAGGGTTTT
1 GTTTAGGGTTTT
22372 AGAGTATTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
94 1 0.01
95 53 0.58
96 14 0.15
97 24 0.26
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (97 bp):
GTTTAGGGTTTTTAAGGAAAAAATCAAATAAATTAAGGTTTAGGGTTACTTAAGTAAATTAATTA
TAAATTTAAAAAAATTTAGATTAGGATTTAGG
Found at i:22988 original size:126 final size:126
Alignment explanation
Indices: 22459--22985 Score: 835
Period size: 126 Copynumber: 4.2 Consensus size: 126
22449 AAAAGCTTCT
* *
22459 ACGTGGACGTTCTTTTGCTACAGTAGTCTCTGAAAAAATAAATTTGAGAAGACGTGTCTGCACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
22524 ATAGTGTCAAAAACGCTTCAAGCAGGATGTATTGTCAGCAAAAGTACTGAAAGAAGCTCTC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
* * * **
22585 ACGTGGACACTTTTTTGCTACAGTAGTATCTG-AAAAATAATTTTGAGAAGACGTGTCTGTGCAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* *
22649 ATAGTGTAAAAAACGCTTCAAGCAGGATGCATTGTT-AGCAAAAGTACTGAAAGAAGCTTCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATT-TTCAGCAAAAGTACTGAAAGAAGCTCCC
* *
22710 ACGTGGACGCTCTTTTGCTACAATAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTACACAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
* * *
22775 ATAGTGGT-AAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAATTACTGGAAGAATCTCCC
66 ATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
* * *
22836 ACGTGGATGCTCTTTTGCTACAGTGGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCATAA
1 ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
22901 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
66 ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
22962 ACGTGGACGCTCTTTTGCTACAGT
1 ACGTGGACGCTCTTTTGCTACAGT
22986 GGTTTTGAAA
Statistics
Matches: 364, Mismatches: 32, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
125 115 0.32
126 247 0.68
127 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (126 bp):
ACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAAAATAATTTTGAGAAGACGTGTCTGCACAA
ATAGTGTCAAAAACGCTTCAAGCAGGATGCATTTTCAGCAAAAGTACTGAAAGAAGCTCCC
Found at i:26172 original size:62 final size:62
Alignment explanation
Indices: 26102--26288 Score: 200
Period size: 62 Copynumber: 3.2 Consensus size: 62
26092 TATAATTACT
26102 TTATTTAAAACAACCTTTTATATTATCACATGAAATAATATAAAAATATTCAAAATGTTGCC
1 TTATTTAAAACAACCTTTTATATTATCACATGAAATAATATAAAAATATTCAAAATGTTGCC
* * * * * *
26164 TTATTTAAAATAA--TTTCCAT-TTAT----T-AAA-AATATAAAAGTAAATT-ATAA--TTACT
1 TTATTTAAAACAACCTTT-TATATTATCACATGAAATAATATAAAA--ATATTCAAAATGTTGCC
*
26217 TTATTTAACACAACCTTTTATATTATCACATGAAATAATATAAAAATATTCAAAATGTTGCC
1 TTATTTAAAACAACCTTTTATATTATCACATGAAATAATATAAAAATATTCAAAATGTTGCC
26279 TTATTTAAAA
1 TTATTTAAAA
26289 TAATTTCCAT
Statistics
Matches: 96, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
53 14 0.15
54 11 0.11
55 13 0.14
56 5 0.05
59 5 0.05
60 13 0.14
61 11 0.11
62 24 0.25
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.40
Consensus pattern (62 bp):
TTATTTAAAACAACCTTTTATATTATCACATGAAATAATATAAAAATATTCAAAATGTTGCC
Found at i:26185 original size:115 final size:116
Alignment explanation
Indices: 26010--26506 Score: 842
Period size: 115 Copynumber: 4.3 Consensus size: 116
26000 TATTTATATT
* * *
26010 TTATTACATGAAATAATAT-AAAATATTCAAAATATTGCTTTATTTAAAATAATTTTCATTTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
26074 T-AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
66 TAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
*
26124 TTATCACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCA-TTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
*
26188 TAAAAATATAAAAGTAAATTATAATTACTTTATTTAACACAACCTTTTATA
66 TAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
*
26239 TTATCACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
*
26304 T-AAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATC
66 TAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
*
26354 TAATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
* *
26419 TAAAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACC-TTTATC
66 T-AAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
* *
26470 TAATTACATGAAATAATATAAAAAGATTCAAAATGTT
1 TTATTACATGAAATAATATAAAAATATTCAAAATGTT
26507 TGTACAAATA
Statistics
Matches: 367, Mismatches: 11, Indels: 8
0.95 0.03 0.02
Matches are distributed among these distances:
114 24 0.07
115 254 0.69
116 48 0.13
117 41 0.11
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (116 bp):
TTATTACATGAAATAATATAAAAATATTCAAAATGTTGCCTTATTTAAAATAATTTCCATTTTAT
TAAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATA
Found at i:27525 original size:7 final size:7
Alignment explanation
Indices: 27513--27539 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
27503 AGTTAAATAA
27513 AAATACT
1 AAATACT
27520 AAATACT
1 AAATACT
27527 AAATACT
1 AAATACT
27534 AAATAC
1 AAATAC
27540 GAATCCACTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATACT
Found at i:28537 original size:15 final size:15
Alignment explanation
Indices: 28517--28547 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28507 TTTTTATTTT
*
28517 AAAAAATAAATTTAG
1 AAAAAATAAAATTAG
28532 AAAAAATAAAATTAG
1 AAAAAATAAAATTAG
28547 A
1 A
28548 GCTTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAAATAAAATTAG
Found at i:28586 original size:22 final size:22
Alignment explanation
Indices: 28574--28623 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
28564 TAACGAGAGT
28574 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
*
28596 TTTGAGA-G-ATTTGAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
28616 TTTGAGAG
1 TTTGAGAG
28624 AATATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.69
21 1 0.04
22 7 0.27
ACGTcount: A:0.40, C:0.00, G:0.30, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:28597 original size:11 final size:11
Alignment explanation
Indices: 28574--28625 Score: 72
Period size: 11 Copynumber: 4.9 Consensus size: 11
28564 TAACGAGAGT
*
28574 TTTGAGAGGAA
1 TTTGAGAGAAA
*
28585 TTTAAGAGAAA
1 TTTGAGAGAAA
28596 TTTGAGAG--A
1 TTTGAGAGAAA
28605 TTTGAGAGAAA
1 TTTGAGAGAAA
28616 TTTGAGAGAA
1 TTTGAGAGAA
28626 TATTGAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
9 9 0.25
11 27 0.75
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.29
Consensus pattern (11 bp):
TTTGAGAGAAA
Found at i:28637 original size:31 final size:31
Alignment explanation
Indices: 28574--28637 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
28564 TAACGAGAGT
* *
28574 TTTGAGAGGAATTTAAGAGAAATTTGAGAGA
1 TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
*
28605 TTTGAGAGAAATTTGAGAG-AATATTGAAAGA
1 TTTGAGAGAAATTTAAGAGAAAT-TTGAAAGA
28636 TT
1 TT
28638 GAAGATTGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.42, C:0.00, G:0.27, T:0.31
Consensus pattern (31 bp):
TTTGAGAGAAATTTAAGAGAAATTTGAAAGA
Done.