Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2104
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: 50098
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Found at i:6962 original size:26 final size:26
Alignment explanation
Indices: 6931--7014 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
6921 GACACCTTAA
*
6931 AAATAACATACAAAAGAGTTTAAAAT
1 AAATAATATACAAAAGAGTTTAAAAT
**
6957 AAATAATATGTAAAAGAGAAATTTAAAAT
1 AAATAATATACAAAAGAG---TTTAAAAT
* *
6986 AAATAATGTACAAAAACAGTTT-AAAT
1 AAATAATATAC-AAAAGAGTTTAAAAT
7012 AAA
1 AAA
7015 AAAATTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 22 0.47
27 3 0.06
29 16 0.34
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATAATATACAAAAGAGTTTAAAAT
Found at i:7756 original size:27 final size:27
Alignment explanation
Indices: 7646--7777 Score: 83
Period size: 27 Copynumber: 5.0 Consensus size: 27
7636 TAAAAAAAAC
* * * * *
7646 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATATGTAAAAT-AT
** *
7674 TTAAAATAAATAACGTAT-AAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
* * * *
7700 TTCAAAATAAGT-A-ATATGTACAGTAG
1 TT-AAAATAAATAATATATGTAAAATAT
7726 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
** *
7753 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATATGTAAAATA
7778 CATAAGACGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 11 0.14
26 20 0.25
27 35 0.44
28 14 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
TTAAAATAAATAATATATGTAAAATAT
Found at i:7851 original size:25 final size:26
Alignment explanation
Indices: 7798--7863 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
7788 AAAAAAAGGA
* * *
7798 TTAAAATAAGTAATA-ATAAAATTAT
1 TTAAAATAAATAATATATAAAATAAC
7823 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
7848 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
7864 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:14894 original size:26 final size:26
Alignment explanation
Indices: 14863--14946 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
14853 GACACCTTAA
*
14863 AAATAACATACAAAAGAGTTTAAAAT
1 AAATAATATACAAAAGAGTTTAAAAT
**
14889 AAATAATATGTAAAAGAGAAATTTAAAAT
1 AAATAATATACAAAAGAG---TTTAAAAT
* *
14918 AAATAATGTACAAAAACAGTTT-AAAT
1 AAATAATATAC-AAAAGAGTTTAAAAT
14944 AAA
1 AAA
14947 AAAATATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 22 0.47
27 3 0.06
29 16 0.34
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATAATATACAAAAGAGTTTAAAAT
Found at i:15689 original size:27 final size:27
Alignment explanation
Indices: 15579--15710 Score: 83
Period size: 27 Copynumber: 5.0 Consensus size: 27
15569 TAAAAAAAAC
* * * * *
15579 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATATGTAAAAT-AT
** *
15607 TTAAAATAAATAACGTAT-AAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
* * * *
15633 TTCAAAATAAGT-A-ATATGTACAGTAG
1 TT-AAAATAAATAATATATGTAAAATAT
15659 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
** *
15686 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATATGTAAAATA
15711 CATAAGACGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 11 0.14
26 20 0.25
27 35 0.44
28 14 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
TTAAAATAAATAATATATGTAAAATAT
Found at i:15784 original size:25 final size:26
Alignment explanation
Indices: 15731--15796 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
15721 AAAAAAAGGA
* * *
15731 TTAAAATAAGTAATA-ATAAAATTAT
1 TTAAAATAAATAATATATAAAATAAC
15756 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
15781 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
15797 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:16290 original size:14 final size:15
Alignment explanation
Indices: 16271--16308 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
16261 CTTGTGATAT
16271 GATATG-CAATCTTA
1 GATATGACAATCTTA
16285 GATATGGTACAATCTTA
1 GATAT-G-ACAATCTTA
16302 GATATGA
1 GATATGA
16309 TATACAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.24
15 2 0.10
16 1 0.05
17 13 0.62
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:16290 original size:19 final size:18
Alignment explanation
Indices: 16266--16322 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
16256 CATATCTTGT
16266 GATATGATATGCAATCTTA
1 GATATGATAT-CAATCTTA
*
16285 GATATGGTA-CAATCTTA
1 GATATGATATCAATCTTA
16302 GATATGATATACAATCTTA
1 GATATGATAT-CAATCTTA
16321 GA
1 GA
16323 AGATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
17 16 0.47
19 18 0.53
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (18 bp):
GATATGATATCAATCTTA
Found at i:17556 original size:26 final size:26
Alignment explanation
Indices: 17527--17608 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
17517 TGGTACAAAT
17527 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
17553 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17579 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17605 TGAT
1 TGAT
17609 GGGCATTTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:25121 original size:11 final size:10
Alignment explanation
Indices: 25103--25150 Score: 60
Period size: 11 Copynumber: 4.6 Consensus size: 10
25093 CTTCTATTTC
25103 AAAAAAAAAG
1 AAAAAAAAAG
25113 AAGAAAAAAAG
1 AA-AAAAAAAG
* *
25124 AAAATAAAAT
1 AAAAAAAAAG
25134 AAAATAAAAAG
1 AAAA-AAAAAG
25145 AAAAAA
1 AAAAAA
25151 GAAAAATGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 14 0.44
11 18 0.56
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:25132 original size:21 final size:21
Alignment explanation
Indices: 25103--25150 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
25093 CTTCTATTTC
25103 AAAAAAAAAGAAGAA-AAAAAG
1 AAAAAAAAAGAA-AATAAAAAG
* *
25124 AAAATAAAATAAAATAAAAAG
1 AAAAAAAAAGAAAATAAAAAG
25145 AAAAAA
1 AAAAAA
25151 GAAAAATGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 2 0.09
21 21 0.91
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.06
Consensus pattern (21 bp):
AAAAAAAAAGAAAATAAAAAG
Found at i:26136 original size:43 final size:41
Alignment explanation
Indices: 26088--26227 Score: 115
Period size: 43 Copynumber: 3.3 Consensus size: 41
26078 CGCATTAATC
26088 CCCTAAGCAGTAGGGTAACAGGTTAAATTTACAGATCTTATCT
1 CCCTAAGCAGTAGGG-AACAGGTTAAA-TTACAGATCTTATCT
** * * * * * *
26131 CCCTAAGCAGTAGTGGAGTAGATCGAAGACT-C-G-CCTTAACC
1 CCCTAAGCAGTAG-GGAACAGGT-TAA-ATTACAGATCTTATCT
*
26172 CCCTAAGCAGTAGGGGAACAGGCTAAAATTACAGATCTTATCT
1 CCCTAAGCAGTA-GGGAACAGG-TTAAATTACAGATCTTATCT
26215 CCCTAAGCAGTAG
1 CCCTAAGCAGTAG
26228 CAGAATAGAT
Statistics
Matches: 73, Mismatches: 16, Indels: 17
0.69 0.15 0.16
Matches are distributed among these distances:
40 2 0.03
41 25 0.34
42 5 0.07
43 35 0.48
44 5 0.07
45 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (41 bp):
CCCTAAGCAGTAGGGAACAGGTTAAATTACAGATCTTATCT
Found at i:26237 original size:84 final size:85
Alignment explanation
Indices: 26082--26285 Score: 302
Period size: 84 Copynumber: 2.4 Consensus size: 85
26072 ATTCAGCGCA
* **
26082 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAATTTACAGATCTTATCTCCCTAAGCAGTAGTGG
1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAG
*
26147 AGTAGAT-CGAAGACTCGCC
66 AATAGATACGAAGACTCGCC
* * *
26166 TTAACCCCCTAAGCAGTAGGGGAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAG
1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAG
*
26231 AATAGATCAACGACGACTCGCC
66 AATAGAT--ACGAAGACTCGCC
*
26253 TTAATCCCCTAAGCAGCAGGGTAACAGGTTAAA
1 TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAA
26286 GTATAGAAGA
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
84 65 0.62
87 40 0.38
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.23
Consensus pattern (85 bp):
TTAATCCCCTAAGCAGTAGGGTAACAGGTTAAAATTACAGATCTTATCTCCCTAAGCAGTAGCAG
AATAGATACGAAGACTCGCC
Found at i:26889 original size:207 final size:207
Alignment explanation
Indices: 26410--27329 Score: 1556
Period size: 207 Copynumber: 4.5 Consensus size: 207
26400 CGGAGAGCAG
* * * *
26410 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTATGATGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
*
26475 TCTTTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
*
26540 AGCAGATCTGGCCTTCAGATG-TTATACTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
26604 TACAAGGAACAA
196 TACAAGGAACAA
* * *
26616 ATCAAAGACATAGCTAATTTGGCTTTCACGTGTTTACGTTAAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
*
26681 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGAGTCTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
*
26746 AGCAGATCTGGCCTTCAGATGTTTATGCTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
26811 TACAAGGAACAA
196 TACAAGGAACAA
* *
26823 ATCGAAGACATAACTGATTTGGCTTTCACGTGTTTATGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* *
26888 TCTCTGTATTGTCAGAAAACAAATCGAAGTTTGGCGTTTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
26953 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
*
27018 TACAATGAACAA
196 TACAAGGAACAA
27030 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* *
27095 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGACAGACATAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
** * * * *
27160 AGCAGATCTAACCTTCAGATGATTAGACTGAAGC-AGATCCAATATGGTTTGGTATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
*
27224 TACAAGGAGCAA
196 TACAAGGAACAA
* * *
27236 ATCGAAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
* *
27301 TCTCTGTATTGTCAGGGAACAAATTGAAG
66 TCTCTGTATTGTCAGAGAACAAATCGAAG
27330 AAGCAGATTT
Statistics
Matches: 673, Mismatches: 40, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
206 269 0.40
207 404 0.60
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (207 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
TACAAGGAACAA
Found at i:27200 original size:413 final size:413
Alignment explanation
Indices: 26410--27329 Score: 1574
Period size: 413 Copynumber: 2.2 Consensus size: 413
26400 CGGAGAGCAG
*
26410 ATCGAAGACATAGCTGATTTGGCTTTCACGTGCTTATGATGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTATGATGAAGCAAATCTAAGATGATTTGGCA
*
26475 TCTTTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
*
26540 AGCAGATCTGGCCTTCAGATGTTATACTGAAGTAAGATCCAAGATGGTTTGGCATCCTTGTGCTT
131 AGCAGATCTGGCCTTCAGATGTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTT
26605 ACAAGGAACAAATCAAAGACATAGCTAATTTGGCTTTCACGTGTTTACGTTAAAGCAAGTCTAAG
196 ACAAGGAACAAATCAAAGACATAGCTAATTTGGCTTTCACGTGTTTACGTTAAAGCAAGTCTAAG
26670 ATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGAGTCTCCATATTCGACGGAG
261 ATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGAGTCTCCATATTCGACGGAG
* ** *
26735 GGCAGACACATAGCAGATCTGGCCTTCAGATGTTTATGCTGAAGCAAGATCCAAGATGGTTTGGC
326 GACAGACACATAGCAGATCTAACCTTCAGATGATTATGCTGAAGCAAGATCCAAGATGGTTTGGC
26800 ATCCTTGTGCTTACAAGGAACAA
391 ATCCTTGTGCTTACAAGGAACAA
* * *
26823 ATCGAAGACATAACTGATTTGGCTTTCACGTGTTTATGTTGAAGCAAGTCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTATGATGAAGCAAATCTAAGATGATTTGGCA
* *
26888 TCTCTGTATTGTCAGAAAACAAATCGAAGTTTGGCGTTTCCATATTCGACGGAGGGCAGACACAT
66 TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
26953 AGCAGATCTGGCCTTCAGATGTTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
131 AGCAGATCTGGCCTTCAGATG-TTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCT
* * * *
27018 TACAATGAACAAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGTTGAAGCAAGTCTAA
195 TACAAGGAACAAATCAAAGACATAGCTAATTTGGCTTTCACGTGTTTACGTTAAAGCAAGTCTAA
*
27083 GATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGA
260 GATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGAGTCTCCATATTCGACGGA
* *
27148 GGACAGACATATAGCAGATCTAACCTTCAGATGATTA-GACTGAAGC-AGATCCAATATGGTTTG
325 GGACAGACACATAGCAGATCTAACCTTCAGATGATTATG-CTGAAGCAAGATCCAAGATGGTTTG
* *
27211 GTATCCTTGTGCTTACAAGGAGCAA
389 GCATCCTTGTGCTTACAAGGAACAA
* * *
27236 ATCGAAGACATAGCTGATTTGGCTTTCGCGTGTTTACGCTGAAGCAAATCTAAGATGATTTGGCA
1 ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTATGATGAAGCAAATCTAAGATGATTTGGCA
* *
27301 TCTCTGTATTGTCAGGGAACAAATTGAAG
66 TCTCTGTATTGTCAGAGAACAAATCGAAG
27330 AAGCAGATTT
Statistics
Matches: 476, Mismatches: 29, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
413 270 0.57
414 206 0.43
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (413 bp):
ATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTATGATGAAGCAAATCTAAGATGATTTGGCA
TCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGCGTCTCCATATTCGACGGAGGGCAGACACAT
AGCAGATCTGGCCTTCAGATGTTATACTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTT
ACAAGGAACAAATCAAAGACATAGCTAATTTGGCTTTCACGTGTTTACGTTAAAGCAAGTCTAAG
ATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTTTGGAGTCTCCATATTCGACGGAG
GACAGACACATAGCAGATCTAACCTTCAGATGATTATGCTGAAGCAAGATCCAAGATGGTTTGGC
ATCCTTGTGCTTACAAGGAACAA
Found at i:27744 original size:19 final size:19
Alignment explanation
Indices: 27719--27809 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
27709 ATTATCTTCA
27719 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
27738 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
27757 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
27774 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
27792 ATGATATACAATCTTAGA
1 ATGATATGCAATCTTAGA
27810 AGATATGATT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 34 0.52
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:27759 original size:14 final size:15
Alignment explanation
Indices: 27740--27795 Score: 60
Period size: 18 Copynumber: 3.5 Consensus size: 15
27730 TCTTAGATGT
27740 GATATG-CAATCTTA
1 GATATGACAATCTTA
27754 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
27771 GATATGATTGCAATCTTA
1 GATATGA---CAATCTTA
27789 GATATGA
1 GATATGA
27796 TATACAATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.17
15 1 0.03
17 14 0.39
18 15 0.42
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:27789 original size:35 final size:37
Alignment explanation
Indices: 27727--27816 Score: 134
Period size: 35 Copynumber: 2.5 Consensus size: 37
27717 CAATGATATG
*
27727 CAATCTTAGATGTGATATGCAATCTTAGATATG-ATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGAATA
27763 CAATCTTAGATATGAT-TGCAATCTTAGATATGATATA
1 CAATCTTAGATATGATATGCAATCTTAGATATGA-ATA
27800 CAATCTTAGA-A-GATATG
1 CAATCTTAGATATGATATG
27817 ATTTTGTAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
35 19 0.38
36 18 0.36
37 13 0.26
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.36
Consensus pattern (37 bp):
CAATCTTAGATATGATATGCAATCTTAGATATGAATA
Found at i:32778 original size:26 final size:26
Alignment explanation
Indices: 32747--32830 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
32737 GACACCTTAA
*
32747 AAATAACATACAAAAGAGTTTAAAAT
1 AAATAATATACAAAAGAGTTTAAAAT
**
32773 AAATAATATGTAAAAGAGAAATTTAAAAT
1 AAATAATATACAAAAGAG---TTTAAAAT
* *
32802 AAATAATGTACAAAAACAGTTT-AAAT
1 AAATAATATAC-AAAAGAGTTTAAAAT
32828 AAA
1 AAA
32831 AAAATTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 22 0.47
27 3 0.06
29 16 0.34
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATAATATACAAAAGAGTTTAAAAT
Found at i:33572 original size:27 final size:27
Alignment explanation
Indices: 33462--33593 Score: 83
Period size: 27 Copynumber: 5.0 Consensus size: 27
33452 TAAAAAAAAC
* * * * *
33462 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATATGTAAAAT-AT
** *
33490 TTAAAATAAATAACGTAT-AAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
* * * *
33516 TTCAAAATAAGT-A-ATATGTACAGTAG
1 TT-AAAATAAATAATATATGTAAAATAT
33542 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
** *
33569 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATATGTAAAATA
33594 CATAAGACGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 11 0.14
26 20 0.25
27 35 0.44
28 14 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
TTAAAATAAATAATATATGTAAAATAT
Found at i:33667 original size:25 final size:26
Alignment explanation
Indices: 33614--33679 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
33604 AAAAAAAGGA
* * *
33614 TTAAAATAAGTAATA-ATAAAATTAT
1 TTAAAATAAATAATATATAAAATAAC
33639 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
33664 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
33680 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:40718 original size:26 final size:26
Alignment explanation
Indices: 40687--40770 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
40677 GACACCTTAA
*
40687 AAATAACATACAAAAGAGTTTAAAAT
1 AAATAATATACAAAAGAGTTTAAAAT
**
40713 AAATAATATGTAAAAGAGAAATTTAAAAT
1 AAATAATATACAAAAGAG---TTTAAAAT
* *
40742 AAATAATGTACAAAAACAGTTT-AAAT
1 AAATAATATAC-AAAAGAGTTTAAAAT
40768 AAA
1 AAA
40771 AAAATTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 22 0.47
27 3 0.06
29 16 0.34
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATAATATACAAAAGAGTTTAAAAT
Found at i:41512 original size:27 final size:27
Alignment explanation
Indices: 41402--41533 Score: 83
Period size: 27 Copynumber: 5.0 Consensus size: 27
41392 TAAAAAAAAC
* * * * *
41402 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATATGTAAAAT-AT
** *
41430 TTAAAATAAATAACGTAT-AAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
* * * *
41456 TTCAAAATAAGT-A-ATATGTACAGTAG
1 TT-AAAATAAATAATATATGTAAAATAT
41482 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
** *
41509 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATATGTAAAATA
41534 CATAAGACGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 11 0.14
26 20 0.25
27 35 0.44
28 14 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
TTAAAATAAATAATATATGTAAAATAT
Found at i:41607 original size:25 final size:26
Alignment explanation
Indices: 41554--41619 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
41544 AAAAAAAGGA
* * *
41554 TTAAAATAAGTAATA-ATAAAATTAT
1 TTAAAATAAATAATATATAAAATAAC
41579 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
41604 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
41620 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:48646 original size:26 final size:26
Alignment explanation
Indices: 48615--48698 Score: 80
Period size: 26 Copynumber: 3.1 Consensus size: 26
48605 GACACCTTAA
*
48615 AAATAACATACAAAAGAGTTTAAAAT
1 AAATAATATACAAAAGAGTTTAAAAT
**
48641 AAATAATATGTAAAAGAGAAATTTAAAAT
1 AAATAATATACAAAAGAG---TTTAAAAT
* *
48670 AAATAATGTACAAAAACAGTTT-AAAT
1 AAATAATATAC-AAAAGAGTTTAAAAT
48696 AAA
1 AAA
48699 AAAATTATAT
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
26 22 0.47
27 3 0.06
29 16 0.34
30 6 0.13
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (26 bp):
AAATAATATACAAAAGAGTTTAAAAT
Found at i:49440 original size:27 final size:27
Alignment explanation
Indices: 49330--49461 Score: 83
Period size: 27 Copynumber: 5.0 Consensus size: 27
49320 TATAAAAAAC
* * * * *
49330 TTAAAATAGATAATACATATATAATGGT
1 TTAAAATAAATAATATATGTAAAAT-AT
** *
49358 TTAAAATAAATAACGTAT-AAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
* * * *
49384 TTCAAAATAAGT-A-ATATGTACAGTAG
1 TT-AAAATAAATAATATATGTAAAATAT
49410 TTAAAATAAATAATATATGTAAAATAT
1 TTAAAATAAATAATATATGTAAAATAT
** *
49437 TTAAAATTTATAATA-ATTTAAAATA
1 TTAAAATAAATAATATATGTAAAATA
49462 CATAAGACGT
Statistics
Matches: 80, Mismatches: 20, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
25 11 0.14
26 20 0.25
27 35 0.44
28 14 0.17
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.36
Consensus pattern (27 bp):
TTAAAATAAATAATATATGTAAAATAT
Found at i:49535 original size:25 final size:26
Alignment explanation
Indices: 49482--49547 Score: 75
Period size: 25 Copynumber: 2.6 Consensus size: 26
49472 AAAAAAAGGA
* * *
49482 TTAAAATAAGTAATA-ATAAAATTAT
1 TTAAAATAAATAATATATAAAATAAC
49507 TTAAAATAAATAATATATAAAA-AAC
1 TTAAAATAAATAATATATAAAATAAC
49532 TTAAAA-AGAATAATAT
1 TTAAAATA-AATAATAT
49548 TAACAGTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 1 0.03
25 29 0.81
26 6 0.17
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAAC
Found at i:50066 original size:20 final size:19
Alignment explanation
Indices: 50015--50072 Score: 75
Period size: 17 Copynumber: 3.1 Consensus size: 19
50005 CATATCTTGT
*
50015 GATATGATATGCAATCTTA
1 GATATGATATACAATCTTA
*
50034 GATATG--GTACAATCTTA
1 GATATGATATACAATCTTA
50051 GATATTGATATACAATCTTA
1 GATA-TGATATACAATCTTA
50071 GA
1 GA
50073 AGATATGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 13 0.39
18 2 0.06
19 6 0.18
20 12 0.36
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGATATACAATCTTA
Done.