Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_57 ID=scaffold_57-JGI_221_v2.0
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: 20157
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.32
Warning! 765 characters in sequence are not A, C, G, or T
Found at i:884 original size:16 final size:16
Alignment explanation
Indices: 843--921 Score: 83
Period size: 16 Copynumber: 5.0 Consensus size: 16
833 AAGTTCAAAT
*
843 TTCATAACTTACGTAA
1 TTCATAACTTACATAA
859 TTTGCATAACTTACATAA
1 -TT-CATAACTTACATAA
877 TTCATAACTTACATAA
1 TTCATAACTTACATAA
**
893 TT--TAA-TTTTATAA
1 TTCATAACTTACATAA
*
906 TACATAACTTACATAA
1 TTCATAACTTACATAA
922 CTTATTAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 7 0.13
14 3 0.06
15 3 0.06
16 22 0.42
17 4 0.08
18 13 0.25
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.41
Consensus pattern (16 bp):
TTCATAACTTACATAA
Found at i:891 original size:9 final size:9
Alignment explanation
Indices: 845--892 Score: 55
Period size: 9 Copynumber: 5.6 Consensus size: 9
835 GTTCAAATTT
845 CATAACTTA
1 CATAACTTA
* * *
854 CGTAATTTG
1 CATAACTTA
863 CATAACTTA
1 CATAACTTA
872 CATAA-TT-
1 CATAACTTA
879 CATAACTTA
1 CATAACTTA
888 CATAA
1 CATAA
893 TTTAATTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
7 5 0.16
8 4 0.13
9 22 0.71
ACGTcount: A:0.42, C:0.19, G:0.04, T:0.35
Consensus pattern (9 bp):
CATAACTTA
Found at i:950 original size:19 final size:19
Alignment explanation
Indices: 926--978 Score: 72
Period size: 18 Copynumber: 2.8 Consensus size: 19
916 ACATAACTTA
926 TTAATATTTATATATAGTT
1 TTAATATTTATATATAGTT
* *
945 TTAATATATATATAT-TTT
1 TTAATATTTATATATAGTT
*
963 TTAAAATTTATATATA
1 TTAATATTTATATATA
979 TATATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (19 bp):
TTAATATTTATATATAGTT
Found at i:977 original size:22 final size:21
Alignment explanation
Indices: 949--992 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
939 ATAGTTTTAA
*
949 TATATATATATTTTTTAAAATT
1 TATATATATA-TATTTAAAATT
971 TATATATATATATTTAAAATT
1 TATATATATATATTTAAAATT
992 T
1 T
993 GATACATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TATATATATATATTTAAAATT
Found at i:1044 original size:23 final size:20
Alignment explanation
Indices: 994--1056 Score: 58
Period size: 23 Copynumber: 3.0 Consensus size: 20
984 TTAAAATTTG
994 ATACATTACATAACTTACATA
1 ATACA-TACATAACTTACATA
*
1015 ACCTACATACATAAACTTACA-C
1 A--TACATACAT-AACTTACATA
*
1037 ATA-ATACATAACTTATATA
1 ATACATACATAACTTACATA
1056 A
1 A
1057 CTTAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
18 7 0.20
19 7 0.20
20 2 0.06
21 1 0.03
22 6 0.17
23 12 0.34
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
ATACATACATAACTTACATA
Found at i:1107 original size:31 final size:31
Alignment explanation
Indices: 1011--1120 Score: 98
Period size: 31 Copynumber: 3.4 Consensus size: 31
1001 ACATAACTTA
* *
1011 CATAACCTACATACATAAA-CTTACA-CATAAT
1 CATAACTTACATACATAAATATTA-ATCAT-AT
* * *
1042 ACATAACTTATATAACTTAAATTTATCAATCATAT
1 -CATAACTTACAT-ACATAAA--TATTAATCATAT
1077 CATAACTTACATACATAAATATTAATCATAT
1 CATAACTTACATACATAAATATTAATCATAT
*
1108 CACAACTTACATA
1 CATAACTTACATA
1121 ACCAACATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
31 23 0.36
32 10 0.16
33 12 0.19
34 11 0.17
35 3 0.05
36 5 0.08
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (31 bp):
CATAACTTACATACATAAATATTAATCATAT
Found at i:1152 original size:24 final size:24
Alignment explanation
Indices: 1118--1176 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
1108 CACAACTTAC
* * *
1118 ATAACCAACATAATGACTTATATA
1 ATAACCTACATAATAACTTACATA
1142 ATAACCTACATAATAACTTACATA
1 ATAACCTACATAATAACTTACATA
1166 ATAA--TACATAA
1 ATAACCTACATAA
1177 CCTACATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
22 7 0.22
24 25 0.78
ACGTcount: A:0.53, C:0.17, G:0.02, T:0.29
Consensus pattern (24 bp):
ATAACCTACATAATAACTTACATA
Found at i:1154 original size:12 final size:12
Alignment explanation
Indices: 1118--1169 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
1108 CACAACTTAC
*
1118 ATAACCAACATA
1 ATAACCTACATA
* * *
1130 ATGACTTATATA
1 ATAACCTACATA
1142 ATAACCTACATA
1 ATAACCTACATA
*
1154 ATAACTTACATA
1 ATAACCTACATA
1166 ATAA
1 ATAA
1170 TACATAACCT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (12 bp):
ATAACCTACATA
Found at i:2560 original size:23 final size:22
Alignment explanation
Indices: 2533--2592 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 22
2523 TGACATTACC
2533 TTTAAACTTATTATTAATATAAT
1 TTTAAA-TTATTATTAATATAAT
* * *
2556 TTTAAAATGTAATA-TACTATTAT
1 TTT-AAAT-TATTATTAATATAAT
2579 TTTAAATTATTATT
1 TTTAAATTATTATT
2593 GACATGTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 4 0.13
22 5 0.17
23 14 0.47
24 7 0.23
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAAATTATTATTAATATAAT
Found at i:6889 original size:35 final size:32
Alignment explanation
Indices: 6843--6921 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 32
6833 GATTTTCTTC
6843 CAAATTATTATTCATTCATTCATAATCGTATGGTA
1 CAAA-TATTATTCATTCA-T-ATAATCGTATGGTA
6878 CAAATA--ATT-ATTCATATAATCGTATGGTA
1 CAAATATTATTCATTCATATAATCGTATGGTA
6907 CAAATAATTATTCAT
1 CAAAT-ATTATTCAT
6922 GAATTTATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
29 19 0.47
30 2 0.05
31 5 0.12
32 6 0.15
33 2 0.05
34 2 0.05
35 4 0.10
ACGTcount: A:0.39, C:0.13, G:0.08, T:0.41
Consensus pattern (32 bp):
CAAATATTATTCATTCATATAATCGTATGGTA
Found at i:6900 original size:29 final size:29
Alignment explanation
Indices: 6864--6921 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6854 TCATTCATTC
6864 ATAATCGTATGGTACAAATAATTATTCAT
1 ATAATCGTATGGTACAAATAATTATTCAT
6893 ATAATCGTATGGTACAAATAATTATTCAT
1 ATAATCGTATGGTACAAATAATTATTCAT
6922 GAATTTATAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (29 bp):
ATAATCGTATGGTACAAATAATTATTCAT
Found at i:8580 original size:6 final size:7
Alignment explanation
Indices: 8555--8588 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
8545 TTGAGTCGGA
*
8555 GAAATAT
1 GAAAAAT
8562 GAAAAAT
1 GAAAAAT
8569 GAAAAAT
1 GAAAAAT
8576 GAAAAAT
1 GAAAAAT
8583 GAAAAA
1 GAAAAA
8589 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
GAAAAAT
Found at i:8594 original size:21 final size:21
Alignment explanation
Indices: 8555--8597 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
8545 TTGAGTCGGA
*
8555 GAAATATGAAAAATGAAAAAT
1 GAAAAATGAAAAATGAAAAAT
*
8576 GAAAAATGAAAAAGTAAAAAAT
1 GAAAAATGAAAAA-TGAAAAAT
8598 AGAGAGGCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (21 bp):
GAAAAATGAAAAATGAAAAAT
Found at i:10037 original size:130 final size:129
Alignment explanation
Indices: 9795--10163 Score: 632
Period size: 130 Copynumber: 2.9 Consensus size: 129
9785 GAACAGATCA
9795 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCT
* *
9860 TCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGTAGTGGAATAGGCT
66 TCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTAGAATAGGCT
9924 GGG-AATATAGCAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTAT
1 GGGAAAT-TA-CAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTAT
*
9988 CTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTAGAATAGGT
64 CTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTAGAATAGGC
10053 T
129 T
* * *
10054 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGATGGCGAATCTTAACT
1 GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCT
* * *
10119 TCAAGTGTAAGGAAGTAGATTTAAGCCACAAATCCTATCTCCCTG
66 TCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTG
10164 AAGTTGTAGT
Statistics
Matches: 228, Mismatches: 9, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
128 3 0.01
129 100 0.44
130 122 0.54
131 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (129 bp):
GGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGAAGCAGATCGAAGACGGCGAATCTTATCT
TCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATATCCCTGGTCAGCAGTAGAATAGGCT
Found at i:10285 original size:44 final size:42
Alignment explanation
Indices: 10236--10792 Score: 232
Period size: 44 Copynumber: 12.8 Consensus size: 42
10226 TCGCATTAAG
* * *
10236 TCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAG-AAGCAGA
* * * * *
10280 TCTTATCCCCCTGAAGTTGCAGTGG-GACAGATCAAAGATGGAAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGAT--GAGA-AGCAGA
* * *
10325 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGAT-TGAAGCCGATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAG-C-A-GA
* * * * *
10369 TCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTA-AAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAG---CAGA
* * * ** * * ** *
10413 TCTTATCTCTCTGAAGTTACAGTAGAGTGGAT-CGCATTAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAGCAGA
* * * * *
10454 TCTTATCTCCCTGAGGTTGCAGCGGAGTAAACTGAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAG-AAGCAGA
* * *
10498 TCTTATCCCCCTGAAGTTGCAGTGG-GACAGATCGAAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGAT-G-AGA-AGCAGA
* * *
10543 TCTTATCTCCCTGAGGTTGCAGTGGAGCAGAT-TGAAGCCAATAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAG-C-A-GA
* * * * *
10587 TCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTA-AAGTAATAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAG---CAGA
* * * ** * * * *
10631 TCTTATCTCTCTGAAGTTGTAGTAGAGTGGAT-CGCATCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAGCAGA
* * * *
10672 TTTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAGG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TGAG-AAGCAGA
* * *
10716 TCTTATCCCCCTGAAGTTGCAGTGG-GACAGATCGAAGATGGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGAT-G-AGA-AGCAGA
* **
10761 TCTTATCTCCCTGAGGTTGCAGTAAAGCAGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT
10793 TAAAGCCGAT
Statistics
Matches: 385, Mismatches: 93, Indels: 69
0.70 0.17 0.13
Matches are distributed among these distances:
41 54 0.14
42 7 0.02
43 10 0.03
44 213 0.55
45 98 0.25
46 3 0.01
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATGAGAAGCAGA
Found at i:10864 original size:218 final size:218
Alignment explanation
Indices: 10149--10836 Score: 1214
Period size: 218 Copynumber: 3.2 Consensus size: 218
10139 TTAAGCCACA
*
10149 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTAAAGTTG
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
* *
10214 CATTAGAGTGGATCGCATTAAGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAG
66 CAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAG
* *
10279 GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCAAAGATGGAAAATCTTATCTCCCTGAGGTTG
131 GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTG
10344 CAGTGGAGCAGATTGAAGCCGAT
196 CAGTGGAGCAGATTGAAGCCGAT
*
10367 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTA
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
* *
10432 CAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGTTGCAGCGGAGTAAACTGAGTAAGCAG
66 CAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAG
10497 GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTG
131 GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTG
*
10562 CAGTGGAGCAGATTGAAGCCAAT
196 CAGTGGAGCAGATTGAAGCCGAT
10585 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
* * *
10650 TAGTAGAGTGGATCGCATCAGGTTTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAG
66 CAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAG
10715 GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTG
131 GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTG
** *
10780 CAGTAAAGCAGATTAAAGCCGAT
196 CAGTGGAGCAGATTGAAGCCGAT
* * *
10803 AATCCTATCCCCCTGAAGTTATAGTGGAGTGGAT
1 AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGAT
10837 CGAAGCACCA
Statistics
Matches: 448, Mismatches: 22, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
218 448 1.00
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (218 bp):
AATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTG
CAGTAGAGTGGATCGCATTAGGTCTTATCTCCCTGAGGTTGCAGCGGAGCAGACTGAGTAAGCAG
GTCTTATCCCCCTGAAGTTGCAGTGGGACAGATCGAAGATGGCAAATCTTATCTCCCTGAGGTTG
CAGTGGAGCAGATTGAAGCCGAT
Found at i:13738 original size:9 final size:9
Alignment explanation
Indices: 13724--13995 Score: 176
Period size: 9 Copynumber: 32.2 Consensus size: 9
13714 AAAAAACAAA
13724 AACTTACAT
1 AACTTACAT
13733 AACTTACAT
1 AACTTACAT
*
13742 AA--TATCCT
1 AACTTA-CAT
*
13750 -ACATA-AT
1 AACTTACAT
13757 AACTTACAT
1 AACTTACAT
13766 AA-TAATACAT
1 AACT--TACAT
*
13776 AACCTACAT
1 AACTTACAT
* *
13785 AAATTAAAT
1 AACTTACAT
*
13794 AAGTTACAT
1 AACTTACAT
*
13803 AA--TACACG
1 AACTTACA-T
* *
13811 AA--AACAAA
1 AACTTAC-AT
13819 AACTTACAT
1 AACTTACAT
13828 AACTTACAT
1 AACTTACAT
13837 AA--TACAT
1 AACTTACAT
13844 AACTTACAT
1 AACTTACAT
* *
13853 AACCTACTT
1 AACTTACAT
13862 AA--TACAT
1 AACTTACAT
13869 AACTTACAT
1 AACTTACAT
*
13878 AA--TACAC
1 AACTTACAT
13885 AACTTACAT
1 AACTTACAT
13894 AACTTACAT
1 AACTTACAT
13903 AA--TACAT
1 AACTTACAT
13910 AACTTACAT
1 AACTTACAT
* *
13919 AACCTACTT
1 AACTTACAT
13928 AA--TACAT
1 AACTTACAT
*
13935 AACTTACAC
1 AACTTACAT
*
13944 AA--TACAC
1 AACTTACAT
13951 AACTTACAT
1 AACTTACAT
13960 AACTTACAT
1 AACTTACAT
13969 AA--TACAT
1 AACTTACAT
13976 AACTTACAT
1 AACTTACAT
* *
13985 GACTTATAT
1 AACTTACAT
13994 AA
1 AA
13996 GACAACTTAC
Statistics
Matches: 210, Mismatches: 27, Indels: 52
0.73 0.09 0.18
Matches are distributed among these distances:
7 54 0.26
8 13 0.06
9 134 0.64
10 9 0.04
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.29
Consensus pattern (9 bp):
AACTTACAT
Found at i:13754 original size:12 final size:12
Alignment explanation
Indices: 13731--13770 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
13721 AAAAACTTAC
*
13731 ATAACTTACATA
1 ATAACCTACATA
*
13743 ATATCCTACATA
1 ATAACCTACATA
*
13755 ATAACTTACATA
1 ATAACCTACATA
13767 ATAA
1 ATAA
13771 TACATAACCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (12 bp):
ATAACCTACATA
Found at i:13808 original size:25 final size:25
Alignment explanation
Indices: 13771--13942 Score: 131
Period size: 25 Copynumber: 6.8 Consensus size: 25
13761 TACATAATAA
* *
13771 TACATAACCTACATAAATTAAATAAGT
1 TACATAA--TACATAAATTACATAACT
* *
13798 TACATAATACACGAAA--ACAAAAACT
1 TACATAATACA-TAAATTAC-ATAACT
13823 TACATAACTTACAT-AA-TACATAACT
1 TACATAA--TACATAAATTACATAACT
*
13848 TACATAACCTAC-TTAA-TACATAACT
1 TACATAA--TACATAAATTACATAACT
* *
13873 TACATAATACACAACTTACATAACT
1 TACATAATACATAAATTACATAACT
* *
13898 TACATAATACATAACTTACATAACC
1 TACATAATACATAAATTACATAACT
* *
13923 TACTTAATACATAACTTACA
1 TACATAATACATAAATTACA
13943 CAATACACAA
Statistics
Matches: 124, Mismatches: 13, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
23 3 0.02
24 3 0.02
25 102 0.82
26 5 0.04
27 11 0.09
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.28
Consensus pattern (25 bp):
TACATAATACATAAATTACATAACT
Found at i:13868 original size:41 final size:40
Alignment explanation
Indices: 13823--13984 Score: 202
Period size: 41 Copynumber: 4.0 Consensus size: 40
13813 AACAAAAACT
* *
13823 TACATAACTTACATAA-TACATAACTTACATAACCTACTTAA
1 TACATAACTTACATAACTACATAA--TACATAACTTACATAA
*
13864 TACATAACTTACATAA-TACACAACTTACATAACTTACATAA
1 TACATAACTTACATAACTACATAA--TACATAACTTACATAA
* *
13905 TACATAACTTACATAACCTACTTAATACATAACTTACACAA
1 TACATAACTTACATAA-CTACATAATACATAACTTACATAA
*
13946 TACACAACTTACATAACTTACATAATACATAACTTACAT
1 TACATAACTTACATAAC-TACATAATACATAACTTACAT
13985 GACTTATATA
Statistics
Matches: 109, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.01
41 103 0.94
43 5 0.05
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (40 bp):
TACATAACTTACATAACTACATAATACATAACTTACATAA
Found at i:13896 original size:66 final size:66
Alignment explanation
Indices: 13819--13984 Score: 323
Period size: 66 Copynumber: 2.5 Consensus size: 66
13809 CGAAAACAAA
*
13819 AACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTACATAATACA
1 AACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTACACAATACA
13884 C
66 C
13885 AACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTACACAATACA
1 AACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTACACAATACA
13950 C
66 C
13951 AACTTACATAACTTACATAATACATAACTTACAT
1 AACTTACATAACTTACATAATACATAACTTACAT
13985 GACTTATATA
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 99 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (66 bp):
AACTTACATAACTTACATAATACATAACTTACATAACCTACTTAATACATAACTTACACAATACA
C
Found at i:13995 original size:25 final size:24
Alignment explanation
Indices: 13880--14007 Score: 95
Period size: 25 Copynumber: 5.2 Consensus size: 24
13870 ACTTACATAA
*
13880 TACACAACTTACATAACTTACATAA--
1 TACATAACTTACATAA--TACA-AACT
*
13905 TACATAACTTACATAACCTACTTAA--
1 TACATAACTTACATAA--TAC-AAACT
*
13930 TACATAACTTACACAATACACAACT
1 TACATAACTTACATAATACA-AACT
13955 TACATAACTTACATAATACATAACT
1 TACATAACTTACATAATACA-AACT
* * *
13980 TACATGACTTATATAAGAC-AACT
1 TACATAACTTACATAATACAAACT
14003 TACAT
1 TACAT
14008 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.16
25 75 0.84
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.30
Consensus pattern (24 bp):
TACATAACTTACATAATACAAACT
Found at i:14124 original size:9 final size:9
Alignment explanation
Indices: 14110--14240 Score: 147
Period size: 9 Copynumber: 15.7 Consensus size: 9
14100 NNNNNNNNAG
14110 ACATAACTT
1 ACATAACTT
*
14119 ACATAAGTT
1 ACATAACTT
14128 ACATAA--T
1 ACATAACTT
14135 ACATAACTT
1 ACATAACTT
14144 ACATAA--T
1 ACATAACTT
14151 ACATAACTT
1 ACATAACTT
14160 ACATAA--T
1 ACATAACTT
14167 ACATAACTT
1 ACATAACTT
*
14176 ACATAATTT
1 ACATAACTT
*
14185 ACTTAA--T
1 ACATAACTT
14192 ACATAACTT
1 ACATAACTT
*
14201 ACATAATTT
1 ACATAACTT
*
14210 ACTTAA--T
1 ACATAACTT
14217 ACATAACTT
1 ACATAACTT
14226 ACATAACTT
1 ACATAACTT
14235 ACATAA
1 ACATAA
14241 ATATATGATA
Statistics
Matches: 105, Mismatches: 7, Indels: 20
0.80 0.05 0.15
Matches are distributed among these distances:
7 33 0.31
9 72 0.69
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (9 bp):
ACATAACTT
Found at i:14139 original size:16 final size:16
Alignment explanation
Indices: 14118--14231 Score: 142
Period size: 16 Copynumber: 7.0 Consensus size: 16
14108 AGACATAACT
*
14118 TACATAAGTTACATAA
1 TACATAACTTACATAA
14134 TACATAACTTACATAA
1 TACATAACTTACATAA
14150 TACATAACTTACATAA
1 TACATAACTTACATAA
14166 TACATAACTTACATAA
1 TACATAACTTACATAA
*
14182 TTTACTTAA--TACATAA
1 --TACATAACTTACATAA
* *
14198 CTTACATAATTTACTTAA
1 --TACATAACTTACATAA
14216 TACATAACTTACATAA
1 TACATAACTTACATAA
14232 CTTACATAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
16 75 0.86
18 12 0.14
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:14144 original size:25 final size:24
Alignment explanation
Indices: 14126--14207 Score: 66
Period size: 25 Copynumber: 3.4 Consensus size: 24
14116 CTTACATAAG
14126 TTACATAATACATAACTTACATAA
1 TTACATAATACATAACTTACATAA
14150 -TACATAACTTACATAA--TACATAA
1 TTACATAA--TACATAACTTACATAA
*
14173 CTTACATAATTTACTTAA--TACATAA
1 -TTACATAA--TACATAACTTACATAA
14198 CTTACATAAT
1 -TTACATAAT
14208 TTACTTAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
23 15 0.29
25 37 0.71
ACGTcount: A:0.48, C:0.17, G:0.00, T:0.35
Consensus pattern (24 bp):
TTACATAATACATAACTTACATAA
Found at i:19887 original size:21 final size:21
Alignment explanation
Indices: 19861--19910 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
19851 CTACAACTTA
** *
19861 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
*
19882 AAGCAGAGGCTGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
19903 AAGCAGAG
1 AAGCAGAG
19911 CAGAGCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.44, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Done.